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File infoFile; if(infoFileName.equals("")) { infoFile = null; }else{ | File infoFile = null; if (infoFileName != null){ | private void processFile(String fileName, int fileType, String infoFileName){ try { HaploData textData; File OutputFile; File inputFile; if(!quietMode && fileName != null){ System.out.println("Using data file " + fileName); } inputFile = new File(fileName); if(!inputFile.exists()){ System.out.println("input file: " + fileName + " does not exist"); System.exit(1); } textData = new HaploData(); Vector result = null; if(fileType == HAPS){ //read in haps file textData.prepareHapsInput(inputFile); } else if (fileType == PED) { //read in ped file /* if(this.arg_ignoreMarkers.size()>0) { for(int i=0;i<this.arg_ignoreMarkers.size();i++){ int index = Integer.parseInt((String)this.arg_ignoreMarkers.get(i)); if(index>0 && index<markerResultArray.length){ markerResultArray[index] = false; if(!this.quietMode) { System.out.println("Ignoring marker " + (index)); } } } }*/ result = textData.linkageToChrom(inputFile, 3, skipCheck); }else{ //read in hapmapfile result = textData.linkageToChrom(inputFile,4,skipCheck); } File infoFile; if(infoFileName.equals("")) { infoFile = null; }else{ infoFile = new File(infoFileName); } if (result != null){ textData.prepareMarkerInput(infoFile,textData.getPedFile().getHMInfo()); }else{ textData.prepareMarkerInput(infoFile,null); } if(!quietMode && infoFile != null){ System.out.println("Using marker file " + infoFile.getName()); } if(outputCheck && result != null){ CheckDataPanel cp = new CheckDataPanel(textData, false); cp.printTable(validateOutputFile(fileName + ".CHECK")); } Vector cust = new Vector(); if(outputType != -1){ textData.generateDPrimeTable(); Haplotype[][] haplos; switch(outputType){ case BLOX_GABRIEL: OutputFile = validateOutputFile(fileName + ".GABRIELblocks"); break; case BLOX_4GAM: OutputFile = validateOutputFile(fileName + ".4GAMblocks"); break; case BLOX_SPINE: OutputFile = validateOutputFile(fileName + ".SPINEblocks"); break; case BLOX_CUSTOM: OutputFile = validateOutputFile(fileName + ".CUSTblocks"); //read in the blocks file File blocksFile = new File(blockFileName); cust = textData.readBlocks(blocksFile); break; default: OutputFile = validateOutputFile(fileName + ".GABRIELblocks"); break; } //this handles output type ALL if(outputType == BLOX_ALL) { OutputFile = validateOutputFile(fileName + ".GABRIELblocks"); textData.guessBlocks(BLOX_GABRIEL); haplos = textData.generateHaplotypes(textData.blocks, 1, false); textData.saveHapsToText(orderHaps(haplos, textData), textData.getMultiDprime(), OutputFile); OutputFile = validateOutputFile(fileName + ".4GAMblocks"); textData.guessBlocks(BLOX_4GAM); haplos = textData.generateHaplotypes(textData.blocks, 1, false); textData.saveHapsToText(orderHaps(haplos, textData), textData.getMultiDprime(), OutputFile); OutputFile = validateOutputFile(fileName + ".SPINEblocks"); textData.guessBlocks(BLOX_SPINE); haplos = textData.generateHaplotypes(textData.blocks, 1, false); textData.saveHapsToText(orderHaps(haplos, textData), textData.getMultiDprime(), OutputFile); }else{ textData.guessBlocks(outputType, cust); haplos = textData.generateHaplotypes(textData.blocks, 1, false); textData.saveHapsToText(orderHaps(haplos, textData), textData.getMultiDprime(), OutputFile); } } if(outputDprime) { OutputFile = validateOutputFile(fileName + ".LD"); if (textData.dpTable != null){ textData.saveDprimeToText(OutputFile, TABLE_TYPE, 0, Chromosome.getSize()); }else{ textData.saveDprimeToText(OutputFile, LIVE_TYPE, 0, Chromosome.getSize()); } } if (outputPNG || outputCompressedPNG){ OutputFile = validateOutputFile(fileName + ".LD.PNG"); if (textData.dpTable == null){ textData.generateDPrimeTable(); textData.guessBlocks(BLOX_CUSTOM, new Vector()); } if (trackFileName != null){ textData.readAnalysisTrack(new File(trackFileName)); } DPrimeDisplay dpd = new DPrimeDisplay(textData); BufferedImage i = dpd.export(0,Chromosome.getSize(),outputCompressedPNG); try{ Jimi.putImage("image/png", i, OutputFile.getName()); }catch(JimiException je){ System.out.println(je.getMessage()); } } //if(fileType){ //TDT.calcTrioTDT(textData.chromosomes); //TODO: Deal with this. why do we calc TDT? and make sure not to do it except when appropriate //} } catch(IOException e){ System.err.println("An error has occured. This probably has to do with file input or output"); } catch(HaploViewException e){ System.err.println(e.getMessage()); } catch(PedFileException pfe) { System.err.println(pfe.getMessage()); } } |
if (f.canWrite()){ System.out.println("File " + f.getName() + " can not be written."); System.exit(1); } | private File validateOutputFile(String fn){ File f = new File(fn); if (f.canWrite()){ System.out.println("File " + f.getName() + " can not be written."); System.exit(1); } if (f.exists() && !quietMode){ System.out.println("File " + f.getName() + " already exists and will be overwritten."); } return f; } |
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protected static void addBodyRow(ProfileManager pm, SQLColumn col, PdfPTable table, | protected void addBodyRow(ProfileManager pm, SQLColumn col, PdfPTable table, | protected static void addBodyRow(ProfileManager pm, SQLColumn col, PdfPTable table, BaseFont bf, Font f, float fsize, float[] widths) throws DocumentException, IOException, ArchitectException, SQLException, InstantiationException, IllegalAccessException { TableProfileResult tProfile = (TableProfileResult) pm.getResult(col.getParentTable()); ColumnProfileResult cProfile = (ColumnProfileResult) pm.getResult(col); DDLGenerator gddl = DDLUtils.createDDLGenerator( col.getParentTable().getParentDatabase().getDataSource()); DecimalFormat pctFormat = new DecimalFormat("0%"); int rowCount = -1; if ( tProfile != null && tProfile.isError() != true ) { rowCount = tProfile.getRowCount(); } java.util.List<ColumnValueCount> topTen = null; if ( cProfile != null && cProfile.isError() != true ) { topTen = cProfile.getValueCount(); } final int ncols = 17; for (int colNo = 0; colNo < ncols; colNo++) { String contents; int alignment; if (colNo == 0) { if ( tProfile == null || tProfile.isError() ) { contents = col.getParentTable().getName() + "\nProfiling Error:\n"; if ( tProfile != null && tProfile.getEx() != null ) contents += tProfile.getEx(); } else { contents = col.getParentTable().getName(); } alignment = Element.ALIGN_LEFT; } else if (colNo == 1) { contents = String.valueOf(rowCount); alignment = Element.ALIGN_RIGHT; } else if (colNo == 2) { contents = col.getName(); alignment = Element.ALIGN_LEFT; } else if (colNo == 3) { contents = gddl.columnType(col); alignment = Element.ALIGN_LEFT; } else if (colNo == 4) { contents = col.isDefinitelyNullable() ? "Y" : "N"; alignment = Element.ALIGN_CENTER; } else if (colNo == 5) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getNullCount()); alignment = Element.ALIGN_RIGHT; } else { contents = "Column Profiling Error"; alignment = Element.ALIGN_LEFT; } } else if (colNo == 6) { if ( cProfile != null && !cProfile.isError() ) { if (rowCount == 0) { contents = "N/A"; alignment = Element.ALIGN_CENTER; } else { contents = pctFormat.format(cProfile.getNullCount() / (double) rowCount); alignment = Element.ALIGN_RIGHT; } } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 7) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getDistinctValueCount()); alignment = Element.ALIGN_RIGHT; } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 8) { if ( cProfile != null && !cProfile.isError() ) { if (rowCount == 0) { contents = "N/A"; alignment = Element.ALIGN_CENTER; } else { contents = pctFormat.format(cProfile.getDistinctValueCount() / (double) rowCount); alignment = Element.ALIGN_RIGHT; } } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 9) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getMinLength()); alignment = Element.ALIGN_RIGHT; } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 10) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getMaxLength()); alignment = Element.ALIGN_RIGHT; } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 11) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getAvgLength()); alignment = Element.ALIGN_RIGHT; } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 12) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getMinValue()); if (cProfile.getMinValue() == null) { alignment = Element.ALIGN_CENTER; } else if (cProfile.getMinValue() instanceof Number) { alignment = Element.ALIGN_RIGHT; } else { alignment = Element.ALIGN_LEFT; } } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 13) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getMaxValue()); if (cProfile.getMaxValue() == null) { alignment = Element.ALIGN_CENTER; } else if (cProfile.getMaxValue() instanceof Number) { alignment = Element.ALIGN_RIGHT; } else { alignment = Element.ALIGN_LEFT; } } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 14) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getAvgValue()); if (cProfile.getAvgValue() == null) { alignment = Element.ALIGN_CENTER; } else if (cProfile.getAvgValue() instanceof Number) { alignment = Element.ALIGN_RIGHT; } else { alignment = Element.ALIGN_LEFT; } } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 15) { if ( cProfile != null && !cProfile.isError() && topTen != null ) { Object value = null; StringBuffer sb = new StringBuffer(); for ( ColumnValueCount cvc : topTen ) { value = cvc.getValue(); sb.append(value).append("\n"); } contents = sb.toString(); if (value == null) { alignment = Element.ALIGN_CENTER; } else if (value instanceof Number) { alignment = Element.ALIGN_RIGHT; } else { alignment = Element.ALIGN_LEFT; } } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 16) { if ( cProfile != null && !cProfile.isError() ) { StringBuffer sb = new StringBuffer(); for ( ColumnValueCount cvc : topTen ) { sb.append(cvc.getCount()).append("\n"); } contents = sb.toString(); alignment = Element.ALIGN_RIGHT; } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else { throw new IllegalStateException("I don't know about column "+colNo); } // update column width to reflect the widest cell widths[colNo] = Math.max(widths[colNo], bf.getWidthPoint((String) contents, fsize)); Phrase phr = new Phrase((String) contents, f); PdfPCell cell = new PdfPCell(phr); cell.setBorder(Rectangle.NO_BORDER); cell.setHorizontalAlignment(alignment); table.addCell(cell); } } |
final int ncols = 17; for (int colNo = 0; colNo < ncols; colNo++) { | for (int colNo = 0; colNo < totalColumn; colNo++) { | protected static void addBodyRow(ProfileManager pm, SQLColumn col, PdfPTable table, BaseFont bf, Font f, float fsize, float[] widths) throws DocumentException, IOException, ArchitectException, SQLException, InstantiationException, IllegalAccessException { TableProfileResult tProfile = (TableProfileResult) pm.getResult(col.getParentTable()); ColumnProfileResult cProfile = (ColumnProfileResult) pm.getResult(col); DDLGenerator gddl = DDLUtils.createDDLGenerator( col.getParentTable().getParentDatabase().getDataSource()); DecimalFormat pctFormat = new DecimalFormat("0%"); int rowCount = -1; if ( tProfile != null && tProfile.isError() != true ) { rowCount = tProfile.getRowCount(); } java.util.List<ColumnValueCount> topTen = null; if ( cProfile != null && cProfile.isError() != true ) { topTen = cProfile.getValueCount(); } final int ncols = 17; for (int colNo = 0; colNo < ncols; colNo++) { String contents; int alignment; if (colNo == 0) { if ( tProfile == null || tProfile.isError() ) { contents = col.getParentTable().getName() + "\nProfiling Error:\n"; if ( tProfile != null && tProfile.getEx() != null ) contents += tProfile.getEx(); } else { contents = col.getParentTable().getName(); } alignment = Element.ALIGN_LEFT; } else if (colNo == 1) { contents = String.valueOf(rowCount); alignment = Element.ALIGN_RIGHT; } else if (colNo == 2) { contents = col.getName(); alignment = Element.ALIGN_LEFT; } else if (colNo == 3) { contents = gddl.columnType(col); alignment = Element.ALIGN_LEFT; } else if (colNo == 4) { contents = col.isDefinitelyNullable() ? "Y" : "N"; alignment = Element.ALIGN_CENTER; } else if (colNo == 5) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getNullCount()); alignment = Element.ALIGN_RIGHT; } else { contents = "Column Profiling Error"; alignment = Element.ALIGN_LEFT; } } else if (colNo == 6) { if ( cProfile != null && !cProfile.isError() ) { if (rowCount == 0) { contents = "N/A"; alignment = Element.ALIGN_CENTER; } else { contents = pctFormat.format(cProfile.getNullCount() / (double) rowCount); alignment = Element.ALIGN_RIGHT; } } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 7) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getDistinctValueCount()); alignment = Element.ALIGN_RIGHT; } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 8) { if ( cProfile != null && !cProfile.isError() ) { if (rowCount == 0) { contents = "N/A"; alignment = Element.ALIGN_CENTER; } else { contents = pctFormat.format(cProfile.getDistinctValueCount() / (double) rowCount); alignment = Element.ALIGN_RIGHT; } } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 9) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getMinLength()); alignment = Element.ALIGN_RIGHT; } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 10) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getMaxLength()); alignment = Element.ALIGN_RIGHT; } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 11) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getAvgLength()); alignment = Element.ALIGN_RIGHT; } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 12) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getMinValue()); if (cProfile.getMinValue() == null) { alignment = Element.ALIGN_CENTER; } else if (cProfile.getMinValue() instanceof Number) { alignment = Element.ALIGN_RIGHT; } else { alignment = Element.ALIGN_LEFT; } } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 13) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getMaxValue()); if (cProfile.getMaxValue() == null) { alignment = Element.ALIGN_CENTER; } else if (cProfile.getMaxValue() instanceof Number) { alignment = Element.ALIGN_RIGHT; } else { alignment = Element.ALIGN_LEFT; } } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 14) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getAvgValue()); if (cProfile.getAvgValue() == null) { alignment = Element.ALIGN_CENTER; } else if (cProfile.getAvgValue() instanceof Number) { alignment = Element.ALIGN_RIGHT; } else { alignment = Element.ALIGN_LEFT; } } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 15) { if ( cProfile != null && !cProfile.isError() && topTen != null ) { Object value = null; StringBuffer sb = new StringBuffer(); for ( ColumnValueCount cvc : topTen ) { value = cvc.getValue(); sb.append(value).append("\n"); } contents = sb.toString(); if (value == null) { alignment = Element.ALIGN_CENTER; } else if (value instanceof Number) { alignment = Element.ALIGN_RIGHT; } else { alignment = Element.ALIGN_LEFT; } } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 16) { if ( cProfile != null && !cProfile.isError() ) { StringBuffer sb = new StringBuffer(); for ( ColumnValueCount cvc : topTen ) { sb.append(cvc.getCount()).append("\n"); } contents = sb.toString(); alignment = Element.ALIGN_RIGHT; } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else { throw new IllegalStateException("I don't know about column "+colNo); } // update column width to reflect the widest cell widths[colNo] = Math.max(widths[colNo], bf.getWidthPoint((String) contents, fsize)); Phrase phr = new Phrase((String) contents, f); PdfPCell cell = new PdfPCell(phr); cell.setBorder(Rectangle.NO_BORDER); cell.setHorizontalAlignment(alignment); table.addCell(cell); } } |
contents = col.isDefinitelyNullable() ? "Y" : "N"; alignment = Element.ALIGN_CENTER; | if ( cProfile != null && !cProfile.isError() ) { if ( col.isDefinitelyNullable() ) { contents = String.valueOf(cProfile.getNullCount()); if (rowCount == 0) { contents += " / N/A"; alignment = Element.ALIGN_CENTER; } else { contents += " / " + pctFormat.format(cProfile.getNullCount() / (double) rowCount); alignment = Element.ALIGN_RIGHT; } } else { contents = "NOT NULL"; } alignment = Element.ALIGN_RIGHT; } else { contents = "Column Profiling Error"; alignment = Element.ALIGN_LEFT; } | protected static void addBodyRow(ProfileManager pm, SQLColumn col, PdfPTable table, BaseFont bf, Font f, float fsize, float[] widths) throws DocumentException, IOException, ArchitectException, SQLException, InstantiationException, IllegalAccessException { TableProfileResult tProfile = (TableProfileResult) pm.getResult(col.getParentTable()); ColumnProfileResult cProfile = (ColumnProfileResult) pm.getResult(col); DDLGenerator gddl = DDLUtils.createDDLGenerator( col.getParentTable().getParentDatabase().getDataSource()); DecimalFormat pctFormat = new DecimalFormat("0%"); int rowCount = -1; if ( tProfile != null && tProfile.isError() != true ) { rowCount = tProfile.getRowCount(); } java.util.List<ColumnValueCount> topTen = null; if ( cProfile != null && cProfile.isError() != true ) { topTen = cProfile.getValueCount(); } final int ncols = 17; for (int colNo = 0; colNo < ncols; colNo++) { String contents; int alignment; if (colNo == 0) { if ( tProfile == null || tProfile.isError() ) { contents = col.getParentTable().getName() + "\nProfiling Error:\n"; if ( tProfile != null && tProfile.getEx() != null ) contents += tProfile.getEx(); } else { contents = col.getParentTable().getName(); } alignment = Element.ALIGN_LEFT; } else if (colNo == 1) { contents = String.valueOf(rowCount); alignment = Element.ALIGN_RIGHT; } else if (colNo == 2) { contents = col.getName(); alignment = Element.ALIGN_LEFT; } else if (colNo == 3) { contents = gddl.columnType(col); alignment = Element.ALIGN_LEFT; } else if (colNo == 4) { contents = col.isDefinitelyNullable() ? "Y" : "N"; alignment = Element.ALIGN_CENTER; } else if (colNo == 5) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getNullCount()); alignment = Element.ALIGN_RIGHT; } else { contents = "Column Profiling Error"; alignment = Element.ALIGN_LEFT; } } else if (colNo == 6) { if ( cProfile != null && !cProfile.isError() ) { if (rowCount == 0) { contents = "N/A"; alignment = Element.ALIGN_CENTER; } else { contents = pctFormat.format(cProfile.getNullCount() / (double) rowCount); alignment = Element.ALIGN_RIGHT; } } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 7) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getDistinctValueCount()); alignment = Element.ALIGN_RIGHT; } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 8) { if ( cProfile != null && !cProfile.isError() ) { if (rowCount == 0) { contents = "N/A"; alignment = Element.ALIGN_CENTER; } else { contents = pctFormat.format(cProfile.getDistinctValueCount() / (double) rowCount); alignment = Element.ALIGN_RIGHT; } } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 9) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getMinLength()); alignment = Element.ALIGN_RIGHT; } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 10) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getMaxLength()); alignment = Element.ALIGN_RIGHT; } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 11) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getAvgLength()); alignment = Element.ALIGN_RIGHT; } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 12) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getMinValue()); if (cProfile.getMinValue() == null) { alignment = Element.ALIGN_CENTER; } else if (cProfile.getMinValue() instanceof Number) { alignment = Element.ALIGN_RIGHT; } else { alignment = Element.ALIGN_LEFT; } } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 13) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getMaxValue()); if (cProfile.getMaxValue() == null) { alignment = Element.ALIGN_CENTER; } else if (cProfile.getMaxValue() instanceof Number) { alignment = Element.ALIGN_RIGHT; } else { alignment = Element.ALIGN_LEFT; } } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 14) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getAvgValue()); if (cProfile.getAvgValue() == null) { alignment = Element.ALIGN_CENTER; } else if (cProfile.getAvgValue() instanceof Number) { alignment = Element.ALIGN_RIGHT; } else { alignment = Element.ALIGN_LEFT; } } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 15) { if ( cProfile != null && !cProfile.isError() && topTen != null ) { Object value = null; StringBuffer sb = new StringBuffer(); for ( ColumnValueCount cvc : topTen ) { value = cvc.getValue(); sb.append(value).append("\n"); } contents = sb.toString(); if (value == null) { alignment = Element.ALIGN_CENTER; } else if (value instanceof Number) { alignment = Element.ALIGN_RIGHT; } else { alignment = Element.ALIGN_LEFT; } } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 16) { if ( cProfile != null && !cProfile.isError() ) { StringBuffer sb = new StringBuffer(); for ( ColumnValueCount cvc : topTen ) { sb.append(cvc.getCount()).append("\n"); } contents = sb.toString(); alignment = Element.ALIGN_RIGHT; } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else { throw new IllegalStateException("I don't know about column "+colNo); } // update column width to reflect the widest cell widths[colNo] = Math.max(widths[colNo], bf.getWidthPoint((String) contents, fsize)); Phrase phr = new Phrase((String) contents, f); PdfPCell cell = new PdfPCell(phr); cell.setBorder(Rectangle.NO_BORDER); cell.setHorizontalAlignment(alignment); table.addCell(cell); } } |
contents = String.valueOf(cProfile.getNullCount()); alignment = Element.ALIGN_RIGHT; } else { contents = "Column Profiling Error"; | contents = String.valueOf(cProfile.getDistinctValueCount()); if (rowCount == 0) { contents += " / N/A"; } else { contents += " / " + pctFormat.format(cProfile.getDistinctValueCount() / (double) rowCount); } alignment = Element.ALIGN_RIGHT; } else { contents = ""; | protected static void addBodyRow(ProfileManager pm, SQLColumn col, PdfPTable table, BaseFont bf, Font f, float fsize, float[] widths) throws DocumentException, IOException, ArchitectException, SQLException, InstantiationException, IllegalAccessException { TableProfileResult tProfile = (TableProfileResult) pm.getResult(col.getParentTable()); ColumnProfileResult cProfile = (ColumnProfileResult) pm.getResult(col); DDLGenerator gddl = DDLUtils.createDDLGenerator( col.getParentTable().getParentDatabase().getDataSource()); DecimalFormat pctFormat = new DecimalFormat("0%"); int rowCount = -1; if ( tProfile != null && tProfile.isError() != true ) { rowCount = tProfile.getRowCount(); } java.util.List<ColumnValueCount> topTen = null; if ( cProfile != null && cProfile.isError() != true ) { topTen = cProfile.getValueCount(); } final int ncols = 17; for (int colNo = 0; colNo < ncols; colNo++) { String contents; int alignment; if (colNo == 0) { if ( tProfile == null || tProfile.isError() ) { contents = col.getParentTable().getName() + "\nProfiling Error:\n"; if ( tProfile != null && tProfile.getEx() != null ) contents += tProfile.getEx(); } else { contents = col.getParentTable().getName(); } alignment = Element.ALIGN_LEFT; } else if (colNo == 1) { contents = String.valueOf(rowCount); alignment = Element.ALIGN_RIGHT; } else if (colNo == 2) { contents = col.getName(); alignment = Element.ALIGN_LEFT; } else if (colNo == 3) { contents = gddl.columnType(col); alignment = Element.ALIGN_LEFT; } else if (colNo == 4) { contents = col.isDefinitelyNullable() ? "Y" : "N"; alignment = Element.ALIGN_CENTER; } else if (colNo == 5) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getNullCount()); alignment = Element.ALIGN_RIGHT; } else { contents = "Column Profiling Error"; alignment = Element.ALIGN_LEFT; } } else if (colNo == 6) { if ( cProfile != null && !cProfile.isError() ) { if (rowCount == 0) { contents = "N/A"; alignment = Element.ALIGN_CENTER; } else { contents = pctFormat.format(cProfile.getNullCount() / (double) rowCount); alignment = Element.ALIGN_RIGHT; } } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 7) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getDistinctValueCount()); alignment = Element.ALIGN_RIGHT; } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 8) { if ( cProfile != null && !cProfile.isError() ) { if (rowCount == 0) { contents = "N/A"; alignment = Element.ALIGN_CENTER; } else { contents = pctFormat.format(cProfile.getDistinctValueCount() / (double) rowCount); alignment = Element.ALIGN_RIGHT; } } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 9) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getMinLength()); alignment = Element.ALIGN_RIGHT; } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 10) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getMaxLength()); alignment = Element.ALIGN_RIGHT; } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 11) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getAvgLength()); alignment = Element.ALIGN_RIGHT; } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 12) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getMinValue()); if (cProfile.getMinValue() == null) { alignment = Element.ALIGN_CENTER; } else if (cProfile.getMinValue() instanceof Number) { alignment = Element.ALIGN_RIGHT; } else { alignment = Element.ALIGN_LEFT; } } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 13) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getMaxValue()); if (cProfile.getMaxValue() == null) { alignment = Element.ALIGN_CENTER; } else if (cProfile.getMaxValue() instanceof Number) { alignment = Element.ALIGN_RIGHT; } else { alignment = Element.ALIGN_LEFT; } } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 14) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getAvgValue()); if (cProfile.getAvgValue() == null) { alignment = Element.ALIGN_CENTER; } else if (cProfile.getAvgValue() instanceof Number) { alignment = Element.ALIGN_RIGHT; } else { alignment = Element.ALIGN_LEFT; } } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 15) { if ( cProfile != null && !cProfile.isError() && topTen != null ) { Object value = null; StringBuffer sb = new StringBuffer(); for ( ColumnValueCount cvc : topTen ) { value = cvc.getValue(); sb.append(value).append("\n"); } contents = sb.toString(); if (value == null) { alignment = Element.ALIGN_CENTER; } else if (value instanceof Number) { alignment = Element.ALIGN_RIGHT; } else { alignment = Element.ALIGN_LEFT; } } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 16) { if ( cProfile != null && !cProfile.isError() ) { StringBuffer sb = new StringBuffer(); for ( ColumnValueCount cvc : topTen ) { sb.append(cvc.getCount()).append("\n"); } contents = sb.toString(); alignment = Element.ALIGN_RIGHT; } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else { throw new IllegalStateException("I don't know about column "+colNo); } // update column width to reflect the widest cell widths[colNo] = Math.max(widths[colNo], bf.getWidthPoint((String) contents, fsize)); Phrase phr = new Phrase((String) contents, f); PdfPCell cell = new PdfPCell(phr); cell.setBorder(Rectangle.NO_BORDER); cell.setHorizontalAlignment(alignment); table.addCell(cell); } } |
if (rowCount == 0) { contents = "N/A"; alignment = Element.ALIGN_CENTER; } else { contents = pctFormat.format(cProfile.getNullCount() / (double) rowCount); alignment = Element.ALIGN_RIGHT; } | contents = String.valueOf(cProfile.getMinLength()); alignment = Element.ALIGN_RIGHT; | protected static void addBodyRow(ProfileManager pm, SQLColumn col, PdfPTable table, BaseFont bf, Font f, float fsize, float[] widths) throws DocumentException, IOException, ArchitectException, SQLException, InstantiationException, IllegalAccessException { TableProfileResult tProfile = (TableProfileResult) pm.getResult(col.getParentTable()); ColumnProfileResult cProfile = (ColumnProfileResult) pm.getResult(col); DDLGenerator gddl = DDLUtils.createDDLGenerator( col.getParentTable().getParentDatabase().getDataSource()); DecimalFormat pctFormat = new DecimalFormat("0%"); int rowCount = -1; if ( tProfile != null && tProfile.isError() != true ) { rowCount = tProfile.getRowCount(); } java.util.List<ColumnValueCount> topTen = null; if ( cProfile != null && cProfile.isError() != true ) { topTen = cProfile.getValueCount(); } final int ncols = 17; for (int colNo = 0; colNo < ncols; colNo++) { String contents; int alignment; if (colNo == 0) { if ( tProfile == null || tProfile.isError() ) { contents = col.getParentTable().getName() + "\nProfiling Error:\n"; if ( tProfile != null && tProfile.getEx() != null ) contents += tProfile.getEx(); } else { contents = col.getParentTable().getName(); } alignment = Element.ALIGN_LEFT; } else if (colNo == 1) { contents = String.valueOf(rowCount); alignment = Element.ALIGN_RIGHT; } else if (colNo == 2) { contents = col.getName(); alignment = Element.ALIGN_LEFT; } else if (colNo == 3) { contents = gddl.columnType(col); alignment = Element.ALIGN_LEFT; } else if (colNo == 4) { contents = col.isDefinitelyNullable() ? "Y" : "N"; alignment = Element.ALIGN_CENTER; } else if (colNo == 5) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getNullCount()); alignment = Element.ALIGN_RIGHT; } else { contents = "Column Profiling Error"; alignment = Element.ALIGN_LEFT; } } else if (colNo == 6) { if ( cProfile != null && !cProfile.isError() ) { if (rowCount == 0) { contents = "N/A"; alignment = Element.ALIGN_CENTER; } else { contents = pctFormat.format(cProfile.getNullCount() / (double) rowCount); alignment = Element.ALIGN_RIGHT; } } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 7) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getDistinctValueCount()); alignment = Element.ALIGN_RIGHT; } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 8) { if ( cProfile != null && !cProfile.isError() ) { if (rowCount == 0) { contents = "N/A"; alignment = Element.ALIGN_CENTER; } else { contents = pctFormat.format(cProfile.getDistinctValueCount() / (double) rowCount); alignment = Element.ALIGN_RIGHT; } } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 9) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getMinLength()); alignment = Element.ALIGN_RIGHT; } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 10) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getMaxLength()); alignment = Element.ALIGN_RIGHT; } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 11) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getAvgLength()); alignment = Element.ALIGN_RIGHT; } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 12) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getMinValue()); if (cProfile.getMinValue() == null) { alignment = Element.ALIGN_CENTER; } else if (cProfile.getMinValue() instanceof Number) { alignment = Element.ALIGN_RIGHT; } else { alignment = Element.ALIGN_LEFT; } } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 13) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getMaxValue()); if (cProfile.getMaxValue() == null) { alignment = Element.ALIGN_CENTER; } else if (cProfile.getMaxValue() instanceof Number) { alignment = Element.ALIGN_RIGHT; } else { alignment = Element.ALIGN_LEFT; } } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 14) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getAvgValue()); if (cProfile.getAvgValue() == null) { alignment = Element.ALIGN_CENTER; } else if (cProfile.getAvgValue() instanceof Number) { alignment = Element.ALIGN_RIGHT; } else { alignment = Element.ALIGN_LEFT; } } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 15) { if ( cProfile != null && !cProfile.isError() && topTen != null ) { Object value = null; StringBuffer sb = new StringBuffer(); for ( ColumnValueCount cvc : topTen ) { value = cvc.getValue(); sb.append(value).append("\n"); } contents = sb.toString(); if (value == null) { alignment = Element.ALIGN_CENTER; } else if (value instanceof Number) { alignment = Element.ALIGN_RIGHT; } else { alignment = Element.ALIGN_LEFT; } } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 16) { if ( cProfile != null && !cProfile.isError() ) { StringBuffer sb = new StringBuffer(); for ( ColumnValueCount cvc : topTen ) { sb.append(cvc.getCount()).append("\n"); } contents = sb.toString(); alignment = Element.ALIGN_RIGHT; } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else { throw new IllegalStateException("I don't know about column "+colNo); } // update column width to reflect the widest cell widths[colNo] = Math.max(widths[colNo], bf.getWidthPoint((String) contents, fsize)); Phrase phr = new Phrase((String) contents, f); PdfPCell cell = new PdfPCell(phr); cell.setBorder(Rectangle.NO_BORDER); cell.setHorizontalAlignment(alignment); table.addCell(cell); } } |
contents = String.valueOf(cProfile.getDistinctValueCount()); | contents = String.valueOf(cProfile.getMaxLength()); | protected static void addBodyRow(ProfileManager pm, SQLColumn col, PdfPTable table, BaseFont bf, Font f, float fsize, float[] widths) throws DocumentException, IOException, ArchitectException, SQLException, InstantiationException, IllegalAccessException { TableProfileResult tProfile = (TableProfileResult) pm.getResult(col.getParentTable()); ColumnProfileResult cProfile = (ColumnProfileResult) pm.getResult(col); DDLGenerator gddl = DDLUtils.createDDLGenerator( col.getParentTable().getParentDatabase().getDataSource()); DecimalFormat pctFormat = new DecimalFormat("0%"); int rowCount = -1; if ( tProfile != null && tProfile.isError() != true ) { rowCount = tProfile.getRowCount(); } java.util.List<ColumnValueCount> topTen = null; if ( cProfile != null && cProfile.isError() != true ) { topTen = cProfile.getValueCount(); } final int ncols = 17; for (int colNo = 0; colNo < ncols; colNo++) { String contents; int alignment; if (colNo == 0) { if ( tProfile == null || tProfile.isError() ) { contents = col.getParentTable().getName() + "\nProfiling Error:\n"; if ( tProfile != null && tProfile.getEx() != null ) contents += tProfile.getEx(); } else { contents = col.getParentTable().getName(); } alignment = Element.ALIGN_LEFT; } else if (colNo == 1) { contents = String.valueOf(rowCount); alignment = Element.ALIGN_RIGHT; } else if (colNo == 2) { contents = col.getName(); alignment = Element.ALIGN_LEFT; } else if (colNo == 3) { contents = gddl.columnType(col); alignment = Element.ALIGN_LEFT; } else if (colNo == 4) { contents = col.isDefinitelyNullable() ? "Y" : "N"; alignment = Element.ALIGN_CENTER; } else if (colNo == 5) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getNullCount()); alignment = Element.ALIGN_RIGHT; } else { contents = "Column Profiling Error"; alignment = Element.ALIGN_LEFT; } } else if (colNo == 6) { if ( cProfile != null && !cProfile.isError() ) { if (rowCount == 0) { contents = "N/A"; alignment = Element.ALIGN_CENTER; } else { contents = pctFormat.format(cProfile.getNullCount() / (double) rowCount); alignment = Element.ALIGN_RIGHT; } } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 7) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getDistinctValueCount()); alignment = Element.ALIGN_RIGHT; } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 8) { if ( cProfile != null && !cProfile.isError() ) { if (rowCount == 0) { contents = "N/A"; alignment = Element.ALIGN_CENTER; } else { contents = pctFormat.format(cProfile.getDistinctValueCount() / (double) rowCount); alignment = Element.ALIGN_RIGHT; } } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 9) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getMinLength()); alignment = Element.ALIGN_RIGHT; } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 10) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getMaxLength()); alignment = Element.ALIGN_RIGHT; } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 11) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getAvgLength()); alignment = Element.ALIGN_RIGHT; } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 12) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getMinValue()); if (cProfile.getMinValue() == null) { alignment = Element.ALIGN_CENTER; } else if (cProfile.getMinValue() instanceof Number) { alignment = Element.ALIGN_RIGHT; } else { alignment = Element.ALIGN_LEFT; } } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 13) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getMaxValue()); if (cProfile.getMaxValue() == null) { alignment = Element.ALIGN_CENTER; } else if (cProfile.getMaxValue() instanceof Number) { alignment = Element.ALIGN_RIGHT; } else { alignment = Element.ALIGN_LEFT; } } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 14) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getAvgValue()); if (cProfile.getAvgValue() == null) { alignment = Element.ALIGN_CENTER; } else if (cProfile.getAvgValue() instanceof Number) { alignment = Element.ALIGN_RIGHT; } else { alignment = Element.ALIGN_LEFT; } } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 15) { if ( cProfile != null && !cProfile.isError() && topTen != null ) { Object value = null; StringBuffer sb = new StringBuffer(); for ( ColumnValueCount cvc : topTen ) { value = cvc.getValue(); sb.append(value).append("\n"); } contents = sb.toString(); if (value == null) { alignment = Element.ALIGN_CENTER; } else if (value instanceof Number) { alignment = Element.ALIGN_RIGHT; } else { alignment = Element.ALIGN_LEFT; } } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 16) { if ( cProfile != null && !cProfile.isError() ) { StringBuffer sb = new StringBuffer(); for ( ColumnValueCount cvc : topTen ) { sb.append(cvc.getCount()).append("\n"); } contents = sb.toString(); alignment = Element.ALIGN_RIGHT; } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else { throw new IllegalStateException("I don't know about column "+colNo); } // update column width to reflect the widest cell widths[colNo] = Math.max(widths[colNo], bf.getWidthPoint((String) contents, fsize)); Phrase phr = new Phrase((String) contents, f); PdfPCell cell = new PdfPCell(phr); cell.setBorder(Rectangle.NO_BORDER); cell.setHorizontalAlignment(alignment); table.addCell(cell); } } |
if (rowCount == 0) { contents = "N/A"; alignment = Element.ALIGN_CENTER; } else { contents = pctFormat.format(cProfile.getDistinctValueCount() / (double) rowCount); alignment = Element.ALIGN_RIGHT; } | contents = String.valueOf(cProfile.getAvgLength()); alignment = Element.ALIGN_RIGHT; | protected static void addBodyRow(ProfileManager pm, SQLColumn col, PdfPTable table, BaseFont bf, Font f, float fsize, float[] widths) throws DocumentException, IOException, ArchitectException, SQLException, InstantiationException, IllegalAccessException { TableProfileResult tProfile = (TableProfileResult) pm.getResult(col.getParentTable()); ColumnProfileResult cProfile = (ColumnProfileResult) pm.getResult(col); DDLGenerator gddl = DDLUtils.createDDLGenerator( col.getParentTable().getParentDatabase().getDataSource()); DecimalFormat pctFormat = new DecimalFormat("0%"); int rowCount = -1; if ( tProfile != null && tProfile.isError() != true ) { rowCount = tProfile.getRowCount(); } java.util.List<ColumnValueCount> topTen = null; if ( cProfile != null && cProfile.isError() != true ) { topTen = cProfile.getValueCount(); } final int ncols = 17; for (int colNo = 0; colNo < ncols; colNo++) { String contents; int alignment; if (colNo == 0) { if ( tProfile == null || tProfile.isError() ) { contents = col.getParentTable().getName() + "\nProfiling Error:\n"; if ( tProfile != null && tProfile.getEx() != null ) contents += tProfile.getEx(); } else { contents = col.getParentTable().getName(); } alignment = Element.ALIGN_LEFT; } else if (colNo == 1) { contents = String.valueOf(rowCount); alignment = Element.ALIGN_RIGHT; } else if (colNo == 2) { contents = col.getName(); alignment = Element.ALIGN_LEFT; } else if (colNo == 3) { contents = gddl.columnType(col); alignment = Element.ALIGN_LEFT; } else if (colNo == 4) { contents = col.isDefinitelyNullable() ? "Y" : "N"; alignment = Element.ALIGN_CENTER; } else if (colNo == 5) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getNullCount()); alignment = Element.ALIGN_RIGHT; } else { contents = "Column Profiling Error"; alignment = Element.ALIGN_LEFT; } } else if (colNo == 6) { if ( cProfile != null && !cProfile.isError() ) { if (rowCount == 0) { contents = "N/A"; alignment = Element.ALIGN_CENTER; } else { contents = pctFormat.format(cProfile.getNullCount() / (double) rowCount); alignment = Element.ALIGN_RIGHT; } } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 7) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getDistinctValueCount()); alignment = Element.ALIGN_RIGHT; } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 8) { if ( cProfile != null && !cProfile.isError() ) { if (rowCount == 0) { contents = "N/A"; alignment = Element.ALIGN_CENTER; } else { contents = pctFormat.format(cProfile.getDistinctValueCount() / (double) rowCount); alignment = Element.ALIGN_RIGHT; } } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 9) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getMinLength()); alignment = Element.ALIGN_RIGHT; } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 10) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getMaxLength()); alignment = Element.ALIGN_RIGHT; } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 11) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getAvgLength()); alignment = Element.ALIGN_RIGHT; } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 12) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getMinValue()); if (cProfile.getMinValue() == null) { alignment = Element.ALIGN_CENTER; } else if (cProfile.getMinValue() instanceof Number) { alignment = Element.ALIGN_RIGHT; } else { alignment = Element.ALIGN_LEFT; } } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 13) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getMaxValue()); if (cProfile.getMaxValue() == null) { alignment = Element.ALIGN_CENTER; } else if (cProfile.getMaxValue() instanceof Number) { alignment = Element.ALIGN_RIGHT; } else { alignment = Element.ALIGN_LEFT; } } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 14) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getAvgValue()); if (cProfile.getAvgValue() == null) { alignment = Element.ALIGN_CENTER; } else if (cProfile.getAvgValue() instanceof Number) { alignment = Element.ALIGN_RIGHT; } else { alignment = Element.ALIGN_LEFT; } } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 15) { if ( cProfile != null && !cProfile.isError() && topTen != null ) { Object value = null; StringBuffer sb = new StringBuffer(); for ( ColumnValueCount cvc : topTen ) { value = cvc.getValue(); sb.append(value).append("\n"); } contents = sb.toString(); if (value == null) { alignment = Element.ALIGN_CENTER; } else if (value instanceof Number) { alignment = Element.ALIGN_RIGHT; } else { alignment = Element.ALIGN_LEFT; } } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 16) { if ( cProfile != null && !cProfile.isError() ) { StringBuffer sb = new StringBuffer(); for ( ColumnValueCount cvc : topTen ) { sb.append(cvc.getCount()).append("\n"); } contents = sb.toString(); alignment = Element.ALIGN_RIGHT; } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else { throw new IllegalStateException("I don't know about column "+colNo); } // update column width to reflect the widest cell widths[colNo] = Math.max(widths[colNo], bf.getWidthPoint((String) contents, fsize)); Phrase phr = new Phrase((String) contents, f); PdfPCell cell = new PdfPCell(phr); cell.setBorder(Rectangle.NO_BORDER); cell.setHorizontalAlignment(alignment); table.addCell(cell); } } |
contents = String.valueOf(cProfile.getMinLength()); alignment = Element.ALIGN_RIGHT; } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 10) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getMaxLength()); alignment = Element.ALIGN_RIGHT; } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 11) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getAvgLength()); alignment = Element.ALIGN_RIGHT; } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 12) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getMinValue()); | protected static void addBodyRow(ProfileManager pm, SQLColumn col, PdfPTable table, BaseFont bf, Font f, float fsize, float[] widths) throws DocumentException, IOException, ArchitectException, SQLException, InstantiationException, IllegalAccessException { TableProfileResult tProfile = (TableProfileResult) pm.getResult(col.getParentTable()); ColumnProfileResult cProfile = (ColumnProfileResult) pm.getResult(col); DDLGenerator gddl = DDLUtils.createDDLGenerator( col.getParentTable().getParentDatabase().getDataSource()); DecimalFormat pctFormat = new DecimalFormat("0%"); int rowCount = -1; if ( tProfile != null && tProfile.isError() != true ) { rowCount = tProfile.getRowCount(); } java.util.List<ColumnValueCount> topTen = null; if ( cProfile != null && cProfile.isError() != true ) { topTen = cProfile.getValueCount(); } final int ncols = 17; for (int colNo = 0; colNo < ncols; colNo++) { String contents; int alignment; if (colNo == 0) { if ( tProfile == null || tProfile.isError() ) { contents = col.getParentTable().getName() + "\nProfiling Error:\n"; if ( tProfile != null && tProfile.getEx() != null ) contents += tProfile.getEx(); } else { contents = col.getParentTable().getName(); } alignment = Element.ALIGN_LEFT; } else if (colNo == 1) { contents = String.valueOf(rowCount); alignment = Element.ALIGN_RIGHT; } else if (colNo == 2) { contents = col.getName(); alignment = Element.ALIGN_LEFT; } else if (colNo == 3) { contents = gddl.columnType(col); alignment = Element.ALIGN_LEFT; } else if (colNo == 4) { contents = col.isDefinitelyNullable() ? "Y" : "N"; alignment = Element.ALIGN_CENTER; } else if (colNo == 5) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getNullCount()); alignment = Element.ALIGN_RIGHT; } else { contents = "Column Profiling Error"; alignment = Element.ALIGN_LEFT; } } else if (colNo == 6) { if ( cProfile != null && !cProfile.isError() ) { if (rowCount == 0) { contents = "N/A"; alignment = Element.ALIGN_CENTER; } else { contents = pctFormat.format(cProfile.getNullCount() / (double) rowCount); alignment = Element.ALIGN_RIGHT; } } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 7) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getDistinctValueCount()); alignment = Element.ALIGN_RIGHT; } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 8) { if ( cProfile != null && !cProfile.isError() ) { if (rowCount == 0) { contents = "N/A"; alignment = Element.ALIGN_CENTER; } else { contents = pctFormat.format(cProfile.getDistinctValueCount() / (double) rowCount); alignment = Element.ALIGN_RIGHT; } } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 9) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getMinLength()); alignment = Element.ALIGN_RIGHT; } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 10) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getMaxLength()); alignment = Element.ALIGN_RIGHT; } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 11) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getAvgLength()); alignment = Element.ALIGN_RIGHT; } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 12) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getMinValue()); if (cProfile.getMinValue() == null) { alignment = Element.ALIGN_CENTER; } else if (cProfile.getMinValue() instanceof Number) { alignment = Element.ALIGN_RIGHT; } else { alignment = Element.ALIGN_LEFT; } } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 13) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getMaxValue()); if (cProfile.getMaxValue() == null) { alignment = Element.ALIGN_CENTER; } else if (cProfile.getMaxValue() instanceof Number) { alignment = Element.ALIGN_RIGHT; } else { alignment = Element.ALIGN_LEFT; } } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 14) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getAvgValue()); if (cProfile.getAvgValue() == null) { alignment = Element.ALIGN_CENTER; } else if (cProfile.getAvgValue() instanceof Number) { alignment = Element.ALIGN_RIGHT; } else { alignment = Element.ALIGN_LEFT; } } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 15) { if ( cProfile != null && !cProfile.isError() && topTen != null ) { Object value = null; StringBuffer sb = new StringBuffer(); for ( ColumnValueCount cvc : topTen ) { value = cvc.getValue(); sb.append(value).append("\n"); } contents = sb.toString(); if (value == null) { alignment = Element.ALIGN_CENTER; } else if (value instanceof Number) { alignment = Element.ALIGN_RIGHT; } else { alignment = Element.ALIGN_LEFT; } } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 16) { if ( cProfile != null && !cProfile.isError() ) { StringBuffer sb = new StringBuffer(); for ( ColumnValueCount cvc : topTen ) { sb.append(cvc.getCount()).append("\n"); } contents = sb.toString(); alignment = Element.ALIGN_RIGHT; } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else { throw new IllegalStateException("I don't know about column "+colNo); } // update column width to reflect the widest cell widths[colNo] = Math.max(widths[colNo], bf.getWidthPoint((String) contents, fsize)); Phrase phr = new Phrase((String) contents, f); PdfPCell cell = new PdfPCell(phr); cell.setBorder(Rectangle.NO_BORDER); cell.setHorizontalAlignment(alignment); table.addCell(cell); } } |
|
} } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 13) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getMaxValue()); | contents = String.valueOf(cProfile.getMinValue()); } } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 10) { if ( cProfile != null && !cProfile.isError() ) { | protected static void addBodyRow(ProfileManager pm, SQLColumn col, PdfPTable table, BaseFont bf, Font f, float fsize, float[] widths) throws DocumentException, IOException, ArchitectException, SQLException, InstantiationException, IllegalAccessException { TableProfileResult tProfile = (TableProfileResult) pm.getResult(col.getParentTable()); ColumnProfileResult cProfile = (ColumnProfileResult) pm.getResult(col); DDLGenerator gddl = DDLUtils.createDDLGenerator( col.getParentTable().getParentDatabase().getDataSource()); DecimalFormat pctFormat = new DecimalFormat("0%"); int rowCount = -1; if ( tProfile != null && tProfile.isError() != true ) { rowCount = tProfile.getRowCount(); } java.util.List<ColumnValueCount> topTen = null; if ( cProfile != null && cProfile.isError() != true ) { topTen = cProfile.getValueCount(); } final int ncols = 17; for (int colNo = 0; colNo < ncols; colNo++) { String contents; int alignment; if (colNo == 0) { if ( tProfile == null || tProfile.isError() ) { contents = col.getParentTable().getName() + "\nProfiling Error:\n"; if ( tProfile != null && tProfile.getEx() != null ) contents += tProfile.getEx(); } else { contents = col.getParentTable().getName(); } alignment = Element.ALIGN_LEFT; } else if (colNo == 1) { contents = String.valueOf(rowCount); alignment = Element.ALIGN_RIGHT; } else if (colNo == 2) { contents = col.getName(); alignment = Element.ALIGN_LEFT; } else if (colNo == 3) { contents = gddl.columnType(col); alignment = Element.ALIGN_LEFT; } else if (colNo == 4) { contents = col.isDefinitelyNullable() ? "Y" : "N"; alignment = Element.ALIGN_CENTER; } else if (colNo == 5) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getNullCount()); alignment = Element.ALIGN_RIGHT; } else { contents = "Column Profiling Error"; alignment = Element.ALIGN_LEFT; } } else if (colNo == 6) { if ( cProfile != null && !cProfile.isError() ) { if (rowCount == 0) { contents = "N/A"; alignment = Element.ALIGN_CENTER; } else { contents = pctFormat.format(cProfile.getNullCount() / (double) rowCount); alignment = Element.ALIGN_RIGHT; } } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 7) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getDistinctValueCount()); alignment = Element.ALIGN_RIGHT; } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 8) { if ( cProfile != null && !cProfile.isError() ) { if (rowCount == 0) { contents = "N/A"; alignment = Element.ALIGN_CENTER; } else { contents = pctFormat.format(cProfile.getDistinctValueCount() / (double) rowCount); alignment = Element.ALIGN_RIGHT; } } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 9) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getMinLength()); alignment = Element.ALIGN_RIGHT; } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 10) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getMaxLength()); alignment = Element.ALIGN_RIGHT; } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 11) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getAvgLength()); alignment = Element.ALIGN_RIGHT; } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 12) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getMinValue()); if (cProfile.getMinValue() == null) { alignment = Element.ALIGN_CENTER; } else if (cProfile.getMinValue() instanceof Number) { alignment = Element.ALIGN_RIGHT; } else { alignment = Element.ALIGN_LEFT; } } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 13) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getMaxValue()); if (cProfile.getMaxValue() == null) { alignment = Element.ALIGN_CENTER; } else if (cProfile.getMaxValue() instanceof Number) { alignment = Element.ALIGN_RIGHT; } else { alignment = Element.ALIGN_LEFT; } } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 14) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getAvgValue()); if (cProfile.getAvgValue() == null) { alignment = Element.ALIGN_CENTER; } else if (cProfile.getAvgValue() instanceof Number) { alignment = Element.ALIGN_RIGHT; } else { alignment = Element.ALIGN_LEFT; } } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 15) { if ( cProfile != null && !cProfile.isError() && topTen != null ) { Object value = null; StringBuffer sb = new StringBuffer(); for ( ColumnValueCount cvc : topTen ) { value = cvc.getValue(); sb.append(value).append("\n"); } contents = sb.toString(); if (value == null) { alignment = Element.ALIGN_CENTER; } else if (value instanceof Number) { alignment = Element.ALIGN_RIGHT; } else { alignment = Element.ALIGN_LEFT; } } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 16) { if ( cProfile != null && !cProfile.isError() ) { StringBuffer sb = new StringBuffer(); for ( ColumnValueCount cvc : topTen ) { sb.append(cvc.getCount()).append("\n"); } contents = sb.toString(); alignment = Element.ALIGN_RIGHT; } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else { throw new IllegalStateException("I don't know about column "+colNo); } // update column width to reflect the widest cell widths[colNo] = Math.max(widths[colNo], bf.getWidthPoint((String) contents, fsize)); Phrase phr = new Phrase((String) contents, f); PdfPCell cell = new PdfPCell(phr); cell.setBorder(Rectangle.NO_BORDER); cell.setHorizontalAlignment(alignment); table.addCell(cell); } } |
} } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 14) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getAvgValue()); | contents = String.valueOf(cProfile.getMaxValue()); } } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 11) { if ( cProfile != null && !cProfile.isError() ) { | protected static void addBodyRow(ProfileManager pm, SQLColumn col, PdfPTable table, BaseFont bf, Font f, float fsize, float[] widths) throws DocumentException, IOException, ArchitectException, SQLException, InstantiationException, IllegalAccessException { TableProfileResult tProfile = (TableProfileResult) pm.getResult(col.getParentTable()); ColumnProfileResult cProfile = (ColumnProfileResult) pm.getResult(col); DDLGenerator gddl = DDLUtils.createDDLGenerator( col.getParentTable().getParentDatabase().getDataSource()); DecimalFormat pctFormat = new DecimalFormat("0%"); int rowCount = -1; if ( tProfile != null && tProfile.isError() != true ) { rowCount = tProfile.getRowCount(); } java.util.List<ColumnValueCount> topTen = null; if ( cProfile != null && cProfile.isError() != true ) { topTen = cProfile.getValueCount(); } final int ncols = 17; for (int colNo = 0; colNo < ncols; colNo++) { String contents; int alignment; if (colNo == 0) { if ( tProfile == null || tProfile.isError() ) { contents = col.getParentTable().getName() + "\nProfiling Error:\n"; if ( tProfile != null && tProfile.getEx() != null ) contents += tProfile.getEx(); } else { contents = col.getParentTable().getName(); } alignment = Element.ALIGN_LEFT; } else if (colNo == 1) { contents = String.valueOf(rowCount); alignment = Element.ALIGN_RIGHT; } else if (colNo == 2) { contents = col.getName(); alignment = Element.ALIGN_LEFT; } else if (colNo == 3) { contents = gddl.columnType(col); alignment = Element.ALIGN_LEFT; } else if (colNo == 4) { contents = col.isDefinitelyNullable() ? "Y" : "N"; alignment = Element.ALIGN_CENTER; } else if (colNo == 5) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getNullCount()); alignment = Element.ALIGN_RIGHT; } else { contents = "Column Profiling Error"; alignment = Element.ALIGN_LEFT; } } else if (colNo == 6) { if ( cProfile != null && !cProfile.isError() ) { if (rowCount == 0) { contents = "N/A"; alignment = Element.ALIGN_CENTER; } else { contents = pctFormat.format(cProfile.getNullCount() / (double) rowCount); alignment = Element.ALIGN_RIGHT; } } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 7) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getDistinctValueCount()); alignment = Element.ALIGN_RIGHT; } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 8) { if ( cProfile != null && !cProfile.isError() ) { if (rowCount == 0) { contents = "N/A"; alignment = Element.ALIGN_CENTER; } else { contents = pctFormat.format(cProfile.getDistinctValueCount() / (double) rowCount); alignment = Element.ALIGN_RIGHT; } } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 9) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getMinLength()); alignment = Element.ALIGN_RIGHT; } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 10) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getMaxLength()); alignment = Element.ALIGN_RIGHT; } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 11) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getAvgLength()); alignment = Element.ALIGN_RIGHT; } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 12) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getMinValue()); if (cProfile.getMinValue() == null) { alignment = Element.ALIGN_CENTER; } else if (cProfile.getMinValue() instanceof Number) { alignment = Element.ALIGN_RIGHT; } else { alignment = Element.ALIGN_LEFT; } } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 13) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getMaxValue()); if (cProfile.getMaxValue() == null) { alignment = Element.ALIGN_CENTER; } else if (cProfile.getMaxValue() instanceof Number) { alignment = Element.ALIGN_RIGHT; } else { alignment = Element.ALIGN_LEFT; } } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 14) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getAvgValue()); if (cProfile.getAvgValue() == null) { alignment = Element.ALIGN_CENTER; } else if (cProfile.getAvgValue() instanceof Number) { alignment = Element.ALIGN_RIGHT; } else { alignment = Element.ALIGN_LEFT; } } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 15) { if ( cProfile != null && !cProfile.isError() && topTen != null ) { Object value = null; StringBuffer sb = new StringBuffer(); for ( ColumnValueCount cvc : topTen ) { value = cvc.getValue(); sb.append(value).append("\n"); } contents = sb.toString(); if (value == null) { alignment = Element.ALIGN_CENTER; } else if (value instanceof Number) { alignment = Element.ALIGN_RIGHT; } else { alignment = Element.ALIGN_LEFT; } } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 16) { if ( cProfile != null && !cProfile.isError() ) { StringBuffer sb = new StringBuffer(); for ( ColumnValueCount cvc : topTen ) { sb.append(cvc.getCount()).append("\n"); } contents = sb.toString(); alignment = Element.ALIGN_RIGHT; } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else { throw new IllegalStateException("I don't know about column "+colNo); } // update column width to reflect the widest cell widths[colNo] = Math.max(widths[colNo], bf.getWidthPoint((String) contents, fsize)); Phrase phr = new Phrase((String) contents, f); PdfPCell cell = new PdfPCell(phr); cell.setBorder(Rectangle.NO_BORDER); cell.setHorizontalAlignment(alignment); table.addCell(cell); } } |
} } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 15) { | contents = String.valueOf(cProfile.getAvgValue()); } } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 12) { | protected static void addBodyRow(ProfileManager pm, SQLColumn col, PdfPTable table, BaseFont bf, Font f, float fsize, float[] widths) throws DocumentException, IOException, ArchitectException, SQLException, InstantiationException, IllegalAccessException { TableProfileResult tProfile = (TableProfileResult) pm.getResult(col.getParentTable()); ColumnProfileResult cProfile = (ColumnProfileResult) pm.getResult(col); DDLGenerator gddl = DDLUtils.createDDLGenerator( col.getParentTable().getParentDatabase().getDataSource()); DecimalFormat pctFormat = new DecimalFormat("0%"); int rowCount = -1; if ( tProfile != null && tProfile.isError() != true ) { rowCount = tProfile.getRowCount(); } java.util.List<ColumnValueCount> topTen = null; if ( cProfile != null && cProfile.isError() != true ) { topTen = cProfile.getValueCount(); } final int ncols = 17; for (int colNo = 0; colNo < ncols; colNo++) { String contents; int alignment; if (colNo == 0) { if ( tProfile == null || tProfile.isError() ) { contents = col.getParentTable().getName() + "\nProfiling Error:\n"; if ( tProfile != null && tProfile.getEx() != null ) contents += tProfile.getEx(); } else { contents = col.getParentTable().getName(); } alignment = Element.ALIGN_LEFT; } else if (colNo == 1) { contents = String.valueOf(rowCount); alignment = Element.ALIGN_RIGHT; } else if (colNo == 2) { contents = col.getName(); alignment = Element.ALIGN_LEFT; } else if (colNo == 3) { contents = gddl.columnType(col); alignment = Element.ALIGN_LEFT; } else if (colNo == 4) { contents = col.isDefinitelyNullable() ? "Y" : "N"; alignment = Element.ALIGN_CENTER; } else if (colNo == 5) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getNullCount()); alignment = Element.ALIGN_RIGHT; } else { contents = "Column Profiling Error"; alignment = Element.ALIGN_LEFT; } } else if (colNo == 6) { if ( cProfile != null && !cProfile.isError() ) { if (rowCount == 0) { contents = "N/A"; alignment = Element.ALIGN_CENTER; } else { contents = pctFormat.format(cProfile.getNullCount() / (double) rowCount); alignment = Element.ALIGN_RIGHT; } } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 7) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getDistinctValueCount()); alignment = Element.ALIGN_RIGHT; } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 8) { if ( cProfile != null && !cProfile.isError() ) { if (rowCount == 0) { contents = "N/A"; alignment = Element.ALIGN_CENTER; } else { contents = pctFormat.format(cProfile.getDistinctValueCount() / (double) rowCount); alignment = Element.ALIGN_RIGHT; } } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 9) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getMinLength()); alignment = Element.ALIGN_RIGHT; } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 10) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getMaxLength()); alignment = Element.ALIGN_RIGHT; } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 11) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getAvgLength()); alignment = Element.ALIGN_RIGHT; } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 12) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getMinValue()); if (cProfile.getMinValue() == null) { alignment = Element.ALIGN_CENTER; } else if (cProfile.getMinValue() instanceof Number) { alignment = Element.ALIGN_RIGHT; } else { alignment = Element.ALIGN_LEFT; } } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 13) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getMaxValue()); if (cProfile.getMaxValue() == null) { alignment = Element.ALIGN_CENTER; } else if (cProfile.getMaxValue() instanceof Number) { alignment = Element.ALIGN_RIGHT; } else { alignment = Element.ALIGN_LEFT; } } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 14) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getAvgValue()); if (cProfile.getAvgValue() == null) { alignment = Element.ALIGN_CENTER; } else if (cProfile.getAvgValue() instanceof Number) { alignment = Element.ALIGN_RIGHT; } else { alignment = Element.ALIGN_LEFT; } } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 15) { if ( cProfile != null && !cProfile.isError() && topTen != null ) { Object value = null; StringBuffer sb = new StringBuffer(); for ( ColumnValueCount cvc : topTen ) { value = cvc.getValue(); sb.append(value).append("\n"); } contents = sb.toString(); if (value == null) { alignment = Element.ALIGN_CENTER; } else if (value instanceof Number) { alignment = Element.ALIGN_RIGHT; } else { alignment = Element.ALIGN_LEFT; } } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 16) { if ( cProfile != null && !cProfile.isError() ) { StringBuffer sb = new StringBuffer(); for ( ColumnValueCount cvc : topTen ) { sb.append(cvc.getCount()).append("\n"); } contents = sb.toString(); alignment = Element.ALIGN_RIGHT; } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else { throw new IllegalStateException("I don't know about column "+colNo); } // update column width to reflect the widest cell widths[colNo] = Math.max(widths[colNo], bf.getWidthPoint((String) contents, fsize)); Phrase phr = new Phrase((String) contents, f); PdfPCell cell = new PdfPCell(phr); cell.setBorder(Rectangle.NO_BORDER); cell.setHorizontalAlignment(alignment); table.addCell(cell); } } |
Object value = null; | protected static void addBodyRow(ProfileManager pm, SQLColumn col, PdfPTable table, BaseFont bf, Font f, float fsize, float[] widths) throws DocumentException, IOException, ArchitectException, SQLException, InstantiationException, IllegalAccessException { TableProfileResult tProfile = (TableProfileResult) pm.getResult(col.getParentTable()); ColumnProfileResult cProfile = (ColumnProfileResult) pm.getResult(col); DDLGenerator gddl = DDLUtils.createDDLGenerator( col.getParentTable().getParentDatabase().getDataSource()); DecimalFormat pctFormat = new DecimalFormat("0%"); int rowCount = -1; if ( tProfile != null && tProfile.isError() != true ) { rowCount = tProfile.getRowCount(); } java.util.List<ColumnValueCount> topTen = null; if ( cProfile != null && cProfile.isError() != true ) { topTen = cProfile.getValueCount(); } final int ncols = 17; for (int colNo = 0; colNo < ncols; colNo++) { String contents; int alignment; if (colNo == 0) { if ( tProfile == null || tProfile.isError() ) { contents = col.getParentTable().getName() + "\nProfiling Error:\n"; if ( tProfile != null && tProfile.getEx() != null ) contents += tProfile.getEx(); } else { contents = col.getParentTable().getName(); } alignment = Element.ALIGN_LEFT; } else if (colNo == 1) { contents = String.valueOf(rowCount); alignment = Element.ALIGN_RIGHT; } else if (colNo == 2) { contents = col.getName(); alignment = Element.ALIGN_LEFT; } else if (colNo == 3) { contents = gddl.columnType(col); alignment = Element.ALIGN_LEFT; } else if (colNo == 4) { contents = col.isDefinitelyNullable() ? "Y" : "N"; alignment = Element.ALIGN_CENTER; } else if (colNo == 5) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getNullCount()); alignment = Element.ALIGN_RIGHT; } else { contents = "Column Profiling Error"; alignment = Element.ALIGN_LEFT; } } else if (colNo == 6) { if ( cProfile != null && !cProfile.isError() ) { if (rowCount == 0) { contents = "N/A"; alignment = Element.ALIGN_CENTER; } else { contents = pctFormat.format(cProfile.getNullCount() / (double) rowCount); alignment = Element.ALIGN_RIGHT; } } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 7) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getDistinctValueCount()); alignment = Element.ALIGN_RIGHT; } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 8) { if ( cProfile != null && !cProfile.isError() ) { if (rowCount == 0) { contents = "N/A"; alignment = Element.ALIGN_CENTER; } else { contents = pctFormat.format(cProfile.getDistinctValueCount() / (double) rowCount); alignment = Element.ALIGN_RIGHT; } } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 9) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getMinLength()); alignment = Element.ALIGN_RIGHT; } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 10) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getMaxLength()); alignment = Element.ALIGN_RIGHT; } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 11) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getAvgLength()); alignment = Element.ALIGN_RIGHT; } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 12) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getMinValue()); if (cProfile.getMinValue() == null) { alignment = Element.ALIGN_CENTER; } else if (cProfile.getMinValue() instanceof Number) { alignment = Element.ALIGN_RIGHT; } else { alignment = Element.ALIGN_LEFT; } } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 13) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getMaxValue()); if (cProfile.getMaxValue() == null) { alignment = Element.ALIGN_CENTER; } else if (cProfile.getMaxValue() instanceof Number) { alignment = Element.ALIGN_RIGHT; } else { alignment = Element.ALIGN_LEFT; } } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 14) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getAvgValue()); if (cProfile.getAvgValue() == null) { alignment = Element.ALIGN_CENTER; } else if (cProfile.getAvgValue() instanceof Number) { alignment = Element.ALIGN_RIGHT; } else { alignment = Element.ALIGN_LEFT; } } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 15) { if ( cProfile != null && !cProfile.isError() && topTen != null ) { Object value = null; StringBuffer sb = new StringBuffer(); for ( ColumnValueCount cvc : topTen ) { value = cvc.getValue(); sb.append(value).append("\n"); } contents = sb.toString(); if (value == null) { alignment = Element.ALIGN_CENTER; } else if (value instanceof Number) { alignment = Element.ALIGN_RIGHT; } else { alignment = Element.ALIGN_LEFT; } } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 16) { if ( cProfile != null && !cProfile.isError() ) { StringBuffer sb = new StringBuffer(); for ( ColumnValueCount cvc : topTen ) { sb.append(cvc.getCount()).append("\n"); } contents = sb.toString(); alignment = Element.ALIGN_RIGHT; } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else { throw new IllegalStateException("I don't know about column "+colNo); } // update column width to reflect the widest cell widths[colNo] = Math.max(widths[colNo], bf.getWidthPoint((String) contents, fsize)); Phrase phr = new Phrase((String) contents, f); PdfPCell cell = new PdfPCell(phr); cell.setBorder(Rectangle.NO_BORDER); cell.setHorizontalAlignment(alignment); table.addCell(cell); } } |
|
value = cvc.getValue(); sb.append(value).append("\n"); | sb.append(cvc.getValue()).append("\n"); | protected static void addBodyRow(ProfileManager pm, SQLColumn col, PdfPTable table, BaseFont bf, Font f, float fsize, float[] widths) throws DocumentException, IOException, ArchitectException, SQLException, InstantiationException, IllegalAccessException { TableProfileResult tProfile = (TableProfileResult) pm.getResult(col.getParentTable()); ColumnProfileResult cProfile = (ColumnProfileResult) pm.getResult(col); DDLGenerator gddl = DDLUtils.createDDLGenerator( col.getParentTable().getParentDatabase().getDataSource()); DecimalFormat pctFormat = new DecimalFormat("0%"); int rowCount = -1; if ( tProfile != null && tProfile.isError() != true ) { rowCount = tProfile.getRowCount(); } java.util.List<ColumnValueCount> topTen = null; if ( cProfile != null && cProfile.isError() != true ) { topTen = cProfile.getValueCount(); } final int ncols = 17; for (int colNo = 0; colNo < ncols; colNo++) { String contents; int alignment; if (colNo == 0) { if ( tProfile == null || tProfile.isError() ) { contents = col.getParentTable().getName() + "\nProfiling Error:\n"; if ( tProfile != null && tProfile.getEx() != null ) contents += tProfile.getEx(); } else { contents = col.getParentTable().getName(); } alignment = Element.ALIGN_LEFT; } else if (colNo == 1) { contents = String.valueOf(rowCount); alignment = Element.ALIGN_RIGHT; } else if (colNo == 2) { contents = col.getName(); alignment = Element.ALIGN_LEFT; } else if (colNo == 3) { contents = gddl.columnType(col); alignment = Element.ALIGN_LEFT; } else if (colNo == 4) { contents = col.isDefinitelyNullable() ? "Y" : "N"; alignment = Element.ALIGN_CENTER; } else if (colNo == 5) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getNullCount()); alignment = Element.ALIGN_RIGHT; } else { contents = "Column Profiling Error"; alignment = Element.ALIGN_LEFT; } } else if (colNo == 6) { if ( cProfile != null && !cProfile.isError() ) { if (rowCount == 0) { contents = "N/A"; alignment = Element.ALIGN_CENTER; } else { contents = pctFormat.format(cProfile.getNullCount() / (double) rowCount); alignment = Element.ALIGN_RIGHT; } } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 7) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getDistinctValueCount()); alignment = Element.ALIGN_RIGHT; } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 8) { if ( cProfile != null && !cProfile.isError() ) { if (rowCount == 0) { contents = "N/A"; alignment = Element.ALIGN_CENTER; } else { contents = pctFormat.format(cProfile.getDistinctValueCount() / (double) rowCount); alignment = Element.ALIGN_RIGHT; } } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 9) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getMinLength()); alignment = Element.ALIGN_RIGHT; } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 10) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getMaxLength()); alignment = Element.ALIGN_RIGHT; } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 11) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getAvgLength()); alignment = Element.ALIGN_RIGHT; } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 12) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getMinValue()); if (cProfile.getMinValue() == null) { alignment = Element.ALIGN_CENTER; } else if (cProfile.getMinValue() instanceof Number) { alignment = Element.ALIGN_RIGHT; } else { alignment = Element.ALIGN_LEFT; } } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 13) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getMaxValue()); if (cProfile.getMaxValue() == null) { alignment = Element.ALIGN_CENTER; } else if (cProfile.getMaxValue() instanceof Number) { alignment = Element.ALIGN_RIGHT; } else { alignment = Element.ALIGN_LEFT; } } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 14) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getAvgValue()); if (cProfile.getAvgValue() == null) { alignment = Element.ALIGN_CENTER; } else if (cProfile.getAvgValue() instanceof Number) { alignment = Element.ALIGN_RIGHT; } else { alignment = Element.ALIGN_LEFT; } } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 15) { if ( cProfile != null && !cProfile.isError() && topTen != null ) { Object value = null; StringBuffer sb = new StringBuffer(); for ( ColumnValueCount cvc : topTen ) { value = cvc.getValue(); sb.append(value).append("\n"); } contents = sb.toString(); if (value == null) { alignment = Element.ALIGN_CENTER; } else if (value instanceof Number) { alignment = Element.ALIGN_RIGHT; } else { alignment = Element.ALIGN_LEFT; } } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 16) { if ( cProfile != null && !cProfile.isError() ) { StringBuffer sb = new StringBuffer(); for ( ColumnValueCount cvc : topTen ) { sb.append(cvc.getCount()).append("\n"); } contents = sb.toString(); alignment = Element.ALIGN_RIGHT; } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else { throw new IllegalStateException("I don't know about column "+colNo); } // update column width to reflect the widest cell widths[colNo] = Math.max(widths[colNo], bf.getWidthPoint((String) contents, fsize)); Phrase phr = new Phrase((String) contents, f); PdfPCell cell = new PdfPCell(phr); cell.setBorder(Rectangle.NO_BORDER); cell.setHorizontalAlignment(alignment); table.addCell(cell); } } |
if (value == null) { alignment = Element.ALIGN_CENTER; } else if (value instanceof Number) { alignment = Element.ALIGN_RIGHT; } else { alignment = Element.ALIGN_LEFT; } } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 16) { | alignment = Element.ALIGN_LEFT; } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 13) { | protected static void addBodyRow(ProfileManager pm, SQLColumn col, PdfPTable table, BaseFont bf, Font f, float fsize, float[] widths) throws DocumentException, IOException, ArchitectException, SQLException, InstantiationException, IllegalAccessException { TableProfileResult tProfile = (TableProfileResult) pm.getResult(col.getParentTable()); ColumnProfileResult cProfile = (ColumnProfileResult) pm.getResult(col); DDLGenerator gddl = DDLUtils.createDDLGenerator( col.getParentTable().getParentDatabase().getDataSource()); DecimalFormat pctFormat = new DecimalFormat("0%"); int rowCount = -1; if ( tProfile != null && tProfile.isError() != true ) { rowCount = tProfile.getRowCount(); } java.util.List<ColumnValueCount> topTen = null; if ( cProfile != null && cProfile.isError() != true ) { topTen = cProfile.getValueCount(); } final int ncols = 17; for (int colNo = 0; colNo < ncols; colNo++) { String contents; int alignment; if (colNo == 0) { if ( tProfile == null || tProfile.isError() ) { contents = col.getParentTable().getName() + "\nProfiling Error:\n"; if ( tProfile != null && tProfile.getEx() != null ) contents += tProfile.getEx(); } else { contents = col.getParentTable().getName(); } alignment = Element.ALIGN_LEFT; } else if (colNo == 1) { contents = String.valueOf(rowCount); alignment = Element.ALIGN_RIGHT; } else if (colNo == 2) { contents = col.getName(); alignment = Element.ALIGN_LEFT; } else if (colNo == 3) { contents = gddl.columnType(col); alignment = Element.ALIGN_LEFT; } else if (colNo == 4) { contents = col.isDefinitelyNullable() ? "Y" : "N"; alignment = Element.ALIGN_CENTER; } else if (colNo == 5) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getNullCount()); alignment = Element.ALIGN_RIGHT; } else { contents = "Column Profiling Error"; alignment = Element.ALIGN_LEFT; } } else if (colNo == 6) { if ( cProfile != null && !cProfile.isError() ) { if (rowCount == 0) { contents = "N/A"; alignment = Element.ALIGN_CENTER; } else { contents = pctFormat.format(cProfile.getNullCount() / (double) rowCount); alignment = Element.ALIGN_RIGHT; } } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 7) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getDistinctValueCount()); alignment = Element.ALIGN_RIGHT; } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 8) { if ( cProfile != null && !cProfile.isError() ) { if (rowCount == 0) { contents = "N/A"; alignment = Element.ALIGN_CENTER; } else { contents = pctFormat.format(cProfile.getDistinctValueCount() / (double) rowCount); alignment = Element.ALIGN_RIGHT; } } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 9) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getMinLength()); alignment = Element.ALIGN_RIGHT; } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 10) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getMaxLength()); alignment = Element.ALIGN_RIGHT; } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 11) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getAvgLength()); alignment = Element.ALIGN_RIGHT; } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 12) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getMinValue()); if (cProfile.getMinValue() == null) { alignment = Element.ALIGN_CENTER; } else if (cProfile.getMinValue() instanceof Number) { alignment = Element.ALIGN_RIGHT; } else { alignment = Element.ALIGN_LEFT; } } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 13) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getMaxValue()); if (cProfile.getMaxValue() == null) { alignment = Element.ALIGN_CENTER; } else if (cProfile.getMaxValue() instanceof Number) { alignment = Element.ALIGN_RIGHT; } else { alignment = Element.ALIGN_LEFT; } } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 14) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getAvgValue()); if (cProfile.getAvgValue() == null) { alignment = Element.ALIGN_CENTER; } else if (cProfile.getAvgValue() instanceof Number) { alignment = Element.ALIGN_RIGHT; } else { alignment = Element.ALIGN_LEFT; } } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 15) { if ( cProfile != null && !cProfile.isError() && topTen != null ) { Object value = null; StringBuffer sb = new StringBuffer(); for ( ColumnValueCount cvc : topTen ) { value = cvc.getValue(); sb.append(value).append("\n"); } contents = sb.toString(); if (value == null) { alignment = Element.ALIGN_CENTER; } else if (value instanceof Number) { alignment = Element.ALIGN_RIGHT; } else { alignment = Element.ALIGN_LEFT; } } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 16) { if ( cProfile != null && !cProfile.isError() ) { StringBuffer sb = new StringBuffer(); for ( ColumnValueCount cvc : topTen ) { sb.append(cvc.getCount()).append("\n"); } contents = sb.toString(); alignment = Element.ALIGN_RIGHT; } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else { throw new IllegalStateException("I don't know about column "+colNo); } // update column width to reflect the widest cell widths[colNo] = Math.max(widths[colNo], bf.getWidthPoint((String) contents, fsize)); Phrase phr = new Phrase((String) contents, f); PdfPCell cell = new PdfPCell(phr); cell.setBorder(Rectangle.NO_BORDER); cell.setHorizontalAlignment(alignment); table.addCell(cell); } } |
StringBuffer truncContents = new StringBuffer(contents.length()); | protected static void addBodyRow(ProfileManager pm, SQLColumn col, PdfPTable table, BaseFont bf, Font f, float fsize, float[] widths) throws DocumentException, IOException, ArchitectException, SQLException, InstantiationException, IllegalAccessException { TableProfileResult tProfile = (TableProfileResult) pm.getResult(col.getParentTable()); ColumnProfileResult cProfile = (ColumnProfileResult) pm.getResult(col); DDLGenerator gddl = DDLUtils.createDDLGenerator( col.getParentTable().getParentDatabase().getDataSource()); DecimalFormat pctFormat = new DecimalFormat("0%"); int rowCount = -1; if ( tProfile != null && tProfile.isError() != true ) { rowCount = tProfile.getRowCount(); } java.util.List<ColumnValueCount> topTen = null; if ( cProfile != null && cProfile.isError() != true ) { topTen = cProfile.getValueCount(); } final int ncols = 17; for (int colNo = 0; colNo < ncols; colNo++) { String contents; int alignment; if (colNo == 0) { if ( tProfile == null || tProfile.isError() ) { contents = col.getParentTable().getName() + "\nProfiling Error:\n"; if ( tProfile != null && tProfile.getEx() != null ) contents += tProfile.getEx(); } else { contents = col.getParentTable().getName(); } alignment = Element.ALIGN_LEFT; } else if (colNo == 1) { contents = String.valueOf(rowCount); alignment = Element.ALIGN_RIGHT; } else if (colNo == 2) { contents = col.getName(); alignment = Element.ALIGN_LEFT; } else if (colNo == 3) { contents = gddl.columnType(col); alignment = Element.ALIGN_LEFT; } else if (colNo == 4) { contents = col.isDefinitelyNullable() ? "Y" : "N"; alignment = Element.ALIGN_CENTER; } else if (colNo == 5) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getNullCount()); alignment = Element.ALIGN_RIGHT; } else { contents = "Column Profiling Error"; alignment = Element.ALIGN_LEFT; } } else if (colNo == 6) { if ( cProfile != null && !cProfile.isError() ) { if (rowCount == 0) { contents = "N/A"; alignment = Element.ALIGN_CENTER; } else { contents = pctFormat.format(cProfile.getNullCount() / (double) rowCount); alignment = Element.ALIGN_RIGHT; } } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 7) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getDistinctValueCount()); alignment = Element.ALIGN_RIGHT; } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 8) { if ( cProfile != null && !cProfile.isError() ) { if (rowCount == 0) { contents = "N/A"; alignment = Element.ALIGN_CENTER; } else { contents = pctFormat.format(cProfile.getDistinctValueCount() / (double) rowCount); alignment = Element.ALIGN_RIGHT; } } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 9) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getMinLength()); alignment = Element.ALIGN_RIGHT; } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 10) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getMaxLength()); alignment = Element.ALIGN_RIGHT; } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 11) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getAvgLength()); alignment = Element.ALIGN_RIGHT; } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 12) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getMinValue()); if (cProfile.getMinValue() == null) { alignment = Element.ALIGN_CENTER; } else if (cProfile.getMinValue() instanceof Number) { alignment = Element.ALIGN_RIGHT; } else { alignment = Element.ALIGN_LEFT; } } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 13) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getMaxValue()); if (cProfile.getMaxValue() == null) { alignment = Element.ALIGN_CENTER; } else if (cProfile.getMaxValue() instanceof Number) { alignment = Element.ALIGN_RIGHT; } else { alignment = Element.ALIGN_LEFT; } } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 14) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getAvgValue()); if (cProfile.getAvgValue() == null) { alignment = Element.ALIGN_CENTER; } else if (cProfile.getAvgValue() instanceof Number) { alignment = Element.ALIGN_RIGHT; } else { alignment = Element.ALIGN_LEFT; } } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 15) { if ( cProfile != null && !cProfile.isError() && topTen != null ) { Object value = null; StringBuffer sb = new StringBuffer(); for ( ColumnValueCount cvc : topTen ) { value = cvc.getValue(); sb.append(value).append("\n"); } contents = sb.toString(); if (value == null) { alignment = Element.ALIGN_CENTER; } else if (value instanceof Number) { alignment = Element.ALIGN_RIGHT; } else { alignment = Element.ALIGN_LEFT; } } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 16) { if ( cProfile != null && !cProfile.isError() ) { StringBuffer sb = new StringBuffer(); for ( ColumnValueCount cvc : topTen ) { sb.append(cvc.getCount()).append("\n"); } contents = sb.toString(); alignment = Element.ALIGN_RIGHT; } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else { throw new IllegalStateException("I don't know about column "+colNo); } // update column width to reflect the widest cell widths[colNo] = Math.max(widths[colNo], bf.getWidthPoint((String) contents, fsize)); Phrase phr = new Phrase((String) contents, f); PdfPCell cell = new PdfPCell(phr); cell.setBorder(Rectangle.NO_BORDER); cell.setHorizontalAlignment(alignment); table.addCell(cell); } } |
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widths[colNo] = Math.max(widths[colNo], bf.getWidthPoint((String) contents, fsize)); Phrase phr = new Phrase((String) contents, f); PdfPCell cell = new PdfPCell(phr); cell.setBorder(Rectangle.NO_BORDER); | for (String contentLine : contents.split("\n")) { if (contentLine.length() > maxCharsInTopN) { contentLine = contentLine.substring(0, maxCharsInTopN) + "..."; } widths[colNo] = Math.max(widths[colNo], bf.getWidthPoint((String) contentLine, fsize)); truncContents.append(contentLine).append("\n"); } PdfPCell cell; if ( colNo == 12 || colNo == 13 ) { cell = new PdfPCell(new Paragraph(truncContents.toString(), f)); cell.setNoWrap(true); } else { Phrase phr = new Phrase(truncContents.toString(), f); cell = new PdfPCell(phr); } | protected static void addBodyRow(ProfileManager pm, SQLColumn col, PdfPTable table, BaseFont bf, Font f, float fsize, float[] widths) throws DocumentException, IOException, ArchitectException, SQLException, InstantiationException, IllegalAccessException { TableProfileResult tProfile = (TableProfileResult) pm.getResult(col.getParentTable()); ColumnProfileResult cProfile = (ColumnProfileResult) pm.getResult(col); DDLGenerator gddl = DDLUtils.createDDLGenerator( col.getParentTable().getParentDatabase().getDataSource()); DecimalFormat pctFormat = new DecimalFormat("0%"); int rowCount = -1; if ( tProfile != null && tProfile.isError() != true ) { rowCount = tProfile.getRowCount(); } java.util.List<ColumnValueCount> topTen = null; if ( cProfile != null && cProfile.isError() != true ) { topTen = cProfile.getValueCount(); } final int ncols = 17; for (int colNo = 0; colNo < ncols; colNo++) { String contents; int alignment; if (colNo == 0) { if ( tProfile == null || tProfile.isError() ) { contents = col.getParentTable().getName() + "\nProfiling Error:\n"; if ( tProfile != null && tProfile.getEx() != null ) contents += tProfile.getEx(); } else { contents = col.getParentTable().getName(); } alignment = Element.ALIGN_LEFT; } else if (colNo == 1) { contents = String.valueOf(rowCount); alignment = Element.ALIGN_RIGHT; } else if (colNo == 2) { contents = col.getName(); alignment = Element.ALIGN_LEFT; } else if (colNo == 3) { contents = gddl.columnType(col); alignment = Element.ALIGN_LEFT; } else if (colNo == 4) { contents = col.isDefinitelyNullable() ? "Y" : "N"; alignment = Element.ALIGN_CENTER; } else if (colNo == 5) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getNullCount()); alignment = Element.ALIGN_RIGHT; } else { contents = "Column Profiling Error"; alignment = Element.ALIGN_LEFT; } } else if (colNo == 6) { if ( cProfile != null && !cProfile.isError() ) { if (rowCount == 0) { contents = "N/A"; alignment = Element.ALIGN_CENTER; } else { contents = pctFormat.format(cProfile.getNullCount() / (double) rowCount); alignment = Element.ALIGN_RIGHT; } } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 7) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getDistinctValueCount()); alignment = Element.ALIGN_RIGHT; } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 8) { if ( cProfile != null && !cProfile.isError() ) { if (rowCount == 0) { contents = "N/A"; alignment = Element.ALIGN_CENTER; } else { contents = pctFormat.format(cProfile.getDistinctValueCount() / (double) rowCount); alignment = Element.ALIGN_RIGHT; } } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 9) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getMinLength()); alignment = Element.ALIGN_RIGHT; } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 10) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getMaxLength()); alignment = Element.ALIGN_RIGHT; } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 11) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getAvgLength()); alignment = Element.ALIGN_RIGHT; } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 12) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getMinValue()); if (cProfile.getMinValue() == null) { alignment = Element.ALIGN_CENTER; } else if (cProfile.getMinValue() instanceof Number) { alignment = Element.ALIGN_RIGHT; } else { alignment = Element.ALIGN_LEFT; } } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 13) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getMaxValue()); if (cProfile.getMaxValue() == null) { alignment = Element.ALIGN_CENTER; } else if (cProfile.getMaxValue() instanceof Number) { alignment = Element.ALIGN_RIGHT; } else { alignment = Element.ALIGN_LEFT; } } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 14) { if ( cProfile != null && !cProfile.isError() ) { contents = String.valueOf(cProfile.getAvgValue()); if (cProfile.getAvgValue() == null) { alignment = Element.ALIGN_CENTER; } else if (cProfile.getAvgValue() instanceof Number) { alignment = Element.ALIGN_RIGHT; } else { alignment = Element.ALIGN_LEFT; } } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 15) { if ( cProfile != null && !cProfile.isError() && topTen != null ) { Object value = null; StringBuffer sb = new StringBuffer(); for ( ColumnValueCount cvc : topTen ) { value = cvc.getValue(); sb.append(value).append("\n"); } contents = sb.toString(); if (value == null) { alignment = Element.ALIGN_CENTER; } else if (value instanceof Number) { alignment = Element.ALIGN_RIGHT; } else { alignment = Element.ALIGN_LEFT; } } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else if (colNo == 16) { if ( cProfile != null && !cProfile.isError() ) { StringBuffer sb = new StringBuffer(); for ( ColumnValueCount cvc : topTen ) { sb.append(cvc.getCount()).append("\n"); } contents = sb.toString(); alignment = Element.ALIGN_RIGHT; } else { contents = ""; alignment = Element.ALIGN_LEFT; } } else { throw new IllegalStateException("I don't know about column "+colNo); } // update column width to reflect the widest cell widths[colNo] = Math.max(widths[colNo], bf.getWidthPoint((String) contents, fsize)); Phrase phr = new Phrase((String) contents, f); PdfPCell cell = new PdfPCell(phr); cell.setBorder(Rectangle.NO_BORDER); cell.setHorizontalAlignment(alignment); table.addCell(cell); } } |
private static void addHeaderRow(PdfPTable table, | private void addHeaderRow(PdfPTable table, | private static void addHeaderRow(PdfPTable table, BaseFont bf, Font f, float fsize, float[] widths) throws DocumentException, IOException, ArchitectException { final String[] headings = new String[] { "Table Name", "Record Count", "Column Name", "Data Type", "Nullable", "Null Count", "% null", "Unique Count", "% unique", "Min Length", "Max Length", "Avg Length", "Min Value", "Max Value", "Avg Value", "Top N Values", "Count" }; int ncols = headings.length; for (int colNo = 0; colNo < ncols; colNo++) { String contents = headings[colNo]; // ensure column width is at least enough for widest word in heading StringTokenizer st = new StringTokenizer(contents); while (st.hasMoreTokens()) { widths[colNo] = Math.max(widths[colNo], bf.getWidthPoint(st.nextToken(), fsize)); } Phrase colTitle = new Phrase(contents, f); PdfPCell cell = new PdfPCell(colTitle); cell.setBorder(Rectangle.BOTTOM | Rectangle.TOP); cell.setBorderWidth(2); cell.setBackgroundColor(new Color(200, 200, 200)); cell.setHorizontalAlignment(Element.ALIGN_CENTER); table.addCell(cell); } table.setHeaderRows(1); } |
final String[] headings = new String[] { "Table Name", "Record Count", "Column Name", "Data Type", "Nullable", "Null Count", "% null", "Unique Count", "% unique", "Min Length", "Max Length", "Avg Length", "Min Value", "Max Value", "Avg Value", "Top N Values", "Count" }; | private static void addHeaderRow(PdfPTable table, BaseFont bf, Font f, float fsize, float[] widths) throws DocumentException, IOException, ArchitectException { final String[] headings = new String[] { "Table Name", "Record Count", "Column Name", "Data Type", "Nullable", "Null Count", "% null", "Unique Count", "% unique", "Min Length", "Max Length", "Avg Length", "Min Value", "Max Value", "Avg Value", "Top N Values", "Count" }; int ncols = headings.length; for (int colNo = 0; colNo < ncols; colNo++) { String contents = headings[colNo]; // ensure column width is at least enough for widest word in heading StringTokenizer st = new StringTokenizer(contents); while (st.hasMoreTokens()) { widths[colNo] = Math.max(widths[colNo], bf.getWidthPoint(st.nextToken(), fsize)); } Phrase colTitle = new Phrase(contents, f); PdfPCell cell = new PdfPCell(colTitle); cell.setBorder(Rectangle.BOTTOM | Rectangle.TOP); cell.setBorderWidth(2); cell.setBackgroundColor(new Color(200, 200, 200)); cell.setHorizontalAlignment(Element.ALIGN_CENTER); table.addCell(cell); } table.setHeaderRows(1); } |
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private static float calcHeaderHeight(PdfPTable table) { | private float calcHeaderHeight(PdfPTable table) { | private static float calcHeaderHeight(PdfPTable table) { int hrows = table.getHeaderRows(); float height = 0f; for (int i = 0; i < hrows; i++) { height += table.getRowHeight(i); } return height; } |
protected static PdfPTable makeNextTable(ProfileManager pm, SQLTable sqlTable, | protected PdfPTable makeNextTable(ProfileManager pm, SQLTable sqlTable, | protected static PdfPTable makeNextTable(ProfileManager pm, SQLTable sqlTable, BaseFont bf, float fsize, float[] widths) throws DocumentException, IOException, ArchitectException, SQLException, InstantiationException, IllegalAccessException { logger.debug("Making next table"); PdfPTable table = new PdfPTable(widths.length); table.setWidthPercentage(100f); Font f = new Font(bf, fsize); TableProfileResult tProfile = (TableProfileResult) pm.getResult(sqlTable); addHeaderRow(table, bf, f, fsize, widths); // body rows for (SQLColumn col : sqlTable.getColumns()) { addBodyRow(pm, col, table, bf, f, fsize, widths); } logger.debug("Finished body rows"); table.setWidths(widths); return table; } |
TableProfileResult tProfile = (TableProfileResult) pm.getResult(sqlTable); | protected static PdfPTable makeNextTable(ProfileManager pm, SQLTable sqlTable, BaseFont bf, float fsize, float[] widths) throws DocumentException, IOException, ArchitectException, SQLException, InstantiationException, IllegalAccessException { logger.debug("Making next table"); PdfPTable table = new PdfPTable(widths.length); table.setWidthPercentage(100f); Font f = new Font(bf, fsize); TableProfileResult tProfile = (TableProfileResult) pm.getResult(sqlTable); addHeaderRow(table, bf, f, fsize, widths); // body rows for (SQLColumn col : sqlTable.getColumns()) { addBodyRow(pm, col, table, bf, f, fsize, widths); } logger.debug("Finished body rows"); table.setWidths(widths); return table; } |
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saveDBCS(); | saveDataSources(); | public void save(ProgressMonitor pm) throws IOException, ArchitectException { out = new PrintWriter(new BufferedWriter(new FileWriter(file))); objectIdMap = new HashMap(); dbcsIdMap = new HashMap(); indent = 0; progress = 0; this.pm = pm; if (pm != null) { pm.setMinimum(0); int pmMax = countSourceTables((SQLObject) sourceDatabases.getModel().getRoot()) + playPen.getPPComponentCount() * 2; logger.debug("Setting progress monitor maximum to "+pmMax); pm.setMaximum(pmMax); pm.setProgress(progress); pm.setMillisToDecideToPopup(500); } try { println("<?xml version=\"1.0\"?>"); println("<architect-project version=\"0.1\">"); indent++; println("<project-name>"+name+"</project-name>"); saveDBCS(); saveSourceDatabases(); saveTargetDatabase(); saveDDLGenerator(); savePlayPen(); indent--; println("</architect-project>"); setModified(false); } finally { if (out != null) out.close(); out = null; if (pm != null) pm.close(); pm = null; } } |
d.addFactoryCreate("architect-project/project-data-sources/data-source", dbcsFactory); d.addCallMethod("architect-project/project-data-sources/data-source/property", "put", 2); d.addCallParam("architect-project/project-data-sources/data-source/property", 0, "key"); d.addCallParam("architect-project/project-data-sources/data-source/property", 1, "value"); | protected Digester setupDigester() { Digester d = new Digester(); d.setValidating(false); d.push(this); // project name d.addCallMethod("architect-project/project-name", "setName", 0); // argument is element body text // source DB connection specs DBCSFactory dbcsFactory = new DBCSFactory(); d.addFactoryCreate("architect-project/project-connection-specs/dbcs", dbcsFactory); d.addSetProperties ("architect-project/project-connection-specs/dbcs", new String[] {"connection-name", "driver-class", "jdbc-url", "user-name", "user-pass", "sequence-number", "single-login"}, new String[] {"displayName", "driverClass", "url", "user", "pass", "seqNo", "singleLogin"}); d.addCallMethod("architect-project/project-connection-specs/dbcs", "setName", 0); // these instances get picked out of the dbcsIdMap by the SQLDatabase factory // source database hierarchy d.addObjectCreate("architect-project/source-databases", LinkedList.class); d.addSetNext("architect-project/source-databases", "setSourceDatabaseList"); SQLDatabaseFactory dbFactory = new SQLDatabaseFactory(); d.addFactoryCreate("architect-project/source-databases/database", dbFactory); d.addSetProperties("architect-project/source-databases/database"); d.addSetNext("architect-project/source-databases/database", "add"); d.addObjectCreate("architect-project/source-databases/database/catalog", SQLCatalog.class); d.addSetProperties("architect-project/source-databases/database/catalog"); d.addSetNext("architect-project/source-databases/database/catalog", "addChild"); d.addObjectCreate("*/schema", SQLSchema.class); d.addSetProperties("*/schema"); d.addSetNext("*/schema", "addChild"); SQLTableFactory tableFactory = new SQLTableFactory(); d.addFactoryCreate("*/table", tableFactory); d.addSetProperties("*/table"); d.addSetNext("*/table", "addChild"); SQLFolderFactory folderFactory = new SQLFolderFactory(); d.addFactoryCreate("*/folder", folderFactory); d.addSetProperties("*/folder"); d.addSetNext("*/folder", "addChild"); SQLColumnFactory columnFactory = new SQLColumnFactory(); d.addFactoryCreate("*/column", columnFactory); d.addSetProperties("*/column"); d.addSetNext("*/column", "addChild"); SQLRelationshipFactory relationshipFactory = new SQLRelationshipFactory(); d.addFactoryCreate("*/relationship", relationshipFactory); d.addSetProperties("*/relationship"); // the factory adds the relationships to the correct PK and FK tables ColumnMappingFactory columnMappingFactory = new ColumnMappingFactory(); d.addFactoryCreate("*/column-mapping", columnMappingFactory); d.addSetProperties("*/column-mapping"); d.addSetNext("*/column-mapping", "addChild"); SQLExceptionFactory exceptionFactory = new SQLExceptionFactory(); d.addFactoryCreate("*/sql-exception", exceptionFactory); d.addSetProperties("*/sql-exception"); d.addSetNext("*/sql-exception", "addChild"); // target database hierarchy d.addFactoryCreate("architect-project/target-database", dbFactory); d.addSetProperties("architect-project/target-database"); d.addSetNext("architect-project/target-database", "setTargetDatabase"); // the play pen TablePaneFactory tablePaneFactory = new TablePaneFactory(); d.addFactoryCreate("architect-project/play-pen/table-pane", tablePaneFactory); // factory will add the tablepanes to the playpen PPRelationshipFactory ppRelationshipFactory = new PPRelationshipFactory(); d.addFactoryCreate("architect-project/play-pen/table-link", ppRelationshipFactory); DDLGeneratorFactory ddlgFactory = new DDLGeneratorFactory(); d.addFactoryCreate("architect-project/ddl-generator", ddlgFactory); d.addSetProperties("architect-project/ddl-generator"); FileFactory fileFactory = new FileFactory(); d.addFactoryCreate("*/file", fileFactory); d.addSetNext("*/file", "setFile"); d.addSetNext("architect-project/ddl-generator", "setDDLGenerator"); return d; } |
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changeBlocks(currentBlockDef); | if (currentBlockDef != BLOX_CUSTOM){ changeBlocks(currentBlockDef); }else{ Vector theBlocks = new Vector(); for (int x = 0; x < currentBlocks.size(); x++){ Vector goodies = new Vector(); int currentBlock[] = (int[])currentBlocks.elementAt(x); for (int marker = 0; marker < currentBlock.length; marker++){ for (int y = 0; y < Chromosome.realIndex.length; y++){ if (Chromosome.realIndex[y] == currentBlock[marker]){ goodies.add(new Integer(y)); } } } int thisBlock[] = new int[goodies.size()]; for (int marker = 0; marker < thisBlock.length; marker++){ thisBlock[marker] = ((Integer)goodies.elementAt(marker)).intValue(); } theBlocks.add(thisBlock); } theData.guessBlocks(BLOX_CUSTOM, theBlocks); } | public void stateChanged(ChangeEvent e) { int tabNum = tabs.getSelectedIndex(); if (tabNum == VIEW_D_NUM || tabNum == VIEW_HAP_NUM){ exportMenuItems[0].setEnabled(true); exportMenuItems[1].setEnabled(true); }else if (tabNum == VIEW_TDT_NUM || tabNum == VIEW_CHECK_NUM){ exportMenuItems[0].setEnabled(true); exportMenuItems[1].setEnabled(false); }else{ exportMenuItems[0].setEnabled(false); exportMenuItems[1].setEnabled(false); } if (tabNum == VIEW_D_NUM){ keyMenu.setEnabled(true); }else{ keyMenu.setEnabled(false); } viewMenuItems[tabs.getSelectedIndex()].setSelected(true); if (checkPanel != null && checkPanel.changed){ window.setCursor(Cursor.getPredefinedCursor(Cursor.WAIT_CURSOR)); JTable table = checkPanel.getTable(); boolean[] markerResults = new boolean[table.getRowCount()]; for (int i = 0; i < table.getRowCount(); i++){ markerResults[i] = ((Boolean)table.getValueAt(i,CheckDataPanel.STATUS_COL)).booleanValue(); } int count = 0; for (int i = 0; i < Chromosome.getSize(); i++){ if (markerResults[i]){ count++; } } Chromosome.realIndex = new int[count]; int k = 0; for (int i =0; i < Chromosome.getSize(); i++){ if (markerResults[i]){ Chromosome.realIndex[k] = i; k++; } } theData.filteredDPrimeTable = theData.getFilteredTable(); //after editing the filtered marker list, needs to be prodded into //resizing correctly Dimension size = dPrimeDisplay.getSize(); Dimension pref = dPrimeDisplay.getPreferredSize(); Rectangle visRect = dPrimeDisplay.getVisibleRect(); if (size.width != pref.width && pref.width > visRect.width){ ((JViewport)dPrimeDisplay.getParent()).setViewSize(pref); } dPrimeDisplay.colorDPrime(currentScheme); hapDisplay.theData = theData; changeBlocks(currentBlockDef); if (tdtPanel != null){ tdtPanel.refreshTable(); } setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR)); checkPanel.changed=false; } if (hapDisplay != null && theData.blocksChanged){ setCursor(Cursor.getPredefinedCursor(Cursor.WAIT_CURSOR)); try{ hapDisplay.getHaps(); }catch(HaploViewException hv){ JOptionPane.showMessageDialog(window, hv.getMessage(), "Error", JOptionPane.ERROR_MESSAGE); } hapScroller.setViewportView(hapDisplay); setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR)); theData.blocksChanged = false; } } |
blockMenuItems[3].setEnabled(false); | public HaploView(){ try{ fc = new JFileChooser(System.getProperty("user.dir")); }catch(NullPointerException n){ try{ UIManager.setLookAndFeel(UIManager.getCrossPlatformLookAndFeelClassName()); fc = new JFileChooser(System.getProperty("user.dir")); UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName()); }catch(Exception e){ } } //menu setup JMenuBar menuBar = new JMenuBar(); setJMenuBar(menuBar); JMenuItem menuItem; //file menu JMenu fileMenu = new JMenu("File"); menuBar.add(fileMenu); menuItem = new JMenuItem(READ_GENOTYPES); setAccelerator(menuItem, 'O', false); menuItem.addActionListener(this); fileMenu.add(menuItem); /* viewGenotypesItem = new JMenuItem(VIEW_GENOTYPES); viewGenotypesItem.addActionListener(this); //viewGenotypesItem.setEnabled(false); fileMenu.add(viewGenotypesItem); */ readMarkerItem = new JMenuItem(READ_MARKERS); setAccelerator(readMarkerItem, 'I', false); readMarkerItem.addActionListener(this); readMarkerItem.setEnabled(false); fileMenu.add(readMarkerItem); analysisItem = new JMenuItem(READ_ANALYSIS_TRACK); setAccelerator(analysisItem, 'A', false); analysisItem.addActionListener(this); analysisItem.setEnabled(false); fileMenu.add(analysisItem); blocksItem = new JMenuItem(READ_BLOCKS_FILE); setAccelerator(blocksItem, 'B', false); blocksItem.addActionListener(this); blocksItem.setEnabled(false); fileMenu.add(blocksItem); /* viewMarkerItem = new JMenuItem(VIEW_MARKERS); viewMarkerItem.addActionListener(this); //viewMarkerItem.setEnabled(false); fileMenu.add(viewMarkerItem); */ fileMenu.addSeparator(); exportMenuItems = new JMenuItem[exportItems.length]; for (int i = 0; i < exportItems.length; i++) { exportMenuItems[i] = new JMenuItem(exportItems[i]); exportMenuItems[i].addActionListener(this); exportMenuItems[i].setEnabled(false); fileMenu.add(exportMenuItems[i]); } fileMenu.addSeparator(); fileMenu.setMnemonic(KeyEvent.VK_F); menuItem = new JMenuItem("Quit"); setAccelerator(menuItem, 'Q', false); menuItem.addActionListener(this); fileMenu.add(menuItem); /// display menu JMenu displayMenu = new JMenu("Display"); displayMenu.setMnemonic(KeyEvent.VK_D); menuBar.add(displayMenu); ButtonGroup group = new ButtonGroup(); viewMenuItems = new JRadioButtonMenuItem[viewItems.length]; for (int i = 0; i < viewItems.length; i++) { viewMenuItems[i] = new JRadioButtonMenuItem(viewItems[i], i == 0); viewMenuItems[i].addActionListener(this); KeyStroke ks = KeyStroke.getKeyStroke('1' + i, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()); viewMenuItems[i].setAccelerator(ks); displayMenu.add(viewMenuItems[i]); viewMenuItems[i].setEnabled(false); group.add(viewMenuItems[i]); } displayMenu.addSeparator(); //a submenu ButtonGroup zg = new ButtonGroup(); JMenu zoomMenu = new JMenu("LD zoom"); zoomMenu.setMnemonic(KeyEvent.VK_Z); zoomMenuItems = new JRadioButtonMenuItem[zoomItems.length]; for (int i = 0; i < zoomItems.length; i++){ zoomMenuItems[i] = new JRadioButtonMenuItem(zoomItems[i], i==0); zoomMenuItems[i].addActionListener(this); zoomMenuItems[i].setActionCommand("zoom" + i); zoomMenu.add(zoomMenuItems[i]); zg.add(zoomMenuItems[i]); } displayMenu.add(zoomMenu); //another submenu ButtonGroup cg = new ButtonGroup(); JMenu colorMenu = new JMenu("LD color scheme"); colorMenu.setMnemonic(KeyEvent.VK_C); colorMenuItems = new JRadioButtonMenuItem[colorItems.length]; for (int i = 0; i< colorItems.length; i++){ colorMenuItems[i] = new JRadioButtonMenuItem(colorItems[i],i==0); colorMenuItems[i].addActionListener(this); colorMenuItems[i].setActionCommand("color" + i); colorMenu.add(colorMenuItems[i]); cg.add(colorMenuItems[i]); } displayMenu.add(colorMenu); //analysis menu JMenu analysisMenu = new JMenu("Analysis"); analysisMenu.setMnemonic(KeyEvent.VK_A); menuBar.add(analysisMenu); //a submenu ButtonGroup bg = new ButtonGroup(); JMenu blockMenu = new JMenu("Define Blocks"); blockMenu.setMnemonic(KeyEvent.VK_B); blockMenuItems = new JRadioButtonMenuItem[blockItems.length]; for (int i = 0; i < blockItems.length; i++){ blockMenuItems[i] = new JRadioButtonMenuItem(blockItems[i], i==0); blockMenuItems[i].addActionListener(this); blockMenuItems[i].setActionCommand("block" + i); blockMenu.add(blockMenuItems[i]); bg.add(blockMenuItems[i]); } blockMenuItems[3].setEnabled(false); analysisMenu.add(blockMenu); clearBlocksItem = new JMenuItem(CLEAR_BLOCKS); setAccelerator(clearBlocksItem, 'C', false); clearBlocksItem.addActionListener(this); clearBlocksItem.setEnabled(false); analysisMenu.add(clearBlocksItem); JMenuItem customizeBlocksItem = new JMenuItem(CUST_BLOCKS); customizeBlocksItem.addActionListener(this); analysisMenu.add(customizeBlocksItem); //color key keyMenu = new JMenu("Key"); menuBar.add(Box.createHorizontalGlue()); menuBar.add(keyMenu); /** NEEDS FIXING helpMenu = new JMenu("Help"); menuBar.add(Box.createHorizontalGlue()); menuBar.add(helpMenu); menuItem = new JMenuItem("Tutorial"); menuItem.addActionListener(this); helpMenu.add(menuItem); **/ /* clearBlocksMenuItem.addActionListener(this); clearBlocksMenuItem.setEnabled(false); toolMenu.add(clearBlocksMenuItem); */ addWindowListener(new WindowAdapter() { public void windowClosing(WindowEvent e){ quit(); } }); addComponentListener(new ResizeListener()); } |
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if (method == BLOX_NONE){ | if (method == BLOX_NONE || method == BLOX_CUSTOM){ | public void changeBlocks(int method){ if (method == BLOX_NONE){ blockMenuItems[BLOX_CUSTOM].setSelected(true); } theData.guessBlocks(method); dPrimeDisplay.repaint(); currentBlockDef = method; try{ if (tabs.getSelectedIndex() == VIEW_HAP_NUM){ hapDisplay.getHaps(); } }catch(HaploViewException hve) { JOptionPane.showMessageDialog(this, hve.getMessage(), "Error", JOptionPane.ERROR_MESSAGE); } hapScroller.setViewportView(hapDisplay); } |
theData.guessBlocks(method); | if (method != BLOX_CUSTOM){ theData.guessBlocks(method); } | public void changeBlocks(int method){ if (method == BLOX_NONE){ blockMenuItems[BLOX_CUSTOM].setSelected(true); } theData.guessBlocks(method); dPrimeDisplay.repaint(); currentBlockDef = method; try{ if (tabs.getSelectedIndex() == VIEW_HAP_NUM){ hapDisplay.getHaps(); } }catch(HaploViewException hve) { JOptionPane.showMessageDialog(this, hve.getMessage(), "Error", JOptionPane.ERROR_MESSAGE); } hapScroller.setViewportView(hapDisplay); } |
if (dPrimeDisplay != null && tabs.getSelectedIndex() == VIEW_D_NUM){ dPrimeDisplay.repaint(); } | changeBlocks(BLOX_CUSTOM); | void readBlocksFile(File file) { try{ Vector cust = theData.readBlocks(file); theData.guessBlocks(BLOX_CUSTOM, cust); if (dPrimeDisplay != null && tabs.getSelectedIndex() == VIEW_D_NUM){ dPrimeDisplay.repaint(); } }catch (HaploViewException hve){ JOptionPane.showMessageDialog(this, hve.getMessage(), "File Error", JOptionPane.ERROR_MESSAGE); }catch (IOException ioe){ JOptionPane.showMessageDialog(this, ioe.getMessage(), "File Error", JOptionPane.ERROR_MESSAGE); } } |
getBody().run(context, output); | invokeBody(output); | public void doTag(final XMLOutput output) throws Exception { this.session = new JellySession( output ); getBody().run(context, output); } |
long minpos = Chromosome.getFilteredMarker(0).getPosition(); long maxpos = Chromosome.getFilteredMarker(Chromosome.getSize()-1).getPosition(); | long minpos = Chromosome.getMarker(0).getPosition(); long maxpos = Chromosome.getMarker(Chromosome.getSize()-1).getPosition(); | public void paintComponent(Graphics g){ Graphics2D g2 = (Graphics2D) g; Dimension size = getSize(); Dimension pref = getPreferredSize(); Rectangle visRect = getVisibleRect(); /* boxSize = ((clipRect.width-2*H_BORDER)/dPrimeTable.length-1); if (boxSize < 12){boxSize=12;} if (boxSize < 25){ printDetails = false; boxRadius = boxSize/2; }else{ boxRadius = boxSize/2 - 1; } */ //okay so this dumb if block is to prevent the ugly repainting //bug when loading markers after the data are already being displayed, //results in a little off-centering for small datasets, but not too bad. //clickxshift and clickyshift are used later to translate from x,y coords //to the pair of markers comparison at those coords if (!(markersLoaded)){ g2.translate((size.width - pref.width) / 2, (size.height - pref.height) / 2); clickXShift = left + (size.width-pref.width)/2; clickYShift = top + (size.height - pref.height)/2; } else { g2.translate((size.width - pref.width) / 2, 0); clickXShift = left + (size.width-pref.width)/2; clickYShift = top; } FontMetrics boxFontMetrics = g.getFontMetrics(boxFont); int diamondX[] = new int[4]; int diamondY[] = new int[4]; Polygon diamond; left = H_BORDER; top = V_BORDER; FontMetrics metrics; int ascent; g2.setColor(this.getBackground()); g2.fillRect(0,0,pref.width,pref.height); g2.setColor(Color.BLACK); BasicStroke thickerStroke = new BasicStroke(1); BasicStroke thinnerStroke = new BasicStroke(0.25f); BasicStroke fatStroke = new BasicStroke(3.0f); if (markersLoaded) { g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON); //// draw the marker locations int wide = (dPrimeTable.length-1) * boxSize; //TODO: talk to kirby about locusview scaling gizmo int lineLeft = wide/20; int lineSpan = (wide/10)*9; long minpos = Chromosome.getFilteredMarker(0).getPosition(); long maxpos = Chromosome.getFilteredMarker(Chromosome.getSize()-1).getPosition(); double spanpos = maxpos - minpos; g2.setStroke(thinnerStroke); g2.setColor(Color.white); g2.fillRect(left + lineLeft, 5, lineSpan, TICK_HEIGHT); g2.setColor(Color.black); g2.drawRect(left + lineLeft, 5, lineSpan, TICK_HEIGHT); for (int i = 0; i < Chromosome.getSize(); i++) { double pos = (Chromosome.getFilteredMarker(i).getPosition() - minpos) / spanpos; int xx = (int) (left + lineLeft + lineSpan*pos); g2.setStroke(thickerStroke); g.drawLine(xx, 5, xx, 5 + TICK_HEIGHT); g2.setStroke(thinnerStroke); g.drawLine(xx, 5 + TICK_HEIGHT, left + i*boxSize, TICK_BOTTOM); } top += TICK_BOTTOM; //// draw the marker names if (printDetails){ g.setFont(markerNameFont); metrics = g.getFontMetrics(); ascent = metrics.getAscent(); widestMarkerName = metrics.stringWidth(Chromosome.getFilteredMarker(0).getName()); for (int x = 1; x < dPrimeTable.length; x++) { int thiswide = metrics.stringWidth(Chromosome.getFilteredMarker(x).getName()); if (thiswide > widestMarkerName) widestMarkerName = thiswide; } g2.translate(left, top + widestMarkerName); g2.rotate(-Math.PI / 2.0); for (int x = 0; x < dPrimeTable.length; x++) { g2.drawString(Chromosome.getFilteredMarker(x).getName(),TEXT_NUMBER_GAP, x*boxSize + ascent/3); } g2.rotate(Math.PI / 2.0); g2.translate(-left, -(top + widestMarkerName)); // move everybody down top += widestMarkerName + TEXT_NUMBER_GAP; } g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_OFF); } //// draw the marker numbers if (printDetails){ g.setFont(markerNumFont); metrics = g.getFontMetrics(); ascent = metrics.getAscent(); for (int x = 0; x < dPrimeTable.length; x++) { String mark = String.valueOf(Chromosome.realIndex[x] + 1); g.drawString(mark, left + x*boxSize - metrics.stringWidth(mark)/2, top + ascent); } top += boxRadius/2; // give a little space between numbers and boxes } //the following values are the bounds on the boxes we want to //display given that the current window is 'visRect' lowX = (visRect.x-clickXShift-(visRect.y + visRect.height-clickYShift))/boxSize; if (lowX < 0) { lowX = 0; } highX = ((visRect.x + visRect.width)/boxSize)+1; if (highX > dPrimeTable.length-1){ highX = dPrimeTable.length-1; } lowY = ((visRect.x-clickXShift)+(visRect.y-clickYShift))/boxSize; if (lowY < lowX+1){ lowY = lowX+1; } highY = (((visRect.x-clickXShift+visRect.width) + (visRect.y-clickYShift+visRect.height))/boxSize)+1; if (highY > dPrimeTable.length){ highY = dPrimeTable.length; } // draw table column by column for (int x = lowX; x < highX; x++) { //always draw the fewest possible boxes if (lowY < x+1){ lowY = x+1; } for (int y = lowY; y < highY; y++) { if (dPrimeTable[x][y] == null){ continue; } double d = dPrimeTable[x][y].getDPrime(); //double l = dPrimeTable[x][y].getLOD(); Color boxColor = dPrimeTable[x][y].getColor(); // draw markers above int xx = left + (x + y) * boxSize / 2; int yy = top + (y - x) * boxSize / 2; diamondX[0] = xx; diamondY[0] = yy - boxRadius; diamondX[1] = xx + boxRadius; diamondY[1] = yy; diamondX[2] = xx; diamondY[2] = yy + boxRadius; diamondX[3] = xx - boxRadius; diamondY[3] = yy; diamond = new Polygon(diamondX, diamondY, 4); g.setColor(boxColor); g.fillPolygon(diamond); if (boxColor == Color.white) { g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON); g.setColor(Color.lightGray); g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_OFF); } if(printDetails){ g.setFont(boxFont); ascent = boxFontMetrics.getAscent(); int val = (int) (d * 100); g.setColor((val < 50) ? Color.gray : Color.black); if (val != 100) { String valu = String.valueOf(val); int widf = boxFontMetrics.stringWidth(valu); g.drawString(valu, xx - widf/2, yy + ascent/2); } } } } //highlight blocks boolean even = true; //g.setColor(new Color(153,255,153)); g.setColor(new Color(51,153,51)); g2.setStroke(fatStroke); for (int i = 0; i < blocks.size(); i++){ int[] theBlock = (int[])blocks.elementAt(i); int first = theBlock[0]; int last = theBlock[theBlock.length-1]; g.drawLine(left + (2*first + 1) * boxSize/2 - boxRadius, top + boxSize/2, left + (first + last) * boxSize/2, top + (last - first) * boxSize/2 + boxRadius); g.drawLine(left + (first + last) * boxSize/2, top + (last - first) * boxSize/2 + boxRadius, left + (2*last - 1) * boxSize/2+boxRadius, top + boxSize/2); for (int j = 0; j < theBlock.length; j++){ g.drawLine(left + (2*theBlock[j]+1) * boxSize/2 - boxRadius, top + boxSize/2, left + (2*theBlock[j]+1) * boxSize/2, top + boxSize/2 - boxRadius); g.drawLine (left + (2*theBlock[j]) * boxSize/2 - boxRadius, top + boxSize/2 - boxRadius, left + (2*theBlock[j]) * boxSize/2, top + boxSize/2); } } g2.setStroke(thickerStroke); if (pref.getWidth() > (2*visRect.width)){ //dataset is big enough to require worldmap if (noImage){ //first time through draw a worldmap if dataset is big: final int WM_MAX_WIDTH = visRect.width/3; double scalefactor; scalefactor = (double)(chartSize.width)/WM_MAX_WIDTH; CompoundBorder wmBorder = new CompoundBorder(BorderFactory.createRaisedBevelBorder(), BorderFactory.createLoweredBevelBorder()); worldmap = new BufferedImage((int)(chartSize.width/scalefactor)+wmBorder.getBorderInsets(this).left*2, (int)(chartSize.height/scalefactor)+wmBorder.getBorderInsets(this).top*2, BufferedImage.TYPE_3BYTE_BGR); Graphics gw = worldmap.getGraphics(); Graphics2D gw2 = (Graphics2D)(gw); gw2.setColor(this.getBackground()); gw2.fillRect(1,1,worldmap.getWidth()-2,worldmap.getHeight()-2); //make a pretty border gw2.setColor(Color.BLACK); wmBorder.paintBorder(this,gw2,0,0,worldmap.getWidth()-1,worldmap.getHeight()-1); ir = wmBorder.getInteriorRectangle(this,0,0,worldmap.getWidth()-1, worldmap.getHeight()-1); double prefBoxSize = boxSize/scalefactor; float[] smallDiamondX = new float[4]; float[] smallDiamondY = new float[4]; GeneralPath gp; for (int x = 0; x < dPrimeTable.length-1; x++){ for (int y = x+1; y < dPrimeTable.length; y++){ if (dPrimeTable[x][y] == null){ continue; } double xx = (x + y)*prefBoxSize/2+wmBorder.getBorderInsets(this).left; double yy = (y - x)*prefBoxSize/2+wmBorder.getBorderInsets(this).top; smallDiamondX[0] = (float)xx; smallDiamondY[0] = (float)(yy - prefBoxSize/2); smallDiamondX[1] = (float)(xx + prefBoxSize/2); smallDiamondY[1] = (float)yy; smallDiamondX[2] = (float)xx; smallDiamondY[2] = (float)(yy + prefBoxSize/2); smallDiamondX[3] = (float)(xx - prefBoxSize/2); smallDiamondY[3] = (float)yy; gp = new GeneralPath(GeneralPath.WIND_EVEN_ODD, smallDiamondX.length); gp.moveTo(smallDiamondX[0],smallDiamondY[0]); for (int i = 1; i < smallDiamondX.length; i++){ gp.lineTo(smallDiamondX[i], smallDiamondY[i]); } gp.closePath(); gw2.setColor(dPrimeTable[x][y].getColor()); gw2.fill(gp); } } noImage = false; } g.drawImage(worldmap,visRect.x, visRect.y + visRect.height - worldmap.getHeight(), this); worldmapRect = new Rectangle(visRect.x, visRect.y+visRect.height-worldmap.getHeight(), worldmap.getWidth(), worldmap.getHeight()); //draw the outline of the viewport g.setColor(Color.BLACK); double hRatio = ir.getWidth()/pref.getWidth(); double vRatio = ir.getHeight()/pref.getHeight(); int hBump = worldmap.getWidth()-ir.width; int vBump = worldmap.getHeight()-ir.height; //bump a few pixels to avoid drawing on the border g.drawRect((int)(visRect.x*hRatio)+hBump/2+visRect.x, (int)(visRect.y*vRatio)+vBump/2+(visRect.y + visRect.height - worldmap.getHeight()), (int)(visRect.width*hRatio), (int)(visRect.height*vRatio)); } } |
for (int i = 0; i < Chromosome.getSize(); i++) { | for (int i = 0; i < Chromosome.getFilteredSize(); i++) { | public void paintComponent(Graphics g){ Graphics2D g2 = (Graphics2D) g; Dimension size = getSize(); Dimension pref = getPreferredSize(); Rectangle visRect = getVisibleRect(); /* boxSize = ((clipRect.width-2*H_BORDER)/dPrimeTable.length-1); if (boxSize < 12){boxSize=12;} if (boxSize < 25){ printDetails = false; boxRadius = boxSize/2; }else{ boxRadius = boxSize/2 - 1; } */ //okay so this dumb if block is to prevent the ugly repainting //bug when loading markers after the data are already being displayed, //results in a little off-centering for small datasets, but not too bad. //clickxshift and clickyshift are used later to translate from x,y coords //to the pair of markers comparison at those coords if (!(markersLoaded)){ g2.translate((size.width - pref.width) / 2, (size.height - pref.height) / 2); clickXShift = left + (size.width-pref.width)/2; clickYShift = top + (size.height - pref.height)/2; } else { g2.translate((size.width - pref.width) / 2, 0); clickXShift = left + (size.width-pref.width)/2; clickYShift = top; } FontMetrics boxFontMetrics = g.getFontMetrics(boxFont); int diamondX[] = new int[4]; int diamondY[] = new int[4]; Polygon diamond; left = H_BORDER; top = V_BORDER; FontMetrics metrics; int ascent; g2.setColor(this.getBackground()); g2.fillRect(0,0,pref.width,pref.height); g2.setColor(Color.BLACK); BasicStroke thickerStroke = new BasicStroke(1); BasicStroke thinnerStroke = new BasicStroke(0.25f); BasicStroke fatStroke = new BasicStroke(3.0f); if (markersLoaded) { g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON); //// draw the marker locations int wide = (dPrimeTable.length-1) * boxSize; //TODO: talk to kirby about locusview scaling gizmo int lineLeft = wide/20; int lineSpan = (wide/10)*9; long minpos = Chromosome.getFilteredMarker(0).getPosition(); long maxpos = Chromosome.getFilteredMarker(Chromosome.getSize()-1).getPosition(); double spanpos = maxpos - minpos; g2.setStroke(thinnerStroke); g2.setColor(Color.white); g2.fillRect(left + lineLeft, 5, lineSpan, TICK_HEIGHT); g2.setColor(Color.black); g2.drawRect(left + lineLeft, 5, lineSpan, TICK_HEIGHT); for (int i = 0; i < Chromosome.getSize(); i++) { double pos = (Chromosome.getFilteredMarker(i).getPosition() - minpos) / spanpos; int xx = (int) (left + lineLeft + lineSpan*pos); g2.setStroke(thickerStroke); g.drawLine(xx, 5, xx, 5 + TICK_HEIGHT); g2.setStroke(thinnerStroke); g.drawLine(xx, 5 + TICK_HEIGHT, left + i*boxSize, TICK_BOTTOM); } top += TICK_BOTTOM; //// draw the marker names if (printDetails){ g.setFont(markerNameFont); metrics = g.getFontMetrics(); ascent = metrics.getAscent(); widestMarkerName = metrics.stringWidth(Chromosome.getFilteredMarker(0).getName()); for (int x = 1; x < dPrimeTable.length; x++) { int thiswide = metrics.stringWidth(Chromosome.getFilteredMarker(x).getName()); if (thiswide > widestMarkerName) widestMarkerName = thiswide; } g2.translate(left, top + widestMarkerName); g2.rotate(-Math.PI / 2.0); for (int x = 0; x < dPrimeTable.length; x++) { g2.drawString(Chromosome.getFilteredMarker(x).getName(),TEXT_NUMBER_GAP, x*boxSize + ascent/3); } g2.rotate(Math.PI / 2.0); g2.translate(-left, -(top + widestMarkerName)); // move everybody down top += widestMarkerName + TEXT_NUMBER_GAP; } g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_OFF); } //// draw the marker numbers if (printDetails){ g.setFont(markerNumFont); metrics = g.getFontMetrics(); ascent = metrics.getAscent(); for (int x = 0; x < dPrimeTable.length; x++) { String mark = String.valueOf(Chromosome.realIndex[x] + 1); g.drawString(mark, left + x*boxSize - metrics.stringWidth(mark)/2, top + ascent); } top += boxRadius/2; // give a little space between numbers and boxes } //the following values are the bounds on the boxes we want to //display given that the current window is 'visRect' lowX = (visRect.x-clickXShift-(visRect.y + visRect.height-clickYShift))/boxSize; if (lowX < 0) { lowX = 0; } highX = ((visRect.x + visRect.width)/boxSize)+1; if (highX > dPrimeTable.length-1){ highX = dPrimeTable.length-1; } lowY = ((visRect.x-clickXShift)+(visRect.y-clickYShift))/boxSize; if (lowY < lowX+1){ lowY = lowX+1; } highY = (((visRect.x-clickXShift+visRect.width) + (visRect.y-clickYShift+visRect.height))/boxSize)+1; if (highY > dPrimeTable.length){ highY = dPrimeTable.length; } // draw table column by column for (int x = lowX; x < highX; x++) { //always draw the fewest possible boxes if (lowY < x+1){ lowY = x+1; } for (int y = lowY; y < highY; y++) { if (dPrimeTable[x][y] == null){ continue; } double d = dPrimeTable[x][y].getDPrime(); //double l = dPrimeTable[x][y].getLOD(); Color boxColor = dPrimeTable[x][y].getColor(); // draw markers above int xx = left + (x + y) * boxSize / 2; int yy = top + (y - x) * boxSize / 2; diamondX[0] = xx; diamondY[0] = yy - boxRadius; diamondX[1] = xx + boxRadius; diamondY[1] = yy; diamondX[2] = xx; diamondY[2] = yy + boxRadius; diamondX[3] = xx - boxRadius; diamondY[3] = yy; diamond = new Polygon(diamondX, diamondY, 4); g.setColor(boxColor); g.fillPolygon(diamond); if (boxColor == Color.white) { g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON); g.setColor(Color.lightGray); g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_OFF); } if(printDetails){ g.setFont(boxFont); ascent = boxFontMetrics.getAscent(); int val = (int) (d * 100); g.setColor((val < 50) ? Color.gray : Color.black); if (val != 100) { String valu = String.valueOf(val); int widf = boxFontMetrics.stringWidth(valu); g.drawString(valu, xx - widf/2, yy + ascent/2); } } } } //highlight blocks boolean even = true; //g.setColor(new Color(153,255,153)); g.setColor(new Color(51,153,51)); g2.setStroke(fatStroke); for (int i = 0; i < blocks.size(); i++){ int[] theBlock = (int[])blocks.elementAt(i); int first = theBlock[0]; int last = theBlock[theBlock.length-1]; g.drawLine(left + (2*first + 1) * boxSize/2 - boxRadius, top + boxSize/2, left + (first + last) * boxSize/2, top + (last - first) * boxSize/2 + boxRadius); g.drawLine(left + (first + last) * boxSize/2, top + (last - first) * boxSize/2 + boxRadius, left + (2*last - 1) * boxSize/2+boxRadius, top + boxSize/2); for (int j = 0; j < theBlock.length; j++){ g.drawLine(left + (2*theBlock[j]+1) * boxSize/2 - boxRadius, top + boxSize/2, left + (2*theBlock[j]+1) * boxSize/2, top + boxSize/2 - boxRadius); g.drawLine (left + (2*theBlock[j]) * boxSize/2 - boxRadius, top + boxSize/2 - boxRadius, left + (2*theBlock[j]) * boxSize/2, top + boxSize/2); } } g2.setStroke(thickerStroke); if (pref.getWidth() > (2*visRect.width)){ //dataset is big enough to require worldmap if (noImage){ //first time through draw a worldmap if dataset is big: final int WM_MAX_WIDTH = visRect.width/3; double scalefactor; scalefactor = (double)(chartSize.width)/WM_MAX_WIDTH; CompoundBorder wmBorder = new CompoundBorder(BorderFactory.createRaisedBevelBorder(), BorderFactory.createLoweredBevelBorder()); worldmap = new BufferedImage((int)(chartSize.width/scalefactor)+wmBorder.getBorderInsets(this).left*2, (int)(chartSize.height/scalefactor)+wmBorder.getBorderInsets(this).top*2, BufferedImage.TYPE_3BYTE_BGR); Graphics gw = worldmap.getGraphics(); Graphics2D gw2 = (Graphics2D)(gw); gw2.setColor(this.getBackground()); gw2.fillRect(1,1,worldmap.getWidth()-2,worldmap.getHeight()-2); //make a pretty border gw2.setColor(Color.BLACK); wmBorder.paintBorder(this,gw2,0,0,worldmap.getWidth()-1,worldmap.getHeight()-1); ir = wmBorder.getInteriorRectangle(this,0,0,worldmap.getWidth()-1, worldmap.getHeight()-1); double prefBoxSize = boxSize/scalefactor; float[] smallDiamondX = new float[4]; float[] smallDiamondY = new float[4]; GeneralPath gp; for (int x = 0; x < dPrimeTable.length-1; x++){ for (int y = x+1; y < dPrimeTable.length; y++){ if (dPrimeTable[x][y] == null){ continue; } double xx = (x + y)*prefBoxSize/2+wmBorder.getBorderInsets(this).left; double yy = (y - x)*prefBoxSize/2+wmBorder.getBorderInsets(this).top; smallDiamondX[0] = (float)xx; smallDiamondY[0] = (float)(yy - prefBoxSize/2); smallDiamondX[1] = (float)(xx + prefBoxSize/2); smallDiamondY[1] = (float)yy; smallDiamondX[2] = (float)xx; smallDiamondY[2] = (float)(yy + prefBoxSize/2); smallDiamondX[3] = (float)(xx - prefBoxSize/2); smallDiamondY[3] = (float)yy; gp = new GeneralPath(GeneralPath.WIND_EVEN_ODD, smallDiamondX.length); gp.moveTo(smallDiamondX[0],smallDiamondY[0]); for (int i = 1; i < smallDiamondX.length; i++){ gp.lineTo(smallDiamondX[i], smallDiamondY[i]); } gp.closePath(); gw2.setColor(dPrimeTable[x][y].getColor()); gw2.fill(gp); } } noImage = false; } g.drawImage(worldmap,visRect.x, visRect.y + visRect.height - worldmap.getHeight(), this); worldmapRect = new Rectangle(visRect.x, visRect.y+visRect.height-worldmap.getHeight(), worldmap.getWidth(), worldmap.getHeight()); //draw the outline of the viewport g.setColor(Color.BLACK); double hRatio = ir.getWidth()/pref.getWidth(); double vRatio = ir.getHeight()/pref.getHeight(); int hBump = worldmap.getWidth()-ir.width; int vBump = worldmap.getHeight()-ir.height; //bump a few pixels to avoid drawing on the border g.drawRect((int)(visRect.x*hRatio)+hBump/2+visRect.x, (int)(visRect.y*vRatio)+vBump/2+(visRect.y + visRect.height - worldmap.getHeight()), (int)(visRect.width*hRatio), (int)(visRect.height*vRatio)); } } |
folderTree.setShowsRootHandles( true ); | folderTree.setShowsRootHandles( false ); | void createUI() { setLayout(new GridBagLayout()); folderTree = new JTree( ); folderTree.setRootVisible( true ); folderTree.setShowsRootHandles( true ); folderTree.setEditable( false ); JScrollPane scrollPane = new JScrollPane( folderTree ); scrollPane.setPreferredSize( new Dimension( 300, 300 ) ); GridBagConstraints c = new GridBagConstraints(); c.gridx = 0; c.gridy = 0; c.gridheight = GridBagConstraints.REMAINDER; c.fill = GridBagConstraints.BOTH; add( scrollPane, c ); JButton addFolderBtn = new JButton( "Add to folder..." ); addFolderBtn.setActionCommand( ADD_ALL_TO_FOLDER_CMD ); addFolderBtn.addActionListener( this ); c = new GridBagConstraints(); c.gridx = 1; c.gridy = 0; add( addFolderBtn, c ); popup = new JPopupMenu(); JMenuItem addAllItem = new JMenuItem( "Add photos" ); addAllItem.addActionListener( this ); addAllItem.setActionCommand( ADD_ALL_TO_THIS_FOLDER_CMD ); JMenuItem removeAllItem = new JMenuItem( "Remove photos" ); removeAllItem.addActionListener( this ); removeAllItem.setActionCommand( REMOVE_ALL_FROM_THIS_FOLDER_CMD ); popup.add( addAllItem ); popup.add( removeAllItem ); MouseListener popupListener = new PopupListener(); folderTree.addMouseListener( popupListener ); } |
TreePath parentPath = e.getTreePath(); folderTree.expandPath( parentPath ); | final TreePath parentPath = e.getTreePath(); SwingUtilities.invokeLater(new java.lang.Runnable() { public void run() { folderTree.expandPath( parentPath ); } }); | public void treeNodesInserted( TreeModelEvent e ) { TreePath parentPath = e.getTreePath(); folderTree.expandPath( parentPath ); } |
g.setFont(boxFont); | g.setFont(popupFont); | public void mousePressed (MouseEvent e) { Rectangle blockselector = new Rectangle(clickXShift-boxRadius,clickYShift - boxRadius, (int)alignedPositions[alignedPositions.length-1]+boxSize, boxSize); //if users right clicks & holds, pop up the info if ((e.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK){ Graphics g = getGraphics(); g.setFont(boxFont); FontMetrics metrics = g.getFontMetrics(); DPrimeTable dPrimeTable = theData.dpTable; final int clickX = e.getX(); final int clickY = e.getY(); final int boxX, boxY; boxX = getPreciseMarkerAt(clickX - clickXShift - (clickY-clickYShift)); boxY = getPreciseMarkerAt(clickX - clickXShift + (clickY-clickYShift)); if ((boxX >= lowX && boxX <= highX) && (boxY > boxX && boxY < highY) && !(wmInteriorRect.contains(clickX,clickY))){ if (dPrimeTable.getLDStats(boxX,boxY) != null){ double[] freqs = dPrimeTable.getLDStats(boxX,boxY).getFreqs(); displayStrings = new Vector(); if (theData.infoKnown){ displayStrings.add(new String ("(" +Chromosome.getMarker(boxX).getName() + ", " + Chromosome.getMarker(boxY).getName() + ")")); double sep = (int)((Chromosome.getMarker(boxY).getPosition() - Chromosome.getMarker(boxX).getPosition())/100); sep /= 10; displayStrings.add(new Double(sep).toString() + " kb"); }else{ displayStrings.add(new String("(" + (Chromosome.realIndex[boxX]+1) + ", " + (Chromosome.realIndex[boxY]+1) + ")")); } displayStrings.add(new String ("D': " + dPrimeTable.getLDStats(boxX,boxY).getDPrime())); displayStrings.add(new String ("LOD: " + dPrimeTable.getLDStats(boxX,boxY).getLOD())); displayStrings.add( new String ("r-squared: " + dPrimeTable.getLDStats(boxX,boxY).getRSquared())); displayStrings.add(new String ("D' conf. bounds: " + dPrimeTable.getLDStats(boxX,boxY).getConfidenceLow() + "-" + dPrimeTable.getLDStats(boxX,boxY).getConfidenceHigh())); //get the alleles for the 4 two-marker haplotypes String[] alleleStrings = new String[4]; String[] alleleMap = {"", "A","C","G","T"}; if (freqs[0] + freqs[1] > freqs[2] + freqs[3]){ alleleStrings[0] = alleleMap[Chromosome.getMarker(boxX).getMajor()]; alleleStrings[1] = alleleMap[Chromosome.getMarker(boxX).getMajor()]; alleleStrings[2] = alleleMap[Chromosome.getMarker(boxX).getMinor()]; alleleStrings[3] = alleleMap[Chromosome.getMarker(boxX).getMinor()]; }else{ alleleStrings[0] = alleleMap[Chromosome.getMarker(boxX).getMinor()]; alleleStrings[1] = alleleMap[Chromosome.getMarker(boxX).getMinor()]; alleleStrings[2] = alleleMap[Chromosome.getMarker(boxX).getMajor()]; alleleStrings[3] = alleleMap[Chromosome.getMarker(boxX).getMajor()]; } if (freqs[0] + freqs[3] > freqs[1] + freqs[2]){ alleleStrings[0] += alleleMap[Chromosome.getMarker(boxY).getMajor()]; alleleStrings[1] += alleleMap[Chromosome.getMarker(boxY).getMinor()]; alleleStrings[2] += alleleMap[Chromosome.getMarker(boxY).getMinor()]; alleleStrings[3] += alleleMap[Chromosome.getMarker(boxY).getMajor()]; }else{ alleleStrings[0] += alleleMap[Chromosome.getMarker(boxY).getMinor()]; alleleStrings[1] += alleleMap[Chromosome.getMarker(boxY).getMajor()]; alleleStrings[2] += alleleMap[Chromosome.getMarker(boxY).getMajor()]; alleleStrings[3] += alleleMap[Chromosome.getMarker(boxY).getMinor()]; } displayStrings.add(new String("Frequencies:")); for (int i = 0; i < 4; i++){ if (freqs[i] > 1.0E-10){ displayStrings.add( new String(alleleStrings[i] + " = " + Math.rint(1000 * freqs[i])/10 + "%")); } } popupExists = true; } } else if (blockselector.contains(clickX, clickY)){ int marker = getPreciseMarkerAt(clickX - clickXShift); int size = 2; if (Chromosome.getMarker(marker).getExtra() != null) size++; displayStrings = new Vector(); if (theData.infoKnown){ displayStrings.add(new String (Chromosome.getMarker(marker).getName())); }else{ displayStrings.add(new String("Marker " + (Chromosome.realIndex[marker]+1))); } displayStrings.add(new String ("MAF: " + Chromosome.getMarker(marker).getMAF())); if (Chromosome.getMarker(marker).getExtra() != null) displayStrings.add(new String (Chromosome.getMarker(marker).getExtra())); popupExists = true; } if (popupExists){ int strlen = 0; for (int x = 0; x < displayStrings.size(); x++){ if (strlen < metrics.stringWidth((String)displayStrings.elementAt(x))){ strlen = metrics.stringWidth((String)displayStrings.elementAt(x)); } } //edge shifts prevent window from popping up partially offscreen int visRightBound = (int)(getVisibleRect().getWidth() + getVisibleRect().getX()); int visBotBound = (int)(getVisibleRect().getHeight() + getVisibleRect().getY()); int rightEdgeShift = 0; if (clickX + strlen + popupLeftMargin +5 > visRightBound){ rightEdgeShift = clickX + strlen + popupLeftMargin + 10 - visRightBound; } int botEdgeShift = 0; if (clickY + displayStrings.size()*metrics.getHeight()+10 > visBotBound){ botEdgeShift = clickY + displayStrings.size()*metrics.getHeight()+15 - visBotBound; } int smallDataVertSlop = 0; if (getPreferredSize().getWidth() < getVisibleRect().width && theData.infoKnown){ smallDataVertSlop = (int)(getVisibleRect().height - getPreferredSize().getHeight())/2; } popupDrawRect = new Rectangle(clickX-rightEdgeShift, clickY-botEdgeShift+smallDataVertSlop, strlen+popupLeftMargin+5, displayStrings.size()*metrics.getHeight()+10); repaint(); } }else if ((e.getModifiers() & InputEvent.BUTTON1_MASK) == InputEvent.BUTTON1_MASK){ int x = e.getX(); int y = e.getY(); if (blockselector.contains(x,y)){ setCursor(Cursor.getPredefinedCursor(Cursor.E_RESIZE_CURSOR)); blockStartX = x; } } } |
g.setFont(popupFont); | public void paintComponent(Graphics g){ DPrimeTable dPrimeTable = theData.dpTable; if (Chromosome.getSize() == 0){ //if there are no valid markers return; } Vector blocks = theData.blocks; Rectangle visRect = getVisibleRect(); //deal with zooming if (chartSize.getWidth() > (3*visRect.width)){ showWM = true; }else{ showWM = false; } if (zoomLevel != 0 || Options.getLDColorScheme() == WMF_SCHEME || Options.getLDColorScheme() == RSQ_SCHEME){ printDPrimeValues = false; } else{ printDPrimeValues = true; } Graphics2D g2 = (Graphics2D) g; Dimension size = getSize(); Dimension pref = getPreferredSize(); g2.setColor(BG_GREY); //if it's a big dataset, resize properly, if it's small make sure to fill whole background if (size.height < pref.height){ g2.fillRect(0,0,pref.width,pref.height); setSize(pref); }else{ g2.fillRect(0,0,size.width, size.height); } g2.setColor(Color.black); //okay so this dumb if block is to prevent the ugly repainting //bug when loading markers after the data are already being displayed, //results in a little off-centering for small datasets, but not too bad. if (!forExport){ if (!theData.infoKnown){ g2.translate((size.width - pref.width) / 2, (size.height - pref.height) / 2); } else { g2.translate((size.width - pref.width) / 2, 0); } } FontMetrics boxFontMetrics = g2.getFontMetrics(boxFont); int diamondX[] = new int[4]; int diamondY[] = new int[4]; Polygon diamond; double lineSpan = alignedPositions[alignedPositions.length-1] - alignedPositions[0]; long minpos = Chromosome.getMarker(0).getPosition(); long maxpos = Chromosome.getMarker(Chromosome.getSize()-1).getPosition(); double spanpos = maxpos - minpos; //See http://www.hapmap.org/cgi-perl/gbrowse/gbrowse_img //for more info on GBrowse img. int imgHeight = 0; if (Options.isGBrowseShown() && Chromosome.getDataChrom() != null){ g2.drawImage(gBrowseImage, H_BORDER,V_BORDER,this); // not sure if this is an imageObserver, however imgHeight = gBrowseImage.getHeight(this) + TRACK_GAP; // get height so we can shift everything down } left = H_BORDER; top = V_BORDER + imgHeight; // push the haplotype display down to make room for gbrowse image. if (forExport){ left -= exportStart * boxSize; } FontMetrics metrics; int ascent; g2.setFont(boldMarkerNameFont); metrics = g2.getFontMetrics(); ascent = metrics.getAscent(); //the following values are the bounds on the boxes we want to //display given that the current window is 'visRect' lowX = getBoundaryMarker(visRect.x-clickXShift-(visRect.y +visRect.height-clickYShift)) - 1; highX = getBoundaryMarker(visRect.x + visRect.width); lowY = getBoundaryMarker((visRect.x-clickXShift)+(visRect.y-clickYShift)) - 1; highY = getBoundaryMarker((visRect.x-clickXShift+visRect.width) + (visRect.y-clickYShift+visRect.height)); if (lowX < 0) { lowX = 0; } if (highX > Chromosome.getSize()-1){ highX = Chromosome.getSize()-1; } if (lowY < lowX+1){ lowY = lowX+1; } if (highY > Chromosome.getSize()){ highY = Chromosome.getSize(); } if (forExport){ lowX = exportStart; lowY = exportStart; highX = exportStop; highY = exportStop; } if (theData.trackExists){ //draw the analysis track above where the marker positions will be marked g2.setColor(Color.white); g2.fill(new Rectangle2D.Double(left, top, lineSpan, TRACK_HEIGHT)); g2.setColor(Color.black); g2.drawRect(left,top,(int)lineSpan,TRACK_HEIGHT); //get the data into an easier format double positions[] = new double[theData.analysisPositions.size()]; double values[] = new double[theData.analysisPositions.size()]; for (int x = 0; x < positions.length; x++){ positions[x] = ((Double)theData.analysisPositions.elementAt(x)).doubleValue(); values[x] = ((Double)theData.analysisValues.elementAt(x)).doubleValue(); } g2.setColor(Color.black); double min = Double.MAX_VALUE; double max = -min; for (int x = 0; x < positions.length; x++){ if(values[x] < min){ min = values[x]; } if (values[x] > max){ max = values[x]; } } double range = max-min; //todo: this is kinda hideous for (int x = 0; x < positions.length - 1; x++){ if (positions[x] >= minpos && positions[x+1] <= maxpos){ g2.draw(new Line2D.Double(lineSpan * Math.abs((positions[x] - minpos)/spanpos) + left, top + TRACK_PALETTE + TRACK_BUMPER - (TRACK_PALETTE * Math.abs((values[x] - min)/range)), lineSpan * Math.abs((positions[x+1] - minpos)/spanpos) + left, top + TRACK_PALETTE + TRACK_BUMPER - (TRACK_PALETTE * Math.abs((values[x+1] - min)/range)))); } } top += TRACK_HEIGHT + TRACK_GAP; } if (theData.infoKnown) { Color green = new Color(0, 127, 0); g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON); //// draw the marker locations g2.setStroke(thinnerStroke); g2.setColor(Color.white); g2.fill(new Rectangle2D.Double(left+1, top+1, lineSpan-1, TICK_HEIGHT-1)); g2.setColor(Color.black); g2.draw(new Rectangle2D.Double(left, top, lineSpan, TICK_HEIGHT)); for (int i = 0; i < Chromosome.getSize(); i++){ double pos = (Chromosome.getMarker(i).getPosition() - minpos) / spanpos; double xx = left + lineSpan*pos; // if we're zoomed, use the line color to indicate whether there is extra data available // (since the marker names are not displayed when zoomed) if (Chromosome.getMarker(i).getExtra() != null && zoomLevel != 0) g2.setColor(green); //draw tick g2.setStroke(thickerStroke); g2.draw(new Line2D.Double(xx, top, xx, top + TICK_HEIGHT)); if (Chromosome.getMarker(i).getExtra() != null && zoomLevel != 0) g2.setStroke(thickerStroke); else g2.setStroke(thinnerStroke); //draw connecting line g2.draw(new Line2D.Double(xx, top + TICK_HEIGHT, left + alignedPositions[i], top+TICK_BOTTOM)); if (Chromosome.getMarker(i).getExtra() != null && zoomLevel != 0) g2.setColor(Color.black); } top += TICK_BOTTOM + TICK_HEIGHT; //// draw the marker names if (printMarkerNames){ widestMarkerName = metrics.stringWidth(Chromosome.getMarker(0).getName()); for (int x = 1; x < Chromosome.getSize(); x++) { int thiswide = metrics.stringWidth(Chromosome.getMarker(x).getName()); if (thiswide > widestMarkerName) widestMarkerName = thiswide; } g2.translate(left, top + widestMarkerName); g2.rotate(-Math.PI / 2.0); for (int x = 0; x < Chromosome.getSize(); x++) { if (theData.isInBlock[x]){ g2.setFont(boldMarkerNameFont); }else{ g2.setFont(markerNameFont); } if (Chromosome.getMarker(x).getExtra() != null) g2.setColor(green); g2.drawString(Chromosome.getMarker(x).getName(),(float)TEXT_GAP, (float)alignedPositions[x] + ascent/3); if (Chromosome.getMarker(x).getExtra() != null) g2.setColor(Color.black); } g2.rotate(Math.PI / 2.0); g2.translate(-left, -(top + widestMarkerName)); // move everybody down top += widestMarkerName + TEXT_GAP; } g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_OFF); } top += blockDispHeight; //// draw the marker numbers if (printMarkerNames){ g2.setFont(markerNumFont); metrics = g2.getFontMetrics(); ascent = metrics.getAscent(); for (int x = 0; x < Chromosome.getSize(); x++) { String mark = String.valueOf(Chromosome.realIndex[x] + 1); g2.drawString(mark, (float)(left + alignedPositions[x] - metrics.stringWidth(mark)/2), (float)(top + ascent)); } top += boxRadius/2; // give a little space between numbers and boxes } //clickxshift and clickyshift are used later to translate from x,y coords //to the pair of markers comparison at those coords if (!(theData.infoKnown)){ clickXShift = left + (size.width-pref.width)/2; clickYShift = top + (size.height - pref.height)/2; } else { clickXShift = left + (size.width-pref.width)/2; clickYShift = top; } // draw table column by column for (int x = lowX; x < highX; x++) { //always draw the fewest possible boxes if (lowY < x+1){ lowY = x+1; } for (int y = lowY; y < highY; y++) { if (dPrimeTable.getLDStats(x,y) == null){ continue; } double d = dPrimeTable.getLDStats(x,y).getDPrime(); //double l = dPrimeTable.getLDStats(x,y).getLOD(); Color boxColor = dPrimeTable.getLDStats(x,y).getColor(); // draw markers above int xx = left + (int)((alignedPositions[x] + alignedPositions[y])/2); int yy = top + (int)((alignedPositions[y] - alignedPositions[x]) / 2); diamondX[0] = xx; diamondY[0] = yy - boxRadius; diamondX[1] = xx + boxRadius; diamondY[1] = yy; diamondX[2] = xx; diamondY[2] = yy + boxRadius; diamondX[3] = xx - boxRadius; diamondY[3] = yy; diamond = new Polygon(diamondX, diamondY, 4); g2.setColor(boxColor); g2.fillPolygon(diamond); if(printDPrimeValues){ g2.setFont(boxFont); ascent = boxFontMetrics.getAscent(); int val = (int) (d * 100); g2.setColor((val < 50) ? Color.gray : Color.black); if (boxColor == Color.darkGray){ g2.setColor(Color.white); } if (val != 100) { String valu = String.valueOf(val); int widf = boxFontMetrics.stringWidth(valu); g.drawString(valu, xx - widf/2, yy + ascent/2); } } } } //highlight blocks g2.setFont(markerNameFont); ascent = g2.getFontMetrics().getAscent(); //g.setColor(new Color(153,255,153)); g2.setColor(Color.black); //g.setColor(new Color(51,153,51)); for (int i = 0; i < blocks.size(); i++){ int[] theBlock = (int[])blocks.elementAt(i); int first = theBlock[0]; int last = theBlock[theBlock.length-1]; //big vee around whole thing g2.setStroke(fatStroke); g2.draw(new Line2D.Double(left + alignedPositions[first] - boxRadius, top, left + (alignedPositions[first] + alignedPositions[last])/2, top + (alignedPositions[last] - alignedPositions[first])/2 + boxRadius)); g2.draw(new Line2D.Double(left + (alignedPositions[first] + alignedPositions[last])/2, top + (alignedPositions[last] - alignedPositions[first])/2 + boxRadius, left + alignedPositions[last] + boxRadius, top)); for (int j = first; j < last; j++){ g2.setStroke(fatStroke); if (theData.isInBlock[j]){ g2.draw(new Line2D.Double(left+alignedPositions[j]-boxSize/2, top-blockDispHeight, left+alignedPositions[j+1]-boxSize/2, top-blockDispHeight)); }else{ g2.draw(new Line2D.Double(left + alignedPositions[j] + boxSize/2, top-blockDispHeight, left+alignedPositions[j+1]-boxSize/2, top-blockDispHeight)); g2.setStroke(dashedFatStroke); g2.draw(new Line2D.Double(left+alignedPositions[j] - boxSize/2, top-blockDispHeight, left+alignedPositions[j] + boxSize/2, top-blockDispHeight)); } } //cap off the end of the block g2.setStroke(fatStroke); g2.draw(new Line2D.Double(left+alignedPositions[last]-boxSize/2, top-blockDispHeight, left+alignedPositions[last]+boxSize/2, top-blockDispHeight)); //lines to connect to block display g2.setStroke(fatStroke); g2.draw(new Line2D.Double(left + alignedPositions[first]-boxSize/2, top-1, left+alignedPositions[first]-boxSize/2, top-blockDispHeight)); g2.draw(new Line2D.Double(left+alignedPositions[last]+boxSize/2, top-1, left+alignedPositions[last]+boxSize/2, top-blockDispHeight)); if (printMarkerNames){ String labelString = new String ("Block " + (i+1)); if (theData.infoKnown){ long blockSize = Chromosome.getMarker(last).getPosition() - Chromosome.getMarker(first).getPosition(); labelString += " (" + blockSize/1000 + " kb)"; } g2.drawString(labelString, (float)(left+alignedPositions[first]-boxSize/2+TEXT_GAP), (float)(top-boxSize/3)); } } g2.setStroke(thickerStroke); //see if the user has right-clicked to popup some marker info if(popupExists){ //dumb bug where little datasets popup the box in the wrong place int smallDatasetSlopH = 0; int smallDatasetSlopV = 0; if (pref.getHeight() < visRect.height){ smallDatasetSlopV = (int)(visRect.height - pref.getHeight())/2; } if (pref.getWidth() < visRect.width){ smallDatasetSlopH = (int)(visRect.width - pref.getWidth())/2; } g2.setColor(Color.white); g2.fillRect(popupDrawRect.x+1-smallDatasetSlopH, popupDrawRect.y+1-smallDatasetSlopV, popupDrawRect.width-1, popupDrawRect.height-1); g2.setColor(Color.black); g2.drawRect(popupDrawRect.x-smallDatasetSlopH, popupDrawRect.y-smallDatasetSlopV, popupDrawRect.width, popupDrawRect.height); for (int x = 0; x < displayStrings.size(); x++){ g.drawString((String)displayStrings.elementAt(x),popupDrawRect.x + popupLeftMargin-smallDatasetSlopH, popupDrawRect.y+((x+1)*metrics.getHeight())-smallDatasetSlopV); } } if (showWM && !forExport){ //dataset is big enough to require worldmap if (wmMaxWidth == 0){ wmMaxWidth = visRect.width/3; } double scalefactor; scalefactor = (double)(chartSize.width)/wmMaxWidth; double prefBoxSize = boxSize/(scalefactor*((double)wmMaxWidth/(double)(wmMaxWidth))); //stick WM_BD in the middle of the blank space at the top of the worldmap final int WM_BD_GAP = (int)(infoHeight/(scalefactor*2)); final int WM_BD_HEIGHT = 2; CompoundBorder wmBorder = new CompoundBorder(BorderFactory.createRaisedBevelBorder(), BorderFactory.createLoweredBevelBorder()); if (noImage){ //first time through draw a worldmap if dataset is big: worldmap = new BufferedImage((int)(chartSize.width/scalefactor)+wmBorder.getBorderInsets(this).left*2, (int)(chartSize.height/scalefactor)+wmBorder.getBorderInsets(this).top*2, BufferedImage.TYPE_3BYTE_BGR); Graphics gw = worldmap.getGraphics(); Graphics2D gw2 = (Graphics2D)(gw); gw2.setColor(BG_GREY); gw2.fillRect(1,1,worldmap.getWidth()-1,worldmap.getHeight()-1); //make a pretty border gw2.setColor(Color.black); wmBorder.paintBorder(this,gw2,0,0,worldmap.getWidth(),worldmap.getHeight()); wmInteriorRect = wmBorder.getInteriorRectangle(this,0,0,worldmap.getWidth(), worldmap.getHeight()); float[] smallDiamondX = new float[4]; float[] smallDiamondY = new float[4]; GeneralPath gp; for (int x = 0; x < Chromosome.getSize()-1; x++){ for (int y = x+1; y < Chromosome.getSize(); y++){ if (dPrimeTable.getLDStats(x,y) == null){ continue; } double xx = ((alignedPositions[y] + alignedPositions[x])/(scalefactor*2)) + wmBorder.getBorderInsets(this).left; double yy = ((alignedPositions[y] - alignedPositions[x] + infoHeight*2)/(scalefactor*2)) + wmBorder.getBorderInsets(this).top; smallDiamondX[0] = (float)xx; smallDiamondY[0] = (float)(yy - prefBoxSize/2); smallDiamondX[1] = (float)(xx + prefBoxSize/2); smallDiamondY[1] = (float)yy; smallDiamondX[2] = (float)xx; smallDiamondY[2] = (float)(yy + prefBoxSize/2); smallDiamondX[3] = (float)(xx - prefBoxSize/2); smallDiamondY[3] = (float)yy; gp = new GeneralPath(GeneralPath.WIND_EVEN_ODD, smallDiamondX.length); gp.moveTo(smallDiamondX[0],smallDiamondY[0]); for (int i = 1; i < smallDiamondX.length; i++){ gp.lineTo(smallDiamondX[i], smallDiamondY[i]); } gp.closePath(); gw2.setColor(dPrimeTable.getLDStats(x,y).getColor()); gw2.fill(gp); } } noImage = false; } //draw block display in worldmap Graphics gw = worldmap.getGraphics(); Graphics2D gw2 = (Graphics2D)(gw); gw2.setColor(BG_GREY); gw2.fillRect(wmBorder.getBorderInsets(this).left, wmBorder.getBorderInsets(this).top+WM_BD_GAP, wmInteriorRect.width, WM_BD_HEIGHT); gw2.setColor(Color.black); boolean even = true; for (int i = 0; i < blocks.size(); i++){ int first = ((int[])blocks.elementAt(i))[0]; int last = ((int[])blocks.elementAt(i))[((int[])blocks.elementAt(i)).length-1]; int voffset; if (even){ voffset = 0; }else{ voffset = WM_BD_HEIGHT/2; } gw2.fillRect(wmBorder.getBorderInsets(this).left - (int)prefBoxSize/2 + (int)(alignedPositions[first]/scalefactor), wmBorder.getBorderInsets(this).top+voffset+WM_BD_GAP, (int)(prefBoxSize + (alignedPositions[last] - alignedPositions[first])/scalefactor), WM_BD_HEIGHT/2); even = !even; } wmResizeCorner = new Rectangle(visRect.x + worldmap.getWidth() - (worldmap.getWidth()-wmInteriorRect.width)/2, visRect.y + visRect.height - worldmap.getHeight(), (worldmap.getWidth()-wmInteriorRect.width)/2, (worldmap.getHeight() -wmInteriorRect.height)/2); g2.drawImage(worldmap,visRect.x, visRect.y + visRect.height - worldmap.getHeight(), this); wmInteriorRect.x = visRect.x + (worldmap.getWidth() - wmInteriorRect.width)/2; wmInteriorRect.y = visRect.y+visRect.height-worldmap.getHeight() + (worldmap.getHeight() - wmInteriorRect.height)/2; //draw the outline of the viewport g2.setColor(Color.black); double hRatio = wmInteriorRect.getWidth()/pref.getWidth(); double vRatio = wmInteriorRect.getHeight()/pref.getHeight(); int hBump = worldmap.getWidth()-wmInteriorRect.width; int vBump = worldmap.getHeight()-wmInteriorRect.height; //bump a few pixels to avoid drawing on the border g2.drawRect((int)(visRect.x*hRatio)+hBump/2+visRect.x, (int)(visRect.y*vRatio)+vBump/2+(visRect.y + visRect.height - worldmap.getHeight()), (int)(visRect.width*hRatio), (int)(visRect.height*vRatio)); } //see if we're drawing a worldmap resize rect if (resizeRectExists){ g2.setColor(Color.black); g2.drawRect(resizeWMRect.x, resizeWMRect.y, resizeWMRect.width, resizeWMRect.height); } //see if we're drawing a block selector rect if (blockRectExists){ g2.setColor(Color.black); g2.setStroke(dashedThinStroke); g2.drawRect(blockRect.x, blockRect.y, blockRect.width, blockRect.height); } } |
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if(description == null) return ""; | public String getDescription() { return description; } |
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if(type.startsWith("[")){ | if(type != null && type.startsWith("[")){ | protected String getDisplayType(String type){ if(type.startsWith("[")){ /* convert to readable name. e.g. [Ljava.lang.String to java.lang.String[]*/ String arrayBraces = ""; while(type.startsWith("[")){ type = type.substring(1); arrayBraces += "[]"; } type = getArrayDisplayType(type) + arrayBraces; } return type; } |
JButton searchButton = new JButton("Search"); | JDefaultButton searchButton = new JDefaultButton("Search"); | public void showSearchDialog(final PlayPen pp) { // XXX need to convert to an ArchitectPanel before switching // this to use ArchitectPanelBuilder. final JDialog d = new JDialog((Frame) SwingUtilities.getAncestorOfClass(JFrame.class, pp), "Find"); ButtonGroup matchType = new ButtonGroup(); matchType.add(substringMatch = new JRadioButton("Substring")); matchType.add(exactMatch = new JRadioButton("Exact Match")); matchType.add(regexMatch = new JRadioButton("Regex")); JPanel matchTypePanel = new JPanel(new GridLayout(1,3)); matchTypePanel.add(substringMatch); matchTypePanel.add(exactMatch); matchTypePanel.add(regexMatch); substringMatch.setSelected(true); ButtonGroup searchType = new ButtonGroup(); searchType.add(tableSearch = new JRadioButton("Tables")); searchType.add(relationshipSearch = new JRadioButton("Relationships")); searchType.add(columnSearch = new JRadioButton("Columns")); searchType.add(allSearch = new JRadioButton("Anything")); JPanel searchTypePanel = new JPanel(new GridLayout(4,1)); searchTypePanel.add(tableSearch); searchTypePanel.add(relationshipSearch); searchTypePanel.add(columnSearch); searchTypePanel.add(allSearch); allSearch.setSelected(true); caseInsensitive = new JCheckBox("Ignoring case"); caseInsensitive.setSelected(true); searchExpression = new JTextField(); JButton searchButton = new JButton("Search"); // searchButton.setDefaultCapable(true); searchButton.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { try { showResults(d, pp); } catch (ArchitectException ex) { ASUtils.showExceptionDialog("Encountered a problem during search", ex); } } }); Action cancelAction = new AbstractAction() { public void actionPerformed(ActionEvent e) { d.setVisible(false); d.dispose(); } }; cancelAction.putValue(Action.NAME, ArchitectPanelBuilder.CANCEL_BUTTON_LABEL); JButton cancelButton = new JButton(cancelAction); ArchitectPanelBuilder.makeJDialogCancellable(d, cancelAction); JPanel buttonPanel = new JPanel(new FlowLayout(FlowLayout.RIGHT)); buttonPanel.add(searchButton); buttonPanel.add(cancelButton); JComponent cp = (JComponent) d.getContentPane(); cp.setLayout(new FormLayout(10, 10)); cp.setBorder(BorderFactory.createEmptyBorder(12, 12, 12, 12)); cp.add(new JLabel("Look for")); cp.add(searchTypePanel); cp.add(new JLabel("Named")); cp.add(searchExpression); cp.add(new JLabel("Comparing by")); cp.add(matchTypePanel); cp.add(new JLabel("")); cp.add(caseInsensitive); cp.add(new JLabel("")); cp.add(buttonPanel); d.getRootPane().setDefaultButton(searchButton); d.pack(); d.setLocationRelativeTo(pp); d.setVisible(true); searchExpression.requestFocus(); } |
int[] block_size; if (theBlock.length < 9){ block_size = new int[1]; block_size[0] = theBlock.length; } else { int ones = theBlock.length%8; int eights = (theBlock.length - ones)/8; if (ones == 0){ block_size = new int[eights]; for (int i = 0; i < eights; i++){ block_size[i]=8; } } else { block_size = new int[eights+1]; for (int i = 0; i < eights-1; i++){ block_size[i]=8; } block_size[eights-1] = (8+ones)/2; block_size[eights] = 8+ones-block_size[eights-1]; } } byte[] thisHap; Vector inputHaploVector = new Vector(); Vector inputHaploTrios = new Vector(); int[] whichVector = new int[chromosomes.size()]; for(int i=0;i<numTrios*4; i+=4) { Chromosome parentAFirst = (Chromosome) chromosomes.elementAt(i); Chromosome parentASecond = (Chromosome) chromosomes.elementAt(i+1); Chromosome parentBFirst = (Chromosome) chromosomes.elementAt(i+2); Chromosome parentBSecond = (Chromosome) chromosomes.elementAt(i+3); boolean tooManyMissingInASegmentA = false; boolean tooManyMissingInASegmentB = false; int totalMissingA = 0; int totalMissingB = 0; int segmentShift = 0; for (int n = 0; n < block_size.length; n++){ int missingA = 0; int missingB = 0; for (int j = 0; j < block_size[n]; j++){ byte AFirstGeno = parentAFirst.getGenotype(theBlock[segmentShift+j]); byte ASecondGeno = parentASecond.getGenotype(theBlock[segmentShift+j]); byte BFirstGeno = parentBFirst.getGenotype(theBlock[segmentShift+j]); byte BSecondGeno = parentBSecond.getGenotype(theBlock[segmentShift+j]); if(AFirstGeno == 0 || ASecondGeno == 0) missingA++; if(BFirstGeno == 0 || BSecondGeno == 0) missingB++; } segmentShift += block_size[n]; if (missingA >= missingLimit){ tooManyMissingInASegmentA = true; } if (missingB >= missingLimit){ tooManyMissingInASegmentB = true; } totalMissingA += missingA; totalMissingB += missingB; } if(!tooManyMissingInASegmentA && totalMissingA <= 1+theBlock.length/3 && !tooManyMissingInASegmentB && totalMissingB <= 1+theBlock.length/3) { whichVector[i] = 2; whichVector[i+1] = 2; whichVector[i+2] = 2; whichVector[i+3] = 2; } else if(!tooManyMissingInASegmentA && totalMissingA <= 1+theBlock.length/3) { whichVector[i] = 1; whichVector[i+1] =1; whichVector[i+2] =0; whichVector[i+3]=0; } else if(!tooManyMissingInASegmentB && totalMissingB <= 1+theBlock.length/3) { whichVector[i] = 0; whichVector[i+1] =0; whichVector[i+2] =1; whichVector[i+3]=1; } else { whichVector[i] = 0; whichVector[i+1] =0; whichVector[i+2] =0; whichVector[i+3]=0; } } for (int i = numTrios*4; i < chromosomes.size(); i++){ Chromosome thisChrom = (Chromosome)chromosomes.elementAt(i); Chromosome nextChrom = (Chromosome)chromosomes.elementAt(++i); boolean tooManyMissingInASegment = false; int totalMissing = 0; int segmentShift = 0; for (int n = 0; n < block_size.length; n++){ int missing = 0; for (int j = 0; j < block_size[n]; j++){ byte theGeno = thisChrom.getGenotype(theBlock[segmentShift+j]); byte nextGeno = nextChrom.getGenotype(theBlock[segmentShift+j]); if(theGeno == 0 || nextGeno == 0) missing++; } segmentShift += block_size[n]; if (missing >= missingLimit){ tooManyMissingInASegment = true; } totalMissing += missing; } if (!tooManyMissingInASegment && totalMissing <= 1+theBlock.length/3){ whichVector[i-1] = 1; whichVector[i] = 1; } } for (int i = 0; i < chromosomes.size(); i++){ Chromosome thisChrom = (Chromosome)chromosomes.elementAt(i); if(whichVector[i] == 1 || whichVector[i] == 2) { thisHap = new byte[theBlock.length]; for (int j = 0; j < theBlock.length; j++){ byte a1 = Chromosome.getMarker(theBlock[j]).getMajor(); byte a2 = Chromosome.getMarker(theBlock[j]).getMinor(); byte theGeno = thisChrom.getGenotype(theBlock[j]); if (theGeno >= 5){ thisHap[j] = 'h'; } else { if (theGeno == a1){ thisHap[j] = '1'; }else if (theGeno == a2){ thisHap[j] = '2'; }else{ thisHap[j] = '0'; } } } if(whichVector[i] == 1) { inputHaploVector.add(thisHap); } else if(whichVector[i] ==2) { inputHaploTrios.add(thisHap); } } } int trioCount = inputHaploTrios.size() / 4; inputHaploTrios.addAll(inputHaploVector); byte[][] input_haplos = (byte[][])inputHaploTrios.toArray(new byte[0][0]); | Haplotype[][] generateHaplotypes(Vector blocks, int hapthresh) throws HaploViewException{ //TODO: output indiv hap estimates Haplotype[][] results = new Haplotype[blocks.size()][]; //String raw = new String(); //String currentLine; this.totalBlocks = blocks.size(); this.blocksDone = 0; for (int k = 0; k < blocks.size(); k++){ this.blocksDone++; int[] preFiltBlock = (int[])blocks.elementAt(k); int[] theBlock; int[] selectedMarkers = new int[0]; int[] equivClass = new int[0]; if (preFiltBlock.length > 30){ equivClass = new int[preFiltBlock.length]; int classCounter = 0; for (int x = 0; x < preFiltBlock.length; x++){ int marker1 = preFiltBlock[x]; //already been lumped into an equivalency class if (equivClass[x] != 0){ continue; } //start a new equivalency class for this SNP classCounter ++; equivClass[x] = classCounter; for (int y = x+1; y < preFiltBlock.length; y++){ int marker2 = preFiltBlock[y]; if (marker1 > marker2){ int tmp = marker1; marker1 = marker2; marker2 = tmp; } if ( dpTable.getLDStats(marker1,marker2).getRSquared() == 1.0){ //these two SNPs are redundant equivClass[y] = classCounter; } } } //parse equivalency classes selectedMarkers = new int[classCounter]; for (int x = 0; x < selectedMarkers.length; x++){ selectedMarkers[x] = -1; } for (int x = 0; x < classCounter; x++){ double genoPC = 1.0; for (int y = 0; y < equivClass.length; y++){ if (equivClass[y] == x+1){ //int[]tossed = new int[3]; if (percentBadGenotypes[preFiltBlock[y]] < genoPC){ selectedMarkers[x] = preFiltBlock[y]; genoPC = percentBadGenotypes[preFiltBlock[y]]; } } } } theBlock = selectedMarkers; //System.out.println("Block " + k + " " + theBlock.length + "/" + preFiltBlock.length); }else{ theBlock = preFiltBlock; } //break up large blocks if needed int[] block_size; if (theBlock.length < 9){ block_size = new int[1]; block_size[0] = theBlock.length; } else { //some base-8 arithmetic int ones = theBlock.length%8; int eights = (theBlock.length - ones)/8; if (ones == 0){ block_size = new int[eights]; for (int i = 0; i < eights; i++){ block_size[i]=8; } } else { block_size = new int[eights+1]; for (int i = 0; i < eights-1; i++){ block_size[i]=8; } block_size[eights-1] = (8+ones)/2; block_size[eights] = 8+ones-block_size[eights-1]; } } byte[] thisHap; Vector inputHaploVector = new Vector(); Vector inputHaploTrios = new Vector(); //whichVector[i] stores a value which indicates which vector chromosome i's genotype should go in //1 indicates inputHaploVector (singletons), 2 indicates inputHaploTrios, //0 indicates none (too much missing data) int[] whichVector = new int[chromosomes.size()]; for(int i=0;i<numTrios*4; i+=4) { Chromosome parentAFirst = (Chromosome) chromosomes.elementAt(i); Chromosome parentASecond = (Chromosome) chromosomes.elementAt(i+1); Chromosome parentBFirst = (Chromosome) chromosomes.elementAt(i+2); Chromosome parentBSecond = (Chromosome) chromosomes.elementAt(i+3); boolean tooManyMissingInASegmentA = false; boolean tooManyMissingInASegmentB = false; int totalMissingA = 0; int totalMissingB = 0; int segmentShift = 0; for (int n = 0; n < block_size.length; n++){ int missingA = 0; int missingB = 0; for (int j = 0; j < block_size[n]; j++){ byte AFirstGeno = parentAFirst.getGenotype(theBlock[segmentShift+j]); byte ASecondGeno = parentASecond.getGenotype(theBlock[segmentShift+j]); byte BFirstGeno = parentBFirst.getGenotype(theBlock[segmentShift+j]); byte BSecondGeno = parentBSecond.getGenotype(theBlock[segmentShift+j]); if(AFirstGeno == 0 || ASecondGeno == 0) missingA++; if(BFirstGeno == 0 || BSecondGeno == 0) missingB++; } segmentShift += block_size[n]; if (missingA >= missingLimit){ tooManyMissingInASegmentA = true; } if (missingB >= missingLimit){ tooManyMissingInASegmentB = true; } totalMissingA += missingA; totalMissingB += missingB; } if(!tooManyMissingInASegmentA && totalMissingA <= 1+theBlock.length/3 && !tooManyMissingInASegmentB && totalMissingB <= 1+theBlock.length/3) { whichVector[i] = 2; whichVector[i+1] = 2; whichVector[i+2] = 2; whichVector[i+3] = 2; } else if(!tooManyMissingInASegmentA && totalMissingA <= 1+theBlock.length/3) { whichVector[i] = 1; whichVector[i+1] =1; whichVector[i+2] =0; whichVector[i+3]=0; } else if(!tooManyMissingInASegmentB && totalMissingB <= 1+theBlock.length/3) { whichVector[i] = 0; whichVector[i+1] =0; whichVector[i+2] =1; whichVector[i+3]=1; } else { whichVector[i] = 0; whichVector[i+1] =0; whichVector[i+2] =0; whichVector[i+3]=0; } } for (int i = numTrios*4; i < chromosomes.size(); i++){ Chromosome thisChrom = (Chromosome)chromosomes.elementAt(i); Chromosome nextChrom = (Chromosome)chromosomes.elementAt(++i); boolean tooManyMissingInASegment = false; int totalMissing = 0; int segmentShift = 0; for (int n = 0; n < block_size.length; n++){ int missing = 0; for (int j = 0; j < block_size[n]; j++){ byte theGeno = thisChrom.getGenotype(theBlock[segmentShift+j]); byte nextGeno = nextChrom.getGenotype(theBlock[segmentShift+j]); if(theGeno == 0 || nextGeno == 0) missing++; } segmentShift += block_size[n]; if (missing >= missingLimit){ tooManyMissingInASegment = true; } totalMissing += missing; } //we want to use chromosomes without too many missing genotypes in a given //subsegment (first term) or without too many missing genotypes in the //whole block (second term) if (!tooManyMissingInASegment && totalMissing <= 1+theBlock.length/3){ whichVector[i-1] = 1; whichVector[i] = 1; } } for (int i = 0; i < chromosomes.size(); i++){ Chromosome thisChrom = (Chromosome)chromosomes.elementAt(i); if(whichVector[i] == 1 || whichVector[i] == 2) { thisHap = new byte[theBlock.length]; for (int j = 0; j < theBlock.length; j++){ byte a1 = Chromosome.getMarker(theBlock[j]).getMajor(); byte a2 = Chromosome.getMarker(theBlock[j]).getMinor(); byte theGeno = thisChrom.getGenotype(theBlock[j]); if (theGeno >= 5){ thisHap[j] = 'h'; } else { if (theGeno == a1){ thisHap[j] = '1'; }else if (theGeno == a2){ thisHap[j] = '2'; }else{ thisHap[j] = '0'; } } } if(whichVector[i] == 1) { inputHaploVector.add(thisHap); } else if(whichVector[i] ==2) { inputHaploTrios.add(thisHap); } } } int trioCount = inputHaploTrios.size() / 4; inputHaploTrios.addAll(inputHaploVector); byte[][] input_haplos = (byte[][])inputHaploTrios.toArray(new byte[0][0]); //kirby patch EM theEM = new EM(); EMReturn EMresults = theEM.full_em_breakup(input_haplos, 4, block_size, 0,trioCount); int p = 0; Haplotype[] tempArray = new Haplotype[EMresults.numHaplos()]; int[][] returnedHaplos = EMresults.getHaplotypes(); double[] returnedFreqs = EMresults.getFrequencies(); for (int i = 0; i < EMresults.numHaplos(); i++){ int[] genos = new int[returnedHaplos[i].length]; for (int j = 0; j < genos.length; j++){ if (returnedHaplos[i][j] == 1){ genos[j] = Chromosome.getMarker(theBlock[j]).getMajor(); }else{ if (Chromosome.getMarker(theBlock[j]).getMinor() == 0){ genos[j] = 8; }else{ genos[j] = Chromosome.getMarker(theBlock[j]).getMinor(); } } } if (selectedMarkers.length > 0){ //we need to reassemble the haplotypes Hashtable hapsHash = new Hashtable(); //add to hash all the genotypes we phased for (int q = 0; q < genos.length; q++){ hapsHash.put(new Integer(theBlock[q]), new Integer(genos[q])); } //now add all the genotypes we didn't bother phasing, based on //which marker they are identical to for (int q = 0; q < equivClass.length; q++){ int currentClass = equivClass[q]-1; if (selectedMarkers[currentClass] == preFiltBlock[q]){ //we alredy added the phased genotypes above continue; } int indexIntoBlock=0; for (int x = 0; x < theBlock.length; x++){ if (theBlock[x] == selectedMarkers[currentClass]){ indexIntoBlock = x; break; } } //this (somewhat laboriously) reconstructs whether to add the minor or major allele //for markers with MAF close to 0.50 we can't use major/minor alleles to match //'em up 'cause these might change given missing data if (Chromosome.getMarker(selectedMarkers[currentClass]).getMAF() > 0.4){ for (int z = 0; z < chromosomes.size(); z++){ Chromosome thisChrom = (Chromosome)chromosomes.elementAt(z); Chromosome nextChrom = (Chromosome)chromosomes.elementAt(++z); int theGeno = thisChrom.getGenotype(selectedMarkers[currentClass]); int nextGeno = nextChrom.getGenotype(selectedMarkers[currentClass]); if (theGeno == nextGeno && theGeno == genos[indexIntoBlock] && thisChrom.getGenotype(preFiltBlock[q]) != 0){ hapsHash.put(new Integer(preFiltBlock[q]), new Integer(thisChrom.getGenotype(preFiltBlock[q]))); } } }else{ if (Chromosome.getMarker(selectedMarkers[currentClass]).getMajor() == genos[indexIntoBlock]){ hapsHash.put(new Integer(preFiltBlock[q]), new Integer(Chromosome.getMarker(preFiltBlock[q]).getMajor())); }else{ hapsHash.put(new Integer(preFiltBlock[q]), new Integer(Chromosome.getMarker(preFiltBlock[q]).getMinor())); } } } genos = new int[preFiltBlock.length]; for (int q = 0; q < preFiltBlock.length; q++){ genos[q] = ((Integer)hapsHash.get(new Integer(preFiltBlock[q]))).intValue(); } } double tempPerc = returnedFreqs[i]; if (tempPerc*100 > hapthresh){ tempArray[p] = new Haplotype(genos, tempPerc, preFiltBlock); p++; } } //make the results array only large enough to hold haps //which pass threshold above results[k] = new Haplotype[p]; for (int z = 0; z < p; z++){ results[k][z] = tempArray[z]; } } return results; } |
|
EM theEM = new EM(); EMReturn EMresults = theEM.full_em_breakup(input_haplos, 4, block_size, 0,trioCount); | EM theEM = new EM(chromosomes,numTrios); theEM.doEM(theBlock); | Haplotype[][] generateHaplotypes(Vector blocks, int hapthresh) throws HaploViewException{ //TODO: output indiv hap estimates Haplotype[][] results = new Haplotype[blocks.size()][]; //String raw = new String(); //String currentLine; this.totalBlocks = blocks.size(); this.blocksDone = 0; for (int k = 0; k < blocks.size(); k++){ this.blocksDone++; int[] preFiltBlock = (int[])blocks.elementAt(k); int[] theBlock; int[] selectedMarkers = new int[0]; int[] equivClass = new int[0]; if (preFiltBlock.length > 30){ equivClass = new int[preFiltBlock.length]; int classCounter = 0; for (int x = 0; x < preFiltBlock.length; x++){ int marker1 = preFiltBlock[x]; //already been lumped into an equivalency class if (equivClass[x] != 0){ continue; } //start a new equivalency class for this SNP classCounter ++; equivClass[x] = classCounter; for (int y = x+1; y < preFiltBlock.length; y++){ int marker2 = preFiltBlock[y]; if (marker1 > marker2){ int tmp = marker1; marker1 = marker2; marker2 = tmp; } if ( dpTable.getLDStats(marker1,marker2).getRSquared() == 1.0){ //these two SNPs are redundant equivClass[y] = classCounter; } } } //parse equivalency classes selectedMarkers = new int[classCounter]; for (int x = 0; x < selectedMarkers.length; x++){ selectedMarkers[x] = -1; } for (int x = 0; x < classCounter; x++){ double genoPC = 1.0; for (int y = 0; y < equivClass.length; y++){ if (equivClass[y] == x+1){ //int[]tossed = new int[3]; if (percentBadGenotypes[preFiltBlock[y]] < genoPC){ selectedMarkers[x] = preFiltBlock[y]; genoPC = percentBadGenotypes[preFiltBlock[y]]; } } } } theBlock = selectedMarkers; //System.out.println("Block " + k + " " + theBlock.length + "/" + preFiltBlock.length); }else{ theBlock = preFiltBlock; } //break up large blocks if needed int[] block_size; if (theBlock.length < 9){ block_size = new int[1]; block_size[0] = theBlock.length; } else { //some base-8 arithmetic int ones = theBlock.length%8; int eights = (theBlock.length - ones)/8; if (ones == 0){ block_size = new int[eights]; for (int i = 0; i < eights; i++){ block_size[i]=8; } } else { block_size = new int[eights+1]; for (int i = 0; i < eights-1; i++){ block_size[i]=8; } block_size[eights-1] = (8+ones)/2; block_size[eights] = 8+ones-block_size[eights-1]; } } byte[] thisHap; Vector inputHaploVector = new Vector(); Vector inputHaploTrios = new Vector(); //whichVector[i] stores a value which indicates which vector chromosome i's genotype should go in //1 indicates inputHaploVector (singletons), 2 indicates inputHaploTrios, //0 indicates none (too much missing data) int[] whichVector = new int[chromosomes.size()]; for(int i=0;i<numTrios*4; i+=4) { Chromosome parentAFirst = (Chromosome) chromosomes.elementAt(i); Chromosome parentASecond = (Chromosome) chromosomes.elementAt(i+1); Chromosome parentBFirst = (Chromosome) chromosomes.elementAt(i+2); Chromosome parentBSecond = (Chromosome) chromosomes.elementAt(i+3); boolean tooManyMissingInASegmentA = false; boolean tooManyMissingInASegmentB = false; int totalMissingA = 0; int totalMissingB = 0; int segmentShift = 0; for (int n = 0; n < block_size.length; n++){ int missingA = 0; int missingB = 0; for (int j = 0; j < block_size[n]; j++){ byte AFirstGeno = parentAFirst.getGenotype(theBlock[segmentShift+j]); byte ASecondGeno = parentASecond.getGenotype(theBlock[segmentShift+j]); byte BFirstGeno = parentBFirst.getGenotype(theBlock[segmentShift+j]); byte BSecondGeno = parentBSecond.getGenotype(theBlock[segmentShift+j]); if(AFirstGeno == 0 || ASecondGeno == 0) missingA++; if(BFirstGeno == 0 || BSecondGeno == 0) missingB++; } segmentShift += block_size[n]; if (missingA >= missingLimit){ tooManyMissingInASegmentA = true; } if (missingB >= missingLimit){ tooManyMissingInASegmentB = true; } totalMissingA += missingA; totalMissingB += missingB; } if(!tooManyMissingInASegmentA && totalMissingA <= 1+theBlock.length/3 && !tooManyMissingInASegmentB && totalMissingB <= 1+theBlock.length/3) { whichVector[i] = 2; whichVector[i+1] = 2; whichVector[i+2] = 2; whichVector[i+3] = 2; } else if(!tooManyMissingInASegmentA && totalMissingA <= 1+theBlock.length/3) { whichVector[i] = 1; whichVector[i+1] =1; whichVector[i+2] =0; whichVector[i+3]=0; } else if(!tooManyMissingInASegmentB && totalMissingB <= 1+theBlock.length/3) { whichVector[i] = 0; whichVector[i+1] =0; whichVector[i+2] =1; whichVector[i+3]=1; } else { whichVector[i] = 0; whichVector[i+1] =0; whichVector[i+2] =0; whichVector[i+3]=0; } } for (int i = numTrios*4; i < chromosomes.size(); i++){ Chromosome thisChrom = (Chromosome)chromosomes.elementAt(i); Chromosome nextChrom = (Chromosome)chromosomes.elementAt(++i); boolean tooManyMissingInASegment = false; int totalMissing = 0; int segmentShift = 0; for (int n = 0; n < block_size.length; n++){ int missing = 0; for (int j = 0; j < block_size[n]; j++){ byte theGeno = thisChrom.getGenotype(theBlock[segmentShift+j]); byte nextGeno = nextChrom.getGenotype(theBlock[segmentShift+j]); if(theGeno == 0 || nextGeno == 0) missing++; } segmentShift += block_size[n]; if (missing >= missingLimit){ tooManyMissingInASegment = true; } totalMissing += missing; } //we want to use chromosomes without too many missing genotypes in a given //subsegment (first term) or without too many missing genotypes in the //whole block (second term) if (!tooManyMissingInASegment && totalMissing <= 1+theBlock.length/3){ whichVector[i-1] = 1; whichVector[i] = 1; } } for (int i = 0; i < chromosomes.size(); i++){ Chromosome thisChrom = (Chromosome)chromosomes.elementAt(i); if(whichVector[i] == 1 || whichVector[i] == 2) { thisHap = new byte[theBlock.length]; for (int j = 0; j < theBlock.length; j++){ byte a1 = Chromosome.getMarker(theBlock[j]).getMajor(); byte a2 = Chromosome.getMarker(theBlock[j]).getMinor(); byte theGeno = thisChrom.getGenotype(theBlock[j]); if (theGeno >= 5){ thisHap[j] = 'h'; } else { if (theGeno == a1){ thisHap[j] = '1'; }else if (theGeno == a2){ thisHap[j] = '2'; }else{ thisHap[j] = '0'; } } } if(whichVector[i] == 1) { inputHaploVector.add(thisHap); } else if(whichVector[i] ==2) { inputHaploTrios.add(thisHap); } } } int trioCount = inputHaploTrios.size() / 4; inputHaploTrios.addAll(inputHaploVector); byte[][] input_haplos = (byte[][])inputHaploTrios.toArray(new byte[0][0]); //kirby patch EM theEM = new EM(); EMReturn EMresults = theEM.full_em_breakup(input_haplos, 4, block_size, 0,trioCount); int p = 0; Haplotype[] tempArray = new Haplotype[EMresults.numHaplos()]; int[][] returnedHaplos = EMresults.getHaplotypes(); double[] returnedFreqs = EMresults.getFrequencies(); for (int i = 0; i < EMresults.numHaplos(); i++){ int[] genos = new int[returnedHaplos[i].length]; for (int j = 0; j < genos.length; j++){ if (returnedHaplos[i][j] == 1){ genos[j] = Chromosome.getMarker(theBlock[j]).getMajor(); }else{ if (Chromosome.getMarker(theBlock[j]).getMinor() == 0){ genos[j] = 8; }else{ genos[j] = Chromosome.getMarker(theBlock[j]).getMinor(); } } } if (selectedMarkers.length > 0){ //we need to reassemble the haplotypes Hashtable hapsHash = new Hashtable(); //add to hash all the genotypes we phased for (int q = 0; q < genos.length; q++){ hapsHash.put(new Integer(theBlock[q]), new Integer(genos[q])); } //now add all the genotypes we didn't bother phasing, based on //which marker they are identical to for (int q = 0; q < equivClass.length; q++){ int currentClass = equivClass[q]-1; if (selectedMarkers[currentClass] == preFiltBlock[q]){ //we alredy added the phased genotypes above continue; } int indexIntoBlock=0; for (int x = 0; x < theBlock.length; x++){ if (theBlock[x] == selectedMarkers[currentClass]){ indexIntoBlock = x; break; } } //this (somewhat laboriously) reconstructs whether to add the minor or major allele //for markers with MAF close to 0.50 we can't use major/minor alleles to match //'em up 'cause these might change given missing data if (Chromosome.getMarker(selectedMarkers[currentClass]).getMAF() > 0.4){ for (int z = 0; z < chromosomes.size(); z++){ Chromosome thisChrom = (Chromosome)chromosomes.elementAt(z); Chromosome nextChrom = (Chromosome)chromosomes.elementAt(++z); int theGeno = thisChrom.getGenotype(selectedMarkers[currentClass]); int nextGeno = nextChrom.getGenotype(selectedMarkers[currentClass]); if (theGeno == nextGeno && theGeno == genos[indexIntoBlock] && thisChrom.getGenotype(preFiltBlock[q]) != 0){ hapsHash.put(new Integer(preFiltBlock[q]), new Integer(thisChrom.getGenotype(preFiltBlock[q]))); } } }else{ if (Chromosome.getMarker(selectedMarkers[currentClass]).getMajor() == genos[indexIntoBlock]){ hapsHash.put(new Integer(preFiltBlock[q]), new Integer(Chromosome.getMarker(preFiltBlock[q]).getMajor())); }else{ hapsHash.put(new Integer(preFiltBlock[q]), new Integer(Chromosome.getMarker(preFiltBlock[q]).getMinor())); } } } genos = new int[preFiltBlock.length]; for (int q = 0; q < preFiltBlock.length; q++){ genos[q] = ((Integer)hapsHash.get(new Integer(preFiltBlock[q]))).intValue(); } } double tempPerc = returnedFreqs[i]; if (tempPerc*100 > hapthresh){ tempArray[p] = new Haplotype(genos, tempPerc, preFiltBlock); p++; } } //make the results array only large enough to hold haps //which pass threshold above results[k] = new Haplotype[p]; for (int z = 0; z < p; z++){ results[k][z] = tempArray[z]; } } return results; } |
Haplotype[] tempArray = new Haplotype[EMresults.numHaplos()]; int[][] returnedHaplos = EMresults.getHaplotypes(); double[] returnedFreqs = EMresults.getFrequencies(); for (int i = 0; i < EMresults.numHaplos(); i++){ | Haplotype[] tempArray = new Haplotype[theEM.numHaplos()]; int[][] returnedHaplos = theEM.getHaplotypes(); double[] returnedFreqs = theEM.getFrequencies(); for (int i = 0; i < theEM.numHaplos(); i++){ | Haplotype[][] generateHaplotypes(Vector blocks, int hapthresh) throws HaploViewException{ //TODO: output indiv hap estimates Haplotype[][] results = new Haplotype[blocks.size()][]; //String raw = new String(); //String currentLine; this.totalBlocks = blocks.size(); this.blocksDone = 0; for (int k = 0; k < blocks.size(); k++){ this.blocksDone++; int[] preFiltBlock = (int[])blocks.elementAt(k); int[] theBlock; int[] selectedMarkers = new int[0]; int[] equivClass = new int[0]; if (preFiltBlock.length > 30){ equivClass = new int[preFiltBlock.length]; int classCounter = 0; for (int x = 0; x < preFiltBlock.length; x++){ int marker1 = preFiltBlock[x]; //already been lumped into an equivalency class if (equivClass[x] != 0){ continue; } //start a new equivalency class for this SNP classCounter ++; equivClass[x] = classCounter; for (int y = x+1; y < preFiltBlock.length; y++){ int marker2 = preFiltBlock[y]; if (marker1 > marker2){ int tmp = marker1; marker1 = marker2; marker2 = tmp; } if ( dpTable.getLDStats(marker1,marker2).getRSquared() == 1.0){ //these two SNPs are redundant equivClass[y] = classCounter; } } } //parse equivalency classes selectedMarkers = new int[classCounter]; for (int x = 0; x < selectedMarkers.length; x++){ selectedMarkers[x] = -1; } for (int x = 0; x < classCounter; x++){ double genoPC = 1.0; for (int y = 0; y < equivClass.length; y++){ if (equivClass[y] == x+1){ //int[]tossed = new int[3]; if (percentBadGenotypes[preFiltBlock[y]] < genoPC){ selectedMarkers[x] = preFiltBlock[y]; genoPC = percentBadGenotypes[preFiltBlock[y]]; } } } } theBlock = selectedMarkers; //System.out.println("Block " + k + " " + theBlock.length + "/" + preFiltBlock.length); }else{ theBlock = preFiltBlock; } //break up large blocks if needed int[] block_size; if (theBlock.length < 9){ block_size = new int[1]; block_size[0] = theBlock.length; } else { //some base-8 arithmetic int ones = theBlock.length%8; int eights = (theBlock.length - ones)/8; if (ones == 0){ block_size = new int[eights]; for (int i = 0; i < eights; i++){ block_size[i]=8; } } else { block_size = new int[eights+1]; for (int i = 0; i < eights-1; i++){ block_size[i]=8; } block_size[eights-1] = (8+ones)/2; block_size[eights] = 8+ones-block_size[eights-1]; } } byte[] thisHap; Vector inputHaploVector = new Vector(); Vector inputHaploTrios = new Vector(); //whichVector[i] stores a value which indicates which vector chromosome i's genotype should go in //1 indicates inputHaploVector (singletons), 2 indicates inputHaploTrios, //0 indicates none (too much missing data) int[] whichVector = new int[chromosomes.size()]; for(int i=0;i<numTrios*4; i+=4) { Chromosome parentAFirst = (Chromosome) chromosomes.elementAt(i); Chromosome parentASecond = (Chromosome) chromosomes.elementAt(i+1); Chromosome parentBFirst = (Chromosome) chromosomes.elementAt(i+2); Chromosome parentBSecond = (Chromosome) chromosomes.elementAt(i+3); boolean tooManyMissingInASegmentA = false; boolean tooManyMissingInASegmentB = false; int totalMissingA = 0; int totalMissingB = 0; int segmentShift = 0; for (int n = 0; n < block_size.length; n++){ int missingA = 0; int missingB = 0; for (int j = 0; j < block_size[n]; j++){ byte AFirstGeno = parentAFirst.getGenotype(theBlock[segmentShift+j]); byte ASecondGeno = parentASecond.getGenotype(theBlock[segmentShift+j]); byte BFirstGeno = parentBFirst.getGenotype(theBlock[segmentShift+j]); byte BSecondGeno = parentBSecond.getGenotype(theBlock[segmentShift+j]); if(AFirstGeno == 0 || ASecondGeno == 0) missingA++; if(BFirstGeno == 0 || BSecondGeno == 0) missingB++; } segmentShift += block_size[n]; if (missingA >= missingLimit){ tooManyMissingInASegmentA = true; } if (missingB >= missingLimit){ tooManyMissingInASegmentB = true; } totalMissingA += missingA; totalMissingB += missingB; } if(!tooManyMissingInASegmentA && totalMissingA <= 1+theBlock.length/3 && !tooManyMissingInASegmentB && totalMissingB <= 1+theBlock.length/3) { whichVector[i] = 2; whichVector[i+1] = 2; whichVector[i+2] = 2; whichVector[i+3] = 2; } else if(!tooManyMissingInASegmentA && totalMissingA <= 1+theBlock.length/3) { whichVector[i] = 1; whichVector[i+1] =1; whichVector[i+2] =0; whichVector[i+3]=0; } else if(!tooManyMissingInASegmentB && totalMissingB <= 1+theBlock.length/3) { whichVector[i] = 0; whichVector[i+1] =0; whichVector[i+2] =1; whichVector[i+3]=1; } else { whichVector[i] = 0; whichVector[i+1] =0; whichVector[i+2] =0; whichVector[i+3]=0; } } for (int i = numTrios*4; i < chromosomes.size(); i++){ Chromosome thisChrom = (Chromosome)chromosomes.elementAt(i); Chromosome nextChrom = (Chromosome)chromosomes.elementAt(++i); boolean tooManyMissingInASegment = false; int totalMissing = 0; int segmentShift = 0; for (int n = 0; n < block_size.length; n++){ int missing = 0; for (int j = 0; j < block_size[n]; j++){ byte theGeno = thisChrom.getGenotype(theBlock[segmentShift+j]); byte nextGeno = nextChrom.getGenotype(theBlock[segmentShift+j]); if(theGeno == 0 || nextGeno == 0) missing++; } segmentShift += block_size[n]; if (missing >= missingLimit){ tooManyMissingInASegment = true; } totalMissing += missing; } //we want to use chromosomes without too many missing genotypes in a given //subsegment (first term) or without too many missing genotypes in the //whole block (second term) if (!tooManyMissingInASegment && totalMissing <= 1+theBlock.length/3){ whichVector[i-1] = 1; whichVector[i] = 1; } } for (int i = 0; i < chromosomes.size(); i++){ Chromosome thisChrom = (Chromosome)chromosomes.elementAt(i); if(whichVector[i] == 1 || whichVector[i] == 2) { thisHap = new byte[theBlock.length]; for (int j = 0; j < theBlock.length; j++){ byte a1 = Chromosome.getMarker(theBlock[j]).getMajor(); byte a2 = Chromosome.getMarker(theBlock[j]).getMinor(); byte theGeno = thisChrom.getGenotype(theBlock[j]); if (theGeno >= 5){ thisHap[j] = 'h'; } else { if (theGeno == a1){ thisHap[j] = '1'; }else if (theGeno == a2){ thisHap[j] = '2'; }else{ thisHap[j] = '0'; } } } if(whichVector[i] == 1) { inputHaploVector.add(thisHap); } else if(whichVector[i] ==2) { inputHaploTrios.add(thisHap); } } } int trioCount = inputHaploTrios.size() / 4; inputHaploTrios.addAll(inputHaploVector); byte[][] input_haplos = (byte[][])inputHaploTrios.toArray(new byte[0][0]); //kirby patch EM theEM = new EM(); EMReturn EMresults = theEM.full_em_breakup(input_haplos, 4, block_size, 0,trioCount); int p = 0; Haplotype[] tempArray = new Haplotype[EMresults.numHaplos()]; int[][] returnedHaplos = EMresults.getHaplotypes(); double[] returnedFreqs = EMresults.getFrequencies(); for (int i = 0; i < EMresults.numHaplos(); i++){ int[] genos = new int[returnedHaplos[i].length]; for (int j = 0; j < genos.length; j++){ if (returnedHaplos[i][j] == 1){ genos[j] = Chromosome.getMarker(theBlock[j]).getMajor(); }else{ if (Chromosome.getMarker(theBlock[j]).getMinor() == 0){ genos[j] = 8; }else{ genos[j] = Chromosome.getMarker(theBlock[j]).getMinor(); } } } if (selectedMarkers.length > 0){ //we need to reassemble the haplotypes Hashtable hapsHash = new Hashtable(); //add to hash all the genotypes we phased for (int q = 0; q < genos.length; q++){ hapsHash.put(new Integer(theBlock[q]), new Integer(genos[q])); } //now add all the genotypes we didn't bother phasing, based on //which marker they are identical to for (int q = 0; q < equivClass.length; q++){ int currentClass = equivClass[q]-1; if (selectedMarkers[currentClass] == preFiltBlock[q]){ //we alredy added the phased genotypes above continue; } int indexIntoBlock=0; for (int x = 0; x < theBlock.length; x++){ if (theBlock[x] == selectedMarkers[currentClass]){ indexIntoBlock = x; break; } } //this (somewhat laboriously) reconstructs whether to add the minor or major allele //for markers with MAF close to 0.50 we can't use major/minor alleles to match //'em up 'cause these might change given missing data if (Chromosome.getMarker(selectedMarkers[currentClass]).getMAF() > 0.4){ for (int z = 0; z < chromosomes.size(); z++){ Chromosome thisChrom = (Chromosome)chromosomes.elementAt(z); Chromosome nextChrom = (Chromosome)chromosomes.elementAt(++z); int theGeno = thisChrom.getGenotype(selectedMarkers[currentClass]); int nextGeno = nextChrom.getGenotype(selectedMarkers[currentClass]); if (theGeno == nextGeno && theGeno == genos[indexIntoBlock] && thisChrom.getGenotype(preFiltBlock[q]) != 0){ hapsHash.put(new Integer(preFiltBlock[q]), new Integer(thisChrom.getGenotype(preFiltBlock[q]))); } } }else{ if (Chromosome.getMarker(selectedMarkers[currentClass]).getMajor() == genos[indexIntoBlock]){ hapsHash.put(new Integer(preFiltBlock[q]), new Integer(Chromosome.getMarker(preFiltBlock[q]).getMajor())); }else{ hapsHash.put(new Integer(preFiltBlock[q]), new Integer(Chromosome.getMarker(preFiltBlock[q]).getMinor())); } } } genos = new int[preFiltBlock.length]; for (int q = 0; q < preFiltBlock.length; q++){ genos[q] = ((Integer)hapsHash.get(new Integer(preFiltBlock[q]))).intValue(); } } double tempPerc = returnedFreqs[i]; if (tempPerc*100 > hapthresh){ tempArray[p] = new Haplotype(genos, tempPerc, preFiltBlock); p++; } } //make the results array only large enough to hold haps //which pass threshold above results[k] = new Haplotype[p]; for (int z = 0; z < p; z++){ results[k][z] = tempArray[z]; } } return results; } |
chroms.add(new Chromosome(ped, indiv, genos, infile.getName())); | chroms.add(new Chromosome(ped, indiv, genos, infile.getName(), 0)); | void prepareHapsInput(File infile) throws IOException, HaploViewException{ //this method is called to suck in data from a file (its only argument) //of genotypes and sets up the Chromosome objects. String currentLine; Vector chroms = new Vector(); byte[] genos = new byte[0]; String ped, indiv; if(infile.length() < 1){ throw new HaploViewException("Genotype file is empty or does not exist: " + infile.getName()); } //read the file: BufferedReader in = new BufferedReader(new FileReader(infile)); int lineCount = 0; int numTokens = 0; boolean even = true; while ((currentLine = in.readLine()) != null){ lineCount++; //each line is expected to be of the format: //ped indiv geno geno geno geno... if (currentLine.length() == 0){ //skip blank lines continue; } even = !even; StringTokenizer st = new StringTokenizer(currentLine); //first two tokens are expected to be ped, indiv if (st.hasMoreTokens()){ ped = st.nextToken(); indiv = st.nextToken(); }else{ throw new HaploViewException("Genotype file error:\nLine " + lineCount + " appears to have fewer than 2 columns."); } //all other tokens are loaded into a vector (they should all be genotypes) genos = new byte[st.countTokens()]; int q = 0; if (numTokens == 0){ numTokens = st.countTokens(); } if (numTokens != st.countTokens()){ throw new HaploViewException("Genotype file error:\nLine " + lineCount + " appears to have an incorrect number of entries"); } while (st.hasMoreTokens()){ String thisGenotype = (String)st.nextElement(); if (thisGenotype.equals("h")) { genos[q] = 9; }else{ try{ genos[q] = Byte.parseByte(thisGenotype); }catch (NumberFormatException nfe){ throw new HaploViewException("Genotype file input error:\ngenotype value \"" + thisGenotype + "\" on line " + lineCount + " not allowed."); } } if (genos[q] < 0 || genos[q] > 9){ throw new HaploViewException("Genotype file input error:\ngenotype value \"" + genos[q] + "\" on line " + lineCount + " not allowed."); } q++; } //a Chromosome is created and added to a vector of chromosomes. //this is what is evetually returned. chroms.add(new Chromosome(ped, indiv, genos, infile.getName())); } if (!even){ //we're missing a line here throw new HaploViewException("Genotype file appears to have an odd number of lines.\n"+ "Each individual is required to have two chromosomes"); } chromosomes = chroms; //initialize realIndex Chromosome.doFilter(genos.length); //wipe clean any existing marker info so we know we're starting clean with a new file Chromosome.markers = null; } |
Writer writer = new OutputStreamWriter( new FileOutputStream( name ), encoding ); | Writer writer = new OutputStreamWriter( new FileOutputStream( name, doAppend ), encoding ); | public void doTag(final XMLOutput output) throws JellyTagException { try { if ( name != null ) { String encoding = (this.encoding != null) ? this.encoding : "UTF-8"; Writer writer = new OutputStreamWriter( new FileOutputStream( name ), encoding ); writeBody(writer); } else if (var != null) { StringWriter writer = new StringWriter(); writeBody(writer); context.setVariable(var, writer.toString()); } else { throw new JellyTagException( "This tag must have either the 'name' or the 'var' variables defined" ); } } catch (FileNotFoundException e) { throw new JellyTagException(e); } catch (UnsupportedEncodingException e) { throw new JellyTagException(e); } catch (SAXException e) { throw new JellyTagException("could not write file",e); } } |
if (haplos == null){ return null; } | public Haplotype[][] filterHaplos(Haplotype[][] haplos) { Haplotype[][] filteredHaplos = new Haplotype[haplos.length][]; for (int i = 0; i < haplos.length; i++){ Vector tempVector = new Vector(); for (int j = 0; j < haplos[i].length; j++){ if (haplos[i][j].getPercentage()*100 > Options.getHaplotypeDisplayThreshold()){ tempVector.add(haplos[i][j]); } } filteredHaplos[i] = new Haplotype[tempVector.size()]; tempVector.copyInto(filteredHaplos[i]); } return filteredHaplos; } |
|
OutputFile = validateOutputFile(fileName + ".4GAMblocks"); textData.guessBlocks(BLOX_4GAM); haplos = textData.generateHaplotypes(textData.blocks, false); filtHaplos = filterHaplos(haplos); textData.pickTags(filtHaplos); textData.saveHapsToText(haplos, textData.computeMultiDprime(filtHaplos), OutputFile);; OutputFile = validateOutputFile(fileName + ".SPINEblocks"); textData.guessBlocks(BLOX_SPINE); haplos = textData.generateHaplotypes(textData.blocks, false); filtHaplos = filterHaplos(haplos); textData.pickTags(filtHaplos); textData.saveHapsToText(haplos, textData.computeMultiDprime(filtHaplos), OutputFile); }else{ textData.guessBlocks(blockOutputType, cust); haplos = textData.generateHaplotypes(textData.blocks, false); filtHaplos = filterHaplos(haplos); textData.pickTags(filtHaplos); textData.saveHapsToText(haplos, textData.computeMultiDprime(filtHaplos), OutputFile); | }else if (!quietMode){ System.out.println("Skipping block output: no valid blocks."); } | private void processFile(String fileName, int fileType, String infoFileName){ try { HaploData textData; File OutputFile; File inputFile; if(!quietMode && fileName != null){ System.out.println("Using data file: " + fileName); } inputFile = new File(fileName); if(!inputFile.exists()){ System.out.println("input file: " + fileName + " does not exist"); System.exit(1); } textData = new HaploData(); //Vector result = null; if(fileType == HAPS){ //read in haps file textData.prepareHapsInput(inputFile); } else if (fileType == PED) { //read in ped file textData.linkageToChrom(inputFile, PED); if(textData.getPedFile().isBogusParents()) { System.out.println("Error: One or more individuals in the file reference non-existent parents.\nThese references have been ignored."); } }else{ //read in hapmapfile textData.linkageToChrom(inputFile,HMP); } File infoFile = null; if (infoFileName != null){ infoFile = new File(infoFileName); } if (fileType != HAPS){ textData.prepareMarkerInput(infoFile,textData.getPedFile().getHMInfo()); }else{ textData.prepareMarkerInput(infoFile,null); } boolean[] markerResults = new boolean[Chromosome.getUnfilteredSize()]; Vector result = null; if (fileType != HAPS){ result = textData.getPedFile().getResults(); //once check has been run we can filter the markers for (int i = 0; i < result.size(); i++){ if ((((MarkerResult)result.get(i)).getRating() > 0 || skipCheck) && Chromosome.getUnfilteredMarker(i).getDupStatus() != 2){ markerResults[i] = true; }else{ markerResults[i] = false; } } }else{ //we haven't done the check (HAPS files) Arrays.fill(markerResults, true); } for (int i = 0; i < excludedMarkers.size(); i++){ int cur = ((Integer)excludedMarkers.elementAt(i)).intValue(); if (cur < 1 || cur > markerResults.length){ System.out.println("Excluded marker out of bounds has been ignored: " + cur + "\nMarkers must be between 1 and N, where N is the total number of markers."); System.exit(1); }else{ markerResults[cur-1] = false; } } Chromosome.doFilter(markerResults); if(!quietMode && infoFile != null){ System.out.println("Using marker information file: " + infoFile.getName()); } if(outputCheck && result != null){ CheckDataPanel cp = new CheckDataPanel(textData); cp.printTable(validateOutputFile(fileName + ".CHECK")); } Vector cust = new Vector(); if(blockOutputType != -1){ textData.generateDPrimeTable(); Haplotype[][] haplos; Haplotype[][] filtHaplos; switch(blockOutputType){ case BLOX_GABRIEL: OutputFile = validateOutputFile(fileName + ".GABRIELblocks"); break; case BLOX_4GAM: OutputFile = validateOutputFile(fileName + ".4GAMblocks"); break; case BLOX_SPINE: OutputFile = validateOutputFile(fileName + ".SPINEblocks"); break; case BLOX_CUSTOM: OutputFile = validateOutputFile(fileName + ".CUSTblocks"); //read in the blocks file File blocksFile = new File(blockFileName); cust = textData.readBlocks(blocksFile); break; case BLOX_ALL: //handled below, so we don't do anything here OutputFile = null; break; default: OutputFile = validateOutputFile(fileName + ".GABRIELblocks"); break; } //this handles output type ALL if(blockOutputType == BLOX_ALL) { OutputFile = validateOutputFile(fileName + ".GABRIELblocks"); textData.guessBlocks(BLOX_GABRIEL); haplos = textData.generateHaplotypes(textData.blocks, false); filtHaplos = filterHaplos(haplos); textData.pickTags(filtHaplos); textData.saveHapsToText(haplos, textData.computeMultiDprime(filtHaplos), OutputFile); OutputFile = validateOutputFile(fileName + ".4GAMblocks"); textData.guessBlocks(BLOX_4GAM); haplos = textData.generateHaplotypes(textData.blocks, false); filtHaplos = filterHaplos(haplos); textData.pickTags(filtHaplos); textData.saveHapsToText(haplos, textData.computeMultiDprime(filtHaplos), OutputFile);; OutputFile = validateOutputFile(fileName + ".SPINEblocks"); textData.guessBlocks(BLOX_SPINE); haplos = textData.generateHaplotypes(textData.blocks, false); filtHaplos = filterHaplos(haplos); textData.pickTags(filtHaplos); textData.saveHapsToText(haplos, textData.computeMultiDprime(filtHaplos), OutputFile); }else{ //guesses blocks based on output type determined above. textData.guessBlocks(blockOutputType, cust); haplos = textData.generateHaplotypes(textData.blocks, false); filtHaplos = filterHaplos(haplos); textData.pickTags(filtHaplos); textData.saveHapsToText(haplos, textData.computeMultiDprime(filtHaplos), OutputFile); } if(Options.getAssocTest() == ASSOC_TRIO || Options.getAssocTest() == ASSOC_CC) { if (blockOutputType == BLOX_ALL){ System.out.println("Haplotype association results cannot be used with block output \"ALL\""); }else{ HaploData.saveHapAssocToText(haplos, validateOutputFile(fileName + ".HAPASSOC")); } } } if(outputDprime) { OutputFile = validateOutputFile(fileName + ".LD"); if (textData.dpTable != null){ textData.saveDprimeToText(OutputFile, TABLE_TYPE, 0, Chromosome.getSize()); }else{ textData.saveDprimeToText(OutputFile, LIVE_TYPE, 0, Chromosome.getSize()); } } if (outputPNG || outputCompressedPNG){ OutputFile = validateOutputFile(fileName + ".LD.PNG"); if (textData.dpTable == null){ textData.generateDPrimeTable(); textData.guessBlocks(BLOX_CUSTOM, new Vector()); } if (trackFileName != null){ textData.readAnalysisTrack(new File(trackFileName)); } DPrimeDisplay dpd = new DPrimeDisplay(textData); BufferedImage i = dpd.export(0,Chromosome.getSize(),outputCompressedPNG); try{ Jimi.putImage("image/png", i, OutputFile.getName()); }catch(JimiException je){ System.out.println(je.getMessage()); } } if(Options.getAssocTest() == ASSOC_TRIO){ Vector tdtResults = TDT.calcTrioTDT(textData.getPedFile()); HaploData.saveMarkerAssocToText(tdtResults, validateOutputFile(fileName + ".ASSOC")); } else if(Options.getAssocTest() == ASSOC_CC) { Vector ccResults = TDT.calcCCTDT(textData.getPedFile()); HaploData.saveMarkerAssocToText(ccResults, validateOutputFile(fileName + ".ASSOC")); } } catch(IOException e){ System.err.println("An error has occured. This probably has to do with file input or output"); } catch(HaploViewException e){ System.err.println(e.getMessage()); } catch(PedFileException pfe) { System.err.println(pfe.getMessage()); } } |
BufferedImage i = dpd.export(0,Chromosome.getSize(),outputCompressedPNG); | BufferedImage i = dpd.export(0,Chromosome.getUnfilteredSize(),outputCompressedPNG); | private void processFile(String fileName, int fileType, String infoFileName){ try { HaploData textData; File OutputFile; File inputFile; if(!quietMode && fileName != null){ System.out.println("Using data file: " + fileName); } inputFile = new File(fileName); if(!inputFile.exists()){ System.out.println("input file: " + fileName + " does not exist"); System.exit(1); } textData = new HaploData(); //Vector result = null; if(fileType == HAPS){ //read in haps file textData.prepareHapsInput(inputFile); } else if (fileType == PED) { //read in ped file textData.linkageToChrom(inputFile, PED); if(textData.getPedFile().isBogusParents()) { System.out.println("Error: One or more individuals in the file reference non-existent parents.\nThese references have been ignored."); } }else{ //read in hapmapfile textData.linkageToChrom(inputFile,HMP); } File infoFile = null; if (infoFileName != null){ infoFile = new File(infoFileName); } if (fileType != HAPS){ textData.prepareMarkerInput(infoFile,textData.getPedFile().getHMInfo()); }else{ textData.prepareMarkerInput(infoFile,null); } boolean[] markerResults = new boolean[Chromosome.getUnfilteredSize()]; Vector result = null; if (fileType != HAPS){ result = textData.getPedFile().getResults(); //once check has been run we can filter the markers for (int i = 0; i < result.size(); i++){ if ((((MarkerResult)result.get(i)).getRating() > 0 || skipCheck) && Chromosome.getUnfilteredMarker(i).getDupStatus() != 2){ markerResults[i] = true; }else{ markerResults[i] = false; } } }else{ //we haven't done the check (HAPS files) Arrays.fill(markerResults, true); } for (int i = 0; i < excludedMarkers.size(); i++){ int cur = ((Integer)excludedMarkers.elementAt(i)).intValue(); if (cur < 1 || cur > markerResults.length){ System.out.println("Excluded marker out of bounds has been ignored: " + cur + "\nMarkers must be between 1 and N, where N is the total number of markers."); System.exit(1); }else{ markerResults[cur-1] = false; } } Chromosome.doFilter(markerResults); if(!quietMode && infoFile != null){ System.out.println("Using marker information file: " + infoFile.getName()); } if(outputCheck && result != null){ CheckDataPanel cp = new CheckDataPanel(textData); cp.printTable(validateOutputFile(fileName + ".CHECK")); } Vector cust = new Vector(); if(blockOutputType != -1){ textData.generateDPrimeTable(); Haplotype[][] haplos; Haplotype[][] filtHaplos; switch(blockOutputType){ case BLOX_GABRIEL: OutputFile = validateOutputFile(fileName + ".GABRIELblocks"); break; case BLOX_4GAM: OutputFile = validateOutputFile(fileName + ".4GAMblocks"); break; case BLOX_SPINE: OutputFile = validateOutputFile(fileName + ".SPINEblocks"); break; case BLOX_CUSTOM: OutputFile = validateOutputFile(fileName + ".CUSTblocks"); //read in the blocks file File blocksFile = new File(blockFileName); cust = textData.readBlocks(blocksFile); break; case BLOX_ALL: //handled below, so we don't do anything here OutputFile = null; break; default: OutputFile = validateOutputFile(fileName + ".GABRIELblocks"); break; } //this handles output type ALL if(blockOutputType == BLOX_ALL) { OutputFile = validateOutputFile(fileName + ".GABRIELblocks"); textData.guessBlocks(BLOX_GABRIEL); haplos = textData.generateHaplotypes(textData.blocks, false); filtHaplos = filterHaplos(haplos); textData.pickTags(filtHaplos); textData.saveHapsToText(haplos, textData.computeMultiDprime(filtHaplos), OutputFile); OutputFile = validateOutputFile(fileName + ".4GAMblocks"); textData.guessBlocks(BLOX_4GAM); haplos = textData.generateHaplotypes(textData.blocks, false); filtHaplos = filterHaplos(haplos); textData.pickTags(filtHaplos); textData.saveHapsToText(haplos, textData.computeMultiDprime(filtHaplos), OutputFile);; OutputFile = validateOutputFile(fileName + ".SPINEblocks"); textData.guessBlocks(BLOX_SPINE); haplos = textData.generateHaplotypes(textData.blocks, false); filtHaplos = filterHaplos(haplos); textData.pickTags(filtHaplos); textData.saveHapsToText(haplos, textData.computeMultiDprime(filtHaplos), OutputFile); }else{ //guesses blocks based on output type determined above. textData.guessBlocks(blockOutputType, cust); haplos = textData.generateHaplotypes(textData.blocks, false); filtHaplos = filterHaplos(haplos); textData.pickTags(filtHaplos); textData.saveHapsToText(haplos, textData.computeMultiDprime(filtHaplos), OutputFile); } if(Options.getAssocTest() == ASSOC_TRIO || Options.getAssocTest() == ASSOC_CC) { if (blockOutputType == BLOX_ALL){ System.out.println("Haplotype association results cannot be used with block output \"ALL\""); }else{ HaploData.saveHapAssocToText(haplos, validateOutputFile(fileName + ".HAPASSOC")); } } } if(outputDprime) { OutputFile = validateOutputFile(fileName + ".LD"); if (textData.dpTable != null){ textData.saveDprimeToText(OutputFile, TABLE_TYPE, 0, Chromosome.getSize()); }else{ textData.saveDprimeToText(OutputFile, LIVE_TYPE, 0, Chromosome.getSize()); } } if (outputPNG || outputCompressedPNG){ OutputFile = validateOutputFile(fileName + ".LD.PNG"); if (textData.dpTable == null){ textData.generateDPrimeTable(); textData.guessBlocks(BLOX_CUSTOM, new Vector()); } if (trackFileName != null){ textData.readAnalysisTrack(new File(trackFileName)); } DPrimeDisplay dpd = new DPrimeDisplay(textData); BufferedImage i = dpd.export(0,Chromosome.getSize(),outputCompressedPNG); try{ Jimi.putImage("image/png", i, OutputFile.getName()); }catch(JimiException je){ System.out.println(je.getMessage()); } } if(Options.getAssocTest() == ASSOC_TRIO){ Vector tdtResults = TDT.calcTrioTDT(textData.getPedFile()); HaploData.saveMarkerAssocToText(tdtResults, validateOutputFile(fileName + ".ASSOC")); } else if(Options.getAssocTest() == ASSOC_CC) { Vector ccResults = TDT.calcCCTDT(textData.getPedFile()); HaploData.saveMarkerAssocToText(ccResults, validateOutputFile(fileName + ".ASSOC")); } } catch(IOException e){ System.err.println("An error has occured. This probably has to do with file input or output"); } catch(HaploViewException e){ System.err.println(e.getMessage()); } catch(PedFileException pfe) { System.err.println(pfe.getMessage()); } } |
if (expectedValue == null && expectedValue == null) { | if (expectedValue == null && actualValue == null) { | public void doTag(XMLOutput output) throws Exception { String message = getBodyText(); Object expectedValue = expected.evaluate(context); Object actualValue = actual.evaluate(context); if (expectedValue == null && expectedValue == null) { return; } if (actualValue != null && expectedValue.equals(actualValue)) { return; } String expressions = "\nExpected expression: " + expected + "\nActual expression: " + actual; failNotEquals(message, expectedValue, actualValue, expressions); } |
message = "File does not exist." | message = "File does not exist."; | public void doTag(XMLOutput output) throws JellyTagException { String message = getBodyText(); if (message == null || message.length() == 0) { message = "File does not exist." } if (file == null) { fail(message, "file given is null"); } else { if (!file.exists()) { fail(message); } } } /** * The file to be tested. If this file exists, the test will pass. * @param aFile the file to test. */ public void setFile(File aFile) { file = aFile; } |
public void setFile(File aFile) { file = aFile; } | public void doTag(XMLOutput output) throws JellyTagException { String message = getBodyText(); if (message == null || message.length() == 0) { message = "File does not exist." } if (file == null) { fail(message, "file given is null"); } else { if (!file.exists()) { fail(message); } } } /** * The file to be tested. If this file exists, the test will pass. * @param aFile the file to test. */ public void setFile(File aFile) { file = aFile; } |
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DateFormat df = new SimpleDateFormat( dateFormatStr ); | DateFormat df = getDateFormat(); | public FuzzyDate parse(String strDate) { DateFormat df = new SimpleDateFormat( dateFormatStr ); FuzzyDate fd = null; try { Date d = df.parse( strDate ); if ( d != null ) { Date midpoint = new Date( d.getTime() + getFuzzyPeriodLength(d) / 2 ); fd = new FuzzyDate( midpoint, ((float)(getFuzzyPeriodLength(d))) / (2*FuzzyDate.MILLIS_IN_DAY) ); } } catch ( ParseException e ) { log.warn( "ParseException: " + e.getMessage() ); } return fd; } |
fd = new FuzzyDate( midpoint, ((float)(getFuzzyPeriodLength(d))) / (2*FuzzyDate.MILLIS_IN_DAY) ); | fd = new FuzzyDate( midpoint, 0.5 * getFloatFuzzyPeriodLength( d ) ); | public FuzzyDate parse(String strDate) { DateFormat df = new SimpleDateFormat( dateFormatStr ); FuzzyDate fd = null; try { Date d = df.parse( strDate ); if ( d != null ) { Date midpoint = new Date( d.getTime() + getFuzzyPeriodLength(d) / 2 ); fd = new FuzzyDate( midpoint, ((float)(getFuzzyPeriodLength(d))) / (2*FuzzyDate.MILLIS_IN_DAY) ); } } catch ( ParseException e ) { log.warn( "ParseException: " + e.getMessage() ); } return fd; } |
iter = foldersNotFound.iterator(); while ( iter.hasNext() ) { PhotoFolder subfolder = (PhotoFolder)iter.next(); subfolder.delete(); } | void indexDirectory( File dir, PhotoFolder folder, int startPercent, int endPercent ) { /** Maintain information how many instances for the photos that were previously added to the folder is found */ HashMap photoInstanceCounts = new HashMap(); if ( folder != null ) { for ( int n = 0; n < folder.getPhotoCount(); n++ ) { photoInstanceCounts.put( folder.getPhoto( n ), new Integer( 0 ) ); } } File files[] = dir.listFiles(); // Count the files int fileCount = 0; int subdirCount = 0; for ( int n = 0; n < files.length; n++ ) { if ( files[n].isDirectory() ) { subdirCount++; } else { fileCount++; } } ProgressCalculator c = new ProgressCalculator( startPercent, endPercent, fileCount, subdirCount ); int nFile = 0; int nDir = 0; for ( int n = 0; n < files.length; n++ ) { File f = files[n]; if ( f.isDirectory() ) { // Create the matching folder PhotoFolder subfolder = null; if ( folder != null ) { subfolder = findSubfolderByName( folder, f.getName() ); if ( subfolder == null ) { subfolder = PhotoFolder.create( f.getName(), folder ); newFolderCount++; } } /* Calclate the start & end percentages to use when indexing this directory. Formula goes so that we estimate that to index current dirctory completely we must index files in subDirCount+1 directories (all subdirs + current directory). So we divide endPercent - startPercent into this many steps) */ int subdirStart = c.getProgress(); nDir++; c.setProcessedSubdirs( nDir ); int subdirEnd = c.getProgress(); indexDirectory( f, subfolder, subdirStart, subdirEnd ); percentComplete = c.getProgress(); } else { if ( f.canRead() ) { currentEvent = new ExtVolIndexerEvent( this ); PhotoInfo p = indexFile( f ); if ( p != null ) { if ( photoInstanceCounts.containsKey( p ) ) { // The photo is already in this folder int refCount = ((Integer)photoInstanceCounts.get( p ) ).intValue(); photoInstanceCounts.remove( p ); photoInstanceCounts.put( p, new Integer( refCount+1 )); } else { // The photo is not yet in this folder folder.addPhoto( p ); photoInstanceCounts.put( p, new Integer( 1 )); } } nFile++; c.setProcessedFiles( nFile ); percentComplete = c.getProgress(); notifyListeners( currentEvent ); } } } /* Check if some of the photos that were in folder before were not found in this directory */ Iterator iter = photoInstanceCounts.keySet().iterator(); while ( iter.hasNext() ) { PhotoInfo p = (PhotoInfo ) iter.next(); int refCount = ((Integer)photoInstanceCounts.get( p )).intValue(); if ( refCount == 0 ) { folder.removePhoto( p ); } } } |
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Object title = attributes.remove("title"); if (title != null) { getWindow().getShell().setText((String)title); } | public void doTag(XMLOutput output) throws MissingAttributeException, JellyTagException { Map attributes = getAttributes(); Object parent = attributes.remove("parent"); if (parent != null) { if (parent instanceof Shell) { this.parent = (Shell) parent; } else { throw new JellyTagException( "The parent attribute is not a Shell, it is of type: " + parent.getClass().getName() + " value: " + parent); } } super.doTag(output); } |
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return new JSR160ServerConnection(jmxc); | return new JSR160ServerConnection(jmxc, jmxc.getMBeanServerConnection()); | public ServerConnection getServerConnection(ApplicationConfig config) throws ConnectionFailedException { try { /* Create an RMI connector client */ HashMap env = new HashMap(); String[] credentials = new String[] {config.getUsername(), config.getPassword()}; env.put("jmx.remote.credentials", credentials); JMXServiceURL url = new JMXServiceURL(config.getURL()); JMXConnector jmxc = JMXConnectorFactory.connect(url, env); return new JSR160ServerConnection(jmxc); } catch (Throwable e) { throw new ConnectionFailedException(e); } } |
Font bigguns = new Font("Default", Font.BOLD, 14); | Font bigguns = new Font("Default", Font.PLAIN, 14); | public UpdateDisplayDialog(HaploView h, String title, UpdateChecker uc) { super(h, title); JPanel contents = new JPanel(); contents.setLayout(new BoxLayout(contents, BoxLayout.Y_AXIS)); Font bigguns = new Font("Default", Font.BOLD, 14); JLabel announceLabel = new JLabel("A newer version of Haploview is available: " + uc.getNewVersion()); announceLabel.setAlignmentX(Component.CENTER_ALIGNMENT); announceLabel.setFont(bigguns); JLabel urlLabel = new JLabel("http://www.broad.mit.edu/mpg/haploview/"); urlLabel.setFont(bigguns); urlLabel.setAlignmentX(Component.CENTER_ALIGNMENT); JScrollPane changeScroller = null; try { JEditorPane changePane = new JEditorPane(); changePane.setEditable(false); changePane.setPage(new URL("http://18.157.34.100:8080/hapchanges.html")); changeScroller = new JScrollPane(changePane); changeScroller.setPreferredSize(new Dimension(150,150)); } catch(IOException ioe) { //if were here then we were able to check for an update, so well just show them a dialog //without listing the changes } contents.add(announceLabel); contents.add(urlLabel); if(changeScroller != null) { changeScroller.setAlignmentX(Component.CENTER_ALIGNMENT); contents.add(changeScroller); } JButton okButton = new JButton("OK"); okButton.addActionListener(this); okButton.setAlignmentX(Component.CENTER_ALIGNMENT); contents.add(okButton); this.setContentPane(contents); this.setLocation(this.getParent().getX() + 100, this.getParent().getY() + 100); this.setModal(true); this.setResizable(false); } |
changeScroller.setPreferredSize(new Dimension(150,150)); | changeScroller.setPreferredSize(new Dimension(250,150)); | public UpdateDisplayDialog(HaploView h, String title, UpdateChecker uc) { super(h, title); JPanel contents = new JPanel(); contents.setLayout(new BoxLayout(contents, BoxLayout.Y_AXIS)); Font bigguns = new Font("Default", Font.BOLD, 14); JLabel announceLabel = new JLabel("A newer version of Haploview is available: " + uc.getNewVersion()); announceLabel.setAlignmentX(Component.CENTER_ALIGNMENT); announceLabel.setFont(bigguns); JLabel urlLabel = new JLabel("http://www.broad.mit.edu/mpg/haploview/"); urlLabel.setFont(bigguns); urlLabel.setAlignmentX(Component.CENTER_ALIGNMENT); JScrollPane changeScroller = null; try { JEditorPane changePane = new JEditorPane(); changePane.setEditable(false); changePane.setPage(new URL("http://18.157.34.100:8080/hapchanges.html")); changeScroller = new JScrollPane(changePane); changeScroller.setPreferredSize(new Dimension(150,150)); } catch(IOException ioe) { //if were here then we were able to check for an update, so well just show them a dialog //without listing the changes } contents.add(announceLabel); contents.add(urlLabel); if(changeScroller != null) { changeScroller.setAlignmentX(Component.CENTER_ALIGNMENT); contents.add(changeScroller); } JButton okButton = new JButton("OK"); okButton.addActionListener(this); okButton.setAlignmentX(Component.CENTER_ALIGNMENT); contents.add(okButton); this.setContentPane(contents); this.setLocation(this.getParent().getX() + 100, this.getParent().getY() + 100); this.setModal(true); this.setResizable(false); } |
contents.add(changeScroller); | JPanel scrollHolder = new JPanel(); scrollHolder.add(changeScroller); contents.add(scrollHolder); | public UpdateDisplayDialog(HaploView h, String title, UpdateChecker uc) { super(h, title); JPanel contents = new JPanel(); contents.setLayout(new BoxLayout(contents, BoxLayout.Y_AXIS)); Font bigguns = new Font("Default", Font.BOLD, 14); JLabel announceLabel = new JLabel("A newer version of Haploview is available: " + uc.getNewVersion()); announceLabel.setAlignmentX(Component.CENTER_ALIGNMENT); announceLabel.setFont(bigguns); JLabel urlLabel = new JLabel("http://www.broad.mit.edu/mpg/haploview/"); urlLabel.setFont(bigguns); urlLabel.setAlignmentX(Component.CENTER_ALIGNMENT); JScrollPane changeScroller = null; try { JEditorPane changePane = new JEditorPane(); changePane.setEditable(false); changePane.setPage(new URL("http://18.157.34.100:8080/hapchanges.html")); changeScroller = new JScrollPane(changePane); changeScroller.setPreferredSize(new Dimension(150,150)); } catch(IOException ioe) { //if were here then we were able to check for an update, so well just show them a dialog //without listing the changes } contents.add(announceLabel); contents.add(urlLabel); if(changeScroller != null) { changeScroller.setAlignmentX(Component.CENTER_ALIGNMENT); contents.add(changeScroller); } JButton okButton = new JButton("OK"); okButton.addActionListener(this); okButton.setAlignmentX(Component.CENTER_ALIGNMENT); contents.add(okButton); this.setContentPane(contents); this.setLocation(this.getParent().getX() + 100, this.getParent().getY() + 100); this.setModal(true); this.setResizable(false); } |
public void run(Context context, XMLOutput output) throws Exception { output.startElement( uri, localName, qname, attributes ); getBody().run(context, output); output.endElement( uri, localName, qname ); } | public void run(JellyContext context, XMLOutput output) throws Exception { output.startElement(uri, localName, qname, attributes); getBody().run(context, output); output.endElement(uri, localName, qname); } | public void run(Context context, XMLOutput output) throws Exception { output.startElement( uri, localName, qname, attributes ); getBody().run(context, output); output.endElement( uri, localName, qname ); } |
int index = attributes.getIndex( "", name ); if ( index > 0 ) { attributes.removeAttribute( index ); } if ( value != null ) { attributes.addAttribute( "", name, name, "CDATA", value.toString() ); } } | int index = attributes.getIndex("", name); if (index >= 0) { attributes.removeAttribute(index); } if (value != null) { attributes.addAttribute("", name, name, "CDATA", value.toString()); } } | public void setAttribute(String name, Object value) { // ### we'll assume that all attributes are in no namespace! // ### this is severely limiting! // ### - Tag attributes should allow for namespace aware int index = attributes.getIndex( "", name ); if ( index > 0 ) { attributes.removeAttribute( index ); } // treat null values as no attribute if ( value != null ) { attributes.addAttribute( "", name, name, "CDATA", value.toString() ); } } |
if (fileType == HAPS){ caller.readPhasedGenotypes(returnStrings); }else if (fileType == PED){ caller.readPedGenotypes(returnStrings, PED); }else if (fileType == DCC){ caller.readPedGenotypes(returnStrings, DCC); } | caller.readGenotypes(returnStrings, fileType); | public void actionPerformed(ActionEvent e) { String command = e.getActionCommand(); if (command==RAW_DATA){ load(PED); }else if (command == PHASED_DATA){ load(HAPS); }else if (command == HAPMAP_DATA){ load(DCC); }else if (command == BROWSE_GENO){ browse(GENO); }else if (command == BROWSE_INFO){ browse(INFO); }else if (command == "OK"){ HaploView caller = (HaploView)this.getParent(); if (doTDT.isSelected()){ if (trioButton.isSelected()){ caller.assocTest = 1; } else { caller.assocTest = 2; } }else{ caller.assocTest = 0; } String[] returnStrings = {genoFileField.getText(), infoFileField.getText(), maxComparisonDistField.getText()}; if (fileType == HAPS){ caller.readPhasedGenotypes(returnStrings); }else if (fileType == PED){ caller.readPedGenotypes(returnStrings, PED); }else if (fileType == DCC){ caller.readPedGenotypes(returnStrings, DCC); } if (caller.dPrimeDisplay != null){ caller.dPrimeDisplay.setVisible(false); } this.dispose(); }else if (command == "Cancel"){ this.dispose(); }else if (command == "tdt"){ if(this.doTDT.isSelected()){ trioButton.setEnabled(true); ccButton.setEnabled(true); }else{ trioButton.setEnabled(false); ccButton.setEnabled(false); } } } |
if ( value.length() > maxLength ) { | if ( value != null && value.length() > maxLength ) { | void checkStringProperty( String propertyName, String value, int maxLength ) throws IllegalArgumentException { if ( value.length() > maxLength ) { throw new IllegalArgumentException( propertyName + " cannot be longer than " + maxLength + " characters" ); } } |
* Populates the schema dropdown box from the schema * parent that doStuff() populated. * @throws ArchitectException | * Populates the schema dropdown box from the schema * parent that doStuff() populated. * * @throws ArchitectException | public void cleanup() throws ArchitectException { setCleanupExceptionMessage("Could not populate catalog dropdown!"); catalogDropdown.removeAllItems(); catalogDropdown.setEnabled(false); // This is either a database, a catalog, or null depending on how db is structured SQLObject schemaParent; if (db.isCatalogContainer()) { for (SQLObject item : (List<SQLObject>) db.getChildren()) { catalogDropdown.addItem(item); } // check if we need to do schemas SQLCatalog cat = (SQLCatalog) catalogDropdown.getSelectedItem(); if (cat == null) { // there are no catalogs (database is completely empty) schemaParent = null; catalogDropdown.setEnabled(false); } else if (cat.isSchemaContainer()) { // there are schemas in this catalog schemaParent = cat; catalogDropdown.setEnabled(true); } else { // there are catalogs, but they don't contain schemas schemaParent = null; catalogDropdown.setEnabled(true); } } else if (db.isSchemaContainer()) { schemaParent = db; catalogDropdown.setEnabled(false); } else { // database contains tables directly schemaParent = null; catalogDropdown.setEnabled(false); } schemaDropdown.removeAllItems(); schemaDropdown.setEnabled(false); if (schemaParent == null) { startCompareAction.setEnabled(isStartable()); } else { // need a final reference to this so we can use it in the inner class final SQLObject finalSchemaParent = schemaParent; new Thread(new Populator() { @Override public void doStuff() throws Exception { ListerProgressBarUpdater progressBarUpdater = new ListerProgressBarUpdater(progressBar, this); new javax.swing.Timer(100, progressBarUpdater).start(); // this populates the schema parent (populate is not visible here) finalSchemaParent.getChildren(); } /** * Populates the schema dropdown box from the schema * parent that doStuff() populated. * @throws ArchitectException */ @Override public void cleanup() throws ArchitectException { setCleanupExceptionMessage("Could not populate schema dropdown!"); for (SQLObject item : (List<SQLObject>) finalSchemaParent.getChildren()) { schemaDropdown.addItem(item); } if (schemaDropdown.getItemCount() > 0) { schemaDropdown.setEnabled(true); } startCompareAction.setEnabled(isStartable()); } }).start(); } } |
} else if (englishButton.isSelected()) { | } else if (englishButton.isSelected()) { int objectCount = 0; | public void actionPerformed(ActionEvent e) { startCompareAction.setEnabled(false); CompareDMFrame cf = null; try { SQLObject left = source.getObjectToCompare(); if (left.getChildType() == SQLTable.class) { sourceTables = left.getChildren(); } else { sourceTables = new ArrayList(); } SQLObject right = target.getObjectToCompare(); if (right.getChildType() == SQLTable.class) { targetTables = right.getChildren(); } else { targetTables = new ArrayList(); } // XXX: should do most or all of this work in a worker thread Map<DiffType, AttributeSet> styles = new HashMap<DiffType, AttributeSet>(); { SimpleAttributeSet att = new SimpleAttributeSet(); StyleConstants.setForeground(att, Color.green); styles.put(DiffType.LEFTONLY, att); att = new SimpleAttributeSet(); StyleConstants.setForeground(att, Color.red); styles.put(DiffType.RIGHTONLY, att); att = new SimpleAttributeSet(); StyleConstants.setForeground(att, Color.black); styles.put(DiffType.SAME, att); att = new SimpleAttributeSet(); StyleConstants.setForeground(att, Color.orange); styles.put(DiffType.MODIFIED, att); } CompareSQL sourceComp = new CompareSQL(sourceTables, targetTables); List<DiffChunk<SQLObject>> diff = sourceComp.generateTableDiffs(); CompareSQL targetComp = new CompareSQL(targetTables, sourceTables); List<DiffChunk<SQLObject>> diff1 = targetComp.generateTableDiffs(); DefaultStyledDocument sourceDoc = new DefaultStyledDocument(); DefaultStyledDocument targetDoc = new DefaultStyledDocument(); if (sqlButton.isSelected()) { throw new UnsupportedOperationException( "We don't support DDL generation yet"); } else if (englishButton.isSelected()) { for (DiffChunk<SQLObject> chunk : diff) { sourceDoc.insertString( sourceDoc.getLength(), chunk.getData().toString()+"\n", styles.get(chunk.getType())); } for (DiffChunk<SQLObject> chunk1 : diff1) { targetDoc.insertString( targetDoc.getLength(), chunk1.getData().toString()+"\n", styles.get(chunk1.getType())); } } else { throw new IllegalStateException( "Don't know what type of output to make"); } // get the title string for the compareDMFrame String compMethod = null; if (sqlButton.isSelected()) { compMethod = "SQL"; } else { compMethod = OUTPUT_ENGLISH; } String titleString = "Comparing " +left.getName() + " to " + right.getName() + " using " + compMethod; cf = new CompareDMFrame( sourceDoc, targetDoc, titleString, source.getDatabase()); cf.pack(); cf.setVisible(true); } catch (ArchitectDiffException ex) { JOptionPane.showMessageDialog( CompareDMPanel.this, "Could not perform the diff:\n"+ex.getMessage(), "Diff Error", JOptionPane.ERROR_MESSAGE); logger.error("Couldn't do diff", ex); } catch (ArchitectException exp) { ASUtils.showExceptionDialog( "StartCompareAction failed", exp); logger.error("StartCompareAction failed", exp); } catch (FileNotFoundException ex) { ASUtils.showExceptionDialog("Your file could not be found.", ex); logger.error("File could not be found.", ex); } catch (IOException ex) { ASUtils.showExceptionDialog("Could not read file", ex); logger.error("Could not read file", ex); } catch (BadLocationException ex) { ASUtils.showExceptionDialog("Could not create document for results", ex); logger.error("Could not create document for results", ex); } catch (Exception ex) { ASUtils.showExceptionDialog("Unxepected Exception!", ex); logger.error("Unxepected Exception!", ex); } finally { this.setEnabled(isStartable()); } } |
sourceDoc.insertString( sourceDoc.getLength(), chunk.getData().toString()+"\n", | if (chunk.getData() instanceof SQLRelationship) { if ( objectCount > 0 ) sourceDoc.insertString(sourceDoc.getLength(), "\n", styles.get(chunk.getType())); SQLRelationship rel = (SQLRelationship) chunk .getData(); sourceDoc.insertString(sourceDoc.getLength(), chunk .getData().toString() + "\n " + rel.getFkTable().getName() + "(" + rel.printKeyColumns(rel.FKCOLUMN) + ")\n refers to " + rel.getPkTable().getName() + "(" + rel.printKeyColumns(rel.PKCOLUMN) + ")", styles.get(chunk.getType())); } else if (chunk.getData() instanceof SQLColumn) { sourceDoc.insertString(sourceDoc.getLength(), " " + chunk.getData().toString(), styles .get(chunk.getType())); } else { if ( objectCount > 0 ) sourceDoc.insertString(sourceDoc.getLength(), "\n", styles.get(chunk.getType())); sourceDoc.insertString(sourceDoc.getLength(), chunk .getData().toString(), styles.get(chunk .getType())); } sourceDoc.insertString(sourceDoc.getLength(), "\n", | public void actionPerformed(ActionEvent e) { startCompareAction.setEnabled(false); CompareDMFrame cf = null; try { SQLObject left = source.getObjectToCompare(); if (left.getChildType() == SQLTable.class) { sourceTables = left.getChildren(); } else { sourceTables = new ArrayList(); } SQLObject right = target.getObjectToCompare(); if (right.getChildType() == SQLTable.class) { targetTables = right.getChildren(); } else { targetTables = new ArrayList(); } // XXX: should do most or all of this work in a worker thread Map<DiffType, AttributeSet> styles = new HashMap<DiffType, AttributeSet>(); { SimpleAttributeSet att = new SimpleAttributeSet(); StyleConstants.setForeground(att, Color.green); styles.put(DiffType.LEFTONLY, att); att = new SimpleAttributeSet(); StyleConstants.setForeground(att, Color.red); styles.put(DiffType.RIGHTONLY, att); att = new SimpleAttributeSet(); StyleConstants.setForeground(att, Color.black); styles.put(DiffType.SAME, att); att = new SimpleAttributeSet(); StyleConstants.setForeground(att, Color.orange); styles.put(DiffType.MODIFIED, att); } CompareSQL sourceComp = new CompareSQL(sourceTables, targetTables); List<DiffChunk<SQLObject>> diff = sourceComp.generateTableDiffs(); CompareSQL targetComp = new CompareSQL(targetTables, sourceTables); List<DiffChunk<SQLObject>> diff1 = targetComp.generateTableDiffs(); DefaultStyledDocument sourceDoc = new DefaultStyledDocument(); DefaultStyledDocument targetDoc = new DefaultStyledDocument(); if (sqlButton.isSelected()) { throw new UnsupportedOperationException( "We don't support DDL generation yet"); } else if (englishButton.isSelected()) { for (DiffChunk<SQLObject> chunk : diff) { sourceDoc.insertString( sourceDoc.getLength(), chunk.getData().toString()+"\n", styles.get(chunk.getType())); } for (DiffChunk<SQLObject> chunk1 : diff1) { targetDoc.insertString( targetDoc.getLength(), chunk1.getData().toString()+"\n", styles.get(chunk1.getType())); } } else { throw new IllegalStateException( "Don't know what type of output to make"); } // get the title string for the compareDMFrame String compMethod = null; if (sqlButton.isSelected()) { compMethod = "SQL"; } else { compMethod = OUTPUT_ENGLISH; } String titleString = "Comparing " +left.getName() + " to " + right.getName() + " using " + compMethod; cf = new CompareDMFrame( sourceDoc, targetDoc, titleString, source.getDatabase()); cf.pack(); cf.setVisible(true); } catch (ArchitectDiffException ex) { JOptionPane.showMessageDialog( CompareDMPanel.this, "Could not perform the diff:\n"+ex.getMessage(), "Diff Error", JOptionPane.ERROR_MESSAGE); logger.error("Couldn't do diff", ex); } catch (ArchitectException exp) { ASUtils.showExceptionDialog( "StartCompareAction failed", exp); logger.error("StartCompareAction failed", exp); } catch (FileNotFoundException ex) { ASUtils.showExceptionDialog("Your file could not be found.", ex); logger.error("File could not be found.", ex); } catch (IOException ex) { ASUtils.showExceptionDialog("Could not read file", ex); logger.error("Could not read file", ex); } catch (BadLocationException ex) { ASUtils.showExceptionDialog("Could not create document for results", ex); logger.error("Could not create document for results", ex); } catch (Exception ex) { ASUtils.showExceptionDialog("Unxepected Exception!", ex); logger.error("Unxepected Exception!", ex); } finally { this.setEnabled(isStartable()); } } |
targetDoc.insertString( targetDoc.getLength(), chunk1.getData().toString()+"\n", | if (chunk1.getData() instanceof SQLRelationship) { if ( objectCount > 0 ) targetDoc.insertString(targetDoc.getLength(), "\n", styles.get(chunk1.getType())); SQLRelationship rel = (SQLRelationship) chunk1 .getData(); targetDoc.insertString(targetDoc.getLength(), chunk1 .getData().toString() + "\n " + rel.getFkTable().getName() + "(" + rel.printKeyColumns(rel.FKCOLUMN) + ")\n refers to " + rel.getPkTable().getName() + "(" + rel.printKeyColumns(rel.PKCOLUMN) + ")", styles.get(chunk1.getType())); } else if (chunk1.getData() instanceof SQLColumn) { targetDoc.insertString(targetDoc.getLength(), " " + chunk1.getData().toString(), styles .get(chunk1.getType())); } else { if ( objectCount > 0 ) targetDoc.insertString(targetDoc.getLength(), "\n", styles.get(chunk1.getType())); targetDoc.insertString(targetDoc.getLength(), chunk1 .getData().toString(), styles.get(chunk1 .getType())); } targetDoc.insertString(targetDoc.getLength(), "\n", | public void actionPerformed(ActionEvent e) { startCompareAction.setEnabled(false); CompareDMFrame cf = null; try { SQLObject left = source.getObjectToCompare(); if (left.getChildType() == SQLTable.class) { sourceTables = left.getChildren(); } else { sourceTables = new ArrayList(); } SQLObject right = target.getObjectToCompare(); if (right.getChildType() == SQLTable.class) { targetTables = right.getChildren(); } else { targetTables = new ArrayList(); } // XXX: should do most or all of this work in a worker thread Map<DiffType, AttributeSet> styles = new HashMap<DiffType, AttributeSet>(); { SimpleAttributeSet att = new SimpleAttributeSet(); StyleConstants.setForeground(att, Color.green); styles.put(DiffType.LEFTONLY, att); att = new SimpleAttributeSet(); StyleConstants.setForeground(att, Color.red); styles.put(DiffType.RIGHTONLY, att); att = new SimpleAttributeSet(); StyleConstants.setForeground(att, Color.black); styles.put(DiffType.SAME, att); att = new SimpleAttributeSet(); StyleConstants.setForeground(att, Color.orange); styles.put(DiffType.MODIFIED, att); } CompareSQL sourceComp = new CompareSQL(sourceTables, targetTables); List<DiffChunk<SQLObject>> diff = sourceComp.generateTableDiffs(); CompareSQL targetComp = new CompareSQL(targetTables, sourceTables); List<DiffChunk<SQLObject>> diff1 = targetComp.generateTableDiffs(); DefaultStyledDocument sourceDoc = new DefaultStyledDocument(); DefaultStyledDocument targetDoc = new DefaultStyledDocument(); if (sqlButton.isSelected()) { throw new UnsupportedOperationException( "We don't support DDL generation yet"); } else if (englishButton.isSelected()) { for (DiffChunk<SQLObject> chunk : diff) { sourceDoc.insertString( sourceDoc.getLength(), chunk.getData().toString()+"\n", styles.get(chunk.getType())); } for (DiffChunk<SQLObject> chunk1 : diff1) { targetDoc.insertString( targetDoc.getLength(), chunk1.getData().toString()+"\n", styles.get(chunk1.getType())); } } else { throw new IllegalStateException( "Don't know what type of output to make"); } // get the title string for the compareDMFrame String compMethod = null; if (sqlButton.isSelected()) { compMethod = "SQL"; } else { compMethod = OUTPUT_ENGLISH; } String titleString = "Comparing " +left.getName() + " to " + right.getName() + " using " + compMethod; cf = new CompareDMFrame( sourceDoc, targetDoc, titleString, source.getDatabase()); cf.pack(); cf.setVisible(true); } catch (ArchitectDiffException ex) { JOptionPane.showMessageDialog( CompareDMPanel.this, "Could not perform the diff:\n"+ex.getMessage(), "Diff Error", JOptionPane.ERROR_MESSAGE); logger.error("Couldn't do diff", ex); } catch (ArchitectException exp) { ASUtils.showExceptionDialog( "StartCompareAction failed", exp); logger.error("StartCompareAction failed", exp); } catch (FileNotFoundException ex) { ASUtils.showExceptionDialog("Your file could not be found.", ex); logger.error("File could not be found.", ex); } catch (IOException ex) { ASUtils.showExceptionDialog("Could not read file", ex); logger.error("Could not read file", ex); } catch (BadLocationException ex) { ASUtils.showExceptionDialog("Could not create document for results", ex); logger.error("Could not create document for results", ex); } catch (Exception ex) { ASUtils.showExceptionDialog("Unxepected Exception!", ex); logger.error("Unxepected Exception!", ex); } finally { this.setEnabled(isStartable()); } } |
ApplicationConfigManager.checkAppNameAlreadyPresent(data.getName()); | public ApplicationConfigData addApplication(ServiceContext context, ApplicationConfigData data){ AccessController.checkAccess(context, ACLConstants.ACL_ADD_APPLICATIONS); /* do the operation */ String appId = ApplicationConfig.getNextApplicationId(); Integer port = data.getPort(); ApplicationConfig config = ApplicationConfigFactory.create(appId, data.getName(), data.getType(), data.getHost(), port, data.getURL(), data.getUsername(), data.getPassword(), null); ApplicationConfigManager.addApplication(config); data.setApplicationId(appId); /* log the operation */ UserActivityLogger.getInstance().logActivity( context.getUser().getUsername(), "Added application "+ "\""+config.getName()+"\""); return data; } |
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getBody().run(context, output); | invokeBody(output); | public void doTag(XMLOutput output) throws Exception { if (log.isDebugEnabled()) { log.debug("running with items: " + items); } if (items != null) { Iterator iter = items.evaluateAsIterator(context); if (log.isDebugEnabled()) { log.debug("Iterating through: " + iter); } // ignore the first items of the iterator for (index = 0; index < begin && iter.hasNext(); index++ ) { iter.next(); } while (iter.hasNext() && index < end) { Object value = iter.next(); if (var != null) { context.setVariable(var, value); } if (indexVar != null) { context.setVariable(indexVar, new Integer(index)); } getBody().run(context, output); // now we need to move to next index index++; for ( int i = 1; i < step; i++, index++ ) { if ( ! iter.hasNext() ) { return; } iter.next(); } } } else { if ( end == Integer.MAX_VALUE && begin == 0 ) { throw new MissingAttributeException( "items" ); } } } |
PhotoCollectionTransferHandler.setLastImportTarget( folder ); | public void drop(DropTargetDropEvent e) { hoverTimer.stop(); // Prevent hover timer from doing an unwanted expandPath or collapsePath if (!isDropAcceptable(e)) { e.rejectDrop(); return; } e.acceptDrop(e.getDropAction()); Transferable transferable = e.getTransferable(); DataFlavor[] flavors = transferable.getTransferDataFlavors(); for (int i = 0; i < flavors.length; i++ ) { DataFlavor flavor = flavors[i]; if (flavor.isMimeTypeEqual(DataFlavor.javaJVMLocalObjectMimeType)) { try { Point pt = e.getLocation(); TreePath pathTarget = tree.getClosestPathForLocation(pt.x, pt.y); PhotoFolder folder = (PhotoFolder) pathTarget.getLastPathComponent(); PhotoInfo[] photos = (PhotoInfo[])transferable.getTransferData(photoInfoFlavor); for ( int n = 0; n < photos.length; n++ ) { folder.addPhoto( photos[n] ); } break; // No need to check remaining flavors } catch (UnsupportedFlavorException ufe) { System.out.println(ufe); e.dropComplete(false); return; } catch (IOException ioe) { System.out.println(ioe); e.dropComplete(false); return; } } } e.dropComplete(true); } |
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System.out.println(first + " " + last + " " + numStrong); | Vector doSFS(){ double cutHighCI = 0.98; double cutLowCI = 0.70; double recHighCI = 0.90; int numStrong = 0; int numRec = 0; int numInGroup = 0; Vector blocks = new Vector(); Vector strongPairs = new Vector(); //first make a list of marker pairs in "strong LD", sorted by distance apart for (int x = 0; x < dPrime.length-1; x++){ for (int y = x+1; y < dPrime.length; y++){ PairwiseLinkage thisPair = dPrime[x][y]; //get the right bits double lod = thisPair.getLOD(); double lowCI = thisPair.getConfidenceLow(); double highCI = thisPair.getConfidenceHigh(); if (lod < -90) continue; //missing data if (highCI < cutHighCI || lowCI < cutLowCI) continue; //must pass "strong LD" test Vector addMe = new Vector(); //a vector of x, y, separation int sep = y - x - 1; //compute separation of two markers addMe.add(String.valueOf(x)); addMe.add(String.valueOf(y)); addMe.add(String.valueOf(sep)); if (strongPairs.size() == 0){ //put first pair first strongPairs.add(addMe); }else{ //sort by descending separation of markers in each pair for (int v = 0; v < strongPairs.size(); v ++){ if (sep >= Integer.parseInt((String)((Vector)strongPairs.elementAt(v)).elementAt(2))){ strongPairs.insertElementAt(addMe, v); break; } } } } } //now take this list of pairs with "strong LD" and construct blocks boolean[] usedInBlock = new boolean[dPrime.length + 1]; for (int v = 0; v < strongPairs.size(); v++){ int first = Integer.parseInt((String)((Vector)strongPairs.elementAt(v)).elementAt(0)); int last = Integer.parseInt((String)((Vector)strongPairs.elementAt(v)).elementAt(1)); //first see if this block overlaps with another: if (usedInBlock[first] || usedInBlock[last]) continue; //test this block. requires 95% of informative markers to be "strong" for (int y = first+1; y <= last; y++){ //loop over columns in row y for (int x = first; x < y; x++){ PairwiseLinkage thisPair = dPrime[x][y]; //get the right bits double lod = thisPair.getLOD(); double lowCI = thisPair.getConfidenceLow(); double highCI = thisPair.getConfidenceHigh(); if (lod < -90) continue; //monomorphic marker error if (lod == 0 && lowCI == 0 && highCI == 0) continue; //skip bad markers if (lowCI > cutLowCI && highCI > cutHighCI) { //System.out.println(first + "\t" + last + "\t" + x + "\t" + y); numStrong++; //strong LD } if (highCI < recHighCI) numRec++; //recombination numInGroup ++; } } //change the definition somewhat for small blocks if (numInGroup > 3){ if (numStrong + numRec < 6) continue; }else if (numInGroup > 2){ if (numStrong + numRec < 3) continue; }else{ if (numStrong + numRec < 1) continue; } if (numStrong/(numStrong + numRec) > 0.95){ //this qualifies as a block //add to the block list, but in order by first marker number: if (blocks.size() == 0){ //put first block first blocks.add(first + " " + last); }else{ //sort by ascending separation of markers in each pair boolean placed = false; for (int b = 0; b < blocks.size(); b ++){ StringTokenizer st = new StringTokenizer((String)blocks.elementAt(b)); if (first < Integer.parseInt(st.nextToken())){ blocks.insertElementAt(first + " " + last, b); placed = true; break; } } //make sure to put in blocks which fall on the tail end if (!placed) blocks.add(first + " " + last); } for (int used = first; used <= last; used++){ usedInBlock[used] = true; } } numStrong = 0; numRec = 0; numInGroup = 0; } return stringVec2intVec(blocks); } |
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numStrong = 0; numRec = 0; numInGroup = 0; | Vector doSFS(){ double cutHighCI = 0.98; double cutLowCI = 0.70; double recHighCI = 0.90; int numStrong = 0; int numRec = 0; int numInGroup = 0; Vector blocks = new Vector(); Vector strongPairs = new Vector(); //first make a list of marker pairs in "strong LD", sorted by distance apart for (int x = 0; x < dPrime.length-1; x++){ for (int y = x+1; y < dPrime.length; y++){ PairwiseLinkage thisPair = dPrime[x][y]; //get the right bits double lod = thisPair.getLOD(); double lowCI = thisPair.getConfidenceLow(); double highCI = thisPair.getConfidenceHigh(); if (lod < -90) continue; //missing data if (highCI < cutHighCI || lowCI < cutLowCI) continue; //must pass "strong LD" test Vector addMe = new Vector(); //a vector of x, y, separation int sep = y - x - 1; //compute separation of two markers addMe.add(String.valueOf(x)); addMe.add(String.valueOf(y)); addMe.add(String.valueOf(sep)); if (strongPairs.size() == 0){ //put first pair first strongPairs.add(addMe); }else{ //sort by descending separation of markers in each pair for (int v = 0; v < strongPairs.size(); v ++){ if (sep >= Integer.parseInt((String)((Vector)strongPairs.elementAt(v)).elementAt(2))){ strongPairs.insertElementAt(addMe, v); break; } } } } } //now take this list of pairs with "strong LD" and construct blocks boolean[] usedInBlock = new boolean[dPrime.length + 1]; for (int v = 0; v < strongPairs.size(); v++){ int first = Integer.parseInt((String)((Vector)strongPairs.elementAt(v)).elementAt(0)); int last = Integer.parseInt((String)((Vector)strongPairs.elementAt(v)).elementAt(1)); //first see if this block overlaps with another: if (usedInBlock[first] || usedInBlock[last]) continue; //test this block. requires 95% of informative markers to be "strong" for (int y = first+1; y <= last; y++){ //loop over columns in row y for (int x = first; x < y; x++){ PairwiseLinkage thisPair = dPrime[x][y]; //get the right bits double lod = thisPair.getLOD(); double lowCI = thisPair.getConfidenceLow(); double highCI = thisPair.getConfidenceHigh(); if (lod < -90) continue; //monomorphic marker error if (lod == 0 && lowCI == 0 && highCI == 0) continue; //skip bad markers if (lowCI > cutLowCI && highCI > cutHighCI) { //System.out.println(first + "\t" + last + "\t" + x + "\t" + y); numStrong++; //strong LD } if (highCI < recHighCI) numRec++; //recombination numInGroup ++; } } //change the definition somewhat for small blocks if (numInGroup > 3){ if (numStrong + numRec < 6) continue; }else if (numInGroup > 2){ if (numStrong + numRec < 3) continue; }else{ if (numStrong + numRec < 1) continue; } if (numStrong/(numStrong + numRec) > 0.95){ //this qualifies as a block //add to the block list, but in order by first marker number: if (blocks.size() == 0){ //put first block first blocks.add(first + " " + last); }else{ //sort by ascending separation of markers in each pair boolean placed = false; for (int b = 0; b < blocks.size(); b ++){ StringTokenizer st = new StringTokenizer((String)blocks.elementAt(b)); if (first < Integer.parseInt(st.nextToken())){ blocks.insertElementAt(first + " " + last, b); placed = true; break; } } //make sure to put in blocks which fall on the tail end if (!placed) blocks.add(first + " " + last); } for (int used = first; used <= last; used++){ usedInBlock[used] = true; } } numStrong = 0; numRec = 0; numInGroup = 0; } return stringVec2intVec(blocks); } |
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ODMG.initODMG( "harri", "", db ); | try { ODMG.initODMG( "harri", "", db ); } catch (PhotovaultException ex) { fail( ex.getMessage() ); } | public void testCreateDB() { File confFile = null; File dbDir = null; // Create an empty configuration file & volume directory try { confFile = File.createTempFile( "photovault_settings_", ".xml" ); confFile.delete(); dbDir = File.createTempFile( "photovault_test_volume", "" ); dbDir.delete(); dbDir.mkdir(); } catch (IOException ex) { ex.printStackTrace(); fail( ex.getMessage() ); } System.setProperty( "photovault.configfile", confFile.getAbsolutePath() ); PhotovaultSettings settings = PhotovaultSettings.getSettings(); PVDatabase db = new PVDatabase(); db.setInstanceType( PVDatabase.TYPE_EMBEDDED ); db.setEmbeddedDirectory( dbDir );// Volume vol = new Volume( "testvolume", dbDir.getAbsolutePath() );// db.addVolume( vol ); settings.addDatabase( db ); settings.saveConfig(); db.createDatabase( "harri", "" ); // Verify that the database can be used by importing a file ODMG.initODMG( "harri", "", db ); File photoFile = new File( "testfiles/test1.jpg" ); PhotoInfo photo = null; try { photo = PhotoInfo.addToDB(photoFile); } catch (PhotoNotFoundException ex) { ex.printStackTrace(); fail( ex.getMessage() ); } photo.setPhotographer( "test" ); try { PhotoInfo photo2 = PhotoInfo.retrievePhotoInfo( photo.getUid() ); Thumbnail thumb = photo2.getThumbnail(); this.assertFalse( "Default thumbnail returned", thumb == Thumbnail.getDefaultThumbnail() ); } catch (PhotoNotFoundException ex) { fail( "Photo not found in database" ); } } |
jPanel1 = new javax.swing.JPanel(); | splashPane = new javax.swing.JPanel(); | private void initComponents() { copyrightPane = new javax.swing.JTabbedPane(); jPanel1 = new javax.swing.JPanel(); splashLabel = new javax.swing.JLabel(); jPanel2 = new javax.swing.JPanel(); jLabel1 = new javax.swing.JLabel(); jLabel2 = new javax.swing.JLabel(); jLabel3 = new javax.swing.JLabel(); jLabel4 = new javax.swing.JLabel(); jLabel5 = new javax.swing.JLabel(); versionLabel = new javax.swing.JLabel(); svnrevLabel = new javax.swing.JLabel(); svnbranchLabel = new javax.swing.JLabel(); buildTimeLabel = new javax.swing.JLabel(); builderLabel = new javax.swing.JLabel(); jPanel3 = new javax.swing.JPanel(); jScrollPane1 = new javax.swing.JScrollPane(); copyrightTextPane = new javax.swing.JTextPane(); setDefaultCloseOperation(javax.swing.WindowConstants.DISPOSE_ON_CLOSE); setTitle("Photovault"); setResizable(false); addMouseListener(new java.awt.event.MouseAdapter() { public void mouseClicked(java.awt.event.MouseEvent evt) { formMouseClicked(evt); } }); copyrightPane.setOpaque(true); copyrightPane.addAncestorListener(new javax.swing.event.AncestorListener() { public void ancestorMoved(javax.swing.event.AncestorEvent evt) { } public void ancestorAdded(javax.swing.event.AncestorEvent evt) { copyrightPaneAncestorAdded(evt); } public void ancestorRemoved(javax.swing.event.AncestorEvent evt) { } }); splashLabel.setText("jLabel1"); splashLabel.addMouseListener(new java.awt.event.MouseAdapter() { public void mouseClicked(java.awt.event.MouseEvent evt) { formMouseClicked(evt); } }); org.jdesktop.layout.GroupLayout jPanel1Layout = new org.jdesktop.layout.GroupLayout(jPanel1); jPanel1.setLayout(jPanel1Layout); jPanel1Layout.setHorizontalGroup( jPanel1Layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING) .add(splashLabel, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, 400, Short.MAX_VALUE) ); jPanel1Layout.setVerticalGroup( jPanel1Layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING) .add(splashLabel, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, 267, Short.MAX_VALUE) ); copyrightPane.addTab("Photovault", jPanel1); jLabel1.setText("Version:"); jLabel2.setText("SVN revision:"); jLabel3.setText("SVN branch:"); jLabel4.setText("Build time:"); jLabel5.setText("Built by:"); versionLabel.setText("jLabel6"); svnrevLabel.setText("jLabel6"); svnbranchLabel.setText("jLabel6"); buildTimeLabel.setText("jLabel6"); builderLabel.setText("jLabel6"); org.jdesktop.layout.GroupLayout jPanel2Layout = new org.jdesktop.layout.GroupLayout(jPanel2); jPanel2.setLayout(jPanel2Layout); jPanel2Layout.setHorizontalGroup( jPanel2Layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING) .add(jPanel2Layout.createSequentialGroup() .add(37, 37, 37) .add(jPanel2Layout.createParallelGroup(org.jdesktop.layout.GroupLayout.TRAILING) .add(jLabel5) .add(jLabel4) .add(jLabel3) .add(jLabel2) .add(jLabel1)) .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED) .add(jPanel2Layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING) .add(versionLabel) .add(svnrevLabel) .add(svnbranchLabel) .add(buildTimeLabel) .add(builderLabel)) .addContainerGap(260, Short.MAX_VALUE)) ); jPanel2Layout.setVerticalGroup( jPanel2Layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING) .add(jPanel2Layout.createSequentialGroup() .addContainerGap() .add(jPanel2Layout.createParallelGroup(org.jdesktop.layout.GroupLayout.BASELINE) .add(jLabel1) .add(versionLabel)) .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED) .add(jPanel2Layout.createParallelGroup(org.jdesktop.layout.GroupLayout.BASELINE) .add(jLabel2) .add(svnrevLabel)) .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED) .add(jPanel2Layout.createParallelGroup(org.jdesktop.layout.GroupLayout.BASELINE) .add(jLabel3) .add(svnbranchLabel)) .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED) .add(jPanel2Layout.createParallelGroup(org.jdesktop.layout.GroupLayout.BASELINE) .add(jLabel4) .add(buildTimeLabel)) .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED) .add(jPanel2Layout.createParallelGroup(org.jdesktop.layout.GroupLayout.BASELINE) .add(jLabel5) .add(builderLabel)) .addContainerGap(162, Short.MAX_VALUE)) ); copyrightPane.addTab("Version info", jPanel2); copyrightTextPane.setEditable(false); jScrollPane1.setViewportView(copyrightTextPane); org.jdesktop.layout.GroupLayout jPanel3Layout = new org.jdesktop.layout.GroupLayout(jPanel3); jPanel3.setLayout(jPanel3Layout); jPanel3Layout.setHorizontalGroup( jPanel3Layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING) .add(jScrollPane1, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, 400, Short.MAX_VALUE) ); jPanel3Layout.setVerticalGroup( jPanel3Layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING) .add(jScrollPane1, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, 267, Short.MAX_VALUE) ); copyrightPane.addTab("Copyright", jPanel3); org.jdesktop.layout.GroupLayout layout = new org.jdesktop.layout.GroupLayout(getContentPane()); getContentPane().setLayout(layout); layout.setHorizontalGroup( layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING) .add(org.jdesktop.layout.GroupLayout.TRAILING, copyrightPane, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, 405, Short.MAX_VALUE) ); layout.setVerticalGroup( layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING) .add(copyrightPane, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, 295, Short.MAX_VALUE) ); pack(); }// </editor-fold>//GEN-END:initComponents |
org.jdesktop.layout.GroupLayout jPanel1Layout = new org.jdesktop.layout.GroupLayout(jPanel1); jPanel1.setLayout(jPanel1Layout); jPanel1Layout.setHorizontalGroup( jPanel1Layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING) | org.jdesktop.layout.GroupLayout splashPaneLayout = new org.jdesktop.layout.GroupLayout(splashPane); splashPane.setLayout(splashPaneLayout); splashPaneLayout.setHorizontalGroup( splashPaneLayout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING) | private void initComponents() { copyrightPane = new javax.swing.JTabbedPane(); jPanel1 = new javax.swing.JPanel(); splashLabel = new javax.swing.JLabel(); jPanel2 = new javax.swing.JPanel(); jLabel1 = new javax.swing.JLabel(); jLabel2 = new javax.swing.JLabel(); jLabel3 = new javax.swing.JLabel(); jLabel4 = new javax.swing.JLabel(); jLabel5 = new javax.swing.JLabel(); versionLabel = new javax.swing.JLabel(); svnrevLabel = new javax.swing.JLabel(); svnbranchLabel = new javax.swing.JLabel(); buildTimeLabel = new javax.swing.JLabel(); builderLabel = new javax.swing.JLabel(); jPanel3 = new javax.swing.JPanel(); jScrollPane1 = new javax.swing.JScrollPane(); copyrightTextPane = new javax.swing.JTextPane(); setDefaultCloseOperation(javax.swing.WindowConstants.DISPOSE_ON_CLOSE); setTitle("Photovault"); setResizable(false); addMouseListener(new java.awt.event.MouseAdapter() { public void mouseClicked(java.awt.event.MouseEvent evt) { formMouseClicked(evt); } }); copyrightPane.setOpaque(true); copyrightPane.addAncestorListener(new javax.swing.event.AncestorListener() { public void ancestorMoved(javax.swing.event.AncestorEvent evt) { } public void ancestorAdded(javax.swing.event.AncestorEvent evt) { copyrightPaneAncestorAdded(evt); } public void ancestorRemoved(javax.swing.event.AncestorEvent evt) { } }); splashLabel.setText("jLabel1"); splashLabel.addMouseListener(new java.awt.event.MouseAdapter() { public void mouseClicked(java.awt.event.MouseEvent evt) { formMouseClicked(evt); } }); org.jdesktop.layout.GroupLayout jPanel1Layout = new org.jdesktop.layout.GroupLayout(jPanel1); jPanel1.setLayout(jPanel1Layout); jPanel1Layout.setHorizontalGroup( jPanel1Layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING) .add(splashLabel, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, 400, Short.MAX_VALUE) ); jPanel1Layout.setVerticalGroup( jPanel1Layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING) .add(splashLabel, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, 267, Short.MAX_VALUE) ); copyrightPane.addTab("Photovault", jPanel1); jLabel1.setText("Version:"); jLabel2.setText("SVN revision:"); jLabel3.setText("SVN branch:"); jLabel4.setText("Build time:"); jLabel5.setText("Built by:"); versionLabel.setText("jLabel6"); svnrevLabel.setText("jLabel6"); svnbranchLabel.setText("jLabel6"); buildTimeLabel.setText("jLabel6"); builderLabel.setText("jLabel6"); org.jdesktop.layout.GroupLayout jPanel2Layout = new org.jdesktop.layout.GroupLayout(jPanel2); jPanel2.setLayout(jPanel2Layout); jPanel2Layout.setHorizontalGroup( jPanel2Layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING) .add(jPanel2Layout.createSequentialGroup() .add(37, 37, 37) .add(jPanel2Layout.createParallelGroup(org.jdesktop.layout.GroupLayout.TRAILING) .add(jLabel5) .add(jLabel4) .add(jLabel3) .add(jLabel2) .add(jLabel1)) .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED) .add(jPanel2Layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING) .add(versionLabel) .add(svnrevLabel) .add(svnbranchLabel) .add(buildTimeLabel) .add(builderLabel)) .addContainerGap(260, Short.MAX_VALUE)) ); jPanel2Layout.setVerticalGroup( jPanel2Layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING) .add(jPanel2Layout.createSequentialGroup() .addContainerGap() .add(jPanel2Layout.createParallelGroup(org.jdesktop.layout.GroupLayout.BASELINE) .add(jLabel1) .add(versionLabel)) .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED) .add(jPanel2Layout.createParallelGroup(org.jdesktop.layout.GroupLayout.BASELINE) .add(jLabel2) .add(svnrevLabel)) .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED) .add(jPanel2Layout.createParallelGroup(org.jdesktop.layout.GroupLayout.BASELINE) .add(jLabel3) .add(svnbranchLabel)) .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED) .add(jPanel2Layout.createParallelGroup(org.jdesktop.layout.GroupLayout.BASELINE) .add(jLabel4) .add(buildTimeLabel)) .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED) .add(jPanel2Layout.createParallelGroup(org.jdesktop.layout.GroupLayout.BASELINE) .add(jLabel5) .add(builderLabel)) .addContainerGap(162, Short.MAX_VALUE)) ); copyrightPane.addTab("Version info", jPanel2); copyrightTextPane.setEditable(false); jScrollPane1.setViewportView(copyrightTextPane); org.jdesktop.layout.GroupLayout jPanel3Layout = new org.jdesktop.layout.GroupLayout(jPanel3); jPanel3.setLayout(jPanel3Layout); jPanel3Layout.setHorizontalGroup( jPanel3Layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING) .add(jScrollPane1, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, 400, Short.MAX_VALUE) ); jPanel3Layout.setVerticalGroup( jPanel3Layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING) .add(jScrollPane1, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, 267, Short.MAX_VALUE) ); copyrightPane.addTab("Copyright", jPanel3); org.jdesktop.layout.GroupLayout layout = new org.jdesktop.layout.GroupLayout(getContentPane()); getContentPane().setLayout(layout); layout.setHorizontalGroup( layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING) .add(org.jdesktop.layout.GroupLayout.TRAILING, copyrightPane, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, 405, Short.MAX_VALUE) ); layout.setVerticalGroup( layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING) .add(copyrightPane, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, 295, Short.MAX_VALUE) ); pack(); }// </editor-fold>//GEN-END:initComponents |
jPanel1Layout.setVerticalGroup( jPanel1Layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING) .add(splashLabel, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, 267, Short.MAX_VALUE) | splashPaneLayout.setVerticalGroup( splashPaneLayout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING) .add(splashLabel, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, 268, Short.MAX_VALUE) | private void initComponents() { copyrightPane = new javax.swing.JTabbedPane(); jPanel1 = new javax.swing.JPanel(); splashLabel = new javax.swing.JLabel(); jPanel2 = new javax.swing.JPanel(); jLabel1 = new javax.swing.JLabel(); jLabel2 = new javax.swing.JLabel(); jLabel3 = new javax.swing.JLabel(); jLabel4 = new javax.swing.JLabel(); jLabel5 = new javax.swing.JLabel(); versionLabel = new javax.swing.JLabel(); svnrevLabel = new javax.swing.JLabel(); svnbranchLabel = new javax.swing.JLabel(); buildTimeLabel = new javax.swing.JLabel(); builderLabel = new javax.swing.JLabel(); jPanel3 = new javax.swing.JPanel(); jScrollPane1 = new javax.swing.JScrollPane(); copyrightTextPane = new javax.swing.JTextPane(); setDefaultCloseOperation(javax.swing.WindowConstants.DISPOSE_ON_CLOSE); setTitle("Photovault"); setResizable(false); addMouseListener(new java.awt.event.MouseAdapter() { public void mouseClicked(java.awt.event.MouseEvent evt) { formMouseClicked(evt); } }); copyrightPane.setOpaque(true); copyrightPane.addAncestorListener(new javax.swing.event.AncestorListener() { public void ancestorMoved(javax.swing.event.AncestorEvent evt) { } public void ancestorAdded(javax.swing.event.AncestorEvent evt) { copyrightPaneAncestorAdded(evt); } public void ancestorRemoved(javax.swing.event.AncestorEvent evt) { } }); splashLabel.setText("jLabel1"); splashLabel.addMouseListener(new java.awt.event.MouseAdapter() { public void mouseClicked(java.awt.event.MouseEvent evt) { formMouseClicked(evt); } }); org.jdesktop.layout.GroupLayout jPanel1Layout = new org.jdesktop.layout.GroupLayout(jPanel1); jPanel1.setLayout(jPanel1Layout); jPanel1Layout.setHorizontalGroup( jPanel1Layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING) .add(splashLabel, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, 400, Short.MAX_VALUE) ); jPanel1Layout.setVerticalGroup( jPanel1Layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING) .add(splashLabel, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, 267, Short.MAX_VALUE) ); copyrightPane.addTab("Photovault", jPanel1); jLabel1.setText("Version:"); jLabel2.setText("SVN revision:"); jLabel3.setText("SVN branch:"); jLabel4.setText("Build time:"); jLabel5.setText("Built by:"); versionLabel.setText("jLabel6"); svnrevLabel.setText("jLabel6"); svnbranchLabel.setText("jLabel6"); buildTimeLabel.setText("jLabel6"); builderLabel.setText("jLabel6"); org.jdesktop.layout.GroupLayout jPanel2Layout = new org.jdesktop.layout.GroupLayout(jPanel2); jPanel2.setLayout(jPanel2Layout); jPanel2Layout.setHorizontalGroup( jPanel2Layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING) .add(jPanel2Layout.createSequentialGroup() .add(37, 37, 37) .add(jPanel2Layout.createParallelGroup(org.jdesktop.layout.GroupLayout.TRAILING) .add(jLabel5) .add(jLabel4) .add(jLabel3) .add(jLabel2) .add(jLabel1)) .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED) .add(jPanel2Layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING) .add(versionLabel) .add(svnrevLabel) .add(svnbranchLabel) .add(buildTimeLabel) .add(builderLabel)) .addContainerGap(260, Short.MAX_VALUE)) ); jPanel2Layout.setVerticalGroup( jPanel2Layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING) .add(jPanel2Layout.createSequentialGroup() .addContainerGap() .add(jPanel2Layout.createParallelGroup(org.jdesktop.layout.GroupLayout.BASELINE) .add(jLabel1) .add(versionLabel)) .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED) .add(jPanel2Layout.createParallelGroup(org.jdesktop.layout.GroupLayout.BASELINE) .add(jLabel2) .add(svnrevLabel)) .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED) .add(jPanel2Layout.createParallelGroup(org.jdesktop.layout.GroupLayout.BASELINE) .add(jLabel3) .add(svnbranchLabel)) .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED) .add(jPanel2Layout.createParallelGroup(org.jdesktop.layout.GroupLayout.BASELINE) .add(jLabel4) .add(buildTimeLabel)) .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED) .add(jPanel2Layout.createParallelGroup(org.jdesktop.layout.GroupLayout.BASELINE) .add(jLabel5) .add(builderLabel)) .addContainerGap(162, Short.MAX_VALUE)) ); copyrightPane.addTab("Version info", jPanel2); copyrightTextPane.setEditable(false); jScrollPane1.setViewportView(copyrightTextPane); org.jdesktop.layout.GroupLayout jPanel3Layout = new org.jdesktop.layout.GroupLayout(jPanel3); jPanel3.setLayout(jPanel3Layout); jPanel3Layout.setHorizontalGroup( jPanel3Layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING) .add(jScrollPane1, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, 400, Short.MAX_VALUE) ); jPanel3Layout.setVerticalGroup( jPanel3Layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING) .add(jScrollPane1, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, 267, Short.MAX_VALUE) ); copyrightPane.addTab("Copyright", jPanel3); org.jdesktop.layout.GroupLayout layout = new org.jdesktop.layout.GroupLayout(getContentPane()); getContentPane().setLayout(layout); layout.setHorizontalGroup( layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING) .add(org.jdesktop.layout.GroupLayout.TRAILING, copyrightPane, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, 405, Short.MAX_VALUE) ); layout.setVerticalGroup( layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING) .add(copyrightPane, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, 295, Short.MAX_VALUE) ); pack(); }// </editor-fold>//GEN-END:initComponents |
copyrightPane.addTab("Photovault", jPanel1); | copyrightPane.addTab("Photovault", splashPane); | private void initComponents() { copyrightPane = new javax.swing.JTabbedPane(); jPanel1 = new javax.swing.JPanel(); splashLabel = new javax.swing.JLabel(); jPanel2 = new javax.swing.JPanel(); jLabel1 = new javax.swing.JLabel(); jLabel2 = new javax.swing.JLabel(); jLabel3 = new javax.swing.JLabel(); jLabel4 = new javax.swing.JLabel(); jLabel5 = new javax.swing.JLabel(); versionLabel = new javax.swing.JLabel(); svnrevLabel = new javax.swing.JLabel(); svnbranchLabel = new javax.swing.JLabel(); buildTimeLabel = new javax.swing.JLabel(); builderLabel = new javax.swing.JLabel(); jPanel3 = new javax.swing.JPanel(); jScrollPane1 = new javax.swing.JScrollPane(); copyrightTextPane = new javax.swing.JTextPane(); setDefaultCloseOperation(javax.swing.WindowConstants.DISPOSE_ON_CLOSE); setTitle("Photovault"); setResizable(false); addMouseListener(new java.awt.event.MouseAdapter() { public void mouseClicked(java.awt.event.MouseEvent evt) { formMouseClicked(evt); } }); copyrightPane.setOpaque(true); copyrightPane.addAncestorListener(new javax.swing.event.AncestorListener() { public void ancestorMoved(javax.swing.event.AncestorEvent evt) { } public void ancestorAdded(javax.swing.event.AncestorEvent evt) { copyrightPaneAncestorAdded(evt); } public void ancestorRemoved(javax.swing.event.AncestorEvent evt) { } }); splashLabel.setText("jLabel1"); splashLabel.addMouseListener(new java.awt.event.MouseAdapter() { public void mouseClicked(java.awt.event.MouseEvent evt) { formMouseClicked(evt); } }); org.jdesktop.layout.GroupLayout jPanel1Layout = new org.jdesktop.layout.GroupLayout(jPanel1); jPanel1.setLayout(jPanel1Layout); jPanel1Layout.setHorizontalGroup( jPanel1Layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING) .add(splashLabel, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, 400, Short.MAX_VALUE) ); jPanel1Layout.setVerticalGroup( jPanel1Layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING) .add(splashLabel, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, 267, Short.MAX_VALUE) ); copyrightPane.addTab("Photovault", jPanel1); jLabel1.setText("Version:"); jLabel2.setText("SVN revision:"); jLabel3.setText("SVN branch:"); jLabel4.setText("Build time:"); jLabel5.setText("Built by:"); versionLabel.setText("jLabel6"); svnrevLabel.setText("jLabel6"); svnbranchLabel.setText("jLabel6"); buildTimeLabel.setText("jLabel6"); builderLabel.setText("jLabel6"); org.jdesktop.layout.GroupLayout jPanel2Layout = new org.jdesktop.layout.GroupLayout(jPanel2); jPanel2.setLayout(jPanel2Layout); jPanel2Layout.setHorizontalGroup( jPanel2Layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING) .add(jPanel2Layout.createSequentialGroup() .add(37, 37, 37) .add(jPanel2Layout.createParallelGroup(org.jdesktop.layout.GroupLayout.TRAILING) .add(jLabel5) .add(jLabel4) .add(jLabel3) .add(jLabel2) .add(jLabel1)) .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED) .add(jPanel2Layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING) .add(versionLabel) .add(svnrevLabel) .add(svnbranchLabel) .add(buildTimeLabel) .add(builderLabel)) .addContainerGap(260, Short.MAX_VALUE)) ); jPanel2Layout.setVerticalGroup( jPanel2Layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING) .add(jPanel2Layout.createSequentialGroup() .addContainerGap() .add(jPanel2Layout.createParallelGroup(org.jdesktop.layout.GroupLayout.BASELINE) .add(jLabel1) .add(versionLabel)) .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED) .add(jPanel2Layout.createParallelGroup(org.jdesktop.layout.GroupLayout.BASELINE) .add(jLabel2) .add(svnrevLabel)) .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED) .add(jPanel2Layout.createParallelGroup(org.jdesktop.layout.GroupLayout.BASELINE) .add(jLabel3) .add(svnbranchLabel)) .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED) .add(jPanel2Layout.createParallelGroup(org.jdesktop.layout.GroupLayout.BASELINE) .add(jLabel4) .add(buildTimeLabel)) .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED) .add(jPanel2Layout.createParallelGroup(org.jdesktop.layout.GroupLayout.BASELINE) .add(jLabel5) .add(builderLabel)) .addContainerGap(162, Short.MAX_VALUE)) ); copyrightPane.addTab("Version info", jPanel2); copyrightTextPane.setEditable(false); jScrollPane1.setViewportView(copyrightTextPane); org.jdesktop.layout.GroupLayout jPanel3Layout = new org.jdesktop.layout.GroupLayout(jPanel3); jPanel3.setLayout(jPanel3Layout); jPanel3Layout.setHorizontalGroup( jPanel3Layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING) .add(jScrollPane1, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, 400, Short.MAX_VALUE) ); jPanel3Layout.setVerticalGroup( jPanel3Layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING) .add(jScrollPane1, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, 267, Short.MAX_VALUE) ); copyrightPane.addTab("Copyright", jPanel3); org.jdesktop.layout.GroupLayout layout = new org.jdesktop.layout.GroupLayout(getContentPane()); getContentPane().setLayout(layout); layout.setHorizontalGroup( layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING) .add(org.jdesktop.layout.GroupLayout.TRAILING, copyrightPane, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, 405, Short.MAX_VALUE) ); layout.setVerticalGroup( layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING) .add(copyrightPane, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, 295, Short.MAX_VALUE) ); pack(); }// </editor-fold>//GEN-END:initComponents |
.addContainerGap(260, Short.MAX_VALUE)) | .addContainerGap(231, Short.MAX_VALUE)) | private void initComponents() { copyrightPane = new javax.swing.JTabbedPane(); jPanel1 = new javax.swing.JPanel(); splashLabel = new javax.swing.JLabel(); jPanel2 = new javax.swing.JPanel(); jLabel1 = new javax.swing.JLabel(); jLabel2 = new javax.swing.JLabel(); jLabel3 = new javax.swing.JLabel(); jLabel4 = new javax.swing.JLabel(); jLabel5 = new javax.swing.JLabel(); versionLabel = new javax.swing.JLabel(); svnrevLabel = new javax.swing.JLabel(); svnbranchLabel = new javax.swing.JLabel(); buildTimeLabel = new javax.swing.JLabel(); builderLabel = new javax.swing.JLabel(); jPanel3 = new javax.swing.JPanel(); jScrollPane1 = new javax.swing.JScrollPane(); copyrightTextPane = new javax.swing.JTextPane(); setDefaultCloseOperation(javax.swing.WindowConstants.DISPOSE_ON_CLOSE); setTitle("Photovault"); setResizable(false); addMouseListener(new java.awt.event.MouseAdapter() { public void mouseClicked(java.awt.event.MouseEvent evt) { formMouseClicked(evt); } }); copyrightPane.setOpaque(true); copyrightPane.addAncestorListener(new javax.swing.event.AncestorListener() { public void ancestorMoved(javax.swing.event.AncestorEvent evt) { } public void ancestorAdded(javax.swing.event.AncestorEvent evt) { copyrightPaneAncestorAdded(evt); } public void ancestorRemoved(javax.swing.event.AncestorEvent evt) { } }); splashLabel.setText("jLabel1"); splashLabel.addMouseListener(new java.awt.event.MouseAdapter() { public void mouseClicked(java.awt.event.MouseEvent evt) { formMouseClicked(evt); } }); org.jdesktop.layout.GroupLayout jPanel1Layout = new org.jdesktop.layout.GroupLayout(jPanel1); jPanel1.setLayout(jPanel1Layout); jPanel1Layout.setHorizontalGroup( jPanel1Layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING) .add(splashLabel, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, 400, Short.MAX_VALUE) ); jPanel1Layout.setVerticalGroup( jPanel1Layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING) .add(splashLabel, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, 267, Short.MAX_VALUE) ); copyrightPane.addTab("Photovault", jPanel1); jLabel1.setText("Version:"); jLabel2.setText("SVN revision:"); jLabel3.setText("SVN branch:"); jLabel4.setText("Build time:"); jLabel5.setText("Built by:"); versionLabel.setText("jLabel6"); svnrevLabel.setText("jLabel6"); svnbranchLabel.setText("jLabel6"); buildTimeLabel.setText("jLabel6"); builderLabel.setText("jLabel6"); org.jdesktop.layout.GroupLayout jPanel2Layout = new org.jdesktop.layout.GroupLayout(jPanel2); jPanel2.setLayout(jPanel2Layout); jPanel2Layout.setHorizontalGroup( jPanel2Layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING) .add(jPanel2Layout.createSequentialGroup() .add(37, 37, 37) .add(jPanel2Layout.createParallelGroup(org.jdesktop.layout.GroupLayout.TRAILING) .add(jLabel5) .add(jLabel4) .add(jLabel3) .add(jLabel2) .add(jLabel1)) .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED) .add(jPanel2Layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING) .add(versionLabel) .add(svnrevLabel) .add(svnbranchLabel) .add(buildTimeLabel) .add(builderLabel)) .addContainerGap(260, Short.MAX_VALUE)) ); jPanel2Layout.setVerticalGroup( jPanel2Layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING) .add(jPanel2Layout.createSequentialGroup() .addContainerGap() .add(jPanel2Layout.createParallelGroup(org.jdesktop.layout.GroupLayout.BASELINE) .add(jLabel1) .add(versionLabel)) .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED) .add(jPanel2Layout.createParallelGroup(org.jdesktop.layout.GroupLayout.BASELINE) .add(jLabel2) .add(svnrevLabel)) .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED) .add(jPanel2Layout.createParallelGroup(org.jdesktop.layout.GroupLayout.BASELINE) .add(jLabel3) .add(svnbranchLabel)) .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED) .add(jPanel2Layout.createParallelGroup(org.jdesktop.layout.GroupLayout.BASELINE) .add(jLabel4) .add(buildTimeLabel)) .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED) .add(jPanel2Layout.createParallelGroup(org.jdesktop.layout.GroupLayout.BASELINE) .add(jLabel5) .add(builderLabel)) .addContainerGap(162, Short.MAX_VALUE)) ); copyrightPane.addTab("Version info", jPanel2); copyrightTextPane.setEditable(false); jScrollPane1.setViewportView(copyrightTextPane); org.jdesktop.layout.GroupLayout jPanel3Layout = new org.jdesktop.layout.GroupLayout(jPanel3); jPanel3.setLayout(jPanel3Layout); jPanel3Layout.setHorizontalGroup( jPanel3Layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING) .add(jScrollPane1, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, 400, Short.MAX_VALUE) ); jPanel3Layout.setVerticalGroup( jPanel3Layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING) .add(jScrollPane1, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, 267, Short.MAX_VALUE) ); copyrightPane.addTab("Copyright", jPanel3); org.jdesktop.layout.GroupLayout layout = new org.jdesktop.layout.GroupLayout(getContentPane()); getContentPane().setLayout(layout); layout.setHorizontalGroup( layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING) .add(org.jdesktop.layout.GroupLayout.TRAILING, copyrightPane, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, 405, Short.MAX_VALUE) ); layout.setVerticalGroup( layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING) .add(copyrightPane, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, 295, Short.MAX_VALUE) ); pack(); }// </editor-fold>//GEN-END:initComponents |
.addContainerGap(162, Short.MAX_VALUE)) | .addContainerGap(157, Short.MAX_VALUE)) | private void initComponents() { copyrightPane = new javax.swing.JTabbedPane(); jPanel1 = new javax.swing.JPanel(); splashLabel = new javax.swing.JLabel(); jPanel2 = new javax.swing.JPanel(); jLabel1 = new javax.swing.JLabel(); jLabel2 = new javax.swing.JLabel(); jLabel3 = new javax.swing.JLabel(); jLabel4 = new javax.swing.JLabel(); jLabel5 = new javax.swing.JLabel(); versionLabel = new javax.swing.JLabel(); svnrevLabel = new javax.swing.JLabel(); svnbranchLabel = new javax.swing.JLabel(); buildTimeLabel = new javax.swing.JLabel(); builderLabel = new javax.swing.JLabel(); jPanel3 = new javax.swing.JPanel(); jScrollPane1 = new javax.swing.JScrollPane(); copyrightTextPane = new javax.swing.JTextPane(); setDefaultCloseOperation(javax.swing.WindowConstants.DISPOSE_ON_CLOSE); setTitle("Photovault"); setResizable(false); addMouseListener(new java.awt.event.MouseAdapter() { public void mouseClicked(java.awt.event.MouseEvent evt) { formMouseClicked(evt); } }); copyrightPane.setOpaque(true); copyrightPane.addAncestorListener(new javax.swing.event.AncestorListener() { public void ancestorMoved(javax.swing.event.AncestorEvent evt) { } public void ancestorAdded(javax.swing.event.AncestorEvent evt) { copyrightPaneAncestorAdded(evt); } public void ancestorRemoved(javax.swing.event.AncestorEvent evt) { } }); splashLabel.setText("jLabel1"); splashLabel.addMouseListener(new java.awt.event.MouseAdapter() { public void mouseClicked(java.awt.event.MouseEvent evt) { formMouseClicked(evt); } }); org.jdesktop.layout.GroupLayout jPanel1Layout = new org.jdesktop.layout.GroupLayout(jPanel1); jPanel1.setLayout(jPanel1Layout); jPanel1Layout.setHorizontalGroup( jPanel1Layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING) .add(splashLabel, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, 400, Short.MAX_VALUE) ); jPanel1Layout.setVerticalGroup( jPanel1Layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING) .add(splashLabel, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, 267, Short.MAX_VALUE) ); copyrightPane.addTab("Photovault", jPanel1); jLabel1.setText("Version:"); jLabel2.setText("SVN revision:"); jLabel3.setText("SVN branch:"); jLabel4.setText("Build time:"); jLabel5.setText("Built by:"); versionLabel.setText("jLabel6"); svnrevLabel.setText("jLabel6"); svnbranchLabel.setText("jLabel6"); buildTimeLabel.setText("jLabel6"); builderLabel.setText("jLabel6"); org.jdesktop.layout.GroupLayout jPanel2Layout = new org.jdesktop.layout.GroupLayout(jPanel2); jPanel2.setLayout(jPanel2Layout); jPanel2Layout.setHorizontalGroup( jPanel2Layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING) .add(jPanel2Layout.createSequentialGroup() .add(37, 37, 37) .add(jPanel2Layout.createParallelGroup(org.jdesktop.layout.GroupLayout.TRAILING) .add(jLabel5) .add(jLabel4) .add(jLabel3) .add(jLabel2) .add(jLabel1)) .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED) .add(jPanel2Layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING) .add(versionLabel) .add(svnrevLabel) .add(svnbranchLabel) .add(buildTimeLabel) .add(builderLabel)) .addContainerGap(260, Short.MAX_VALUE)) ); jPanel2Layout.setVerticalGroup( jPanel2Layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING) .add(jPanel2Layout.createSequentialGroup() .addContainerGap() .add(jPanel2Layout.createParallelGroup(org.jdesktop.layout.GroupLayout.BASELINE) .add(jLabel1) .add(versionLabel)) .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED) .add(jPanel2Layout.createParallelGroup(org.jdesktop.layout.GroupLayout.BASELINE) .add(jLabel2) .add(svnrevLabel)) .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED) .add(jPanel2Layout.createParallelGroup(org.jdesktop.layout.GroupLayout.BASELINE) .add(jLabel3) .add(svnbranchLabel)) .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED) .add(jPanel2Layout.createParallelGroup(org.jdesktop.layout.GroupLayout.BASELINE) .add(jLabel4) .add(buildTimeLabel)) .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED) .add(jPanel2Layout.createParallelGroup(org.jdesktop.layout.GroupLayout.BASELINE) .add(jLabel5) .add(builderLabel)) .addContainerGap(162, Short.MAX_VALUE)) ); copyrightPane.addTab("Version info", jPanel2); copyrightTextPane.setEditable(false); jScrollPane1.setViewportView(copyrightTextPane); org.jdesktop.layout.GroupLayout jPanel3Layout = new org.jdesktop.layout.GroupLayout(jPanel3); jPanel3.setLayout(jPanel3Layout); jPanel3Layout.setHorizontalGroup( jPanel3Layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING) .add(jScrollPane1, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, 400, Short.MAX_VALUE) ); jPanel3Layout.setVerticalGroup( jPanel3Layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING) .add(jScrollPane1, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, 267, Short.MAX_VALUE) ); copyrightPane.addTab("Copyright", jPanel3); org.jdesktop.layout.GroupLayout layout = new org.jdesktop.layout.GroupLayout(getContentPane()); getContentPane().setLayout(layout); layout.setHorizontalGroup( layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING) .add(org.jdesktop.layout.GroupLayout.TRAILING, copyrightPane, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, 405, Short.MAX_VALUE) ); layout.setVerticalGroup( layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING) .add(copyrightPane, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, 295, Short.MAX_VALUE) ); pack(); }// </editor-fold>//GEN-END:initComponents |
.add(jScrollPane1, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, 267, Short.MAX_VALUE) | .add(jScrollPane1, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, 268, Short.MAX_VALUE) | private void initComponents() { copyrightPane = new javax.swing.JTabbedPane(); jPanel1 = new javax.swing.JPanel(); splashLabel = new javax.swing.JLabel(); jPanel2 = new javax.swing.JPanel(); jLabel1 = new javax.swing.JLabel(); jLabel2 = new javax.swing.JLabel(); jLabel3 = new javax.swing.JLabel(); jLabel4 = new javax.swing.JLabel(); jLabel5 = new javax.swing.JLabel(); versionLabel = new javax.swing.JLabel(); svnrevLabel = new javax.swing.JLabel(); svnbranchLabel = new javax.swing.JLabel(); buildTimeLabel = new javax.swing.JLabel(); builderLabel = new javax.swing.JLabel(); jPanel3 = new javax.swing.JPanel(); jScrollPane1 = new javax.swing.JScrollPane(); copyrightTextPane = new javax.swing.JTextPane(); setDefaultCloseOperation(javax.swing.WindowConstants.DISPOSE_ON_CLOSE); setTitle("Photovault"); setResizable(false); addMouseListener(new java.awt.event.MouseAdapter() { public void mouseClicked(java.awt.event.MouseEvent evt) { formMouseClicked(evt); } }); copyrightPane.setOpaque(true); copyrightPane.addAncestorListener(new javax.swing.event.AncestorListener() { public void ancestorMoved(javax.swing.event.AncestorEvent evt) { } public void ancestorAdded(javax.swing.event.AncestorEvent evt) { copyrightPaneAncestorAdded(evt); } public void ancestorRemoved(javax.swing.event.AncestorEvent evt) { } }); splashLabel.setText("jLabel1"); splashLabel.addMouseListener(new java.awt.event.MouseAdapter() { public void mouseClicked(java.awt.event.MouseEvent evt) { formMouseClicked(evt); } }); org.jdesktop.layout.GroupLayout jPanel1Layout = new org.jdesktop.layout.GroupLayout(jPanel1); jPanel1.setLayout(jPanel1Layout); jPanel1Layout.setHorizontalGroup( jPanel1Layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING) .add(splashLabel, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, 400, Short.MAX_VALUE) ); jPanel1Layout.setVerticalGroup( jPanel1Layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING) .add(splashLabel, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, 267, Short.MAX_VALUE) ); copyrightPane.addTab("Photovault", jPanel1); jLabel1.setText("Version:"); jLabel2.setText("SVN revision:"); jLabel3.setText("SVN branch:"); jLabel4.setText("Build time:"); jLabel5.setText("Built by:"); versionLabel.setText("jLabel6"); svnrevLabel.setText("jLabel6"); svnbranchLabel.setText("jLabel6"); buildTimeLabel.setText("jLabel6"); builderLabel.setText("jLabel6"); org.jdesktop.layout.GroupLayout jPanel2Layout = new org.jdesktop.layout.GroupLayout(jPanel2); jPanel2.setLayout(jPanel2Layout); jPanel2Layout.setHorizontalGroup( jPanel2Layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING) .add(jPanel2Layout.createSequentialGroup() .add(37, 37, 37) .add(jPanel2Layout.createParallelGroup(org.jdesktop.layout.GroupLayout.TRAILING) .add(jLabel5) .add(jLabel4) .add(jLabel3) .add(jLabel2) .add(jLabel1)) .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED) .add(jPanel2Layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING) .add(versionLabel) .add(svnrevLabel) .add(svnbranchLabel) .add(buildTimeLabel) .add(builderLabel)) .addContainerGap(260, Short.MAX_VALUE)) ); jPanel2Layout.setVerticalGroup( jPanel2Layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING) .add(jPanel2Layout.createSequentialGroup() .addContainerGap() .add(jPanel2Layout.createParallelGroup(org.jdesktop.layout.GroupLayout.BASELINE) .add(jLabel1) .add(versionLabel)) .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED) .add(jPanel2Layout.createParallelGroup(org.jdesktop.layout.GroupLayout.BASELINE) .add(jLabel2) .add(svnrevLabel)) .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED) .add(jPanel2Layout.createParallelGroup(org.jdesktop.layout.GroupLayout.BASELINE) .add(jLabel3) .add(svnbranchLabel)) .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED) .add(jPanel2Layout.createParallelGroup(org.jdesktop.layout.GroupLayout.BASELINE) .add(jLabel4) .add(buildTimeLabel)) .addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED) .add(jPanel2Layout.createParallelGroup(org.jdesktop.layout.GroupLayout.BASELINE) .add(jLabel5) .add(builderLabel)) .addContainerGap(162, Short.MAX_VALUE)) ); copyrightPane.addTab("Version info", jPanel2); copyrightTextPane.setEditable(false); jScrollPane1.setViewportView(copyrightTextPane); org.jdesktop.layout.GroupLayout jPanel3Layout = new org.jdesktop.layout.GroupLayout(jPanel3); jPanel3.setLayout(jPanel3Layout); jPanel3Layout.setHorizontalGroup( jPanel3Layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING) .add(jScrollPane1, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, 400, Short.MAX_VALUE) ); jPanel3Layout.setVerticalGroup( jPanel3Layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING) .add(jScrollPane1, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, 267, Short.MAX_VALUE) ); copyrightPane.addTab("Copyright", jPanel3); org.jdesktop.layout.GroupLayout layout = new org.jdesktop.layout.GroupLayout(getContentPane()); getContentPane().setLayout(layout); layout.setHorizontalGroup( layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING) .add(org.jdesktop.layout.GroupLayout.TRAILING, copyrightPane, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, 405, Short.MAX_VALUE) ); layout.setVerticalGroup( layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING) .add(copyrightPane, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, 295, Short.MAX_VALUE) ); pack(); }// </editor-fold>//GEN-END:initComponents |
versionLabel.setText( prop.getProperty( "build.version", "unknown" ) ); | String version = prop.getProperty( "build.version", "unknown" ); String versionTag = prop.getProperty( "build.version_tag", "unknown" ); versionLabel.setText( version + " (" + versionTag + ")" ); | void setupInfo() { URL buildPropertyURL = AboutDlg.class.getClassLoader().getResource( "buildinfo.properties"); Properties prop = new Properties(); try { InputStream is = buildPropertyURL.openStream(); prop.load( is ); } catch (IOException e ) { // Cannot read the properties for some reason. // Do nothing, use the default values instead. } svnrevLabel.setText( prop.getProperty( "svn.revision", "unknown" ) ); svnbranchLabel.setText( prop.getProperty( "svn.info.url", "unknown" ) ); buildTimeLabel.setText( prop.getProperty( "build.time", "unknown" ) ); builderLabel.setText( prop.getProperty( "build.user", "unknown" ) ); versionLabel.setText( prop.getProperty( "build.version", "unknown" ) ); builderLabel.setText( prop.getProperty( "build.user", "unknown" ) ); // Set up the splash screen image URL splashImageURL = AboutDlg.class.getClassLoader().getResource( "splash.jpg" ); Icon splash = new ImageIcon( splashImageURL ); splashLabel.setIcon( splash ); splashLabel.setText( null ); // Set the copyright text URL copyrightTextURL = AboutDlg.class.getClassLoader().getResource( "copyright.html" ); try { copyrightTextPane.setPage( copyrightTextURL ); } catch ( IOException e ) {} } |
table1.changeColumnIndex(table1.getColumnIndex(c1), 2); | table1.changeColumnIndex(table1.getColumnIndex(c1), 2, false); | public void testFireDbChildrenInserted() throws Exception { SQLTable table1 = db.getTableByName("REGRESSION_TEST1"); SQLColumn c1 = table1.getColumn(0); Folder folder = table1.getColumnsFolder(); TestSQLObjectListener test1 = new TestSQLObjectListener(); folder.addSQLObjectListener(test1); TestSQLObjectListener test2 = new TestSQLObjectListener(); folder.addSQLObjectListener(test2); assertEquals(test1.getInsertedCount(), 0); assertEquals(test1.getRemovedCount(), 0); assertEquals(test1.getChangedCount(), 0); assertEquals(test1.getStructureChangedCount(), 0); assertEquals(test2.getInsertedCount(), 0); assertEquals(test2.getRemovedCount(), 0); assertEquals(test2.getChangedCount(), 0); assertEquals(test2.getStructureChangedCount(), 0); SQLColumn tmpCol = new SQLColumn(); table1.addColumn(tmpCol); table1.changeColumnIndex(table1.getColumnIndex(c1), 2); assertEquals(test1.getInsertedCount(), 2); assertEquals(test1.getRemovedCount(), 1); assertEquals(test1.getChangedCount(), 0); assertEquals(test1.getStructureChangedCount(), 0); assertEquals(test2.getInsertedCount(), 2); assertEquals(test2.getRemovedCount(), 1); assertEquals(test2.getChangedCount(), 0); assertEquals(test2.getStructureChangedCount(), 0); folder.removeSQLObjectListener(test1); table1.changeColumnIndex(table1.getColumnIndex(c1), 1); assertEquals(test1.getInsertedCount(), 2); assertEquals(test1.getRemovedCount(), 1); assertEquals(test1.getChangedCount(), 0); assertEquals(test1.getStructureChangedCount(), 0); assertEquals(test2.getInsertedCount(), 3); assertEquals(test2.getRemovedCount(), 2); assertEquals(test2.getChangedCount(), 0); assertEquals(test2.getStructureChangedCount(), 0); table1.removeColumn(tmpCol); assertEquals(test2.getInsertedCount(), 3); assertEquals(test2.getRemovedCount(), 3); assertEquals(test2.getChangedCount(), 0); assertEquals(test2.getStructureChangedCount(), 0); } |
table1.changeColumnIndex(table1.getColumnIndex(c1), 1); | table1.changeColumnIndex(table1.getColumnIndex(c1), 1, false); | public void testFireDbChildrenInserted() throws Exception { SQLTable table1 = db.getTableByName("REGRESSION_TEST1"); SQLColumn c1 = table1.getColumn(0); Folder folder = table1.getColumnsFolder(); TestSQLObjectListener test1 = new TestSQLObjectListener(); folder.addSQLObjectListener(test1); TestSQLObjectListener test2 = new TestSQLObjectListener(); folder.addSQLObjectListener(test2); assertEquals(test1.getInsertedCount(), 0); assertEquals(test1.getRemovedCount(), 0); assertEquals(test1.getChangedCount(), 0); assertEquals(test1.getStructureChangedCount(), 0); assertEquals(test2.getInsertedCount(), 0); assertEquals(test2.getRemovedCount(), 0); assertEquals(test2.getChangedCount(), 0); assertEquals(test2.getStructureChangedCount(), 0); SQLColumn tmpCol = new SQLColumn(); table1.addColumn(tmpCol); table1.changeColumnIndex(table1.getColumnIndex(c1), 2); assertEquals(test1.getInsertedCount(), 2); assertEquals(test1.getRemovedCount(), 1); assertEquals(test1.getChangedCount(), 0); assertEquals(test1.getStructureChangedCount(), 0); assertEquals(test2.getInsertedCount(), 2); assertEquals(test2.getRemovedCount(), 1); assertEquals(test2.getChangedCount(), 0); assertEquals(test2.getStructureChangedCount(), 0); folder.removeSQLObjectListener(test1); table1.changeColumnIndex(table1.getColumnIndex(c1), 1); assertEquals(test1.getInsertedCount(), 2); assertEquals(test1.getRemovedCount(), 1); assertEquals(test1.getChangedCount(), 0); assertEquals(test1.getStructureChangedCount(), 0); assertEquals(test2.getInsertedCount(), 3); assertEquals(test2.getRemovedCount(), 2); assertEquals(test2.getChangedCount(), 0); assertEquals(test2.getStructureChangedCount(), 0); table1.removeColumn(tmpCol); assertEquals(test2.getInsertedCount(), 3); assertEquals(test2.getRemovedCount(), 3); assertEquals(test2.getChangedCount(), 0); assertEquals(test2.getStructureChangedCount(), 0); } |
for (int i = 0; i < model.getChildCount(); i++) { model.getChild(i).removeSQLObjectListener(tableListModel); | for (int i = 0; i < model.getColumnsFolder().getChildCount(); i++) { model.getColumnsFolder().getChild(i).removeSQLObjectListener(tableListModel); | protected void cleanup() { try { for (int i = 0; i < model.getChildCount(); i++) { model.getChild(i).removeSQLObjectListener(tableListModel); } } catch (ArchitectException e) { logger.error("Caught exception removing treemodel from column listener list"); } model.removeSQLObjectListener(tableListModel); } |
model.removeSQLObjectListener(tableListModel); | model.getColumnsFolder().removeSQLObjectListener(tableListModel); | protected void cleanup() { try { for (int i = 0; i < model.getChildCount(); i++) { model.getChild(i).removeSQLObjectListener(tableListModel); } } catch (ArchitectException e) { logger.error("Caught exception removing treemodel from column listener list"); } model.removeSQLObjectListener(tableListModel); } |
boolean addToPK = false; int pkSize = getPkSize(); if (getColumns().size() > 0 && pos < pkSize) { addToPK = true; normalizePrimaryKey(); for (int i = pos; i < pkSize; i++) { ((SQLColumn) getColumns().get(i)).primaryKeySeq = new Integer(i + 1); } } col.setParent(null); if (addToPK) { col.nullable = DatabaseMetaData.columnNoNulls; col.primaryKeySeq = new Integer(pos); } else { col.primaryKeySeq = null; | if (isMagicEnabled()) { boolean addToPK = false; int pkSize = getPkSize(); if (getColumns().size() > 0 && pos < pkSize) { addToPK = true; normalizePrimaryKey(); for (int i = pos; i < pkSize; i++) { ((SQLColumn) getColumns().get(i)).primaryKeySeq = new Integer(i + 1); } } col.setParent(null); if (addToPK) { col.nullable = DatabaseMetaData.columnNoNulls; col.primaryKeySeq = new Integer(pos); } else { col.primaryKeySeq = null; } | private void addColumnImpl(int pos, SQLColumn col) throws ArchitectException { if (getColumnIndex(col) != -1) { col.addReference(); return; } boolean addToPK = false; int pkSize = getPkSize(); if (getColumns().size() > 0 && pos < pkSize) { addToPK = true; normalizePrimaryKey(); for (int i = pos; i < pkSize; i++) { ((SQLColumn) getColumns().get(i)).primaryKeySeq = new Integer(i + 1); } } col.setParent(null); if (addToPK) { col.nullable = DatabaseMetaData.columnNoNulls; col.primaryKeySeq = new Integer(pos); } else { col.primaryKeySeq = null; } columnsFolder.addChild(pos, col); } |
SQLColumn col = (SQLColumn) columnsFolder.children.remove(oldIdx); columnsFolder.fireDbChildRemoved(oldIdx, col); columnsFolder.children.add(newIdx, col); if (putInPK) { col.primaryKeySeq = new Integer(1); } else { col.primaryKeySeq = null; } normalizePrimaryKey(); columnsFolder.fireDbChildInserted(newIdx, col); | try { startCompoundEdit("Changing column index"); SQLColumn col = (SQLColumn) columnsFolder.children.get(oldIdx); Integer oldPkSeq = col.primaryKeySeq; Integer interimPkSeq; if (putInPK) { interimPkSeq = new Integer(1); } else { interimPkSeq = null; } col.primaryKeySeq = interimPkSeq; col.fireDbObjectChanged("primaryKeySeq", oldPkSeq, interimPkSeq); columnsFolder.children.remove(oldIdx); columnsFolder.fireDbChildRemoved(oldIdx, col); columnsFolder.children.add(newIdx, col); columnsFolder.fireDbChildInserted(newIdx, col); normalizePrimaryKey(); } finally { endCompoundEdit("Changing column index"); } | public void changeColumnIndex(int oldIdx, int newIdx, boolean putInPK) throws ArchitectException { // remove and add the column directly, then manually fire the event. // This is necessary because the relationships prevent deletion of locked keys. SQLColumn col = (SQLColumn) columnsFolder.children.remove(oldIdx); columnsFolder.fireDbChildRemoved(oldIdx, col); columnsFolder.children.add(newIdx, col); if (putInPK) { col.primaryKeySeq = new Integer(1); // will get sane value when normalized } else { col.primaryKeySeq = null; } normalizePrimaryKey(); columnsFolder.fireDbChildInserted(newIdx, col); } |
String oldName = getName(); try { startCompoundEdit("Table Name Change"); super.setName(argName); if (primaryKeyName == null || primaryKeyName.equals("") || primaryKeyName.equals(oldName+"_pk")) { setPrimaryKeyName( getName()+"_pk"); } } finally { endCompoundEdit("Ending table name compound edit"); } | if (!isMagicEnabled()) { super.setName(argName); } else try { String oldName = getName(); startCompoundEdit("Table Name Change"); super.setName(argName); if (primaryKeyName == null || primaryKeyName.equals("") || primaryKeyName.equals(oldName+"_pk")) { setPrimaryKeyName( getName()+"_pk"); } } finally { endCompoundEdit("Ending table name compound edit"); } | public void setName(String argName) { String oldName = getName(); try { startCompoundEdit("Table Name Change"); super.setName(argName); if (primaryKeyName == null || primaryKeyName.equals("") || primaryKeyName.equals(oldName+"_pk")) { setPrimaryKeyName( getName()+"_pk"); } } finally { endCompoundEdit("Ending table name compound edit"); } } |
if (l == null) throw new NullPointerException("You can't add a null listener"); | public void addSQLObjectListener(SQLObjectListener l) { if (getSQLObjectListeners().contains(l)) { if (logger.isDebugEnabled()) { logger.debug("NOT Adding duplicate listener "+l+" to SQLObject "+this); } return; } getSQLObjectListeners().add(l); } |
|
for(Enumeration enum=request.getAttributeNames(); enum.hasMoreElements();){ String attribute = (String)enum.nextElement(); | for(Enumeration en=request.getAttributeNames(); en.hasMoreElements();){ String attribute = (String)en.nextElement(); | private ActionForward handleDebugMode(HttpServletRequest request, HttpServletResponse response, ActionForward resultForward) throws IOException { if("true".equals(request.getParameter("debug.xml"))){ response.setContentType("text/xml"); XMLEncoder encoder = new XMLEncoder(response.getOutputStream()); for(Enumeration enum=request.getAttributeNames(); enum.hasMoreElements();){ String attribute = (String)enum.nextElement(); Object attrValue = request.getAttribute(attribute); encoder.writeObject(attribute); encoder.writeObject(attrValue); } encoder.writeObject(request); encoder.close(); resultForward = null; } |
return resultForward; } | private ActionForward handleDebugMode(HttpServletRequest request, HttpServletResponse response, ActionForward resultForward) throws IOException { if("true".equals(request.getParameter("debug.xml"))){ response.setContentType("text/xml"); XMLEncoder encoder = new XMLEncoder(response.getOutputStream()); for(Enumeration enum=request.getAttributeNames(); enum.hasMoreElements();){ String attribute = (String)enum.nextElement(); Object attrValue = request.getAttribute(attribute); encoder.writeObject(attribute); encoder.writeObject(attrValue); } encoder.writeObject(request); encoder.close(); resultForward = null; } |
|
try { Collection selectedPhotos = view.getSelection(); if ( selectedPhotos.size() > 1 ) { int n = JOptionPane.showConfirmDialog( parentFrame, "You have selected " + selectedPhotos.size() + " photos\n" + "Are you sure that you want to\ndisplay all of them at once?", "Open multiple photos", JOptionPane.YES_NO_OPTION ); if ( n != JOptionPane.YES_OPTION ) { return; | Collection selectedPhotos = view.getSelection(); if ( selectedPhotos.size() > 1 ) { int n = JOptionPane.showConfirmDialog( parentFrame, "You have selected " + selectedPhotos.size() + " photos\n" + "Are you sure that you want to\ndisplay all of them at once?", "Open multiple photos", JOptionPane.YES_NO_OPTION ); if ( n != JOptionPane.YES_OPTION ) { return; } } Cursor oldCursor = c.getCursor(); c.setCursor( new Cursor( Cursor.WAIT_CURSOR ) ); Iterator iter = selectedPhotos.iterator(); JAIPhotoViewer viewer = null; while ( iter.hasNext() ) { try { viewer = null; PhotoInfo photo = (PhotoInfo) iter.next(); JFrame frame = new JFrame( "Photo" ); viewer = new JAIPhotoViewer(); frame.getContentPane().add( viewer, BorderLayout.CENTER ); frame.setDefaultCloseOperation( JFrame.DISPOSE_ON_CLOSE ); final JAIPhotoViewer pv = viewer; frame.addWindowListener( new WindowAdapter() { public void windowClosing( WindowEvent e ) { pv.setPhoto( null ); } } ); viewer.setPhoto( photo ); frame.pack(); frame.setVisible( true ); } catch ( Throwable e ) { log.warn( "Error while trying to show a photo: " + e ); e.printStackTrace(); if ( viewer != null ) { viewer.setPhoto( null ); | public void actionPerformed( ActionEvent ev ) { Frame parentFrame = null; Container c = view.getTopLevelAncestor(); if ( c instanceof Frame ) { parentFrame = (Frame) c; } try { Collection selectedPhotos = view.getSelection(); if ( selectedPhotos.size() > 1 ) { // If user wants to open many photos at once ask for confirmation // Try to find the frame in which this component is in int n = JOptionPane.showConfirmDialog( parentFrame, "You have selected " + selectedPhotos.size() + " photos\n" + "Are you sure that you want to\ndisplay all of them at once?", "Open multiple photos", JOptionPane.YES_NO_OPTION ); if ( n != JOptionPane.YES_OPTION ) { return; } } Cursor oldCursor = c.getCursor(); c.setCursor( new Cursor( Cursor.WAIT_CURSOR ) ); Iterator iter = selectedPhotos.iterator(); while ( iter.hasNext() ) { PhotoInfo photo = (PhotoInfo) iter.next(); JFrame frame = new JFrame( "Photo" ); final JAIPhotoViewer viewer = new JAIPhotoViewer(); frame.getContentPane().add( viewer, BorderLayout.CENTER ); frame.setDefaultCloseOperation( JFrame.DISPOSE_ON_CLOSE ); // This is a WAR for a memory management problem. For // some reason the frame and objects owned by it seem // not to be garbage collected. So we free the large // image buffers to avoid massive memory leak. frame.addWindowListener( new WindowAdapter() { public void windowClosing( WindowEvent e ) { viewer.setPhoto( null ); } } ); viewer.setPhoto( photo ); frame.pack(); frame.setVisible( true ); } c.setCursor( oldCursor ); } catch ( Throwable e ) { System.err.println( "Out of memory error" ); log.warn( e ); e.printStackTrace(); } } |
Cursor oldCursor = c.getCursor(); c.setCursor( new Cursor( Cursor.WAIT_CURSOR ) ); Iterator iter = selectedPhotos.iterator(); while ( iter.hasNext() ) { PhotoInfo photo = (PhotoInfo) iter.next(); JFrame frame = new JFrame( "Photo" ); final JAIPhotoViewer viewer = new JAIPhotoViewer(); frame.getContentPane().add( viewer, BorderLayout.CENTER ); frame.setDefaultCloseOperation( JFrame.DISPOSE_ON_CLOSE ); frame.addWindowListener( new WindowAdapter() { public void windowClosing( WindowEvent e ) { viewer.setPhoto( null ); } } ); viewer.setPhoto( photo ); frame.pack(); frame.setVisible( true ); } c.setCursor( oldCursor ); } catch ( Throwable e ) { System.err.println( "Out of memory error" ); log.warn( e ); e.printStackTrace(); } | c.setCursor( oldCursor ); | public void actionPerformed( ActionEvent ev ) { Frame parentFrame = null; Container c = view.getTopLevelAncestor(); if ( c instanceof Frame ) { parentFrame = (Frame) c; } try { Collection selectedPhotos = view.getSelection(); if ( selectedPhotos.size() > 1 ) { // If user wants to open many photos at once ask for confirmation // Try to find the frame in which this component is in int n = JOptionPane.showConfirmDialog( parentFrame, "You have selected " + selectedPhotos.size() + " photos\n" + "Are you sure that you want to\ndisplay all of them at once?", "Open multiple photos", JOptionPane.YES_NO_OPTION ); if ( n != JOptionPane.YES_OPTION ) { return; } } Cursor oldCursor = c.getCursor(); c.setCursor( new Cursor( Cursor.WAIT_CURSOR ) ); Iterator iter = selectedPhotos.iterator(); while ( iter.hasNext() ) { PhotoInfo photo = (PhotoInfo) iter.next(); JFrame frame = new JFrame( "Photo" ); final JAIPhotoViewer viewer = new JAIPhotoViewer(); frame.getContentPane().add( viewer, BorderLayout.CENTER ); frame.setDefaultCloseOperation( JFrame.DISPOSE_ON_CLOSE ); // This is a WAR for a memory management problem. For // some reason the frame and objects owned by it seem // not to be garbage collected. So we free the large // image buffers to avoid massive memory leak. frame.addWindowListener( new WindowAdapter() { public void windowClosing( WindowEvent e ) { viewer.setPhoto( null ); } } ); viewer.setPhoto( photo ); frame.pack(); frame.setVisible( true ); } c.setCursor( oldCursor ); } catch ( Throwable e ) { System.err.println( "Out of memory error" ); log.warn( e ); e.printStackTrace(); } } |
viewer.setPhoto( null ); } | pv.setPhoto( null ); } | public void windowClosing( WindowEvent e ) { viewer.setPhoto( null ); } |
headingJLabel.setBackground(new Color(117, 138, 155)); | headingJLabel.setBackground(new Color(117, 138, 155, 255)); | void addHeading(final String headingText) { if(null == headingJLabel) { headingJLabel = LabelFactory.create(headingText, UIConstants.DefaultFontBold); headingJLabel.setBackground(new Color(117, 138, 155)); headingJLabel.setForeground(Color.WHITE); headingJLabel.setIcon(getHeadingIcon()); headingJLabel.setOpaque(true); } // h: 24 px // x indent: 29 px final GridBagConstraints c = new GridBagConstraints(); c.anchor = GridBagConstraints.WEST; c.gridx = 0; c.weightx = 1.0; c.fill = GridBagConstraints.HORIZONTAL; avatar.add(headingJLabel, c.clone()); } |
private Fixture(final ArtifactModel aModel, final JabberId closedBy, | private Fixture(final ContainerModel cModel, final JabberId closedBy, | private Fixture(final ArtifactModel aModel, final JabberId closedBy, final Calendar closedOn, final InternalContainerModel cInternalModel, final Long containerId, final Integer eTeamSize) { this.aModel = aModel; this.closedBy = closedBy; this.closedOn = closedOn; this.cInternalModel = cInternalModel; this.containerId = containerId; this.eTeamSize = eTeamSize; } |
this.aModel = aModel; | this.cModel = cModel; | private Fixture(final ArtifactModel aModel, final JabberId closedBy, final Calendar closedOn, final InternalContainerModel cInternalModel, final Long containerId, final Integer eTeamSize) { this.aModel = aModel; this.closedBy = closedBy; this.closedOn = closedOn; this.cInternalModel = cInternalModel; this.containerId = containerId; this.eTeamSize = eTeamSize; } |
datum = new Fixture(aModel, jUnitX.getJabberId(), currentDateTime(), | datum = new Fixture(cModel, jUnitX.getJabberId(), currentDateTime(), | protected void setUp() throws Exception { super.setUp(); login(); final ContainerModel cModel = getContainerModel(); final ArtifactModel aModel = getArtifactModel(); final ModelTestUser jUnitX = ModelTestUser.getX(); final Container container = createContainer(NAME); final Document document = addDocument(container, getInputFiles()[0]); addTeam(container); modifyDocument(document); cModel.publish(container.getId()); aModel.sendKey(container.getId(), jUnitX.getJabberId()); datum = new Fixture(aModel, jUnitX.getJabberId(), currentDateTime(), getInternalContainerModel(), container.getId(), aModel.readTeam(container.getId()).size()); } |
aModel.readTeam(container.getId()).size()); | cModel.readTeam(container.getId()).size()); | protected void setUp() throws Exception { super.setUp(); login(); final ContainerModel cModel = getContainerModel(); final ArtifactModel aModel = getArtifactModel(); final ModelTestUser jUnitX = ModelTestUser.getX(); final Container container = createContainer(NAME); final Document document = addDocument(container, getInputFiles()[0]); addTeam(container); modifyDocument(document); cModel.publish(container.getId()); aModel.sendKey(container.getId(), jUnitX.getJabberId()); datum = new Fixture(aModel, jUnitX.getJabberId(), currentDateTime(), getInternalContainerModel(), container.getId(), aModel.readTeam(container.getId()).size()); } |
Set<User> team; | List<User> team; | public void testHandleClose() { Set<User> team; try { datum.cInternalModel.handleClose(datum.containerId, datum.closedBy, datum.closedOn); } catch(final ParityException px) { fail(createFailMessage(px)); } final Container container = datum.cInternalModel.read(datum.containerId); assertNotNull(NAME, container); assertEquals(NAME + " [CONTAINER STATE DOES NOT MATCH EXPECTATION]", container.getState(), ArtifactState.CLOSED); team = datum.aModel.readTeam(datum.containerId); assertNotNull(NAME, team); assertEquals(NAME + " [TEAM SIZE DOES NOT MATCH EXPECTATION]", datum.eTeamSize.intValue(), team.size()); } |
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