h4iku/coconut_java2006_preprocessed · Datasets at Hugging Face

pageFormat = job.defaultPage();

pageFormat = new PageFormat(); pageFormat.setPaper(new Paper()); pageFormat.getPaper().setImageableArea(50, 50, pageFormat.getWidth()-(50*2), pageFormat.getHeight()-(50*2));

public PrintPanel(PlayPen pp) { super(); setOpaque(true); setLayout(new BoxLayout(this, BoxLayout.X_AXIS)); this.pp = pp; add(new PrintPreviewPanel()); job = PrinterJob.getPrinterJob(); jobAttributes = new HashPrintRequestAttributeSet(); pageFormat = job.defaultPage(); JPanel formPanel = new JPanel(new FormLayout()); formPanel.add(new JLabel("Printer")); formPanel.add(printerBox = new JComboBox(PrinterJob.lookupPrintServices())); printerBox.setSelectedItem(getPreferredPrinter()); formPanel.add(new JLabel("Page Format")); String pf = paperToPrintable(pageFormat); formPanel.add(pageFormatLabel = new JLabel(pf.toString())); formPanel.add(new JLabel("Change Page Format")); formPanel.add(pageFormatButton = new JButton("Change Page Format")); pageFormatButton.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { setPageFormat(job.pageDialog(jobAttributes)); } }); formPanel.add(zoomLabel = new JLabel("Scaling = 100%")); formPanel.add(zoomSlider = new JSlider(JSlider.HORIZONTAL, 1, 300, 100)); setZoom(1.0); zoomSlider.addChangeListener(this); add(formPanel); }

setPageFormat(job.pageDialog(jobAttributes));

setPageFormat(job.pageDialog(pageFormat));

public PrintPanel(PlayPen pp) { super(); setOpaque(true); setLayout(new BoxLayout(this, BoxLayout.X_AXIS)); this.pp = pp; add(new PrintPreviewPanel()); job = PrinterJob.getPrinterJob(); jobAttributes = new HashPrintRequestAttributeSet(); pageFormat = job.defaultPage(); JPanel formPanel = new JPanel(new FormLayout()); formPanel.add(new JLabel("Printer")); formPanel.add(printerBox = new JComboBox(PrinterJob.lookupPrintServices())); printerBox.setSelectedItem(getPreferredPrinter()); formPanel.add(new JLabel("Page Format")); String pf = paperToPrintable(pageFormat); formPanel.add(pageFormatLabel = new JLabel(pf.toString())); formPanel.add(new JLabel("Change Page Format")); formPanel.add(pageFormatButton = new JButton("Change Page Format")); pageFormatButton.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { setPageFormat(job.pageDialog(jobAttributes)); } }); formPanel.add(zoomLabel = new JLabel("Scaling = 100%")); formPanel.add(zoomSlider = new JSlider(JSlider.HORIZONTAL, 1, 300, 100)); setZoom(1.0); zoomSlider.addChangeListener(this); add(formPanel); }

pageCountLabel = new JLabel("Page Count: "+getNumberOfPages()); formPanel.add(pageCountLabel);

public PrintPanel(PlayPen pp) { super(); setOpaque(true); setLayout(new BoxLayout(this, BoxLayout.X_AXIS)); this.pp = pp; add(new PrintPreviewPanel()); job = PrinterJob.getPrinterJob(); jobAttributes = new HashPrintRequestAttributeSet(); pageFormat = job.defaultPage(); JPanel formPanel = new JPanel(new FormLayout()); formPanel.add(new JLabel("Printer")); formPanel.add(printerBox = new JComboBox(PrinterJob.lookupPrintServices())); printerBox.setSelectedItem(getPreferredPrinter()); formPanel.add(new JLabel("Page Format")); String pf = paperToPrintable(pageFormat); formPanel.add(pageFormatLabel = new JLabel(pf.toString())); formPanel.add(new JLabel("Change Page Format")); formPanel.add(pageFormatButton = new JButton("Change Page Format")); pageFormatButton.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { setPageFormat(job.pageDialog(jobAttributes)); } }); formPanel.add(zoomLabel = new JLabel("Scaling = 100%")); formPanel.add(zoomSlider = new JSlider(JSlider.HORIZONTAL, 1, 300, 100)); setZoom(1.0); zoomSlider.addChangeListener(this); add(formPanel); }

setPageFormat(job.pageDialog(jobAttributes));

setPageFormat(job.pageDialog(pageFormat));

public void actionPerformed(ActionEvent e) { setPageFormat(job.pageDialog(jobAttributes)); }

g2.drawString("Page "+pageIndex+" of "+(pagesAcross*pagesDown), (float) (leftMargin+10.0), (float) (topMargin+10.0)); logger.debug("Printing page "+(pageIndex+1)+" of "+(pagesAcross*pagesDown) +" at ["+col+","+row+"]");

AffineTransform backupXform = g2.getTransform();

public int print(Graphics graphics, PageFormat pageFormat, int pageIndex) throws PrinterException { Graphics2D g2 = (Graphics2D) graphics; if (pageIndex < pagesAcross*pagesDown) { double leftMargin = pageFormat.getImageableX(); double topMargin = pageFormat.getImageableY(); double width = pageFormat.getImageableWidth(); double height = pageFormat.getImageableHeight(); // which page we're printing in the big grid int col = pageIndex % pagesAcross; int row = pageIndex / pagesAcross; g2.drawString("Page "+pageIndex+" of "+(pagesAcross*pagesDown), (float) (leftMargin+10.0), (float) (topMargin+10.0)); logger.debug("Printing page "+(pageIndex+1)+" of "+(pagesAcross*pagesDown) +" at ["+col+","+row+"]"); g2.translate(leftMargin - col*width, topMargin - row*height); g2.scale(zoom, zoom); pp.print(g2); return PAGE_EXISTS; } else { return NO_SUCH_PAGE; } }

g2.setTransform(backupXform); if (printPageNumbersBox.isSelected()) { g2.drawString("Page "+(pageIndex+1)+" of "+(pagesAcross*pagesDown), (float) (leftMargin+10.0), (float) (topMargin+10.0)); }

public int print(Graphics graphics, PageFormat pageFormat, int pageIndex) throws PrinterException { Graphics2D g2 = (Graphics2D) graphics; if (pageIndex < pagesAcross*pagesDown) { double leftMargin = pageFormat.getImageableX(); double topMargin = pageFormat.getImageableY(); double width = pageFormat.getImageableWidth(); double height = pageFormat.getImageableHeight(); // which page we're printing in the big grid int col = pageIndex % pagesAcross; int row = pageIndex / pagesAcross; g2.drawString("Page "+pageIndex+" of "+(pagesAcross*pagesDown), (float) (leftMargin+10.0), (float) (topMargin+10.0)); logger.debug("Printing page "+(pageIndex+1)+" of "+(pagesAcross*pagesDown) +" at ["+col+","+row+"]"); g2.translate(leftMargin - col*width, topMargin - row*height); g2.scale(zoom, zoom); pp.print(g2); return PAGE_EXISTS; } else { return NO_SUCH_PAGE; } }

pageCountLabel.setText("Page Count: "+getNumberOfPages());

public void validateLayout() { // widths are in points (1/72 inch units) Dimension ppSize = pp.getPreferredSize(); double ppWidth = ppSize.width; double ppHeight = ppSize.height; double paperWidth = pageFormat.getImageableWidth(); double paperHeight = pageFormat.getImageableHeight(); pagesAcross = (int) Math.ceil(zoom * ppWidth / paperWidth); pagesDown = (int) Math.ceil(zoom * ppHeight / paperHeight); }

int tabNum = tabs.getSelectedIndex(); if (tabNum == VIEW_D_NUM || tabNum == VIEW_HAP_NUM){

HaploviewTab tab = (HaploviewTab)tabs.getSelectedComponent(); if (tab.equals(ldTab) || tab.equals(hapsTab)){

public void stateChanged(ChangeEvent e) { if (tabs.getSelectedIndex() != -1){ window.setCursor(Cursor.getPredefinedCursor(Cursor.WAIT_CURSOR)); 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_ASSOC_NUM || tabNum == VIEW_CHECK_NUM || tabNum == VIEW_TAGGER_NUM){ exportMenuItems[0].setEnabled(true); exportMenuItems[1].setEnabled(false); }else{ exportMenuItems[0].setEnabled(false); exportMenuItems[1].setEnabled(false); } //if we've adjusted the haps display thresh we need to change the haps ass panel if (tabNum == VIEW_ASSOC_NUM){ JTabbedPane metaAssoc= (JTabbedPane)tabs.getComponentAt(tabNum); //this is the haps ass tab inside the assoc super-tab HaploAssocPanel htp = (HaploAssocPanel) metaAssoc.getComponent(1); if (htp.initialHaplotypeDisplayThreshold != Options.getHaplotypeDisplayThreshold()){ htp.makeTable(new AssociationTestSet(theData.getHaplotypes(), null)); permutationPanel.setBlocksChanged(); if (custAssocPanel == null){ //change tests if we don't have a custom set AssociationTestSet permSet = new AssociationTestSet(); permSet.cat(tdtPanel.getTestSet()); permSet.cat(hapAssocPanel.getTestSet()); permutationPanel.setTestSet(new PermutationTestSet(0,theData.getSavedEMs(),theData.getPedFile(),permSet)); } } } if (tabNum == VIEW_D_NUM){ keyMenu.setEnabled(true); }else{ keyMenu.setEnabled(false); } viewMenuItems[tabs.getSelectedIndex()].setSelected(true); if (checkPanel != null && checkPanel.changed){ //first store up the current blocks Vector currentBlocks = new Vector(); for (int blocks = 0; blocks < theData.blocks.size(); blocks++){ int thisBlock[] = (int[]) theData.blocks.elementAt(blocks); int thisBlockReal[] = new int[thisBlock.length]; for (int marker = 0; marker < thisBlock.length; marker++){ thisBlockReal[marker] = Chromosome.realIndex[thisBlock[marker]]; } currentBlocks.add(thisBlockReal); } Chromosome.doFilter(checkPanel.getMarkerResults()); //after editing the filtered marker list, needs to be prodded into //resizing correctly dPrimeDisplay.computePreferredSize(); dPrimeDisplay.colorDPrime(); hapDisplay.theData = theData; if (currentBlockDef != BLOX_CUSTOM){ changeBlocks(currentBlockDef); }else{ //adjust the blocks 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++){ //we only keep markers from the input that are "good" from checkdata //we also realign the input file to the current "good" subset since input is //indexed of all possible markers in the dataset 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(); } if (thisBlock.length > 1){ theBlocks.add(thisBlock); } } theData.guessBlocks(BLOX_CUSTOM, theBlocks); } if (tdtPanel != null){ tdtPanel.refreshTable(); } if (taggerConfigPanel != null){ taggerConfigPanel.refreshTable(); } if(permutationPanel != null) { permutationPanel.setBlocksChanged(); if (custAssocPanel == null){ //change tests if we don't have a custom set AssociationTestSet permSet = new AssociationTestSet(); permSet.cat(tdtPanel.getTestSet()); permSet.cat(hapAssocPanel.getTestSet()); permutationPanel.setTestSet(new PermutationTestSet(0,theData.getSavedEMs(),theData.getPedFile(),permSet)); } } checkPanel.changed=false; } if (hapDisplay != null && theData.blocksChanged){ try{ hapDisplay.getHaps(); if(Options.getAssocTest() != ASSOC_NONE) { //this is the haps ass tab inside the assoc super-tab hapAssocPanel.makeTable(new AssociationTestSet(theData.getHaplotypes(), null)); permutationPanel.setBlocksChanged(); if (custAssocPanel == null){ //change tests if we don't have a custom set AssociationTestSet permSet = new AssociationTestSet(); permSet.cat(tdtPanel.getTestSet()); permSet.cat(hapAssocPanel.getTestSet()); permutationPanel.setTestSet(new PermutationTestSet(0,theData.getSavedEMs(),theData.getPedFile(),permSet)); } } }catch(HaploViewException hv){ JOptionPane.showMessageDialog(window, hv.getMessage(), "Error", JOptionPane.ERROR_MESSAGE); } hapScroller.setViewportView(hapDisplay); theData.blocksChanged = false; } setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR)); } }

}else if (tabNum == VIEW_ASSOC_NUM || tabNum == VIEW_CHECK_NUM || tabNum == VIEW_TAGGER_NUM){

}else if (tab.equals(associationTab) || tab.equals(checkTab) || tab.equals(taggerTab)){

public void stateChanged(ChangeEvent e) { if (tabs.getSelectedIndex() != -1){ window.setCursor(Cursor.getPredefinedCursor(Cursor.WAIT_CURSOR)); 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_ASSOC_NUM || tabNum == VIEW_CHECK_NUM || tabNum == VIEW_TAGGER_NUM){ exportMenuItems[0].setEnabled(true); exportMenuItems[1].setEnabled(false); }else{ exportMenuItems[0].setEnabled(false); exportMenuItems[1].setEnabled(false); } //if we've adjusted the haps display thresh we need to change the haps ass panel if (tabNum == VIEW_ASSOC_NUM){ JTabbedPane metaAssoc= (JTabbedPane)tabs.getComponentAt(tabNum); //this is the haps ass tab inside the assoc super-tab HaploAssocPanel htp = (HaploAssocPanel) metaAssoc.getComponent(1); if (htp.initialHaplotypeDisplayThreshold != Options.getHaplotypeDisplayThreshold()){ htp.makeTable(new AssociationTestSet(theData.getHaplotypes(), null)); permutationPanel.setBlocksChanged(); if (custAssocPanel == null){ //change tests if we don't have a custom set AssociationTestSet permSet = new AssociationTestSet(); permSet.cat(tdtPanel.getTestSet()); permSet.cat(hapAssocPanel.getTestSet()); permutationPanel.setTestSet(new PermutationTestSet(0,theData.getSavedEMs(),theData.getPedFile(),permSet)); } } } if (tabNum == VIEW_D_NUM){ keyMenu.setEnabled(true); }else{ keyMenu.setEnabled(false); } viewMenuItems[tabs.getSelectedIndex()].setSelected(true); if (checkPanel != null && checkPanel.changed){ //first store up the current blocks Vector currentBlocks = new Vector(); for (int blocks = 0; blocks < theData.blocks.size(); blocks++){ int thisBlock[] = (int[]) theData.blocks.elementAt(blocks); int thisBlockReal[] = new int[thisBlock.length]; for (int marker = 0; marker < thisBlock.length; marker++){ thisBlockReal[marker] = Chromosome.realIndex[thisBlock[marker]]; } currentBlocks.add(thisBlockReal); } Chromosome.doFilter(checkPanel.getMarkerResults()); //after editing the filtered marker list, needs to be prodded into //resizing correctly dPrimeDisplay.computePreferredSize(); dPrimeDisplay.colorDPrime(); hapDisplay.theData = theData; if (currentBlockDef != BLOX_CUSTOM){ changeBlocks(currentBlockDef); }else{ //adjust the blocks 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++){ //we only keep markers from the input that are "good" from checkdata //we also realign the input file to the current "good" subset since input is //indexed of all possible markers in the dataset 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(); } if (thisBlock.length > 1){ theBlocks.add(thisBlock); } } theData.guessBlocks(BLOX_CUSTOM, theBlocks); } if (tdtPanel != null){ tdtPanel.refreshTable(); } if (taggerConfigPanel != null){ taggerConfigPanel.refreshTable(); } if(permutationPanel != null) { permutationPanel.setBlocksChanged(); if (custAssocPanel == null){ //change tests if we don't have a custom set AssociationTestSet permSet = new AssociationTestSet(); permSet.cat(tdtPanel.getTestSet()); permSet.cat(hapAssocPanel.getTestSet()); permutationPanel.setTestSet(new PermutationTestSet(0,theData.getSavedEMs(),theData.getPedFile(),permSet)); } } checkPanel.changed=false; } if (hapDisplay != null && theData.blocksChanged){ try{ hapDisplay.getHaps(); if(Options.getAssocTest() != ASSOC_NONE) { //this is the haps ass tab inside the assoc super-tab hapAssocPanel.makeTable(new AssociationTestSet(theData.getHaplotypes(), null)); permutationPanel.setBlocksChanged(); if (custAssocPanel == null){ //change tests if we don't have a custom set AssociationTestSet permSet = new AssociationTestSet(); permSet.cat(tdtPanel.getTestSet()); permSet.cat(hapAssocPanel.getTestSet()); permutationPanel.setTestSet(new PermutationTestSet(0,theData.getSavedEMs(),theData.getPedFile(),permSet)); } } }catch(HaploViewException hv){ JOptionPane.showMessageDialog(window, hv.getMessage(), "Error", JOptionPane.ERROR_MESSAGE); } hapScroller.setViewportView(hapDisplay); theData.blocksChanged = false; } setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR)); } }

if (tabNum == VIEW_ASSOC_NUM){ JTabbedPane metaAssoc= (JTabbedPane)tabs.getComponentAt(tabNum);

if (tab.equals(associationTab)){ JTabbedPane metaAssoc = (JTabbedPane)associationTab.getComponent(0);

public void stateChanged(ChangeEvent e) { if (tabs.getSelectedIndex() != -1){ window.setCursor(Cursor.getPredefinedCursor(Cursor.WAIT_CURSOR)); 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_ASSOC_NUM || tabNum == VIEW_CHECK_NUM || tabNum == VIEW_TAGGER_NUM){ exportMenuItems[0].setEnabled(true); exportMenuItems[1].setEnabled(false); }else{ exportMenuItems[0].setEnabled(false); exportMenuItems[1].setEnabled(false); } //if we've adjusted the haps display thresh we need to change the haps ass panel if (tabNum == VIEW_ASSOC_NUM){ JTabbedPane metaAssoc= (JTabbedPane)tabs.getComponentAt(tabNum); //this is the haps ass tab inside the assoc super-tab HaploAssocPanel htp = (HaploAssocPanel) metaAssoc.getComponent(1); if (htp.initialHaplotypeDisplayThreshold != Options.getHaplotypeDisplayThreshold()){ htp.makeTable(new AssociationTestSet(theData.getHaplotypes(), null)); permutationPanel.setBlocksChanged(); if (custAssocPanel == null){ //change tests if we don't have a custom set AssociationTestSet permSet = new AssociationTestSet(); permSet.cat(tdtPanel.getTestSet()); permSet.cat(hapAssocPanel.getTestSet()); permutationPanel.setTestSet(new PermutationTestSet(0,theData.getSavedEMs(),theData.getPedFile(),permSet)); } } } if (tabNum == VIEW_D_NUM){ keyMenu.setEnabled(true); }else{ keyMenu.setEnabled(false); } viewMenuItems[tabs.getSelectedIndex()].setSelected(true); if (checkPanel != null && checkPanel.changed){ //first store up the current blocks Vector currentBlocks = new Vector(); for (int blocks = 0; blocks < theData.blocks.size(); blocks++){ int thisBlock[] = (int[]) theData.blocks.elementAt(blocks); int thisBlockReal[] = new int[thisBlock.length]; for (int marker = 0; marker < thisBlock.length; marker++){ thisBlockReal[marker] = Chromosome.realIndex[thisBlock[marker]]; } currentBlocks.add(thisBlockReal); } Chromosome.doFilter(checkPanel.getMarkerResults()); //after editing the filtered marker list, needs to be prodded into //resizing correctly dPrimeDisplay.computePreferredSize(); dPrimeDisplay.colorDPrime(); hapDisplay.theData = theData; if (currentBlockDef != BLOX_CUSTOM){ changeBlocks(currentBlockDef); }else{ //adjust the blocks 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++){ //we only keep markers from the input that are "good" from checkdata //we also realign the input file to the current "good" subset since input is //indexed of all possible markers in the dataset 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(); } if (thisBlock.length > 1){ theBlocks.add(thisBlock); } } theData.guessBlocks(BLOX_CUSTOM, theBlocks); } if (tdtPanel != null){ tdtPanel.refreshTable(); } if (taggerConfigPanel != null){ taggerConfigPanel.refreshTable(); } if(permutationPanel != null) { permutationPanel.setBlocksChanged(); if (custAssocPanel == null){ //change tests if we don't have a custom set AssociationTestSet permSet = new AssociationTestSet(); permSet.cat(tdtPanel.getTestSet()); permSet.cat(hapAssocPanel.getTestSet()); permutationPanel.setTestSet(new PermutationTestSet(0,theData.getSavedEMs(),theData.getPedFile(),permSet)); } } checkPanel.changed=false; } if (hapDisplay != null && theData.blocksChanged){ try{ hapDisplay.getHaps(); if(Options.getAssocTest() != ASSOC_NONE) { //this is the haps ass tab inside the assoc super-tab hapAssocPanel.makeTable(new AssociationTestSet(theData.getHaplotypes(), null)); permutationPanel.setBlocksChanged(); if (custAssocPanel == null){ //change tests if we don't have a custom set AssociationTestSet permSet = new AssociationTestSet(); permSet.cat(tdtPanel.getTestSet()); permSet.cat(hapAssocPanel.getTestSet()); permutationPanel.setTestSet(new PermutationTestSet(0,theData.getSavedEMs(),theData.getPedFile(),permSet)); } } }catch(HaploViewException hv){ JOptionPane.showMessageDialog(window, hv.getMessage(), "Error", JOptionPane.ERROR_MESSAGE); } hapScroller.setViewportView(hapDisplay); theData.blocksChanged = false; } setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR)); } }

if (tabNum == VIEW_D_NUM){

if (tab.equals(ldTab)){

public void stateChanged(ChangeEvent e) { if (tabs.getSelectedIndex() != -1){ window.setCursor(Cursor.getPredefinedCursor(Cursor.WAIT_CURSOR)); 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_ASSOC_NUM || tabNum == VIEW_CHECK_NUM || tabNum == VIEW_TAGGER_NUM){ exportMenuItems[0].setEnabled(true); exportMenuItems[1].setEnabled(false); }else{ exportMenuItems[0].setEnabled(false); exportMenuItems[1].setEnabled(false); } //if we've adjusted the haps display thresh we need to change the haps ass panel if (tabNum == VIEW_ASSOC_NUM){ JTabbedPane metaAssoc= (JTabbedPane)tabs.getComponentAt(tabNum); //this is the haps ass tab inside the assoc super-tab HaploAssocPanel htp = (HaploAssocPanel) metaAssoc.getComponent(1); if (htp.initialHaplotypeDisplayThreshold != Options.getHaplotypeDisplayThreshold()){ htp.makeTable(new AssociationTestSet(theData.getHaplotypes(), null)); permutationPanel.setBlocksChanged(); if (custAssocPanel == null){ //change tests if we don't have a custom set AssociationTestSet permSet = new AssociationTestSet(); permSet.cat(tdtPanel.getTestSet()); permSet.cat(hapAssocPanel.getTestSet()); permutationPanel.setTestSet(new PermutationTestSet(0,theData.getSavedEMs(),theData.getPedFile(),permSet)); } } } if (tabNum == VIEW_D_NUM){ keyMenu.setEnabled(true); }else{ keyMenu.setEnabled(false); } viewMenuItems[tabs.getSelectedIndex()].setSelected(true); if (checkPanel != null && checkPanel.changed){ //first store up the current blocks Vector currentBlocks = new Vector(); for (int blocks = 0; blocks < theData.blocks.size(); blocks++){ int thisBlock[] = (int[]) theData.blocks.elementAt(blocks); int thisBlockReal[] = new int[thisBlock.length]; for (int marker = 0; marker < thisBlock.length; marker++){ thisBlockReal[marker] = Chromosome.realIndex[thisBlock[marker]]; } currentBlocks.add(thisBlockReal); } Chromosome.doFilter(checkPanel.getMarkerResults()); //after editing the filtered marker list, needs to be prodded into //resizing correctly dPrimeDisplay.computePreferredSize(); dPrimeDisplay.colorDPrime(); hapDisplay.theData = theData; if (currentBlockDef != BLOX_CUSTOM){ changeBlocks(currentBlockDef); }else{ //adjust the blocks 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++){ //we only keep markers from the input that are "good" from checkdata //we also realign the input file to the current "good" subset since input is //indexed of all possible markers in the dataset 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(); } if (thisBlock.length > 1){ theBlocks.add(thisBlock); } } theData.guessBlocks(BLOX_CUSTOM, theBlocks); } if (tdtPanel != null){ tdtPanel.refreshTable(); } if (taggerConfigPanel != null){ taggerConfigPanel.refreshTable(); } if(permutationPanel != null) { permutationPanel.setBlocksChanged(); if (custAssocPanel == null){ //change tests if we don't have a custom set AssociationTestSet permSet = new AssociationTestSet(); permSet.cat(tdtPanel.getTestSet()); permSet.cat(hapAssocPanel.getTestSet()); permutationPanel.setTestSet(new PermutationTestSet(0,theData.getSavedEMs(),theData.getPedFile(),permSet)); } } checkPanel.changed=false; } if (hapDisplay != null && theData.blocksChanged){ try{ hapDisplay.getHaps(); if(Options.getAssocTest() != ASSOC_NONE) { //this is the haps ass tab inside the assoc super-tab hapAssocPanel.makeTable(new AssociationTestSet(theData.getHaplotypes(), null)); permutationPanel.setBlocksChanged(); if (custAssocPanel == null){ //change tests if we don't have a custom set AssociationTestSet permSet = new AssociationTestSet(); permSet.cat(tdtPanel.getTestSet()); permSet.cat(hapAssocPanel.getTestSet()); permutationPanel.setTestSet(new PermutationTestSet(0,theData.getSavedEMs(),theData.getPedFile(),permSet)); } } }catch(HaploViewException hv){ JOptionPane.showMessageDialog(window, hv.getMessage(), "Error", JOptionPane.ERROR_MESSAGE); } hapScroller.setViewportView(hapDisplay); theData.blocksChanged = false; } setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR)); } }

export(tabs.getSelectedIndex(), PNG_MODE, 0, Chromosome.getUnfilteredSize());

export((HaploviewTab)tabs.getSelectedComponent(), PNG_MODE, 0, Chromosome.getUnfilteredSize());

public void actionPerformed(ActionEvent e) { String command = e.getActionCommand(); if (command.equals(READ_GENOTYPES)){ ReadDataDialog readDialog = new ReadDataDialog("Open new data", this); readDialog.pack(); readDialog.setVisible(true); } else if (command.equals(READ_MARKERS)){ //JFileChooser fc = new JFileChooser(System.getProperty("user.dir")); fc.setSelectedFile(new File("")); int returnVal = fc.showOpenDialog(this); if (returnVal == JFileChooser.APPROVE_OPTION) { readMarkers(fc.getSelectedFile(),null); } }else if (command.equals(READ_ANALYSIS_TRACK)){ fc.setSelectedFile(new File("")); int returnVal = fc.showOpenDialog(this); if (returnVal == JFileChooser.APPROVE_OPTION){ readAnalysisFile(fc.getSelectedFile()); } }else if (command.equals(DOWNLOAD_GBROWSE)){ GBrowseDialog gbd = new GBrowseDialog(this, "Connect to HapMap Info Server"); gbd.pack(); gbd.setVisible(true); }else if (command.equals(GBROWSE_OPTS)){ GBrowseOptionDialog gbod = new GBrowseOptionDialog(this, "HapMap Info Track Options"); gbod.pack(); gbod.setVisible(true); }else if (command.equals(READ_BLOCKS_FILE)){ fc.setSelectedFile(new File("")); if (fc.showOpenDialog(this) == JFileChooser.APPROVE_OPTION){ readBlocksFile(fc.getSelectedFile()); } }else if (command.equals(CUST_BLOCKS)){ TweakBlockDefsDialog tweakDialog = new TweakBlockDefsDialog("Customize Blocks", this); tweakDialog.pack(); tweakDialog.setVisible(true); }else if (command.equals(CLEAR_BLOCKS)){ changeBlocks(BLOX_NONE); //blockdef clauses }else if (command.startsWith("block")){ int method = Integer.valueOf(command.substring(5)).intValue(); changeBlocks(method); //zooming clauses }else if (command.startsWith("zoom")){ dPrimeDisplay.zoom(Integer.valueOf(command.substring(4)).intValue()); //coloring clauses }else if (command.startsWith("color")){ Options.setLDColorScheme(Integer.valueOf(command.substring(5)).intValue()); dPrimeDisplay.colorDPrime(); changeKey(); //exporting clauses }else if (command.equals(EXPORT_PNG)){ export(tabs.getSelectedIndex(), PNG_MODE, 0, Chromosome.getUnfilteredSize()); }else if (command.equals(EXPORT_TEXT)){ export(tabs.getSelectedIndex(), TXT_MODE, 0, Chromosome.getUnfilteredSize()); }else if (command.equals(EXPORT_OPTIONS)){ ExportDialog exDialog = new ExportDialog(this); exDialog.pack(); exDialog.setVisible(true); }else if (command.equals("Select All")){ checkPanel.selectAll(); }else if (command.equals("Rescore Markers")){ String cut = cdc.hwcut.getText(); if (cut.equals("")){ cut = "0"; } CheckData.hwCut = Double.parseDouble(cut); cut = cdc.genocut.getText(); if (cut.equals("")){ cut="0"; } CheckData.failedGenoCut = Integer.parseInt(cut); cut = cdc.mendcut.getText(); if (cut.equals("")){ cut="0"; } CheckData.numMendErrCut = Integer.parseInt(cut); cut = cdc.mafcut.getText(); if (cut.equals("")){ cut="0"; } CheckData.mafCut = Double.parseDouble(cut); checkPanel.redoRatings(); JTable jt = checkPanel.getTable(); jt.repaint(); }else if (command.equals("LD Display Spacing")){ ProportionalSpacingDialog spaceDialog = new ProportionalSpacingDialog(this, "Adjust LD Spacing"); spaceDialog.pack(); spaceDialog.setVisible(true); }else if (command.equals("About Haploview")){ JOptionPane.showMessageDialog(this, ABOUT_STRING, "About Haploview", JOptionPane.INFORMATION_MESSAGE); } else if(command.equals("Check for update")) { final SwingWorker worker = new SwingWorker(){ UpdateChecker uc; String unableToConnect; public Object construct() { uc = new UpdateChecker(); try { uc.checkForUpdate(); } catch(IOException ioe) { unableToConnect = ioe.getMessage(); } return null; } public void finished() { window.setCursor(new Cursor(Cursor.DEFAULT_CURSOR)); if(uc != null) { if(unableToConnect != null) { JOptionPane.showMessageDialog(window, "An error occured while checking for update.\n " + unableToConnect , "Update Check", JOptionPane.ERROR_MESSAGE); } else if(uc.isNewVersionAvailable()) { UpdateDisplayDialog udp = new UpdateDisplayDialog(window,"Update Check",uc); udp.pack(); udp.setVisible(true); } else { JOptionPane.showMessageDialog(window, "Your version of Haploview is up to date.", "Update Check", JOptionPane.INFORMATION_MESSAGE); } } } }; setCursor(new Cursor(Cursor.WAIT_CURSOR)); worker.start(); }else if (command.equals("Quit")){ quit(); } else { for (int i = 0; i < viewItems.length; i++) { if (command.equals(viewItems[i])) tabs.setSelectedIndex(i); } } }

export(tabs.getSelectedIndex(), TXT_MODE, 0, Chromosome.getUnfilteredSize());

export((HaploviewTab)tabs.getSelectedComponent(), TXT_MODE, 0, Chromosome.getUnfilteredSize());

public void actionPerformed(ActionEvent e) { String command = e.getActionCommand(); if (command.equals(READ_GENOTYPES)){ ReadDataDialog readDialog = new ReadDataDialog("Open new data", this); readDialog.pack(); readDialog.setVisible(true); } else if (command.equals(READ_MARKERS)){ //JFileChooser fc = new JFileChooser(System.getProperty("user.dir")); fc.setSelectedFile(new File("")); int returnVal = fc.showOpenDialog(this); if (returnVal == JFileChooser.APPROVE_OPTION) { readMarkers(fc.getSelectedFile(),null); } }else if (command.equals(READ_ANALYSIS_TRACK)){ fc.setSelectedFile(new File("")); int returnVal = fc.showOpenDialog(this); if (returnVal == JFileChooser.APPROVE_OPTION){ readAnalysisFile(fc.getSelectedFile()); } }else if (command.equals(DOWNLOAD_GBROWSE)){ GBrowseDialog gbd = new GBrowseDialog(this, "Connect to HapMap Info Server"); gbd.pack(); gbd.setVisible(true); }else if (command.equals(GBROWSE_OPTS)){ GBrowseOptionDialog gbod = new GBrowseOptionDialog(this, "HapMap Info Track Options"); gbod.pack(); gbod.setVisible(true); }else if (command.equals(READ_BLOCKS_FILE)){ fc.setSelectedFile(new File("")); if (fc.showOpenDialog(this) == JFileChooser.APPROVE_OPTION){ readBlocksFile(fc.getSelectedFile()); } }else if (command.equals(CUST_BLOCKS)){ TweakBlockDefsDialog tweakDialog = new TweakBlockDefsDialog("Customize Blocks", this); tweakDialog.pack(); tweakDialog.setVisible(true); }else if (command.equals(CLEAR_BLOCKS)){ changeBlocks(BLOX_NONE); //blockdef clauses }else if (command.startsWith("block")){ int method = Integer.valueOf(command.substring(5)).intValue(); changeBlocks(method); //zooming clauses }else if (command.startsWith("zoom")){ dPrimeDisplay.zoom(Integer.valueOf(command.substring(4)).intValue()); //coloring clauses }else if (command.startsWith("color")){ Options.setLDColorScheme(Integer.valueOf(command.substring(5)).intValue()); dPrimeDisplay.colorDPrime(); changeKey(); //exporting clauses }else if (command.equals(EXPORT_PNG)){ export(tabs.getSelectedIndex(), PNG_MODE, 0, Chromosome.getUnfilteredSize()); }else if (command.equals(EXPORT_TEXT)){ export(tabs.getSelectedIndex(), TXT_MODE, 0, Chromosome.getUnfilteredSize()); }else if (command.equals(EXPORT_OPTIONS)){ ExportDialog exDialog = new ExportDialog(this); exDialog.pack(); exDialog.setVisible(true); }else if (command.equals("Select All")){ checkPanel.selectAll(); }else if (command.equals("Rescore Markers")){ String cut = cdc.hwcut.getText(); if (cut.equals("")){ cut = "0"; } CheckData.hwCut = Double.parseDouble(cut); cut = cdc.genocut.getText(); if (cut.equals("")){ cut="0"; } CheckData.failedGenoCut = Integer.parseInt(cut); cut = cdc.mendcut.getText(); if (cut.equals("")){ cut="0"; } CheckData.numMendErrCut = Integer.parseInt(cut); cut = cdc.mafcut.getText(); if (cut.equals("")){ cut="0"; } CheckData.mafCut = Double.parseDouble(cut); checkPanel.redoRatings(); JTable jt = checkPanel.getTable(); jt.repaint(); }else if (command.equals("LD Display Spacing")){ ProportionalSpacingDialog spaceDialog = new ProportionalSpacingDialog(this, "Adjust LD Spacing"); spaceDialog.pack(); spaceDialog.setVisible(true); }else if (command.equals("About Haploview")){ JOptionPane.showMessageDialog(this, ABOUT_STRING, "About Haploview", JOptionPane.INFORMATION_MESSAGE); } else if(command.equals("Check for update")) { final SwingWorker worker = new SwingWorker(){ UpdateChecker uc; String unableToConnect; public Object construct() { uc = new UpdateChecker(); try { uc.checkForUpdate(); } catch(IOException ioe) { unableToConnect = ioe.getMessage(); } return null; } public void finished() { window.setCursor(new Cursor(Cursor.DEFAULT_CURSOR)); if(uc != null) { if(unableToConnect != null) { JOptionPane.showMessageDialog(window, "An error occured while checking for update.\n " + unableToConnect , "Update Check", JOptionPane.ERROR_MESSAGE); } else if(uc.isNewVersionAvailable()) { UpdateDisplayDialog udp = new UpdateDisplayDialog(window,"Update Check",uc); udp.pack(); udp.setVisible(true); } else { JOptionPane.showMessageDialog(window, "Your version of Haploview is up to date.", "Update Check", JOptionPane.INFORMATION_MESSAGE); } } } }; setCursor(new Cursor(Cursor.WAIT_CURSOR)); worker.start(); }else if (command.equals("Quit")){ quit(); } else { for (int i = 0; i < viewItems.length; i++) { if (command.equals(viewItems[i])) tabs.setSelectedIndex(i); } } }

if (tabs.getSelectedIndex() == VIEW_HAP_NUM){

if (tabs.getSelectedComponent().equals(hapsTab)){

public void changeBlocks(int method){ if (method == BLOX_NONE || method == BLOX_CUSTOM){ blockMenuItems[BLOX_CUSTOM].setSelected(true); } if (method != BLOX_CUSTOM){ 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); }

void export(int tabNum, int format, int start, int stop){

void export(HaploviewTab tab, int format, int start, int stop){

void export(int tabNum, int format, int start, int stop){ fc.setSelectedFile(new File("")); if (fc.showSaveDialog(this) == JFileChooser.APPROVE_OPTION){ File outfile = fc.getSelectedFile(); if (format == PNG_MODE || format == COMPRESSED_PNG_MODE){ BufferedImage image = null; if (tabNum == VIEW_D_NUM){ try { if (format == PNG_MODE){ image = dPrimeDisplay.export(start, stop, false); }else{ image = dPrimeDisplay.export(start, stop, true); } } catch(HaploViewException hve) { JOptionPane.showMessageDialog(this, hve.getMessage(), "Export Error", JOptionPane.ERROR_MESSAGE); } }else if (tabNum == VIEW_HAP_NUM){ image = hapDisplay.export(); }else{ image = new BufferedImage(1,1,BufferedImage.TYPE_3BYTE_BGR); } if (image != null){ try{ String filename = outfile.getPath(); if (! (filename.endsWith(".png") || filename.endsWith(".PNG"))){ filename += ".png"; } Jimi.putImage("image/png", image, filename); }catch(JimiException je){ JOptionPane.showMessageDialog(this, je.getMessage(), "Error", JOptionPane.ERROR_MESSAGE); } } } else if (format == TXT_MODE){ try{ if (tabNum == VIEW_D_NUM){ theData.saveDprimeToText(outfile, TABLE_TYPE, start, stop); }else if (tabNum == VIEW_HAP_NUM){ theData.saveHapsToText(hapDisplay.filteredHaplos,hapDisplay.multidprimeArray, outfile); }else if (tabNum == VIEW_CHECK_NUM){ checkPanel.printTable(outfile); }else if (tabNum == VIEW_ASSOC_NUM){ Component selectedTab = ((JTabbedPane)tabs.getComponent(tabNum)).getSelectedComponent(); if(selectedTab == tdtPanel){ tdtPanel.getTestSet().saveSNPsToText(outfile); }else if (selectedTab == hapAssocPanel){ hapAssocPanel.getTestSet().saveHapsToText(outfile); }else if (selectedTab == permutationPanel){ permutationPanel.export(outfile); }else if (selectedTab == custAssocPanel){ custAssocPanel.getTestSet().saveResultsToText(outfile); } }else if (tabNum == VIEW_TAGGER_NUM){ taggerConfigPanel.export(outfile); } }catch(IOException ioe){ JOptionPane.showMessageDialog(this, ioe.getMessage(), "Error", JOptionPane.ERROR_MESSAGE); }catch(HaploViewException he){ JOptionPane.showMessageDialog(this, he.getMessage(), "Error", JOptionPane.ERROR_MESSAGE); } } } }

if (tabNum == VIEW_D_NUM){

if (tab.equals(ldTab)){

void export(int tabNum, int format, int start, int stop){ fc.setSelectedFile(new File("")); if (fc.showSaveDialog(this) == JFileChooser.APPROVE_OPTION){ File outfile = fc.getSelectedFile(); if (format == PNG_MODE || format == COMPRESSED_PNG_MODE){ BufferedImage image = null; if (tabNum == VIEW_D_NUM){ try { if (format == PNG_MODE){ image = dPrimeDisplay.export(start, stop, false); }else{ image = dPrimeDisplay.export(start, stop, true); } } catch(HaploViewException hve) { JOptionPane.showMessageDialog(this, hve.getMessage(), "Export Error", JOptionPane.ERROR_MESSAGE); } }else if (tabNum == VIEW_HAP_NUM){ image = hapDisplay.export(); }else{ image = new BufferedImage(1,1,BufferedImage.TYPE_3BYTE_BGR); } if (image != null){ try{ String filename = outfile.getPath(); if (! (filename.endsWith(".png") || filename.endsWith(".PNG"))){ filename += ".png"; } Jimi.putImage("image/png", image, filename); }catch(JimiException je){ JOptionPane.showMessageDialog(this, je.getMessage(), "Error", JOptionPane.ERROR_MESSAGE); } } } else if (format == TXT_MODE){ try{ if (tabNum == VIEW_D_NUM){ theData.saveDprimeToText(outfile, TABLE_TYPE, start, stop); }else if (tabNum == VIEW_HAP_NUM){ theData.saveHapsToText(hapDisplay.filteredHaplos,hapDisplay.multidprimeArray, outfile); }else if (tabNum == VIEW_CHECK_NUM){ checkPanel.printTable(outfile); }else if (tabNum == VIEW_ASSOC_NUM){ Component selectedTab = ((JTabbedPane)tabs.getComponent(tabNum)).getSelectedComponent(); if(selectedTab == tdtPanel){ tdtPanel.getTestSet().saveSNPsToText(outfile); }else if (selectedTab == hapAssocPanel){ hapAssocPanel.getTestSet().saveHapsToText(outfile); }else if (selectedTab == permutationPanel){ permutationPanel.export(outfile); }else if (selectedTab == custAssocPanel){ custAssocPanel.getTestSet().saveResultsToText(outfile); } }else if (tabNum == VIEW_TAGGER_NUM){ taggerConfigPanel.export(outfile); } }catch(IOException ioe){ JOptionPane.showMessageDialog(this, ioe.getMessage(), "Error", JOptionPane.ERROR_MESSAGE); }catch(HaploViewException he){ JOptionPane.showMessageDialog(this, he.getMessage(), "Error", JOptionPane.ERROR_MESSAGE); } } } }

}else if (tabNum == VIEW_HAP_NUM){

}else if (tab.equals(hapsTab)){

void export(int tabNum, int format, int start, int stop){ fc.setSelectedFile(new File("")); if (fc.showSaveDialog(this) == JFileChooser.APPROVE_OPTION){ File outfile = fc.getSelectedFile(); if (format == PNG_MODE || format == COMPRESSED_PNG_MODE){ BufferedImage image = null; if (tabNum == VIEW_D_NUM){ try { if (format == PNG_MODE){ image = dPrimeDisplay.export(start, stop, false); }else{ image = dPrimeDisplay.export(start, stop, true); } } catch(HaploViewException hve) { JOptionPane.showMessageDialog(this, hve.getMessage(), "Export Error", JOptionPane.ERROR_MESSAGE); } }else if (tabNum == VIEW_HAP_NUM){ image = hapDisplay.export(); }else{ image = new BufferedImage(1,1,BufferedImage.TYPE_3BYTE_BGR); } if (image != null){ try{ String filename = outfile.getPath(); if (! (filename.endsWith(".png") || filename.endsWith(".PNG"))){ filename += ".png"; } Jimi.putImage("image/png", image, filename); }catch(JimiException je){ JOptionPane.showMessageDialog(this, je.getMessage(), "Error", JOptionPane.ERROR_MESSAGE); } } } else if (format == TXT_MODE){ try{ if (tabNum == VIEW_D_NUM){ theData.saveDprimeToText(outfile, TABLE_TYPE, start, stop); }else if (tabNum == VIEW_HAP_NUM){ theData.saveHapsToText(hapDisplay.filteredHaplos,hapDisplay.multidprimeArray, outfile); }else if (tabNum == VIEW_CHECK_NUM){ checkPanel.printTable(outfile); }else if (tabNum == VIEW_ASSOC_NUM){ Component selectedTab = ((JTabbedPane)tabs.getComponent(tabNum)).getSelectedComponent(); if(selectedTab == tdtPanel){ tdtPanel.getTestSet().saveSNPsToText(outfile); }else if (selectedTab == hapAssocPanel){ hapAssocPanel.getTestSet().saveHapsToText(outfile); }else if (selectedTab == permutationPanel){ permutationPanel.export(outfile); }else if (selectedTab == custAssocPanel){ custAssocPanel.getTestSet().saveResultsToText(outfile); } }else if (tabNum == VIEW_TAGGER_NUM){ taggerConfigPanel.export(outfile); } }catch(IOException ioe){ JOptionPane.showMessageDialog(this, ioe.getMessage(), "Error", JOptionPane.ERROR_MESSAGE); }catch(HaploViewException he){ JOptionPane.showMessageDialog(this, he.getMessage(), "Error", JOptionPane.ERROR_MESSAGE); } } } }

}else if (tabNum == VIEW_CHECK_NUM){

}else if (tab.equals(checkTab)){

void export(int tabNum, int format, int start, int stop){ fc.setSelectedFile(new File("")); if (fc.showSaveDialog(this) == JFileChooser.APPROVE_OPTION){ File outfile = fc.getSelectedFile(); if (format == PNG_MODE || format == COMPRESSED_PNG_MODE){ BufferedImage image = null; if (tabNum == VIEW_D_NUM){ try { if (format == PNG_MODE){ image = dPrimeDisplay.export(start, stop, false); }else{ image = dPrimeDisplay.export(start, stop, true); } } catch(HaploViewException hve) { JOptionPane.showMessageDialog(this, hve.getMessage(), "Export Error", JOptionPane.ERROR_MESSAGE); } }else if (tabNum == VIEW_HAP_NUM){ image = hapDisplay.export(); }else{ image = new BufferedImage(1,1,BufferedImage.TYPE_3BYTE_BGR); } if (image != null){ try{ String filename = outfile.getPath(); if (! (filename.endsWith(".png") || filename.endsWith(".PNG"))){ filename += ".png"; } Jimi.putImage("image/png", image, filename); }catch(JimiException je){ JOptionPane.showMessageDialog(this, je.getMessage(), "Error", JOptionPane.ERROR_MESSAGE); } } } else if (format == TXT_MODE){ try{ if (tabNum == VIEW_D_NUM){ theData.saveDprimeToText(outfile, TABLE_TYPE, start, stop); }else if (tabNum == VIEW_HAP_NUM){ theData.saveHapsToText(hapDisplay.filteredHaplos,hapDisplay.multidprimeArray, outfile); }else if (tabNum == VIEW_CHECK_NUM){ checkPanel.printTable(outfile); }else if (tabNum == VIEW_ASSOC_NUM){ Component selectedTab = ((JTabbedPane)tabs.getComponent(tabNum)).getSelectedComponent(); if(selectedTab == tdtPanel){ tdtPanel.getTestSet().saveSNPsToText(outfile); }else if (selectedTab == hapAssocPanel){ hapAssocPanel.getTestSet().saveHapsToText(outfile); }else if (selectedTab == permutationPanel){ permutationPanel.export(outfile); }else if (selectedTab == custAssocPanel){ custAssocPanel.getTestSet().saveResultsToText(outfile); } }else if (tabNum == VIEW_TAGGER_NUM){ taggerConfigPanel.export(outfile); } }catch(IOException ioe){ JOptionPane.showMessageDialog(this, ioe.getMessage(), "Error", JOptionPane.ERROR_MESSAGE); }catch(HaploViewException he){ JOptionPane.showMessageDialog(this, he.getMessage(), "Error", JOptionPane.ERROR_MESSAGE); } } } }

}else if (tabNum == VIEW_ASSOC_NUM){ Component selectedTab = ((JTabbedPane)tabs.getComponent(tabNum)).getSelectedComponent();

}else if (tab.equals(associationTab)){ Component selectedTab = ((JTabbedPane)associationTab.getComponent(0)).getSelectedComponent();

void export(int tabNum, int format, int start, int stop){ fc.setSelectedFile(new File("")); if (fc.showSaveDialog(this) == JFileChooser.APPROVE_OPTION){ File outfile = fc.getSelectedFile(); if (format == PNG_MODE || format == COMPRESSED_PNG_MODE){ BufferedImage image = null; if (tabNum == VIEW_D_NUM){ try { if (format == PNG_MODE){ image = dPrimeDisplay.export(start, stop, false); }else{ image = dPrimeDisplay.export(start, stop, true); } } catch(HaploViewException hve) { JOptionPane.showMessageDialog(this, hve.getMessage(), "Export Error", JOptionPane.ERROR_MESSAGE); } }else if (tabNum == VIEW_HAP_NUM){ image = hapDisplay.export(); }else{ image = new BufferedImage(1,1,BufferedImage.TYPE_3BYTE_BGR); } if (image != null){ try{ String filename = outfile.getPath(); if (! (filename.endsWith(".png") || filename.endsWith(".PNG"))){ filename += ".png"; } Jimi.putImage("image/png", image, filename); }catch(JimiException je){ JOptionPane.showMessageDialog(this, je.getMessage(), "Error", JOptionPane.ERROR_MESSAGE); } } } else if (format == TXT_MODE){ try{ if (tabNum == VIEW_D_NUM){ theData.saveDprimeToText(outfile, TABLE_TYPE, start, stop); }else if (tabNum == VIEW_HAP_NUM){ theData.saveHapsToText(hapDisplay.filteredHaplos,hapDisplay.multidprimeArray, outfile); }else if (tabNum == VIEW_CHECK_NUM){ checkPanel.printTable(outfile); }else if (tabNum == VIEW_ASSOC_NUM){ Component selectedTab = ((JTabbedPane)tabs.getComponent(tabNum)).getSelectedComponent(); if(selectedTab == tdtPanel){ tdtPanel.getTestSet().saveSNPsToText(outfile); }else if (selectedTab == hapAssocPanel){ hapAssocPanel.getTestSet().saveHapsToText(outfile); }else if (selectedTab == permutationPanel){ permutationPanel.export(outfile); }else if (selectedTab == custAssocPanel){ custAssocPanel.getTestSet().saveResultsToText(outfile); } }else if (tabNum == VIEW_TAGGER_NUM){ taggerConfigPanel.export(outfile); } }catch(IOException ioe){ JOptionPane.showMessageDialog(this, ioe.getMessage(), "Error", JOptionPane.ERROR_MESSAGE); }catch(HaploViewException he){ JOptionPane.showMessageDialog(this, he.getMessage(), "Error", JOptionPane.ERROR_MESSAGE); } } } }

}else if (tabNum == VIEW_TAGGER_NUM){

}else if (tab.equals(taggerTab)){

void export(int tabNum, int format, int start, int stop){ fc.setSelectedFile(new File("")); if (fc.showSaveDialog(this) == JFileChooser.APPROVE_OPTION){ File outfile = fc.getSelectedFile(); if (format == PNG_MODE || format == COMPRESSED_PNG_MODE){ BufferedImage image = null; if (tabNum == VIEW_D_NUM){ try { if (format == PNG_MODE){ image = dPrimeDisplay.export(start, stop, false); }else{ image = dPrimeDisplay.export(start, stop, true); } } catch(HaploViewException hve) { JOptionPane.showMessageDialog(this, hve.getMessage(), "Export Error", JOptionPane.ERROR_MESSAGE); } }else if (tabNum == VIEW_HAP_NUM){ image = hapDisplay.export(); }else{ image = new BufferedImage(1,1,BufferedImage.TYPE_3BYTE_BGR); } if (image != null){ try{ String filename = outfile.getPath(); if (! (filename.endsWith(".png") || filename.endsWith(".PNG"))){ filename += ".png"; } Jimi.putImage("image/png", image, filename); }catch(JimiException je){ JOptionPane.showMessageDialog(this, je.getMessage(), "Error", JOptionPane.ERROR_MESSAGE); } } } else if (format == TXT_MODE){ try{ if (tabNum == VIEW_D_NUM){ theData.saveDprimeToText(outfile, TABLE_TYPE, start, stop); }else if (tabNum == VIEW_HAP_NUM){ theData.saveHapsToText(hapDisplay.filteredHaplos,hapDisplay.multidprimeArray, outfile); }else if (tabNum == VIEW_CHECK_NUM){ checkPanel.printTable(outfile); }else if (tabNum == VIEW_ASSOC_NUM){ Component selectedTab = ((JTabbedPane)tabs.getComponent(tabNum)).getSelectedComponent(); if(selectedTab == tdtPanel){ tdtPanel.getTestSet().saveSNPsToText(outfile); }else if (selectedTab == hapAssocPanel){ hapAssocPanel.getTestSet().saveHapsToText(outfile); }else if (selectedTab == permutationPanel){ permutationPanel.export(outfile); }else if (selectedTab == custAssocPanel){ custAssocPanel.getTestSet().saveResultsToText(outfile); } }else if (tabNum == VIEW_TAGGER_NUM){ taggerConfigPanel.export(outfile); } }catch(IOException ioe){ JOptionPane.showMessageDialog(this, ioe.getMessage(), "Error", JOptionPane.ERROR_MESSAGE); }catch(HaploViewException he){ JOptionPane.showMessageDialog(this, he.getMessage(), "Error", JOptionPane.ERROR_MESSAGE); } } } }

if (dPrimeDisplay != null && tabs.getSelectedIndex() == VIEW_D_NUM){

if (dPrimeDisplay != null && tabs.getSelectedComponent().equals(ldTab)){

void readAnalysisFile(File inFile){ try{ theData.readAnalysisTrack(inFile); }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); } dPrimeDisplay.computePreferredSize(); if (dPrimeDisplay != null && tabs.getSelectedIndex() == VIEW_D_NUM){ dPrimeDisplay.repaint(); } }

int currentTab = VIEW_D_NUM;

HaploviewTab currentTab = ldTab;

void readGenotypes(String[] inputOptions, int type){ //input is a 2 element array with //inputOptions[0] = ped file //inputOptions[1] = info file (null if none) //inputOptions[2] = custom association test list file (null if none) //type is either 3 or 4 for ped and hapmap files respectively final File inFile = new File(inputOptions[0]); final AssociationTestSet customAssocSet; try { if (inputOptions[2] != null && inputOptions[1] == null){ throw new HaploViewException("A marker information file is required if a tests file is specified."); } this.setCursor(Cursor.getPredefinedCursor(Cursor.WAIT_CURSOR)); if (inFile.length() < 1){ throw new HaploViewException("Genotype file is empty or nonexistent: " + inFile.getName()); } if (type == HAPS_FILE){ //these are not available for non ped files viewMenuItems[VIEW_CHECK_NUM].setEnabled(false); viewMenuItems[VIEW_ASSOC_NUM].setEnabled(false); Options.setAssocTest(ASSOC_NONE); } theData = new HaploData(); if (type == HAPS_FILE){ theData.prepareHapsInput(new File(inputOptions[0])); }else{ theData.linkageToChrom(inFile, type); } if(type != HAPS_FILE && theData.getPedFile().isBogusParents()) { JOptionPane.showMessageDialog(this, "One or more individuals in the file reference non-existent parents.\nThese references have been ignored.", "File Error", JOptionPane.ERROR_MESSAGE); } //deal with marker information theData.infoKnown = false; File markerFile; if (inputOptions[1] == null){ markerFile = null; }else{ markerFile = new File(inputOptions[1]); } //turn on/off gbrowse menu if (Options.isGBrowseShown()){ gbEditItem.setEnabled(true); }else{ gbEditItem.setEnabled(false); } checkPanel = null; if (type == HAPS_FILE){ readMarkers(markerFile, null); //initialize realIndex Chromosome.doFilter(Chromosome.getUnfilteredSize()); customAssocSet = null; }else{ readMarkers(markerFile, theData.getPedFile().getHMInfo()); //we read the file in first, so we can whitelist all the markers in the custom test set HashSet whiteListedCustomMarkers = new HashSet(); if (inputOptions[2] != null){ customAssocSet = new AssociationTestSet(inputOptions[2]); whiteListedCustomMarkers = customAssocSet.getWhitelist(); }else{ customAssocSet = null; } theData.setWhiteList(whiteListedCustomMarkers); checkPanel = new CheckDataPanel(this); checkPanel.setAlignmentX(Component.CENTER_ALIGNMENT); //set up the indexing to take into account skipped markers. Chromosome.doFilter(checkPanel.getMarkerResults()); } //let's start the math final SwingWorker worker = new SwingWorker(){ public Object construct(){ dPrimeDisplay=null; changeKey(); theData.generateDPrimeTable(); theData.guessBlocks(BLOX_GABRIEL); //theData.guessBlocks(BLOX_NONE); //for debugging, doesn't call blocks at first blockMenuItems[0].setSelected(true); zoomMenuItems[0].setSelected(true); theData.blocksChanged = false; Container contents = getContentPane(); contents.removeAll(); int currentTab = VIEW_D_NUM; /*if (!(tabs == null)){ currentTab = tabs.getSelectedIndex(); } */ tabs = new JTabbedPane(); tabs.addChangeListener(new TabChangeListener()); //first, draw the D' picture JPanel panel = new JPanel(); panel.setLayout(new BoxLayout(panel, BoxLayout.Y_AXIS)); dPrimeDisplay = new DPrimeDisplay(window); JScrollPane dPrimeScroller = new JScrollPane(dPrimeDisplay); dPrimeScroller.getViewport().setScrollMode(JViewport.BLIT_SCROLL_MODE); dPrimeScroller.getVerticalScrollBar().setUnitIncrement(60); dPrimeScroller.getHorizontalScrollBar().setUnitIncrement(60); panel.add(dPrimeScroller); tabs.addTab(viewItems[VIEW_D_NUM], panel); viewMenuItems[VIEW_D_NUM].setEnabled(true); //compute and show haps on next tab panel = new JPanel(); panel.setLayout(new BoxLayout(panel, BoxLayout.Y_AXIS)); try { hapDisplay = new HaplotypeDisplay(theData); } catch(HaploViewException e) { JOptionPane.showMessageDialog(window, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE); } HaplotypeDisplayController hdc = new HaplotypeDisplayController(hapDisplay); hapScroller = new JScrollPane(hapDisplay); hapScroller.getVerticalScrollBar().setUnitIncrement(60); hapScroller.getHorizontalScrollBar().setUnitIncrement(60); panel.add(hapScroller); panel.add(hdc); tabs.addTab(viewItems[VIEW_HAP_NUM], panel); viewMenuItems[VIEW_HAP_NUM].setEnabled(true); displayMenu.setEnabled(true); analysisMenu.setEnabled(true); //check data panel if (checkPanel != null){ JPanel metaCheckPanel = new JPanel(); metaCheckPanel.setLayout(new BoxLayout(metaCheckPanel, BoxLayout.Y_AXIS)); metaCheckPanel.add(checkPanel); cdc = new CheckDataController(window); metaCheckPanel.add(cdc); tabs.addTab(viewItems[VIEW_CHECK_NUM], metaCheckPanel); viewMenuItems[VIEW_CHECK_NUM].setEnabled(true); currentTab=VIEW_CHECK_NUM; } //tagger display taggerConfigPanel = new TaggerConfigPanel(theData); JPanel metaTagPanel = new JPanel(); metaTagPanel.setLayout(new BoxLayout(metaTagPanel,BoxLayout.Y_AXIS)); metaTagPanel.add(taggerConfigPanel); JTabbedPane tagTabs = new JTabbedPane(); tagTabs.add("Configuration",metaTagPanel); JPanel resMetaPanel = new JPanel(); resMetaPanel.setLayout(new BoxLayout(resMetaPanel,BoxLayout.Y_AXIS)); TaggerResultsPanel tagResultsPanel = new TaggerResultsPanel(); taggerConfigPanel.addActionListener(tagResultsPanel); resMetaPanel.add(tagResultsPanel); tagTabs.addTab("Results",resMetaPanel); tabs.addTab(VIEW_TAGGER,tagTabs); viewMenuItems[VIEW_TAGGER_NUM].setEnabled(true); //Association panel if(Options.getAssocTest() != ASSOC_NONE) { JTabbedPane metaAssoc = new JTabbedPane(); try{ tdtPanel = new TDTPanel(new AssociationTestSet(theData.getPedFile(), null, Chromosome.getAllMarkers())); } catch(PedFileException e) { JOptionPane.showMessageDialog(window, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE); } metaAssoc.add("Single Marker", tdtPanel); hapAssocPanel = new HaploAssocPanel(new AssociationTestSet(theData.getHaplotypes(), null)); metaAssoc.add("Haplotypes", hapAssocPanel); //custom association tests custAssocPanel = null; if(customAssocSet != null) { try { customAssocSet.runFileTests(theData, tdtPanel.getTestSet().getMarkerAssociationResults()); custAssocPanel = new CustomAssocPanel(customAssocSet); metaAssoc.addTab("Custom",custAssocPanel); metaAssoc.setSelectedComponent(custAssocPanel); } catch (HaploViewException e) { JOptionPane.showMessageDialog(window, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE); } } AssociationTestSet permSet; boolean cust = false; if (custAssocPanel != null){ permSet = custAssocPanel.getTestSet(); cust = true; }else{ permSet = new AssociationTestSet(); permSet.cat(tdtPanel.getTestSet()); permSet.cat(hapAssocPanel.getTestSet()); } permutationPanel = new PermutationTestPanel(new PermutationTestSet(0,theData.getSavedEMs(), theData.getPedFile(),permSet), cust); metaAssoc.add(permutationPanel,"Permutation Tests"); tabs.addTab(VIEW_ASSOC, metaAssoc); viewMenuItems[VIEW_ASSOC_NUM].setEnabled(true); } tabs.setSelectedIndex(currentTab); contents.add(tabs); repaint(); setVisible(true); theData.finished = true; setTitle(TITLE_STRING + " -- " + inFile.getName()); return null; } }; timer = new javax.swing.Timer(50, new ActionListener(){ public void actionPerformed(ActionEvent evt){ if (theData.finished){ timer.stop(); for (int i = 0; i < blockMenuItems.length; i++){ blockMenuItems[i].setEnabled(true); } clearBlocksItem.setEnabled(true); readMarkerItem.setEnabled(true); blocksItem.setEnabled(true); exportMenuItems[2].setEnabled(true); setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR)); } } }); worker.start(); timer.start(); }catch(IOException ioexec) { JOptionPane.showMessageDialog(this, ioexec.getMessage(), "File Error", JOptionPane.ERROR_MESSAGE); setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR)); }catch(PedFileException pfe){ JOptionPane.showMessageDialog(this, pfe.getMessage(), "File Error", JOptionPane.ERROR_MESSAGE); setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR)); }catch (HaploViewException hve){ JOptionPane.showMessageDialog(this, hve.getMessage(), "File Error", JOptionPane.ERROR_MESSAGE); setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR)); } }

JPanel panel = new JPanel(); panel.setLayout(new BoxLayout(panel, BoxLayout.Y_AXIS));

void readGenotypes(String[] inputOptions, int type){ //input is a 2 element array with //inputOptions[0] = ped file //inputOptions[1] = info file (null if none) //inputOptions[2] = custom association test list file (null if none) //type is either 3 or 4 for ped and hapmap files respectively final File inFile = new File(inputOptions[0]); final AssociationTestSet customAssocSet; try { if (inputOptions[2] != null && inputOptions[1] == null){ throw new HaploViewException("A marker information file is required if a tests file is specified."); } this.setCursor(Cursor.getPredefinedCursor(Cursor.WAIT_CURSOR)); if (inFile.length() < 1){ throw new HaploViewException("Genotype file is empty or nonexistent: " + inFile.getName()); } if (type == HAPS_FILE){ //these are not available for non ped files viewMenuItems[VIEW_CHECK_NUM].setEnabled(false); viewMenuItems[VIEW_ASSOC_NUM].setEnabled(false); Options.setAssocTest(ASSOC_NONE); } theData = new HaploData(); if (type == HAPS_FILE){ theData.prepareHapsInput(new File(inputOptions[0])); }else{ theData.linkageToChrom(inFile, type); } if(type != HAPS_FILE && theData.getPedFile().isBogusParents()) { JOptionPane.showMessageDialog(this, "One or more individuals in the file reference non-existent parents.\nThese references have been ignored.", "File Error", JOptionPane.ERROR_MESSAGE); } //deal with marker information theData.infoKnown = false; File markerFile; if (inputOptions[1] == null){ markerFile = null; }else{ markerFile = new File(inputOptions[1]); } //turn on/off gbrowse menu if (Options.isGBrowseShown()){ gbEditItem.setEnabled(true); }else{ gbEditItem.setEnabled(false); } checkPanel = null; if (type == HAPS_FILE){ readMarkers(markerFile, null); //initialize realIndex Chromosome.doFilter(Chromosome.getUnfilteredSize()); customAssocSet = null; }else{ readMarkers(markerFile, theData.getPedFile().getHMInfo()); //we read the file in first, so we can whitelist all the markers in the custom test set HashSet whiteListedCustomMarkers = new HashSet(); if (inputOptions[2] != null){ customAssocSet = new AssociationTestSet(inputOptions[2]); whiteListedCustomMarkers = customAssocSet.getWhitelist(); }else{ customAssocSet = null; } theData.setWhiteList(whiteListedCustomMarkers); checkPanel = new CheckDataPanel(this); checkPanel.setAlignmentX(Component.CENTER_ALIGNMENT); //set up the indexing to take into account skipped markers. Chromosome.doFilter(checkPanel.getMarkerResults()); } //let's start the math final SwingWorker worker = new SwingWorker(){ public Object construct(){ dPrimeDisplay=null; changeKey(); theData.generateDPrimeTable(); theData.guessBlocks(BLOX_GABRIEL); //theData.guessBlocks(BLOX_NONE); //for debugging, doesn't call blocks at first blockMenuItems[0].setSelected(true); zoomMenuItems[0].setSelected(true); theData.blocksChanged = false; Container contents = getContentPane(); contents.removeAll(); int currentTab = VIEW_D_NUM; /*if (!(tabs == null)){ currentTab = tabs.getSelectedIndex(); } */ tabs = new JTabbedPane(); tabs.addChangeListener(new TabChangeListener()); //first, draw the D' picture JPanel panel = new JPanel(); panel.setLayout(new BoxLayout(panel, BoxLayout.Y_AXIS)); dPrimeDisplay = new DPrimeDisplay(window); JScrollPane dPrimeScroller = new JScrollPane(dPrimeDisplay); dPrimeScroller.getViewport().setScrollMode(JViewport.BLIT_SCROLL_MODE); dPrimeScroller.getVerticalScrollBar().setUnitIncrement(60); dPrimeScroller.getHorizontalScrollBar().setUnitIncrement(60); panel.add(dPrimeScroller); tabs.addTab(viewItems[VIEW_D_NUM], panel); viewMenuItems[VIEW_D_NUM].setEnabled(true); //compute and show haps on next tab panel = new JPanel(); panel.setLayout(new BoxLayout(panel, BoxLayout.Y_AXIS)); try { hapDisplay = new HaplotypeDisplay(theData); } catch(HaploViewException e) { JOptionPane.showMessageDialog(window, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE); } HaplotypeDisplayController hdc = new HaplotypeDisplayController(hapDisplay); hapScroller = new JScrollPane(hapDisplay); hapScroller.getVerticalScrollBar().setUnitIncrement(60); hapScroller.getHorizontalScrollBar().setUnitIncrement(60); panel.add(hapScroller); panel.add(hdc); tabs.addTab(viewItems[VIEW_HAP_NUM], panel); viewMenuItems[VIEW_HAP_NUM].setEnabled(true); displayMenu.setEnabled(true); analysisMenu.setEnabled(true); //check data panel if (checkPanel != null){ JPanel metaCheckPanel = new JPanel(); metaCheckPanel.setLayout(new BoxLayout(metaCheckPanel, BoxLayout.Y_AXIS)); metaCheckPanel.add(checkPanel); cdc = new CheckDataController(window); metaCheckPanel.add(cdc); tabs.addTab(viewItems[VIEW_CHECK_NUM], metaCheckPanel); viewMenuItems[VIEW_CHECK_NUM].setEnabled(true); currentTab=VIEW_CHECK_NUM; } //tagger display taggerConfigPanel = new TaggerConfigPanel(theData); JPanel metaTagPanel = new JPanel(); metaTagPanel.setLayout(new BoxLayout(metaTagPanel,BoxLayout.Y_AXIS)); metaTagPanel.add(taggerConfigPanel); JTabbedPane tagTabs = new JTabbedPane(); tagTabs.add("Configuration",metaTagPanel); JPanel resMetaPanel = new JPanel(); resMetaPanel.setLayout(new BoxLayout(resMetaPanel,BoxLayout.Y_AXIS)); TaggerResultsPanel tagResultsPanel = new TaggerResultsPanel(); taggerConfigPanel.addActionListener(tagResultsPanel); resMetaPanel.add(tagResultsPanel); tagTabs.addTab("Results",resMetaPanel); tabs.addTab(VIEW_TAGGER,tagTabs); viewMenuItems[VIEW_TAGGER_NUM].setEnabled(true); //Association panel if(Options.getAssocTest() != ASSOC_NONE) { JTabbedPane metaAssoc = new JTabbedPane(); try{ tdtPanel = new TDTPanel(new AssociationTestSet(theData.getPedFile(), null, Chromosome.getAllMarkers())); } catch(PedFileException e) { JOptionPane.showMessageDialog(window, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE); } metaAssoc.add("Single Marker", tdtPanel); hapAssocPanel = new HaploAssocPanel(new AssociationTestSet(theData.getHaplotypes(), null)); metaAssoc.add("Haplotypes", hapAssocPanel); //custom association tests custAssocPanel = null; if(customAssocSet != null) { try { customAssocSet.runFileTests(theData, tdtPanel.getTestSet().getMarkerAssociationResults()); custAssocPanel = new CustomAssocPanel(customAssocSet); metaAssoc.addTab("Custom",custAssocPanel); metaAssoc.setSelectedComponent(custAssocPanel); } catch (HaploViewException e) { JOptionPane.showMessageDialog(window, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE); } } AssociationTestSet permSet; boolean cust = false; if (custAssocPanel != null){ permSet = custAssocPanel.getTestSet(); cust = true; }else{ permSet = new AssociationTestSet(); permSet.cat(tdtPanel.getTestSet()); permSet.cat(hapAssocPanel.getTestSet()); } permutationPanel = new PermutationTestPanel(new PermutationTestSet(0,theData.getSavedEMs(), theData.getPedFile(),permSet), cust); metaAssoc.add(permutationPanel,"Permutation Tests"); tabs.addTab(VIEW_ASSOC, metaAssoc); viewMenuItems[VIEW_ASSOC_NUM].setEnabled(true); } tabs.setSelectedIndex(currentTab); contents.add(tabs); repaint(); setVisible(true); theData.finished = true; setTitle(TITLE_STRING + " -- " + inFile.getName()); return null; } }; timer = new javax.swing.Timer(50, new ActionListener(){ public void actionPerformed(ActionEvent evt){ if (theData.finished){ timer.stop(); for (int i = 0; i < blockMenuItems.length; i++){ blockMenuItems[i].setEnabled(true); } clearBlocksItem.setEnabled(true); readMarkerItem.setEnabled(true); blocksItem.setEnabled(true); exportMenuItems[2].setEnabled(true); setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR)); } } }); worker.start(); timer.start(); }catch(IOException ioexec) { JOptionPane.showMessageDialog(this, ioexec.getMessage(), "File Error", JOptionPane.ERROR_MESSAGE); setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR)); }catch(PedFileException pfe){ JOptionPane.showMessageDialog(this, pfe.getMessage(), "File Error", JOptionPane.ERROR_MESSAGE); setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR)); }catch (HaploViewException hve){ JOptionPane.showMessageDialog(this, hve.getMessage(), "File Error", JOptionPane.ERROR_MESSAGE); setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR)); } }

panel.add(dPrimeScroller); tabs.addTab(viewItems[VIEW_D_NUM], panel);

ldTab = new HaploviewTab(dPrimeScroller); tabs.addTab(VIEW_DPRIME, ldTab);

void readGenotypes(String[] inputOptions, int type){ //input is a 2 element array with //inputOptions[0] = ped file //inputOptions[1] = info file (null if none) //inputOptions[2] = custom association test list file (null if none) //type is either 3 or 4 for ped and hapmap files respectively final File inFile = new File(inputOptions[0]); final AssociationTestSet customAssocSet; try { if (inputOptions[2] != null && inputOptions[1] == null){ throw new HaploViewException("A marker information file is required if a tests file is specified."); } this.setCursor(Cursor.getPredefinedCursor(Cursor.WAIT_CURSOR)); if (inFile.length() < 1){ throw new HaploViewException("Genotype file is empty or nonexistent: " + inFile.getName()); } if (type == HAPS_FILE){ //these are not available for non ped files viewMenuItems[VIEW_CHECK_NUM].setEnabled(false); viewMenuItems[VIEW_ASSOC_NUM].setEnabled(false); Options.setAssocTest(ASSOC_NONE); } theData = new HaploData(); if (type == HAPS_FILE){ theData.prepareHapsInput(new File(inputOptions[0])); }else{ theData.linkageToChrom(inFile, type); } if(type != HAPS_FILE && theData.getPedFile().isBogusParents()) { JOptionPane.showMessageDialog(this, "One or more individuals in the file reference non-existent parents.\nThese references have been ignored.", "File Error", JOptionPane.ERROR_MESSAGE); } //deal with marker information theData.infoKnown = false; File markerFile; if (inputOptions[1] == null){ markerFile = null; }else{ markerFile = new File(inputOptions[1]); } //turn on/off gbrowse menu if (Options.isGBrowseShown()){ gbEditItem.setEnabled(true); }else{ gbEditItem.setEnabled(false); } checkPanel = null; if (type == HAPS_FILE){ readMarkers(markerFile, null); //initialize realIndex Chromosome.doFilter(Chromosome.getUnfilteredSize()); customAssocSet = null; }else{ readMarkers(markerFile, theData.getPedFile().getHMInfo()); //we read the file in first, so we can whitelist all the markers in the custom test set HashSet whiteListedCustomMarkers = new HashSet(); if (inputOptions[2] != null){ customAssocSet = new AssociationTestSet(inputOptions[2]); whiteListedCustomMarkers = customAssocSet.getWhitelist(); }else{ customAssocSet = null; } theData.setWhiteList(whiteListedCustomMarkers); checkPanel = new CheckDataPanel(this); checkPanel.setAlignmentX(Component.CENTER_ALIGNMENT); //set up the indexing to take into account skipped markers. Chromosome.doFilter(checkPanel.getMarkerResults()); } //let's start the math final SwingWorker worker = new SwingWorker(){ public Object construct(){ dPrimeDisplay=null; changeKey(); theData.generateDPrimeTable(); theData.guessBlocks(BLOX_GABRIEL); //theData.guessBlocks(BLOX_NONE); //for debugging, doesn't call blocks at first blockMenuItems[0].setSelected(true); zoomMenuItems[0].setSelected(true); theData.blocksChanged = false; Container contents = getContentPane(); contents.removeAll(); int currentTab = VIEW_D_NUM; /*if (!(tabs == null)){ currentTab = tabs.getSelectedIndex(); } */ tabs = new JTabbedPane(); tabs.addChangeListener(new TabChangeListener()); //first, draw the D' picture JPanel panel = new JPanel(); panel.setLayout(new BoxLayout(panel, BoxLayout.Y_AXIS)); dPrimeDisplay = new DPrimeDisplay(window); JScrollPane dPrimeScroller = new JScrollPane(dPrimeDisplay); dPrimeScroller.getViewport().setScrollMode(JViewport.BLIT_SCROLL_MODE); dPrimeScroller.getVerticalScrollBar().setUnitIncrement(60); dPrimeScroller.getHorizontalScrollBar().setUnitIncrement(60); panel.add(dPrimeScroller); tabs.addTab(viewItems[VIEW_D_NUM], panel); viewMenuItems[VIEW_D_NUM].setEnabled(true); //compute and show haps on next tab panel = new JPanel(); panel.setLayout(new BoxLayout(panel, BoxLayout.Y_AXIS)); try { hapDisplay = new HaplotypeDisplay(theData); } catch(HaploViewException e) { JOptionPane.showMessageDialog(window, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE); } HaplotypeDisplayController hdc = new HaplotypeDisplayController(hapDisplay); hapScroller = new JScrollPane(hapDisplay); hapScroller.getVerticalScrollBar().setUnitIncrement(60); hapScroller.getHorizontalScrollBar().setUnitIncrement(60); panel.add(hapScroller); panel.add(hdc); tabs.addTab(viewItems[VIEW_HAP_NUM], panel); viewMenuItems[VIEW_HAP_NUM].setEnabled(true); displayMenu.setEnabled(true); analysisMenu.setEnabled(true); //check data panel if (checkPanel != null){ JPanel metaCheckPanel = new JPanel(); metaCheckPanel.setLayout(new BoxLayout(metaCheckPanel, BoxLayout.Y_AXIS)); metaCheckPanel.add(checkPanel); cdc = new CheckDataController(window); metaCheckPanel.add(cdc); tabs.addTab(viewItems[VIEW_CHECK_NUM], metaCheckPanel); viewMenuItems[VIEW_CHECK_NUM].setEnabled(true); currentTab=VIEW_CHECK_NUM; } //tagger display taggerConfigPanel = new TaggerConfigPanel(theData); JPanel metaTagPanel = new JPanel(); metaTagPanel.setLayout(new BoxLayout(metaTagPanel,BoxLayout.Y_AXIS)); metaTagPanel.add(taggerConfigPanel); JTabbedPane tagTabs = new JTabbedPane(); tagTabs.add("Configuration",metaTagPanel); JPanel resMetaPanel = new JPanel(); resMetaPanel.setLayout(new BoxLayout(resMetaPanel,BoxLayout.Y_AXIS)); TaggerResultsPanel tagResultsPanel = new TaggerResultsPanel(); taggerConfigPanel.addActionListener(tagResultsPanel); resMetaPanel.add(tagResultsPanel); tagTabs.addTab("Results",resMetaPanel); tabs.addTab(VIEW_TAGGER,tagTabs); viewMenuItems[VIEW_TAGGER_NUM].setEnabled(true); //Association panel if(Options.getAssocTest() != ASSOC_NONE) { JTabbedPane metaAssoc = new JTabbedPane(); try{ tdtPanel = new TDTPanel(new AssociationTestSet(theData.getPedFile(), null, Chromosome.getAllMarkers())); } catch(PedFileException e) { JOptionPane.showMessageDialog(window, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE); } metaAssoc.add("Single Marker", tdtPanel); hapAssocPanel = new HaploAssocPanel(new AssociationTestSet(theData.getHaplotypes(), null)); metaAssoc.add("Haplotypes", hapAssocPanel); //custom association tests custAssocPanel = null; if(customAssocSet != null) { try { customAssocSet.runFileTests(theData, tdtPanel.getTestSet().getMarkerAssociationResults()); custAssocPanel = new CustomAssocPanel(customAssocSet); metaAssoc.addTab("Custom",custAssocPanel); metaAssoc.setSelectedComponent(custAssocPanel); } catch (HaploViewException e) { JOptionPane.showMessageDialog(window, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE); } } AssociationTestSet permSet; boolean cust = false; if (custAssocPanel != null){ permSet = custAssocPanel.getTestSet(); cust = true; }else{ permSet = new AssociationTestSet(); permSet.cat(tdtPanel.getTestSet()); permSet.cat(hapAssocPanel.getTestSet()); } permutationPanel = new PermutationTestPanel(new PermutationTestSet(0,theData.getSavedEMs(), theData.getPedFile(),permSet), cust); metaAssoc.add(permutationPanel,"Permutation Tests"); tabs.addTab(VIEW_ASSOC, metaAssoc); viewMenuItems[VIEW_ASSOC_NUM].setEnabled(true); } tabs.setSelectedIndex(currentTab); contents.add(tabs); repaint(); setVisible(true); theData.finished = true; setTitle(TITLE_STRING + " -- " + inFile.getName()); return null; } }; timer = new javax.swing.Timer(50, new ActionListener(){ public void actionPerformed(ActionEvent evt){ if (theData.finished){ timer.stop(); for (int i = 0; i < blockMenuItems.length; i++){ blockMenuItems[i].setEnabled(true); } clearBlocksItem.setEnabled(true); readMarkerItem.setEnabled(true); blocksItem.setEnabled(true); exportMenuItems[2].setEnabled(true); setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR)); } } }); worker.start(); timer.start(); }catch(IOException ioexec) { JOptionPane.showMessageDialog(this, ioexec.getMessage(), "File Error", JOptionPane.ERROR_MESSAGE); setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR)); }catch(PedFileException pfe){ JOptionPane.showMessageDialog(this, pfe.getMessage(), "File Error", JOptionPane.ERROR_MESSAGE); setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR)); }catch (HaploViewException hve){ JOptionPane.showMessageDialog(this, hve.getMessage(), "File Error", JOptionPane.ERROR_MESSAGE); setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR)); } }

panel = new JPanel(); panel.setLayout(new BoxLayout(panel, BoxLayout.Y_AXIS));

void readGenotypes(String[] inputOptions, int type){ //input is a 2 element array with //inputOptions[0] = ped file //inputOptions[1] = info file (null if none) //inputOptions[2] = custom association test list file (null if none) //type is either 3 or 4 for ped and hapmap files respectively final File inFile = new File(inputOptions[0]); final AssociationTestSet customAssocSet; try { if (inputOptions[2] != null && inputOptions[1] == null){ throw new HaploViewException("A marker information file is required if a tests file is specified."); } this.setCursor(Cursor.getPredefinedCursor(Cursor.WAIT_CURSOR)); if (inFile.length() < 1){ throw new HaploViewException("Genotype file is empty or nonexistent: " + inFile.getName()); } if (type == HAPS_FILE){ //these are not available for non ped files viewMenuItems[VIEW_CHECK_NUM].setEnabled(false); viewMenuItems[VIEW_ASSOC_NUM].setEnabled(false); Options.setAssocTest(ASSOC_NONE); } theData = new HaploData(); if (type == HAPS_FILE){ theData.prepareHapsInput(new File(inputOptions[0])); }else{ theData.linkageToChrom(inFile, type); } if(type != HAPS_FILE && theData.getPedFile().isBogusParents()) { JOptionPane.showMessageDialog(this, "One or more individuals in the file reference non-existent parents.\nThese references have been ignored.", "File Error", JOptionPane.ERROR_MESSAGE); } //deal with marker information theData.infoKnown = false; File markerFile; if (inputOptions[1] == null){ markerFile = null; }else{ markerFile = new File(inputOptions[1]); } //turn on/off gbrowse menu if (Options.isGBrowseShown()){ gbEditItem.setEnabled(true); }else{ gbEditItem.setEnabled(false); } checkPanel = null; if (type == HAPS_FILE){ readMarkers(markerFile, null); //initialize realIndex Chromosome.doFilter(Chromosome.getUnfilteredSize()); customAssocSet = null; }else{ readMarkers(markerFile, theData.getPedFile().getHMInfo()); //we read the file in first, so we can whitelist all the markers in the custom test set HashSet whiteListedCustomMarkers = new HashSet(); if (inputOptions[2] != null){ customAssocSet = new AssociationTestSet(inputOptions[2]); whiteListedCustomMarkers = customAssocSet.getWhitelist(); }else{ customAssocSet = null; } theData.setWhiteList(whiteListedCustomMarkers); checkPanel = new CheckDataPanel(this); checkPanel.setAlignmentX(Component.CENTER_ALIGNMENT); //set up the indexing to take into account skipped markers. Chromosome.doFilter(checkPanel.getMarkerResults()); } //let's start the math final SwingWorker worker = new SwingWorker(){ public Object construct(){ dPrimeDisplay=null; changeKey(); theData.generateDPrimeTable(); theData.guessBlocks(BLOX_GABRIEL); //theData.guessBlocks(BLOX_NONE); //for debugging, doesn't call blocks at first blockMenuItems[0].setSelected(true); zoomMenuItems[0].setSelected(true); theData.blocksChanged = false; Container contents = getContentPane(); contents.removeAll(); int currentTab = VIEW_D_NUM; /*if (!(tabs == null)){ currentTab = tabs.getSelectedIndex(); } */ tabs = new JTabbedPane(); tabs.addChangeListener(new TabChangeListener()); //first, draw the D' picture JPanel panel = new JPanel(); panel.setLayout(new BoxLayout(panel, BoxLayout.Y_AXIS)); dPrimeDisplay = new DPrimeDisplay(window); JScrollPane dPrimeScroller = new JScrollPane(dPrimeDisplay); dPrimeScroller.getViewport().setScrollMode(JViewport.BLIT_SCROLL_MODE); dPrimeScroller.getVerticalScrollBar().setUnitIncrement(60); dPrimeScroller.getHorizontalScrollBar().setUnitIncrement(60); panel.add(dPrimeScroller); tabs.addTab(viewItems[VIEW_D_NUM], panel); viewMenuItems[VIEW_D_NUM].setEnabled(true); //compute and show haps on next tab panel = new JPanel(); panel.setLayout(new BoxLayout(panel, BoxLayout.Y_AXIS)); try { hapDisplay = new HaplotypeDisplay(theData); } catch(HaploViewException e) { JOptionPane.showMessageDialog(window, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE); } HaplotypeDisplayController hdc = new HaplotypeDisplayController(hapDisplay); hapScroller = new JScrollPane(hapDisplay); hapScroller.getVerticalScrollBar().setUnitIncrement(60); hapScroller.getHorizontalScrollBar().setUnitIncrement(60); panel.add(hapScroller); panel.add(hdc); tabs.addTab(viewItems[VIEW_HAP_NUM], panel); viewMenuItems[VIEW_HAP_NUM].setEnabled(true); displayMenu.setEnabled(true); analysisMenu.setEnabled(true); //check data panel if (checkPanel != null){ JPanel metaCheckPanel = new JPanel(); metaCheckPanel.setLayout(new BoxLayout(metaCheckPanel, BoxLayout.Y_AXIS)); metaCheckPanel.add(checkPanel); cdc = new CheckDataController(window); metaCheckPanel.add(cdc); tabs.addTab(viewItems[VIEW_CHECK_NUM], metaCheckPanel); viewMenuItems[VIEW_CHECK_NUM].setEnabled(true); currentTab=VIEW_CHECK_NUM; } //tagger display taggerConfigPanel = new TaggerConfigPanel(theData); JPanel metaTagPanel = new JPanel(); metaTagPanel.setLayout(new BoxLayout(metaTagPanel,BoxLayout.Y_AXIS)); metaTagPanel.add(taggerConfigPanel); JTabbedPane tagTabs = new JTabbedPane(); tagTabs.add("Configuration",metaTagPanel); JPanel resMetaPanel = new JPanel(); resMetaPanel.setLayout(new BoxLayout(resMetaPanel,BoxLayout.Y_AXIS)); TaggerResultsPanel tagResultsPanel = new TaggerResultsPanel(); taggerConfigPanel.addActionListener(tagResultsPanel); resMetaPanel.add(tagResultsPanel); tagTabs.addTab("Results",resMetaPanel); tabs.addTab(VIEW_TAGGER,tagTabs); viewMenuItems[VIEW_TAGGER_NUM].setEnabled(true); //Association panel if(Options.getAssocTest() != ASSOC_NONE) { JTabbedPane metaAssoc = new JTabbedPane(); try{ tdtPanel = new TDTPanel(new AssociationTestSet(theData.getPedFile(), null, Chromosome.getAllMarkers())); } catch(PedFileException e) { JOptionPane.showMessageDialog(window, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE); } metaAssoc.add("Single Marker", tdtPanel); hapAssocPanel = new HaploAssocPanel(new AssociationTestSet(theData.getHaplotypes(), null)); metaAssoc.add("Haplotypes", hapAssocPanel); //custom association tests custAssocPanel = null; if(customAssocSet != null) { try { customAssocSet.runFileTests(theData, tdtPanel.getTestSet().getMarkerAssociationResults()); custAssocPanel = new CustomAssocPanel(customAssocSet); metaAssoc.addTab("Custom",custAssocPanel); metaAssoc.setSelectedComponent(custAssocPanel); } catch (HaploViewException e) { JOptionPane.showMessageDialog(window, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE); } } AssociationTestSet permSet; boolean cust = false; if (custAssocPanel != null){ permSet = custAssocPanel.getTestSet(); cust = true; }else{ permSet = new AssociationTestSet(); permSet.cat(tdtPanel.getTestSet()); permSet.cat(hapAssocPanel.getTestSet()); } permutationPanel = new PermutationTestPanel(new PermutationTestSet(0,theData.getSavedEMs(), theData.getPedFile(),permSet), cust); metaAssoc.add(permutationPanel,"Permutation Tests"); tabs.addTab(VIEW_ASSOC, metaAssoc); viewMenuItems[VIEW_ASSOC_NUM].setEnabled(true); } tabs.setSelectedIndex(currentTab); contents.add(tabs); repaint(); setVisible(true); theData.finished = true; setTitle(TITLE_STRING + " -- " + inFile.getName()); return null; } }; timer = new javax.swing.Timer(50, new ActionListener(){ public void actionPerformed(ActionEvent evt){ if (theData.finished){ timer.stop(); for (int i = 0; i < blockMenuItems.length; i++){ blockMenuItems[i].setEnabled(true); } clearBlocksItem.setEnabled(true); readMarkerItem.setEnabled(true); blocksItem.setEnabled(true); exportMenuItems[2].setEnabled(true); setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR)); } } }); worker.start(); timer.start(); }catch(IOException ioexec) { JOptionPane.showMessageDialog(this, ioexec.getMessage(), "File Error", JOptionPane.ERROR_MESSAGE); setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR)); }catch(PedFileException pfe){ JOptionPane.showMessageDialog(this, pfe.getMessage(), "File Error", JOptionPane.ERROR_MESSAGE); setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR)); }catch (HaploViewException hve){ JOptionPane.showMessageDialog(this, hve.getMessage(), "File Error", JOptionPane.ERROR_MESSAGE); setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR)); } }

panel.add(hapScroller); panel.add(hdc); tabs.addTab(viewItems[VIEW_HAP_NUM], panel);

hapsTab = new HaploviewTab(hapScroller); hapsTab.add(hdc); tabs.addTab(VIEW_HAPLOTYPES, hapsTab);

void readGenotypes(String[] inputOptions, int type){ //input is a 2 element array with //inputOptions[0] = ped file //inputOptions[1] = info file (null if none) //inputOptions[2] = custom association test list file (null if none) //type is either 3 or 4 for ped and hapmap files respectively final File inFile = new File(inputOptions[0]); final AssociationTestSet customAssocSet; try { if (inputOptions[2] != null && inputOptions[1] == null){ throw new HaploViewException("A marker information file is required if a tests file is specified."); } this.setCursor(Cursor.getPredefinedCursor(Cursor.WAIT_CURSOR)); if (inFile.length() < 1){ throw new HaploViewException("Genotype file is empty or nonexistent: " + inFile.getName()); } if (type == HAPS_FILE){ //these are not available for non ped files viewMenuItems[VIEW_CHECK_NUM].setEnabled(false); viewMenuItems[VIEW_ASSOC_NUM].setEnabled(false); Options.setAssocTest(ASSOC_NONE); } theData = new HaploData(); if (type == HAPS_FILE){ theData.prepareHapsInput(new File(inputOptions[0])); }else{ theData.linkageToChrom(inFile, type); } if(type != HAPS_FILE && theData.getPedFile().isBogusParents()) { JOptionPane.showMessageDialog(this, "One or more individuals in the file reference non-existent parents.\nThese references have been ignored.", "File Error", JOptionPane.ERROR_MESSAGE); } //deal with marker information theData.infoKnown = false; File markerFile; if (inputOptions[1] == null){ markerFile = null; }else{ markerFile = new File(inputOptions[1]); } //turn on/off gbrowse menu if (Options.isGBrowseShown()){ gbEditItem.setEnabled(true); }else{ gbEditItem.setEnabled(false); } checkPanel = null; if (type == HAPS_FILE){ readMarkers(markerFile, null); //initialize realIndex Chromosome.doFilter(Chromosome.getUnfilteredSize()); customAssocSet = null; }else{ readMarkers(markerFile, theData.getPedFile().getHMInfo()); //we read the file in first, so we can whitelist all the markers in the custom test set HashSet whiteListedCustomMarkers = new HashSet(); if (inputOptions[2] != null){ customAssocSet = new AssociationTestSet(inputOptions[2]); whiteListedCustomMarkers = customAssocSet.getWhitelist(); }else{ customAssocSet = null; } theData.setWhiteList(whiteListedCustomMarkers); checkPanel = new CheckDataPanel(this); checkPanel.setAlignmentX(Component.CENTER_ALIGNMENT); //set up the indexing to take into account skipped markers. Chromosome.doFilter(checkPanel.getMarkerResults()); } //let's start the math final SwingWorker worker = new SwingWorker(){ public Object construct(){ dPrimeDisplay=null; changeKey(); theData.generateDPrimeTable(); theData.guessBlocks(BLOX_GABRIEL); //theData.guessBlocks(BLOX_NONE); //for debugging, doesn't call blocks at first blockMenuItems[0].setSelected(true); zoomMenuItems[0].setSelected(true); theData.blocksChanged = false; Container contents = getContentPane(); contents.removeAll(); int currentTab = VIEW_D_NUM; /*if (!(tabs == null)){ currentTab = tabs.getSelectedIndex(); } */ tabs = new JTabbedPane(); tabs.addChangeListener(new TabChangeListener()); //first, draw the D' picture JPanel panel = new JPanel(); panel.setLayout(new BoxLayout(panel, BoxLayout.Y_AXIS)); dPrimeDisplay = new DPrimeDisplay(window); JScrollPane dPrimeScroller = new JScrollPane(dPrimeDisplay); dPrimeScroller.getViewport().setScrollMode(JViewport.BLIT_SCROLL_MODE); dPrimeScroller.getVerticalScrollBar().setUnitIncrement(60); dPrimeScroller.getHorizontalScrollBar().setUnitIncrement(60); panel.add(dPrimeScroller); tabs.addTab(viewItems[VIEW_D_NUM], panel); viewMenuItems[VIEW_D_NUM].setEnabled(true); //compute and show haps on next tab panel = new JPanel(); panel.setLayout(new BoxLayout(panel, BoxLayout.Y_AXIS)); try { hapDisplay = new HaplotypeDisplay(theData); } catch(HaploViewException e) { JOptionPane.showMessageDialog(window, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE); } HaplotypeDisplayController hdc = new HaplotypeDisplayController(hapDisplay); hapScroller = new JScrollPane(hapDisplay); hapScroller.getVerticalScrollBar().setUnitIncrement(60); hapScroller.getHorizontalScrollBar().setUnitIncrement(60); panel.add(hapScroller); panel.add(hdc); tabs.addTab(viewItems[VIEW_HAP_NUM], panel); viewMenuItems[VIEW_HAP_NUM].setEnabled(true); displayMenu.setEnabled(true); analysisMenu.setEnabled(true); //check data panel if (checkPanel != null){ JPanel metaCheckPanel = new JPanel(); metaCheckPanel.setLayout(new BoxLayout(metaCheckPanel, BoxLayout.Y_AXIS)); metaCheckPanel.add(checkPanel); cdc = new CheckDataController(window); metaCheckPanel.add(cdc); tabs.addTab(viewItems[VIEW_CHECK_NUM], metaCheckPanel); viewMenuItems[VIEW_CHECK_NUM].setEnabled(true); currentTab=VIEW_CHECK_NUM; } //tagger display taggerConfigPanel = new TaggerConfigPanel(theData); JPanel metaTagPanel = new JPanel(); metaTagPanel.setLayout(new BoxLayout(metaTagPanel,BoxLayout.Y_AXIS)); metaTagPanel.add(taggerConfigPanel); JTabbedPane tagTabs = new JTabbedPane(); tagTabs.add("Configuration",metaTagPanel); JPanel resMetaPanel = new JPanel(); resMetaPanel.setLayout(new BoxLayout(resMetaPanel,BoxLayout.Y_AXIS)); TaggerResultsPanel tagResultsPanel = new TaggerResultsPanel(); taggerConfigPanel.addActionListener(tagResultsPanel); resMetaPanel.add(tagResultsPanel); tagTabs.addTab("Results",resMetaPanel); tabs.addTab(VIEW_TAGGER,tagTabs); viewMenuItems[VIEW_TAGGER_NUM].setEnabled(true); //Association panel if(Options.getAssocTest() != ASSOC_NONE) { JTabbedPane metaAssoc = new JTabbedPane(); try{ tdtPanel = new TDTPanel(new AssociationTestSet(theData.getPedFile(), null, Chromosome.getAllMarkers())); } catch(PedFileException e) { JOptionPane.showMessageDialog(window, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE); } metaAssoc.add("Single Marker", tdtPanel); hapAssocPanel = new HaploAssocPanel(new AssociationTestSet(theData.getHaplotypes(), null)); metaAssoc.add("Haplotypes", hapAssocPanel); //custom association tests custAssocPanel = null; if(customAssocSet != null) { try { customAssocSet.runFileTests(theData, tdtPanel.getTestSet().getMarkerAssociationResults()); custAssocPanel = new CustomAssocPanel(customAssocSet); metaAssoc.addTab("Custom",custAssocPanel); metaAssoc.setSelectedComponent(custAssocPanel); } catch (HaploViewException e) { JOptionPane.showMessageDialog(window, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE); } } AssociationTestSet permSet; boolean cust = false; if (custAssocPanel != null){ permSet = custAssocPanel.getTestSet(); cust = true; }else{ permSet = new AssociationTestSet(); permSet.cat(tdtPanel.getTestSet()); permSet.cat(hapAssocPanel.getTestSet()); } permutationPanel = new PermutationTestPanel(new PermutationTestSet(0,theData.getSavedEMs(), theData.getPedFile(),permSet), cust); metaAssoc.add(permutationPanel,"Permutation Tests"); tabs.addTab(VIEW_ASSOC, metaAssoc); viewMenuItems[VIEW_ASSOC_NUM].setEnabled(true); } tabs.setSelectedIndex(currentTab); contents.add(tabs); repaint(); setVisible(true); theData.finished = true; setTitle(TITLE_STRING + " -- " + inFile.getName()); return null; } }; timer = new javax.swing.Timer(50, new ActionListener(){ public void actionPerformed(ActionEvent evt){ if (theData.finished){ timer.stop(); for (int i = 0; i < blockMenuItems.length; i++){ blockMenuItems[i].setEnabled(true); } clearBlocksItem.setEnabled(true); readMarkerItem.setEnabled(true); blocksItem.setEnabled(true); exportMenuItems[2].setEnabled(true); setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR)); } } }); worker.start(); timer.start(); }catch(IOException ioexec) { JOptionPane.showMessageDialog(this, ioexec.getMessage(), "File Error", JOptionPane.ERROR_MESSAGE); setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR)); }catch(PedFileException pfe){ JOptionPane.showMessageDialog(this, pfe.getMessage(), "File Error", JOptionPane.ERROR_MESSAGE); setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR)); }catch (HaploViewException hve){ JOptionPane.showMessageDialog(this, hve.getMessage(), "File Error", JOptionPane.ERROR_MESSAGE); setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR)); } }

JPanel metaCheckPanel = new JPanel(); metaCheckPanel.setLayout(new BoxLayout(metaCheckPanel, BoxLayout.Y_AXIS)); metaCheckPanel.add(checkPanel);

checkTab = new HaploviewTab(checkPanel);

void readGenotypes(String[] inputOptions, int type){ //input is a 2 element array with //inputOptions[0] = ped file //inputOptions[1] = info file (null if none) //inputOptions[2] = custom association test list file (null if none) //type is either 3 or 4 for ped and hapmap files respectively final File inFile = new File(inputOptions[0]); final AssociationTestSet customAssocSet; try { if (inputOptions[2] != null && inputOptions[1] == null){ throw new HaploViewException("A marker information file is required if a tests file is specified."); } this.setCursor(Cursor.getPredefinedCursor(Cursor.WAIT_CURSOR)); if (inFile.length() < 1){ throw new HaploViewException("Genotype file is empty or nonexistent: " + inFile.getName()); } if (type == HAPS_FILE){ //these are not available for non ped files viewMenuItems[VIEW_CHECK_NUM].setEnabled(false); viewMenuItems[VIEW_ASSOC_NUM].setEnabled(false); Options.setAssocTest(ASSOC_NONE); } theData = new HaploData(); if (type == HAPS_FILE){ theData.prepareHapsInput(new File(inputOptions[0])); }else{ theData.linkageToChrom(inFile, type); } if(type != HAPS_FILE && theData.getPedFile().isBogusParents()) { JOptionPane.showMessageDialog(this, "One or more individuals in the file reference non-existent parents.\nThese references have been ignored.", "File Error", JOptionPane.ERROR_MESSAGE); } //deal with marker information theData.infoKnown = false; File markerFile; if (inputOptions[1] == null){ markerFile = null; }else{ markerFile = new File(inputOptions[1]); } //turn on/off gbrowse menu if (Options.isGBrowseShown()){ gbEditItem.setEnabled(true); }else{ gbEditItem.setEnabled(false); } checkPanel = null; if (type == HAPS_FILE){ readMarkers(markerFile, null); //initialize realIndex Chromosome.doFilter(Chromosome.getUnfilteredSize()); customAssocSet = null; }else{ readMarkers(markerFile, theData.getPedFile().getHMInfo()); //we read the file in first, so we can whitelist all the markers in the custom test set HashSet whiteListedCustomMarkers = new HashSet(); if (inputOptions[2] != null){ customAssocSet = new AssociationTestSet(inputOptions[2]); whiteListedCustomMarkers = customAssocSet.getWhitelist(); }else{ customAssocSet = null; } theData.setWhiteList(whiteListedCustomMarkers); checkPanel = new CheckDataPanel(this); checkPanel.setAlignmentX(Component.CENTER_ALIGNMENT); //set up the indexing to take into account skipped markers. Chromosome.doFilter(checkPanel.getMarkerResults()); } //let's start the math final SwingWorker worker = new SwingWorker(){ public Object construct(){ dPrimeDisplay=null; changeKey(); theData.generateDPrimeTable(); theData.guessBlocks(BLOX_GABRIEL); //theData.guessBlocks(BLOX_NONE); //for debugging, doesn't call blocks at first blockMenuItems[0].setSelected(true); zoomMenuItems[0].setSelected(true); theData.blocksChanged = false; Container contents = getContentPane(); contents.removeAll(); int currentTab = VIEW_D_NUM; /*if (!(tabs == null)){ currentTab = tabs.getSelectedIndex(); } */ tabs = new JTabbedPane(); tabs.addChangeListener(new TabChangeListener()); //first, draw the D' picture JPanel panel = new JPanel(); panel.setLayout(new BoxLayout(panel, BoxLayout.Y_AXIS)); dPrimeDisplay = new DPrimeDisplay(window); JScrollPane dPrimeScroller = new JScrollPane(dPrimeDisplay); dPrimeScroller.getViewport().setScrollMode(JViewport.BLIT_SCROLL_MODE); dPrimeScroller.getVerticalScrollBar().setUnitIncrement(60); dPrimeScroller.getHorizontalScrollBar().setUnitIncrement(60); panel.add(dPrimeScroller); tabs.addTab(viewItems[VIEW_D_NUM], panel); viewMenuItems[VIEW_D_NUM].setEnabled(true); //compute and show haps on next tab panel = new JPanel(); panel.setLayout(new BoxLayout(panel, BoxLayout.Y_AXIS)); try { hapDisplay = new HaplotypeDisplay(theData); } catch(HaploViewException e) { JOptionPane.showMessageDialog(window, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE); } HaplotypeDisplayController hdc = new HaplotypeDisplayController(hapDisplay); hapScroller = new JScrollPane(hapDisplay); hapScroller.getVerticalScrollBar().setUnitIncrement(60); hapScroller.getHorizontalScrollBar().setUnitIncrement(60); panel.add(hapScroller); panel.add(hdc); tabs.addTab(viewItems[VIEW_HAP_NUM], panel); viewMenuItems[VIEW_HAP_NUM].setEnabled(true); displayMenu.setEnabled(true); analysisMenu.setEnabled(true); //check data panel if (checkPanel != null){ JPanel metaCheckPanel = new JPanel(); metaCheckPanel.setLayout(new BoxLayout(metaCheckPanel, BoxLayout.Y_AXIS)); metaCheckPanel.add(checkPanel); cdc = new CheckDataController(window); metaCheckPanel.add(cdc); tabs.addTab(viewItems[VIEW_CHECK_NUM], metaCheckPanel); viewMenuItems[VIEW_CHECK_NUM].setEnabled(true); currentTab=VIEW_CHECK_NUM; } //tagger display taggerConfigPanel = new TaggerConfigPanel(theData); JPanel metaTagPanel = new JPanel(); metaTagPanel.setLayout(new BoxLayout(metaTagPanel,BoxLayout.Y_AXIS)); metaTagPanel.add(taggerConfigPanel); JTabbedPane tagTabs = new JTabbedPane(); tagTabs.add("Configuration",metaTagPanel); JPanel resMetaPanel = new JPanel(); resMetaPanel.setLayout(new BoxLayout(resMetaPanel,BoxLayout.Y_AXIS)); TaggerResultsPanel tagResultsPanel = new TaggerResultsPanel(); taggerConfigPanel.addActionListener(tagResultsPanel); resMetaPanel.add(tagResultsPanel); tagTabs.addTab("Results",resMetaPanel); tabs.addTab(VIEW_TAGGER,tagTabs); viewMenuItems[VIEW_TAGGER_NUM].setEnabled(true); //Association panel if(Options.getAssocTest() != ASSOC_NONE) { JTabbedPane metaAssoc = new JTabbedPane(); try{ tdtPanel = new TDTPanel(new AssociationTestSet(theData.getPedFile(), null, Chromosome.getAllMarkers())); } catch(PedFileException e) { JOptionPane.showMessageDialog(window, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE); } metaAssoc.add("Single Marker", tdtPanel); hapAssocPanel = new HaploAssocPanel(new AssociationTestSet(theData.getHaplotypes(), null)); metaAssoc.add("Haplotypes", hapAssocPanel); //custom association tests custAssocPanel = null; if(customAssocSet != null) { try { customAssocSet.runFileTests(theData, tdtPanel.getTestSet().getMarkerAssociationResults()); custAssocPanel = new CustomAssocPanel(customAssocSet); metaAssoc.addTab("Custom",custAssocPanel); metaAssoc.setSelectedComponent(custAssocPanel); } catch (HaploViewException e) { JOptionPane.showMessageDialog(window, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE); } } AssociationTestSet permSet; boolean cust = false; if (custAssocPanel != null){ permSet = custAssocPanel.getTestSet(); cust = true; }else{ permSet = new AssociationTestSet(); permSet.cat(tdtPanel.getTestSet()); permSet.cat(hapAssocPanel.getTestSet()); } permutationPanel = new PermutationTestPanel(new PermutationTestSet(0,theData.getSavedEMs(), theData.getPedFile(),permSet), cust); metaAssoc.add(permutationPanel,"Permutation Tests"); tabs.addTab(VIEW_ASSOC, metaAssoc); viewMenuItems[VIEW_ASSOC_NUM].setEnabled(true); } tabs.setSelectedIndex(currentTab); contents.add(tabs); repaint(); setVisible(true); theData.finished = true; setTitle(TITLE_STRING + " -- " + inFile.getName()); return null; } }; timer = new javax.swing.Timer(50, new ActionListener(){ public void actionPerformed(ActionEvent evt){ if (theData.finished){ timer.stop(); for (int i = 0; i < blockMenuItems.length; i++){ blockMenuItems[i].setEnabled(true); } clearBlocksItem.setEnabled(true); readMarkerItem.setEnabled(true); blocksItem.setEnabled(true); exportMenuItems[2].setEnabled(true); setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR)); } } }); worker.start(); timer.start(); }catch(IOException ioexec) { JOptionPane.showMessageDialog(this, ioexec.getMessage(), "File Error", JOptionPane.ERROR_MESSAGE); setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR)); }catch(PedFileException pfe){ JOptionPane.showMessageDialog(this, pfe.getMessage(), "File Error", JOptionPane.ERROR_MESSAGE); setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR)); }catch (HaploViewException hve){ JOptionPane.showMessageDialog(this, hve.getMessage(), "File Error", JOptionPane.ERROR_MESSAGE); setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR)); } }

metaCheckPanel.add(cdc); tabs.addTab(viewItems[VIEW_CHECK_NUM], metaCheckPanel);

checkTab.add(cdc); tabs.addTab(VIEW_CHECK_PANEL, checkTab);

void readGenotypes(String[] inputOptions, int type){ //input is a 2 element array with //inputOptions[0] = ped file //inputOptions[1] = info file (null if none) //inputOptions[2] = custom association test list file (null if none) //type is either 3 or 4 for ped and hapmap files respectively final File inFile = new File(inputOptions[0]); final AssociationTestSet customAssocSet; try { if (inputOptions[2] != null && inputOptions[1] == null){ throw new HaploViewException("A marker information file is required if a tests file is specified."); } this.setCursor(Cursor.getPredefinedCursor(Cursor.WAIT_CURSOR)); if (inFile.length() < 1){ throw new HaploViewException("Genotype file is empty or nonexistent: " + inFile.getName()); } if (type == HAPS_FILE){ //these are not available for non ped files viewMenuItems[VIEW_CHECK_NUM].setEnabled(false); viewMenuItems[VIEW_ASSOC_NUM].setEnabled(false); Options.setAssocTest(ASSOC_NONE); } theData = new HaploData(); if (type == HAPS_FILE){ theData.prepareHapsInput(new File(inputOptions[0])); }else{ theData.linkageToChrom(inFile, type); } if(type != HAPS_FILE && theData.getPedFile().isBogusParents()) { JOptionPane.showMessageDialog(this, "One or more individuals in the file reference non-existent parents.\nThese references have been ignored.", "File Error", JOptionPane.ERROR_MESSAGE); } //deal with marker information theData.infoKnown = false; File markerFile; if (inputOptions[1] == null){ markerFile = null; }else{ markerFile = new File(inputOptions[1]); } //turn on/off gbrowse menu if (Options.isGBrowseShown()){ gbEditItem.setEnabled(true); }else{ gbEditItem.setEnabled(false); } checkPanel = null; if (type == HAPS_FILE){ readMarkers(markerFile, null); //initialize realIndex Chromosome.doFilter(Chromosome.getUnfilteredSize()); customAssocSet = null; }else{ readMarkers(markerFile, theData.getPedFile().getHMInfo()); //we read the file in first, so we can whitelist all the markers in the custom test set HashSet whiteListedCustomMarkers = new HashSet(); if (inputOptions[2] != null){ customAssocSet = new AssociationTestSet(inputOptions[2]); whiteListedCustomMarkers = customAssocSet.getWhitelist(); }else{ customAssocSet = null; } theData.setWhiteList(whiteListedCustomMarkers); checkPanel = new CheckDataPanel(this); checkPanel.setAlignmentX(Component.CENTER_ALIGNMENT); //set up the indexing to take into account skipped markers. Chromosome.doFilter(checkPanel.getMarkerResults()); } //let's start the math final SwingWorker worker = new SwingWorker(){ public Object construct(){ dPrimeDisplay=null; changeKey(); theData.generateDPrimeTable(); theData.guessBlocks(BLOX_GABRIEL); //theData.guessBlocks(BLOX_NONE); //for debugging, doesn't call blocks at first blockMenuItems[0].setSelected(true); zoomMenuItems[0].setSelected(true); theData.blocksChanged = false; Container contents = getContentPane(); contents.removeAll(); int currentTab = VIEW_D_NUM; /*if (!(tabs == null)){ currentTab = tabs.getSelectedIndex(); } */ tabs = new JTabbedPane(); tabs.addChangeListener(new TabChangeListener()); //first, draw the D' picture JPanel panel = new JPanel(); panel.setLayout(new BoxLayout(panel, BoxLayout.Y_AXIS)); dPrimeDisplay = new DPrimeDisplay(window); JScrollPane dPrimeScroller = new JScrollPane(dPrimeDisplay); dPrimeScroller.getViewport().setScrollMode(JViewport.BLIT_SCROLL_MODE); dPrimeScroller.getVerticalScrollBar().setUnitIncrement(60); dPrimeScroller.getHorizontalScrollBar().setUnitIncrement(60); panel.add(dPrimeScroller); tabs.addTab(viewItems[VIEW_D_NUM], panel); viewMenuItems[VIEW_D_NUM].setEnabled(true); //compute and show haps on next tab panel = new JPanel(); panel.setLayout(new BoxLayout(panel, BoxLayout.Y_AXIS)); try { hapDisplay = new HaplotypeDisplay(theData); } catch(HaploViewException e) { JOptionPane.showMessageDialog(window, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE); } HaplotypeDisplayController hdc = new HaplotypeDisplayController(hapDisplay); hapScroller = new JScrollPane(hapDisplay); hapScroller.getVerticalScrollBar().setUnitIncrement(60); hapScroller.getHorizontalScrollBar().setUnitIncrement(60); panel.add(hapScroller); panel.add(hdc); tabs.addTab(viewItems[VIEW_HAP_NUM], panel); viewMenuItems[VIEW_HAP_NUM].setEnabled(true); displayMenu.setEnabled(true); analysisMenu.setEnabled(true); //check data panel if (checkPanel != null){ JPanel metaCheckPanel = new JPanel(); metaCheckPanel.setLayout(new BoxLayout(metaCheckPanel, BoxLayout.Y_AXIS)); metaCheckPanel.add(checkPanel); cdc = new CheckDataController(window); metaCheckPanel.add(cdc); tabs.addTab(viewItems[VIEW_CHECK_NUM], metaCheckPanel); viewMenuItems[VIEW_CHECK_NUM].setEnabled(true); currentTab=VIEW_CHECK_NUM; } //tagger display taggerConfigPanel = new TaggerConfigPanel(theData); JPanel metaTagPanel = new JPanel(); metaTagPanel.setLayout(new BoxLayout(metaTagPanel,BoxLayout.Y_AXIS)); metaTagPanel.add(taggerConfigPanel); JTabbedPane tagTabs = new JTabbedPane(); tagTabs.add("Configuration",metaTagPanel); JPanel resMetaPanel = new JPanel(); resMetaPanel.setLayout(new BoxLayout(resMetaPanel,BoxLayout.Y_AXIS)); TaggerResultsPanel tagResultsPanel = new TaggerResultsPanel(); taggerConfigPanel.addActionListener(tagResultsPanel); resMetaPanel.add(tagResultsPanel); tagTabs.addTab("Results",resMetaPanel); tabs.addTab(VIEW_TAGGER,tagTabs); viewMenuItems[VIEW_TAGGER_NUM].setEnabled(true); //Association panel if(Options.getAssocTest() != ASSOC_NONE) { JTabbedPane metaAssoc = new JTabbedPane(); try{ tdtPanel = new TDTPanel(new AssociationTestSet(theData.getPedFile(), null, Chromosome.getAllMarkers())); } catch(PedFileException e) { JOptionPane.showMessageDialog(window, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE); } metaAssoc.add("Single Marker", tdtPanel); hapAssocPanel = new HaploAssocPanel(new AssociationTestSet(theData.getHaplotypes(), null)); metaAssoc.add("Haplotypes", hapAssocPanel); //custom association tests custAssocPanel = null; if(customAssocSet != null) { try { customAssocSet.runFileTests(theData, tdtPanel.getTestSet().getMarkerAssociationResults()); custAssocPanel = new CustomAssocPanel(customAssocSet); metaAssoc.addTab("Custom",custAssocPanel); metaAssoc.setSelectedComponent(custAssocPanel); } catch (HaploViewException e) { JOptionPane.showMessageDialog(window, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE); } } AssociationTestSet permSet; boolean cust = false; if (custAssocPanel != null){ permSet = custAssocPanel.getTestSet(); cust = true; }else{ permSet = new AssociationTestSet(); permSet.cat(tdtPanel.getTestSet()); permSet.cat(hapAssocPanel.getTestSet()); } permutationPanel = new PermutationTestPanel(new PermutationTestSet(0,theData.getSavedEMs(), theData.getPedFile(),permSet), cust); metaAssoc.add(permutationPanel,"Permutation Tests"); tabs.addTab(VIEW_ASSOC, metaAssoc); viewMenuItems[VIEW_ASSOC_NUM].setEnabled(true); } tabs.setSelectedIndex(currentTab); contents.add(tabs); repaint(); setVisible(true); theData.finished = true; setTitle(TITLE_STRING + " -- " + inFile.getName()); return null; } }; timer = new javax.swing.Timer(50, new ActionListener(){ public void actionPerformed(ActionEvent evt){ if (theData.finished){ timer.stop(); for (int i = 0; i < blockMenuItems.length; i++){ blockMenuItems[i].setEnabled(true); } clearBlocksItem.setEnabled(true); readMarkerItem.setEnabled(true); blocksItem.setEnabled(true); exportMenuItems[2].setEnabled(true); setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR)); } } }); worker.start(); timer.start(); }catch(IOException ioexec) { JOptionPane.showMessageDialog(this, ioexec.getMessage(), "File Error", JOptionPane.ERROR_MESSAGE); setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR)); }catch(PedFileException pfe){ JOptionPane.showMessageDialog(this, pfe.getMessage(), "File Error", JOptionPane.ERROR_MESSAGE); setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR)); }catch (HaploViewException hve){ JOptionPane.showMessageDialog(this, hve.getMessage(), "File Error", JOptionPane.ERROR_MESSAGE); setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR)); } }

currentTab=VIEW_CHECK_NUM; } taggerConfigPanel = new TaggerConfigPanel(theData); JPanel metaTagPanel = new JPanel(); metaTagPanel.setLayout(new BoxLayout(metaTagPanel,BoxLayout.Y_AXIS)); metaTagPanel.add(taggerConfigPanel); JTabbedPane tagTabs = new JTabbedPane(); tagTabs.add("Configuration",metaTagPanel); JPanel resMetaPanel = new JPanel(); resMetaPanel.setLayout(new BoxLayout(resMetaPanel,BoxLayout.Y_AXIS)); TaggerResultsPanel tagResultsPanel = new TaggerResultsPanel(); taggerConfigPanel.addActionListener(tagResultsPanel); resMetaPanel.add(tagResultsPanel); tagTabs.addTab("Results",resMetaPanel); tabs.addTab(VIEW_TAGGER,tagTabs); viewMenuItems[VIEW_TAGGER_NUM].setEnabled(true);

currentTab=checkTab; } if (theData.infoKnown){ taggerConfigPanel = new TaggerConfigPanel(theData); JPanel metaTagPanel = new JPanel(); metaTagPanel.setLayout(new BoxLayout(metaTagPanel,BoxLayout.Y_AXIS)); metaTagPanel.add(taggerConfigPanel); JTabbedPane tagTabs = new JTabbedPane(); tagTabs.add("Configuration",metaTagPanel); JPanel resMetaPanel = new JPanel(); resMetaPanel.setLayout(new BoxLayout(resMetaPanel,BoxLayout.Y_AXIS)); TaggerResultsPanel tagResultsPanel = new TaggerResultsPanel(); taggerConfigPanel.addActionListener(tagResultsPanel); resMetaPanel.add(tagResultsPanel); tagTabs.addTab("Results",resMetaPanel); taggerTab = new HaploviewTab(tagTabs); tabs.addTab(VIEW_TAGGER,taggerTab); viewMenuItems[VIEW_TAGGER_NUM].setEnabled(true); }

void readGenotypes(String[] inputOptions, int type){ //input is a 2 element array with //inputOptions[0] = ped file //inputOptions[1] = info file (null if none) //inputOptions[2] = custom association test list file (null if none) //type is either 3 or 4 for ped and hapmap files respectively final File inFile = new File(inputOptions[0]); final AssociationTestSet customAssocSet; try { if (inputOptions[2] != null && inputOptions[1] == null){ throw new HaploViewException("A marker information file is required if a tests file is specified."); } this.setCursor(Cursor.getPredefinedCursor(Cursor.WAIT_CURSOR)); if (inFile.length() < 1){ throw new HaploViewException("Genotype file is empty or nonexistent: " + inFile.getName()); } if (type == HAPS_FILE){ //these are not available for non ped files viewMenuItems[VIEW_CHECK_NUM].setEnabled(false); viewMenuItems[VIEW_ASSOC_NUM].setEnabled(false); Options.setAssocTest(ASSOC_NONE); } theData = new HaploData(); if (type == HAPS_FILE){ theData.prepareHapsInput(new File(inputOptions[0])); }else{ theData.linkageToChrom(inFile, type); } if(type != HAPS_FILE && theData.getPedFile().isBogusParents()) { JOptionPane.showMessageDialog(this, "One or more individuals in the file reference non-existent parents.\nThese references have been ignored.", "File Error", JOptionPane.ERROR_MESSAGE); } //deal with marker information theData.infoKnown = false; File markerFile; if (inputOptions[1] == null){ markerFile = null; }else{ markerFile = new File(inputOptions[1]); } //turn on/off gbrowse menu if (Options.isGBrowseShown()){ gbEditItem.setEnabled(true); }else{ gbEditItem.setEnabled(false); } checkPanel = null; if (type == HAPS_FILE){ readMarkers(markerFile, null); //initialize realIndex Chromosome.doFilter(Chromosome.getUnfilteredSize()); customAssocSet = null; }else{ readMarkers(markerFile, theData.getPedFile().getHMInfo()); //we read the file in first, so we can whitelist all the markers in the custom test set HashSet whiteListedCustomMarkers = new HashSet(); if (inputOptions[2] != null){ customAssocSet = new AssociationTestSet(inputOptions[2]); whiteListedCustomMarkers = customAssocSet.getWhitelist(); }else{ customAssocSet = null; } theData.setWhiteList(whiteListedCustomMarkers); checkPanel = new CheckDataPanel(this); checkPanel.setAlignmentX(Component.CENTER_ALIGNMENT); //set up the indexing to take into account skipped markers. Chromosome.doFilter(checkPanel.getMarkerResults()); } //let's start the math final SwingWorker worker = new SwingWorker(){ public Object construct(){ dPrimeDisplay=null; changeKey(); theData.generateDPrimeTable(); theData.guessBlocks(BLOX_GABRIEL); //theData.guessBlocks(BLOX_NONE); //for debugging, doesn't call blocks at first blockMenuItems[0].setSelected(true); zoomMenuItems[0].setSelected(true); theData.blocksChanged = false; Container contents = getContentPane(); contents.removeAll(); int currentTab = VIEW_D_NUM; /*if (!(tabs == null)){ currentTab = tabs.getSelectedIndex(); } */ tabs = new JTabbedPane(); tabs.addChangeListener(new TabChangeListener()); //first, draw the D' picture JPanel panel = new JPanel(); panel.setLayout(new BoxLayout(panel, BoxLayout.Y_AXIS)); dPrimeDisplay = new DPrimeDisplay(window); JScrollPane dPrimeScroller = new JScrollPane(dPrimeDisplay); dPrimeScroller.getViewport().setScrollMode(JViewport.BLIT_SCROLL_MODE); dPrimeScroller.getVerticalScrollBar().setUnitIncrement(60); dPrimeScroller.getHorizontalScrollBar().setUnitIncrement(60); panel.add(dPrimeScroller); tabs.addTab(viewItems[VIEW_D_NUM], panel); viewMenuItems[VIEW_D_NUM].setEnabled(true); //compute and show haps on next tab panel = new JPanel(); panel.setLayout(new BoxLayout(panel, BoxLayout.Y_AXIS)); try { hapDisplay = new HaplotypeDisplay(theData); } catch(HaploViewException e) { JOptionPane.showMessageDialog(window, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE); } HaplotypeDisplayController hdc = new HaplotypeDisplayController(hapDisplay); hapScroller = new JScrollPane(hapDisplay); hapScroller.getVerticalScrollBar().setUnitIncrement(60); hapScroller.getHorizontalScrollBar().setUnitIncrement(60); panel.add(hapScroller); panel.add(hdc); tabs.addTab(viewItems[VIEW_HAP_NUM], panel); viewMenuItems[VIEW_HAP_NUM].setEnabled(true); displayMenu.setEnabled(true); analysisMenu.setEnabled(true); //check data panel if (checkPanel != null){ JPanel metaCheckPanel = new JPanel(); metaCheckPanel.setLayout(new BoxLayout(metaCheckPanel, BoxLayout.Y_AXIS)); metaCheckPanel.add(checkPanel); cdc = new CheckDataController(window); metaCheckPanel.add(cdc); tabs.addTab(viewItems[VIEW_CHECK_NUM], metaCheckPanel); viewMenuItems[VIEW_CHECK_NUM].setEnabled(true); currentTab=VIEW_CHECK_NUM; } //tagger display taggerConfigPanel = new TaggerConfigPanel(theData); JPanel metaTagPanel = new JPanel(); metaTagPanel.setLayout(new BoxLayout(metaTagPanel,BoxLayout.Y_AXIS)); metaTagPanel.add(taggerConfigPanel); JTabbedPane tagTabs = new JTabbedPane(); tagTabs.add("Configuration",metaTagPanel); JPanel resMetaPanel = new JPanel(); resMetaPanel.setLayout(new BoxLayout(resMetaPanel,BoxLayout.Y_AXIS)); TaggerResultsPanel tagResultsPanel = new TaggerResultsPanel(); taggerConfigPanel.addActionListener(tagResultsPanel); resMetaPanel.add(tagResultsPanel); tagTabs.addTab("Results",resMetaPanel); tabs.addTab(VIEW_TAGGER,tagTabs); viewMenuItems[VIEW_TAGGER_NUM].setEnabled(true); //Association panel if(Options.getAssocTest() != ASSOC_NONE) { JTabbedPane metaAssoc = new JTabbedPane(); try{ tdtPanel = new TDTPanel(new AssociationTestSet(theData.getPedFile(), null, Chromosome.getAllMarkers())); } catch(PedFileException e) { JOptionPane.showMessageDialog(window, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE); } metaAssoc.add("Single Marker", tdtPanel); hapAssocPanel = new HaploAssocPanel(new AssociationTestSet(theData.getHaplotypes(), null)); metaAssoc.add("Haplotypes", hapAssocPanel); //custom association tests custAssocPanel = null; if(customAssocSet != null) { try { customAssocSet.runFileTests(theData, tdtPanel.getTestSet().getMarkerAssociationResults()); custAssocPanel = new CustomAssocPanel(customAssocSet); metaAssoc.addTab("Custom",custAssocPanel); metaAssoc.setSelectedComponent(custAssocPanel); } catch (HaploViewException e) { JOptionPane.showMessageDialog(window, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE); } } AssociationTestSet permSet; boolean cust = false; if (custAssocPanel != null){ permSet = custAssocPanel.getTestSet(); cust = true; }else{ permSet = new AssociationTestSet(); permSet.cat(tdtPanel.getTestSet()); permSet.cat(hapAssocPanel.getTestSet()); } permutationPanel = new PermutationTestPanel(new PermutationTestSet(0,theData.getSavedEMs(), theData.getPedFile(),permSet), cust); metaAssoc.add(permutationPanel,"Permutation Tests"); tabs.addTab(VIEW_ASSOC, metaAssoc); viewMenuItems[VIEW_ASSOC_NUM].setEnabled(true); } tabs.setSelectedIndex(currentTab); contents.add(tabs); repaint(); setVisible(true); theData.finished = true; setTitle(TITLE_STRING + " -- " + inFile.getName()); return null; } }; timer = new javax.swing.Timer(50, new ActionListener(){ public void actionPerformed(ActionEvent evt){ if (theData.finished){ timer.stop(); for (int i = 0; i < blockMenuItems.length; i++){ blockMenuItems[i].setEnabled(true); } clearBlocksItem.setEnabled(true); readMarkerItem.setEnabled(true); blocksItem.setEnabled(true); exportMenuItems[2].setEnabled(true); setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR)); } } }); worker.start(); timer.start(); }catch(IOException ioexec) { JOptionPane.showMessageDialog(this, ioexec.getMessage(), "File Error", JOptionPane.ERROR_MESSAGE); setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR)); }catch(PedFileException pfe){ JOptionPane.showMessageDialog(this, pfe.getMessage(), "File Error", JOptionPane.ERROR_MESSAGE); setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR)); }catch (HaploViewException hve){ JOptionPane.showMessageDialog(this, hve.getMessage(), "File Error", JOptionPane.ERROR_MESSAGE); setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR)); } }

tabs.addTab(VIEW_ASSOC, metaAssoc);

associationTab = new HaploviewTab(metaAssoc); tabs.addTab(VIEW_ASSOC, associationTab);

void readGenotypes(String[] inputOptions, int type){ //input is a 2 element array with //inputOptions[0] = ped file //inputOptions[1] = info file (null if none) //inputOptions[2] = custom association test list file (null if none) //type is either 3 or 4 for ped and hapmap files respectively final File inFile = new File(inputOptions[0]); final AssociationTestSet customAssocSet; try { if (inputOptions[2] != null && inputOptions[1] == null){ throw new HaploViewException("A marker information file is required if a tests file is specified."); } this.setCursor(Cursor.getPredefinedCursor(Cursor.WAIT_CURSOR)); if (inFile.length() < 1){ throw new HaploViewException("Genotype file is empty or nonexistent: " + inFile.getName()); } if (type == HAPS_FILE){ //these are not available for non ped files viewMenuItems[VIEW_CHECK_NUM].setEnabled(false); viewMenuItems[VIEW_ASSOC_NUM].setEnabled(false); Options.setAssocTest(ASSOC_NONE); } theData = new HaploData(); if (type == HAPS_FILE){ theData.prepareHapsInput(new File(inputOptions[0])); }else{ theData.linkageToChrom(inFile, type); } if(type != HAPS_FILE && theData.getPedFile().isBogusParents()) { JOptionPane.showMessageDialog(this, "One or more individuals in the file reference non-existent parents.\nThese references have been ignored.", "File Error", JOptionPane.ERROR_MESSAGE); } //deal with marker information theData.infoKnown = false; File markerFile; if (inputOptions[1] == null){ markerFile = null; }else{ markerFile = new File(inputOptions[1]); } //turn on/off gbrowse menu if (Options.isGBrowseShown()){ gbEditItem.setEnabled(true); }else{ gbEditItem.setEnabled(false); } checkPanel = null; if (type == HAPS_FILE){ readMarkers(markerFile, null); //initialize realIndex Chromosome.doFilter(Chromosome.getUnfilteredSize()); customAssocSet = null; }else{ readMarkers(markerFile, theData.getPedFile().getHMInfo()); //we read the file in first, so we can whitelist all the markers in the custom test set HashSet whiteListedCustomMarkers = new HashSet(); if (inputOptions[2] != null){ customAssocSet = new AssociationTestSet(inputOptions[2]); whiteListedCustomMarkers = customAssocSet.getWhitelist(); }else{ customAssocSet = null; } theData.setWhiteList(whiteListedCustomMarkers); checkPanel = new CheckDataPanel(this); checkPanel.setAlignmentX(Component.CENTER_ALIGNMENT); //set up the indexing to take into account skipped markers. Chromosome.doFilter(checkPanel.getMarkerResults()); } //let's start the math final SwingWorker worker = new SwingWorker(){ public Object construct(){ dPrimeDisplay=null; changeKey(); theData.generateDPrimeTable(); theData.guessBlocks(BLOX_GABRIEL); //theData.guessBlocks(BLOX_NONE); //for debugging, doesn't call blocks at first blockMenuItems[0].setSelected(true); zoomMenuItems[0].setSelected(true); theData.blocksChanged = false; Container contents = getContentPane(); contents.removeAll(); int currentTab = VIEW_D_NUM; /*if (!(tabs == null)){ currentTab = tabs.getSelectedIndex(); } */ tabs = new JTabbedPane(); tabs.addChangeListener(new TabChangeListener()); //first, draw the D' picture JPanel panel = new JPanel(); panel.setLayout(new BoxLayout(panel, BoxLayout.Y_AXIS)); dPrimeDisplay = new DPrimeDisplay(window); JScrollPane dPrimeScroller = new JScrollPane(dPrimeDisplay); dPrimeScroller.getViewport().setScrollMode(JViewport.BLIT_SCROLL_MODE); dPrimeScroller.getVerticalScrollBar().setUnitIncrement(60); dPrimeScroller.getHorizontalScrollBar().setUnitIncrement(60); panel.add(dPrimeScroller); tabs.addTab(viewItems[VIEW_D_NUM], panel); viewMenuItems[VIEW_D_NUM].setEnabled(true); //compute and show haps on next tab panel = new JPanel(); panel.setLayout(new BoxLayout(panel, BoxLayout.Y_AXIS)); try { hapDisplay = new HaplotypeDisplay(theData); } catch(HaploViewException e) { JOptionPane.showMessageDialog(window, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE); } HaplotypeDisplayController hdc = new HaplotypeDisplayController(hapDisplay); hapScroller = new JScrollPane(hapDisplay); hapScroller.getVerticalScrollBar().setUnitIncrement(60); hapScroller.getHorizontalScrollBar().setUnitIncrement(60); panel.add(hapScroller); panel.add(hdc); tabs.addTab(viewItems[VIEW_HAP_NUM], panel); viewMenuItems[VIEW_HAP_NUM].setEnabled(true); displayMenu.setEnabled(true); analysisMenu.setEnabled(true); //check data panel if (checkPanel != null){ JPanel metaCheckPanel = new JPanel(); metaCheckPanel.setLayout(new BoxLayout(metaCheckPanel, BoxLayout.Y_AXIS)); metaCheckPanel.add(checkPanel); cdc = new CheckDataController(window); metaCheckPanel.add(cdc); tabs.addTab(viewItems[VIEW_CHECK_NUM], metaCheckPanel); viewMenuItems[VIEW_CHECK_NUM].setEnabled(true); currentTab=VIEW_CHECK_NUM; } //tagger display taggerConfigPanel = new TaggerConfigPanel(theData); JPanel metaTagPanel = new JPanel(); metaTagPanel.setLayout(new BoxLayout(metaTagPanel,BoxLayout.Y_AXIS)); metaTagPanel.add(taggerConfigPanel); JTabbedPane tagTabs = new JTabbedPane(); tagTabs.add("Configuration",metaTagPanel); JPanel resMetaPanel = new JPanel(); resMetaPanel.setLayout(new BoxLayout(resMetaPanel,BoxLayout.Y_AXIS)); TaggerResultsPanel tagResultsPanel = new TaggerResultsPanel(); taggerConfigPanel.addActionListener(tagResultsPanel); resMetaPanel.add(tagResultsPanel); tagTabs.addTab("Results",resMetaPanel); tabs.addTab(VIEW_TAGGER,tagTabs); viewMenuItems[VIEW_TAGGER_NUM].setEnabled(true); //Association panel if(Options.getAssocTest() != ASSOC_NONE) { JTabbedPane metaAssoc = new JTabbedPane(); try{ tdtPanel = new TDTPanel(new AssociationTestSet(theData.getPedFile(), null, Chromosome.getAllMarkers())); } catch(PedFileException e) { JOptionPane.showMessageDialog(window, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE); } metaAssoc.add("Single Marker", tdtPanel); hapAssocPanel = new HaploAssocPanel(new AssociationTestSet(theData.getHaplotypes(), null)); metaAssoc.add("Haplotypes", hapAssocPanel); //custom association tests custAssocPanel = null; if(customAssocSet != null) { try { customAssocSet.runFileTests(theData, tdtPanel.getTestSet().getMarkerAssociationResults()); custAssocPanel = new CustomAssocPanel(customAssocSet); metaAssoc.addTab("Custom",custAssocPanel); metaAssoc.setSelectedComponent(custAssocPanel); } catch (HaploViewException e) { JOptionPane.showMessageDialog(window, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE); } } AssociationTestSet permSet; boolean cust = false; if (custAssocPanel != null){ permSet = custAssocPanel.getTestSet(); cust = true; }else{ permSet = new AssociationTestSet(); permSet.cat(tdtPanel.getTestSet()); permSet.cat(hapAssocPanel.getTestSet()); } permutationPanel = new PermutationTestPanel(new PermutationTestSet(0,theData.getSavedEMs(), theData.getPedFile(),permSet), cust); metaAssoc.add(permutationPanel,"Permutation Tests"); tabs.addTab(VIEW_ASSOC, metaAssoc); viewMenuItems[VIEW_ASSOC_NUM].setEnabled(true); } tabs.setSelectedIndex(currentTab); contents.add(tabs); repaint(); setVisible(true); theData.finished = true; setTitle(TITLE_STRING + " -- " + inFile.getName()); return null; } }; timer = new javax.swing.Timer(50, new ActionListener(){ public void actionPerformed(ActionEvent evt){ if (theData.finished){ timer.stop(); for (int i = 0; i < blockMenuItems.length; i++){ blockMenuItems[i].setEnabled(true); } clearBlocksItem.setEnabled(true); readMarkerItem.setEnabled(true); blocksItem.setEnabled(true); exportMenuItems[2].setEnabled(true); setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR)); } } }); worker.start(); timer.start(); }catch(IOException ioexec) { JOptionPane.showMessageDialog(this, ioexec.getMessage(), "File Error", JOptionPane.ERROR_MESSAGE); setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR)); }catch(PedFileException pfe){ JOptionPane.showMessageDialog(this, pfe.getMessage(), "File Error", JOptionPane.ERROR_MESSAGE); setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR)); }catch (HaploViewException hve){ JOptionPane.showMessageDialog(this, hve.getMessage(), "File Error", JOptionPane.ERROR_MESSAGE); setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR)); } }

tabs.setSelectedIndex(currentTab);

tabs.setSelectedComponent(currentTab);

void readGenotypes(String[] inputOptions, int type){ //input is a 2 element array with //inputOptions[0] = ped file //inputOptions[1] = info file (null if none) //inputOptions[2] = custom association test list file (null if none) //type is either 3 or 4 for ped and hapmap files respectively final File inFile = new File(inputOptions[0]); final AssociationTestSet customAssocSet; try { if (inputOptions[2] != null && inputOptions[1] == null){ throw new HaploViewException("A marker information file is required if a tests file is specified."); } this.setCursor(Cursor.getPredefinedCursor(Cursor.WAIT_CURSOR)); if (inFile.length() < 1){ throw new HaploViewException("Genotype file is empty or nonexistent: " + inFile.getName()); } if (type == HAPS_FILE){ //these are not available for non ped files viewMenuItems[VIEW_CHECK_NUM].setEnabled(false); viewMenuItems[VIEW_ASSOC_NUM].setEnabled(false); Options.setAssocTest(ASSOC_NONE); } theData = new HaploData(); if (type == HAPS_FILE){ theData.prepareHapsInput(new File(inputOptions[0])); }else{ theData.linkageToChrom(inFile, type); } if(type != HAPS_FILE && theData.getPedFile().isBogusParents()) { JOptionPane.showMessageDialog(this, "One or more individuals in the file reference non-existent parents.\nThese references have been ignored.", "File Error", JOptionPane.ERROR_MESSAGE); } //deal with marker information theData.infoKnown = false; File markerFile; if (inputOptions[1] == null){ markerFile = null; }else{ markerFile = new File(inputOptions[1]); } //turn on/off gbrowse menu if (Options.isGBrowseShown()){ gbEditItem.setEnabled(true); }else{ gbEditItem.setEnabled(false); } checkPanel = null; if (type == HAPS_FILE){ readMarkers(markerFile, null); //initialize realIndex Chromosome.doFilter(Chromosome.getUnfilteredSize()); customAssocSet = null; }else{ readMarkers(markerFile, theData.getPedFile().getHMInfo()); //we read the file in first, so we can whitelist all the markers in the custom test set HashSet whiteListedCustomMarkers = new HashSet(); if (inputOptions[2] != null){ customAssocSet = new AssociationTestSet(inputOptions[2]); whiteListedCustomMarkers = customAssocSet.getWhitelist(); }else{ customAssocSet = null; } theData.setWhiteList(whiteListedCustomMarkers); checkPanel = new CheckDataPanel(this); checkPanel.setAlignmentX(Component.CENTER_ALIGNMENT); //set up the indexing to take into account skipped markers. Chromosome.doFilter(checkPanel.getMarkerResults()); } //let's start the math final SwingWorker worker = new SwingWorker(){ public Object construct(){ dPrimeDisplay=null; changeKey(); theData.generateDPrimeTable(); theData.guessBlocks(BLOX_GABRIEL); //theData.guessBlocks(BLOX_NONE); //for debugging, doesn't call blocks at first blockMenuItems[0].setSelected(true); zoomMenuItems[0].setSelected(true); theData.blocksChanged = false; Container contents = getContentPane(); contents.removeAll(); int currentTab = VIEW_D_NUM; /*if (!(tabs == null)){ currentTab = tabs.getSelectedIndex(); } */ tabs = new JTabbedPane(); tabs.addChangeListener(new TabChangeListener()); //first, draw the D' picture JPanel panel = new JPanel(); panel.setLayout(new BoxLayout(panel, BoxLayout.Y_AXIS)); dPrimeDisplay = new DPrimeDisplay(window); JScrollPane dPrimeScroller = new JScrollPane(dPrimeDisplay); dPrimeScroller.getViewport().setScrollMode(JViewport.BLIT_SCROLL_MODE); dPrimeScroller.getVerticalScrollBar().setUnitIncrement(60); dPrimeScroller.getHorizontalScrollBar().setUnitIncrement(60); panel.add(dPrimeScroller); tabs.addTab(viewItems[VIEW_D_NUM], panel); viewMenuItems[VIEW_D_NUM].setEnabled(true); //compute and show haps on next tab panel = new JPanel(); panel.setLayout(new BoxLayout(panel, BoxLayout.Y_AXIS)); try { hapDisplay = new HaplotypeDisplay(theData); } catch(HaploViewException e) { JOptionPane.showMessageDialog(window, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE); } HaplotypeDisplayController hdc = new HaplotypeDisplayController(hapDisplay); hapScroller = new JScrollPane(hapDisplay); hapScroller.getVerticalScrollBar().setUnitIncrement(60); hapScroller.getHorizontalScrollBar().setUnitIncrement(60); panel.add(hapScroller); panel.add(hdc); tabs.addTab(viewItems[VIEW_HAP_NUM], panel); viewMenuItems[VIEW_HAP_NUM].setEnabled(true); displayMenu.setEnabled(true); analysisMenu.setEnabled(true); //check data panel if (checkPanel != null){ JPanel metaCheckPanel = new JPanel(); metaCheckPanel.setLayout(new BoxLayout(metaCheckPanel, BoxLayout.Y_AXIS)); metaCheckPanel.add(checkPanel); cdc = new CheckDataController(window); metaCheckPanel.add(cdc); tabs.addTab(viewItems[VIEW_CHECK_NUM], metaCheckPanel); viewMenuItems[VIEW_CHECK_NUM].setEnabled(true); currentTab=VIEW_CHECK_NUM; } //tagger display taggerConfigPanel = new TaggerConfigPanel(theData); JPanel metaTagPanel = new JPanel(); metaTagPanel.setLayout(new BoxLayout(metaTagPanel,BoxLayout.Y_AXIS)); metaTagPanel.add(taggerConfigPanel); JTabbedPane tagTabs = new JTabbedPane(); tagTabs.add("Configuration",metaTagPanel); JPanel resMetaPanel = new JPanel(); resMetaPanel.setLayout(new BoxLayout(resMetaPanel,BoxLayout.Y_AXIS)); TaggerResultsPanel tagResultsPanel = new TaggerResultsPanel(); taggerConfigPanel.addActionListener(tagResultsPanel); resMetaPanel.add(tagResultsPanel); tagTabs.addTab("Results",resMetaPanel); tabs.addTab(VIEW_TAGGER,tagTabs); viewMenuItems[VIEW_TAGGER_NUM].setEnabled(true); //Association panel if(Options.getAssocTest() != ASSOC_NONE) { JTabbedPane metaAssoc = new JTabbedPane(); try{ tdtPanel = new TDTPanel(new AssociationTestSet(theData.getPedFile(), null, Chromosome.getAllMarkers())); } catch(PedFileException e) { JOptionPane.showMessageDialog(window, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE); } metaAssoc.add("Single Marker", tdtPanel); hapAssocPanel = new HaploAssocPanel(new AssociationTestSet(theData.getHaplotypes(), null)); metaAssoc.add("Haplotypes", hapAssocPanel); //custom association tests custAssocPanel = null; if(customAssocSet != null) { try { customAssocSet.runFileTests(theData, tdtPanel.getTestSet().getMarkerAssociationResults()); custAssocPanel = new CustomAssocPanel(customAssocSet); metaAssoc.addTab("Custom",custAssocPanel); metaAssoc.setSelectedComponent(custAssocPanel); } catch (HaploViewException e) { JOptionPane.showMessageDialog(window, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE); } } AssociationTestSet permSet; boolean cust = false; if (custAssocPanel != null){ permSet = custAssocPanel.getTestSet(); cust = true; }else{ permSet = new AssociationTestSet(); permSet.cat(tdtPanel.getTestSet()); permSet.cat(hapAssocPanel.getTestSet()); } permutationPanel = new PermutationTestPanel(new PermutationTestSet(0,theData.getSavedEMs(), theData.getPedFile(),permSet), cust); metaAssoc.add(permutationPanel,"Permutation Tests"); tabs.addTab(VIEW_ASSOC, metaAssoc); viewMenuItems[VIEW_ASSOC_NUM].setEnabled(true); } tabs.setSelectedIndex(currentTab); contents.add(tabs); repaint(); setVisible(true); theData.finished = true; setTitle(TITLE_STRING + " -- " + inFile.getName()); return null; } }; timer = new javax.swing.Timer(50, new ActionListener(){ public void actionPerformed(ActionEvent evt){ if (theData.finished){ timer.stop(); for (int i = 0; i < blockMenuItems.length; i++){ blockMenuItems[i].setEnabled(true); } clearBlocksItem.setEnabled(true); readMarkerItem.setEnabled(true); blocksItem.setEnabled(true); exportMenuItems[2].setEnabled(true); setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR)); } } }); worker.start(); timer.start(); }catch(IOException ioexec) { JOptionPane.showMessageDialog(this, ioexec.getMessage(), "File Error", JOptionPane.ERROR_MESSAGE); setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR)); }catch(PedFileException pfe){ JOptionPane.showMessageDialog(this, pfe.getMessage(), "File Error", JOptionPane.ERROR_MESSAGE); setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR)); }catch (HaploViewException hve){ JOptionPane.showMessageDialog(this, hve.getMessage(), "File Error", JOptionPane.ERROR_MESSAGE); setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR)); } }

int currentTab = VIEW_D_NUM;

HaploviewTab currentTab = ldTab;

public Object construct(){ dPrimeDisplay=null; changeKey(); theData.generateDPrimeTable(); theData.guessBlocks(BLOX_GABRIEL); //theData.guessBlocks(BLOX_NONE); //for debugging, doesn't call blocks at first blockMenuItems[0].setSelected(true); zoomMenuItems[0].setSelected(true); theData.blocksChanged = false; Container contents = getContentPane(); contents.removeAll(); int currentTab = VIEW_D_NUM; /*if (!(tabs == null)){ currentTab = tabs.getSelectedIndex(); } */ tabs = new JTabbedPane(); tabs.addChangeListener(new TabChangeListener()); //first, draw the D' picture JPanel panel = new JPanel(); panel.setLayout(new BoxLayout(panel, BoxLayout.Y_AXIS)); dPrimeDisplay = new DPrimeDisplay(window); JScrollPane dPrimeScroller = new JScrollPane(dPrimeDisplay); dPrimeScroller.getViewport().setScrollMode(JViewport.BLIT_SCROLL_MODE); dPrimeScroller.getVerticalScrollBar().setUnitIncrement(60); dPrimeScroller.getHorizontalScrollBar().setUnitIncrement(60); panel.add(dPrimeScroller); tabs.addTab(viewItems[VIEW_D_NUM], panel); viewMenuItems[VIEW_D_NUM].setEnabled(true); //compute and show haps on next tab panel = new JPanel(); panel.setLayout(new BoxLayout(panel, BoxLayout.Y_AXIS)); try { hapDisplay = new HaplotypeDisplay(theData); } catch(HaploViewException e) { JOptionPane.showMessageDialog(window, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE); } HaplotypeDisplayController hdc = new HaplotypeDisplayController(hapDisplay); hapScroller = new JScrollPane(hapDisplay); hapScroller.getVerticalScrollBar().setUnitIncrement(60); hapScroller.getHorizontalScrollBar().setUnitIncrement(60); panel.add(hapScroller); panel.add(hdc); tabs.addTab(viewItems[VIEW_HAP_NUM], panel); viewMenuItems[VIEW_HAP_NUM].setEnabled(true); displayMenu.setEnabled(true); analysisMenu.setEnabled(true); //check data panel if (checkPanel != null){ JPanel metaCheckPanel = new JPanel(); metaCheckPanel.setLayout(new BoxLayout(metaCheckPanel, BoxLayout.Y_AXIS)); metaCheckPanel.add(checkPanel); cdc = new CheckDataController(window); metaCheckPanel.add(cdc); tabs.addTab(viewItems[VIEW_CHECK_NUM], metaCheckPanel); viewMenuItems[VIEW_CHECK_NUM].setEnabled(true); currentTab=VIEW_CHECK_NUM; } //tagger display taggerConfigPanel = new TaggerConfigPanel(theData); JPanel metaTagPanel = new JPanel(); metaTagPanel.setLayout(new BoxLayout(metaTagPanel,BoxLayout.Y_AXIS)); metaTagPanel.add(taggerConfigPanel); JTabbedPane tagTabs = new JTabbedPane(); tagTabs.add("Configuration",metaTagPanel); JPanel resMetaPanel = new JPanel(); resMetaPanel.setLayout(new BoxLayout(resMetaPanel,BoxLayout.Y_AXIS)); TaggerResultsPanel tagResultsPanel = new TaggerResultsPanel(); taggerConfigPanel.addActionListener(tagResultsPanel); resMetaPanel.add(tagResultsPanel); tagTabs.addTab("Results",resMetaPanel); tabs.addTab(VIEW_TAGGER,tagTabs); viewMenuItems[VIEW_TAGGER_NUM].setEnabled(true); //Association panel if(Options.getAssocTest() != ASSOC_NONE) { JTabbedPane metaAssoc = new JTabbedPane(); try{ tdtPanel = new TDTPanel(new AssociationTestSet(theData.getPedFile(), null, Chromosome.getAllMarkers())); } catch(PedFileException e) { JOptionPane.showMessageDialog(window, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE); } metaAssoc.add("Single Marker", tdtPanel); hapAssocPanel = new HaploAssocPanel(new AssociationTestSet(theData.getHaplotypes(), null)); metaAssoc.add("Haplotypes", hapAssocPanel); //custom association tests custAssocPanel = null; if(customAssocSet != null) { try { customAssocSet.runFileTests(theData, tdtPanel.getTestSet().getMarkerAssociationResults()); custAssocPanel = new CustomAssocPanel(customAssocSet); metaAssoc.addTab("Custom",custAssocPanel); metaAssoc.setSelectedComponent(custAssocPanel); } catch (HaploViewException e) { JOptionPane.showMessageDialog(window, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE); } } AssociationTestSet permSet; boolean cust = false; if (custAssocPanel != null){ permSet = custAssocPanel.getTestSet(); cust = true; }else{ permSet = new AssociationTestSet(); permSet.cat(tdtPanel.getTestSet()); permSet.cat(hapAssocPanel.getTestSet()); } permutationPanel = new PermutationTestPanel(new PermutationTestSet(0,theData.getSavedEMs(), theData.getPedFile(),permSet), cust); metaAssoc.add(permutationPanel,"Permutation Tests"); tabs.addTab(VIEW_ASSOC, metaAssoc); viewMenuItems[VIEW_ASSOC_NUM].setEnabled(true); } tabs.setSelectedIndex(currentTab); contents.add(tabs); repaint(); setVisible(true); theData.finished = true; setTitle(TITLE_STRING + " -- " + inFile.getName()); return null; }