@Test(expected = IllegalArgumentException.class) public void noZero( ) { KeyValue kv = new KeyValue("8675904"); String now = SimulationData.createCanonicalSmoldynOutputFileName(kv, 0, 0); System.out.println("never see " + now); }
public static String createCanonicalSmoldynOutputFileName(KeyValue fieldDataKey,int jobIndex,int timeIndex){ if (timeIndex > 0) { String rval = createSimIDWithJobIndex(fieldDataKey,jobIndex,false) + String.format("_%03d",timeIndex) + SimDataConstants.SMOLDYN_OUTPUT_FILE_EXTENSION; return rval; } throw new IllegalArgumentException("smoldyn output index must be > 0"); }
SimulationData extends VCData { public static String createCanonicalSmoldynOutputFileName(KeyValue fieldDataKey,int jobIndex,int timeIndex){ if (timeIndex > 0) { String rval = createSimIDWithJobIndex(fieldDataKey,jobIndex,false) + String.format("_%03d",timeIndex) + SimDataConstants.SMOLDYN_OUTPUT_FILE_EXTENSION; return rval; } throw new IllegalArgumentException("smoldyn output index must be > 0"); } }
SimulationData extends VCData { public static String createCanonicalSmoldynOutputFileName(KeyValue fieldDataKey,int jobIndex,int timeIndex){ if (timeIndex > 0) { String rval = createSimIDWithJobIndex(fieldDataKey,jobIndex,false) + String.format("_%03d",timeIndex) + SimDataConstants.SMOLDYN_OUTPUT_FILE_EXTENSION; return rval; } throw new IllegalArgumentException("smoldyn output index must be > 0"); } SimulationData(VCDataIdentifier argVCDataID, File primaryUserDir, File secondaryUserDir,SimDataAmplistorInfo simDataAmplistorInfo); }
SimulationData extends VCData { public static String createCanonicalSmoldynOutputFileName(KeyValue fieldDataKey,int jobIndex,int timeIndex){ if (timeIndex > 0) { String rval = createSimIDWithJobIndex(fieldDataKey,jobIndex,false) + String.format("_%03d",timeIndex) + SimDataConstants.SMOLDYN_OUTPUT_FILE_EXTENSION; return rval; } throw new IllegalArgumentException("smoldyn output index must be > 0"); } SimulationData(VCDataIdentifier argVCDataID, File primaryUserDir, File secondaryUserDir,SimDataAmplistorInfo simDataAmplistorInfo); static VCDataIdentifier createScanFriendlyVCDataID(VCDataIdentifier inVCDID); AnnotatedFunction simplifyFunction(AnnotatedFunction function); synchronized long getDataBlockTimeStamp(int dataType, double timepoint); synchronized double[] getDataTimesPostProcess(OutputContext outputContext); synchronized double[] getDataTimes(); SymbolTableEntry getEntry(String identifier); AnnotatedFunction getFunction(OutputContext outputContext,String identifier); AnnotatedFunction[] getFunctions(OutputContext outputContext); synchronized boolean getIsODEData(); File getLogFilePrivate(); synchronized CartesianMesh getPostProcessingMesh(String varName,OutputContext outputContext); synchronized CartesianMesh getMesh(); synchronized ODEDataBlock getODEDataBlock(); synchronized ParticleDataBlock getParticleDataBlock(double time); synchronized boolean getParticleDataExists(); synchronized VCDataIdentifier getResultsInfoObject(); synchronized SimDataBlock getSimDataBlock(OutputContext outputContext, String varName, double time); synchronized long getSizeInBytes(); synchronized DataIdentifier[] getVarAndFunctionDataIdentifiers(OutputContext outputContext); boolean isChombo(); @Override boolean isMovingBoundary(); @Override boolean isComsol(); synchronized void removeAllResults(); static String createCanonicalSimFilePathName(KeyValue fieldDataKey,int timeIndex,int jobIndex,boolean isOldStyle); static String createCanonicalSimTaskXMLFilePathName(KeyValue fieldDataKey,int jobIndex,boolean isOldStyle); static String createCanonicalFieldDataLogFileName(KeyValue fieldDataKey); static String createCanonicalFieldFunctionSyntax(String externalDataIdentifierName,String varName,double beginTime,String extDataIdVariableTypeName); static String createCanonicalSimZipFileName(KeyValue fieldDataKey,Integer zipIndex,int jobIndex,boolean isOldStyle,boolean bHDF5); static String createCanonicalSimLogFileName(KeyValue fieldDataKey,int jobIndex,boolean isOldStyle); static String createCanonicalSmoldynOutputFileName(KeyValue fieldDataKey,int jobIndex,int timeIndex); static String createCanonicalPostProcessFileName(VCDataIdentifier vcdID); static String createCanonicalNFSimOutputFileName(KeyValue fieldDataKey,int jobIndex); static String createCanonicalMeshFileName(KeyValue fieldDataKey,int jobIndex,boolean isOldStyle); static String createCanonicalMeshMetricsFileName(KeyValue fieldDataKey,int jobIndex,boolean isOldStyle); static String createCanonicalMovingBoundaryOutputFileName(KeyValue fieldDataKey,int jobIndex,boolean isOldStyle); static String createCanonicalComsolOutputFileName(KeyValue fieldDataKey,int jobIndex,boolean isOldStyle); static String createCanonicalFunctionsFileName(KeyValue fieldDataKey,int jobIndex,boolean isOldStyle); static String createCanonicalSubdomainFileName(KeyValue fieldDataKey,int jobIndex,boolean isOldStyle); static String createCanonicalResampleFileName(SimResampleInfoProvider simResampleInfoProvider,FieldFunctionArguments fieldFuncArgs); static String createSimIDWithJobIndex(KeyValue fieldDataKey,int jobIndex,boolean isOldStyle); void getEntries(Map<String, SymbolTableEntry> entryMap); boolean isPostProcessing(OutputContext outputContext,String varName); File getDataProcessingOutputSourceFileHDF5(); File getFieldDataFile(SimResampleInfoProvider simResampleInfoProvider,FieldFunctionArguments fieldFunctionArguments); File getMeshFile(boolean bHDF5); File getFunctionsFile(boolean bFirst); File getZipFile(boolean bHDF5,Integer zipIndex); File getSubdomainFile(); File getLogFile(); File getSmoldynOutputFile(int timeIndex); @Override ChomboFiles getChomboFiles(); @Override VCellSimFiles getVCellSimFiles(); @Override MovingBoundarySimFiles getMovingBoundarySimFiles(); @Override ComsolSimFiles getComsolSimFiles(); VCDataIdentifier getVcDataId(); synchronized SimDataBlock getChomboExtrapolatedValues(String varName, double time); static final VariableType getVariableTypeFromLength(CartesianMesh mesh, int dataLength); static String getDefaultFieldDataFileNameForSimulation(FieldFunctionArguments fieldFuncArgs); }
SimulationData extends VCData { public static String createCanonicalSmoldynOutputFileName(KeyValue fieldDataKey,int jobIndex,int timeIndex){ if (timeIndex > 0) { String rval = createSimIDWithJobIndex(fieldDataKey,jobIndex,false) + String.format("_%03d",timeIndex) + SimDataConstants.SMOLDYN_OUTPUT_FILE_EXTENSION; return rval; } throw new IllegalArgumentException("smoldyn output index must be > 0"); } SimulationData(VCDataIdentifier argVCDataID, File primaryUserDir, File secondaryUserDir,SimDataAmplistorInfo simDataAmplistorInfo); static VCDataIdentifier createScanFriendlyVCDataID(VCDataIdentifier inVCDID); AnnotatedFunction simplifyFunction(AnnotatedFunction function); synchronized long getDataBlockTimeStamp(int dataType, double timepoint); synchronized double[] getDataTimesPostProcess(OutputContext outputContext); synchronized double[] getDataTimes(); SymbolTableEntry getEntry(String identifier); AnnotatedFunction getFunction(OutputContext outputContext,String identifier); AnnotatedFunction[] getFunctions(OutputContext outputContext); synchronized boolean getIsODEData(); File getLogFilePrivate(); synchronized CartesianMesh getPostProcessingMesh(String varName,OutputContext outputContext); synchronized CartesianMesh getMesh(); synchronized ODEDataBlock getODEDataBlock(); synchronized ParticleDataBlock getParticleDataBlock(double time); synchronized boolean getParticleDataExists(); synchronized VCDataIdentifier getResultsInfoObject(); synchronized SimDataBlock getSimDataBlock(OutputContext outputContext, String varName, double time); synchronized long getSizeInBytes(); synchronized DataIdentifier[] getVarAndFunctionDataIdentifiers(OutputContext outputContext); boolean isChombo(); @Override boolean isMovingBoundary(); @Override boolean isComsol(); synchronized void removeAllResults(); static String createCanonicalSimFilePathName(KeyValue fieldDataKey,int timeIndex,int jobIndex,boolean isOldStyle); static String createCanonicalSimTaskXMLFilePathName(KeyValue fieldDataKey,int jobIndex,boolean isOldStyle); static String createCanonicalFieldDataLogFileName(KeyValue fieldDataKey); static String createCanonicalFieldFunctionSyntax(String externalDataIdentifierName,String varName,double beginTime,String extDataIdVariableTypeName); static String createCanonicalSimZipFileName(KeyValue fieldDataKey,Integer zipIndex,int jobIndex,boolean isOldStyle,boolean bHDF5); static String createCanonicalSimLogFileName(KeyValue fieldDataKey,int jobIndex,boolean isOldStyle); static String createCanonicalSmoldynOutputFileName(KeyValue fieldDataKey,int jobIndex,int timeIndex); static String createCanonicalPostProcessFileName(VCDataIdentifier vcdID); static String createCanonicalNFSimOutputFileName(KeyValue fieldDataKey,int jobIndex); static String createCanonicalMeshFileName(KeyValue fieldDataKey,int jobIndex,boolean isOldStyle); static String createCanonicalMeshMetricsFileName(KeyValue fieldDataKey,int jobIndex,boolean isOldStyle); static String createCanonicalMovingBoundaryOutputFileName(KeyValue fieldDataKey,int jobIndex,boolean isOldStyle); static String createCanonicalComsolOutputFileName(KeyValue fieldDataKey,int jobIndex,boolean isOldStyle); static String createCanonicalFunctionsFileName(KeyValue fieldDataKey,int jobIndex,boolean isOldStyle); static String createCanonicalSubdomainFileName(KeyValue fieldDataKey,int jobIndex,boolean isOldStyle); static String createCanonicalResampleFileName(SimResampleInfoProvider simResampleInfoProvider,FieldFunctionArguments fieldFuncArgs); static String createSimIDWithJobIndex(KeyValue fieldDataKey,int jobIndex,boolean isOldStyle); void getEntries(Map<String, SymbolTableEntry> entryMap); boolean isPostProcessing(OutputContext outputContext,String varName); File getDataProcessingOutputSourceFileHDF5(); File getFieldDataFile(SimResampleInfoProvider simResampleInfoProvider,FieldFunctionArguments fieldFunctionArguments); File getMeshFile(boolean bHDF5); File getFunctionsFile(boolean bFirst); File getZipFile(boolean bHDF5,Integer zipIndex); File getSubdomainFile(); File getLogFile(); File getSmoldynOutputFile(int timeIndex); @Override ChomboFiles getChomboFiles(); @Override VCellSimFiles getVCellSimFiles(); @Override MovingBoundarySimFiles getMovingBoundarySimFiles(); @Override ComsolSimFiles getComsolSimFiles(); VCDataIdentifier getVcDataId(); synchronized SimDataBlock getChomboExtrapolatedValues(String varName, double time); static final VariableType getVariableTypeFromLength(CartesianMesh mesh, int dataLength); static String getDefaultFieldDataFileNameForSimulation(FieldFunctionArguments fieldFuncArgs);  }