public abstract class TransformTaxaTables extends TaxaCountModule
BLJ_OPTIONS
GZIP_EXT, LOG_EXT, PDF_EXT, RETURN, SH_EXT, TAB_DELIM, TSV_EXT, TXT_EXT
LOG_DIR, MAIN_SCRIPT_PREFIX, NO_VERSION, OUTPUT_DIR, RES_DIR, TEMP_DIR
Constructor and Description |
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TransformTaxaTables() |
Modifier and Type | Method and Description |
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protected List<String> |
filterSamples(TaxaLevelTable inputData)
Filter out any samples in which all values are 0.
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protected List<String> |
filterTaxa(TaxaLevelTable inputData) |
protected File |
getOutputFile(File inputFile) |
protected abstract String |
getProcessSuffix() |
void |
runModule()
This method executes the modules primary Java routine.
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protected abstract TaxaLevelTable |
transform(TaxaLevelTable inputData,
List<String> filteredSampleIDs,
List<String> filteredTaxaIDs)
Transform a table of values.
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filterByProcessLevel, getDetails, getInputFiles, getPreRequisiteModules, isTaxaModule, isValidInputModule
buildScript, executeTask, getDockerImageName, getDockerImageOwner, getDockerImageTag, getWorkerScriptFunctions, markStatus, moduleComplete, moduleFailed, runBioLockJ_CMD
buildScriptForPairedReads, checkDependencies, getJobParams, getMainScript, getRuntimeParams, getScriptDir, getScriptErrors, getSummary, getTimeout, hasScripts, isValidProp
addGeneralProperty, addGeneralProperty, addGeneralProperty, addNewProperty, addNewProperty, cacheInputFiles, cleanUp, compareTo, equals, findModuleInputFiles, getAlias, getDescription, getFileCache, getID, getLogDir, getMenuPlacement, getMetadata, getModuleDir, getOutputDir, getPostRequisiteModules, getPropDefault, getPropDescMap, getPropType, getPropTypeMap, getResourceDir, getTempDir, getTitle, hashCode, init, listProps, setAlias, toString
clone, finalize, getClass, notify, notifyAll, wait, wait, wait
buildScriptForPairedReads, getJobParams, getMainScript, getScriptDir, getScriptErrors, getTimeout
checkDependencies, cleanUp, getAlias, getID, getLogDir, getMetadata, getModuleDir, getOutputDir, getPostRequisiteModules, getPropDefault, getResourceDir, getSummary, getTempDir, init, setAlias, version
public void runModule() throws Exception
JavaModule
runModule
in interface JavaModule
runModule
in class JavaModuleImpl
Exception
- thrown if any runtime error occursprotected abstract TaxaLevelTable transform(TaxaLevelTable inputData, List<String> filteredSampleIDs, List<String> filteredTaxaIDs) throws Exception
inputData
- the data to be transformed without filteringfilteredSampleIDs
- Sample ids after filteringfilteredTaxaIDs
- Taxa names after filteringException
protected List<String> filterSamples(TaxaLevelTable inputData)
inputData
- protected List<String> filterTaxa(TaxaLevelTable inputData)
protected abstract String getProcessSuffix()