biolockj.module.report.taxa

Class TaxaCountModule

java.lang.Object

biolockj.module.BioModuleImpl

biolockj.module.ScriptModuleImpl

biolockj.module.JavaModuleImpl

biolockj.module.report.taxa.TaxaCountModule

All Implemented Interfaces:

BioModule, JavaModule, ScriptModule, Comparable<BioModule>

Direct Known Subclasses:

AddMetadataToTaxaTables, NormalizeTaxaTables

public abstract class TaxaCountModule
extends JavaModuleImpl

TBD

Field Summary

Fields inherited from class biolockj.module.JavaModuleImpl

BLJ_OPTIONS

Fields inherited from class biolockj.module.BioModuleImpl

GZIP_EXT, LOG_EXT, PDF_EXT, RETURN, SH_EXT, TAB_DELIM, TSV_EXT, TXT_EXT

Fields inherited from interface biolockj.module.ScriptModule

SCRIPT_BATCH_SIZE, SCRIPT_DEFAULT_HEADER, SCRIPT_NUM_THREADS, SCRIPT_PERMISSIONS, SCRIPT_TIMEOUT

Fields inherited from interface biolockj.module.BioModule

MAIN_SCRIPT_PREFIX, OUTPUT_DIR, TEMP_DIR

Constructor Summary

Constructors

Constructor and Description
TaxaCountModule()

Method Summary

Modifier and Type	Method and Description
protected static List<File>	filterByProcessLevel(List<File> files) Pipelines may include taxa tables + normalized taxa tables (or log normalized taxa tables).
List<File>	getInputFiles() BioModule BioModuleImpl.getInputFiles() is called to initialize upon first call and cached.
List<String>	getPreRequisiteModules() Require taxonomy table module as prerequisite
boolean	isTaxaModule(BioModule module) Check the module output directory for taxonomy table files generated by BioLockJ.
boolean	isValidInputModule(BioModule module) If module is a SeqModule input must contain sequence data.

Methods inherited from class biolockj.module.JavaModuleImpl

buildScript, executeTask, getSource, getWorkerScriptFunctions, markStatus, moduleComplete, moduleFailed, runModule

Methods inherited from class biolockj.module.ScriptModuleImpl

buildScriptForPairedReads, checkDependencies, getJobParams, getMainScript, getRuntimeParams, getScriptDir, getScriptErrors, getSummary, getTimeout, hasScripts

Methods inherited from class biolockj.module.BioModuleImpl

cacheInputFiles, cleanUp, compareTo, equals, findModuleInputFiles, getFileCache, getID, getModuleDir, getOutputDir, getPostRequisiteModules, getTempDir, init, toString, validateFileNameUnique

Methods inherited from class java.lang.Object

clone, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface biolockj.module.ScriptModule

buildScriptForPairedReads, getJobParams, getMainScript, getScriptDir, getScriptErrors, getTimeout

Methods inherited from interface biolockj.module.BioModule

checkDependencies, cleanUp, getID, getModuleDir, getOutputDir, getPostRequisiteModules, getSummary, getTempDir, init

Constructor Detail

TaxaCountModule

public TaxaCountModule()

Method Detail

getInputFiles

public List<File> getInputFiles()
                         throws Exception

Description copied from class: BioModuleImpl

BioModule BioModuleImpl.getInputFiles() is called to initialize upon first call and cached.

Specified by:

getInputFiles in interface BioModule

Overrides:

getInputFiles in class BioModuleImpl

Returns:

Input files

Throws:

Exception - if unable to obtain input files

getPreRequisiteModules

public List<String> getPreRequisiteModules()
                                    throws Exception

Require taxonomy table module as prerequisite

Specified by:

getPreRequisiteModules in interface BioModule

Overrides:

getPreRequisiteModules in class BioModuleImpl

Returns:

List of BioModule Class Names

Throws:

Exception - if invalid Class names are returned as prerequisites

isTaxaModule

public boolean isTaxaModule(BioModule module)

Check the module output directory for taxonomy table files generated by BioLockJ.

Parameters:

module - BioModule

Returns:

TRUE if module generated taxonomy table files

isValidInputModule

public boolean isValidInputModule(BioModule module)

Description copied from class: JavaModuleImpl

If module is a SeqModule input must contain sequence data.

Specified by:

isValidInputModule in interface BioModule

Overrides:

isValidInputModule in class JavaModuleImpl

Parameters:

module - BioModule that ran before the current BioModule

Returns:

boolean TRUE if the previousModule output is acceptable input for the current BioModule

filterByProcessLevel

protected static List<File> filterByProcessLevel(List<File> files)

Pipelines may include taxa tables + normalized taxa tables (or log normalized taxa tables). Standard modules will always want the most processed modules (log-norm is top preference, then normalized, lastly raw counts). The purpose of includes less processes normalized tables is merely to provide the required input for the R_PlotEffectSize module (which find the correct tables in an R function).

Parameters:

files - List of taxa table files

Returns:

List of taxa tables (only 1/level)