biolockj.module.report.otu

Class OtuCountModule

java.lang.Object

biolockj.module.BioModuleImpl

biolockj.module.ScriptModuleImpl

biolockj.module.JavaModuleImpl

biolockj.module.report.otu.OtuCountModule

All Implemented Interfaces:

BioModule, JavaModule, ScriptModule, Comparable<BioModule>

Direct Known Subclasses:

BuildTaxaTables, CompileOtuCounts, RarefyOtuCounts, RemoveLowOtuCounts, RemoveScarceOtuCounts

public abstract class OtuCountModule
extends JavaModuleImpl

OtuCount modules reads OTU count assignment tables (1 file/sample) with 2 columns.
Col1: Full OTU pathway spanning top to bottom level Col2: Count (# of reads) for the sample.

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
OtuCountModule()

Method Summary

Modifier and Type	Method and Description
List<File>	getInputFiles() BioModule BioModuleImpl.getInputFiles() is called to initialize upon first call and cached.
protected boolean	isOtuModule(BioModule module) Check the module to determine if it generated OTU count files.
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, getPreRequisiteModules, 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, getPreRequisiteModules, getSummary, getTempDir, init

Constructor Detail

OtuCountModule

public OtuCountModule()

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

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

isOtuModule

protected boolean isOtuModule(BioModule module)

Check the module to determine if it generated OTU count files.

Parameters:

module - BioModule

Returns:

TRUE if module generated OTU count files