biolockj.module.report.humann2

Class Humann2CountModule

java.lang.Object

biolockj.module.BioModuleImpl

biolockj.module.ScriptModuleImpl

biolockj.module.JavaModuleImpl

biolockj.module.report.humann2.Humann2CountModule

All Implemented Interfaces:

BioModule, JavaModule, ScriptModule, Comparable<BioModule>

Direct Known Subclasses:

AddMetadataToPathwayTables, RemoveLowPathwayCounts, RemoveScarcePathwayCounts

public abstract class Humann2CountModule
extends JavaModuleImpl

This abstract superclass is extended by all other modules in this package.
Shared method implementations are defined to ensure uniform adoption of dependencies and prerequisites.

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
Humann2CountModule()

Method Summary

Modifier and Type	Method and Description
void	checkDependencies() Validate module dependencies: Require Config. exists Require Config. is positive integer Require Config. is positive integer Verify Config. is positive integer if set
List<File>	getInputFiles() BioModule BioModuleImpl.getInputFiles() is called to initialize upon first call and cached.
List<String>	getPreRequisiteModules() Module prerequisite: Humann2Parser
protected boolean	isHumann2CountModule(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, 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

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

Constructor Detail

Humann2CountModule

public Humann2CountModule()

Method Detail

checkDependencies

public void checkDependencies()
                       throws Exception

Description copied from class: ScriptModuleImpl

Validate module dependencies:

• Require Config. exists
• Require Config. is positive integer
• Require Config. is positive integer
• Verify Config. is positive integer if set

Specified by:

checkDependencies in interface BioModule

Overrides:

checkDependencies in class ScriptModuleImpl

Throws:

Exception - thrown if missing or invalid dependencies are found

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

Module prerequisite: Humann2Parser

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

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

isHumann2CountModule

protected boolean isHumann2CountModule(BioModule module)

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

Parameters:

module - BioModule

Returns:

TRUE if module generated OTU count files