biolockj.module

Class SeqModuleImpl

java.lang.Object

biolockj.module.BioModuleImpl

biolockj.module.ScriptModuleImpl

biolockj.module.SeqModuleImpl

All Implemented Interfaces:

BioModule, ScriptModule, SeqModule, Comparable<BioModule>

Direct Known Subclasses:

AwkFastaConverter, BuildQiimeMapping, ClassifierModuleImpl, GenomeAssembly, Gunzipper, KneadData, PearMergeReads

public abstract class SeqModuleImpl
extends ScriptModuleImpl
implements SeqModule

Superclass for SeqModules that take sequence files as input for pre-processing prior to classification.

Field Summary

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.BioModule

LOG_DIR, MAIN_SCRIPT_PREFIX, NO_VERSION, OUTPUT_DIR, RES_DIR, TEMP_DIR

Constructor Summary

Constructors

Constructor and Description
SeqModuleImpl()

Method Summary

Modifier and Type	Method and Description
List<File>	getInputFiles() Return getSeqFiles(Collection) to filter standard module input files.
List<File>	getSeqFiles(Collection<File> files) Return only sequence files for sample IDs found in the metadata file. If Config."metadata.required" = "Y", an error is thrown to list the files that cannot be matched to a metadata row.
String	getSummary() Add database info if module is a DatabaseModule
boolean	isValidInputModule(BioModule module) In the early stages of the pipeline, starting with the very 1st module ImportMetadata, most modules expect sequence files as input.

Methods inherited from class biolockj.module.ScriptModuleImpl

buildScript, buildScriptForPairedReads, checkDependencies, executeTask, getJobParams, getMainScript, getRuntimeParams, getScriptDir, getScriptErrors, getTimeout, getWorkerScriptFunctions, hasScripts, isValidProp

Methods inherited from class biolockj.module.BioModuleImpl

addGeneralProperty, addGeneralProperty, addGeneralProperty, addNewProperty, addNewProperty, cacheInputFiles, cleanUp, compareTo, equals, findModuleInputFiles, getAlias, getDescription, getDetails, getDockerImageOwner, getDockerImageTag, getFileCache, getID, getLogDir, getMenuPlacement, getMetadata, getModuleDir, getOutputDir, getPostRequisiteModules, getPreRequisiteModules, getPropDefault, getPropDescMap, getPropType, getPropTypeMap, getResourceDir, getTempDir, getTitle, hashCode, init, listProps, setAlias, toString

Methods inherited from class java.lang.Object

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

Methods inherited from interface biolockj.module.ScriptModule

buildScript, buildScriptForPairedReads, getJobParams, getMainScript, getScriptDir, getScriptErrors, getTimeout, getWorkerScriptFunctions

Methods inherited from interface biolockj.module.BioModule

checkDependencies, cleanUp, executeTask, getAlias, getDockerImageName, getDockerImageOwner, getDockerImageTag, getID, getLogDir, getMetadata, getModuleDir, getOutputDir, getPostRequisiteModules, getPreRequisiteModules, getPropDefault, getResourceDir, getTempDir, init, setAlias, version

Constructor Detail

SeqModuleImpl

public SeqModuleImpl()

Method Detail

getInputFiles

public List<File> getInputFiles()

Return getSeqFiles(Collection) to filter standard module input files.

Specified by:

getInputFiles in interface BioModule

Overrides:

getInputFiles in class BioModuleImpl

Returns:

Input files

Throws:

SequnceFormatException

getSeqFiles

public List<File> getSeqFiles(Collection<File> files)
                       throws SequnceFormatException

Description copied from interface: SeqModule

Return only sequence files for sample IDs found in the metadata file.
If Config."metadata.required" = "Y", an error is thrown to list the files that cannot be matched to a metadata row.

Specified by:

getSeqFiles in interface SeqModule

Parameters:

files - Module input files

Returns:

Module sequence files

Throws:

SequnceFormatException - If Config."metadata.required" = "Y" but sequence files found that do not have a corresponding record in the metadata file or if invalid metadata prevents parsing SEQ files.

getSummary

public String getSummary()
                  throws Exception

Add database info if module is a DatabaseModule

Specified by:

getSummary in interface BioModule

Overrides:

getSummary in class ScriptModuleImpl

Returns:

Summary of BioModule execution

Throws:

Exception - if any error occurs

isValidInputModule

public boolean isValidInputModule(BioModule module)

Description copied from class: BioModuleImpl

In the early stages of the pipeline, starting with the very 1st module ImportMetadata, most modules expect sequence files as input. This method returns false if the previousModule only produced a new metadata file, such as ImportMetadata or RegisterNumReads. When BioModuleImpl.getInputFiles() is called, this method determines if the previousModule output is valid input for the current BioModule. The default implementation of this method returns FALSE if the previousModule only generates a new metadata file.

Specified by:

isValidInputModule in interface BioModule

Overrides:

isValidInputModule in class BioModuleImpl

Parameters:

module - BioModule that ran before the current BioModule

Returns:

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