biolockj.module.classifier

Class ClassifierModuleImpl

java.lang.Object

biolockj.module.BioModuleImpl

biolockj.module.ScriptModuleImpl

biolockj.module.SeqModuleImpl

biolockj.module.classifier.ClassifierModuleImpl

All Implemented Interfaces:

BioModule, ClassifierModule, DatabaseModule, ScriptModule, SeqModule, Comparable<BioModule>

Direct Known Subclasses:

Humann2Classifier, Kraken2Classifier, KrakenClassifier, Metaphlan2Classifier, QiimeClassifier, RdpClassifier

public abstract class ClassifierModuleImpl
extends SeqModuleImpl
implements ClassifierModule, DatabaseModule

This is the superclass for all WGS and 16S biolockj.module.classifier BioModules.

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.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
ClassifierModuleImpl()

Method Summary

Modifier and Type	Method and Description
void	checkDependencies() Validate module dependencies: Call getClassifierExe() to verify the executable Call getClassifierParams() to verify the runtime parameters are valid Call validateModuleOrder() to validate module configuration order.
abstract String	getClassifierExe() Get the executable required to classify your samples.
abstract List<String>	getClassifierParams() Get optional list of parameters to append whenever the classifier executable is called.
protected String	getClassifierType() This method returns the classifier class name in lower case, after "classifier" is removed. The remaining text should uniquely identify the name of the program. The basic deployment will return one of: (rdp, qiime, kraken, metaphlan2, or humann2).
abstract File	getDB() Return database directory, if multiple databases are configured, they must share a common parent directory and the common parent directory is returned by this method.
List<String>	getPostRequisiteModules() This method returns the corresponding Parser module associated with the classifier.
String	getSummary() Add database info if module is a DatabaseModule
protected void	validateModuleOrder() Validate that no biolockj.module.seq modules run after this classifier unless a new classifier branch is started.

Methods inherited from class biolockj.module.SeqModuleImpl

getInputFiles, getSeqFiles, isValidInputModule

Methods inherited from class biolockj.module.ScriptModuleImpl

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

Methods inherited from class biolockj.module.BioModuleImpl

cacheInputFiles, cleanUp, compareTo, equals, findModuleInputFiles, getFileCache, getID, getModuleDir, getOutputDir, 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.SeqModule

getSeqFiles

Methods inherited from interface biolockj.module.ScriptModule

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

Methods inherited from interface biolockj.module.BioModule

cleanUp, executeTask, getID, getInputFiles, getModuleDir, getOutputDir, getPreRequisiteModules, getTempDir, init, isValidInputModule

Constructor Detail

ClassifierModuleImpl

public ClassifierModuleImpl()

Method Detail

checkDependencies

public void checkDependencies()
                       throws Exception

Validate module dependencies:

• Call getClassifierExe() to verify the executable
• Call getClassifierParams() to verify the runtime parameters are valid
• Call validateModuleOrder() to validate module configuration order.
• Call BioModule.checkDependencies() to validate script dependencies.

Specified by:

checkDependencies in interface BioModule

Overrides:

checkDependencies in class ScriptModuleImpl

Throws:

Exception - thrown if missing or invalid dependencies are found

getClassifierExe

public abstract String getClassifierExe()
                                 throws Exception

Description copied from interface: ClassifierModule

Get the executable required to classify your samples.

Specified by:

getClassifierExe in interface ClassifierModule

Returns:

Command to execute classifier program

Throws:

Exception - if the classifier program undefined or invalid

getClassifierParams

public abstract List<String> getClassifierParams()
                                          throws Exception

Description copied from interface: ClassifierModule

Get optional list of parameters to append whenever the classifier executable is called.

Specified by:

getClassifierParams in interface ClassifierModule

Returns:

Runtime parameters

Throws:

Exception - thrown if parameters defined are invalid

getDB

public abstract File getDB()
                    throws Exception

Description copied from interface: DatabaseModule

Return database directory, if multiple databases are configured, they must share a common parent directory and the common parent directory is returned by this method.

Specified by:

getDB in interface DatabaseModule

Returns:

Database directory

Throws:

Exception - thrown if any runtime error occurs

getPostRequisiteModules

public List<String> getPostRequisiteModules()
                                     throws Exception

This method returns the corresponding Parser module associated with the classifier. The Parser module name is built using the same prefix used in the Classifier module

For example RdpClassifier, will return the RdpParser.

Specified by:

getPostRequisiteModules in interface BioModule

Overrides:

getPostRequisiteModules in class BioModuleImpl

Returns:

List of BioModules

Throws:

Exception - if invalid Class names are returned as post-requisites

getSummary

public String getSummary()
                  throws Exception

Description copied from class: SeqModuleImpl

Add database info if module is a DatabaseModule

Specified by:

getSummary in interface BioModule

Overrides:

getSummary in class SeqModuleImpl

Returns:

Summary of BioModule execution

Throws:

Exception - if any error occurs

getClassifierType

protected String getClassifierType()

This method returns the classifier class name in lower case, after "classifier" is removed.
The remaining text should uniquely identify the name of the program.
The basic deployment will return one of: (rdp, qiime, kraken, metaphlan2, or humann2).

Returns:

String - options { rdp, qiime, kraken, kraken2, metaphlan2, or humann2 }

validateModuleOrder

protected void validateModuleOrder()
                            throws Exception

Validate that no biolockj.module.seq modules run after this classifier unless a new classifier branch is started.

Throws:

Exception - if modules are out of order