biolockj.module.diversity

Class ShannonDiversity

java.lang.Object

biolockj.module.BioModuleImpl

biolockj.module.ScriptModuleImpl

biolockj.module.JavaModuleImpl

biolockj.module.report.taxa.TaxaCountModule

biolockj.module.report.taxa.TransformTaxaTables

biolockj.module.diversity.ShannonDiversity

All Implemented Interfaces:

ApiModule, BioModule, JavaModule, ScriptModule, Comparable<BioModule>

public class ShannonDiversity
extends TransformTaxaTables
implements ApiModule

Field Summary

Fields

Modifier and Type	Field and Description
static String	SHANNON_COLUMN

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.BioModule

LOG_DIR, MAIN_SCRIPT_PREFIX, NO_VERSION, OUTPUT_DIR, RES_DIR, TEMP_DIR

Constructor Summary

Constructors

Constructor and Description
ShannonDiversity()

Method Summary

Modifier and Type	Method and Description
protected List<String>	filterTaxa(TaxaLevelTable inputData)
String	getCitationString() At a minimum, this should return the name and/or url for the wrapped tool.
String	getDescription() Briefly describe what this module does.
protected String	getProcessSuffix()
boolean	isValidInputModule(BioModule module) If module is a SeqModule input must contain sequence data.
protected TaxaLevelTable	transform(TaxaLevelTable inputData, List<String> filteredSampleIDs, List<String> filteredTaxaIDs) Transform a table of values.
String	version() Changes to a module class should be accompanied by a increment in version.

Methods inherited from class biolockj.module.report.taxa.TransformTaxaTables

filterSamples, getOutputFile, runModule

Methods inherited from class biolockj.module.report.taxa.TaxaCountModule

filterByProcessLevel, getDetails, getInputFiles, getPreRequisiteModules, isTaxaModule

Methods inherited from class biolockj.module.JavaModuleImpl

buildScript, executeTask, getDockerImageName, getDockerImageOwner, getDockerImageTag, getWorkerScriptFunctions, markStatus, moduleComplete, moduleFailed, runBioLockJ_CMD

Methods inherited from class biolockj.module.ScriptModuleImpl

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

Methods inherited from class biolockj.module.BioModuleImpl

addGeneralProperty, addGeneralProperty, addGeneralProperty, addNewProperty, addNewProperty, cacheInputFiles, cleanUp, compareTo, equals, findModuleInputFiles, getAlias, getDescription, getFileCache, getID, getLogDir, getMenuPlacement, getMetadata, getModuleDir, getOutputDir, getPostRequisiteModules, 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.api.ApiModule

getDescription, getDetails, getMenuPlacement, getPropType, getTitle, isValidProp, listProps

Methods inherited from interface biolockj.module.BioModule

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

Methods inherited from interface biolockj.module.ScriptModule

buildScriptForPairedReads, getJobParams, getMainScript, getScriptDir, getScriptErrors, getTimeout

Field Detail

SHANNON_COLUMN

public static final String SHANNON_COLUMN

See Also:

Constant Field Values

Constructor Detail

ShannonDiversity

public ShannonDiversity()

Method Detail

transform

protected TaxaLevelTable transform(TaxaLevelTable inputData,
                                   List<String> filteredSampleIDs,
                                   List<String> filteredTaxaIDs)
                            throws Exception

Description copied from class: TransformTaxaTables

Transform a table of values. The transform method may or may not make use of the values that were filtered out.

Specified by:

transform in class TransformTaxaTables

Parameters:

inputData - the data to be transformed without filtering

filteredSampleIDs - Sample ids after filtering

filteredTaxaIDs - Taxa names after filtering

Returns:

A

Throws:

Exception

filterTaxa

protected List<String> filterTaxa(TaxaLevelTable inputData)

Overrides:

filterTaxa in class TransformTaxaTables

getDescription

public String getDescription()

Description copied from interface: ApiModule

Briefly describe what this module does. A more detailed description may be returned by getDetails.

Specified by:

getDescription in interface ApiModule

Returns:

getCitationString

public String getCitationString()

Description copied from interface: ApiModule

At a minimum, this should return the name and/or url for the wrapped tool. For BioLockJ home-grown modules, it can cite BioLockJ and give the current version. Ideally this will include the version for the wrapped tool. Tool version may require using a stored variable that can be filled in during execution; and the string that is returned pre-execution may not have the version.

Specified by:

getCitationString in interface ApiModule

Returns:

version

public String version()

Description copied from interface: BioModule

Changes to a module class should be accompanied by a increment in version. The is a string and open form, but using the major.minor.patch semantic versioning is recommended.

Specified by:

version in interface BioModule

Returns:

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 TaxaCountModule

Parameters:

module - BioModule that ran before the current BioModule

Returns:

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

getProcessSuffix

protected String getProcessSuffix()

Specified by:

getProcessSuffix in class TransformTaxaTables