biolockj.module.report.taxa

Class LogTransformTaxaTables

java.lang.Object

biolockj.module.BioModuleImpl

biolockj.module.ScriptModuleImpl

biolockj.module.JavaModuleImpl

biolockj.module.report.taxa.TaxaCountModule

biolockj.module.report.taxa.TransformTaxaTables

biolockj.module.report.taxa.LogTransformTaxaTables

All Implemented Interfaces:

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

public class LogTransformTaxaTables
extends TransformTaxaTables
implements ApiModule

This utility is used to log-transform the raw OTU counts on Log10 or Log-e scales.

GUI Module Name

Log Transform Taxa Tables

Field Summary

Fields

Modifier and Type	Field and Description
protected static String	LOG_10 Log 10 display string a supported value for: "report.logBase"
protected static String	LOG_E Log e display string a supported value for: "report.logBase"

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
LogTransformTaxaTables()

Method Summary

Modifier and Type	Method and Description
void	checkDependencies() Verify Config."report.logBase" property is valid (if defined) with a value = (e or 10).
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	getLogBase() Get the Log base (10 or e)
protected String	getProcessSuffix()
String	getSummary() Returns summary message to be displayed by Email module so must not contain confidential info.
Boolean	isValidProp(String property) Tests to see if the value val is valid for property prop; primarily tests format.
protected TaxaLevelTable	transform(TaxaLevelTable inputData, List<String> filteredSampleIDs, List<String> filteredTaxaIDs) Log transform the data

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

filterSamples, filterTaxa, getOutputFile, runModule

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

filterByProcessLevel, getDetails, getInputFiles, getPreRequisiteModules, isTaxaModule, isValidInputModule

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, getJobParams, getMainScript, getRuntimeParams, getScriptDir, getScriptErrors, getTimeout, hasScripts

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, listProps

Methods inherited from interface biolockj.module.BioModule

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

Methods inherited from interface biolockj.module.ScriptModule

buildScriptForPairedReads, getJobParams, getMainScript, getScriptDir, getScriptErrors, getTimeout

Field Detail

LOG_10

protected static final String LOG_10

Log 10 display string a supported value for: "report.logBase"

See Also:

Constant Field Values

LOG_E

protected static final String LOG_E

Log e display string a supported value for: "report.logBase"

See Also:

Constant Field Values

Constructor Detail

LogTransformTaxaTables

public LogTransformTaxaTables()

Method Detail

checkDependencies

public void checkDependencies()
                       throws Exception

Verify Config."report.logBase" property is valid (if defined) with a value = (e or 10).

Specified by:

checkDependencies in interface BioModule

Overrides:

checkDependencies in class ScriptModuleImpl

Throws:

ConfigFormatException - if REPORT_LOG_BASE is not set to a valid option (e or 10)

Exception - thrown if missing or invalid dependencies are found

isValidProp

public Boolean isValidProp(String property)
                    throws Exception

Description copied from interface: ApiModule

Tests to see if the value val is valid for property prop; primarily tests format. This is designed for individual properties. To make sure property values are compatible, use BioModule.checkDependencies(). Using switch/case or a stack of if/else is recommended. Within each case, call any/all method that is used by this module to access the value from the config file, leveraging the checks in the Config.get* methods. This method should never actually return false. If the value is not valid, it should throw an exception that includes a helpful message about whats not valid. As part of a throwable, that message is passed along to wherever the call started. Any time that "false" is actually the desired form, this method should be wrapped in a try/catch.

Specified by:

isValidProp in interface ApiModule

Overrides:

isValidProp in class ScriptModuleImpl

Returns:

true if value is recognized and good, false/Exception if it is recognized and invalid, null if prop is not recognized.

Throws:

Exception

transform

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

Log transform the data

Specified by:

transform in class TransformTaxaTables

Parameters:

otuTable - OTU raw count table

Returns:

A

Throws:

Exception - if unable to construct LogTransformTaxaTables

getProcessSuffix

protected String getProcessSuffix()

Specified by:

getProcessSuffix in class TransformTaxaTables

getLogBase

protected String getLogBase()

Get the Log base (10 or e)

Returns:

Log base

getSummary

public String getSummary()
                  throws Exception

Description copied from class: ScriptModuleImpl

Returns summary message to be displayed by Email module so must not contain confidential info. ModuleUtil provides summary metrics on output files

Specified by:

getSummary in interface BioModule

Overrides:

getSummary in class ScriptModuleImpl

Returns:

Summary of BioModule execution

Throws:

Exception - if any error occurs

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: