biolockj.module.report.taxa

Class BuildTaxaTables

java.lang.Object

biolockj.module.BioModuleImpl

biolockj.module.ScriptModuleImpl

biolockj.module.JavaModuleImpl

biolockj.module.report.otu.OtuCountModule

biolockj.module.report.taxa.BuildTaxaTables

All Implemented Interfaces:

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

public class BuildTaxaTables
extends OtuCountModule
implements ApiModule

Many R BioModules expect separate tables containing log-normalized taxa counts for each taxonomy level. This module reads the most recent OTU count files generated by any previous BioModule.

GUI Module Name

Build Taxa Tables

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.BioModule

LOG_DIR, MAIN_SCRIPT_PREFIX, NO_VERSION, OUTPUT_DIR, RES_DIR, TEMP_DIR

Constructor Summary

Constructors

Constructor and Description
BuildTaxaTables()

Method Summary

Modifier and Type	Method and Description
protected void	buildTaxonomyTables(TreeMap<String,TreeMap<String,Long>> sampleOtuCounts) Build taxonomy tables from the sampleTaxaCounts.
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.
String	getDetails() A extension of getDescription.
String	getSummary() Returns summary message to be displayed by Email module so must not contain confidential info.
void	runModule() This method executes the modules primary Java routine.

Methods inherited from class biolockj.module.report.otu.OtuCountModule

getInputFiles, isOtuModule, 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, checkDependencies, getJobParams, getMainScript, getRuntimeParams, getScriptDir, getScriptErrors, 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, 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.api.ApiModule

getDescription, 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, getTempDir, init, isValidInputModule, setAlias, version

Methods inherited from interface biolockj.module.ScriptModule

buildScriptForPairedReads, getJobParams, getMainScript, getScriptDir, getScriptErrors, getTimeout

Constructor Detail

BuildTaxaTables

public BuildTaxaTables()

Method Detail

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

runModule

public void runModule()
               throws Exception

Description copied from interface: JavaModule

This method executes the modules primary Java routine.

Specified by:

runModule in interface JavaModule

Specified by:

runModule in class JavaModuleImpl

Throws:

Exception - thrown if any runtime error occurs

buildTaxonomyTables

protected void buildTaxonomyTables(TreeMap<String,TreeMap<String,Long>> sampleOtuCounts)
                            throws Exception

Build taxonomy tables from the sampleTaxaCounts.

Parameters:

sampleOtuCounts - TreeMap(SampleId, TreeMap(OTU, count)) OTU counts for every sample

Throws:

Exception - if errors occur

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:

getDetails

public String getDetails()

Description copied from interface: ApiModule

A extension of getDescription. Beyond the brief description, give details such as the interaction between properties.

Specified by:

getDetails in interface ApiModule

Overrides:

getDetails in class BioModuleImpl

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: