biolockj.module.report.otu

Class CompileOtuCounts

java.lang.Object

biolockj.module.BioModuleImpl

biolockj.module.ScriptModuleImpl

biolockj.module.JavaModuleImpl

biolockj.module.report.otu.OtuCountModule

biolockj.module.report.otu.CompileOtuCounts

All Implemented Interfaces:

BioModule, JavaModule, ScriptModule, Comparable<BioModule>

public class CompileOtuCounts
extends OtuCountModule

This BioModule compiles the counts from all OTU count files into a single summary OTU count file containing OTU counts for the entire dataset.

GUI Module Name

Compile OTU Counts

Field Summary

Fields

Modifier and Type	Field and Description
static String	SUMMARY Output file prefix: "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.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
CompileOtuCounts()

Method Summary

Modifier and Type	Method and Description
protected void	buildSummaryOtuCountFile(TreeMap<String,Long> otuCounts) Build Summary OTU count file for all samples.
protected TreeMap<String,Long>	compileOtuCounts(Collection<File> files) Compile OTU counts from the individual sample OTU count files
protected String	getMaxOtusPerSample() Find the maximum OTU count per sample.
protected String	getMinOtusPerSample() Find the minimum OTU count per sample.
String	getSummary() Add summary with unique OTU counts/level.
protected File	getSummaryOtuFile() Get the summary output file
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, getSource, getWorkerScriptFunctions, markStatus, moduleComplete, moduleFailed

Methods inherited from class biolockj.module.ScriptModuleImpl

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

Methods inherited from class biolockj.module.BioModuleImpl

cacheInputFiles, cleanUp, compareTo, equals, findModuleInputFiles, getFileCache, getID, getModuleDir, getOutputDir, getPostRequisiteModules, 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.ScriptModule

buildScriptForPairedReads, getJobParams, getMainScript, getScriptDir, getScriptErrors, getTimeout

Methods inherited from interface biolockj.module.BioModule

checkDependencies, cleanUp, getID, getModuleDir, getOutputDir, getPostRequisiteModules, getPreRequisiteModules, getTempDir, init

Field Detail

SUMMARY

public static final String SUMMARY

Output file prefix: "summary"

See Also:

Constant Field Values

Constructor Detail

CompileOtuCounts

public CompileOtuCounts()

Method Detail

getSummary

public String getSummary()
                  throws Exception

Add summary with unique OTU counts/level.

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

buildSummaryOtuCountFile

protected void buildSummaryOtuCountFile(TreeMap<String,Long> otuCounts)
                                 throws Exception

Build Summary OTU count file for all samples.

Parameters:

otuCounts - OTU-count mapping

Throws:

Exception - if errors occur

compileOtuCounts

protected TreeMap<String,Long> compileOtuCounts(Collection<File> files)
                                         throws Exception

Compile OTU counts from the individual sample OTU count files

Parameters:

files - Collection of OTU count files

Returns:

TreeMap(OTU, count)

Throws:

Exception - if errors occur

getMaxOtusPerSample

protected String getMaxOtusPerSample()

Find the maximum OTU count per sample.

Returns:

Max OTU per sample.

getMinOtusPerSample

protected String getMinOtusPerSample()

Find the minimum OTU count per sample.

Returns:

Min OTU per sample.

getSummaryOtuFile

protected File getSummaryOtuFile()

Get the summary output file

Returns:

OTU summary file