compbio.runner.disorder

Class GlobPlot

java.lang.Object

compbio.engine.client.SkeletalExecutable<GlobPlot>

compbio.runner.disorder.GlobPlot

All Implemented Interfaces:

Executable<GlobPlot>, PipedExecutable<GlobPlot>

public class GlobPlot
extends SkeletalExecutable<GlobPlot>
implements PipedExecutable<GlobPlot>

./GlobPipe.py SmoothFrame DOMjoinFrame DOMpeakFrame DISjoinFrame DISpeakFrame FASTAfile' Optimised for ELM: ./GlobPlot.py 10 8 75 8 8 sequence_file' Webserver settings: ./GlobPlot.py 10 15 74 4 5 sequence_file' Hard-coded values are 10 15 74 4 5. Changing these values are not recommended by developers, apart from smoothing window. However, the binary, GlobPlot depends on - Tisean which is not happy with arbitrary changes to these values, so changing them can lead to problems. May be we can offer preset? This is not a standard GlobPlot! The script has been modified!

Nested Class Summary

Nested classes/interfaces inherited from interface compbio.engine.client.Executable

Executable.ExecProvider

Field Summary

Fields

Modifier and Type	Field and Description
private static org.apache.log4j.Logger	log

Fields inherited from class compbio.engine.client.SkeletalExecutable

cbuilder, ERROR, errorFile, INPUT, inputFile, OUTPUT, outputFile, ph

Constructor Summary

Constructors

Constructor and Description
GlobPlot()

Method Summary

Modifier and Type	Method and Description
ScoreManager	getResults(java.lang.String workDirectory)
java.lang.Class<GlobPlot>	getType()
GlobPlot	setInput(java.lang.String inFile)

Methods inherited from class compbio.engine.client.SkeletalExecutable

addParameters, equals, getClusterCpuNum, getClusterJobSettings, getCreatedFiles, getError, getInput, getLimit, getLimits, getOutput, getParameters, hashCode, isErrorSet, isInputSet, isOutputSet, loadRunConfiguration, setError, setOutput, setParameter, toString

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface compbio.engine.client.Executable

addParameters, getClusterJobSettings, getCreatedFiles, getError, getInput, getLimit, getLimits, getOutput, getParameters, loadRunConfiguration

Field Detail

log

private static org.apache.log4j.Logger log

Constructor Detail

GlobPlot

public GlobPlot()

Method Detail

getResults

public ScoreManager getResults(java.lang.String workDirectory)
                        throws ResultNotAvailableException

Specified by:

getResults in interface Executable<GlobPlot>

Throws:

ResultNotAvailableException

setInput

public GlobPlot setInput(java.lang.String inFile)

Overrides:

setInput in class SkeletalExecutable<GlobPlot>

getType

public java.lang.Class<GlobPlot> getType()

Specified by:

getType in class SkeletalExecutable<GlobPlot>

Returns:

subclasses must return their type