de.mpg.biochem.mars.kcp.commands

Class KCPCommand

java.lang.Object

org.scijava.module.AbstractModule

org.scijava.module.DefaultMutableModule

org.scijava.command.DynamicCommand

de.mpg.biochem.mars.kcp.commands.KCPCommand

All Implemented Interfaces:

java.lang.Runnable, org.scijava.Cancelable, org.scijava.command.Command, org.scijava.Contextual, org.scijava.Initializable, org.scijava.module.Module, org.scijava.module.MutableModule, org.scijava.plugin.SciJavaPlugin

public class KCPCommand
extends org.scijava.command.DynamicCommand
implements org.scijava.command.Command, org.scijava.Initializable

Field Summary

Fields inherited from class org.scijava.command.DynamicCommand

moduleService, pluginService

Constructor Summary

Constructors

Constructor and Description
KCPCommand()

Method Summary

Modifier and Type	Method and Description
MoleculeArchive<Molecule,MarsMetadata,MoleculeArchiveProperties<Molecule,MarsMetadata>,MoleculeArchiveIndex<Molecule,MarsMetadata>>	getArchive()
java.lang.String	getBackgroundRegion()
boolean	getCalculateBackgroundSigma()
double	getConfidenceLevel()
boolean	getFitSteps()
double	getGlobalSigma()
java.lang.String	getIncludeTags()
java.lang.String	getRegionSource()
java.lang.String	getTags()
int	getThreads()
java.lang.String	getXColumn()
java.lang.String	getYColumn()
void	initialize()
void	run()
void	setAnalyzeRegion(boolean region)
void	setArchive(MoleculeArchive<Molecule,MarsMetadata,MoleculeArchiveProperties<Molecule,MarsMetadata>,MoleculeArchiveIndex<Molecule,MarsMetadata>> archive)
void	setBackgroundRegion(java.lang.String backgroundRegion)
void	setCalculateBackgroundSigma(boolean calcBackgroundSigma)
void	setConfidenceLevel(double confidenceLevel)
void	setFitSteps(boolean step_analysis)
void	setGlobalSigma(double global_sigma)
void	setIncludeTags(java.lang.String include)
void	setRegion(java.lang.String regionName)
void	setRegionSource(java.lang.String regionSource)
void	setTags(java.lang.String tags)
void	setThreads(int nThreads)
void	setXColumn(java.lang.String xColumn)
void	setYColumn(java.lang.String yColumn)

Methods inherited from class org.scijava.command.DynamicCommand

cancel, context, getCancelReason, getContext, getInfo, getInput, getOutput, isCanceled, saveInputs, setContext, setInput, setOutput, uncancel

Methods inherited from class org.scijava.module.AbstractModule

cancel, getDelegateObject, getInputs, getOutputs, isInputResolved, isOutputResolved, preview, resolveInput, resolveOutput, setInputs, setOutputs, unresolveInput, unresolveOutput

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface org.scijava.module.MutableModule

addInput, addInput, addOutput, addOutput, removeInput, removeOutput

Methods inherited from interface org.scijava.module.Module

cancel, getDelegateObject, getInputs, getOutputs, isInputResolved, isOutputResolved, isResolved, preview, resolveInput, resolveOutput, setInputs, setOutputs, setResolved, unresolveInput, unresolveOutput

Constructor Detail

KCPCommand

public KCPCommand()

Method Detail

initialize

public void initialize()

Specified by:

initialize in interface org.scijava.Initializable

Specified by:

initialize in interface org.scijava.module.Module

Overrides:

initialize in class org.scijava.module.AbstractModule

run

public void run()

Specified by:

run in interface java.lang.Runnable

Specified by:

run in interface org.scijava.module.MutableModule

setArchive

public void setArchive(MoleculeArchive<Molecule,MarsMetadata,MoleculeArchiveProperties<Molecule,MarsMetadata>,MoleculeArchiveIndex<Molecule,MarsMetadata>> archive)

getArchive

public MoleculeArchive<Molecule,MarsMetadata,MoleculeArchiveProperties<Molecule,MarsMetadata>,MoleculeArchiveIndex<Molecule,MarsMetadata>> getArchive()

setXColumn

public void setXColumn(java.lang.String xColumn)

getXColumn

public java.lang.String getXColumn()

setYColumn

public void setYColumn(java.lang.String yColumn)

getYColumn

public java.lang.String getYColumn()

setConfidenceLevel

public void setConfidenceLevel(double confidenceLevel)

getConfidenceLevel

public double getConfidenceLevel()

setGlobalSigma

public void setGlobalSigma(double global_sigma)

getGlobalSigma

public double getGlobalSigma()

setRegionSource

public void setRegionSource(java.lang.String regionSource)

getRegionSource

public java.lang.String getRegionSource()

setCalculateBackgroundSigma

public void setCalculateBackgroundSigma(boolean calcBackgroundSigma)

getCalculateBackgroundSigma

public boolean getCalculateBackgroundSigma()

setBackgroundRegion

public void setBackgroundRegion(java.lang.String backgroundRegion)

getBackgroundRegion

public java.lang.String getBackgroundRegion()

setAnalyzeRegion

public void setAnalyzeRegion(boolean region)

setRegion

public void setRegion(java.lang.String regionName)

setIncludeTags

public void setIncludeTags(java.lang.String include)

getIncludeTags

public java.lang.String getIncludeTags()

setTags

public void setTags(java.lang.String tags)

getTags

public java.lang.String getTags()

setFitSteps

public void setFitSteps(boolean step_analysis)

getFitSteps

public boolean getFitSteps()

setThreads

public void setThreads(int nThreads)

getThreads

public int getThreads()