edu.cornell.med.icb.tissueinfo.similarity
Class AnnotateClustersMode

java.lang.Object
  edu.cornell.med.icb.cli.UseModality<TiSimOptions>
      edu.cornell.med.icb.tissueinfo.similarity.TiSimMode
          edu.cornell.med.icb.tissueinfo.similarity.AnnotateClustersMode

public class AnnotateClustersMode
extends TiSimMode

Calculates tissue weights for a set of clusters generated by ClusterMode.

Author:

Fabien Campagne Date: Sep 11, 2007 Time: 10:31:14 AM

Constructor Summary

AnnotateClustersMode()

Method Summary

void	defineOptions(com.martiansoftware.jsap.JSAP jsap)
void	interpretArguments(com.martiansoftware.jsap.JSAP jsap, com.martiansoftware.jsap.JSAPResult result, TiSimOptions options)
void	process(TiSimOptions options) Process with options.

Methods inherited from class edu.cornell.med.icb.tissueinfo.similarity.TiSimMode

setupEngine, setupEngine

Methods inherited from class edu.cornell.med.icb.cli.UseModality

addHelpFlag, checkPrintHelp, getExecutedModality, getOriginalArgs, printHelp, process, registerMode, setOriginalArgs, setTestingMode

Methods inherited from class java.lang.Object

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

Constructor Detail

AnnotateClustersMode

public AnnotateClustersMode()

Method Detail

defineOptions

public void defineOptions(com.martiansoftware.jsap.JSAP jsap)
                   throws com.martiansoftware.jsap.JSAPException

Overrides:

defineOptions in class TiSimMode

Throws:

com.martiansoftware.jsap.JSAPException

interpretArguments

public void interpretArguments(com.martiansoftware.jsap.JSAP jsap,
                               com.martiansoftware.jsap.JSAPResult result,
                               TiSimOptions options)

Overrides:

interpretArguments in class TiSimMode

process

public void process(TiSimOptions options)

Description copied from class: TiSimMode

Process with options. This method may exit the JVM at any time.

Overrides:

process in class TiSimMode

Parameters:

options - some options