MDACC
Biostatistics

org.mdanderson.biostat.geneclust
Class Simulation

java.lang.Object
  extended byorg.mdanderson.biostat.geneclust.SProcess
      extended byorg.mdanderson.biostat.geneclust.Simulation

public abstract class Simulation
extends SProcess


Field Summary
protected  String classificationFileName
           
protected  int gapTolerance
           
protected  int numClustersToExtract
           
protected  int numPermutations
           
protected  int percentSupervision
           
protected  int percentToShave
           
protected  String performSupervised
           
protected  String writeMatrix
           
 
Fields inherited from class org.mdanderson.biostat.geneclust.SProcess
dialog
 
Constructor Summary
Simulation(SimulationDialog dialog, boolean isPerformSupervised, int percentSupervision, String classificationPathName, int numClustersToExtract, int percentToShave, int numPermutations, int gapTolerance, boolean isWriteMatrix)
          Class constructor specifying (way too many) simulation parameters...
 
Method Summary
protected  void writeSinterpreterGenericInput(org.mdanderson.biostat.geneclust.SBufferedWriter bw)
          Writes mode-indifferent S interpreter input data to the output stream.
protected  void writeSinterpreterInit(org.mdanderson.biostat.geneclust.SBufferedWriter bw)
          Writes the S interpreter initialization code.
 
Methods inherited from class org.mdanderson.biostat.geneclust.SProcess
getDialog, run, writeSinterpreterInput, writeSinterpreterInterrupt, writeSinterpreterTermination
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

performSupervised

protected String performSupervised

percentSupervision

protected int percentSupervision

classificationFileName

protected String classificationFileName

numClustersToExtract

protected int numClustersToExtract

percentToShave

protected int percentToShave

numPermutations

protected int numPermutations

gapTolerance

protected int gapTolerance

writeMatrix

protected String writeMatrix
Constructor Detail

Simulation

public Simulation(SimulationDialog dialog,
                  boolean isPerformSupervised,
                  int percentSupervision,
                  String classificationPathName,
                  int numClustersToExtract,
                  int percentToShave,
                  int numPermutations,
                  int gapTolerance,
                  boolean isWriteMatrix)
Class constructor specifying (way too many) simulation parameters...

Parameters:
dialog - dialog allows monitoring of sim progress
isPerformSupervised - if true, perform supervised shaving
percentSupervision - percent supervision to use
classificationPathName - classification for supervised shaving
numClustersToExtract - number of clusters to extract
percentToShave - percent to shave
numPermutations - number of permutations
gapTolerance - gap tolerance
isWriteMatrix - if true, write matrix to disk. This is only useful in demo mode.
Throws:
NullPointerException - if dialog is null
Method Detail

writeSinterpreterInit

protected void writeSinterpreterInit(org.mdanderson.biostat.geneclust.SBufferedWriter bw)
                              throws IOException
Writes the S interpreter initialization code. It sets S interpreter options and global variables, dynamically loads the C library, and initializes the S interpreter graphics environment.

Parameters:
bw - output stream writer
Throws:
IOException - if an error occurs while writing

writeSinterpreterGenericInput

protected void writeSinterpreterGenericInput(org.mdanderson.biostat.geneclust.SBufferedWriter bw)
                                      throws IOException
Writes mode-indifferent S interpreter input data to the output stream.

Parameters:
bw - output stream writer
Throws:
IOException - if an error occurs while writing

MDACC
Biostatistics

Copyright © 2002 M.D. Anderson Cancer Center. All Rights Reserved.