org.mdanderson.biostat.geneclust
Class Simulation
java.lang.Object
org.mdanderson.biostat.geneclust.SProcess
org.mdanderson.biostat.geneclust.Simulation
- public abstract class Simulation
- extends SProcess
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 java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
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
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 progressisPerformSupervised
- if true, perform supervised shavingpercentSupervision
- percent supervision to useclassificationPathName
- classification for supervised shavingnumClustersToExtract
- number of clusters to extractpercentToShave
- percent to shavenumPermutations
- number of permutationsgapTolerance
- gap toleranceisWriteMatrix
- if true, write matrix to disk. This is
only useful in demo mode.
- Throws:
NullPointerException
- if dialog is null
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
Copyright © 2002 M.D. Anderson Cancer Center. All Rights Reserved.