org.mdanderson.biostat.geneclust
public abstract class Simulation extends SProcess
Modifier and Type | Field and Description |
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protected String |
classificationFileName |
protected int |
gapTolerance |
protected int |
numClustersToExtract |
protected int |
numPermutations |
protected int |
percentSupervision |
protected int |
percentToShave |
protected String |
performSupervised |
protected String |
writeMatrix |
Constructor and Description |
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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...
|
Modifier and Type | Method and Description |
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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.
|
getDialog, run, writeSinterpreterInput, writeSinterpreterInterrupt, writeSinterpreterTermination
protected String performSupervised
protected int percentSupervision
protected String classificationFileName
protected int numClustersToExtract
protected int percentToShave
protected int numPermutations
protected int gapTolerance
protected String writeMatrix
public Simulation(SimulationDialog dialog, boolean isPerformSupervised, int percentSupervision, String classificationPathName, int numClustersToExtract, int percentToShave, int numPermutations, int gapTolerance, boolean isWriteMatrix)
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.NullPointerException
- if dialog is nullprotected void writeSinterpreterInit(org.mdanderson.biostat.geneclust.SBufferedWriter bw) throws IOException
bw
- output stream writerIOException
- if an error occurs while writingprotected void writeSinterpreterGenericInput(org.mdanderson.biostat.geneclust.SBufferedWriter bw) throws IOException
bw
- output stream writerIOException
- if an error occurs while writingCopyright © 2002 M.D. Anderson Cancer Center. All Rights Reserved.