org.geworkbench.util.pathwaydecoder.mutualinformation
Class MutualInformationLibrary

java.lang.Object
  extended by org.geworkbench.util.pathwaydecoder.mutualinformation.MutualInformationLibrary

public class MutualInformationLibrary
extends java.lang.Object

Title: Bioworks

Description: Modular Application Framework for Gene Expession, Sequence and Genotype Analysis

Copyright: Copyright (c) 2003 -2004

Company: Columbia University

Version:
1.0
Author:
not attributable

Method Summary
 void create(java.lang.String theMatrix, java.lang.String output, int mArrayNo, int[] mArrayId)
          Create the adjacency matrix from a file based matrix
 void createConstrainedHigh(java.lang.String theMatrix, int controlId, double percent)
           
 void createConstrainedHigh(java.lang.String theMatrix, java.lang.String geneAffyId, double percent)
           
 void createConstrainedLow(java.lang.String theMatrix, int controlId, double percent)
           
 void createConstrainedLow(java.lang.String theMatrix, java.lang.String geneAffyId, double percent)
           
 double getCompletion()
           
 boolean initialized()
           
 void setParams(double mean, double sigma, double threshold, double miErrorPercent, boolean reduce)
           
 void stop()
           
 void test()
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Method Detail

initialized

public boolean initialized()

create

public void create(java.lang.String theMatrix,
                   java.lang.String output,
                   int mArrayNo,
                   int[] mArrayId)
Create the adjacency matrix from a file based matrix

Parameters:
theMatrix - String the name of the Gene Expression matrix
output - String the name of the output Adjancency Matrix
mArrayNo - int the number of microarrays to use
mArrayId - int[] the ids of the microarrays to use
reduce - boolean if true, remove non-nearest neighbors

createConstrainedHigh

public void createConstrainedHigh(java.lang.String theMatrix,
                                  int controlId,
                                  double percent)

createConstrainedLow

public void createConstrainedLow(java.lang.String theMatrix,
                                 int controlId,
                                 double percent)

createConstrainedHigh

public void createConstrainedHigh(java.lang.String theMatrix,
                                  java.lang.String geneAffyId,
                                  double percent)

createConstrainedLow

public void createConstrainedLow(java.lang.String theMatrix,
                                 java.lang.String geneAffyId,
                                 double percent)

setParams

public void setParams(double mean,
                      double sigma,
                      double threshold,
                      double miErrorPercent,
                      boolean reduce)

getCompletion

public double getCompletion()

stop

public void stop()

test

public void test()