org.geworkbench.util.pathwaydecoder.mutualinformation
Class AdjacencyMatrix

java.lang.Object
  extended by org.geworkbench.util.pathwaydecoder.mutualinformation.AdjacencyMatrix
All Implemented Interfaces:
java.io.Serializable

public class AdjacencyMatrix
extends java.lang.Object
implements java.io.Serializable

AdjacencyMatrix

This class needs deep cleaning-up.

Version:
$Id$
Author:
not attributable
See Also:
Serialized Form

Constructor Summary
AdjacencyMatrix()
           
 
Method Summary
 void add(int geneId1, int geneId2, float edge)
          Adds and edge between geneId1 and geneId2
 void add(java.lang.String geneId1, java.lang.String geneId2, boolean isGene1InMicroarray, boolean isGene2InMicroarray, float edge)
          Adds and edge between geneId1 and geneId2
 void addDirectional(int geneId1, int geneId2, java.lang.String interaction)
           
 void addDirectional(java.lang.String geneId1, java.lang.String geneId2, boolean isGene1InMicroarray, boolean isGene2InMicroarray, java.lang.String interaction)
           
 void addGeneRow(int geneId)
           
 java.util.HashMap<java.lang.Integer,java.lang.Float> get(int geneId)
          Returns a map with all the edges to geneId
 float get(int geneId1, int geneId2)
          returns the strength of the edge between geneId1 and geneId2 (0.0 == no edge)
 int getConnectionNo()
           
 java.util.HashMap<java.lang.Integer,java.util.HashMap<java.lang.Integer,java.lang.Float>> getGeneRows()
           
 java.util.HashMap<java.lang.String,java.util.HashMap<java.lang.String,java.lang.Float>> getGeneRowsNotInMicroarray()
           
 java.util.HashMap<java.lang.Integer,java.util.HashMap<java.lang.Integer,java.lang.String>> getInteractionMap()
           
 java.util.HashMap<java.lang.String,java.util.HashMap<java.lang.String,java.lang.String>> getInteractionNotInMicroarrayMap()
           
 java.util.Set<java.lang.Integer> getKeys()
           
 java.lang.String getLabel()
           
 int getMappedId(int geneId)
           
 DSMicroarraySet<DSMicroarray> getMicroarraySet()
           
 void setLabel(java.lang.String name)
           
 void setMicroarraySet(DSMicroarraySet<DSMicroarray> microarraySet)
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

AdjacencyMatrix

public AdjacencyMatrix()
Method Detail

getGeneRows

public java.util.HashMap<java.lang.Integer,java.util.HashMap<java.lang.Integer,java.lang.Float>> getGeneRows()

getGeneRowsNotInMicroarray

public java.util.HashMap<java.lang.String,java.util.HashMap<java.lang.String,java.lang.Float>> getGeneRowsNotInMicroarray()

get

public float get(int geneId1,
                 int geneId2)
returns the strength of the edge between geneId1 and geneId2 (0.0 == no edge)

Parameters:
geneId1 - int
geneId2 - int
Returns:
float

getInteractionMap

public java.util.HashMap<java.lang.Integer,java.util.HashMap<java.lang.Integer,java.lang.String>> getInteractionMap()

getInteractionNotInMicroarrayMap

public java.util.HashMap<java.lang.String,java.util.HashMap<java.lang.String,java.lang.String>> getInteractionNotInMicroarrayMap()

get

public java.util.HashMap<java.lang.Integer,java.lang.Float> get(int geneId)
Returns a map with all the edges to geneId

Parameters:
geneId - int
Returns:
HashMap

addGeneRow

public void addGeneRow(int geneId)

getLabel

public java.lang.String getLabel()

setLabel

public void setLabel(java.lang.String name)

add

public void add(int geneId1,
                int geneId2,
                float edge)
Adds and edge between geneId1 and geneId2

Parameters:
geneId1 - int
geneId2 - int
edge - float

add

public void add(java.lang.String geneId1,
                java.lang.String geneId2,
                boolean isGene1InMicroarray,
                boolean isGene2InMicroarray,
                float edge)
Adds and edge between geneId1 and geneId2

Parameters:
geneId1 - String
geneId2 - String
edge - float

addDirectional

public void addDirectional(int geneId1,
                           int geneId2,
                           java.lang.String interaction)
Parameters:
geneId1 - int
geneId2 - int
interaction - String

addDirectional

public void addDirectional(java.lang.String geneId1,
                           java.lang.String geneId2,
                           boolean isGene1InMicroarray,
                           boolean isGene2InMicroarray,
                           java.lang.String interaction)
Parameters:
geneId1 - String
geneId2 - String
interaction - String

getMappedId

public int getMappedId(int geneId)

getKeys

public java.util.Set<java.lang.Integer> getKeys()

getConnectionNo

public int getConnectionNo()

setMicroarraySet

public void setMicroarraySet(DSMicroarraySet<DSMicroarray> microarraySet)

getMicroarraySet

public DSMicroarraySet<DSMicroarray> getMicroarraySet()