org.geworkbench.util.pathwaydecoder.mutualinformation
Class AdjacencyMatrix

java.lang.Object
  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()