baseCode.bio.geneset
Class GeneAnnotations

java.lang.Object
  baseCode.bio.geneset.GeneAnnotations

public class GeneAnnotations

extends java.lang.Object

Reads tab-delimited file to create maps of probes to classes, classes to probes, probes to genes, genes to probes.

Maintains the following important data structures, all derived from the input file:

 
  
   
    
     
      
       
        
         
          
           
                                                    probe->Classes -- each value is a Set of the Classes that a probe belongs to.
                                                    Classes->probe -- each value is a Set of the probes that belong to a class
                                                    probe->gene -- each value is the gene name corresponding to the probe.
                                                    gene->list of probes -- each value is a list of probes corresponding to a gene
                                                    probe->description -- each value is a text description of the probe (actually...of the gene)
                
            
           
          
         
        
       
      
     
    
   
  
 

Copyright (c) 2004 Columbia University

Version:

$Id: GeneAnnotations.java,v 1.7 2004/12/27 22:25:56 pavlidis Exp $

Author:

Paul Pavlidis, Shamhil Merchant, Homin Lee

Constructor Summary

GeneAnnotations(GeneAnnotations geneData, java.util.Set activeProbes)
This is for creating GeneAnnotations by pruning a copy.

GeneAnnotations(java.io.InputStream stream, java.util.Set activeGenes, StatusViewer messenger)
Make a new GeneAnnotations that only includes the probes in the parameter 'probes'.

GeneAnnotations(java.lang.String fileName, java.util.Set activeGenes, StatusViewer messenger)

GeneAnnotations(java.lang.String filename, StatusViewer messenger)
This is for creating GeneAnnotations by reading from a file

Method Summary

void	addClass(java.lang.String id, java.util.ArrayList probesForNew) Add a class
boolean	geneSetExists(java.lang.String id) Returns true if the class is in the classToProbe map
java.util.Map	geneSetToRedundantMap()
java.util.ArrayList	getClassToProbes(java.lang.String id)
java.util.ArrayList	getGeneProbeList(java.lang.String g) Get a list of the probes that correspond to a particular gene.
java.lang.String	getGeneSetByIndex(int i) Get a class by an integer index i from the sorted list.
java.util.Map	getGeneSetToGeneMap()
java.util.Map	getGeneSetToProbeMap()
java.util.Map	getGeneToGeneSetMap()
java.util.Map	getGeneToProbeList()
java.lang.String	getProbeDescription(java.lang.String p) Get the description for a gene.
java.lang.String	getProbeGeneName(java.lang.String p) Get the gene that a probe belongs to.
java.util.Map	getProbeToGeneMap()
java.util.Map	getProbeToGeneSetMap()
java.util.List	getSelectedProbes()
java.util.List	getSelectedSets()
void	modifyClass(java.lang.String classId, java.util.ArrayList probesForNew) Redefine a class.
int	numAnnotatedGenes() Compute how many genes have Gene set annotations.
int	numGenes() How many genes are in the file?
int	numGeneSets() Get the number of classes.
int	numGenesInGeneSet(java.lang.String id) Get the number of genes in a gene set, identified by id.
int	numProbesForGene(java.lang.String g) Get how many probes point to the same gene.
int	numProbesInGeneSet(java.lang.String id) Get the number of probes in a gene set, identified by id.
void	print(java.io.Writer out) Print out the gene annotations in the same format we got them in, but if the gene sets have been modified, this will be reflected.
void	removeClassFromMaps(java.lang.String id) Remove a gene set (class) from all the maps that reference it.
void	resetSelectedProbes() Set the selected gene set to be the entire set.
void	resetSelectedSets() Set the selected gene set to be the entire set.
int	selectedProbes()
int	selectedSets()
void	selectProbes(java.lang.String searchOn) Create a selected probes list based on a search string.
void	selectSets(java.lang.String searchOn, GONames goData)
void	sortGeneSets() Sort the gene sets, filling out the sortedGeneSets.
java.util.List	sortGeneSetsBySize()
javax.swing.table.TableModel	toTableModel()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

GeneAnnotations

public GeneAnnotations(java.lang.String filename,
                       StatusViewer messenger)
                throws java.io.IOException

This is for creating GeneAnnotations by reading from a file

Parameters:

filename - String

messenger - StatusViewer to print status updates to.

Throws:

java.io.IOException

GeneAnnotations

public GeneAnnotations(GeneAnnotations geneData,
                       java.util.Set activeProbes)

This is for creating GeneAnnotations by pruning a copy.

Parameters:

geneData - GeneAnnotations copy to prune from

activeProbes - Set only include these probes

GeneAnnotations

public GeneAnnotations(java.io.InputStream stream,
                       java.util.Set activeGenes,
                       StatusViewer messenger)
                throws java.io.IOException

Make a new GeneAnnotations that only includes the probes in the parameter 'probes'.

Parameters:

stream -

activeGenes - Only genes in this set are left.

Throws:

java.io.IOException

GeneAnnotations

public GeneAnnotations(java.lang.String fileName,
                       java.util.Set activeGenes,
                       StatusViewer messenger)
                throws java.io.IOException

Parameters:

fileName -

Method Detail

getProbeToGeneMap

public java.util.Map getProbeToGeneMap()

Returns:

Map

getGeneToProbeList

public java.util.Map getGeneToProbeList()

Returns:

Map

getGeneSetToProbeMap

public java.util.Map getGeneSetToProbeMap()

Returns:

Map

getClassToProbes

public java.util.ArrayList getClassToProbes(java.lang.String id)

Parameters:

id - String class id

Returns:

ArrayList list of probes in class

sortGeneSets

public void sortGeneSets()

Sort the gene sets, filling out the sortedGeneSets. This should be called after any changes have been made to the classToProbeMap. The sort is just in order of id.

sortGeneSetsBySize

public java.util.List sortGeneSetsBySize()

Returns:

getProbeToGeneSetMap

public java.util.Map getProbeToGeneSetMap()

Returns:

Map

geneSetToRedundantMap

public java.util.Map geneSetToRedundantMap()

Returns:

Map

getProbeGeneName

public java.lang.String getProbeGeneName(java.lang.String p)

Get the gene that a probe belongs to.

Parameters:

p - String

Returns:

String

getProbeDescription

public java.lang.String getProbeDescription(java.lang.String p)

Get the description for a gene.

Parameters:

p - String

Returns:

String

getGeneProbeList

public java.util.ArrayList getGeneProbeList(java.lang.String g)

Get a list of the probes that correspond to a particular gene.

Parameters:

g - String a gene name

Returns:

ArrayList list of the probes for gene g

getGeneSetByIndex

public java.lang.String getGeneSetByIndex(int i)

Get a class by an integer index i from the sorted list.

Parameters:

i -

Returns:

geneSetExists

public boolean geneSetExists(java.lang.String id)

Returns true if the class is in the classToProbe map

Parameters:

id - String a class id

Returns:

boolean

numProbesForGene

public int numProbesForGene(java.lang.String g)

Get how many probes point to the same gene. This is like the old "numReplicates".

Parameters:

g -

Returns:

numGeneSets

public int numGeneSets()

Get the number of classes. This is computed from the sortedGeneSets.

Returns:

numGenes

public int numGenes()

How many genes are in the file?

numProbesInGeneSet

public int numProbesInGeneSet(java.lang.String id)

Get the number of probes in a gene set, identified by id.

Parameters:

id - String a class id

Returns:

int number of probes in the class

numGenesInGeneSet

public int numGenesInGeneSet(java.lang.String id)

Get the number of genes in a gene set, identified by id.

Parameters:

id - String a class id

Returns:

int number of genes in the class

addClass

public void addClass(java.lang.String id,
                     java.util.ArrayList probesForNew)

Add a class

Parameters:

id - String class to be added

probesForNew - ArrayList user-defined list of members.

modifyClass

public void modifyClass(java.lang.String classId,
                        java.util.ArrayList probesForNew)

Redefine a class.

Parameters:

classId - String class to be modified

probesForNew - ArrayList current user-defined list of members. The "real" version of the class is modified to look like this one.

toTableModel

public javax.swing.table.TableModel toTableModel()

Returns:

selectProbes

public void selectProbes(java.lang.String searchOn)

Create a selected probes list based on a search string.

Parameters:

searchOn - A string to be searched.

resetSelectedProbes

public void resetSelectedProbes()

Set the selected gene set to be the entire set.

getSelectedProbes

public java.util.List getSelectedProbes()

Returns:

the list of selected probes.

selectedProbes

public int selectedProbes()

Returns:

the number of probes currently on the 'selected' list.

selectSets

public void selectSets(java.lang.String searchOn,
                       GONames goData)

Parameters:

searchOn -

goData -

resetSelectedSets

public void resetSelectedSets()

Set the selected gene set to be the entire set.

getSelectedSets

public java.util.List getSelectedSets()

Returns:

list of selected sets.

selectedSets

public int selectedSets()

Returns:

the number of sets currently on the 'selected' list.

print

public void print(java.io.Writer out)
           throws java.io.IOException

Print out the gene annotations in the same format we got them in, but if the gene sets have been modified, this will be reflected.

Parameters:

out -

Throws:

java.io.IOException

getGeneSetToGeneMap

public java.util.Map getGeneSetToGeneMap()

Returns:

Returns the classToGeneMap.

getGeneToGeneSetMap

public java.util.Map getGeneToGeneSetMap()

Returns:

Returns the geneToClassMap.

numAnnotatedGenes

public int numAnnotatedGenes()

Compute how many genes have Gene set annotations.

Returns:

removeClassFromMaps

public void removeClassFromMaps(java.lang.String id)

Remove a gene set (class) from all the maps that reference it.

Parameters:

id -