Class EditedGeneList

java.lang.Object
  |
  +--EditedGeneList

class EditedGeneList

extends java.lang.Object

Class to edit the Edited Gene List. The EGL is Filter.editedCL gene list. Operations include adding, removing, setting it to Filter.workingCL, etc.

This work was produced by Peter Lemkin of the National Cancer Institute, an agency of the United States Government. As a work of the United States Government there is no associated copyright. It is offered as open source software under the Mozilla Public License (version 1.1) subject to the limitations noted in the accompanying LEGAL file. This notice must be included with the code. The MAExplorer Mozilla and Legal files are available on http://maexplorer.sourceforge.net/.

Version:

$Date: 2003/04/03 21:01:40 $ $Revision: 1.6 $

Author:

P. Lemkin (NCI), G. Thornwall (SAIC), NCI-Frederick, Frederick, MD

See Also:

MAExplorer Home, GeneClass, GeneList

Field Summary

private Filter	fc link to global Filter instance
private GeneClass	gct link to global GeneClass instance
private MAExplorer	mae link to global MAExplorer instance
private Maps	map link to global Maps instance
(package private) int	maxGenes max # genes/gene list
private GeneList	tmpCL temporary gene list for computations

Constructor Summary

(package private)

EditedGeneList(MAExplorer mae) EditedGeneList() - constructor

Method Summary

(package private) boolean	addGeneByRegion(Gene gene) addGenesByRegion() - add genes to editedCL if they are in the region in the pseudoarray image or scatterplot [TODO]
(package private) boolean	addGeneToEditedCL(Gene gene) addGeneToEditedCL() - add gene to editedCL if not in CL by gene
(package private) boolean	addGeneToEditedCL(int mid) addGeneToEditedCL() - add gene to editedCL if not in CL by mid
(package private) boolean	processEditCommand(int mouseKeyMods) processEditCommand() - do an 'edited gene list' add/remove command:
(package private) boolean	removeGeneFromEditedCL(Gene gene) removeGeneFromEditedCL() - remove gene from the editedCL by gene.
(package private) boolean	removeGeneFromEditedCL(int mid) removeGeneFromEditedCL() - remove gene from the editedCL by mid.
(package private) boolean	setEGLfromGeneListStr(java.lang.String[] geneNameList) setEGLfromGeneListStr() - set the EGL from the gene list string names.

Methods inherited from class java.lang.Object

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

Field Detail

mae

private MAExplorer mae

link to global MAExplorer instance

map

private Maps map

link to global Maps instance

fc

private Filter fc

link to global Filter instance

gct

private GeneClass gct

link to global GeneClass instance

tmpCL

private GeneList tmpCL

temporary gene list for computations

maxGenes

int maxGenes

max # genes/gene list

Constructor Detail

EditedGeneList

EditedGeneList(MAExplorer mae)

EditedGeneList() - constructor

Parameters:

mae - is the MAExplorer instance

Method Detail

removeGeneFromEditedCL

boolean removeGeneFromEditedCL(int mid)

removeGeneFromEditedCL() - remove gene from the editedCL by mid.

Parameters:

mid - is the Master Gene Index if not -1

Returns:

true if removed it.

See Also:

removeGeneFromEditedCL(int)

removeGeneFromEditedCL

boolean removeGeneFromEditedCL(Gene gene)

removeGeneFromEditedCL() - remove gene from the editedCL by gene.

Parameters:

gene - is the Gene instance

Returns:

true if removed it.

See Also:

GeneBitSet.updateListGeneBitSets(), GeneList.rmvGene(Gene)

addGeneToEditedCL

boolean addGeneToEditedCL(int mid)

addGeneToEditedCL() - add gene to editedCL if not in CL by mid

Parameters:

mid - is the Master Gene Index if not -1

Returns:

true if aded it.

addGeneToEditedCL

boolean addGeneToEditedCL(Gene gene)

addGeneToEditedCL() - add gene to editedCL if not in CL by gene

Parameters:

gene - is the Gene instance

Returns:

true if added it.

See Also:

GeneList.addGene(Gene), GeneBitSet.updateListGeneBitSets()

addGeneByRegion

boolean addGeneByRegion(Gene gene)

addGenesByRegion() - add genes to editedCL if they are in the region in the pseudoarray image or scatterplot [TODO]

Parameters:

gene - is the Gene instance

Returns:

true if added it.

processEditCommand

boolean processEditCommand(int mouseKeyMods)

processEditCommand() - do an 'edited gene list' add/remove command:

   CTRL/MOUSE to add genes to editedCL
   SHIFT/MOUSE to remove genes from editedCL

Parameters:

mouseKeyModes - key modifiers

Returns:

true if successful

See Also:

Filter.computeWorkingGeneList(), GeneList.isGeneInGeneList(Gene), Component.repaint(), Component.repaint(), Util.showMsg(java.lang.String), addGeneToEditedCL(int), removeGeneFromEditedCL(int)

setEGLfromGeneListStr

boolean setEGLfromGeneListStr(java.lang.String[] geneNameList)

setEGLfromGeneListStr() - set the EGL from the gene list string names. This allows MULTIPLE instances of gene to be added to EGL.

Parameters:

geneNameList - is string list of genes by Gene_Name

Returns:

true if succeed.

See Also:

GeneList.setGeneListFromGeneNameArray(java.lang.String[])