Class GeneClass

java.lang.Object
  |
  +--GeneClass

class GeneClass

extends java.lang.Object

The GeneClass sets up GeneLists for operating on classes of genes. These belong to both built-in and user-defined gene class. The methods available copy gene genes to the special gene sets and maintain a popup status window. The built-in gene classes are divided into fixed and dynamic special gene classes.
1. Fixed gene classes depending on original GIPO data - can't be changed or deleted

allGenesCL - "ALL GENES"

allNamedGenesCL - "ALL NAMED GENES",

similarESTsCL - "ESTs similar to genes"

ESTsCL - "ESTs"

allGenesAndESTsCL - "All genes and ESTs"

goodGenesCL - "Good genes"

replicateGenesCL - "Replicate genes"

housekeepingGenesCL - "HousekeepingGenes"

calDNACL - "Calibration DNA"

yourPlatesCL - "Your plates"

emptyWellCL - "Empty wells"

2. Special user assignable gene classes are - may be changed but not deleted

userFilterGeneSetCL - "User Filter Gene Set",

editedCL - "Edited Gene List"

normCL - "Normalization Gene Set"

2. Regular user creatable gene classes - may be changed and deleted Users can create as many user defined sets as they wish that may be either changed or deleted.

NOTE: All of these GeneLists live in GeneClass rather than in Filter.

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: 2003/07/07 21:40:41 $ / $Revision: 1.10 $

Author:

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

See Also:

MAExplorer Home, GeneList, GeneBitSet

Field Summary

private GeneBitSet	allClBS working bit set of all genes
(package private) GeneList	allGenesAndESTsCL special list of All genes and ESTs
(package private) GeneList	allGenesCL special list of all genes
(package private) GeneList	allNamedGenesCL special list of all named genes
(package private) GeneList	calDNACL special list of calibration DNA
(package private) int	curGeneClass current Gene class selected.
(package private) static java.lang.String	curGeneClassName Name of current Gene Class
(package private) static java.lang.String[]	defClassName
(package private) GeneList	editedCL "edited gene list"
(package private) GeneList	emptyWellCL special list of "EmptyWell" genes
(package private) GeneList	ESTsCL special list of unknown ESTs
(package private) GeneList[]	geneClassCLS Gene index lists for each gene class.
(package private) static java.lang.String[]	geneClassName List of GeneClass names [0:nbrGC-1]
(package private) Table	gincDB (opt.) Table of gene classes if it exists
(package private) GeneList	goodGenesCL special list of good genes
(package private) GeneList	housekeepingGenesCL special list of all housekeeping genes
(package private) int	idxAllGenes index for special class in the list
(package private) int	idxAllGenesAndESTs index for special class in the list
(package private) int	idxAllNamedGenes index for special class in the list
(package private) int	idxCalDNA index for special class in the list
(package private) static int	idxCurGeneClass index of current GeneClass
(package private) int	idxEGL index for special class in the list
(package private) int	idxEmptyWell index for special class in the list
(package private) int	idxESTs index for special class in the list
(package private) int	idxGoodGenes index for special class in the list
(package private) int	idxHousekeepingGenes index for special class in the list
(package private) int	idxNormGeneSet index for special class in the list
(package private) int	idxReplicateGenes index for special class in the list
(package private) int	idxSimilarESTs index for special class in the list
(package private) int	idxUserFilterGeneSet index for special class in the list
(package private) int	idxYourPlates index for special class in the list
private MAExplorer	mae link to global instance
private Maps	map link to global instance
(package private) static int	nbrGC # of all gene classes
(package private) static int[]	nbrGenesInGC size of the corresponding GeneClass.
(package private) static int	NDEF_CLASS_NAMES
(package private) static int	nFixedGC # of fixed special built-in gene
(package private) GeneList	normCL "Normalization genes"
(package private) static int	nSpecialGC # of all special built-in gene classes including variable
(package private) GeneList	replicateGenesCL special list of replicate genes
(package private) GeneList	similarESTsCL special list of ESTs similar to genes
(package private) GeneList	userFilterGeneSetCL "Filter by user Filter Gene Set"
(package private) GeneList	yourPlatesCL special list of "your plate" genes

Constructor Summary

(package private)

GeneClass(MAExplorer mae) GeneClass() - constructor to create gene class database

Method Summary

(package private) void	assignGeneNames2StaticGeneList() assignGeneNames2StaticGeneList() - assign Gene_Names' to map.midStaticCL list now that the gene lists exist in the map.midStaticCL list.
(package private) GeneList	getGeneListOfCurrentGeneClass() getGeneListOfCurrentGeneClass() - get the current GeneClass Gene List
(package private) GeneList	getGeneListOfGeneClass(java.lang.String geneClassName) getGeneListOfGeneClass() - return a Gene List for the gene class
(package private) int	lookupGeneClassIdx(java.lang.String geneClass) lookupGeneClassIdx() - lookup index of gene class if exists.
private void	readGeneClassCloneIDGeneNameGeneClassFile() readGeneClassCloneIDGeneNameGeneClassFile() - build table data Read data from mae.geneIdNameClassFile.
private boolean	readGeneClassTableFile() readGeneClassTableFile() - read mae.geneClassNamesFile into database If the file is not available, then use the default data in this Class.
(package private) int	setCurrentGeneClassName(java.lang.String newGeneClass) setCurrentGeneClassName() - set the "current GeneClass"
(package private) void	setupDefaultGeneClass_GeneBitSets() setupDefaultGeneClass_GeneBitSets() - called at end of init() to set up gene sets.
(package private) void	setupSpecialGeneLists() setupSpecialGeneLists() - set up default special gene class cases.
(package private) void	updateStdGenePartitions() updateStdGenePartitions() - setup all of the special gene sets.

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 instance

map

private Maps map

link to global instance

allClBS

private GeneBitSet allClBS

working bit set of all genes

gincDB

Table gincDB

(opt.) Table of gene classes if it exists

allGenesCL

GeneList allGenesCL

special list of all genes

allNamedGenesCL

GeneList allNamedGenesCL

special list of all named genes

similarESTsCL

GeneList similarESTsCL

special list of ESTs similar to genes

ESTsCL

GeneList ESTsCL

special list of unknown ESTs

allGenesAndESTsCL

GeneList allGenesAndESTsCL

special list of All genes and ESTs

goodGenesCL

GeneList goodGenesCL

special list of good genes

replicateGenesCL

GeneList replicateGenesCL

special list of replicate genes

housekeepingGenesCL

GeneList housekeepingGenesCL

special list of all housekeeping genes

calDNACL

GeneList calDNACL

special list of calibration DNA

yourPlatesCL

GeneList yourPlatesCL

special list of "your plate" genes

emptyWellCL

GeneList emptyWellCL

special list of "EmptyWell" genes

userFilterGeneSetCL

GeneList userFilterGeneSetCL

"Filter by user Filter Gene Set"

editedCL

GeneList editedCL

"edited gene list"

normCL

GeneList normCL

"Normalization genes"

geneClassCLS

GeneList[] geneClassCLS

Gene index lists for each gene class. [geneClassNameIdx][nbrGenesInGC] the values are from GridCoords.gid2mid[]

curGeneClassName

static java.lang.String curGeneClassName

Name of current Gene Class

geneClassName

static java.lang.String[] geneClassName

List of GeneClass names [0:nbrGC-1]

nbrGenesInGC

static int[] nbrGenesInGC

size of the corresponding GeneClass.

idxCurGeneClass

static int idxCurGeneClass

index of current GeneClass

nSpecialGC

static int nSpecialGC

# of all special built-in gene classes including variable

nFixedGC

static int nFixedGC

# of fixed special built-in gene

nbrGC

static int nbrGC

# of all gene classes

defClassName

static final java.lang.String[] defClassName

NDEF_CLASS_NAMES

static final int NDEF_CLASS_NAMES

idxAllGenes

int idxAllGenes

index for special class in the list

idxAllNamedGenes

int idxAllNamedGenes

index for special class in the list

idxSimilarESTs

int idxSimilarESTs

index for special class in the list

idxESTs

int idxESTs

index for special class in the list

idxAllGenesAndESTs

int idxAllGenesAndESTs

index for special class in the list

idxGoodGenes

int idxGoodGenes

index for special class in the list

idxReplicateGenes

int idxReplicateGenes

index for special class in the list

idxHousekeepingGenes

int idxHousekeepingGenes

index for special class in the list

idxCalDNA

int idxCalDNA

index for special class in the list

idxYourPlates

int idxYourPlates

index for special class in the list

idxEmptyWell

int idxEmptyWell

index for special class in the list

idxUserFilterGeneSet

int idxUserFilterGeneSet

index for special class in the list

idxEGL

int idxEGL

index for special class in the list

idxNormGeneSet

int idxNormGeneSet

index for special class in the list

curGeneClass

int curGeneClass

current Gene class selected. class 0 is the class of ALL GENES. class 1 is the class of ALL NAMED GENES with full GeneBank Ids.

Constructor Detail

GeneClass

GeneClass(MAExplorer mae)

GeneClass() - constructor to create gene class database

Parameters:

mae - is instance of MAExplorer

See Also:

readGeneClassTableFile()

Method Detail

setupSpecialGeneLists

void setupSpecialGeneLists()

setupSpecialGeneLists() - set up default special gene class cases. The default curGeneClass is "ALL GENES".

See Also:

GeneList, lookupGeneClassIdx(java.lang.String), updateStdGenePartitions()

setupDefaultGeneClass_GeneBitSets

void setupDefaultGeneClass_GeneBitSets()

setupDefaultGeneClass_GeneBitSets() - called at end of init() to set up gene sets. Create initial Gene Sets which will appear in userBS[] list. NOTE: keep in sync with new default bit sets.

See Also:

UserState.restoreGeneSets(), GeneBitSet.assignCLtoUserBS(java.lang.String, GeneList)

readGeneClassTableFile

private boolean readGeneClassTableFile()

readGeneClassTableFile() - read mae.geneClassNamesFile into database If the file is not available, then use the default data in this Class. Also setup the special gene lists.
[TODO] This will be replace with GeneOntology data....

Returns:

true if succeed.

See Also:

Table, Table.lookupFieldIdxAndRemapFieldName(java.lang.String, java.lang.String), setupSpecialGeneLists()

readGeneClassCloneIDGeneNameGeneClassFile

private void readGeneClassCloneIDGeneNameGeneClassFile()

readGeneClassCloneIDGeneNameGeneClassFile() - build table data Read data from mae.geneIdNameClassFile. This contains fields:

       Master_Id    Master_Gene_Name    Gene_Class

See Also:

GeneList, GeneList.addGene(Gene), GeneList.shortenGeneList(), GipoTable.getMIDfromMaster_IDhashTable(java.lang.String), Table, SimpleTable.lookupFieldIdx(java.lang.String)

lookupGeneClassIdx

int lookupGeneClassIdx(java.lang.String geneClass)

lookupGeneClassIdx() - lookup index of gene class if exists.

Parameters:

geneClass - is the name of the gene class to look up

Returns:

index if found, if not return -1

getGeneListOfGeneClass

GeneList getGeneListOfGeneClass(java.lang.String geneClassName)

getGeneListOfGeneClass() - return a Gene List for the gene class

Parameters:

geneClassName - is the name of the gene class to retrieve

Returns:

gene class else null if problem

See Also:

lookupGeneClassIdx(java.lang.String)

setCurrentGeneClassName

int setCurrentGeneClassName(java.lang.String newGeneClass)

setCurrentGeneClassName() - set the "current GeneClass"

Parameters:

newGeneClass - is the name of the new gene class to create

Returns:

index of new class, -1 if illegal.

See Also:

GeneList.copy(GeneList, GeneList), lookupGeneClassIdx(java.lang.String)

getGeneListOfCurrentGeneClass

GeneList getGeneListOfCurrentGeneClass()

getGeneListOfCurrentGeneClass() - get the current GeneClass Gene List

Returns:

gene list of the current gene class

See Also:

lookupGeneClassIdx(java.lang.String)

updateStdGenePartitions

void updateStdGenePartitions()

updateStdGenePartitions() - setup all of the special gene sets. NOTE: the special gene lists should have been been setup previously. NOTE: we do NOT setup UserFilterGeneSetCL, editedCL or normCL - which must be done elsewhere in specialized classes.

See Also:

GeneList.addGene(Gene)

assignGeneNames2StaticGeneList

void assignGeneNames2StaticGeneList()

assignGeneNames2StaticGeneList() - assign Gene_Names' to map.midStaticCL list now that the gene lists exist in the map.midStaticCL list.

See Also:

GipoTable.getMIDfromMaster_IDhashTable(java.lang.String), SimpleTable.lookupFieldIdx(java.lang.String)