Class GeneList

java.lang.Object
  |
  +--GeneList

class GeneList

extends java.lang.Object

The GeneList class manipulate lists of genes (clones, oligos, etc). A GeneList contains a subset of all genes in the database. It contains both a GeneBitSet bitset and an mList[0:length-1] containing MIDs sorted by whatever criteria are desired. The the index of mList[] does NOT imply the 1:1 ordering of genes as it is for midStaticCL.mList[] and GridCoords.gid2fgrc[].
Note: all gene GeneList instances have a GeneBitSet but may or may not have a mList[].

This class represents an individual gene list entry.

Note: gene sets are part of GeneLists and are implemented as GeneBitSet instances. Binary set operations are handled at the bit set level and are order N/64 using 64-bit long-word logical operations instead being O(N*N) if convolving mList[]'s are required.

In the places where we must work with an explicit mList[], the mList[] is defined otherwise it is set to null. Therefore, operations which update the bitSet will also update the mList[] if it is not null.

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: 2003/07/18 17:15:04 $ / $Revision: 1.12 $

Author:

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

See Also:

MAExplorer Home

Field Summary

(package private) GeneBitSet	bitSet
(package private) java.lang.String	cName instance: name of gene list
private static GeneList[]	geneSets list of all gene lists
(package private) int	length # of genes used in this gene list
private MAExplorer	mae link to global MAExplorer instance
(package private) int	MAX_GENE_LISTS max # of gene lists(or sets) to allow
(package private) static int	maxGeneListSize & number of geneSets
(package private) static int	maxGeneSets # of gene sets - keep title in gene set
(package private) int	maxSize maximum allocation size
(package private) Gene[]	mList instance: (opt) sorted list of Gene objects.
private static GeneList	tempSetCL temporary GeneList used in set operations
(package private) static int	useGeneSetIndex GeneSet to use for Current Gene Class.

Constructor Summary

(package private)	GeneList(MAExplorer mae, int maxGeneListSize) GeneList() - constructor to specify list sizes with both mList[] and bitSet.
(package private)	GeneList(MAExplorer mae, int maxGeneListSize, java.lang.String cName) GeneList() - constructor to make new Gene named list with both mList[] and bitSet.
(package private)	GeneList(MAExplorer mae, int maxGeneListSize, java.lang.String cName, boolean createMlistFlag) GeneList() - constructor to make new Gene named list with bitSet but optional mList[].

Method Summary

(package private) boolean	addGene(Gene c) addGene() - add Gene to gene list bitSet, and mList[] if it exists.
private void	allocGeneList(int maxGeneListSize, java.lang.String cName, boolean createMlistFlag) allocGeneList() - constructor to make new Gene named list with bitSet, but optional mList[].
(package private) void	cleanup() cleanup() - cleanup global static allocated variables in this class.
(package private) boolean	clear() clear() - clear gene list length and bitSet, but keep mList[] data
(package private) boolean	clearMlist() clearMlist() - clear gene mList[] entries to null.
(package private) boolean	clearNull() clearNull() - clear bitSet and gene mList[], set entries to null.
(package private) boolean	compressGeneList() compressGeneList() - compress the mList[] by removing nulls if any.
(package private) boolean	copy(GeneList c1, GeneList c2) copy() - copy GeneList mList[] and bitSets of c2 to c1.
(package private) boolean	copySorted(GeneList c1, GeneList c2) copySorted() - copy GeneList mList[] sorted, and bitSets of c2 to c1.
(package private) boolean	difference(GeneList c1, GeneList c2, GeneList c3) difference() - compute difference of gene lists (c2 - c1)==> c3.
(package private) Gene[]	getGeneList() getGeneList() - get gene mList[] data as Gene[].
(package private) GeneList	getGeneListByName(java.lang.String geneListName) getGeneListByName() - get GeneList if geneListName is a valid GeneList cName.
(package private) boolean	intersection(GeneList c1, GeneList c2, GeneList c3) intersection() - compute intersection of GeneLists (c1 & c2) ==> c3.
(package private) boolean	isGeneInGeneList(Gene c) isGeneInGeneList() - test if gene is in GeneList.
(package private) boolean	isGIDinGeneList(int gid) isGIDinGeneList() - test if GridCoords gid in GeneList.
(package private) boolean	isMIDinGeneList(int mid) isMIDinGeneList() - test if Gene id (mid) is in GeneList.
(package private) boolean	rmvGene(Gene c) rmvGene() - remove Gene from gene list and bitSet.
(package private) boolean	setGene(Gene c, int idx) setGene() - set Gene to specific gene list mList[idx].
(package private) boolean	setGeneListFromGeneNameArray(java.lang.String[] geneNameList) setGeneListFromGeneNameArray() - set the GeneList from array of gene names.
(package private) boolean	shortenGeneList() shortenGeneList() - shorten the mList[] to save space.
(package private) boolean	union(GeneList c1, GeneList c2, GeneList c3) union() - compute union of gene lists (c1 & c2) ==> c3.

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

MAX_GENE_LISTS

final int MAX_GENE_LISTS

max # of gene lists(or sets) to allow

maxGeneSets

static int maxGeneSets

# of gene sets - keep title in gene set

useGeneSetIndex

static int useGeneSetIndex

GeneSet to use for Current Gene Class. If there is a gene set, let it be >0. 0 is the set of ALL GENES

maxGeneListSize

static int maxGeneListSize

& number of geneSets

geneSets

private static GeneList[] geneSets

list of all gene lists

tempSetCL

private static GeneList tempSetCL

temporary GeneList used in set operations

cName

java.lang.String cName

instance: name of gene list

mList

Gene[] mList

instance: (opt) sorted list of Gene objects. allocated [0:maxSize-1] active [0:length-1]

bitSet

GeneBitSet bitSet

maxSize

int maxSize

maximum allocation size

length

int length

# of genes used in this gene list

Constructor Detail

GeneList

GeneList(MAExplorer mae,
         int maxGeneListSize)

GeneList() - constructor to specify list sizes with both mList[] and bitSet.

Parameters:

mae - is instance of MAExplorer

maxGeneListSize - is max size of any gene list

See Also:

allocGeneList(int, java.lang.String, boolean)

GeneList

GeneList(MAExplorer mae,
         int maxGeneListSize,
         java.lang.String cName)

GeneList() - constructor to make new Gene named list with both mList[] and bitSet.

Parameters:

mae - is instance of MAExplorer

maxGeneListSize - is max size of any gene list

cName - is name of the gene list

See Also:

allocGeneList(int, java.lang.String, boolean)

GeneList

GeneList(MAExplorer mae,
         int maxGeneListSize,
         java.lang.String cName,
         boolean createMlistFlag)

GeneList() - constructor to make new Gene named list with bitSet but optional mList[].

Parameters:

mae - is instance of MAExplorer

maxGeneListSize - is max size of any gene list

cName - is name of the gene list

createMlistFlag - creates the mList[] if true

See Also:

allocGeneList(int, java.lang.String, boolean)

Method Detail

allocGeneList

private void allocGeneList(int maxGeneListSize,
                           java.lang.String cName,
                           boolean createMlistFlag)

allocGeneList() - constructor to make new Gene named list with bitSet, but optional mList[].

Parameters:

maxGeneListSize - is max size of any gene list

cName - is name of the gene list

createMlistFlag - creates the mList[] if true

See Also:

GeneBitSet

setGene

boolean setGene(Gene c,
                int idx)

setGene() - set Gene to specific gene list mList[idx]. It also extends the list. NOTE: There may be mList[] entries with null values. So be careful when use the list.

Parameters:

c - is the gene instance

idx - is the index of where to put it in the mList[]

Returns:

true if set, false if any problems.

See Also:

GeneBitSet.setItem(int)

addGene

boolean addGene(Gene c)

addGene() - add Gene to gene list bitSet, and mList[] if it exists.

Parameters:

c - is the gene instance

Returns:

true if added, false if already in the list

See Also:

GeneBitSet.addItem(int), GeneBitSet.isItemInGeneBitSet(int)

rmvGene

boolean rmvGene(Gene c)

rmvGene() - remove Gene from gene list and bitSet.

Parameters:

c - is the gene instance

Returns:

true if removed it, false if not found.

See Also:

GeneBitSet.isItemInGeneBitSet(int), GeneBitSet.rmvItem(int)

setGeneListFromGeneNameArray

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

setGeneListFromGeneNameArray() - set the GeneList from array of gene names. This allows MULTIPLE instances of gene to be added to the GeneList.

Parameters:

geneNameList - is the string list of gene names

Returns:

TRUE if succeed.

See Also:

GipoTable.getAllMIDsForGene(java.lang.String, int), addGene(Gene), clear()

shortenGeneList

boolean shortenGeneList()

shortenGeneList() - shorten the mList[] to save space. Reallocate a new array and shorten it. This does not affect the bitSet.

Returns:

true if succeed

compressGeneList

boolean compressGeneList()

compressGeneList() - compress the mList[] by removing nulls if any. This does not affect the bitSet.

Returns:

true if succeed

See Also:

GeneBitSet.copyCLtoBS(GeneBitSet, GeneList, boolean)

isGeneInGeneList

boolean isGeneInGeneList(Gene c)

isGeneInGeneList() - test if gene is in GeneList. Uses bit sets so don't have to enumerate the mList[] to check.

Parameters:

c - is the Gene to test

Returns:

true if gene is in the GeneList.

See Also:

GeneBitSet.isItemInGeneBitSet(int)

isMIDinGeneList

boolean isMIDinGeneList(int mid)

isMIDinGeneList() - test if Gene id (mid) is in GeneList. Uses bit sets so don't have to enumerate the mList[] to check.

Parameters:

mid - is the MID of gene to test

Returns:

true if gene is in the gene list

See Also:

GeneBitSet.isItemInGeneBitSet(int)

isGIDinGeneList

boolean isGIDinGeneList(int gid)

isGIDinGeneList() - test if GridCoords gid in GeneList. Uses bit sets so don't have to enumerate the mList[] to check.

Parameters:

gid - is the GID of gene to test

Returns:

true if gene is in the gene list

See Also:

GeneBitSet.isItemInGeneBitSet(int)

getGeneList

Gene[] getGeneList()

getGeneList() - get gene mList[] data as Gene[]. Make mList[] if required.

Returns:

list of Genes

See Also:

GeneBitSet.cvtBStoCL(GeneList)

getGeneListByName

GeneList getGeneListByName(java.lang.String geneListName)

getGeneListByName() - get GeneList if geneListName is a valid GeneList cName.

Returns:

gene list or null if invalid name

clear

boolean clear()

clear() - clear gene list length and bitSet, but keep mList[] data

Returns:

true if successful.

See Also:

GeneBitSet.clearNull()

clearMlist

boolean clearMlist()

clearMlist() - clear gene mList[] entries to null.

Returns:

true if successful.

clearNull

boolean clearNull()

clearNull() - clear bitSet and gene mList[], set entries to null.

Returns:

true if successful.

See Also:

GeneBitSet.clearNull(), clearMlist()

copySorted

boolean copySorted(GeneList c1,
                   GeneList c2)

copySorted() - copy GeneList mList[] sorted, and bitSets of c2 to c1. You can rename c1 if the name is not null, else it keeps old name.

Parameters:

c1 - is first gene list

c2 - is 2nd gene list

Returns:

true if succeed.

See Also:

GeneBitSet.copyBStoBS(GeneBitSet, GeneBitSet)

copy

boolean copy(GeneList c1,
             GeneList c2)

copy() - copy GeneList mList[] and bitSets of c2 to c1.

Parameters:

c1 - is first gene list

c2 - is 2nd gene list

Returns:

true if succeed.

See Also:

GeneBitSet.copyBStoBS(GeneBitSet, GeneBitSet), GeneBitSet.copyBStoCL(GeneList, GeneBitSet)

union

boolean union(GeneList c1,
              GeneList c2,
              GeneList c3)

union() - compute union of gene lists (c1 & c2) ==> c3. Then, copy the results into c3. Note: c1 or c2 can be the same as c3. It will copy the result AFTER it has been computed.

Parameters:

c1 - is first gene list

c2 - is 2nd gene list

c3 - is 2nd gene list

Returns:

true if successful.

See Also:

GeneBitSet.copyBStoBS(GeneBitSet, GeneBitSet), GeneBitSet.copyBStoCL(GeneList, GeneBitSet), GeneBitSet.union(GeneBitSet, GeneBitSet, GeneBitSet)

intersection

boolean intersection(GeneList c1,
                     GeneList c2,
                     GeneList c3)

intersection() - compute intersection of GeneLists (c1 & c2) ==> c3. Then, copy the results into c3. Note: c1 or c2 can be the same as c3. It will copy the result AFTER it has been computed.

Parameters:

c1 - is first gene list

c2 - is 2nd gene list

c3 - is 2nd gene list

Returns:

true if successful.

See Also:

GeneBitSet.copyBStoBS(GeneBitSet, GeneBitSet), GeneBitSet.copyBStoCL(GeneList, GeneBitSet), GeneBitSet.intersection(GeneBitSet, GeneBitSet, GeneBitSet)

difference

boolean difference(GeneList c1,
                   GeneList c2,
                   GeneList c3)

difference() - compute difference of gene lists (c2 - c1)==> c3. Then, copy the result into c3. Note: c1 or c2 can be the same as c3. It will copy the result AFTER it has been computed.

Parameters:

c1 - is first gene list

c2 - is 2nd gene list

c3 - is 2nd gene list

Returns:

true if successful.

See Also:

GeneBitSet.copyBStoBS(GeneBitSet, GeneBitSet), GeneBitSet.copyBStoCL(GeneList, GeneBitSet), GeneBitSet.difference(GeneBitSet, GeneBitSet, GeneBitSet)

cleanup

void cleanup()

cleanup() - cleanup global static allocated variables in this class. If statics are added later to this class, then set them to null here.