Class Maps

java.lang.Object
  |
  +--Maps

class Maps

extends java.lang.Object

The Maps class holds various gene maps for mapping: GID, MID, GCRF, gene names. Specifically, gid, mid, gangGid, cloneID, gene_name mapping and hash lookup tables. The mapping tables are allocated here but populated elsewhere, and used throughout MAExplorer.

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: 2002/12/11 17:23:26 $ $Revision: $

Author:

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

See Also:

MAExplorer Home, GridCoords, GeneList

Field Summary

private Config	cfg link to global Config instance
(package private) int[][][][]	fgrc2gid map: [f][g][r][c] to gid (GridCoords index GID).
(package private) static java.lang.String[]	fName list of alphabetic names of Names of fields
(package private) GridCoords[]	gid2fgrc map: gid (GridCoords index) to [f][g][r][c] values in GridCoords object.
(package private) int[]	gid2mid map: gid (gridCoords index) to mid (Master Gene index).
(package private) GeneList	gidStaticCL map: GridCoords gid index to list of genes.
(package private) int[]	gidToGangGid map: gid (GridCoords index) to the Gang gid.
(package private) static java.lang.String[]	gName list of alphabetic names of Names of grids
private MAExplorer	mae link to global MAExplorer instance
(package private) int	maxGeneHashTableSize size of gene hash table estimated as 1.5*maxGenes - only to 1st instance
(package private) int	maxGenes maximum number of genes (estimated as maxGRIDS*maxGROWS*maxGCOLS)
(package private) int	maxMIDs maximum # of Master Gene IDs = size of gene (i.e clone,oligo, etc) list
(package private) int	maxSpots maximum # of spots estimated as maxFIELDS*maxGRIDS*maxGROWS*maxGCOL
(package private) int	maxSpotsFound max # spots found.
(package private) int[]	mid2gid map: mid (Master Gene index) to gid (gridCoords index) This is created by: GeneTable.setupMIDlist() It is used for lookup by: GeneTable.getGeneListOfGeneClass()
(package private) java.util.Hashtable	mid2MasterIdHashtable hash table of Master Gene IDs (MID) of size maxGeneHashTableSize.
(package private) GeneList	midStaticCL map: mid index to list of genes i.e.

Constructor Summary

(package private)

Maps(MAExplorer mae) Maps() - constructor that allocates mapping tables calc size from F*G*R*C These is populated @GipoTable.setupMapLookupTables().

Method Summary

private void	allocateMapArrays() allocateMapArrays() - Allocate the map arrays and hash tables
(package private) int	lookupMIDfrom_dbEST(java.lang.String name) lookupMIDfrom_dbEST() - lookup mid from dbEST 3' or 5' ID.
(package private) int	lookupMIDfromCloneID(java.lang.String name) lookupMIDfromCloneID() - lookup mid from CloneID Note this returns the first instance of the gene found if there are duplicates.
(package private) int	lookupMIDfromGenBankACC(java.lang.String name) lookupMIDfromGenBankACC() - lookup mid from GenBank ACC ID.
(package private) int	lookupMIDfromGeneName(java.lang.String name) lookupMIDfromGeneName() - lookup mid from Gene Name.
(package private) int	lookupMIDfromLocusID(java.lang.String name) lookupMIDfromLocusID() - lookup mid from Locus ID Note this returns the first instance of the gene found if there are duplicates.
(package private) int	lookupMIDfromRefSeqID(java.lang.String name) lookupMIDfromRefSeqID() - lookup mid from RefSeq ID Note this returns the first instance of the gene found if there are duplicates.
(package private) int	lookupMIDfromSwissProtID(java.lang.String name) lookupMIDfromSwissProtID() - lookup mid from SwissProt ID Note this returns the first instance of the gene found if there are duplicates.
(package private) int	lookupMIDfromUniGeneID(java.lang.String name) lookupMIDfromUniGeneID() - lookup mid from UniGene ID Note this returns the first instance of the gene found if there are duplicates.
(package private) int[]	lookupMIDlistFrom_dbEST(java.lang.String name) lookupMIDlistFrom_dbEST() - lookup mid list from dbEST 3' or 5' ID.
(package private) int[]	lookupMIDListFromCloneID(java.lang.String name) lookupMIDlistFromCloneID() - lookup mid list from CloneID.
(package private) int[]	lookupMIDlistFromGenBankACC(java.lang.String name) lookupMIDlistFromGenBankACC() - lookup mid list from GenBank ID.
(package private) int[]	lookupMIDListFromGeneName(java.lang.String name) lookupMIDlistFromGeneName() - lookup mid list from Gene Name.
(package private) int[]	lookupMIDListFromLocusID(java.lang.String name) lookupMIDlistFromLocusID() - lookup mid list from Locus ID.
(package private) int[]	lookupMIDListFromRefSeqID(java.lang.String name) lookupMIDlistFromRefSeqID() - lookup mid list from RefSeq ID.
(package private) int[]	lookupMIDListFromSwissProtID(java.lang.String name) lookupMIDlistFromSwissProtID() - lookup mid list from SwissProt ID.
(package private) int[]	lookupMIDListFromUniGeneID(java.lang.String name) lookupMIDlistFromUniGeneID() - lookup mid list from UniGene ID.

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

cfg

private Config cfg

link to global Config instance

fName

static final java.lang.String[] fName

list of alphabetic names of Names of fields

gName

static final java.lang.String[] gName

list of alphabetic names of Names of grids

maxGeneHashTableSize

int maxGeneHashTableSize

size of gene hash table estimated as 1.5*maxGenes - only to 1st instance

maxMIDs

int maxMIDs

maximum # of Master Gene IDs = size of gene (i.e clone,oligo, etc) list

maxGenes

int maxGenes

maximum number of genes (estimated as maxGRIDS*maxGROWS*maxGCOLS)

maxSpots

int maxSpots

maximum # of spots estimated as maxFIELDS*maxGRIDS*maxGROWS*maxGCOL

maxSpotsFound

int maxSpotsFound

max # spots found. Set by GridCoords.createIndexToGridCoordMap

gid2fgrc

GridCoords[] gid2fgrc

map: gid (GridCoords index) to [f][g][r][c] values in GridCoords object. This is created by: GridCoords.createIndexToGridCoordMap() It is searched by: cfg.lookupHPoords()

fgrc2gid

int[][][][] fgrc2gid

map: [f][g][r][c] to gid (GridCoords index GID). estimate as [maxFIELDS+1][maxGRIDS+1][maxGROWS+1][maxGCOLS+1] This is created by: GridCoords.createIndexToGridCoordMap() It is NOT searched - just used as lookup.

gidToGangGid

int[] gidToGangGid

map: gid (GridCoords index) to the Gang gid. This is created by: GridCoords.createIndexToGridCoordMap() It is NOT searched - juse used as lookup.

gid2mid

int[] gid2mid

map: gid (gridCoords index) to mid (Master Gene index). NOTE mid is a small number < maxGenes - it is NOT the numeric equivalent of MasterID! This is created by: GeneTable.setupMIDlist(). It is searched by: ???? NOTYET!.

mid2gid

int[] mid2gid

map: mid (Master Gene index) to gid (gridCoords index) This is created by: GeneTable.setupMIDlist() It is used for lookup by: GeneTable.getGeneListOfGeneClass()

midStaticCL

GeneList midStaticCL

map: mid index to list of genes i.e. Maps.midStatCL.mList[mid] This STATIC map is created by: GeneTable.setupMIDlist()

gidStaticCL

GeneList gidStaticCL

map: GridCoords gid index to list of genes. i.e. Maps.gidStatCL.mList[gid] This STATIC map is created by: GeneTable.setupMIDlist()

mid2MasterIdHashtable

java.util.Hashtable mid2MasterIdHashtable

hash table of Master Gene IDs (MID) of size maxGeneHashTableSize. The value is an Integer value mid which is the index midStaticCL[]. This is created by: GeneTable.setupMIDlist(). It is searched by: GeneTable.getMIDfromMasterIDname(MasterID).

Constructor Detail

Maps

Maps(MAExplorer mae)

Maps() - constructor that allocates mapping tables calc size from F*G*R*C These is populated @GipoTable.setupMapLookupTables().

Parameters:

mae - is instance of MAExplorer

See Also:

allocateMapArrays()

Method Detail

allocateMapArrays

private void allocateMapArrays()

allocateMapArrays() - Allocate the map arrays and hash tables

See Also:

FileIO.logMsgln(java.lang.String), GeneList

lookupMIDfromGeneName

int lookupMIDfromGeneName(java.lang.String name)

lookupMIDfromGeneName() - lookup mid from Gene Name. Note this returns the first instance of the gene found if there are duplicates.

Parameters:

name - of gene to look up

Returns:

mid if found else -1

lookupMIDListFromGeneName

int[] lookupMIDListFromGeneName(java.lang.String name)

lookupMIDlistFromGeneName() - lookup mid list from Gene Name. Note this returns the first instance of the gene found if there are duplicates.

Parameters:

name - of gene to look up

Returns:

mid list if found, else null

lookupMIDfromCloneID

int lookupMIDfromCloneID(java.lang.String name)

lookupMIDfromCloneID() - lookup mid from CloneID Note this returns the first instance of the gene found if there are duplicates.

Parameters:

name - of gene to look up

Returns:

mid if found else -1

lookupMIDListFromCloneID

int[] lookupMIDListFromCloneID(java.lang.String name)

lookupMIDlistFromCloneID() - lookup mid list from CloneID. Note this returns the first instance of the gene found if there are duplicates.

Parameters:

name - of gene to look up

Returns:

mid list if found, else null

lookupMIDfromUniGeneID

int lookupMIDfromUniGeneID(java.lang.String name)

lookupMIDfromUniGeneID() - lookup mid from UniGene ID Note this returns the first instance of the gene found if there are duplicates.

Parameters:

name - of gene to look up

Returns:

mid if found else -1

lookupMIDListFromUniGeneID

int[] lookupMIDListFromUniGeneID(java.lang.String name)

lookupMIDlistFromUniGeneID() - lookup mid list from UniGene ID. Note this returns the first instance of the gene found if there are duplicates.

Parameters:

name - of gene to look up

Returns:

mid list if found, else null

lookupMIDfromRefSeqID

int lookupMIDfromRefSeqID(java.lang.String name)

lookupMIDfromRefSeqID() - lookup mid from RefSeq ID Note this returns the first instance of the gene found if there are duplicates.

Parameters:

name - of gene to look up

Returns:

mid if found else -1

lookupMIDListFromRefSeqID

int[] lookupMIDListFromRefSeqID(java.lang.String name)

lookupMIDlistFromRefSeqID() - lookup mid list from RefSeq ID. Note this returns the first instance of the gene found if there are duplicates.

Parameters:

name - of gene to look up

Returns:

mid list if found, else null

lookupMIDfromLocusID

int lookupMIDfromLocusID(java.lang.String name)

lookupMIDfromLocusID() - lookup mid from Locus ID Note this returns the first instance of the gene found if there are duplicates.

Parameters:

name - of gene to look up

Returns:

mid if found else -1

lookupMIDListFromLocusID

int[] lookupMIDListFromLocusID(java.lang.String name)

lookupMIDlistFromLocusID() - lookup mid list from Locus ID. Note this returns the first instance of the gene found if there are duplicates.

Parameters:

name - of gene to look up

Returns:

mid list if found, else null

lookupMIDfromSwissProtID

int lookupMIDfromSwissProtID(java.lang.String name)

lookupMIDfromSwissProtID() - lookup mid from SwissProt ID Note this returns the first instance of the gene found if there are duplicates.

Parameters:

name - of gene to look up

Returns:

mid if found else -1

lookupMIDListFromSwissProtID

int[] lookupMIDListFromSwissProtID(java.lang.String name)

lookupMIDlistFromSwissProtID() - lookup mid list from SwissProt ID. Note this returns the first instance of the gene found if there are duplicates.

Parameters:

name - of gene to look up

Returns:

mid list if found, else null

lookupMIDfromGenBankACC

int lookupMIDfromGenBankACC(java.lang.String name)

lookupMIDfromGenBankACC() - lookup mid from GenBank ACC ID. Note this returns the first instance of the gene found if there are duplicates.

Parameters:

name - of gene to look up

Returns:

mid if found else -1

lookupMIDlistFromGenBankACC

int[] lookupMIDlistFromGenBankACC(java.lang.String name)

lookupMIDlistFromGenBankACC() - lookup mid list from GenBank ID. Note this returns the first instance of the gene found if there are duplicates.

Parameters:

name - of gene to look up

Returns:

mid list if found, else null

lookupMIDfrom_dbEST

int lookupMIDfrom_dbEST(java.lang.String name)

lookupMIDfrom_dbEST() - lookup mid from dbEST 3' or 5' ID. Note this returns the first instance of the gene found if there are duplicates.

Parameters:

name - of gene to look up

Returns:

mid if found else -1

lookupMIDlistFrom_dbEST

int[] lookupMIDlistFrom_dbEST(java.lang.String name)

lookupMIDlistFrom_dbEST() - lookup mid list from dbEST 3' or 5' ID. Note this returns the first instance of the gene found if there are duplicates.

Parameters:

name - of gene to look up

Returns:

mid list if found, else null