Class GipoTable

java.lang.Object
  |
  +--SimpleTable
        |
        +--Table
              |
              +--GipoTable

class GipoTable

extends Table

The GipoTable class read sthe tab-delimited GipoTable file. GIPO is Gene In Plate Order file or the array Print file (sometimes called GAL or Gene Array List, etc). It then sets up the gene mappings in the Maps.midStaticCL.mList[0:maxGenes-1] gene list. The GipoTable maps FRGC coordinates and Plate data to Gene Id data, genomic ID and gene name data.

It reads the GeneInPlateOrder table includeing gene (clone, oligo) data from a FILE/URL. This table is obtained (possibly edited) derived from the array maker (vendor) for the corresponding micro array.

 This is a tab delimited file consisting of the following fields
 (which may not all be present or may have different names):
   (opt) "field", 
   "grid", "grid col", "grid row", "plate", "plate row",
   "plate col", "Clone ID", 

 NOTE: (J. Powell, mAdb/CIT), Clone_ID's may be "IMAGE:#", "ATCC:#", or
 an unknown # (eg. Pl#R#C#", etc).

 The (opt) "NAME_GCR" and (opt) "QualCheck" are used by NIA.

 Note either "grid", "grid col", "grid row" or "NAME_GCR" must
 be specified.
 

 The following fields extend the GIPO file 
 (Fields formerly in GeneNames class reading the GeneNames.txt file).
     "Unigene cluster ID", "Gene Class", "Unigene cluster name"

 The following fields extend the GIPO file:
    "GenBankAcc", "dbEst5", "GenBankAcc5'", "dbEst3'", "GeneBankAcc3'"

 Note: there may be additional fields that are included in thye GIPO file
 that could be used by Plugins, 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: 2003/07/07 21:40:41 $ $Revision: 1.11 $

Author:

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

See Also:

MAExplorer Home, Table

Field Summary

private Config	cfg link to global Config instance
(package private) int	cloneIdIdx index for "Clone ID"
(package private) int	dbESTid3Idx index for "dbEst3'"
(package private) int	dbESTid5Idx index for "dbEst5'"
(package private) int	fieldIdx index for "field"
(package private) int	GenBankAcc3Idx index for "GenBankAcc3'" or "GeneBankAcc3'"
(package private) int	GenBankAcc5Idx index for "GenBankAcc5'" or "GeneBankAcc5'"
(package private) int	GenBankAccIdx index for "GenBankAcc" or "GeneBankAcc"
(package private) int	Gene_ClassIdx index for "Gene Class"
(package private) int	GeneNameIdx index for "GeneName"
(package private) int[]	gid2GipoTableRow contains index of row in tData[], lookup by grid index (gid), of size maxGTmapSize
(package private) int	grid_colIdx index for "grid col"
(package private) int	grid_rowIdx index for "grid row"
(package private) int	gridIdx index for "grid"
(package private) static int	GT_BAD_MID analyzable bad clone id, good gene name
(package private) static int	GT_BAD_SPOT non-analyzable gene,, e.g.
(package private) static int	GT_DUP_SPOT analyzable genes, duplicated gene.
(package private) static int	GT_GOOD analyzable, good gene/clone id.
(package private) int	locationIdx index for "Location"
(package private) int	LocusLinkIdIdx index for "LocusID"
private MAExplorer	mae link to global MAExplorer instance
private java.lang.String	maeTbl name of remapped table name
private Maps	map link to global Maps instance
(package private) int	masterIdIdx generic Master_ID index
(package private) int	masterNameIdx generic Master_Gene_Name index
(package private) int	maxGTmapSize Sizeof gid2GipoTableRow[1:map.maxSpots]
(package private) int	nameGRCIdx index for "NAME_GRC" - NIA
private int	nGenesUpdated when copy data to static gene list
(package private) int	OmimIdIdx index for "OMIM" ID
(package private) int	plate_colIdx index for "plate col"
(package private) int	plate_rowIdx index for "plate row"
(package private) int	plateIdx index for "plate name"
(package private) int	qualCheckIdx index for "QualCheck" - NIA
(package private) int	RefSeqIdIdx index for "RefSeq" ID
(package private) int	SwissProtIdx index for "SwissProtID"
(package private) int	Unigene_cluster_IDidx index for "Unigene cluster ID"
(package private) int	Unigene_cluster_nameIdx index for "Unigene cluster name"

Fields inherited from class Table

bufSize, fileOKflag, fio

Fields inherited from class SimpleTable

fileName, msg, tCols, tData, tFields, title, tRows

Constructor Summary

(package private)

GipoTable(MAExplorer mae, java.lang.String fileName) GipoTable() - constructor to read the GIPO table.

Method Summary

(package private) boolean	copyGBCTdataToStaticGeneDB() copyGBCTdataToStaticGeneDB() - setupMaster_ID mid to GipoTable table row lookup table.
(package private) boolean	copyGeneNamesTableFile() copyGeneNamesTableFile() - copy gene names into static Gene database map.midStaticCL.mList
(package private) int[]	getAllMIDsForGene(java.lang.String name, int matchByIdx) getAllMIDsForGene() - get Gene midList[] for gene name.
(package private) int	getMIDfromMaster_IDhashTable(java.lang.String Master_ID) getMIDfromMaster_IDhashTable() - get Gene index (mid) given Master_ID.
private void	setupFieldIndexes() setupFieldIndexes() - lookup field name indexes for GIPO Table fields
private void	setupMapLookupTables() setupMapLookupTables() - reparse FGRC to GipoTable table row idx from tData[][].

Methods inherited from class Table

copyTable, createFileTable, getArrayOfTabDelimitedTokens, getData, getTableRowsSubset, getTableRowsSubset, insertTblInULHCtable, lookupFieldIdxAndRemapFieldName, makeTabDelimReport, readTable, storeDataBufParser

Methods inherited from class SimpleTable

freeTable, getTableRowFieldByRowIdx, getTableRowFieldIdxByRowIdx, lookupFieldIdx, setFieldData, setRowData, trimWhitespace

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

cfg

private Config cfg

link to global Config instance

maeTbl

private final java.lang.String maeTbl

name of remapped table name

locationIdx

int locationIdx

index for "Location"

plateIdx

int plateIdx

index for "plate name"

plate_rowIdx

int plate_rowIdx

index for "plate row"

plate_colIdx

int plate_colIdx

index for "plate col"

fieldIdx

int fieldIdx

index for "field"

gridIdx

int gridIdx

index for "grid"

grid_colIdx

int grid_colIdx

index for "grid col"

grid_rowIdx

int grid_rowIdx

index for "grid row"

LocusLinkIdIdx

int LocusLinkIdIdx

index for "LocusID"

cloneIdIdx

int cloneIdIdx

index for "Clone ID"

OmimIdIdx

int OmimIdIdx

index for "OMIM" ID

RefSeqIdIdx

int RefSeqIdIdx

index for "RefSeq" ID

nameGRCIdx

int nameGRCIdx

index for "NAME_GRC" - NIA

qualCheckIdx

int qualCheckIdx

index for "QualCheck" - NIA

GeneNameIdx

int GeneNameIdx

index for "GeneName"

Unigene_cluster_IDidx

int Unigene_cluster_IDidx

index for "Unigene cluster ID"

Unigene_cluster_nameIdx

int Unigene_cluster_nameIdx

index for "Unigene cluster name"

Gene_ClassIdx

int Gene_ClassIdx

index for "Gene Class"

dbESTid3Idx

int dbESTid3Idx

index for "dbEst3'"

dbESTid5Idx

int dbESTid5Idx

index for "dbEst5'"

GenBankAccIdx

int GenBankAccIdx

index for "GenBankAcc" or "GeneBankAcc"

GenBankAcc3Idx

int GenBankAcc3Idx

index for "GenBankAcc3'" or "GeneBankAcc3'"

GenBankAcc5Idx

int GenBankAcc5Idx

index for "GenBankAcc5'" or "GeneBankAcc5'"

SwissProtIdx

int SwissProtIdx

index for "SwissProtID"

masterIdIdx

int masterIdIdx

generic Master_ID index

masterNameIdx

int masterNameIdx

generic Master_Gene_Name index

nGenesUpdated

private int nGenesUpdated

when copy data to static gene list

maxGTmapSize

int maxGTmapSize

Sizeof gid2GipoTableRow[1:map.maxSpots]

gid2GipoTableRow

int[] gid2GipoTableRow

contains index of row in tData[], lookup by grid index (gid), of size maxGTmapSize

GT_GOOD

static final int GT_GOOD

analyzable, good gene/clone id.

GT_BAD_MID

static final int GT_BAD_MID

analyzable bad clone id, good gene name

GT_BAD_SPOT

static final int GT_BAD_SPOT

non-analyzable gene,, e.g. empty spots, or filled with internal testing material

GT_DUP_SPOT

static final int GT_DUP_SPOT

analyzable genes, duplicated gene. Only one of duplicates is flagged with this

Constructor Detail

GipoTable

GipoTable(MAExplorer mae,
          java.lang.String fileName)

GipoTable() - constructor to read the GIPO table.

Parameters:

mae - is instance of MAExplorer

fileName - is the full path name of the GIPO file

See Also:

MAExplorer.logDRYROTerr(java.lang.String), Util.popupDryrotMsgsAndQuit(), setupFieldIndexes(), setupMapLookupTables()

Method Detail

setupFieldIndexes

private void setupFieldIndexes()

setupFieldIndexes() - lookup field name indexes for GIPO Table fields

See Also:

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

setupMapLookupTables

private void setupMapLookupTables()

setupMapLookupTables() - reparse FGRC to GipoTable table row idx from tData[][]. Create FGRC to GT table row lookup table gid2GipoTableRow[gid] map. Also create hash table list of Master_ID names indexed by GridCoords index (gid) by inserting (gid,masterIDname) into the

    mae.mp.gid2CloneIdHashtable.

This will only point to the first gene. If there are additional copies of that gene, then put them in a replicate gene list.

This also sets up the primary GeneList maps which are used by all other gene lists when saving gene index (mid):

    map.midStaticCL[0:maxGenes-1],
    map.gidStaticCL[0:maxSpots-1].

Update the map.gid2mid[] which maps either F1 or F2 gid to mid.

See Also:

Gene, Gene.assignMasterID(int), Gene.assignMasterGeneName(int), Gene.setplateData(java.lang.String, java.lang.String, java.lang.String), GeneList.clearNull(), GeneList.setGene(Gene, int), GridCoords.cvtNAME_GCR2FGRC(int, java.lang.String), MAExplorer.logDRYROTerr(java.lang.String), Util.popupDryrotMsgsAndQuit(), getMIDfromMaster_IDhashTable(java.lang.String)

getMIDfromMaster_IDhashTable

int getMIDfromMaster_IDhashTable(java.lang.String Master_ID)

getMIDfromMaster_IDhashTable() - get Gene index (mid) given Master_ID. NOTE: this may NOT be unique if there genes are multiple spotted and are not part of the (F1,F2) duplicates. Return MID if found, else -1 if not found.

getAllMIDsForGene

int[] getAllMIDsForGene(java.lang.String name,
                        int matchByIdx)

getAllMIDsForGene() - get Gene midList[] for gene name. NOTE: genes may not be unique if they are multiply spotted (not counting the (F1,F2) duplicates if they exist).String

Parameters:

name - - gene name

matchByIdx - - gipo.XXXXIdx value for the different fields.

Returns:

list of indices else null if not found.

copyGeneNamesTableFile

boolean copyGeneNamesTableFile()

copyGeneNamesTableFile() - copy gene names into static Gene database map.midStaticCL.mList

Returns:

true if succeed.

See Also:

GeneList.addGene(Gene), GeneClass.lookupGeneClassIdx(java.lang.String), getMIDfromMaster_IDhashTable(java.lang.String)

copyGBCTdataToStaticGeneDB

boolean copyGBCTdataToStaticGeneDB()

copyGBCTdataToStaticGeneDB() - setupMaster_ID mid to GipoTable table row lookup table. This sets up the mid2GenBankGeneDataRow[gid] map.

Returns:

true if succeed

See Also:

getMIDfromMaster_IDhashTable(java.lang.String)