Class SpotFeatures

java.lang.Object
  |
  +--SpotFeatures

class SpotFeatures

extends java.lang.Object

The SpotFeatures class and methods to get spot feature String information. This includes gene clone ID, gene name, genomic id info, GIPO address, plate address, normalized intensity data, ratios, 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 21:40:40 $ $Revision: 1.8 $

Author:

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

See Also:

MAExplorer Home

Field Summary

private static CompositeDatabase	cdb link to global instance
private static Config	cfg link to global instance of Config
(package private) java.lang.String	cloneID lookup I.M.A.G.E.
(package private) java.lang.String	dbESTid3 lookup dbEST id 3'
(package private) java.lang.String	dbESTid5 lookup dbEST id 5'
(package private) static java.lang.String	featuresStr Strings generated by getSpotFeatures()
(package private) java.lang.String	GenBankAcc lookup GenBank Acc
(package private) java.lang.String	GenBankAcc3 lookup GenBank Acc 3'
(package private) java.lang.String	GenBankAcc5 lookup GenBank Acc 5'
(package private) java.lang.String	geneClass lookup "Gene_Class"
(package private) java.lang.String	geneName lookup "Gene_Name"
(package private) static java.lang.String	genomicDataStr Strings generated by getSpotFeatures()
(package private) java.lang.String	LocusID lookup LocusLink LocusID
private static MAExplorer	mae link to global MAExplorer instance
private static Maps	map link to global Maps instance
(package private) java.lang.String	masterID lookup master Gene identifier
(package private) java.lang.String	plate lookup corresponding plate
(package private) java.lang.String	plate_col lookup corresponding plate_col
(package private) java.lang.String	plate_row lookup corresponding plate_row
(package private) java.lang.String	SwissProt lookup SwissProtID
(package private) java.lang.String	UGclusterName lookup "UGclusterName" name
(package private) java.lang.String	Unigene_ID lookup "Unigene_ID" name
(package private) static java.lang.String	xygStr Strings generated by getSpotFeatures()

Constructor Summary

(package private)

SpotFeatures(MAExplorer mae) SpotFeatures() - constructor

Method Summary

(package private) static java.lang.String	getCurGeneFeaturedata() getCurGeneFeaturedata() - get spot feature summary of current gene.
(package private) static java.lang.String	getCurGeneGenomicdata() getCurGeneGenomicdata() - get spot feature summary of current gene.
(package private) static java.lang.String	getCurGeneXYGdata() getCurGeneXYGdata() - get spot quantitation summary of current gene.
(package private) java.lang.String	getPlate(int gid) getPlate(gid) - return the Plate coords Grid[r,c] as B3,4 etc.
(package private) java.lang.String	getSpotFeatures(java.awt.Point xy, MaHybridSample ms) getSpotFeatures() - get spot coords and features associated with spot at (x,y)
(package private) java.lang.String	getSpotFeaturesLine(int gid) getSpotFeaturesLine() - get spot coords and features associated with spot gid.
(package private) java.lang.String	getSpotGenomicData(java.awt.Point xy, MaHybridSample ms) getSpotGenomicData() - get additional genomic name features by (x,y) coordindate of current spot for sample if the features exist.
(package private) java.lang.String	getSpotGenomicLine(int gid) getSpotGenomicLine() - get additional Genomic name features by GID if they exist.
(package private) java.lang.String	getSpotMeasurementStr(int gid, MaHybridSample ms) getSpotMeasurementStr() - return pretty-print spot measurement string.
(package private) java.lang.String	getXYG(java.awt.Point xy, MaHybridSample ms) getXYG() - return pretty-print string for status of x,y,grayvalue string.
(package private) boolean	setGenomicData(int gid) setGenomicData() - get genomic data from GID gene into local variables of spotFeatures.
(package private) void	showValidSpotInfo(java.awt.Point xyObj, MaHybridSample ms) showValidSpotInfo() - show spot gene info if valid obj else no-op

Methods inherited from class java.lang.Object

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

Field Detail

mae

private static MAExplorer mae

link to global MAExplorer instance

map

private static Maps map

link to global Maps instance

cdb

private static CompositeDatabase cdb

link to global instance

cfg

private static Config cfg

link to global instance of Config

plate

java.lang.String plate

lookup corresponding plate

plate_row

java.lang.String plate_row

lookup corresponding plate_row

plate_col

java.lang.String plate_col

lookup corresponding plate_col

masterID

java.lang.String masterID

lookup master Gene identifier

LocusID

java.lang.String LocusID

lookup LocusLink LocusID

Unigene_ID

java.lang.String Unigene_ID

lookup "Unigene_ID" name

cloneID

java.lang.String cloneID

lookup I.M.A.G.E. Clone Id

dbESTid3

java.lang.String dbESTid3

lookup dbEST id 3'

dbESTid5

java.lang.String dbESTid5

lookup dbEST id 5'

GenBankAcc

java.lang.String GenBankAcc

lookup GenBank Acc

GenBankAcc3

java.lang.String GenBankAcc3

lookup GenBank Acc 3'

GenBankAcc5

java.lang.String GenBankAcc5

lookup GenBank Acc 5'

SwissProt

java.lang.String SwissProt

lookup SwissProtID

geneName

java.lang.String geneName

lookup "Gene_Name"

UGclusterName

java.lang.String UGclusterName

lookup "UGclusterName" name

geneClass

java.lang.String geneClass

lookup "Gene_Class"

xygStr

static java.lang.String xygStr

Strings generated by getSpotFeatures()

featuresStr

static java.lang.String featuresStr

Strings generated by getSpotFeatures()

genomicDataStr

static java.lang.String genomicDataStr

Strings generated by getSpotFeatures()

Constructor Detail

SpotFeatures

SpotFeatures(MAExplorer mae)

SpotFeatures() - constructor

Parameters:

mae - is instance of MAExplorer

Method Detail

getSpotMeasurementStr

java.lang.String getSpotMeasurementStr(int gid,
                                       MaHybridSample ms)

getSpotMeasurementStr() - return pretty-print spot measurement string. This includes state dependent reporting of x,y,grayvalue. This method will generate different strings depending on various state settings including normalization, single or sets of HP data, Intensity or ratio data, etc.

Parameters:

gid - is the Grid Index (GID) of spot to report

ms - sample being tested to which the xy spot applies

Returns:

pretty-print string for data for the point xy in sample ms

See Also:

GridCoords.cvtGID2str(int, boolean), HPxyData.updateDataAndStat(int), MaHybridSample.getDataByGID(int, boolean, int), Util.cvf2s(float, int)

getXYG

java.lang.String getXYG(java.awt.Point xy,
                        MaHybridSample ms)

getXYG() - return pretty-print string for status of x,y,grayvalue string. This method will generate different strings depending on various state settings including normalization, single or sets of HP data, Intensity or ratio data, etc.

Parameters:

xy - is the coordinates close to spot being requested

ms - sample being tested to which the xy spot applies

Returns:

pretty-print string for data for the point xy in sample ms

See Also:

CompositeDatabase.lookupHPcoords(int, int, int, boolean, MaHybridSample), ScrollableImageCanvas.setObjState(MaHybridSample, int, int), getSpotMeasurementStr(int, MaHybridSample)

getSpotFeaturesLine

java.lang.String getSpotFeaturesLine(int gid)

getSpotFeaturesLine() - get spot coords and features associated with spot gid.

Parameters:

gid - is the Grid Index (GID) of spot to report

ms - sample being tested to which the xy spot applies

Returns:

spot features string otherwise "" if no spot specified.

See Also:

Gene.lookupIDbyName(java.lang.String), getPlate(int), setGenomicData(int)

getSpotFeatures

java.lang.String getSpotFeatures(java.awt.Point xy,
                                 MaHybridSample ms)

getSpotFeatures() - get spot coords and features associated with spot at (x,y)

Parameters:

xy - is the pseudoarray image coordinates close to spot being requested

ms - sample being tested to which the xy spot applies

Returns:

spot features string otherwise "" if no actual spot was specified.

See Also:

CompositeDatabase.lookupHPcoords(int, int, int, boolean, MaHybridSample), getSpotFeaturesLine(int)

getSpotGenomicLine

java.lang.String getSpotGenomicLine(int gid)

getSpotGenomicLine() - get additional Genomic name features by GID if they exist. These include GeneName, UniGeneName, GeneClass, ...

Parameters:

gid - is the Grid Index (GID) of spot to report

Returns:

spot genomic data otherwise "" if no actual spot was specified.

See Also:

setGenomicData(int)

getSpotGenomicData

java.lang.String getSpotGenomicData(java.awt.Point xy,
                                    MaHybridSample ms)

getSpotGenomicData() - get additional genomic name features by (x,y) coordindate of current spot for sample if the features exist. These include: GeneName, UGclusterName, GeneClass, ...

Parameters:

xy - is the pseudoarray image coordinates close to spot being requested

ms - sample being tested to which the xy spot applies

Returns:

spot genomic data otherwise "" if no actual spot was specified.

See Also:

CompositeDatabase.lookupHPcoords(int, int, int, boolean, MaHybridSample), getSpotGenomicLine(int)

getPlate

java.lang.String getPlate(int gid)

getPlate(gid) - return the Plate coords Grid[r,c] as B3,4 etc.

Parameters:

gid - is the grid index

Returns:

plate name otherwise "" if no actual spot was specified.

setGenomicData

boolean setGenomicData(int gid)

setGenomicData() - get genomic data from GID gene into local variables of spotFeatures.

Parameters:

gid - is the Grid Index (GID) of spot to report

Returns:

true if were able to get data

showValidSpotInfo

void showValidSpotInfo(java.awt.Point xyObj,
                       MaHybridSample ms)

showValidSpotInfo() - show spot gene info if valid obj else no-op

Parameters:

xyObj - is the pseudoarray image coordinates close to spot being requested

ms - sample being tested to which the xyObj spot applies

See Also:

Util.showFeatures(java.lang.String, java.lang.String), Util.showMsg(java.lang.String), getXYG(java.awt.Point, MaHybridSample), getSpotFeatures(java.awt.Point, MaHybridSample), getSpotGenomicData(java.awt.Point, MaHybridSample)

getCurGeneXYGdata

static java.lang.String getCurGeneXYGdata()

getCurGeneXYGdata() - get spot quantitation summary of current gene. The format depends on the normalization, single or multiple X, Y sets pseudoarray image mode, etc. See the Reference manual.

Returns:

string report if current gene (spot) defined else ""

See Also:

getXYG(java.awt.Point, MaHybridSample)

getCurGeneFeaturedata

static java.lang.String getCurGeneFeaturedata()

getCurGeneFeaturedata() - get spot feature summary of current gene. The format depends on GIPO and other data available for the gene. See the Reference Manual for examples.

Returns:

string report if valid spot else ""

See Also:

getSpotFeatures(java.awt.Point, MaHybridSample)

getCurGeneGenomicdata

static java.lang.String getCurGeneGenomicdata()

getCurGeneGenomicdata() - get spot feature summary of current gene. The format depends on GIPO and other data available for the gene. See the Reference Manual for examples.

Returns:

string report if valid spot else ""

See Also:

getSpotGenomicData(java.awt.Point, MaHybridSample)