Class Config

java.lang.Object
  |
  +--Config

class Config

extends java.lang.Object

The class holds MAExplorer configuration variables that constitute par of the global state. Data is read from the MaConfiguration.txt (or whatever it is called) input file when MAExplorer is first started. Then (navem,value) data read from the .mae startup file (in the case of the stand-alone system) or from s (in the case of APPLETS) may overide this.

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: 2003/06/27 17:59:46 $ $Revision: 1.25 $

Author:

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

See Also:

MAExplorer Home, ConfigTable, GetParams

Field Summary

(package private) java.lang.String	baseCgiURLgeneClassNames PARAM "baseCgiURLgeneClassNames"
(package private) java.lang.String	baseCgiURLgeneIdNameClass PARAM "baseCgiURLgeneIdNameClass"
(package private) java.lang.String	baseCgiURLgipo PARAM "baseCgiURLgipo"
(package private) java.lang.String	baseCgiURLquant PARAM "baseCgiURLquant"
(package private) java.lang.String	baseCgiURLsamples PARAM "baseCgiURLsamples"
(package private) java.lang.String	calDNAname PARAM "calDNAname" (opt) calibration DNA name
(package private) float	clusterDistThr Threshold PARAM: cluster distance Filter threshold
(package private) java.lang.String	configFile Configuration file where we got the config data ...
(package private) java.lang.String	database PARAM "databaseName"
(package private) java.lang.String	dbEstURL base addr PARAM "dbEstURL"
(package private) java.lang.String	dbSubset PARAM "dbSubset" database subset
(package private) static int	DEF_CANVAS_HSIZE default uArray canvas horizontal size
(package private) static int	DEF_CANVAS_VSIZE default uArray canvas vertical size
(package private) static float	DEF_CLUSTER_DIST Default cluster distance
(package private) static float	DEF_DIFF_THR DEFAULT Diff(HP-X,HP-Y) in [minNorm:maxNorm] as fct.
(package private) static int	DEF_MAX_INTENSITY default maximum intensity.
(package private) static int	DEF_NBR_CLUSTERS Default # of clusters
(package private) static float	DEF_P_VALUE_THR DEFAULT: t-test threshold
(package private) static int	DEF_RADIUS Default spot radius (-1)
(package private) static float	DEF_SPOT_CV_THR DEFAULT: SPOT CV threshold
(package private) float	detValueSpotThr Threshold PARAM: "detValueSpotThr" continuous spot Detection Value threshold
private boolean	didGetParms Flag: once only code for single call to getStateParamValues()
(package private) float	diffThr Threshold PARAM: diff (HP-X,HP-Y) Filter threshold
(package private) java.lang.String	Elist HP-E list
(package private) java.lang.String	emptyWellName PARAM "emptyWellName" (opt) what you call "EmptyWell"
(package private) java.lang.String	fluoresLbl1 PARAM "fluorescentLbl1" (Cy3) or F1
(package private) java.lang.String	fluoresLbl2 PARAM "fluorescentLbl2" (Cy5) or F2
(package private) java.lang.String	fontFamily PARAM "fontFamily" 'SansSerif'
(package private) java.lang.String	gbid2LocusLinkURL base addr PARAM "gbid2LocusLinkURL"
(package private) java.lang.String	genBankAccURL base addr PARAM "genBankAccURL"
(package private) java.lang.String	genBankCloneURL base addr PARAM "genBankCloneURL"
(package private) java.lang.String	genBankCloneURLepilogue base addr PARAM "genBankCloneURLepilogue"
(package private) java.lang.String	geneCardURL base addr PARAM "geneCardURL"
(package private) static boolean	genGridsFromNbrGenes Flag: generate grid coords from nbrGENES
(package private) java.lang.String	geoFullDataTableURL Get full HTML list of a specific GEO microarray platform.
(package private) java.lang.String	geoListOfPlatformsURL Get HTML list of www.ncbi.nlm.nih.gov/geo Gene Express Omnibus GEO microarray platforms numbered GPL4, GPL5, ..."
(package private) java.lang.String	geoPlatformID GEO platform Identifier of the form "GPL"+.
(package private) java.lang.String	gipoFile PARAM "gipoFile" or URL
private GetParams	gp link to global instance of GetParams
(package private) java.lang.String	histologyURL base addr PARAM "histologyURL"
(package private) static boolean	ignoreExtraFIELDS Flag: ignore extra fields > maxFIELDS.
(package private) java.lang.String	IMAGE2GenBankURL base addr PARAM "IMAGE2GenBankURL"
(package private) java.lang.String	IMAGE2unigeneURL base addr PARAM "IMAGE2unigeneURL"
(package private) java.lang.String	jaxURL base addr PARAM "jaxURL"
(package private) java.lang.String	locusLinkURL base addr PARAM "locusLinkURL"
(package private) float	lowRangeScaleFactor Scale factor for pseudoarray image.
(package private) java.lang.String	maAnalysisProg PARAM default M.A.
(package private) java.lang.String	mAdbURL base addr PARAM "mAdbURL"
private MAExplorer	mae link to global instance of MAExplorer
(package private) java.lang.String	maInfoFile PARAM "maInfoFile" or URL (opt)
(package private) static float	MAX_CLUSTER_DIST Maximum cluster distance
(package private) static int	MAX_NBR_CLUSTERS Maximum # of clusters
(package private) static int	MAX_RADIUS MAximum spot radius allowed
(package private) java.awt.Dimension	maxCalcPseudoArraySize Computed maximum pseudoarray canvas size, null if not using pseudoarrays as (width,height) required given the array geometry.
(package private) int	maxFIELDS PARAM fields left and right
(package private) int	maxGCOLS PARAM grid rows
(package private) int	maxGenesToRpt PARAM Max # of genes to report in highest or lowest # genes
(package private) int	maxGRIDS PARAM grids labeled A, B, ..., H
(package private) int	maxGROWS PARAM grid cols
(package private) float	maxQualCheck Set from .quant file data: Maximum QualCheck Value
(package private) java.lang.String	medMinerURL base addr PARAM "medMinerURL"
(package private) java.lang.String	medMinerURLepilogue base addr PARAM "medMinerURLepilogue"
(package private) static float	MIN_CLUSTER_DIST Minimum cluster distance
(package private) static int	MIN_NBR_CLUSTERS Minimum # of clusters
(package private) static int	MIN_RADIUS Minimum spot radius allowed
(package private) float	minQualCheck Set from .quant file data: Minimum QualCheck Value
(package private) java.lang.String	modelsURL base addr PARAM "modelsURL"
(package private) int	nbrGENES PARAM specified # of genes
(package private) int	nbrOfClustersThr Threshold PARAM: # of clusters threshold
(package private) int	nbrSPOTS PARAM specified # of spots
(package private) int	nGenomicMenus size of sGenomicMenu[]
(package private) int	nHelpMenus size of sHelpMenu[]
(package private) int	nPluginMenus size of sPluginMenus[]
(package private) java.lang.String	omimURL base addr PARAM "omimURL"
(package private) float	pctOKthr Threshold PARAM: "pctOKthr" % spot intensity OK threshold
(package private) java.lang.String	pirURL base addr PARAM "pirURL"
(package private) float	pValueThr Threshold PARAM: p-value threshold for t-test Filter
(package private) float	qualThr Threshold PARAM: "qualThr" continuous QualCheck threshold
(package private) java.lang.String	quantFileExt PARAM "quantFileExt" i.e.
(package private) java.lang.String	RatioHP HP to use for normalization
(package private) java.lang.String	sampDBfile PARAM "samplesDBfile"
(package private) java.lang.String[]	sGenomicIDreq PARAM ID required entries ("GenomicIDreq"+i).
(package private) java.lang.String[]	sGenomicMenu PARAM menu entries "GenomicMenu"+i.
(package private) java.lang.String[]	sGenomicURL PARAM URL entries "GenomicURL"+i
(package private) java.lang.String[]	sGenomicURLepilogue PARAM: URL entries "GenomicURLepilogue"+i
(package private) java.lang.String[]	sHelpMenu PARAM menu entries "HelpMenu"+i
(package private) java.lang.String[]	sHelpURL PARAM URL entries "HelpURL"+i
(package private) java.lang.String[]	sPluginCallAtStartup PARAM menu entries "PluginCallAtStartup"+i.
(package private) java.lang.String[]	sPluginClassFile PARAM menu entries "PluginClassFile"+i.
(package private) java.lang.String[]	sPluginMenuName PARAM menu entries "PluginMenuName"+i.
(package private) java.lang.String[]	sPluginMenuStubName PARAM menu entries "PluginMenuStubName"+i.
(package private) float	spotCVthr Threshold PARAM: Spot CV threshold 2*|f1-f2|/(f1+f2) for Filter
(package private) java.lang.String	swissProtURL base addr PARAM "swissProtURL"
(package private) java.lang.String	uniGeneClusterIdURL base addr PARAM "uniGeneClusterIdURL"
(package private) java.lang.String	unigeneSpecies PARAM "species" UniGene Species code
(package private) java.lang.String	uniGeneURL base addr PARAM "uniGeneURL"
(package private) java.lang.String	writeFileCGIurl base addr PARAM "writeFileCGIurl"
(package private) java.lang.String	Xlist HP-X set
(package private) java.lang.String	Ylist HP-Y set
(package private) java.lang.String	yourPlateName PARAM "yourPlateName" (opt) your plate name

Constructor Summary

(package private)

Config(MAExplorer mae, java.lang.String configFile) Config() - constructor to make it accessible.

Method Summary

(package private) java.awt.Dimension	computeMaxCanvasSize() computeMaxCanvasSize() - compute the maximum pseudoArray Canvas size
(package private) void	getAdditionalParams() getAdditionalParams() - get additional params from .mae file or Applet etc.
(package private) void	getStateParamValues() getStateParamValues() - get non-file state PARAMs
(package private) void	readPARAMvalues(java.lang.String path) readPARAMvalues() - read applet PARAM values overiding configuration file.
(package private) boolean	setDefaultURLs(java.lang.String species) setDefaultURLs() - set default URLs based on species
(package private) void	setupFullpathFilenames() setupFullpathFilenames() - add the full path to the file names
(package private) static void	setupPathBase(MAExplorer mae) setupPathBase() - set mae.(fileBasePath, isWorkingMAE) from codeBase.

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 of MAExplorer

gp

private GetParams gp

link to global instance of GetParams

didGetParms

private boolean didGetParms

Flag: once only code for single call to getStateParamValues()

DEF_CANVAS_HSIZE

static final int DEF_CANVAS_HSIZE

default uArray canvas horizontal size

DEF_CANVAS_VSIZE

static final int DEF_CANVAS_VSIZE

default uArray canvas vertical size

DEF_MAX_INTENSITY

static final int DEF_MAX_INTENSITY

default maximum intensity. This is replaced by actual maximum...

DEF_RADIUS

static final int DEF_RADIUS

Default spot radius (-1)

MIN_RADIUS

static final int MIN_RADIUS

Minimum spot radius allowed

MAX_RADIUS

static final int MAX_RADIUS

MAximum spot radius allowed

DEF_CLUSTER_DIST

static final float DEF_CLUSTER_DIST

Default cluster distance

MIN_CLUSTER_DIST

static final float MIN_CLUSTER_DIST

Minimum cluster distance

MAX_CLUSTER_DIST

static final float MAX_CLUSTER_DIST

Maximum cluster distance

DEF_NBR_CLUSTERS

static final int DEF_NBR_CLUSTERS

Default # of clusters

MIN_NBR_CLUSTERS

static final int MIN_NBR_CLUSTERS

Minimum # of clusters

MAX_NBR_CLUSTERS

static final int MAX_NBR_CLUSTERS

Maximum # of clusters

DEF_P_VALUE_THR

static final float DEF_P_VALUE_THR

DEFAULT: t-test threshold

DEF_SPOT_CV_THR

static final float DEF_SPOT_CV_THR

DEFAULT: SPOT CV threshold

DEF_DIFF_THR

static final float DEF_DIFF_THR

DEFAULT Diff(HP-X,HP-Y) in [minNorm:maxNorm] as fct. Norm method

database

java.lang.String database

PARAM "databaseName"

dbSubset

java.lang.String dbSubset

PARAM "dbSubset" database subset

maAnalysisProg

java.lang.String maAnalysisProg

PARAM default M.A. analysis pgm

unigeneSpecies

java.lang.String unigeneSpecies

PARAM "species" UniGene Species code

writeFileCGIurl

java.lang.String writeFileCGIurl

base addr PARAM "writeFileCGIurl"

genBankCloneURL

java.lang.String genBankCloneURL

base addr PARAM "genBankCloneURL"

genBankCloneURLepilogue

java.lang.String genBankCloneURLepilogue

base addr PARAM "genBankCloneURLepilogue"

uniGeneURL

java.lang.String uniGeneURL

base addr PARAM "uniGeneURL"

uniGeneClusterIdURL

java.lang.String uniGeneClusterIdURL

base addr PARAM "uniGeneClusterIdURL"

omimURL

java.lang.String omimURL

base addr PARAM "omimURL"

dbEstURL

java.lang.String dbEstURL

base addr PARAM "dbEstURL"

mAdbURL

java.lang.String mAdbURL

base addr PARAM "mAdbURL"

gbid2LocusLinkURL

java.lang.String gbid2LocusLinkURL

base addr PARAM "gbid2LocusLinkURL"

locusLinkURL

java.lang.String locusLinkURL

base addr PARAM "locusLinkURL"

jaxURL

java.lang.String jaxURL

base addr PARAM "jaxURL"

genBankAccURL

java.lang.String genBankAccURL

base addr PARAM "genBankAccURL"

medMinerURL

java.lang.String medMinerURL

base addr PARAM "medMinerURL"

medMinerURLepilogue

java.lang.String medMinerURLepilogue

base addr PARAM "medMinerURLepilogue"

swissProtURL

java.lang.String swissProtURL

base addr PARAM "swissProtURL"

pirURL

java.lang.String pirURL

base addr PARAM "pirURL"

IMAGE2unigeneURL

java.lang.String IMAGE2unigeneURL

base addr PARAM "IMAGE2unigeneURL"

IMAGE2GenBankURL

java.lang.String IMAGE2GenBankURL

base addr PARAM "IMAGE2GenBankURL"

geoListOfPlatformsURL

java.lang.String geoListOfPlatformsURL

Get HTML list of www.ncbi.nlm.nih.gov/geo Gene Express Omnibus GEO microarray platforms numbered GPL4, GPL5, ..."

geoFullDataTableURL

java.lang.String geoFullDataTableURL

Get full HTML list of a specific GEO microarray platform. Append the platoform. e.g. "GPL80"

geoPlatformID

java.lang.String geoPlatformID

GEO platform Identifier of the form "GPL"+. E.g. GPL80

geneCardURL

java.lang.String geneCardURL

base addr PARAM "geneCardURL"

histologyURL

java.lang.String histologyURL

base addr PARAM "histologyURL"

modelsURL

java.lang.String modelsURL

base addr PARAM "modelsURL"

nHelpMenus

int nHelpMenus

size of sHelpMenu[]

sHelpMenu

java.lang.String[] sHelpMenu

PARAM menu entries "HelpMenu"+i

sHelpURL

java.lang.String[] sHelpURL

PARAM URL entries "HelpURL"+i

nGenomicMenus

int nGenomicMenus

size of sGenomicMenu[]

sGenomicMenu

java.lang.String[] sGenomicMenu

PARAM menu entries "GenomicMenu"+i. An example might be "FlyBase"

sGenomicURL

java.lang.String[] sGenomicURL

PARAM URL entries "GenomicURL"+i

sGenomicURLepilogue

java.lang.String[] sGenomicURLepilogue

PARAM: URL entries "GenomicURLepilogue"+i

sGenomicIDreq

java.lang.String[] sGenomicIDreq

PARAM ID required entries ("GenomicIDreq"+i). These should be within the legal list of identifiers. Eg Clone_ID, GenBankAcc, etc. An example of a new GIPO id might be "FlyBaseID".

nPluginMenus

int nPluginMenus

size of sPluginMenus[]

sPluginMenuName

java.lang.String[] sPluginMenuName

PARAM menu entries "PluginMenuName"+i. E.g. "New sample report"

sPluginMenuStubName

java.lang.String[] sPluginMenuStubName

PARAM menu entries "PluginMenuStubName"+i. E.g. "ReportMenu:sample"

sPluginClassFile

java.lang.String[] sPluginClassFile

PARAM menu entries "PluginClassFile"+i. E.g. "NewReport.class"

sPluginCallAtStartup

java.lang.String[] sPluginCallAtStartup

PARAM menu entries "PluginCallAtStartup"+i. E.g. "TRUE", "FALSE" or "BOTH" of "InstallInMenu", "RunOnStartup", "NoInstall"

configFile

java.lang.String configFile

Configuration file where we got the config data ...

quantFileExt

java.lang.String quantFileExt

PARAM "quantFileExt" i.e. ".quant" file extension default

sampDBfile

java.lang.String sampDBfile

PARAM "samplesDBfile"

maInfoFile

java.lang.String maInfoFile

PARAM "maInfoFile" or URL (opt)

gipoFile

java.lang.String gipoFile

PARAM "gipoFile" or URL

baseCgiURLquant

java.lang.String baseCgiURLquant

PARAM "baseCgiURLquant"

baseCgiURLsamples

java.lang.String baseCgiURLsamples

PARAM "baseCgiURLsamples"

baseCgiURLgipo

java.lang.String baseCgiURLgipo

PARAM "baseCgiURLgipo"

baseCgiURLgeneClassNames

java.lang.String baseCgiURLgeneClassNames

PARAM "baseCgiURLgeneClassNames"

baseCgiURLgeneIdNameClass

java.lang.String baseCgiURLgeneIdNameClass

PARAM "baseCgiURLgeneIdNameClass"

calDNAname

java.lang.String calDNAname

PARAM "calDNAname" (opt) calibration DNA name

yourPlateName

java.lang.String yourPlateName

PARAM "yourPlateName" (opt) your plate name

emptyWellName

java.lang.String emptyWellName

PARAM "emptyWellName" (opt) what you call "EmptyWell"

Xlist

java.lang.String Xlist

HP-X set

Ylist

java.lang.String Ylist

HP-Y set

Elist

java.lang.String Elist

HP-E list

RatioHP

java.lang.String RatioHP

HP to use for normalization

fontFamily

java.lang.String fontFamily

PARAM "fontFamily" 'SansSerif'

fluoresLbl1

java.lang.String fluoresLbl1

PARAM "fluorescentLbl1" (Cy3) or F1

fluoresLbl2

java.lang.String fluoresLbl2

PARAM "fluorescentLbl2" (Cy5) or F2

maxGenesToRpt

int maxGenesToRpt

PARAM Max # of genes to report in highest or lowest # genes

nbrGENES

int nbrGENES

PARAM specified # of genes

nbrSPOTS

int nbrSPOTS

PARAM specified # of spots

maxFIELDS

int maxFIELDS

PARAM fields left and right

maxGRIDS

int maxGRIDS

PARAM grids labeled A, B, ..., H

maxGCOLS

int maxGCOLS

PARAM grid rows

maxGROWS

int maxGROWS

PARAM grid cols

nbrOfClustersThr

int nbrOfClustersThr

Threshold PARAM: # of clusters threshold

minQualCheck

float minQualCheck

Set from .quant file data: Minimum QualCheck Value

maxQualCheck

float maxQualCheck

Set from .quant file data: Maximum QualCheck Value

qualThr

float qualThr

Threshold PARAM: "qualThr" continuous QualCheck threshold

detValueSpotThr

float detValueSpotThr

Threshold PARAM: "detValueSpotThr" continuous spot Detection Value threshold

pctOKthr

float pctOKthr

Threshold PARAM: "pctOKthr" % spot intensity OK threshold

diffThr

float diffThr

Threshold PARAM: diff (HP-X,HP-Y) Filter threshold

clusterDistThr

float clusterDistThr

Threshold PARAM: cluster distance Filter threshold

pValueThr

float pValueThr

Threshold PARAM: p-value threshold for t-test Filter

spotCVthr

float spotCVthr

Threshold PARAM: Spot CV threshold 2*|f1-f2|/(f1+f2) for Filter

lowRangeScaleFactor

float lowRangeScaleFactor

Scale factor for pseudoarray image. The low-range scale factor for scaling the low portion of the dynmaic range.

genGridsFromNbrGenes

static boolean genGridsFromNbrGenes

Flag: generate grid coords from nbrGENES

ignoreExtraFIELDS

static boolean ignoreExtraFIELDS

Flag: ignore extra fields > maxFIELDS. This means that you can treat multi-field data as if it only had one field.

maxCalcPseudoArraySize

java.awt.Dimension maxCalcPseudoArraySize

Computed maximum pseudoarray canvas size, null if not using pseudoarrays as (width,height) required given the array geometry.

Constructor Detail

Config

Config(MAExplorer mae,
       java.lang.String configFile)

Config() - constructor to make it accessible.

Parameters:

mae - is the MAExplorer instance

configFile - is the full path filename for configuation file

Method Detail

setDefaultURLs

boolean setDefaultURLs(java.lang.String species)

setDefaultURLs() - set default URLs based on species

Parameters:

species - name (UniGene 2 letter codes)

Returns:

true if succeed

getStateParamValues

void getStateParamValues()

getStateParamValues() - get non-file state PARAMs

See Also:

GetParams.getNumberedParamList(java.lang.String), GetParams.getParamVal(java.lang.String), GetParams.setDefParam(java.lang.String, boolean), MAExplorer.logDRYROTerr(java.lang.String), Util.cvs2f(java.lang.String), Util.cvs2i(java.lang.String), Util.popupDryrotMsgsAndQuit(), getAdditionalParams(), setDefaultURLs(java.lang.String)

getAdditionalParams

void getAdditionalParams()

getAdditionalParams() - get additional params from .mae file or Applet etc. put there by (File | SaveAsDB).

See Also:

GetParams.setDefParam(java.lang.String, boolean)

readPARAMvalues

void readPARAMvalues(java.lang.String path)

readPARAMvalues() - read applet PARAM values overiding configuration file.

Parameters:

path - of configuration file

See Also:

GetParams.getParamVal(java.lang.String), MAExplorer.logDRYROTerr(java.lang.String), getStateParamValues()

setupPathBase

static void setupPathBase(MAExplorer mae)

setupPathBase() - set mae.(fileBasePath, isWorkingMAE) from codeBase.

Parameters:

mae - is the MAExplorer instance

setupFullpathFilenames

void setupFullpathFilenames()

setupFullpathFilenames() - add the full path to the file names

See Also:

readPARAMvalues(java.lang.String)

computeMaxCanvasSize

java.awt.Dimension computeMaxCanvasSize()

computeMaxCanvasSize() - compute the maximum pseudoArray Canvas size

Returns:

maximum pseudoarray canvas size, null if not using pseudoarrays as (width,height) required given the array geometry.