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Class ProtPlot

java.lang.Object
  |
  +--ProtPlot

public class ProtPlot
extends java.lang.Object

Class ProtPlot.java is the main class. ProtPlot generates an interactive virtual protein 2D Map plot in a 2D-gel format. The data is based on a database of derived Max EST expression over a variety of tissue types from data obtained from the CGAP, UniGene and SWISS-PROT data. ProtPlot data is contained in a set of tissue-specific (PRotPlot) .prp files described in the documentation.

NOTE: see http://TMAP.sourceforge.net/index.html for documentation.

This work was produced by Peter Lemkin of the National Cancer Institute, an agency of the United States Government and Djamel Medjahed (SAIC-Frederick). 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.

Version:: $Date: 2002/10/14 20:17:17 $ $Revision: $
Author:: P. Lemkin (NCI), Djamel Medjahed (SAIC), NCI-Frederick, Frederick, MD
See Also:: ProtPlot Home
This work was derived from MAExplorer under the Mozilla 1.1 Open Source Public License by Peter Lemkin of the National Cancer Institute, an agency of the United States Government subject to the limitations noted in the accompanying LEGAL file. See licence info on http://maexplorer.sourceforge.org/

Field Summary

boolean autoUpdateFlag
          if we are to auto update reports, else use Update button if available

java.lang.String browserTitle
          browser title

java.lang.String buttonFontFamily
          default button font family name

Cluster clust
          Instance of Cluster

java.lang.String clusterNameSetFile
          File name of Cluster Named Protein set file if it exists

(package private) static java.lang.String COG_URL


static boolean CONSOLE_FLAG
          Always TRUE

int curMPID
          Current mPid for current sample proteins index.

Protein curMProt
          current Master Protein object if any

int curPID
          current pid protein id if any.

int curSample
          current index of the ReadPRP PRP database

java.lang.String curSampleNameFile
          Name of the current sample Name File

static boolean DBUG_6_SAMPLES
          DBUG max # of 6 samples to test multiple samples

static boolean DBUG_LOCALHOST_HOMEPAGE
          Debug Update commands using LOCALHOST_HOMEPAGE_URL

static boolean DEBUG
          general purpose debugging

static int DEBUG_MENU_CMDS
          DEBUG_MENU_CMDS value set to enable new commands being debugged 0 to enable command, -1 to disable it, -2 to not show them in the menu.

(package private) static java.lang.String DEF_CUR_SAMPLE_PRP_FILE
          Default .prp startup file if none specified

(package private) static java.lang.String DEF_SAMPLEX_PRP_FILE
          Default sample X .prp file if none specified

(package private) static java.lang.String DEF_SAMPLEY_PRP_FILE
          Default sample Y .prp file if none specified

boolean displayXYscatterplotFlag
          "Display (X vs Y) else (Mw vs pI) scatterplot [CB]"

int distMode
          distance computation method using the DIST_xxxx values

float distThreshold
          Distance threshold for similarity clustering

int distThrValUB
          (Distance Threshold) Vertical slider initial value Upper Bound

java.lang.String docCodeBase
          Where the Reference Manual is kept

static int DRAW_BOX
          Plotting type: box

static int DRAW_CIRCLE
          Plotting type: circle

static int DRAW_PLUS
          Plotting type: plus

boolean dupsInXYsetsFlag
          flag set if there are samples that are in both the X and Y sample sets when call recalcSampleIdxLists().

EventHandlerPRP eh
          instance of EventHandlerPRP

(package private) ExprProfilePopup epp
          popup expression profile window if enabled

long exprProfileBits
          selected current expression list bits of selected samples

int expValLB
          (Expression-ratio) Vertical slider Expression initial value Lower Bound

int expValUB
          (Expression-ratio) Vertical slider Expression initial value Lower Bound

(package private) static java.lang.String FAMILY_NAMES_FILE
          Name of file with tab-delim list of protein families (name, bits)

java.lang.String familyNamesFile
          protein family name file

Filter fil
          Instance of Data Filter.

static java.lang.String fileSeparator
          paths, "/" or "|", or ":", depends on OS.

java.lang.String filterNameSetFile
          File name of Filter Named Protein set file if it exists

FileIOPRP fio
          Instance of major classes for global data access.

static int FRAME_HEIGHT
          Frame height

static int FRAME_WIDTH
          Frame width

(package private) static java.lang.String GENBANK_BASEURL


java.lang.String genBankServerBase
          GenBank server

GetListOfPRPs glp
          Get a list of .prp file names

java.util.Hashtable hashMPIDs
          Hash table of Master Proteins for proteins from all PRP databases

(package private) static java.lang.String HOMEPAGE_URL
          Home page for ProtPlot

int hsValLB
          (MW) Horizontal slider initial value Lower Bound

int hsValUB
          (MW) Horizontal slider initial value Upper Bound

int[] idxSampleEPlist
          list of indices of samples used in the sampleEPlist[0:nSampleEPlist-1]

int[] idxSampleXlist
          list of indices of samples used in the X set [0:nSampleXlist-1]

int[] idxSampleYlist
          list of indices of samples used in the Y set [0:nSampleYlist-1]

boolean isWinPCflag
          set to TRUE if any Windows PC

(package private) static java.lang.String LOCALHOST_HOMEPAGE_URL
          local site Home page for ProtPlot

boolean logMWscalingFlag
          scale MW by log

MathPRP math
          math package

static int MAX_FAMILIES
          max # protein class names

static int MAX_NEAREST_PROTEINS
          Max # proteins to cluster in similarity cluster plot

static int MAX_PROTEINS
          maximum # of protein spots ever seen in the union of all .prp DBs

static int MAX_PRP_FILES
          Max # of PRP databases that may be read at one time

static int MAX_SAPARAMS
          max # of stand-alone parameters

static int MAX_TISSUES
          max # tissue names

float maxExprVal
          Expression range scroller - Expression upper bound [0.0:1.0]

int maxProteinsFound
          maximum # of proteins found in any one sample

float maxRatioSample
          Expression-ratio (X/Y) range of actual samples- upper bound

float maxRatioVal
          Expression-ratio (X/Y) range scroller - Ratio upper bound

java.lang.String menuFontFamily
          default menu item font family name

float[][] mExprVector
          Master Protein List [0:nMasterPids-1][0:nSamples-1] of protein expression values from all PRP DBs

float minExprVal
          Expression range scroller - Expression lower bound [0.0:1.0]

float minRatioSample
          Expression-ratio (X/Y) range of actual samples - lower bound

float minRatioVal
          Expression-ratio (X/Y) range scroller - Ratio lower bound

int[][] mPid2PidMap
          Map of mPids to pids for specific samples [0:nMasterPids-1][0:nSamples-1].

int[] mPidFiltered
          Is list [0:nMpidFiltered] of all mPids that passed the data filter and are used by the current sample (for a single sample) or by a set of samples (e.g.

int[] mPidSamples
          Is list [0:nMpidSamples] of all mPids used by the current sample (for a single sample) or by a set of samples (e.g.

int[] mPidSimilarCluster
          List [0:nMpidSimilarCluster-1] of mPids similar to the current protein curMPID

Protein[] mProtList
          Master Protein List [0:nMasterPids-1] of proteins from all PRP databases indexed by mPid value.

java.lang.String[] mProtSwissProtAcc
          Master Protein List [0:nMasterPids-1] of protein SWISS-PROT Acc #s from all PRP DBs is indexed by mPid value.

java.lang.String[] mProtSwissProtId
          Master Protein List [0:nMasterPids-1] of protein IDs from all PRP DBs is indexed by mPid value.

boolean mReady
          ready to analyze

int[] nbrProteins
          List of # proteins/sample [0:nPRPs-1]

static boolean NEVER
          Always FALSE

int nMasterPids
          Number of proteins in the Master Protein List mPid[]

int nMpidFiltered
          size of mPidSamples[] list.

int nMpidSamples
          size of mPidSamples[] list.

int nMpidSimilarCluster
          # of clustered proteins

boolean noArgsFlag
          set if there are no args specified

int nOverDaltonLimit
          Number of proteins found that are > 200K daltons

int nPRPs
          # of PRP file names

int nSampleEPlist
          # of samples used in the expression vector sampleEPlist[0:nPRPs-1]

int nSamples
          Number of ReadPRP instances of PRP databases

int nSampleXlist
          # of samples used in the X set sampleXlist[0:nPRPs-1]

int nSampleYlist
          # of samples used in the Y set sampleYlist[0:nPRPs-1]

private static int nSAparam
          # of stand-alone params

int nSavedClusterMPIDs
          # of saved clustered proteins

int nSavedFilterMPIDs
          # of saved Filtered proteins

static java.lang.String osName
          operating system Windows, SUNOS, etc

boolean outsideRatioRangeFlag
          Filter by (X/Y) of samples X & samples Y outside of [minRation:maxRatio] sliders

static java.lang.String prjPRPdir
          standalone startup PRP/ Directory

(package private) static java.lang.String PRO_CLASS_BASE_URL


java.lang.String proClassServerBase
          PIR lookup on our server

Protein prot
          Clone instances

(package private) static java.lang.String PROTPLOT_STATE_FILE
          name of the ProtPlot state file

java.util.Hashtable protPlotStateHT
          Hash table of the ProtPlot state read from stateFile ".prpstate" if not null

java.lang.String protServerBase
          top level codebase for ProtPlot server

java.lang.String[] prpFileNames
          List of PRP file names [0:nPRPs-1]

java.lang.String prpListNamesFile
          File containing the list of .prp files to use

java.lang.String[] prpNames
          List of PRP names [0:nPRPs-1]

float pValueThr
          The p-Value threshold slider value in the range of 0.0 to 1.0

int pValueThrUB
          (pValue Threshold) Vertical slider initial value Upper Bound

int ratioValLB
          (Expression-ratio) Vertical slider (sX/xY ratio) initial value Lower Bound

int ratioValUB
          (Expression-ratio) Vertical slider (sX/xY ratio) initial value Upper Bound

ReadPRP[] rdList
          List [0:nSamples-1] of ReadPRP instances of PRP databases

boolean requireAtLeastNsamplesFlag
          "Filter by requiring at least N samples [RB]" checkbox for thresholdNsamples

boolean requireAtMostNsamplesFlag
          "Filter by requiring at most N samples [RB]" checkbox for thresholdNsamples

ReadFamilies rf
          ReadFamilies

ReportPRP rpt
          instance of ReportPRP

static ShowStringPopup rptPopup
          Current report string popup instance.

ReadTissues rt
          ReadTissues

boolean[] sampleEPlist
          list of samples used in the expression vector [0:nPRPs-1]

java.lang.String sampleNameFileX
          Name of the current sample Name File X

java.lang.String sampleNameFileY
          Name of the current sample Name File Y

int sampleX
          current index of the ReadPRP PRP database (X/Y) ratio sample X

boolean[] sampleXlist
          boolean list of samples used in the X set [0:nPRPs-1]

int sampleY
          current index of the ReadPRP PRP database (X/Y) ratio sample Y

boolean[] sampleYlist
          list of samples used in the Y set [0:nPRPs-1]

private static java.lang.String[] saName
          [0:nSAparam-1] name

private static java.lang.String[] saValue
          [0:nSAparam-1] value

int[] savedClusterMPIDs
          List [0:nSavedClusterMPIDs-1] of mPids of saved clustered proteins

boolean[] savedClusterMPIDsMap
          boolean map of saved clustered MPIDs

int[] savedClusterNbrMPIDs
          List [0:nSavedClusterMPIDs-1] of cluster numberssy of saved clustered proteins

java.lang.String savedClusterSeedSP_ACC
          saved cluster SP-ACC

int[] savedFilterMPIDs
          List [0:nSavedFilterMPIDs-1] of mPids of saved Filtered proteins

boolean[] savedFilterMPIDsMap
          boolean map of saved clustered MPIDs

int scrHeight
          screen size height

int scrWidth
          screen size width

boolean showAllXYproteinsIfNullSamplesFlag
          "Show all X and Y samples if doing X/Y filtering [CB]" checkbox

boolean showClusteredProteinsFlag
          "Show clustered proteins by black boxes [CB] flag

boolean showWebPageFlag
          Allow access to Web if click on spot

boolean sortAssendingFlag
          "Sort report assending order[CB]"

ShowScatterPlotPopup spp
          main window containing the 2D plot and menu bar

StatisticsPRP stat
          statistics package

static java.lang.String stateFile
          Current state file.

static java.lang.String stateName
          Current state name is the stateFile without the ".prpstate"

boolean statusAreaIsVisibleFlag
          The 3 Status lines area visibility flag.

PopupStatusWindow statusPopup
          Holds the popup window status lines

(package private) static java.lang.String SWISS2D_BASEURL
          Hardwired URLs and file names

java.lang.String swissProtServerBase
          swiss prot server

java.lang.String textFontFamily
          default text font family name

int thresholdNsamples
          Number of samples threshold slider

int thresholdSproteins
          Number of proteins/sample (S) threshold slider

(package private) static java.lang.String TISSUE_NAMES_FILE
          Name of file with tab-delim list of tissues (name, bits)

java.lang.String tissueNamesFile
          tissue name file

(package private) static java.lang.String TMAP_JAR_VERSION_FILE
          name of file containing the latest ProtPlot.jar version #

static java.lang.String TOTAL_PRP_EXTENSION
          Only read PRP files with this file extension.

static float UNDER_DALTON_LIMIT
          default bound for toggling data base between xxx_tot.prp and the subset <= this limit.

static boolean USE_FAMILIES_FILE_FLAG
          Set if read protein Family data from FAMILY_NAMES_FILE

static boolean USE_LINEAR_SCROLLING
          use linear else non-linear scroller scaling

boolean useCmapRatioModeFlag
          plot samplesX/sampleY ratio range color map in the scatterplot

boolean useDichromasyFlag
          color blind filter

boolean useEPsetExprModeFlag
          Show mean EP set sample expression

boolean useExponentialMapFlag
          If enabled, it generates a non-linear colormap using the eMap[gray] function to generate a 10 color eColor[0:9] set of colors stored in cMap[0:155].

boolean useExprFlag
          "Expression/Location" checkbox

boolean useExprModeFlag
          plot the current sample expression data in the scatterplot

boolean useExprProfilePlotModeFlag
          if true, then popup expression profile in epp

boolean useFamilyANDflag
          use AND else OR of Family filters

long useFamilyBits
          selected current protein family bits

boolean useFamilyFilterFlag
          enable gene Family name filtering

boolean useFilterByXY_KStestFlag
          "Filter by X & Y sets Kolmogorov-Smirnov test results [RB]"

boolean useFilterByXYsetMissingProteinsFlag
          "Filter by X & Y sets missing proteins [CB]"

boolean useFilterByXYtTestFlag
          "Filter by X & Y sets t-test results [RB]"

boolean useFilterExprRangeFlag
          "Filter by Expression range" checkbox filters

boolean useFiltersFlag
          "Filter/NoFilter" checkbox for ANY active filters

boolean useGenBankFlag
          GenBank Web access

static java.lang.String useHomeServer
          ProtPlot home server to use

static boolean useInitialStateFileFlag
          Only read initial state file if this is set

boolean useLocalDocFlag
          Flag to use local Doc/ directory for help else to use ProtPlot server

boolean useMouseOverFlag
          "useMouseOver" for popup tracking balloons

boolean useProClassFlag
          access ProClass if click on spot

boolean usePRPlistFilterFlag
          enable gene PRP list name filtering

boolean usePseudocolorFlag
          "Use pseudocolor else grayscale for expression, checkbox

boolean useRatioModeFlag
          Show ratio X/Y or X-set/Y-set, else single sample expression or mean EP set expression

static java.lang.String userDir
          user directory where project was started.

boolean useRGratioModeFlag
          plot samplesX/sampleY ratio (Red=X + Green=Y) data in the scatterplot

boolean useSavedClusterFlag
          Use saved clustered set of proteins in data filter

boolean useSavedFilterFlag
          Use saved filtered set of proteins in data filter

boolean useSingleExprModeFlag
          Show single sample expression

boolean useSwissProtFlag
          access SwissProt if click on spot

boolean useTissueANDflag
          use AND else OR of tissue filters

long useTissueBits
          selected current tissues bits

boolean useTissueFilterFlag
          enable Tissue name filtering

boolean useTotPRPflag
          if true, access all proteins, otherwise filter out all proteins > UNDER_DALTON_LIMIT Daltons.

boolean useVariableRadiusFlag
          use variable radius for drawing spots proportional to the expression else all the same size

boolean useXYsetCmapRatioModeFlag
          plot X-Set-samples /X-Set-samples ratio range color map scatterplot

boolean useXYsetDataFlag
          use X / Y sets of samples else use single X / Y samples

UtilPRP util
          Utility instance

static java.lang.String VERSION


java.lang.String versionStateFile
          Version of the read from stateFile ".prpstate" if not null

static java.lang.String verStr


int vsValLB
          (pI) Vertical slider initial value Lower Bound

int vsValUB
          (pI) Vertical slider initial value Upper Bound

java.lang.String xCondLabel
          plot label: (className,mnData,sdData,cvData) X (set) for current protein if previously called the t-test

java.lang.String xCondName
          condition name for all X set members

java.lang.String yCondLabel
          plot label: (className,mnData,stdData,cvData) Y (set) for current protein if previously called the t-test

java.lang.String yCondName
          condition name for all Y set members

Constructor Summary

ProtPlot()


Method Summary

(package private) void ()


void calcMPID2PIDmap()
          calcMPID2PIDmap() - generate the mPid to pid map for all samples.

private void clearDynamicState()
          clearDynamicState() - reset dynamic state variables in prp instance

int getPRPindexByFileName(java.lang.String fileName)
          getPRPindexByFileName() - lookup the PRP index by file name

int getPRPindexByName(java.lang.String name)
          getPRPindexByName() - lookup the PRP index by file name

boolean getStateValue(java.lang.String key, boolean def)
          getStateValue() - get boolean PARAM and use default if not found.

private float getStateValue(java.lang.String key, float def)
          getStateValue() - get float PARAM and use default if not found.

int getStateValue(java.lang.String key, int def)
          getStateValue() - get int PARAM and use default if not found.

private long getStateValue(java.lang.String key, long def)
          getStateValue() - get float PARAM and use default if not found.

java.lang.String getStateValue(java.lang.String key, java.lang.String def)
          getStateValue() - get PARAM and use default if not found.

void init()
          init() - allocate,clear state, read PARAMs, build GUI and start things off.

static void main(java.lang.String[] args)
          main() - for ProtPlot started by standalone application.

void quit()
          quit() - kill this application

boolean readEntirePRPdatabase()
          readEntirePRPdatabase() - read the entire database.

boolean recalcEPsampleIdxLists()
          recalcEPsampleIdxLists() - recompute the idxSampleEPlist[] NOTE: this does NOT use the #proteins/sample sizing.

boolean recalcXYsampleIdxLists()
          recalcXYsampleIdxLists() - recompute idxSampleXlist[] & idxSampleYlist[] NOTE: this does NOT use the #proteins/sample sizing.

void resetDefaultstate(boolean resetFlag)
          resetDefaultstate() - Reinitialize global user state Anything in this method should be able to be set during runtime from the "Reset" menu.

void setAllParamDefaults()
          setAllParamDefaults() - reset all parameter defaults using the built in values if can not find the parameter in the prp.stateFile file

void setDefaultXYEPsets(java.lang.String xKeyword, java.lang.String yKeyword, java.lang.String epKeyword)
          setDefaultXYEPsets() - set the default X, Y, EP sample sets by keywords If the keyword is null, then do not set the set.

(package private) void setSamplesListsFromState()
          setSamplesListsFromState() - read the sample lists from the state data has already been read int hash table

boolean setStatusAreaVisible(boolean flag)
          setStatusAreaVisible() - show or hide three status lines in status popup

Methods inherited from class java.lang.Object

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

Field Detail

VERSION

public static final java.lang.String VERSION

verStr

public static final java.lang.String verStr

DBUG_6_SAMPLES

public static boolean DBUG_6_SAMPLES

DBUG max # of 6 samples to test multiple samples

CONSOLE_FLAG

public static boolean CONSOLE_FLAG

Always TRUE

NEVER

public static boolean NEVER

Always FALSE

DEBUG

public static boolean DEBUG

general purpose debugging

DEBUG_MENU_CMDS

public static int DEBUG_MENU_CMDS

DEBUG_MENU_CMDS value set to enable new commands being debugged 0 to enable command, -1 to disable it, -2 to not show them in the menu.

USE_FAMILIES_FILE_FLAG

public static boolean USE_FAMILIES_FILE_FLAG

Set if read protein Family data from FAMILY_NAMES_FILE

USE_LINEAR_SCROLLING

public static boolean USE_LINEAR_SCROLLING

use linear else non-linear scroller scaling

DBUG_LOCALHOST_HOMEPAGE

public static boolean DBUG_LOCALHOST_HOMEPAGE

Debug Update commands using LOCALHOST_HOMEPAGE_URL

SWISS2D_BASEURL

static final java.lang.String SWISS2D_BASEURL

Hardwired URLs and file names

PRO_CLASS_BASE_URL

static final java.lang.String PRO_CLASS_BASE_URL

GENBANK_BASEURL

static final java.lang.String GENBANK_BASEURL

COG_URL

static final java.lang.String COG_URL

DEF_CUR_SAMPLE_PRP_FILE

static final java.lang.String DEF_CUR_SAMPLE_PRP_FILE

Default .prp startup file if none specified

DEF_SAMPLEX_PRP_FILE

static final java.lang.String DEF_SAMPLEX_PRP_FILE

Default sample X .prp file if none specified

DEF_SAMPLEY_PRP_FILE

static final java.lang.String DEF_SAMPLEY_PRP_FILE

Default sample Y .prp file if none specified

HOMEPAGE_URL

static final java.lang.String HOMEPAGE_URL

Home page for ProtPlot

LOCALHOST_HOMEPAGE_URL

static final java.lang.String LOCALHOST_HOMEPAGE_URL

local site Home page for ProtPlot

PROTPLOT_STATE_FILE

static final java.lang.String PROTPLOT_STATE_FILE

name of the ProtPlot state file

FAMILY_NAMES_FILE

static final java.lang.String FAMILY_NAMES_FILE

Name of file with tab-delim list of protein families (name, bits)

TISSUE_NAMES_FILE

static final java.lang.String TISSUE_NAMES_FILE

Name of file with tab-delim list of tissues (name, bits)

TMAP_JAR_VERSION_FILE

static final java.lang.String TMAP_JAR_VERSION_FILE

name of file containing the latest ProtPlot.jar version #

UNDER_DALTON_LIMIT

public static final float UNDER_DALTON_LIMIT

default bound for toggling data base between xxx_tot.prp and the subset <= this limit.

TOTAL_PRP_EXTENSION

public static java.lang.String TOTAL_PRP_EXTENSION

Only read PRP files with this file extension. Set it to null to read ALL ".prp" files in the PRP/ directory.

MAX_SAPARAMS

public static final int MAX_SAPARAMS

max # of stand-alone parameters

MAX_FAMILIES

public static final int MAX_FAMILIES

max # protein class names

MAX_TISSUES

public static final int MAX_TISSUES

max # tissue names

MAX_PROTEINS

public static final int MAX_PROTEINS

maximum # of protein spots ever seen in the union of all .prp DBs

MAX_PRP_FILES

public static final int MAX_PRP_FILES

Max # of PRP databases that may be read at one time

MAX_NEAREST_PROTEINS

public static final int MAX_NEAREST_PROTEINS

Max # proteins to cluster in similarity cluster plot

clust

public Cluster clust

Instance of Cluster

eh

public EventHandlerPRP eh

instance of EventHandlerPRP

fil

public Filter fil

Instance of Data Filter.

fio

public FileIOPRP fio

Instance of major classes for global data access.

glp

public GetListOfPRPs glp

Get a list of .prp file names

statusPopup

public PopupStatusWindow statusPopup

Holds the popup window status lines

prot

public Protein prot

Clone instances

rpt

public ReportPRP rpt

instance of ReportPRP

rf

public ReadFamilies rf

ReadFamilies

rt

public ReadTissues rt

ReadTissues

spp

public ShowScatterPlotPopup spp

main window containing the 2D plot and menu bar

epp

ExprProfilePopup epp

popup expression profile window if enabled

util

public UtilPRP util

Utility instance

math

public MathPRP math

math package

stat

public StatisticsPRP stat

statistics package

rptPopup

public static ShowStringPopup rptPopup

Current report string popup instance. Needed to replace existing report

useHomeServer

public static java.lang.String useHomeServer

ProtPlot home server to use

useInitialStateFileFlag

public static boolean useInitialStateFileFlag

Only read initial state file if this is set

protPlotStateHT

public java.util.Hashtable protPlotStateHT

Hash table of the ProtPlot state read from stateFile ".prpstate" if not null

versionStateFile

public java.lang.String versionStateFile

Version of the read from stateFile ".prpstate" if not null

textFontFamily

public java.lang.String textFontFamily

default text font family name

menuFontFamily

public java.lang.String menuFontFamily

default menu item font family name

buttonFontFamily

public java.lang.String buttonFontFamily

default button font family name

nPRPs

public int nPRPs

# of PRP file names

prpFileNames

public java.lang.String[] prpFileNames

List of PRP file names [0:nPRPs-1]

prpNames

public java.lang.String[] prpNames

List of PRP names [0:nPRPs-1]

nbrProteins

public int[] nbrProteins

List of # proteins/sample [0:nPRPs-1]

rdList

public ReadPRP[] rdList

List [0:nSamples-1] of ReadPRP instances of PRP databases

nSamples

public int nSamples

Number of ReadPRP instances of PRP databases

curSample

public int curSample

current index of the ReadPRP PRP database

sampleX

public int sampleX

current index of the ReadPRP PRP database (X/Y) ratio sample X

sampleY

public int sampleY

current index of the ReadPRP PRP database (X/Y) ratio sample Y

curSampleNameFile

public java.lang.String curSampleNameFile

Name of the current sample Name File

sampleNameFileX

public java.lang.String sampleNameFileX

Name of the current sample Name File X

sampleNameFileY

public java.lang.String sampleNameFileY

Name of the current sample Name File Y

useSavedClusterFlag

public boolean useSavedClusterFlag

Use saved clustered set of proteins in data filter

useSavedFilterFlag

public boolean useSavedFilterFlag

Use saved filtered set of proteins in data filter

useTotPRPflag

public boolean useTotPRPflag

if true, access all proteins, otherwise filter out all proteins > UNDER_DALTON_LIMIT Daltons.

useXYsetDataFlag

public boolean useXYsetDataFlag

use X / Y sets of samples else use single X / Y samples

useRatioModeFlag

public boolean useRatioModeFlag

Show ratio X/Y or X-set/Y-set, else single sample expression or mean EP set expression

useSingleExprModeFlag

public boolean useSingleExprModeFlag

Show single sample expression

useEPsetExprModeFlag

public boolean useEPsetExprModeFlag

Show mean EP set sample expression

useRGratioModeFlag

public boolean useRGratioModeFlag

plot samplesX/sampleY ratio (Red=X + Green=Y) data in the scatterplot

useCmapRatioModeFlag

public boolean useCmapRatioModeFlag

plot samplesX/sampleY ratio range color map in the scatterplot

useXYsetCmapRatioModeFlag

public boolean useXYsetCmapRatioModeFlag

plot X-Set-samples /X-Set-samples ratio range color map scatterplot

displayXYscatterplotFlag

public boolean displayXYscatterplotFlag

"Display (X vs Y) else (Mw vs pI) scatterplot [CB]"

useExprModeFlag

public boolean useExprModeFlag

plot the current sample expression data in the scatterplot

outsideRatioRangeFlag

public boolean outsideRatioRangeFlag

Filter by (X/Y) of samples X & samples Y outside of [minRation:maxRatio] sliders

useExponentialMapFlag

public boolean useExponentialMapFlag

If enabled, it generates a non-linear colormap using the eMap[gray] function to generate a 10 color eColor[0:9] set of colors stored in cMap[0:155].

useExprProfilePlotModeFlag

public boolean useExprProfilePlotModeFlag

if true, then popup expression profile in epp

mProtList

public Protein[] mProtList

Master Protein List [0:nMasterPids-1] of proteins from all PRP databases indexed by mPid value.

mProtSwissProtId

public java.lang.String[] mProtSwissProtId

Master Protein List [0:nMasterPids-1] of protein IDs from all PRP DBs is indexed by mPid value.

mProtSwissProtAcc

public java.lang.String[] mProtSwissProtAcc

Master Protein List [0:nMasterPids-1] of protein SWISS-PROT Acc #s from all PRP DBs is indexed by mPid value.

nMasterPids

public int nMasterPids

Number of proteins in the Master Protein List mPid[]

maxProteinsFound

public int maxProteinsFound

maximum # of proteins found in any one sample

nOverDaltonLimit

public int nOverDaltonLimit

Number of proteins found that are > 200K daltons

mExprVector

public float[][] mExprVector

Master Protein List [0:nMasterPids-1][0:nSamples-1] of protein expression values from all PRP DBs

mPid2PidMap

public int[][] mPid2PidMap

Map of mPids to pids for specific samples [0:nMasterPids-1][0:nSamples-1]. This is created AFTER all data has been read in.

mPidSamples

public int[] mPidSamples

Is list [0:nMpidSamples] of all mPids used by the current sample (for a single sample) or by a set of samples (e.g. SampleX and SampleY). It could be extended to any arbitrary subset of samples.

nMpidSamples

public int nMpidSamples

size of mPidSamples[] list.

mPidFiltered

public int[] mPidFiltered

Is list [0:nMpidFiltered] of all mPids that passed the data filter and are used by the current sample (for a single sample) or by a set of samples (e.g. SampleX and SampleY). It could be extended to any arbitrary subset of samples.

nMpidFiltered

public int nMpidFiltered

size of mPidSamples[] list.

hashMPIDs

public java.util.Hashtable hashMPIDs

Hash table of Master Proteins for proteins from all PRP databases

xCondLabel

public java.lang.String xCondLabel

plot label: (className,mnData,sdData,cvData) X (set) for current protein if previously called the t-test

yCondLabel

public java.lang.String yCondLabel

plot label: (className,mnData,stdData,cvData) Y (set) for current protein if previously called the t-test

xCondName

public java.lang.String xCondName

condition name for all X set members

yCondName

public java.lang.String yCondName

condition name for all Y set members

sampleEPlist

public boolean[] sampleEPlist

list of samples used in the expression vector [0:nPRPs-1]

idxSampleEPlist

public int[] idxSampleEPlist

list of indices of samples used in the sampleEPlist[0:nSampleEPlist-1]

nSampleEPlist

public int nSampleEPlist

# of samples used in the expression vector sampleEPlist[0:nPRPs-1]

dupsInXYsetsFlag

public boolean dupsInXYsetsFlag

flag set if there are samples that are in both the X and Y sample sets when call recalcSampleIdxLists().

sampleXlist

public boolean[] sampleXlist

boolean list of samples used in the X set [0:nPRPs-1]

idxSampleXlist

public int[] idxSampleXlist

list of indices of samples used in the X set [0:nSampleXlist-1]

nSampleXlist

public int nSampleXlist

# of samples used in the X set sampleXlist[0:nPRPs-1]

sampleYlist

public boolean[] sampleYlist

list of samples used in the Y set [0:nPRPs-1]

idxSampleYlist

public int[] idxSampleYlist

list of indices of samples used in the Y set [0:nSampleYlist-1]

nSampleYlist

public int nSampleYlist

# of samples used in the Y set sampleYlist[0:nPRPs-1]

saName

private static java.lang.String[] saName

[0:nSAparam-1] name

saValue

private static java.lang.String[] saValue

[0:nSAparam-1] value

nSAparam

private static int nSAparam

# of stand-alone params

scrWidth

public int scrWidth

screen size width

scrHeight

public int scrHeight

screen size height

osName

public static java.lang.String osName

operating system Windows, SUNOS, etc

protServerBase

public java.lang.String protServerBase

top level codebase for ProtPlot server

proClassServerBase

public java.lang.String proClassServerBase

PIR lookup on our server

swissProtServerBase

public java.lang.String swissProtServerBase

swiss prot server

genBankServerBase

public java.lang.String genBankServerBase

GenBank server

useLocalDocFlag

public boolean useLocalDocFlag

Flag to use local Doc/ directory for help else to use ProtPlot server

familyNamesFile

public java.lang.String familyNamesFile

protein family name file

tissueNamesFile

public java.lang.String tissueNamesFile

tissue name file

prpListNamesFile

public java.lang.String prpListNamesFile

File containing the list of .prp files to use

userDir

public static java.lang.String userDir

user directory where project was started. From System.getProperty("user.dir")+fileSeparator

prjPRPdir

public static java.lang.String prjPRPdir

standalone startup PRP/ Directory

stateFile

public static java.lang.String stateFile

Current state file. Defaults to PROTPLOT_STATE_FILE

stateName

public static java.lang.String stateName

Current state name is the stateFile without the ".prpstate"

clusterNameSetFile

public java.lang.String clusterNameSetFile

File name of Cluster Named Protein set file if it exists

filterNameSetFile

public java.lang.String filterNameSetFile

File name of Filter Named Protein set file if it exists

fileSeparator

public static java.lang.String fileSeparator

paths, "/" or "|", or ":", depends on OS. From System.getProperty("file.separator")

noArgsFlag

public boolean noArgsFlag

set if there are no args specified

statusAreaIsVisibleFlag

public boolean statusAreaIsVisibleFlag

The 3 Status lines area visibility flag.

useDichromasyFlag

public boolean useDichromasyFlag

color blind filter

usePseudocolorFlag

public boolean usePseudocolorFlag

"Use pseudocolor else grayscale for expression, checkbox

useVariableRadiusFlag

public boolean useVariableRadiusFlag

use variable radius for drawing spots proportional to the expression else all the same size

autoUpdateFlag

public boolean autoUpdateFlag

if we are to auto update reports, else use Update button if available

showClusteredProteinsFlag

public boolean showClusteredProteinsFlag

"Show clustered proteins by black boxes [CB] flag

sortAssendingFlag

public boolean sortAssendingFlag

"Sort report assending order[CB]"

useSwissProtFlag

public boolean useSwissProtFlag

access SwissProt if click on spot

useProClassFlag

public boolean useProClassFlag

access ProClass if click on spot

useGenBankFlag

public boolean useGenBankFlag

GenBank Web access

showWebPageFlag

public boolean showWebPageFlag

Allow access to Web if click on spot

isWinPCflag

public boolean isWinPCflag

set to TRUE if any Windows PC

docCodeBase

public java.lang.String docCodeBase

Where the Reference Manual is kept

browserTitle

public java.lang.String browserTitle

browser title

minExprVal

public float minExprVal

Expression range scroller - Expression lower bound [0.0:1.0]

maxExprVal

public float maxExprVal

Expression range scroller - Expression upper bound [0.0:1.0]

maxRatioVal

public float maxRatioVal

Expression-ratio (X/Y) range scroller - Ratio upper bound

minRatioVal

public float minRatioVal

Expression-ratio (X/Y) range scroller - Ratio lower bound

maxRatioSample

public float maxRatioSample

Expression-ratio (X/Y) range of actual samples- upper bound

minRatioSample

public float minRatioSample

Expression-ratio (X/Y) range of actual samples - lower bound

FRAME_HEIGHT

public static final int FRAME_HEIGHT

Frame height

FRAME_WIDTH

public static final int FRAME_WIDTH

Frame width

DRAW_PLUS

public static final int DRAW_PLUS

Plotting type: plus

DRAW_CIRCLE

public static final int DRAW_CIRCLE

Plotting type: circle

DRAW_BOX

public static final int DRAW_BOX

Plotting type: box

mReady

public boolean mReady

ready to analyze

useMouseOverFlag

public boolean useMouseOverFlag

"useMouseOver" for popup tracking balloons

logMWscalingFlag

public boolean logMWscalingFlag

scale MW by log

useFiltersFlag

public boolean useFiltersFlag

"Filter/NoFilter" checkbox for ANY active filters

useFilterExprRangeFlag

public boolean useFilterExprRangeFlag

"Filter by Expression range" checkbox filters

useExprFlag

public boolean useExprFlag

"Expression/Location" checkbox

requireAtLeastNsamplesFlag

public boolean requireAtLeastNsamplesFlag

"Filter by requiring at least N samples [RB]" checkbox for thresholdNsamples

requireAtMostNsamplesFlag

public boolean requireAtMostNsamplesFlag

"Filter by requiring at most N samples [RB]" checkbox for thresholdNsamples

showAllXYproteinsIfNullSamplesFlag

public boolean showAllXYproteinsIfNullSamplesFlag

"Show all X and Y samples if doing X/Y filtering [CB]" checkbox

useFamilyANDflag

public boolean useFamilyANDflag

use AND else OR of Family filters

useTissueANDflag

public boolean useTissueANDflag

use AND else OR of tissue filters

useFilterByXYsetMissingProteinsFlag

public boolean useFilterByXYsetMissingProteinsFlag

"Filter by X & Y sets missing proteins [CB]"

useFilterByXYtTestFlag

public boolean useFilterByXYtTestFlag

"Filter by X & Y sets t-test results [RB]"

useFilterByXY_KStestFlag

public boolean useFilterByXY_KStestFlag

"Filter by X & Y sets Kolmogorov-Smirnov test results [RB]"

usePRPlistFilterFlag

public boolean usePRPlistFilterFlag

enable gene PRP list name filtering

useFamilyFilterFlag

public boolean useFamilyFilterFlag

enable gene Family name filtering

useTissueFilterFlag

public boolean useTissueFilterFlag

enable Tissue name filtering

exprProfileBits

public long exprProfileBits

selected current expression list bits of selected samples

useFamilyBits

public long useFamilyBits

selected current protein family bits

useTissueBits

public long useTissueBits

selected current tissues bits

curPID

public int curPID

current pid protein id if any. -1 means none.

curMPID

public int curMPID

Current mPid for current sample proteins index. -1 means inone. *.

curMProt

public Protein curMProt

current Master Protein object if any

nMpidSimilarCluster

public int nMpidSimilarCluster

# of clustered proteins

mPidSimilarCluster

public int[] mPidSimilarCluster

List [0:nMpidSimilarCluster-1] of mPids similar to the current protein curMPID

nSavedClusterMPIDs

public int nSavedClusterMPIDs

# of saved clustered proteins

savedClusterSeedSP_ACC

public java.lang.String savedClusterSeedSP_ACC

saved cluster SP-ACC

savedClusterMPIDs

public int[] savedClusterMPIDs

List [0:nSavedClusterMPIDs-1] of mPids of saved clustered proteins

savedClusterNbrMPIDs

public int[] savedClusterNbrMPIDs

List [0:nSavedClusterMPIDs-1] of cluster numberssy of saved clustered proteins

savedClusterMPIDsMap

public boolean[] savedClusterMPIDsMap

boolean map of saved clustered MPIDs

nSavedFilterMPIDs

public int nSavedFilterMPIDs

# of saved Filtered proteins

savedFilterMPIDs

public int[] savedFilterMPIDs

List [0:nSavedFilterMPIDs-1] of mPids of saved Filtered proteins

savedFilterMPIDsMap

public boolean[] savedFilterMPIDsMap

boolean map of saved clustered MPIDs

distThreshold

public float distThreshold

Distance threshold for similarity clustering

distMode

public int distMode

distance computation method using the DIST_xxxx values

thresholdNsamples

public int thresholdNsamples

Number of samples threshold slider

thresholdSproteins

public int thresholdSproteins

Number of proteins/sample (S) threshold slider

pValueThr

public float pValueThr

The p-Value threshold slider value in the range of 0.0 to 1.0

hsValLB

public int hsValLB

(MW) Horizontal slider initial value Lower Bound

hsValUB

public int hsValUB

(MW) Horizontal slider initial value Upper Bound

vsValLB

public int vsValLB

(pI) Vertical slider initial value Lower Bound

vsValUB

public int vsValUB

(pI) Vertical slider initial value Upper Bound

expValLB

public int expValLB

(Expression-ratio) Vertical slider Expression initial value Lower Bound

expValUB

public int expValUB

(Expression-ratio) Vertical slider Expression initial value Lower Bound

ratioValLB

public int ratioValLB

(Expression-ratio) Vertical slider (sX/xY ratio) initial value Lower Bound

ratioValUB

public int ratioValUB

(Expression-ratio) Vertical slider (sX/xY ratio) initial value Upper Bound

distThrValUB

public int distThrValUB

(Distance Threshold) Vertical slider initial value Upper Bound

pValueThrUB

public int pValueThrUB

(pValue Threshold) Vertical slider initial value Upper Bound

Constructor Detail

ProtPlot

public ProtPlot()

Method Detail

void ()

Overrides:: in class java.lang.Object

main

public static void main(java.lang.String[] args)

main() - for ProtPlot started by standalone application.

clearDynamicState

private void clearDynamicState()

clearDynamicState() - reset dynamic state variables in prp instance

resetDefaultstate

public void resetDefaultstate(boolean resetFlag)

resetDefaultstate() - Reinitialize global user state Anything in this method should be able to be set during runtime from the "Reset" menu. If called from the MENU, call Config again to reset from state file.

Parameters:: resetFlag - is true if this is secondary reset, not first time.

setSamplesListsFromState

void setSamplesListsFromState()

setSamplesListsFromState() - read the sample lists from the state data has already been read int hash table

setDefaultXYEPsets

public void setDefaultXYEPsets(java.lang.String xKeyword,
                               java.lang.String yKeyword,
                               java.lang.String epKeyword)

setDefaultXYEPsets() - set the default X, Y, EP sample sets by keywords If the keyword is null, then do not set the set.

Parameters:: xKeyword - to use to define the X set of samples; yKeyword - to use to define the Y set of samples; epKeyword - to use to define the EP set of samples

recalcXYsampleIdxLists

public boolean recalcXYsampleIdxLists()

recalcXYsampleIdxLists() - recompute idxSampleXlist[] & idxSampleYlist[] NOTE: this does NOT use the #proteins/sample sizing. This should be called whenever the X, Y, or EP sets are changed!!!! A side effect is to set boolean dupsInXYsetsFlag if indices have any duplicate samples shared between X and Y sets.

Returns:: true if successful

recalcEPsampleIdxLists

public boolean recalcEPsampleIdxLists()

recalcEPsampleIdxLists() - recompute the idxSampleEPlist[] NOTE: this does NOT use the #proteins/sample sizing. This should be called whenever the EP sets are changed!!!!

Returns:: true if successful

setAllParamDefaults

public void setAllParamDefaults()

setAllParamDefaults() - reset all parameter defaults using the built in values if can not find the parameter in the prp.stateFile file

init

public void init()

init() - allocate,clear state, read PARAMs, build GUI and start things off. Clear state, read PARAMs, build GUI and start things off. This code can be called repeatedly to restart ProtPlot on a difference saCodeBase.

readEntirePRPdatabase

public boolean readEntirePRPdatabase()

readEntirePRPdatabase() - read the entire database. Read the list of .prp file names taking the TOTAL_PRP_EXTENSION into account to build DB from xxx_tot.prp.

Returns:: true if ok

getStateValue

public java.lang.String getStateValue(java.lang.String key,
                                      java.lang.String def)

getStateValue() - get PARAM and use default if not found.

getStateValue

public int getStateValue(java.lang.String key,
                         int def)

getStateValue() - get int PARAM and use default if not found.

getStateValue

private long getStateValue(java.lang.String key,
                           long def)

getStateValue() - get float PARAM and use default if not found.

getStateValue

private float getStateValue(java.lang.String key,
                            float def)

getStateValue() - get float PARAM and use default if not found.

getStateValue

public boolean getStateValue(java.lang.String key,
                             boolean def)

getStateValue() - get boolean PARAM and use default if not found.

getPRPindexByFileName

public int getPRPindexByFileName(java.lang.String fileName)

getPRPindexByFileName() - lookup the PRP index by file name

Parameters:: fileName - of PRP file to search
Returns:: index if succeed, -1 if failed

getPRPindexByName

public int getPRPindexByName(java.lang.String name)

getPRPindexByName() - lookup the PRP index by file name

Parameters:: name - of PRP sample to search
Returns:: index if succeed, -1 if failed

setStatusAreaVisible

public boolean setStatusAreaVisible(boolean flag)

setStatusAreaVisible() - show or hide three status lines in status popup

calcMPID2PIDmap

public void calcMPID2PIDmap()

calcMPID2PIDmap() - generate the mPid to pid map for all samples. The mPid2PidMap[0:nMasterPids-1][0:nSamples-1] map enables looking up pids given mPid for any sample. Entries where there is no data are set to -1. This is created AFTER all data has been read in.

quit

public void quit()

quit() - kill this application

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Field Summary
`boolean`	`autoUpdateFlag` if we are to auto update reports, else use Update button if available
`java.lang.String`	`browserTitle` browser title
`java.lang.String`	`buttonFontFamily` default button font family name
`Cluster`	`clust` Instance of Cluster
`java.lang.String`	`clusterNameSetFile` File name of Cluster Named Protein set file if it exists
`(package private) static java.lang.String`	`COG_URL`
`static boolean`	`CONSOLE_FLAG` Always TRUE
`int`	`curMPID` Current mPid for current sample proteins index.
`Protein`	`curMProt` current Master Protein object if any
`int`	`curPID` current pid protein id if any.
`int`	`curSample` current index of the ReadPRP PRP database
`java.lang.String`	`curSampleNameFile` Name of the current sample Name File
`static boolean`	`DBUG_6_SAMPLES` DBUG max # of 6 samples to test multiple samples
`static boolean`	`DBUG_LOCALHOST_HOMEPAGE` Debug Update commands using LOCALHOST_HOMEPAGE_URL
`static boolean`	`DEBUG` general purpose debugging
`static int`	`DEBUG_MENU_CMDS` DEBUG_MENU_CMDS value set to enable new commands being debugged 0 to enable command, -1 to disable it, -2 to not show them in the menu.
`(package private) static java.lang.String`	`DEF_CUR_SAMPLE_PRP_FILE` Default .prp startup file if none specified
`(package private) static java.lang.String`	`DEF_SAMPLEX_PRP_FILE` Default sample X .prp file if none specified
`(package private) static java.lang.String`	`DEF_SAMPLEY_PRP_FILE` Default sample Y .prp file if none specified
`boolean`	`displayXYscatterplotFlag` "Display (X vs Y) else (Mw vs pI) scatterplot [CB]"
`int`	`distMode` distance computation method using the DIST_xxxx values
`float`	`distThreshold` Distance threshold for similarity clustering
`int`	`distThrValUB` (Distance Threshold) Vertical slider initial value Upper Bound
`java.lang.String`	`docCodeBase` Where the Reference Manual is kept
`static int`	`DRAW_BOX` Plotting type: box
`static int`	`DRAW_CIRCLE` Plotting type: circle
`static int`	`DRAW_PLUS` Plotting type: plus
`boolean`	`dupsInXYsetsFlag` flag set if there are samples that are in both the X and Y sample sets when call recalcSampleIdxLists().
`EventHandlerPRP`	`eh` instance of EventHandlerPRP
`(package private) ExprProfilePopup`	`epp` popup expression profile window if enabled
`long`	`exprProfileBits` selected current expression list bits of selected samples
`int`	`expValLB` (Expression-ratio) Vertical slider Expression initial value Lower Bound
`int`	`expValUB` (Expression-ratio) Vertical slider Expression initial value Lower Bound
`(package private) static java.lang.String`	`FAMILY_NAMES_FILE` Name of file with tab-delim list of protein families (name, bits)
`java.lang.String`	`familyNamesFile` protein family name file
`Filter`	`fil` Instance of Data Filter.
`static java.lang.String`	`fileSeparator` paths, "/" or "\|", or ":", depends on OS.
`java.lang.String`	`filterNameSetFile` File name of Filter Named Protein set file if it exists
`FileIOPRP`	`fio` Instance of major classes for global data access.
`static int`	`FRAME_HEIGHT` Frame height
`static int`	`FRAME_WIDTH` Frame width
`(package private) static java.lang.String`	`GENBANK_BASEURL`
`java.lang.String`	`genBankServerBase` GenBank server
`GetListOfPRPs`	`glp` Get a list of .prp file names
`java.util.Hashtable`	`hashMPIDs` Hash table of Master Proteins for proteins from all PRP databases
`(package private) static java.lang.String`	`HOMEPAGE_URL` Home page for ProtPlot
`int`	`hsValLB` (MW) Horizontal slider initial value Lower Bound
`int`	`hsValUB` (MW) Horizontal slider initial value Upper Bound
`int[]`	`idxSampleEPlist` list of indices of samples used in the sampleEPlist[0:nSampleEPlist-1]
`int[]`	`idxSampleXlist` list of indices of samples used in the X set [0:nSampleXlist-1]
`int[]`	`idxSampleYlist` list of indices of samples used in the Y set [0:nSampleYlist-1]
`boolean`	`isWinPCflag` set to TRUE if any Windows PC
`(package private) static java.lang.String`	`LOCALHOST_HOMEPAGE_URL` local site Home page for ProtPlot
`boolean`	`logMWscalingFlag` scale MW by log
`MathPRP`	`math` math package
`static int`	`MAX_FAMILIES` max # protein class names
`static int`	`MAX_NEAREST_PROTEINS` Max # proteins to cluster in similarity cluster plot
`static int`	`MAX_PROTEINS` maximum # of protein spots ever seen in the union of all .prp DBs
`static int`	`MAX_PRP_FILES` Max # of PRP databases that may be read at one time
`static int`	`MAX_SAPARAMS` max # of stand-alone parameters
`static int`	`MAX_TISSUES` max # tissue names
`float`	`maxExprVal` Expression range scroller - Expression upper bound [0.0:1.0]
`int`	`maxProteinsFound` maximum # of proteins found in any one sample
`float`	`maxRatioSample` Expression-ratio (X/Y) range of actual samples- upper bound
`float`	`maxRatioVal` Expression-ratio (X/Y) range scroller - Ratio upper bound
`java.lang.String`	`menuFontFamily` default menu item font family name
`float[][]`	`mExprVector` Master Protein List [0:nMasterPids-1][0:nSamples-1] of protein expression values from all PRP DBs
`float`	`minExprVal` Expression range scroller - Expression lower bound [0.0:1.0]
`float`	`minRatioSample` Expression-ratio (X/Y) range of actual samples - lower bound
`float`	`minRatioVal` Expression-ratio (X/Y) range scroller - Ratio lower bound
`int[][]`	`mPid2PidMap` Map of mPids to pids for specific samples [0:nMasterPids-1][0:nSamples-1].
`int[]`	`mPidFiltered` Is list [0:nMpidFiltered] of all mPids that passed the data filter and are used by the current sample (for a single sample) or by a set of samples (e.g.
`int[]`	`mPidSamples` Is list [0:nMpidSamples] of all mPids used by the current sample (for a single sample) or by a set of samples (e.g.
`int[]`	`mPidSimilarCluster` List [0:nMpidSimilarCluster-1] of mPids similar to the current protein curMPID
`Protein[]`	`mProtList` Master Protein List [0:nMasterPids-1] of proteins from all PRP databases indexed by mPid value.
`java.lang.String[]`	`mProtSwissProtAcc` Master Protein List [0:nMasterPids-1] of protein SWISS-PROT Acc #s from all PRP DBs is indexed by mPid value.
`java.lang.String[]`	`mProtSwissProtId` Master Protein List [0:nMasterPids-1] of protein IDs from all PRP DBs is indexed by mPid value.
`boolean`	`mReady` ready to analyze
`int[]`	`nbrProteins` List of # proteins/sample [0:nPRPs-1]
`static boolean`	`NEVER` Always FALSE
`int`	`nMasterPids` Number of proteins in the Master Protein List mPid[]
`int`	`nMpidFiltered` size of mPidSamples[] list.
`int`	`nMpidSamples` size of mPidSamples[] list.
`int`	`nMpidSimilarCluster` # of clustered proteins
`boolean`	`noArgsFlag` set if there are no args specified
`int`	`nOverDaltonLimit` Number of proteins found that are > 200K daltons
`int`	`nPRPs` # of PRP file names
`int`	`nSampleEPlist` # of samples used in the expression vector sampleEPlist[0:nPRPs-1]
`int`	`nSamples` Number of ReadPRP instances of PRP databases
`int`	`nSampleXlist` # of samples used in the X set sampleXlist[0:nPRPs-1]
`int`	`nSampleYlist` # of samples used in the Y set sampleYlist[0:nPRPs-1]
`private static int`	`nSAparam` # of stand-alone params
`int`	`nSavedClusterMPIDs` # of saved clustered proteins
`int`	`nSavedFilterMPIDs` # of saved Filtered proteins
`static java.lang.String`	`osName` operating system Windows, SUNOS, etc
`boolean`	`outsideRatioRangeFlag` Filter by (X/Y) of samples X & samples Y outside of [minRation:maxRatio] sliders
`static java.lang.String`	`prjPRPdir` standalone startup PRP/ Directory
`(package private) static java.lang.String`	`PRO_CLASS_BASE_URL`
`java.lang.String`	`proClassServerBase` PIR lookup on our server
`Protein`	`prot` Clone instances
`(package private) static java.lang.String`	`PROTPLOT_STATE_FILE` name of the ProtPlot state file
`java.util.Hashtable`	`protPlotStateHT` Hash table of the ProtPlot state read from stateFile ".prpstate" if not null
`java.lang.String`	`protServerBase` top level codebase for ProtPlot server
`java.lang.String[]`	`prpFileNames` List of PRP file names [0:nPRPs-1]
`java.lang.String`	`prpListNamesFile` File containing the list of .prp files to use
`java.lang.String[]`	`prpNames` List of PRP names [0:nPRPs-1]
`float`	`pValueThr` The p-Value threshold slider value in the range of 0.0 to 1.0
`int`	`pValueThrUB` (pValue Threshold) Vertical slider initial value Upper Bound
`int`	`ratioValLB` (Expression-ratio) Vertical slider (sX/xY ratio) initial value Lower Bound
`int`	`ratioValUB` (Expression-ratio) Vertical slider (sX/xY ratio) initial value Upper Bound
`ReadPRP[]`	`rdList` List [0:nSamples-1] of ReadPRP instances of PRP databases
`boolean`	`requireAtLeastNsamplesFlag` "Filter by requiring at least N samples [RB]" checkbox for thresholdNsamples
`boolean`	`requireAtMostNsamplesFlag` "Filter by requiring at most N samples [RB]" checkbox for thresholdNsamples
`ReadFamilies`	`rf` ReadFamilies
`ReportPRP`	`rpt` instance of ReportPRP
`static ShowStringPopup`	`rptPopup` Current report string popup instance.
`ReadTissues`	`rt` ReadTissues
`boolean[]`	`sampleEPlist` list of samples used in the expression vector [0:nPRPs-1]
`java.lang.String`	`sampleNameFileX` Name of the current sample Name File X
`java.lang.String`	`sampleNameFileY` Name of the current sample Name File Y
`int`	`sampleX` current index of the ReadPRP PRP database (X/Y) ratio sample X
`boolean[]`	`sampleXlist` boolean list of samples used in the X set [0:nPRPs-1]
`int`	`sampleY` current index of the ReadPRP PRP database (X/Y) ratio sample Y
`boolean[]`	`sampleYlist` list of samples used in the Y set [0:nPRPs-1]
`private static java.lang.String[]`	`saName` [0:nSAparam-1] name
`private static java.lang.String[]`	`saValue` [0:nSAparam-1] value
`int[]`	`savedClusterMPIDs` List [0:nSavedClusterMPIDs-1] of mPids of saved clustered proteins
`boolean[]`	`savedClusterMPIDsMap` boolean map of saved clustered MPIDs
`int[]`	`savedClusterNbrMPIDs` List [0:nSavedClusterMPIDs-1] of cluster numberssy of saved clustered proteins
`java.lang.String`	`savedClusterSeedSP_ACC` saved cluster SP-ACC
`int[]`	`savedFilterMPIDs` List [0:nSavedFilterMPIDs-1] of mPids of saved Filtered proteins
`boolean[]`	`savedFilterMPIDsMap` boolean map of saved clustered MPIDs
`int`	`scrHeight` screen size height
`int`	`scrWidth` screen size width
`boolean`	`showAllXYproteinsIfNullSamplesFlag` "Show all X and Y samples if doing X/Y filtering [CB]" checkbox
`boolean`	`showClusteredProteinsFlag` "Show clustered proteins by black boxes [CB] flag
`boolean`	`showWebPageFlag` Allow access to Web if click on spot
`boolean`	`sortAssendingFlag` "Sort report assending order[CB]"
`ShowScatterPlotPopup`	`spp` main window containing the 2D plot and menu bar
`StatisticsPRP`	`stat` statistics package
`static java.lang.String`	`stateFile` Current state file.
`static java.lang.String`	`stateName` Current state name is the stateFile without the ".prpstate"
`boolean`	`statusAreaIsVisibleFlag` The 3 Status lines area visibility flag.
`PopupStatusWindow`	`statusPopup` Holds the popup window status lines
`(package private) static java.lang.String`	`SWISS2D_BASEURL` Hardwired URLs and file names
`java.lang.String`	`swissProtServerBase` swiss prot server
`java.lang.String`	`textFontFamily` default text font family name
`int`	`thresholdNsamples` Number of samples threshold slider
`int`	`thresholdSproteins` Number of proteins/sample (S) threshold slider
`(package private) static java.lang.String`	`TISSUE_NAMES_FILE` Name of file with tab-delim list of tissues (name, bits)
`java.lang.String`	`tissueNamesFile` tissue name file
`(package private) static java.lang.String`	`TMAP_JAR_VERSION_FILE` name of file containing the latest ProtPlot.jar version #
`static java.lang.String`	`TOTAL_PRP_EXTENSION` Only read PRP files with this file extension.
`static float`	`UNDER_DALTON_LIMIT` default bound for toggling data base between xxx_tot.prp and the subset <= this limit.
`static boolean`	`USE_FAMILIES_FILE_FLAG` Set if read protein Family data from FAMILY_NAMES_FILE
`static boolean`	`USE_LINEAR_SCROLLING` use linear else non-linear scroller scaling
`boolean`	`useCmapRatioModeFlag` plot samplesX/sampleY ratio range color map in the scatterplot
`boolean`	`useDichromasyFlag` color blind filter
`boolean`	`useEPsetExprModeFlag` Show mean EP set sample expression
`boolean`	`useExponentialMapFlag` If enabled, it generates a non-linear colormap using the eMap[gray] function to generate a 10 color eColor[0:9] set of colors stored in cMap[0:155].
`boolean`	`useExprFlag` "Expression/Location" checkbox
`boolean`	`useExprModeFlag` plot the current sample expression data in the scatterplot
`boolean`	`useExprProfilePlotModeFlag` if true, then popup expression profile in epp
`boolean`	`useFamilyANDflag` use AND else OR of Family filters
`long`	`useFamilyBits` selected current protein family bits
`boolean`	`useFamilyFilterFlag` enable gene Family name filtering
`boolean`	`useFilterByXY_KStestFlag` "Filter by X & Y sets Kolmogorov-Smirnov test results [RB]"
`boolean`	`useFilterByXYsetMissingProteinsFlag` "Filter by X & Y sets missing proteins [CB]"
`boolean`	`useFilterByXYtTestFlag` "Filter by X & Y sets t-test results [RB]"
`boolean`	`useFilterExprRangeFlag` "Filter by Expression range" checkbox filters
`boolean`	`useFiltersFlag` "Filter/NoFilter" checkbox for ANY active filters
`boolean`	`useGenBankFlag` GenBank Web access
`static java.lang.String`	`useHomeServer` ProtPlot home server to use
`static boolean`	`useInitialStateFileFlag` Only read initial state file if this is set
`boolean`	`useLocalDocFlag` Flag to use local Doc/ directory for help else to use ProtPlot server
`boolean`	`useMouseOverFlag` "useMouseOver" for popup tracking balloons
`boolean`	`useProClassFlag` access ProClass if click on spot
`boolean`	`usePRPlistFilterFlag` enable gene PRP list name filtering
`boolean`	`usePseudocolorFlag` "Use pseudocolor else grayscale for expression, checkbox
`boolean`	`useRatioModeFlag` Show ratio X/Y or X-set/Y-set, else single sample expression or mean EP set expression
`static java.lang.String`	`userDir` user directory where project was started.
`boolean`	`useRGratioModeFlag` plot samplesX/sampleY ratio (Red=X + Green=Y) data in the scatterplot
`boolean`	`useSavedClusterFlag` Use saved clustered set of proteins in data filter
`boolean`	`useSavedFilterFlag` Use saved filtered set of proteins in data filter
`boolean`	`useSingleExprModeFlag` Show single sample expression
`boolean`	`useSwissProtFlag` access SwissProt if click on spot
`boolean`	`useTissueANDflag` use AND else OR of tissue filters
`long`	`useTissueBits` selected current tissues bits
`boolean`	`useTissueFilterFlag` enable Tissue name filtering
`boolean`	`useTotPRPflag` if true, access all proteins, otherwise filter out all proteins > UNDER_DALTON_LIMIT Daltons.
`boolean`	`useVariableRadiusFlag` use variable radius for drawing spots proportional to the expression else all the same size
`boolean`	`useXYsetCmapRatioModeFlag` plot X-Set-samples /X-Set-samples ratio range color map scatterplot
`boolean`	`useXYsetDataFlag` use X / Y sets of samples else use single X / Y samples
`UtilPRP`	`util` Utility instance
`static java.lang.String`	`VERSION`
`java.lang.String`	`versionStateFile` Version of the read from stateFile ".prpstate" if not null
`static java.lang.String`	`verStr`
`int`	`vsValLB` (pI) Vertical slider initial value Lower Bound
`int`	`vsValUB` (pI) Vertical slider initial value Upper Bound
`java.lang.String`	`xCondLabel` plot label: (className,mnData,sdData,cvData) X (set) for current protein if previously called the t-test
`java.lang.String`	`xCondName` condition name for all X set members
`java.lang.String`	`yCondLabel` plot label: (className,mnData,stdData,cvData) Y (set) for current protein if previously called the t-test
`java.lang.String`	`yCondName` condition name for all Y set members

Method Summary
`(package private) void`	`()`
`void`	`calcMPID2PIDmap()` calcMPID2PIDmap() - generate the mPid to pid map for all samples.
`private void`	`clearDynamicState()` clearDynamicState() - reset dynamic state variables in prp instance
`int`	`getPRPindexByFileName(java.lang.String fileName)` getPRPindexByFileName() - lookup the PRP index by file name
`int`	`getPRPindexByName(java.lang.String name)` getPRPindexByName() - lookup the PRP index by file name
`boolean`	`getStateValue(java.lang.String key, boolean def)` getStateValue() - get boolean PARAM and use default if not found.
`private float`	`getStateValue(java.lang.String key, float def)` getStateValue() - get float PARAM and use default if not found.
`int`	`getStateValue(java.lang.String key, int def)` getStateValue() - get int PARAM and use default if not found.
`private long`	`getStateValue(java.lang.String key, long def)` getStateValue() - get float PARAM and use default if not found.
`java.lang.String`	`getStateValue(java.lang.String key, java.lang.String def)` getStateValue() - get PARAM and use default if not found.
`void`	`init()` init() - allocate,clear state, read PARAMs, build GUI and start things off.
`static void`	`main(java.lang.String[] args)` main() - for ProtPlot started by standalone application.
`void`	`quit()` quit() - kill this application
`boolean`	`readEntirePRPdatabase()` readEntirePRPdatabase() - read the entire database.
`boolean`	`recalcEPsampleIdxLists()` recalcEPsampleIdxLists() - recompute the idxSampleEPlist[] NOTE: this does NOT use the #proteins/sample sizing.
`boolean`	`recalcXYsampleIdxLists()` recalcXYsampleIdxLists() - recompute idxSampleXlist[] & idxSampleYlist[] NOTE: this does NOT use the #proteins/sample sizing.
`void`	`resetDefaultstate(boolean resetFlag)` resetDefaultstate() - Reinitialize global user state Anything in this method should be able to be set during runtime from the "Reset" menu.
`void`	`setAllParamDefaults()` setAllParamDefaults() - reset all parameter defaults using the built in values if can not find the parameter in the prp.stateFile file
`void`	`setDefaultXYEPsets(java.lang.String xKeyword, java.lang.String yKeyword, java.lang.String epKeyword)` setDefaultXYEPsets() - set the default X, Y, EP sample sets by keywords If the keyword is null, then do not set the set.
`(package private) void`	`setSamplesListsFromState()` setSamplesListsFromState() - read the sample lists from the state data has already been read int hash table
`boolean`	`setStatusAreaVisible(boolean flag)` setStatusAreaVisible() - show or hide three status lines in status popup