CmpSpots
Class CmpSpots

java.lang.Object
  CmpSpots.Cmpglb
      CmpSpots.CmpSpots

public class CmpSpots
extends Cmpglb

Class CmpSpots.java is a 2D PAGE SAMPLE spot pairing program for Open2Dprot

This code was derived and refactored from GELLAB-II cmpgl2 C language files "Version November 9, 1999", and the Open2Dprot CmpSpots program Java files.

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 Open2Dprot Mozilla and Legal files are available on http://Open2Dprot.sourceforge.net/.

Version:

$Date: 2005/12/22 11:41:31 $ $Revision: 1.38 $

Author:

P. Lemkin, NCI-Frederick, Frederick, MD, 21702

Field Summary

Fields inherited from class CmpSpots.Cmpglb

acc, accDatabaseFile, accFile, accFormatMode, AP, applicationName, argsV, asgn, banner, bannerTitle, baseImageFileNameRsample, baseImageFileNameSample, batchDir, cacheDir, cmpspotsURL, commutativeLMSswitch, CONSOLE_FLAG, CP, cs, data, DATE, dbLM, dbRsample, dbSample, DBUG_ALL_SSF_SPOTS, DBUG_APPEND, DBUG_ASSIGN_CODES, DBUG_ASSIGN_SSF_TO_LMS, DBUG_COMPUTE_RADII, DBUG_CONSOLE, DBUG_DUMP_LM_SET_SPOTS, DBUG_DUMP_PREFACE_EPILOGUE, DBUG_DUMP_SPF, DBUG_FIND_LMS_IN_SSFS, DBUG_FREE_0200000, DBUG_FREE_04000, DBUG_INITIAL_SPOT_PAIRING, DBUG_PRINT_AT, DBUG_PRINT_FULL_NODE_INFO, DBUG_PRINT_LMS_SET_SPOTS, DBUG_PRINT_LMS_SPOT_MAPPING, DBUG_READ_LANDMARKS, DBUG_READ_SSF_DATA, DBUG_SECONDARY_PAIRING, DBUG_SPECIFIC_SPOTS, DBUG_SWITCH_ANALYSIS, DBUG_SWITCHES, dBugBits, dbugBitsHelpStr, dBugLMsetList, debugSwitch, defaultSwitch, demoFileList, demoSwitch, docFileList, dtdSwitch, EP, fileSeparator, fio, fourSqrtPi, GS, ini, inPixFileRsample, inPixFileSample, inputFormatSwitch, isCsamplePrimeSwitch, jarFileList, jarLibrFileList, landmarkDatabaseFile, latchLandmarkSpotSwitch, legalImageFileExtens, LM, LMSETCOLOR, lmsFile, lmsFormatMode, MAX_LM_LATCH_THR, maxLatchDist, nbrAltLMSSwitch, nDbugLMsetList, NEVER, nlmDB, nSwitches, OPTBKGROUND, osName, pair, pair2ndary, paramH, pix, pix1, pix2, pixFileExtn, PP, ppxDir, pra, projDir, projDirSwitch, propertiesFile, propertiesFileSwitch, ps, PUBLISH, rdbmsDir, REVISION, rRoiDbug, rRoiDbugSwitch, RSAMPLE, rsampleName, rsampleSwitch, SAMPLE, sampleName, sampleSwitch, secondaryPairingSwitch, simplePixFileRsample, simplePixFileSample, sort, SP, spfFormatMode, spfFormatSwitch, spfOutputFile, spfOutputPrefaceFile, SPOTBOXCOLOR, sRoiDbug, sRoiDbugSwitch, ssfFileRsample, ssfFileSample, ssfFormatMode, ssfInputEpilogueFileRsample, ssfInputEpilogueFileSample, ssfInputFileRsample, ssfInputFileSample, ssfInputPrefaceFileRsample, ssfInputPrefaceFileSample, startTime, sw, switchOptCBvalue, switchOptData, switchOptValue, thrPPswitch, thrSPswitch, timerSwitch, tmpDir, updateSwitch, US, usageSwitch, USE_DEMO_DATA, useAccFileSwitch, useHistGUISwitch, useLmsFileSwitch, usePercentDensitySwitch, usePopupGUISwitch, userDir, util, VERSION, xmlDir

Constructor Summary

CmpSpots()

Method Summary

private boolean	lookupSampleEntryInAccDB(java.lang.String accNameData, java.lang.String accFieldName, java.lang.String accFile, DbSample dbSsf) lookupSampleEntryInAccDB() - lookup the sample image name in the accession DB.
static void	main(java.lang.String[] args) main() - for CmpSpots 2D spot-pairing program for Open2Dprot.
private int	pairSpotsBetweenSamples(java.lang.String[] args) pairSpotsBetweenSamples() - pair the two samples spot lists.
void	popupImageViewer() popupImageViewer() - popup the image viewer after the images were computed by the spot pairing.
private char[]	readSsfImage(java.lang.String imageFile, DbSample dbSsf) readSsfImage() - read the SSF image and set image status in the dbSsf instance
private static void	resetResources(boolean fullResetFlag) resetResources() - reset any resources that must be reset for the next run of the spot pairing.
private java.lang.String[]	setupDebugSwitches(java.lang.String[] argv) setupDebugSwitches() - setup the debug switches
private static java.lang.String[]	setupDemoSwitches(java.lang.String[] argv) setupDemoSwitches() - setup the demo switches for the "gel-HM-019" (HUMAN-AML) and "gel-HM-071" (Human-ALL) samples
private static java.lang.String[]	setupMinDefaultsSwitches(java.lang.String[] argv) setupMinDefaultsSwitches() - add the minimum default switches.

Methods inherited from class CmpSpots.Cmpglb

get2D, get2D, initGlb, resetGlb, set2D

Methods inherited from class java.lang.Object

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

Constructor Detail

CmpSpots

public CmpSpots()

Method Detail

main

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

main() - for CmpSpots 2D spot-pairing program for Open2Dprot.

Parameters:

args - is the argument list of command line

See Also:

CmpIni.switchAnalysis(java.lang.String[]), CmpReportPopup.setOutFileToCloseOnKill(java.io.FileWriter), CmpReportPopup.setSaveAsFile(java.lang.String), CmpReportPopup.waitForUserClose(), CmpShowImage.showImageGUI(java.lang.String), FileIO#makeProjectDirs, Switches#cvtSwitchListToStr, Switches#getSwitchOptionsTableStr, Switches#mergeSwitches, Util#appendPRmsg, Util#getPrettyPrintCurrentDateStr, Util#showReportStatus, pairSpotsBetweenSamples(java.lang.String[]), resetResources(boolean), setupDebugSwitches(java.lang.String[]), setupMinDefaultsSwitches(java.lang.String[]), setupDemoSwitches(java.lang.String[])

pairSpotsBetweenSamples

private int pairSpotsBetweenSamples(java.lang.String[] args)

pairSpotsBetweenSamples() - pair the two samples spot lists.

Returns:

exit code. It is 0 if succeed, else non-zero for errors this gets passed to System.exit(exit code).

See Also:

CmpAssign.assignSSFtoLMS(), CmpIni.additionalInit(), CmpIni.initSwitchOptionsData(), CmpIni.postProcessSwitches(), CmpIni.switchAnalysis(java.lang.String[]), CmpPair.findLMSinSsfs(), CmpPair.initialSpotPairing(), CmpPairSecondary.secondarySpotPairing(), DbAccession#loadAccessionDatabase, DbAccession#lookupSampleInAccDB, DbLM#computeLMSradii, DbLM#cvLMSIdx2Name, DbLM#lookupSamplePairLMS, DbLM#readLandmarkDatabase, DbPairSamples#setPairSamples, DbPairSamples#setPairingThresholds, DbPairSamples#writeEntireSPF, DbSample#assignRsampleToAllSpotsInSpotList, DbSample#readSSFdata, DbSample#setSampleNames, FileIO#discoverFileExtension, FileIO#makeProjectDirs, PopupFileDialog#popupFileDialog, Util#appendPRmsg, Util#calcStatusTimesReport, Util#fatalExit, Util#showReportStatus, lookupSampleEntryInAccDB(java.lang.String, java.lang.String, java.lang.String, DbSample)

lookupSampleEntryInAccDB

private boolean lookupSampleEntryInAccDB(java.lang.String accNameData,
                                         java.lang.String accFieldName,
                                         java.lang.String accFile,
                                         DbSample dbSsf)

lookupSampleEntryInAccDB() - lookup the sample image name in the accession DB.

Parameters:

accNameData - is the sample image name to search for. Do not specify the file extension.

accFieldName - is the accession field name

accFile - is the name of the accession file

dbSsf - is the SSF instance to use

Returns:

true if succeed

readSsfImage

private char[] readSsfImage(java.lang.String imageFile,
                            DbSample dbSsf)

readSsfImage() - read the SSF image and set image status in the dbSsf instance

Parameters:

imageFile - to read

dbSsf - to update

Returns:

image array

See Also:

PixReader#clearImageReader, PixReader#getCharPix, PixReader#readImageFile

resetResources

private static void resetResources(boolean fullResetFlag)

resetResources() - reset any resources that must be reset for the next run of the spot pairing.

Parameters:

fullResetFlag - force new resource allocation

See Also:

DbLM#init, DbSample#init, CmpData.reset(), Cmpglb.resetGlb()

setupMinDefaultsSwitches

private static java.lang.String[] setupMinDefaultsSwitches(java.lang.String[] argv)

setupMinDefaultsSwitches() - add the minimum default switches.

Parameters:

argv - is list of original switches

Returns:

new argV merged switch list

See Also:

Switches#mergeSwitches, Util#cvs2Array

setupDemoSwitches

private static java.lang.String[] setupDemoSwitches(java.lang.String[] argv)

setupDemoSwitches() - setup the demo switches for the "gel-HM-019" (HUMAN-AML) and "gel-HM-071" (Human-ALL) samples

Parameters:

argv - is list of original switches

Returns:

new argV merged switch list

See Also:

Switches#mergeSwitches, Util#cvs2Array

setupDebugSwitches

private java.lang.String[] setupDebugSwitches(java.lang.String[] argv)

setupDebugSwitches() - setup the debug switches

Parameters:

argv - list of original switches

Returns:

new argV merged switch list

See Also:

Switches#mergeSwitches, Util#cvs2Array

popupImageViewer

public void popupImageViewer()

popupImageViewer() - popup the image viewer after the images were computed by the spot pairing.

See Also:

CmpShowImage.setPixDatabase(java.lang.String[], java.lang.String[], java.lang.String[], char[][], int, java.lang.String, int[], int[], boolean), CmpShowImage.showImageGUI(java.lang.String)