Accession.Accglb
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java.lang.Object
public class Accglb
Class Accglb is the base class that specifies global variables used by all of the other Open2Dprot Accession program classes.
This code was derived and refactored from GELLAB-II C language files and the Open2Dprot Seg2Dgel and Accession 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/.
| Field Summary | |
|---|---|
static DbAccession |
acc
|
static java.lang.String |
accDatabaseFile
full path Accession database file |
static java.lang.String |
accessionURL
Hardwired Open2Dprot server connection Switch to S.F. |
static java.lang.String |
accFile
Accession database file without the path. |
static int |
accFormatMode
Accession DB file modes: Allowed: IO_FORMAT_TAB_DELIM, IO_FORMAT_XML |
(package private) static boolean |
ADD_WINDUMP
Use the winDump option in the ROI GUI. |
(package private) static boolean |
ALLOW_CALIBRATION
Allow access to Calibration popup window |
(package private) static boolean |
ALLOW_SAVE_DB
Allow saving modified Accession database file |
static java.lang.String |
applicationName
name of the application |
static java.lang.String[] |
argsV
Total command list arg list originally set fro main(args) |
static java.lang.String |
banner
The full version data banner with todays date |
static java.lang.String |
bannerTitle
The short version data banner for popup titles |
static java.lang.String |
batchDir
Batch temporary data files used in exec'ing pipeline modules directory {projDir}/batch/ |
static DbSpot |
bkgrdSpot
Sample Background spot used in spot measurements if not null. |
static java.lang.String |
cacheDir
Cache database directory {projDir}/cache/ |
static boolean |
changedAccDBnameFlag
Flag indicating changed the Accession DB data name |
static boolean |
CONSOLE_FLAG
|
static Accession |
cs
instance of the main class |
static AccData |
data
|
static java.lang.String |
DATE
CVS Version date |
static DbSample |
dbRsample
Rsample state parameters read from files. |
static DbSample |
dbSample
Sample state parameters read from files. |
static boolean |
DBUG_APPEND
Debugging append text flag |
static boolean |
DBUG_CONSOLE
Debugging console text flag |
static int |
DBUG_FREE_0100
Debug code: -free- |
static int |
DBUG_FREE_01000
Debug code: -free- |
static int |
DBUG_FREE_010000
Debug code: -free- |
static int |
DBUG_FREE_0100000
Debug code: -free- |
static int |
DBUG_FREE_01000000
Debug code: -free- |
static int |
DBUG_FREE_020
Debug code: -free- |
static int |
DBUG_FREE_0200
Debug code: -free- |
static int |
DBUG_FREE_02000
Debug code: -free- |
static int |
DBUG_FREE_020000
Debug code: -free- |
static int |
DBUG_FREE_02000000
Debug code: -free- |
static int |
DBUG_FREE_04
Debug code: compute the landmark sets 1/2 radii |
static int |
DBUG_FREE_040
Debug code: -free- |
static int |
DBUG_FREE_0400
Debug code: -free- |
static int |
DBUG_FREE_04000
Debug code: -free- |
static int |
DBUG_FREE_040000
Debug code: -free- |
static int |
DBUG_FREE_0400000
Debug code: -free- |
static int |
DBUG_MAIN
Debug code: main() |
static int |
DBUG_PRINT_AT
Debug code: -printAt() debugging |
static int |
DBUG_SWITCH_ANALYSIS
Debug code: analyze command line switches |
static boolean |
DBUG_SWITCHES
Debugging switches |
static java.lang.String[] |
dbugBitName
Debug bits name from the parsed Accession.dbug file |
static int |
dBugBits
-DEBUG:bits |
static java.lang.String |
dbugBitsHelpStr
Debug bit options help for error messages |
static int[] |
dbugBitValues
Debug bits values from the parsed Accession.dbug file |
static boolean |
debugSwitch
The parsed of Command line switches |
static boolean |
defaultSwitch
The parsed of Command line switches |
static java.lang.String[] |
demoFileList
List of demo/ files downloadable from the server |
static boolean |
demoSwitch
The parsed of Command line switches |
static int |
distLatchThr
minimum distance for spot to latch |
static java.lang.String[] |
docFileList
List of documentation files downloadable from the server |
static boolean |
dtdSwitch
The parsed of Command line switches |
static java.lang.String |
fileSeparator
File separator: Property("file.separator") |
static FileIO |
fio
|
static float |
fourSqrtPi
Constant 4*sqrt(PI) constant used in computing spot volume |
static AccIni |
ini
|
static java.lang.String |
inPixFileRsample
original Rsample input image file with full path and .tif, .tiff, .jpg, .gif or .ppx file extensions. |
static java.lang.String |
inPixFileSample
original Sample input image file with full path and .tif, .tiff, .jpg, .gif or .ppx file extensions. |
static boolean |
inputFormatSwitch
The parsed of Command line switches |
static java.lang.String[] |
jarFileList
List of program .jar files downloadable from the server |
static java.lang.String[] |
jarLibrFileList
List of library .jar files downloadable from the server |
static java.lang.String[] |
legalImageFileExtens
List of legal sample image file extensions |
static boolean |
makeBkupCopyFlag
The parsed of Command line switches |
(package private) static int |
MAX_WEDGE_STEPS
default # of peak wedge calibration table steps |
static boolean |
needToSaveAccessionDataFlag
Flag indicates need to save the Accession DB data |
static boolean |
NEVER
NEVER and CONSOLE_FLAG - debugging variables - must not be final! |
static int |
nSwitches
the number of Command line switches |
static int |
OPTBKGROUND
Shift background grayscale away from 0 so graphics show up better... |
static java.lang.String |
osName
name of this operating system: Property("os.name") |
static PixReader |
pix
|
static java.lang.String |
pixFileExtn
Output images are either ".gif" or ".jpg" [TODO] change this to .jpg with JPEG writer. |
static java.lang.String |
ppxDir
Original sample images directory {projDir}/ppx/ |
static AccReportPopup |
pra
generic popup report |
static java.lang.String |
projDir
Project directory that is either userDir, specified by -projDir:{path}, or extracted from the input file path it the image is in a "/ppx/" subdirectory. |
static boolean |
projDirSwitch
The parsed of Command line switches |
static java.lang.String |
propertiesFile
Current startup properties file containing default switches if it exists. |
static boolean |
propertiesFileSwitch
The parsed of Command line switches |
(package private) static boolean |
PUBLISH
NOTE: overide the following debugging options if publishing on net. |
static java.lang.String |
rdbmsDir
RDBMS database directory {projDir}/rdbms/ |
static java.lang.String |
REVISION
CVS Revision |
static int |
RSAMPLE
The index for the Rsample (Reference Sample) |
static java.lang.String |
rsampleName
Name of Rsample that does not include either the file extension or the path. |
static boolean |
rsampleSwitch
The parsed of Command line switches |
static int |
SAMPLE
The index for the Sample to be paired with the Rsample |
static java.lang.String |
sampleName
Name of Sample that does not include either the file extension or the path. |
static boolean |
sampleSwitch
The parsed of Command line switches |
static java.lang.String |
simplePixFileRsample
Simple Rsample original Rsample input image file with .tif, .tiff, .jpg, .gif or .ppx file extensions. |
static java.lang.String |
simplePixFileSample
Simple original Sample input image file with .tif, .tiff, .jpg, .gif or .ppx file extensions. |
static boolean |
sortSpotListFlag
Sort the measured spots in assending order by density |
static int |
spfFormatMode
SPF output file modes: Allowed: IO_FORMAT_FULL, IO_FORMAT_GELLAB, IO_FORMAT_TAB_DELIM, IO_FORMAT_XML |
static int |
spotBoxSize
spot measurement box size |
static int |
ssfCWX1
SSF computing window used with -ssfCW: |
static int |
ssfCWX2
SSF computing window used with -ssfCW: |
static int |
ssfCWY1
SSF computing window used with -ssfCW: |
static int |
ssfCWY2
SSF computing window used with -ssfCW: |
static java.lang.String |
ssfFileRsample
SSF input file for G1 sample (i.e., Rsample) |
static java.lang.String |
ssfFileSample
SSF input file for G2 sample (i.e., Sample) |
static int |
ssfFormatMode
SSF input file modes: Allowed: IO_FORMAT_TAB_DELIM, IO_FORMAT_XML |
static java.lang.String |
ssfInputEpilogueFileRsample
full tab-delim G1 EPILOGUE xml/Rsample Spot Segmentation File full path |
static java.lang.String |
ssfInputEpilogueFileSample
full tab-delim G2 EPILOGUE xml/Sample Segmentation File full path |
static java.lang.String |
ssfInputFileRsample
xml/ Rsample G1 Spot Segmentation File full path |
static java.lang.String |
ssfInputFileSample
xml/ Sample G2 Spot Segmentation File full path |
static java.lang.String |
ssfInputPrefaceFileRsample
full tab-delim G1 PREFACE xml/Rsample Spot Segmentation File full path |
static java.lang.String |
ssfInputPrefaceFileSample
full tab-delim G2 PREFACE xml/Sample Spot Segmentation File full path |
static long |
startTime
starting time in epoch msec time |
static java.lang.String[] |
sw
Command line + Accession.properties state switches |
(package private) static boolean[] |
switchOptCBvalue
The switchOptcCBvalue[0:nData-1] is used by the Report Popup that in turn may call PopupOptions. |
(package private) static java.lang.String[] |
switchOptData
The switchOptData[0:(2*nData)-1] is used by the Report Popup that in turn may call PopupOptions. |
(package private) static java.lang.String[] |
switchOptValue
The switchOptValue[0:nData-1] is used by the Report Popup that in turn may call PopupOptions. |
static boolean |
timerSwitch
The parsed of Command line switches |
static java.lang.String |
tmpDir
Tmp images directory {projDir}/tmp/ |
static boolean |
updateSwitch
The parsed of Command line switches |
static boolean |
usageSwitch
The parsed of Command line switches |
(package private) static boolean |
USE_DEMO_DATA
Use the demo data by enabling the -demo flag and data. |
static boolean |
useAccFileSwitch
The parsed of Command line switches |
static boolean |
useCommonSpotSizeFlag
When recompute all spot measurements in the spot list, use the same square spot size (i.e., spotBoxSize). |
static java.lang.String |
userDir
current User directory: getProperty("user.dir")+fileSeparator |
static boolean |
useSpotBkbrdCorrectionFlag
When recompute all spot measurements in the spot list, do spot density background correction |
static Util |
util
instance of utility class |
static java.lang.String |
VERSION
Manually define Version number |
static java.lang.String |
xmlDate
XML accession file date "Date" |
static java.lang.String |
xmlDBname
XML accession file database name value for "DatabaseName" |
static java.lang.String |
xmlDir
Directory {projDir}/xml/ use to accession, landmark, SSF, SPF, CSD and other database files. |
| Constructor Summary | |
|---|---|
Accglb()
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| Method Summary | |
|---|---|
static void |
initGlb()
initGlb() - intialize any resources that must be set upon startup [TODO] Could move some of the above static defs here... |
static void |
resetGlb()
resetGlb() - reset any resources that must be reset for the next run of the program. |
static void |
showReportStatus(java.lang.String opr)
showReportStatus() - display the msg in popup report line display And update the timer for the opr |
| Methods inherited from class java.lang.Object |
|---|
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
| Field Detail |
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public static Accession cs
public static final java.lang.String applicationName
static boolean PUBLISH
static boolean USE_DEMO_DATA
static boolean ADD_WINDUMP
static boolean ALLOW_SAVE_DB
static boolean ALLOW_CALIBRATION
public static final boolean DBUG_APPEND
public static boolean DBUG_SWITCHES
public static final boolean DBUG_CONSOLE
public static java.lang.String DATE
public static java.lang.String REVISION
public static java.lang.String VERSION
public static boolean NEVER
public static boolean CONSOLE_FLAG
static final int MAX_WEDGE_STEPS
public static final java.lang.String accessionURL
public static java.lang.String[] jarFileList
public static java.lang.String[] jarLibrFileList
public static java.lang.String[] docFileList
public static java.lang.String[] demoFileList
public static final int DBUG_SWITCH_ANALYSIS
public static final int DBUG_PRINT_AT
public static final int DBUG_FREE_04
public static final int DBUG_FREE_020
public static final int DBUG_FREE_040
public static final int DBUG_FREE_0100
public static final int DBUG_FREE_0200
public static final int DBUG_FREE_0400
public static final int DBUG_FREE_01000
public static final int DBUG_FREE_02000
public static final int DBUG_FREE_04000
public static final int DBUG_FREE_010000
public static final int DBUG_FREE_020000
public static final int DBUG_FREE_040000
public static final int DBUG_FREE_0100000
public static final int DBUG_MAIN
public static final int DBUG_FREE_0400000
public static final int DBUG_FREE_01000000
public static final int DBUG_FREE_02000000
public static final java.lang.String dbugBitsHelpStr
public static final int OPTBKGROUND
public static final int RSAMPLE
public static final int SAMPLE
public static int spfFormatMode
public static int ssfFormatMode
public static int accFormatMode
public static DbAccession acc
public static AccData data
public static AccIni ini
public static FileIO fio
public static PixReader pix
public static Util util
public static AccReportPopup pra
public static DbSample dbRsample
public static DbSample dbSample
public static java.lang.String bannerTitle
public static java.lang.String banner
public static java.lang.String rsampleName
public static java.lang.String sampleName
public static final java.lang.String[] legalImageFileExtens
public static java.lang.String accDatabaseFile
public static java.lang.String accFile
public static java.lang.String xmlDBname
public static java.lang.String xmlDate
public static java.lang.String ssfFileRsample
public static java.lang.String ssfFileSample
public static boolean needToSaveAccessionDataFlag
public static boolean changedAccDBnameFlag
public static java.lang.String propertiesFile
public static java.lang.String pixFileExtn
public static java.lang.String simplePixFileRsample
public static java.lang.String simplePixFileSample
public static java.lang.String inPixFileRsample
public static java.lang.String inPixFileSample
public static java.lang.String ssfInputFileRsample
public static java.lang.String ssfInputPrefaceFileRsample
public static java.lang.String ssfInputEpilogueFileRsample
public static java.lang.String ssfInputFileSample
public static java.lang.String ssfInputPrefaceFileSample
public static java.lang.String ssfInputEpilogueFileSample
public static java.lang.String osName
public static java.lang.String fileSeparator
public static java.lang.String userDir
public static java.lang.String projDir
public static java.lang.String batchDir
public static java.lang.String cacheDir
public static java.lang.String ppxDir
public static java.lang.String rdbmsDir
public static java.lang.String tmpDir
public static java.lang.String xmlDir
public static java.lang.String[] argsV
public static java.lang.String[] sw
public static int nSwitches
public static boolean useAccFileSwitch
public static boolean makeBkupCopyFlag
public static boolean debugSwitch
public static boolean defaultSwitch
public static boolean demoSwitch
public static boolean dtdSwitch
public static boolean inputFormatSwitch
public static boolean projDirSwitch
public static boolean propertiesFileSwitch
public static boolean rsampleSwitch
public static boolean sampleSwitch
public static boolean timerSwitch
public static boolean updateSwitch
public static boolean usageSwitch
public static int dBugBits
public static int[] dbugBitValues
public static java.lang.String[] dbugBitName
public static int ssfCWX1
public static int ssfCWY1
public static int ssfCWX2
public static int ssfCWY2
public static float fourSqrtPi
public static int distLatchThr
public static int spotBoxSize
public static boolean useCommonSpotSizeFlag
public static boolean useSpotBkbrdCorrectionFlag
sp.densityPrime= sp.density - (sp.area*sp.mnBackground).
Use sp.densityPrime rather than sp.density in computing the
calibration by spot list.
public static boolean sortSpotListFlag
public static DbSpot bkgrdSpot
public static long startTime
static java.lang.String[] switchOptData
static boolean[] switchOptCBvalue
static java.lang.String[] switchOptValue
| Constructor Detail |
|---|
public Accglb()
| Method Detail |
|---|
public static void initGlb()
public static void resetGlb()
public static void showReportStatus(java.lang.String opr)
opr - to display
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