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java.lang.Object Seg2Dgel.Sg2glb
public class Sg2glb
Class Sg2glb is the base class that specifies global variables used by all of the other Seg2Dgel 2D gel segmenter classes.
This code was derived and refactored from GELLABII sg2gii C language 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 if exists which is xmlDir+accFile 
static boolean 
accDatabaseSwitch
The parsed of Command line + gel.rc state switches 
static java.lang.String 
accFile
Accession database file if exists 
static int 
accFormatMode
Accession file input file format mode set by the command line switch accessionDB:accession.txt or accessionDB:accession.xml This then gets mapped to either FileIO.IO_FORMAT_XML or IO_FORMAT_TAB_DELIMITED. 
static boolean 
allowTouchingEdgesSwitch
The parsed of Command line + gel.rc state switches 
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 boolean 
averageODSwitch
The parsed of Command line + gel.rc state switches 
static Sg2avg 
avg

static java.lang.String 
avgPixFile
tmp/average image file 
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 
baseImageFileName
Base file name is the original gel input image file without the directory and WITHOUT the file extension. 
static long 
baseStatusTime
base starting time in epoch msec time for the status reports 
static java.lang.String 
batchDir
Batch temporary data files used in exec'ing pipeline modules directory {projDir}/batch/ 
static int[] 
bfav
Average buffered images  unsigned 16bit line buffers [0:pixWidth1] 
static int[] 
bfavm
Average buffered images  unsigned 16bit line buffers [0:pixWidth1] 
static int[] 
bfavm1
Average buffered images  unsigned 16bit line buffers [0:pixWidth1] 
static int[] 
bfavp
Average buffered images  unsigned 16bit line buffers [0:pixWidth1] 
static int[] 
bfavp1
Average buffered images  unsigned 16bit line buffers [0:pixWidth1] 
static int[] 
bfog
Input image  16bit unsigned char in int[] line buffers for buffered images [0:pixWidth1] 
static int[] 
bfogm
Input image  16bit unsigned char in int[] line buffers for buffered images [0:pixWidth1] 
static int[] 
bfogm1
Input image  16bit unsigned char in int[] line buffers for buffered images [0:pixWidth1] 
static int[] 
bfogm2
Input image  16bit unsigned char in int[] line buffers for buffered images [0:pixWidth1] 
static int[] 
bfogm3
Input image  16bit unsigned char in int[] line buffers for buffered images [0:pixWidth1] 
static int[] 
bfogm4
Input image  16bit unsigned char in int[] line buffers for buffered images [0:pixWidth1] 
static int[] 
bfogm5
Input image  16bit unsigned char in int[] line buffers for buffered images [0:pixWidth1] 
static int[] 
bfogp
Input image  16bit unsigned char in int[] line buffers for buffered images [0:pixWidth1] 
static int[] 
bfogp1
Input image  16bit unsigned char in int[] line buffers for buffered images [0:pixWidth1] 
static int[] 
bfogp2
Input image  16bit unsigned char in int[] line buffers for buffered images [0:pixWidth1] 
static int[] 
bfogp3
Input image  16bit unsigned char in int[] line buffers for buffered images [0:pixWidth1] 
static int[] 
bfogp4
Input image  16bit unsigned char in int[] line buffers for buffered images [0:pixWidth1] 
static int[] 
bfogp5
Input image  16bit unsigned char in int[] line buffers for buffered images [0:pixWidth1] 
static Sg2bkg 
bkg

static int 
BKGRD_CODE
pixel code for the CC background pixel 
static boolean 
bkgrdCorrectionSwitch
The parsed of Command line + gel.rc state switches 
static java.lang.String 
bkgrdPixFile
tmp/notch filter background image file 
static boolean 
bkgrdSizeFlag
The parsed of Command line + gel.rc state switches 
static int 
BLACK
Pixel color for black 
static boolean 
boundaryInSSFSwitch
The parsed of Command line + gel.rc state switches 
static int[] 
bufbkg
Background buffered image  unsigned 16bit line buffer [0:pixWidth1] 
static int[] 
bufcc
Restof buffered image  unsigned 16bit line buffer [0:pixWidth1] 
static int[] 
bufmag
Magnitude buffered image  unsigned 16bit line buffer [0:pixWidth1] 
static int[] 
bufrest
Restof buffered image  unsigned 16bit line buffer [0:pixWidth1] 
static int 
c11
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c12
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c13
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c14
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c15
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c16
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c17
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c18
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c19
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c1a
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c1b
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c1c
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c1d
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c1e
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c1f
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c1g
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c1h
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c21
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c22
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c23
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c24
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c25
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c26
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c27
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c28
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c29
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c2a
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c2b
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c2c
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c2d
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c2e
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c2f
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c2g
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c2h
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c31
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c32
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c33
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c34
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c35
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c36
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c37
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c38
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c39
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c3a
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c3b
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c3c
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c3d
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c3e
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c3f
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c3g
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c3h
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c41
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c42
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c43
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c44
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c45
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c46
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c47
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c48
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c49
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c4a
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c4b
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c4c
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c4d
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c4e
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c4f
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c4g
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c4h
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c51
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c52
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c53
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c54
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c55
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c56
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c57
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c58
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c59
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c5a
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c5b
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c5c
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c5d
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c5e
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c5f
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c5g
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c5h
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c61
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c62
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c63
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c64
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c65
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c66
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c67
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c68
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c69
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c6a
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c6b
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c6c
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c6d
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c6e
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c6f
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c6g
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c6h
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c71
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c72
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c73
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c74
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c75
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c76
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c77
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c78
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c79
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c7a
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c7b
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c7c
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c7d
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c7e
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c7f
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c7g
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c7h
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c81
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c82
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c83
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c84
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c85
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c86
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c87
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c88
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c89
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c8a
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c8b
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c8c
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c8d
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c8e
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c8f
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c8g
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c8h
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c91
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c92
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c93
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c94
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c95
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c96
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c97
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c98
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c99
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c9a
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c9b
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c9c
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c9d
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c9e
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c9f
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c9g
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
c9h
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
ca1
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
ca2
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
ca3
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
ca4
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
ca5
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
ca6
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
ca7
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
ca8
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
ca9
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
caa
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
cab
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
cac
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static java.lang.String 
cacheDir
Cache database directory {projDir}/cache/ 
static int 
cad
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
cae
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
caf
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
cag
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
cah
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static CalibrateOD 
cal

static int[] 
cal2gray
map pixel gray values to calibration value (e.g., OD) by scaling it as: OD*1000 to gray Size [0:maxGrayPixel] 
static java.lang.String 
calFile
[DEPRICATE] cal/<.cal calibration file> 
static int 
cb1
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
cb2
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
cb3
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
cb4
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
cb5
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
cb6
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
cb7
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
cb8
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
cb9
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
cba
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
cbb
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
cbc
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
cbd
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
cbe
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
cbf
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
cbg
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
cbh
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static Sg2cc 
cc

static int 
cc1
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
cc2
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
cc3
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
cc4
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
cc5
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
cc6
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
cc7
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
cc8
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
cc9
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
cca
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
ccb
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
ccc
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
ccd
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
cce
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
ccf
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
ccg
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
cch
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
ccMinSize
Parameter threshold min # pixels/CC spot 
static boolean 
ccMinSizeSwitch
The parsed of Command line + gel.rc state switches 
static int 
ccNum
initial central core spot number 
static java.lang.String 
ccPixFile
tmp/central core image file 
static int 
cd1
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
cd2
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
cd3
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
cd4
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
cd5
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
cd6
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
cd7
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
cd8
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
cd9
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
cda
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
cdb
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
cdc
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
cdd
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
cde
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
cdf
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
cdg
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static int 
cdh
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood 
static boolean 
computingWindowSwitch
The parsed of Command line + gel.rc state switches 
static char 
coneOfSilenceMode
The filter type set by the command line switch laplacian:B,{PC}, 
static boolean 
CONSOLE_FLAG

static boolean 
ctlCorePixSwitch
The parsed of Command line + gel.rc state switches 
static int 
cwx1
ULHC X computing window for entire input gel image 
static int 
cwx2
LRHC X computing window for entire input gel image 
static int 
cwy1
ULHC Y computing window for entire input gel image 
static int 
cwy2
LRHC Y computing window for entire input gel image 
static Sg2data 
data

static java.lang.String 
DATE
CVS Version date 
static DbSample 
dbSample
Current sample being analyzed 
static DbSpot 
dbSpot
Current spot being analyzed 
static Sg2dbug 
dbug

static int 
DBUG_ADD_INTERIOR_CC_PIXELS
Trace inner loop of addInteriorCCpixels() to 
static int 
DBUG_BND_ANALYSIS
Trace findBoundary(), pushXYboundary(), resetBnd() 
static int 
DBUG_CALC_FEATURES
Trace calcFeatures() where compute spot values from the images & FBL 
static int 
DBUG_CHAIN_CODE_RLM_ANALYSIS
Trace pairChainCodeNotches(), findMinMaxPeaksInRLM()and findPairedNotches_in_RLM() 
(package private) static boolean 
DBUG_CONSOLE
Debugging console text flag 
static int 
DBUG_CVT_BND_TO_CHAINCODE
Trace cvtBoundaryToChainCode(), cvtChainCode_to_nextXY() 
static int 
DBUG_DRAW_NOTCH_PAIR_LINE
Trace drawLineBetweenNotchPair() to 
static int 
DBUG_DRAW_SAT_SPOT_BND
Trace draw boundary of saturated spot CC 
static int 
DBUG_DUMP_CC_PPX
Trace dump CC images at key points if enabled in code 
static int 
DBUG_FILL_CORNERS
Trace fillCorners() to fill corners in the current PCC 
static int 
DBUG_FILL_HOLES_IN_PCC_CONCAVITIES
Trace fillHolesInPCCconcavities() to filler corners in PCC concavities 
static int 
DBUG_FIND_BND_NOTCHES_IN_CHAIN_CODE
Trace findNotches_in_chainCode() to 
static int 
DBUG_FIND_SPOT_LIST
Trace findSpotList() to find spots 
static int 
DBUG_INNER_LOOP_FIND_SPOT
Trace inner loop of findSpot() to 
static int 
DBUG_MAX_PROPAGATE
Trace maxPropagate() to expand from the CC to the PCC 
static int 
DBUG_NBR_COMPONENTS
Trace numberComponents() to number components in the central core 
static int 
DBUG_PIX_DBCODE
Trace dbugPixDBcode() to print small NxN pixel windows that match the [dbx1:dbx2, dby1:dby2] window. 
static int 
DBUG_PRINT_GRAY2CAL_MAP
Trace print gray2cal[] to print the gray2cal[] map 
static int 
DBUG_PROP_SAT_SPOTS
Trace propSaturatedSpot() to 
static int 
DBUG_PROP_SPOT_TO_2ND_MAXIMA
Trace propSpotTo2ndDrivMaxima() to prop CC to 2nd maxima to make PCC 
static int 
DBUG_PUSH_XY_INTO_FBL
Trace pushXYintoFBL() to 
static int 
DBUG_RMV_CONCAVITIES
Trace rmvConcavities() to remove concavities in the central core 
static int 
DBUG_RMV_INTERIOR_CC_PIXELS
Trace inner loop of rmvInteriorCCpixels() to 
static int 
DBUG_ROUND_CORNERS
Trace roundCorners() to round corners of the PCC 
static int 
DBUG_SPLIT_CHECK_SPOT
Trace splitCheckSpot() to check and split a spot if it is needed 
static int 
DBUG_SPLIT_PIX_BY_FBL_BND_ANALSIS
Trace splitPixByFBLboundaryAnal() to 
static boolean 
DBUG_SWITCHES
Debugging switches 
static int 
dbugBits
Parameter threshold DEBUG:bits 
static java.lang.String 
dbugBitsHelpStr
Debug bit options help for error messages 
static boolean 
dbugBitsPixFlag
Special test for DBUG_PIX_NXN bit to to print windows that match the [dbx1:dbx2, dby1:dby2] window. 
static int 
dbx1
Debugging window for debug: window 
static int 
dbx2
Debugging window for debug: window 
static int 
dby1
Debugging window for debug: window 
static int 
dby2
Debugging window for debug: window 
static boolean 
debugSwitch
The parsed of Command line + gel.rc state switches 
static boolean 
defaultSwitch
The parsed of Command line + gel.rc state switches 
static int 
defaultTypeCode
Default type for default: 
static boolean 
deleteIsolatedPixelsSwitch
The parsed of Command line + gel.rc state switches 
static java.lang.String[] 
demoFileList
List of demo/ files downloadable from the server 
static boolean 
demoSwitch
The parsed of Command line + gel.rc state switches 
static int 
DFT_2D_GEL
Default data type 2Dgel 
static int 
DFT_2D_LC_MS
Default data type 2DLCMS 
static int 
DFT_NO_DB
Default data type Nodatabase 
static boolean 
didPropSaturatedSpots
For debugging  to avoid repropagating split spots 
static boolean 
didSplitSpotFlag
For debugging  to abort seg and dump intermediate images. 
static boolean 
diffODSwitch
The parsed of Command line + gel.rc state switches 
static java.lang.String[] 
docFileList
List of documentation files downloadable from the server 
static boolean 
dotsSwitch
The parsed of Command line + gel.rc state switches 
static int 
dpx1
Debugging window for pixdump: window 
static int 
dpx2
Debugging window for pixdump: window 
static int 
dpy1
Debugging window for pixdump: window 
static int 
dpy2
Debugging window for pixdump: window 
static Sg2draw 
draw

static char 
drawBoundaryOverlayType
The drawing overlay type is set by the command line switch drawBoundaryt:{O  Z} 
static boolean 
drawBoundarySwitch
The parsed of Command line + gel.rc state switches 
static char 
drawDotOverlayType
The drawing overlay type is set by the command line switch drawDot:{O  Z} 
static char 
drawMEROverlayType
The drawing overlay type is set by the command line switch drawMinEnclRect:{O  Z} 
static boolean 
drawMERSwitch
The parsed of Command line + gel.rc state switches 
static char 
drawPlusOverlayType
The drawing overlay type is set by the command line switch drawPlus:{O  Z} 
static boolean 
drawPlusSwitch
The parsed of Command line + gel.rc state switches 
static boolean 
drawSxSyEllipseSwitch
The parsed of Command line + gel.rc state switches 
static char 
drawSxSyOverlayType
The drawing overlay type is set by the command line switch drawSxSyEllipse:{O  Z} 
static boolean 
drawTitleSwitch
The parsed of Command line + gel.rc state switches 
static boolean 
dtdSwitch
The parsed of Command line + gel.rc state switches 
(package private) static boolean 
ENABLE_DEVELOPER_DEBUGGING
Enable developer debugging when do initial startup. 
(package private) static boolean 
ENABLE_SATURATED_SPOTS
Enable debugging saturatedSpots analysis 
(package private) static boolean 
ENABLE_SPOT_SPLITTING
Enable debugging splitSpots analysis 
static Sg2fbl 
fbl

static java.lang.String 
fileSeparator
File separator: Property("file.separator") 
static FileIO 
fio

static Sg2fnd 
fnd

static float 
fourSqrtPi
Constant 4*sqrt(PI) constant used in computing spot volume 
static int[] 
gHist
Histogram of pix4 AVERAGE Size [0:maxGrayPixel+1] 
static float 
glbPercentThr
Parameters and thresholds 
static int[] 
gray2cal

static int 
gridSize
Parameter threshold grid size i.e. 
static Sg2hash 
hashFBL
Hash table for FBL used to quickly determine if an (x,y) coord is in the FBL. 
static int 
HASHFBLPRIME
Initial prime #size of Final Blob List (FBL) hash table. 
static Sg2hash 
hashWS
Hash table for WS used to quickly determine if an (x,y) coord is in the Working Stack (WS). 
static float 
histThreshold
Parameters and thresholds 
static int 
i0R
Extended 5x5 neighborhood for 3x3 'Busse' filter 
static int 
i10
Gray scale intensity 3X3 neighborhood 
static int 
i11
Gray scale intensity 3X3 neighborhood 
static int 
i12
Gray scale intensity 3X3 neighborhood 
static int 
i13
Gray scale intensity 3X3 neighborhood 
static int 
i14
Gray scale intensity 3X3 neighborhood 
static int 
i15
Gray scale intensity 3X3 neighborhood 
static int 
i16
Gray scale intensity 3X3 neighborhood 
static int 
i17
Gray scale intensity 3X3 neighborhood 
static int 
i18
Gray scale intensity 3X3 neighborhood 
static int 
i2U
Extended 5x5 neighborhood for 3x3 'Busse' filter 
static int 
i4L
Extended 5x5 neighborhood for 3x3 'Busse' filter 
static int 
i6D
Extended 5x5 neighborhood for 3x3 'Busse' filter 
static Sg2ini 
ini

static java.lang.String 
inPixFile
original gel input image file with full path and .tif, .tiff, .jpg, .gif or .ppx file extensions. 
static int 
ISOLATED_PIXEL_CODE
pixel code for guard region splitting previously merged spots 
static int 
j11
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j12
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j13
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j14
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j15
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j16
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j17
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j18
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j19
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j1a
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j1b
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j1c
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j1d
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j1e
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j1f
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j1g
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j1h
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j21
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j22
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j23
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j24
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j25
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j26
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j27
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j28
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j29
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j2a
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j2b
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j2c
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j2d
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j2e
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j2f
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j2g
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j2h
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j31
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j32
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j33
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j34
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j35
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j36
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j37
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j38
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j39
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j3a
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j3b
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j3c
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j3d
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j3e
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j3f
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j3g
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j3h
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j41
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j42
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j43
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j44
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j45
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j46
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j47
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j48
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j49
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j4a
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j4b
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j4c
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j4d
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j4e
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j4f
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j4g
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j4h
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j51
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j52
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j53
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j54
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j55
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j56
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j57
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j58
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j59
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j5a
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j5b
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j5c
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j5d
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j5e
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j5f
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j5g
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j5h
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j61
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j62
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j63
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j64
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j65
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j66
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j67
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j68
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j69
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j6a
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j6b
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j6c
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j6d
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j6e
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j6f
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j6g
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j6h
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j71
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j72
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j73
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j74
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j75
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j76
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j77
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j78
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j79
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j7a
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j7b
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j7c
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j7d
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j7e
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j7f
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j7g
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j7h
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j81
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j82
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j83
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j84
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j85
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j86
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j87
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j88
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j89
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j8a
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j8b
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j8c
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j8d
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j8e
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j8f
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j8g
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j8h
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j91
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j92
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j93
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j94
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j95
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j96
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j97
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j98
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j99
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j9a
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j9b
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j9c
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j9d
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j9e
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j9f
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j9g
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
j9h
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
ja1
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
ja2
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
ja3
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
ja4
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
ja5
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
ja6
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
ja7
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
ja8
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
ja9
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
jaa
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
jab
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
jac
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
jad
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
jae
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
jaf
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
jag
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
jah
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static java.lang.String[] 
jarFileList
List of .jar files downloadable from the server 
static java.lang.String[] 
jarLibrFileList
List of library .jar files downloadable from the server 
static int 
jb1
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
jb2
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
jb3
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
jb4
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
jb5
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
jb6
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
jb7
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
jb8
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
jb9
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
jba
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
jbb
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
jbc
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
jbd
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
jbe
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
jbf
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
jbg
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
jbh
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
jc1
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
jc2
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
jc3
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
jc4
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
jc5
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
jc6
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
jc7
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
jc8
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
jc9
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
jca
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
jcb
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
jcc
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
jcd
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
jce
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
jcf
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
jcg
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
jch
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
jd1
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
jd2
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
jd3
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
jd4
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
jd5
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
jd6
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
jd7
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
jd8
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
jd9
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
jda
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
jdb
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
jdc
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
jdd
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
jde
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
jdf
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
jdg
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static int 
jdh
Grayscale intensity data for other filters for up to a 13x17 neighborhood 
static boolean 
keepInputImageSwitch
The parsed of Command line + gel.rc state switches 
static int 
KILL_SPOT_CODE
pixel code for deleted spot in central core if NEQ sizing (0 if noDelete) 
static int 
killSpotColor
Spot color used for deleted spots. 
static boolean 
laplacianSwitch
The parsed of Command line + gel.rc state switches 
static java.lang.String[] 
legalImageFileExtens
List of legal gel image file extensions 
static int 
lineLaplacianHeight
Height for laplacian:L, 
static int 
lineLaplacianWidth
Width for laplacian:{HV}, 
static int 
lowPassSize
The low pass filter width (3x3, 5x5, 7x7, 13x17(13)) lowpassFilter: 
static boolean 
lowpassSwitch
The parsed of Command line + gel.rc state switches 
static boolean 
lp13xZZSwitch
The parsed of Command line + gel.rc state switches 
static boolean 
lp3x3Switch
The parsed of Command line + gel.rc state switches 
static boolean 
lp5x5Switch
The parsed of Command line + gel.rc state switches 
static boolean 
lp7x7Switch
The parsed of Command line + gel.rc state switches 
static java.lang.String 
mag2ndPixFile
tmp/magnitude of 2nd directive image file 
static int 
MAX_BUFFERED_SPOTS
max # spots to buffer in memory when converting the list of spots to string representations. 
static int 
MAX_CC_CODE
pixel code for maximum labeled central core (CC) pixel 
static int 
MAX_INTERIOR_FBL_SIZE
Max interior of spot size. 
static int 
MAX_PCC_CODE
pixel code for maximum labeled propagated central core (PCC) pixel 
static int 
maxColsToPrint
Parameter threshold max # cols width to print winDump 
static int 
maxGhist
Histogram statistics [for use in FUTURE] 
static int 
maxGrayPixel
max Gray Pixel value in the image is (1< 
static int 
MAXSUBSPOTS
max # subspots a spot can split into 
static int 
meanGhist
Histogram statistics [for use in FUTURE] 
static int 
merx1
The final spot minimum enclosing rectangle captured when computeFeatures() when it copies the mer[xy]p[12] data that is then copied to the mer[xy][12] 
static int 
merx2
The final spot minimum enclosing rectangle captured when computeFeatures() when it copies the mer[xy]p[12] data that is then copied to the mer[xy][12] 
static int 
merxp1
Working minimum enclosing rectangle created as we do saveFPL() or pushFBL() calls. 
static int 
merxp2
Working minimum enclosing rectangle created as we do saveFPL() or pushFBL() calls. 
static int 
mery1
The final spot minimum enclosing rectangle captured when computeFeatures() when it copies the mer[xy]p[12] data that is then copied to the mer[xy][12] 
static int 
mery2
The final spot minimum enclosing rectangle captured when computeFeatures() when it copies the mer[xy]p[12] data that is then copied to the mer[xy][12] 
static int 
meryp1
Working minimum enclosing rectangle created as we do saveFPL() or pushFBL() calls. 
static int 
meryp2
Working minimum enclosing rectangle created as we do saveFPL() or pushFBL() calls. 
static int 
MHISTSIZE
Size of histogram for splitting algorithm 
static int 
MIN_CC_CODE
pixel code for minimum labeled central core (CC) pixel 
static int 
MIN_PCC_CODE
pixel code for minimum labeled propagated central core (PCC) pixel 
static int 
MINBLOBAREA
used in findAllSpots() 
static int 
minGhist
Histogram statistics [for use in FUTURE] 
static int 
MINSPLITSPOTSIZE
Minimum spot CC size of spot for it to be allowed to be a candidate for spot splitting. 
static int 
nBitsPerPixel
# of bits/pixel in the image 
static int 
nBkgrdSize
Parameter threshold background:32, Size of sq. 
static int 
nBytesPerPixel
# of bytes/pixel in the image 
static boolean 
NEVER
NEVER and CONSOLE_FLAG  debugging variables  must not be final! 
static Sg2ngh 
ngh

static Sg2notch 
notch

static int 
nPixels
total # of pixels in image = pixWidth*pixHeight 
static int 
nStatusName
# of Report status names saved when do util.showReportStatus(name) calls. 
static int 
nSwitches
the number of Command line + gel.rc state switches 
static boolean 
optimizeInteriorFBLSwitch
The parsed of Command line + gel.rc state switches 
static java.lang.String 
osName
name of this operating system: Property("os.name") 
static ParamHash 
paramH

static int 
PCC_BASE_CODE
pixel code for guard region splitting previously merged spots 
static PixReader 
pix

static char[] 
pix1
original gel image 16bit unsigned char in int[], or nBitsPerPixel scaled to 16bits. 
static char[] 
pix2
magnitude Laplacian image with mag2ndPixFile. 
static char[] 
pix3
central core image with ccPixFile. 
static char[] 
pix4
Averaged gel image after gaussian smoothing with avgPixFile. 
static char[] 
pix5
Segmented spots output Z image with no background with segPixFile. 
static char[] 
pix6
Background OD image with bkgrdPixFile. 
static char[] 
pix7
Restof output image with restOfPixFile. 
static java.lang.String 
pixDir
Original image directory used in picking off project diredctory. 
static boolean 
pixDumpSwitch
The parsed of Command line + gel.rc state switches 
static float 
pixelSizeMicrons
Pixel resolution in the gel image in microns/pixel 
static java.lang.String 
pixFileExtn
Output images are either ".gif" or ".jpg" [TODO] change this to .jpg with JPEG writer. 
static int 
pixHeight
Input gel image size: height 
static int 
pixWidth
Input gel image size: width 
static java.lang.String 
ppxDir
Original sample images directory {projDir}/ppx/ 
static Sg2reportPopup 
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 + gel.rc state switches 
static java.lang.String 
propertiesFile
Current startup properties file containing default switches if it exists. 
static boolean 
propertiesFileSwitch
The parsed of Command line + gel.rc state switches 
static int 
pTileGhist
Histogram statistics [for use in FUTURE] 
(package private) static boolean 
PUBLISH
NOTE: overide the following debugging options if publishing on net. 
static boolean 
quickEstimateSwitch
The parsed of Command line + gel.rc state switches 
static java.lang.String 
rdbmsDir
RDBMS database directory {projDir}/rdbms/ 
static Sg2rest 
rest

static java.lang.String 
restOfPixFile
tmp/central core image file 
static boolean 
restOfPixSwitch
The parsed of Command line + gel.rc state switches 
static java.lang.String 
REVISION
CVS Revision 
static java.lang.String 
rlmCWfile
tmp/RML CW file 
static boolean 
rmvDprimeSizingSwitch
The parsed of Command line + gel.rc state switches 
static boolean 
sampleSwitch
The parsed of Command line + gel.rc state switches 
static Sg2sat 
sat

static boolean 
saturatedSpotSwitch
The parsed of Command line + gel.rc state switches 
static int 
scaledMaxOD
This is the max value index for cal2gray[] it is computed as cal2gray.length1 
static java.lang.String 
seg2dgelURL
Hardwired Open2Dprot server connection Switch to S.F. 
static java.lang.String 
segPixFile
tmp/segmented image image file 
static boolean 
segPixSwitch
The parsed of Command line + gel.rc state switches 
static Seg2Dgel 
sg2

static java.lang.String 
simpleFileName
Simple file name is the original gel input image file without the directory and WITH the file extension. 
static float 
sizeFractionGaussianWidth
Parameters and thresholds 
static Sort 
sort

static Sg2split 
split

static boolean 
splitLargeCCfblByBndAnalSwitch
The parsed of Command line + gel.rc state switches 
static boolean 
splitLargeCCfblByRLManalSwitch
The parsed of Command line + gel.rc state switches 
static boolean 
splitLargeCCfblByThreshAnalSwitch
The parsed of Command line + gel.rc state switches 
static int 
splitMinCCsize
Parameter threshold lower CC bound for splitting spots 
static boolean 
splitSpotSwitch
The parsed of Command line + gel.rc state switches 
static int 
spotNumber
initial spot number 
static int 
ssfFormatMode
SSF output file format mode set by the command line switch ssfFormat:<{FLTX}> where mode is either 'F', 'L', 'T' or 'X'. 
static boolean 
ssfFormatSwitch
The parsed of Command line + gel.rc state switches 
static java.lang.String 
ssfOutputEpilogueFile
full tabdelim EPILOGUE xml/ Sample Spotlist File full path 
static java.lang.String 
ssfOutputFile
xml/ Sample Spotlist File full path 
static java.lang.String 
ssfOutputPrefaceFile
full tabdelim PREFACE xml/ Sample Spotlist File full path 
static long 
startTime
starting time in epoch msec time 
static long[] 
statusMemoryFree
Report status memory Free. 
static long[] 
statusMemoryTot
Report status memory Total. 
static java.lang.String[] 
statusName
Report status names saved when do util.showReportStatus(name) calls. 
static long[] 
statusStartTime
Report status starting times entries in epoch msec time Saved when do util.showReportStatus(name) calls. 
static java.lang.String[] 
sw
Command line + Seg2Dgel.properties state switches 
(package private) static boolean[] 
switchOptCBvalue
The switchOptcCBvalue[0:nData1] 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:nData1] is used by the Report Popup that in turn may call PopupOptions. 
static float 
t1Area
Parameter: Lower spot area sizing threshold thrArea:a1, 
static float 
t1Density
Parameter: Lower spot integrated density sizing threshold thrDensity:d1, 
static float 
t1Range
Parameter: Lower spot maxmin density sizing threshold thrRange:d1, 
static float 
t1SxSyRatio
Parameter: Lower spot Sx/Sy sizing threshold thrSxSyRatio:s1, 
static float 
t2Area
Parameter: Upper spot area sizing threshold thrArea:,a2 
static float 
t2Density
Parameter: Upper spot integrated density sizing threshold thrDensity:,d2 
static float 
t2Range
Parameter: Upper spot maxmin density sizing threshold thrRange:,d2 
static float 
t2SxSyRatio
Parameter: Upper spot mSx/Sy sizing threshold thrSxSyRatio:,s2 
static int 
TEST_LARGE_IMAGE
Temporary debugging flag for debugging specific large saturated images in findSpot() if this value is >0. 
static boolean 
thrAreaSwitch
The parsed of Command line + gel.rc state switches 
static boolean 
thrDensitySwitch
The parsed of Command line + gel.rc state switches 
static boolean 
thrRangeSwitch
The parsed of Command line + gel.rc state switches 
static boolean 
thrSxSyRatioSwitch
The parsed of Command line + gel.rc state switches 
static boolean 
timerSwitch
The parsed of Command line + gel.rc state switches 
static java.lang.String 
tmpDir
Tmp images directory {projDir}/tmp/ 
static int 
UNLABELED_CC_CODE
pixel code for unlabeled central core (CC)pixel 
static boolean 
updateSwitch
The parsed of Command line + gel.rc state switches 
static boolean 
usageSwitch
The parsed of Command line + gel.rc state switches 
static boolean 
USE_13X13
Use 13x17 or 13x13 filters  BUT NOT BOTH !!!!! 
static boolean 
USE_BKGD_AND_ISOLATED_PIXEL_BACKGROUND
Define background as a pixel as either BKGRD_CODE or ISOLATED_PIXEL_CODE otherwise it is just BKGRD_CODE. 
(package private) static boolean 
USE_DEMO_DATA
Use the demo data by enabling the demo flag and data. 
(package private) static boolean 
USE_DOM_XML_SSF
Use DOM/JDOM/... 
static boolean 
use3x3laplacianSwitch
The parsed of Command line + gel.rc state switches 
static boolean 
use5x5laplacianSwitch
The parsed of Command line + gel.rc state switches 
static boolean 
useBkgdAndIsolatedPixelFlag
Define background as a pixel as either BKGRD_CODE or ISOLATED_PIXEL_CODE otherwise it is just BKGRD_CODE. 
static boolean 
useBusseLaplacianSwitch
The parsed of Command line + gel.rc state switches 
static boolean 
useCopyOfPix1ForPix5Switch
The parsed of Command line + gel.rc state switches 
static boolean 
useHistGUISwitch
The parsed of Command line + gel.rc state switches 
static boolean 
useHorizLineLaplacianSwitch
The parsed of Command line + gel.rc state switches 
static boolean 
usePopupGUISwitch
The parsed of Command line + gel.rc state switches 
static java.lang.String 
userDir
current User directory: getProperty("user.dir")+fileSeparator 
static boolean 
useVertLineLaplacianSwitch
The parsed of Command line + gel.rc state switches 
static Util 
util

static java.lang.String 
VERSION
Manually define Version number 
static int 
WHITE
Pixel color for white 
static int 
widthWindmp
Parameter threshold windmp window size 
static int 
windmpStepSize
Parameter threshold windmp sampling size. 
static Sg2wrk 
wrk

static int 
wXsize
Width offset for threshold Gaussian filter size. 
static int 
wYsize
Height offset for threshold Gaussian filter size. 
static int 
xDbug
current spot being analyzed w/debug 
static java.lang.String 
xmlDir
Directory {projDir}/xml/ use to accession, landmark, SSF, SPF, CSD and other database files. 
static int[] 
xPentrance

static int[] 
xPexit

static int 
yDbug
current spot being analyzed w/debug 
static int[] 
yPentrance

static int[] 
yPexit

static int 
yTitle

Constructor Summary  

Sg2glb()

Method Summary  

static int 
get2D(char[] pix,
int x,
int y)
get2D()  get the pixel at pix(x,y) computed at (y+pixelWidth+x) 
static int 
get2D(int[] pix,
int x,
int y)
get2D()  get the pixel at pix(x,y) computed at (y+pixelWidth+x) 
static int[] 
getPixLineBuf(int[] lineBuf,
char[] pix,
int y)
getPixLineBuf()  get the line y from int[] pix into lineBuf[]. 
static int[] 
getPixLineBuf(int[] lineBuf,
int[] pix,
int y)
getPixLineBuf()  get the line y from int[] pix into lineBuf[]. 
static void 
initGlb()
initGlb()  intialize any resources that must be set upon startup [TODO] Could move some of the above static defs here... 
static boolean 
isDBwindow()
isDBwindow()  test if (xDbug,yDbug) is inside the debug window. 
static boolean 
isDBwindow(int x,
int y)
isDBwindow()  test if (x,y) is inside the debug window. 
static int 
put2Dbuf(int[] buf,
int x,
int g)
put2Dbuf()  save pixel value g at buf[x] 
static void 
resetGlb()
resetGlb()  reset any resources that must be reset for the next run of the segmenter. 
static int 
set2D(char[] pix,
int x,
int y,
int g)
set2D()  save the pixel value g at pix(x,y) computed at (y+pixelWidth+x) 
static int 
set2D(int[] pix,
int x,
int y,
int g)
set2D()  save the pixel value g at pix(x,y) computed at (y+pixelWidth+x) 
static boolean 
setPixLineBuf(int[] lineBuf,
char[] pix,
int y)
setPixLineBuf()  save the line y from int[] pix from lineBuf[] 
static boolean 
setPixLineBuf(int[] lineBuf,
int[] pix,
int y)
setPixLineBuf()  save the line y from int[] pix from lineBuf[] 
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 

public static final java.lang.String applicationName
static boolean PUBLISH
static boolean USE_DEMO_DATA
static boolean ENABLE_DEVELOPER_DEBUGGING
static boolean ENABLE_SPOT_SPLITTING
static boolean ENABLE_SATURATED_SPOTS
static boolean USE_DOM_XML_SSF
public static int TEST_LARGE_IMAGE
public static boolean DBUG_SWITCHES
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
public static final java.lang.String seg2dgelURL
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 MAX_BUFFERED_SPOTS
public static final int MAXSUBSPOTS
public static final int MAX_INTERIOR_FBL_SIZE
public static final int HASHFBLPRIME
public static final int MINSPLITSPOTSIZE
public static final int MHISTSIZE
public static final int MINBLOBAREA
public static final boolean USE_13X13
public static final int WHITE
public static final int BLACK
public static final boolean USE_BKGD_AND_ISOLATED_PIXEL_BACKGROUND
public static final int BKGRD_CODE
public static final int UNLABELED_CC_CODE
public static final int MIN_CC_CODE
public static final int MAX_CC_CODE
public static final int PCC_BASE_CODE
public static final int MIN_PCC_CODE
public static final int MAX_PCC_CODE
public static final int KILL_SPOT_CODE
public static final int ISOLATED_PIXEL_CODE
public static final int DFT_NO_DB
public static final int DFT_2D_GEL
public static final int DFT_2D_LC_MS
public static final int DBUG_PIX_DBCODE
public static final int DBUG_FIND_SPOT_LIST
public static final int DBUG_PROP_SAT_SPOTS
public static final int DBUG_SPLIT_CHECK_SPOT
public static final int DBUG_RMV_CONCAVITIES
public static final int DBUG_NBR_COMPONENTS
public static final int DBUG_MAX_PROPAGATE
public static final int DBUG_FILL_CORNERS
public static final int DBUG_FILL_HOLES_IN_PCC_CONCAVITIES
public static final int DBUG_ROUND_CORNERS
public static final int DBUG_PROP_SPOT_TO_2ND_MAXIMA
public static final int DBUG_PRINT_GRAY2CAL_MAP
public static final int DBUG_RMV_INTERIOR_CC_PIXELS
public static final int DBUG_CALC_FEATURES
public static final int DBUG_ADD_INTERIOR_CC_PIXELS
public static final int DBUG_INNER_LOOP_FIND_SPOT
public static final int DBUG_SPLIT_PIX_BY_FBL_BND_ANALSIS
public static final int DBUG_BND_ANALYSIS
public static final int DBUG_CVT_BND_TO_CHAINCODE
public static final int DBUG_FIND_BND_NOTCHES_IN_CHAIN_CODE
public static final int DBUG_CHAIN_CODE_RLM_ANALYSIS
public static final int DBUG_DRAW_NOTCH_PAIR_LINE
public static final int DBUG_PUSH_XY_INTO_FBL
public static final int DBUG_DRAW_SAT_SPOT_BND
public static final int DBUG_DUMP_CC_PPX
public static final java.lang.String dbugBitsHelpStr
public static Seg2Dgel sg2
public static Sg2avg avg
public static Sg2bkg bkg
public static Sg2cc cc
public static Sg2data data
public static Sg2dbug dbug
public static Sg2draw draw
public static Sg2fbl fbl
public static Sg2fnd fnd
public static Sg2ini ini
public static Sg2ngh ngh
public static Sg2notch notch
public static Sg2rest rest
public static Sg2sat sat
public static Sg2split split
public static Sg2wrk wrk
public static CalibrateOD cal
public static DbAccession acc
public static DbSample dbSample
public static DbSpot dbSpot
public static FileIO fio
public static ParamHash paramH
public static PixReader pix
public static Sort sort
public static Util util
public static Sg2reportPopup pra
public static java.lang.String bannerTitle
public static java.lang.String banner
public static final java.lang.String[] legalImageFileExtens
public static java.lang.String accFile
public static java.lang.String accDatabaseFile
public static java.lang.String propertiesFile
public static java.lang.String pixFileExtn
public static java.lang.String inPixFile
public static java.lang.String simpleFileName
public static java.lang.String baseImageFileName
public static java.lang.String avgPixFile
public static java.lang.String calFile
public static java.lang.String ccPixFile
public static java.lang.String mag2ndPixFile
public static java.lang.String bkgrdPixFile
public static java.lang.String segPixFile
public static java.lang.String restOfPixFile
public static java.lang.String ssfOutputFile
public static java.lang.String ssfOutputPrefaceFile
public static java.lang.String ssfOutputEpilogueFile
public static java.lang.String rlmCWfile
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 pixDir
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 accDatabaseSwitch
public static boolean allowTouchingEdgesSwitch
public static boolean averageODSwitch
public static boolean bkgrdSizeFlag
public static boolean bkgrdCorrectionSwitch
public static boolean boundaryInSSFSwitch
public static boolean ccMinSizeSwitch
public static boolean ctlCorePixSwitch
public static boolean computingWindowSwitch
public static boolean debugSwitch
public static boolean defaultSwitch
public static boolean demoSwitch
public static boolean drawTitleSwitch
public static boolean diffODSwitch
public static boolean deleteIsolatedPixelsSwitch
public static boolean dotsSwitch
public static boolean drawPlusSwitch
public static boolean drawBoundarySwitch
public static boolean drawMERSwitch
public static boolean drawSxSyEllipseSwitch
public static boolean ssfFormatSwitch
public static boolean dtdSwitch
public static boolean keepInputImageSwitch
public static boolean laplacianSwitch
public static boolean lowpassSwitch
public static boolean lp3x3Switch
public static boolean lp5x5Switch
public static boolean lp7x7Switch
public static boolean lp13xZZSwitch
public static boolean pixDumpSwitch
public static boolean projDirSwitch
public static boolean propertiesFileSwitch
public static boolean optimizeInteriorFBLSwitch
public static boolean restOfPixSwitch
public static boolean rmvDprimeSizingSwitch
public static boolean quickEstimateSwitch
public static boolean sampleSwitch
public static boolean saturatedSpotSwitch
public static boolean segPixSwitch
public static boolean splitSpotSwitch
public static boolean splitLargeCCfblByBndAnalSwitch
public static boolean splitLargeCCfblByRLManalSwitch
public static boolean splitLargeCCfblByThreshAnalSwitch
public static boolean thrAreaSwitch
public static boolean thrDensitySwitch
public static boolean thrRangeSwitch
public static boolean thrSxSyRatioSwitch
public static boolean timerSwitch
public static boolean updateSwitch
public static boolean usePopupGUISwitch
public static boolean useHistGUISwitch
public static boolean useCopyOfPix1ForPix5Switch
public static boolean use3x3laplacianSwitch
public static boolean use5x5laplacianSwitch
public static boolean useBusseLaplacianSwitch
public static boolean useHorizLineLaplacianSwitch
public static boolean useVertLineLaplacianSwitch
public static boolean usageSwitch
public static char coneOfSilenceMode
public static char drawDotOverlayType
public static char drawPlusOverlayType
public static char drawBoundaryOverlayType
public static char drawMEROverlayType
public static char drawSxSyOverlayType
public static int defaultTypeCode
public static int lowPassSize
public static int accFormatMode
public static int ssfFormatMode
public static boolean didSplitSpotFlag
public static boolean didPropSaturatedSpots
public static boolean useBkgdAndIsolatedPixelFlag
public static boolean dbugBitsPixFlag
public static float fourSqrtPi
public static int ccMinSize
public static int gridSize
public static int dbugBits
public static int splitMinCCsize
public static int nBkgrdSize
public static int widthWindmp
public static int maxColsToPrint
public static int windmpStepSize
public static int wXsize
public static int wYsize
public static int lineLaplacianWidth
public static int lineLaplacianHeight
public static float glbPercentThr
public static float sizeFractionGaussianWidth
public static float histThreshold
public static float t1Area
public static float t2Area
public static float t1Density
public static float t2Density
public static float t1Range
public static float t2Range
public static float t1SxSyRatio
public static float t2SxSyRatio
public static int ccNum
public static int spotNumber
public static int yTitle
public static Sg2hash hashFBL
public static Sg2hash hashWS
public static long startTime
public static long[] statusStartTime
public static long[] statusMemoryTot
public static long[] statusMemoryFree
public static java.lang.String[] statusName
public static int nStatusName
public static long baseStatusTime
public static int killSpotColor
deleteIsolatedPixels killSpotColor   true KILL_SPOT_CODE false BKGRD_CODE
public static int cwx1
public static int cwx2
public static int cwy1
public static int cwy2
public static int merx1
public static int merx2
public static int mery1
public static int mery2
public static int meryp1
public static int meryp2
public static int merxp1
public static int merxp2
public static int dpx1
public static int dpx2
public static int dpy1
public static int dpy2
public static int dbx1
public static int dbx2
public static int dby1
public static int dby2
public static int xDbug
public static int yDbug
public static int[] xPentrance
public static int[] xPexit
public static int[] yPentrance
public static int[] yPexit
public static float pixelSizeMicrons
public static int pixWidth
public static int pixHeight
public static int nPixels
public static int nBytesPerPixel
public static int nBitsPerPixel
public static int maxGrayPixel
public static int[] gray2cal
public static int[] cal2gray
public static int scaledMaxOD
public static int[] gHist
public static int minGhist
public static int maxGhist
public static int meanGhist
public static int pTileGhist
public static char[] pix1
public static char[] pix2
public static char[] pix3
public static char[] pix4
public static char[] pix5
public static char[] pix6
public static char[] pix7
public static int[] bfogm5
postfix line relative to y   m5 y5 m4 y4 m3 y3 m2 y2 m1 y1  y p1 y+1 p2 y+2 p3 y+3 p4 y+4 p5 y+5
public static int[] bfogm4
postfix line relative to y   m5 y5 m4 y4 m3 y3 m2 y2 m1 y1  y p1 y+1 p2 y+2 p3 y+3 p4 y+4 p5 y+5
public static int[] bfogm3
postfix line relative to y   m5 y5 m4 y4 m3 y3 m2 y2 m1 y1  y p1 y+1 p2 y+2 p3 y+3 p4 y+4 p5 y+5
public static int[] bfogm2
postfix line relative to y   m5 y5 m4 y4 m3 y3 m2 y2 m1 y1  y p1 y+1 p2 y+2 p3 y+3 p4 y+4 p5 y+5
public static int[] bfogm1
postfix line relative to y   m5 y5 m4 y4 m3 y3 m2 y2 m1 y1  y p1 y+1 p2 y+2 p3 y+3 p4 y+4 p5 y+5
public static int[] bfogm
postfix line relative to y   m5 y5 m4 y4 m3 y3 m2 y2 m1 y1  y p1 y+1 p2 y+2 p3 y+3 p4 y+4 p5 y+5
public static int[] bfog
postfix line relative to y   m5 y5 m4 y4 m3 y3 m2 y2 m1 y1  y p1 y+1 p2 y+2 p3 y+3 p4 y+4 p5 y+5
public static int[] bfogp
postfix line relative to y   m5 y5 m4 y4 m3 y3 m2 y2 m1 y1  y p1 y+1 p2 y+2 p3 y+3 p4 y+4 p5 y+5
public static int[] bfogp1
postfix line relative to y   m5 y5 m4 y4 m3 y3 m2 y2 m1 y1  y p1 y+1 p2 y+2 p3 y+3 p4 y+4 p5 y+5
public static int[] bfogp2
postfix line relative to y   m5 y5 m4 y4 m3 y3 m2 y2 m1 y1  y p1 y+1 p2 y+2 p3 y+3 p4 y+4 p5 y+5
public static int[] bfogp3
postfix line relative to y   m5 y5 m4 y4 m3 y3 m2 y2 m1 y1  y p1 y+1 p2 y+2 p3 y+3 p4 y+4 p5 y+5
public static int[] bfogp4
postfix line relative to y   m5 y5 m4 y4 m3 y3 m2 y2 m1 y1  y p1 y+1 p2 y+2 p3 y+3 p4 y+4 p5 y+5
public static int[] bfogp5
postfix line relative to y   m5 y5 m4 y4 m3 y3 m2 y2 m1 y1  y p1 y+1 p2 y+2 p3 y+3 p4 y+4 p5 y+5
public static int[] bfavm1
postfix line relative to y   avm1 y2 avm y1 av y avp y+1 av1 y+2
public static int[] bfavm
postfix line relative to y   avm1 y2 avm y1 av y avp y+1 av1 y+2
public static int[] bfav
postfix line relative to y   avm1 y2 avm y1 av y avp y+1 av1 y+2
public static int[] bfavp
postfix line relative to y   avm1 y2 avm y1 av y avp y+1 av1 y+2
public static int[] bfavp1
postfix line relative to y   avm1 y2 avm y1 av y avp y+1 av1 y+2
public static int[] bufbkg
public static int[] bufmag
public static int[] bufrest
public static int[] bufcc
public static int i10
i13 i12 i11 i14 i18 i10 i15 i16 i17
public static int i11
i13 i12 i11 i14 i18 i10 i15 i16 i17
public static int i12
i13 i12 i11 i14 i18 i10 i15 i16 i17
public static int i13
i13 i12 i11 i14 i18 i10 i15 i16 i17
public static int i14
i13 i12 i11 i14 i18 i10 i15 i16 i17
public static int i15
i13 i12 i11 i14 i18 i10 i15 i16 i17
public static int i16
i13 i12 i11 i14 i18 i10 i15 i16 i17
public static int i17
i13 i12 i11 i14 i18 i10 i15 i16 i17
public static int i18
i13 i12 i11 i14 i18 i10 i15 i16 i17
public static int i4L
i2U i13 i12 i11 i4L i14 i18 i10 i0R i15 i16 i17 i6D
public static int i0R
i2U i13 i12 i11 i4L i14 i18 i10 i0R i15 i16 i17 i6D
public static int i2U
i2U i13 i12 i11 i4L i14 i18 i10 i0R i15 i16 i17 i6D
public static int i6D
i2U i13 i12 i11 i4L i14 i18 i10 i0R i15 i16 i17 i6D
public static int c11
public static int c12
public static int c13
public static int c14
public static int c15
public static int c16
public static int c17
public static int c18
public static int c19
public static int c1a
public static int c1b
public static int c1c
public static int c1d
public static int c1e
public static int c1f
public static int c1g
public static int c1h
public static int c21
public static int c22
public static int c23
public static int c24
public static int c25
public static int c26
public static int c27
public static int c28
public static int c29
public static int c2a
public static int c2b
public static int c2c
public static int c2d
public static int c2e
public static int c2f
public static int c2g
public static int c2h
public static int c31
public static int c32
public static int c33
public static int c34
public static int c35
public static int c36
public static int c37
public static int c38
public static int c39
public static int c3a
public static int c3b
public static int c3c
public static int c3d
public static int c3e
public static int c3f
public static int c3g
public static int c3h
public static int c41
public static int c42
public static int c43
public static int c44
public static int c45
public static int c46
public static int c47
public static int c48
public static int c49
public static int c4a
public static int c4b
public static int c4c
public static int c4d
public static int c4e
public static int c4f
public static int c4g
public static int c4h
public static int c51
public static int c52
public static int c53
public static int c54
public static int c55
public static int c56
public static int c57
public static int c58
public static int c59
public static int c5a
public static int c5b
public static int c5c
public static int c5d
public static int c5e
public static int c5f
public static int c5g
public static int c5h
public static int c61
public static int c62
public static int c63
public static int c64
public static int c65
public static int c66
public static int c67
public static int c68
public static int c69
public static int c6a
public static int c6b
public static int c6c
public static int c6d
public static int c6e
public static int c6f
public static int c6g
public static int c6h
public static int c71
public static int c72
public static int c73
public static int c74
public static int c75
public static int c76
public static int c77
public static int c78
public static int c79
public static int c7a
public static int c7b
public static int c7c
public static int c7d
public static int c7e
public static int c7f
public static int c7g
public static int c7h
public static int c81
public static int c82
public static int c83
public static int c84
public static int c85
public static int c86
public static int c87
public static int c88
public static int c89
public static int c8a
public static int c8b
public static int c8c
public static int c8d
public static int c8e
public static int c8f
public static int c8g
public static int c8h
public static int c91
public static int c92
public static int c93
public static int c94
public static int c95
public static int c96
public static int c97
public static int c98
public static int c99
public static int c9a
public static int c9b
public static int c9c
public static int c9d
public static int c9e
public static int c9f
public static int c9g
public static int c9h
public static int ca1
public static int ca2
public static int ca3
public static int ca4
public static int ca5
public static int ca6
public static int ca7
public static int ca8
public static int ca9
public static int caa
public static int cab
public static int cac
public static int cad
public static int cae
public static int caf
public static int cag
public static int cah
public static int cb1
public static int cb2
public static int cb3
public static int cb4
public static int cb5
public static int cb6
public static int cb7
public static int cb8
public static int cb9
public static int cba
public static int cbb
public static int cbc
public static int cbd
public static int cbe
public static int cbf
public static int cbg
public static int cbh
public static int cc1
public static int cc2
public static int cc3
public static int cc4
public static int cc5
public static int cc6
public static int cc7
public static int cc8
public static int cc9
public static int cca
public static int ccb
public static int ccc
public static int ccd
public static int cce
public static int ccf
public static int ccg
public static int cch
public static int cd1
public static int cd2
public static int cd3
public static int cd4
public static int cd5
public static int cd6
public static int cd7
public static int cd8
public static int cd9
public static int cda
public static int cdb
public static int cdc
public static int cdd
public static int cde
public static int cdf
public static int cdg
public static int cdh
public static int j11
public static int j12
public static int j13
public static int j14
public static int j15
public static int j16
public static int j17
public static int j18
public static int j19
public static int j1a
public static int j1b
public static int j1c
public static int j1d
public static int j1e
public static int j1f
public static int j1g
public static int j1h
public static int j21
public static int j22
public static int j23
public static int j24
public static int j25
public static int j26
public static int j27
public static int j28
public static int j29
public static int j2a
public static int j2b
public static int j2c
public static int j2d
public static int j2e
public static int j2f
public static int j2g
public static int j2h
public static int j31
public static int j32
public static int j33
public static int j34
public static int j35
public static int j36
public static int j37
public static int j38
public static int j39
public static int j3a
public static int j3b
public static int j3c
public static int j3d
public static int j3e
public static int j3f
public static int j3g
public static int j3h
public static int j41
public static int j42
public static int j43
public static int j44
public static int j45
public static int j46
public static int j47
public static int j48
public static int j49
public static int j4a
public static int j4b
public static int j4c
public static int j4d
public static int j4e
public static int j4f
public static int j4g
public static int j4h
public static int j51
public static int j52
public static int j53
public static int j54
public static int j55
public static int j56
public static int j57
public static int j58
public static int j59
public static int j5a
public static int j5b
public static int j5c
public static int j5d
public static int j5e
public static int j5f
public static int j5g
public static int j5h
public static int j61
public static int j62
public static int j63
public static int j64
public static int j65
public static int j66
public static int j67
public static int j68
public static int j69
public static int j6a
public static int j6b
public static int j6c
public static int j6d
public static int j6e
public static int j6f
public static int j6g
public static int j6h
public static int j71
public static int j72
public static int j73
public static int j74
public static int j75
public static int j76
public static int j77
public static int j78
public static int j79
public static int j7a
public static int j7b
public static int j7c
public static int j7d
public static int j7e
public static int j7f
public static int j7g
public static int j7h
public static int j81
public static int j82
public static int j83
public static int j84
public static int j85
public static int j86
public static int j87
public static int j88
public static int j89
public static int j8a
public static int j8b
public static int j8c
public static int j8d
public static int j8e
public static int j8f
public static int j8g
public static int j8h
public static int j91
public static int j92
public static int j93
public static int j94
public static int j95
public static int j96
public static int j97
public static int j98
public static int j99
public static int j9a
public static int j9b
public static int j9c
public static int j9d
public static int j9e
public static int j9f
public static int j9g
public static int j9h
public static int ja1
public static int ja2
public static int ja3
public static int ja4
public static int ja5
public static int ja6
public static int ja7
public static int ja8
public static int ja9
public static int jaa
public static int jab
public static int jac
public static int jad
public static int jae
public static int jaf
public static int jag
public static int jah
public static int jb1
public static int jb2
public static int jb3
public static int jb4
public static int jb5
public static int jb6
public static int jb7
public static int jb8
public static int jb9
public static int jba
public static int jbb
public static int jbc
public static int jbd
public static int jbe
public static int jbf
public static int jbg
public static int jbh
public static int jc1
public static int jc2
public static int jc3
public static int jc4
public static int jc5
public static int jc6
public static int jc7
public static int jc8
public static int jc9
public static int jca
public static int jcb
public static int jcc
public static int jcd
public static int jce
public static int jcf
public static int jcg
public static int jch
public static int jd1
public static int jd2
public static int jd3
public static int jd4
public static int jd5
public static int jd6
public static int jd7
public static int jd8
public static int jd9
public static int jda
public static int jdb
public static int jdc
public static int jdd
public static int jde
public static int jdf
public static int jdg
public static int jdh
static java.lang.String[] switchOptData
static boolean[] switchOptCBvalue
static java.lang.String[] switchOptValue
Constructor Detail 

public Sg2glb()
Method Detail 

public static void initGlb()
public static void resetGlb()
public static final int[] getPixLineBuf(int[] lineBuf, int[] pix, int y)
lineBuf
 array predefined of [pixWidth].pix
 is the image buffery
 is the line to use
public static final int[] getPixLineBuf(int[] lineBuf, char[] pix, int y)
lineBuf
 array predefined of [pixWidth].pix
 is the image buffery
 is the line to use
public static final boolean setPixLineBuf(int[] lineBuf, int[] pix, int y)
lineBuf
 array predefined of [pixWidth]pix
 is the image buffery
 is the line to use
public static final boolean setPixLineBuf(int[] lineBuf, char[] pix, int y)
lineBuf
 array predefined of [pixWidth]pix
 is the image buffery
 is the line to use
public static final int get2D(int[] pix, int x, int y)
pix
 is the image bufferx
 of pixely
 of pixel
public static final int get2D(char[] pix, int x, int y)
pix
 is the image bufferx
 of pixely
 of pixel
public static final int set2D(int[] pix, int x, int y, int g)
pix
 is the image bufferx
 of pixely
 of pixelg
 is new int value to save
public static final int set2D(char[] pix, int x, int y, int g)
pix
 is the image bufferx
 of pixely
 of pixelg
 is new int value to save
public static final int put2Dbuf(int[] buf, int x, int g)
pix
 is the image bufferx
 of pixelg
 is new int value to save
public static final boolean isDBwindow()
public static final boolean isDBwindow(int x, int y)
x
 is value to testy
 is value to test
public static void showReportStatus(java.lang.String opr)
opr
 to display


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