Seg2Dgel
Class Sg2glb

java.lang.Object
  Seg2Dgel.Sg2glb

Direct Known Subclasses:

Seg2Dgel, Sg2avg, Sg2bkg, Sg2cc, Sg2data, Sg2dbug, Sg2draw, Sg2fbl, Sg2fnd, Sg2hash, Sg2ini, Sg2ngh, Sg2notch, Sg2rest, Sg2sat, Sg2split, Sg2wrk

public class Sg2glb
extends java.lang.Object

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 GELLAB-II 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/.

Version:

$Date: 2005/12/22 00:41:56 $ $Revision: 1.32 $

Author:

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

See Also:

Open2Dprot Home

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 16-bit line buffers [0:pixWidth-1]
static int[]	bfavm Average buffered images - unsigned 16-bit line buffers [0:pixWidth-1]
static int[]	bfavm1 Average buffered images - unsigned 16-bit line buffers [0:pixWidth-1]
static int[]	bfavp Average buffered images - unsigned 16-bit line buffers [0:pixWidth-1]
static int[]	bfavp1 Average buffered images - unsigned 16-bit line buffers [0:pixWidth-1]
static int[]	bfog Input image - 16-bit unsigned char in int[] line buffers for buffered images [0:pixWidth-1]
static int[]	bfogm Input image - 16-bit unsigned char in int[] line buffers for buffered images [0:pixWidth-1]
static int[]	bfogm1 Input image - 16-bit unsigned char in int[] line buffers for buffered images [0:pixWidth-1]
static int[]	bfogm2 Input image - 16-bit unsigned char in int[] line buffers for buffered images [0:pixWidth-1]
static int[]	bfogm3 Input image - 16-bit unsigned char in int[] line buffers for buffered images [0:pixWidth-1]
static int[]	bfogm4 Input image - 16-bit unsigned char in int[] line buffers for buffered images [0:pixWidth-1]
static int[]	bfogm5 Input image - 16-bit unsigned char in int[] line buffers for buffered images [0:pixWidth-1]
static int[]	bfogp Input image - 16-bit unsigned char in int[] line buffers for buffered images [0:pixWidth-1]
static int[]	bfogp1 Input image - 16-bit unsigned char in int[] line buffers for buffered images [0:pixWidth-1]
static int[]	bfogp2 Input image - 16-bit unsigned char in int[] line buffers for buffered images [0:pixWidth-1]
static int[]	bfogp3 Input image - 16-bit unsigned char in int[] line buffers for buffered images [0:pixWidth-1]
static int[]	bfogp4 Input image - 16-bit unsigned char in int[] line buffers for buffered images [0:pixWidth-1]
static int[]	bfogp5 Input image - 16-bit unsigned char in int[] line buffers for buffered images [0:pixWidth-1]
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 16-bit line buffer [0:pixWidth-1]
static int[]	bufcc Rest-of buffered image - unsigned 16-bit line buffer [0:pixWidth-1]
static int[]	bufmag Magnitude buffered image - unsigned 16-bit line buffer [0:pixWidth-1]
static int[]	bufrest Rest-of buffered image - unsigned 16-bit line buffer [0:pixWidth-1]
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,{P|C}, switch where type is either 'C' or 'P'.
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