Constant Field Values

Contents

• Seg2Dgel.*

Seg2Dgel.*

Seg2Dgel.Sg2data

private static final boolean

FPU_ROUNDS

true

Seg2Dgel.Sg2drawHistogram

public static final int	HIST_HEIGHT	500
public static final int	HIST_WIDTH	400
static final long	serialVersionUID	0L

Seg2Dgel.Sg2glb

public static final java.lang.String	applicationName	"Seg2Dgel"
public static final int	BKGRD_CODE	0
public static final int	BLACK	255
public static final int	DBUG_ADD_INTERIOR_CC_PIXELS	16384
public static final int	DBUG_BND_ANALYSIS	131072
public static final int	DBUG_CALC_FEATURES	8192
public static final int	DBUG_CHAIN_CODE_RLM_ANALYSIS	1048576
static final boolean	DBUG_CONSOLE	true
public static final int	DBUG_CVT_BND_TO_CHAINCODE	262144
public static final int	DBUG_DRAW_NOTCH_PAIR_LINE	2097152
public static final int	DBUG_DRAW_SAT_SPOT_BND	8388608
public static final int	DBUG_DUMP_CC_PPX	16777216
public static final int	DBUG_FILL_CORNERS	128
public static final int	DBUG_FILL_HOLES_IN_PCC_CONCAVITIES	256
public static final int	DBUG_FIND_BND_NOTCHES_IN_CHAIN_CODE	524288
public static final int	DBUG_FIND_SPOT_LIST	2
public static final int	DBUG_INNER_LOOP_FIND_SPOT	32768
public static final int	DBUG_MAX_PROPAGATE	64
public static final int	DBUG_NBR_COMPONENTS	32
public static final int	DBUG_PIX_DBCODE	1
public static final int	DBUG_PRINT_GRAY2CAL_MAP	2048
public static final int	DBUG_PROP_SAT_SPOTS	4
public static final int	DBUG_PROP_SPOT_TO_2ND_MAXIMA	1024
public static final int	DBUG_PUSH_XY_INTO_FBL	4194304
public static final int	DBUG_RMV_CONCAVITIES	16
public static final int	DBUG_RMV_INTERIOR_CC_PIXELS	4096
public static final int	DBUG_ROUND_CORNERS	512
public static final int	DBUG_SPLIT_CHECK_SPOT	8
public static final int	DBUG_SPLIT_PIX_BY_FBL_BND_ANALSIS	65536
public static final java.lang.String	dbugBitsHelpStr	"Debug bits for -debug switch for the Seg2Dgel program -\nOpen2Dprot project 2D Electrophoresis Gel Spot Segmenter\n==========================================================\n\n---------------------------------------------------------------------\n| Note: This pre-alpha level software is under construction and |\n| will change. Not all functionality described is fully implemented |\n| or fully debugged. |\n---------------------------------------------------------------------\n\nDebugging option bits used with the \'-dbug:<bits>\' command line command\n-----------------------------------------------------------------------\n\nThe following are the orthogonal -debug option code bits in octal.\nThis means you can add them together (in octal) and use that number.\n\n Octal code Methods traced\n ========== ================\nbit: 01 = dbugPixDBcode()\nbit: 02 = findSpotList()\nbit: 04 = propSaturatedSpot()\nbit: 010 = splitCheckSpot()\nbit: 020 = rmvConcavities()\nbit: 040 = numberComponents()\nbit: 0100 = maxPropagate()\nbit: 0200 = fillCorners()\nbit: 0400 = fillHolesInPCCconcavities()\nbit: 01000 = roundCorners()\nbit: 02000 = propSpotTo2ndDrivMaxima()\nbit: 04000 = print gray2cal[]\nbit: 010000 = rmvInteriorCCpixels()\nbit: 020000 = calcFeatures()\nbit: 040000 = addInteriorCCpixels\nbit: 0100000 = inner loop of findSpot()\nbit: 0200000 = splitPixByFBLboundaryAnal()\nbit: 0400000 = findBoundary(), pushXYboundary(), resetBnd()\nbit: 01000000 = cvtBoundaryToChainCode(), cvtChainCode_to_nextXY()\nbit: 02000000 = findNotches_in_chainCode()\nbit: 04000000 = pairChainCodeNotches(), findMinMaxPeaksInRLM(), findPairedNotches_in_RLM()\nbit: 010000000 = drawLineBetweenNotchPair()\nbit: 020000000 = pushXYintoFBL()\nbit: 040000000 = draw Boundary Of Saturated Spots CC\nbit: 0100000000 = dump CC images At Key Points If Enabled In Code.\nbit: 0200000000 = trace Garbage Collection Calling Method.\n\n=======================================================================\n\n"
public static final int	DFT_2D_GEL	2
public static final int	DFT_2D_LC_MS	3
public static final int	DFT_NO_DB	1
public static final int	HASHFBLPRIME	409
public static final int	ISOLATED_PIXEL_CODE	255
public static final int	KILL_SPOT_CODE	254
public static final int	MAX_BUFFERED_SPOTS	5000
public static final int	MAX_CC_CODE	99
public static final int	MAX_INTERIOR_FBL_SIZE	1024
public static final int	MAX_PCC_CODE	199
public static final int	MAXSUBSPOTS	100
public static final int	MHISTSIZE	65526
public static final int	MIN_CC_CODE	2
public static final int	MIN_PCC_CODE	102
public static final int	MINBLOBAREA	10
public static final int	MINSPLITSPOTSIZE	15
public static final int	PCC_BASE_CODE	100
public static final java.lang.String	seg2dgelURL	"http://open2dprot.sourceforge.net/Seg2Dgel/"
public static final int	UNLABELED_CC_CODE	1
public static final boolean	USE_13X13	true
public static final boolean	USE_BKGD_AND_ISOLATED_PIXEL_BACKGROUND	false
public static final int	WHITE	0

Seg2Dgel.Sg2ngh

private static final float

ALPHA

1.0f

Seg2Dgel.Sg2notch

public static final int	BND_MIN_NOTCH_ALIGN_ANGLE_THR	15
public static final int	BND_MIN_NOTCH_ALIGN_RATIO_THR	2
public static final int	BND_MIN_NOTCH_ANGLE_DIFF_THR	50
public static final int	BND_MIN_NOTCH_PEAK_DIST_THR	5
public static final int	BND_MIN_NOTCH_STRENGTH_THR	4
public static final int	BND_NOTCH_DIST_OFFSET	10
public static final int	INITIAL_MAXNOTCHES	50

Seg2Dgel.Seg2Dgel.Sg2reportPopup

static final long

serialVersionUID

0L

Seg2Dgel.Sg2showImage

static final int	DIST_THR	5
public static final boolean	ENABLE_ZOOM	true
public static final int	HIST_HEIGHT	500
public static final int	HIST_IMAGE_DENSITY	1
public static final int	HIST_NONE	0
public static final int	HIST_SPOT_AREA	2
public static final int	HIST_SPOT_MAX_DENSITY	9
public static final int	HIST_SPOT_MIN_DENSITY	8
public static final int	HIST_SPOT_MNBKGRD	3
public static final int	HIST_SPOT_MNDENSITY	4
public static final int	HIST_SPOT_SX_SY_RATIO_RANGE	11
public static final int	HIST_SPOT_TOT_DENSITY	5
public static final int	HIST_SPOT_TOT_DENSITY_PRIME	6
public static final int	HIST_SPOT_TOT_DENSITY_RANGE	10
public static final int	HIST_SPOT_VOLUME	7
public static final int	HIST_WIDTH	400
public static final int	IS_HEIGHT	460
public static final int	IS_WIDTH	490
static final int	NCOLS	80
static final int	NROWS	14
public final int	ROI_CW	1
public final int	ROI_DBUG	3
public final int	ROI_ND	2
public final int	ROI_NONE	0
public final int	ROI_PIXDUMP	4
public final int	ROI_WORKING	5
static final long	serialVersionUID	0L
public final int	VIEW_HEIGHT	730
public final int	VIEW_WIDTH_NO_HIST	790
public final int	VIEW_WIDTH_WITH_HIST	915

Seg2Dgel.Sg2viewImage

static final int	DIST_THR	5
public static final boolean	ENABLE_ZOOM	true
public static final int	HIST_HEIGHT	500
public static final int	HIST_WIDTH	400
public static final int	IS_HEIGHT	460
public static final int	IS_WIDTH	490
public final int	MAX_ROI	4
static final int	NCOLS	80
static final int	NROWS	14
public final int	ROI_CW	1
public final int	ROI_DBUG	3
public final int	ROI_ND	2
public final int	ROI_NONE	0
public final int	ROI_PIXDUMP	4
static final long	serialVersionUID	0L
public final int	VIEW_HEIGHT	720