Serialized Form
chromosome
java.lang.String chromosome
start
int start
end
int end
notes
java.lang.String notes
hits
java.util.HashSet hits
gcContent
boolean[] gcContent
chromosome
java.lang.String chromosome
start
int start
end
int end
middle
int middle
score
double score
type
int type
Class trans.roc.Sgr extends java.lang.Object implements Serializable |
chromosome
java.lang.String chromosome
position
int position
score
double score
gataParams
GATAParams gataParams
annoParams
AnnoSpecParams annoParams
g2
java.awt.Graphics2D g2
scaleBar
ScaleBar scaleBar
genericGlyphs
GenericGlyph[][] genericGlyphs
geneGlyphs
GeneRepGlyph[] geneGlyphs
console
Console console
viewPort
javax.swing.JViewport viewPort
thinStroke
java.awt.BasicStroke thinStroke
normalStroke
java.awt.BasicStroke normalStroke
fatStroke
java.awt.BasicStroke fatStroke
dashStroke
java.awt.BasicStroke dashStroke
scaleBarStroke
java.awt.BasicStroke scaleBarStroke
trackStrokes
java.awt.BasicStroke[] trackStrokes
font
java.awt.Font font
DNAColor
java.awt.Color DNAColor
RNAColor
java.awt.Color RNAColor
proteinColor
java.awt.Color proteinColor
labelColor
java.awt.Color labelColor
scaleLineColor
java.awt.Color scaleLineColor
normalDNALines
java.awt.geom.Line2D.Double[] normalDNALines
thinDNALines
java.awt.geom.Line2D.Double[] thinDNALines
fatRNALines
java.awt.geom.Line2D.Double[] fatRNALines
thinRNALines
java.awt.geom.Line2D.Double[] thinRNALines
dottedProteinLines
java.awt.geom.Line2D.Double[] dottedProteinLines
thinProteinLines
java.awt.geom.Line2D.Double[] thinProteinLines
scaleLines
java.awt.geom.Line2D.Double[] scaleLines
labels
java.util.ArrayList labels
trackLabels
java.util.ArrayList[] trackLabels
anyGenericGlyphs
boolean anyGenericGlyphs
trackVis
boolean[] trackVis
trackLabelVis
boolean[] trackLabelVis
numberTracks
int numberTracks
panel
AlignerInputPanel panel
A
int A
B
int B
C
int C
D
int D
E
int E
F
int F
G
int G
H
int H
I
int I
J
int J
K
int K
L
int L
sizeTextFields
int sizeTextFields
xRight
int xRight
furthestRight
int furthestRight
furthestDown
int furthestDown
finalBaseName
java.lang.String finalBaseName
stats
double[] stats
refF
javax.swing.JTextField refF
refBrows
javax.swing.JButton refBrows
compF
javax.swing.JTextField compF
compBrows
javax.swing.JButton compBrows
bl2F
javax.swing.JTextField bl2F
bl2FBrows
javax.swing.JButton bl2FBrows
objF
javax.swing.JTextField objF
objBrows
javax.swing.JButton objBrows
baseNameF
javax.swing.JTextField baseNameF
baseNameBrows
javax.swing.JButton baseNameBrows
matSpin
javax.swing.JSpinner matSpin
misSpin
javax.swing.JSpinner misSpin
createSpin
javax.swing.JSpinner createSpin
extSpin
javax.swing.JSpinner extSpin
maskYes
javax.swing.JRadioButton maskYes
maskNo
javax.swing.JRadioButton maskNo
extractYes
javax.swing.JRadioButton extractYes
extractNo
javax.swing.JRadioButton extractNo
winTexF
javax.swing.JTextField winTexF
scoreTexF
javax.swing.JTextField scoreTexF
bitTexF
javax.swing.JTextField bitTexF
refTexF
javax.swing.JTextField refTexF
compTexF
javax.swing.JTextField compTexF
help
javax.swing.JButton help
reset
javax.swing.JButton reset
go
javax.swing.JButton go
chooser
javax.swing.JFileChooser chooser
chooserDirectories
javax.swing.JFileChooser chooserDirectories
frame
javax.swing.JFrame frame
ap
AlignerPreferences ap
gata
GATAligner gata
refSeq
java.lang.String refSeq
compSeq
java.lang.String compSeq
bl2SeqProg
java.lang.String bl2SeqProg
storageLoc
java.lang.String storageLoc
baseName
java.lang.String baseName
match
java.lang.Integer match
misMatch
java.lang.Integer misMatch
create
java.lang.Integer create
extend
java.lang.Integer extend
mask
java.lang.String mask
extract
java.lang.String extract
window
java.lang.String window
score
java.lang.String score
refStart
java.lang.String refStart
compStart
java.lang.String compStart
seq1
java.lang.String seq1
startSeq1
int startSeq1
stopSeq1
int stopSeq1
seq2
java.lang.String seq2
startSeq2
int startSeq2
stopSeq2
int stopSeq2
score
int score
bitScore
double bitScore
expect
java.lang.String expect
orientation
int orientation
AP
AlignParams AP
coordinates
int[] coordinates
oriWord
java.lang.String oriWord
shapes
java.util.ArrayList shapes
LA
LocalAlignment LA
realStartRef
double realStartRef
realStartComp
double realStartComp
relStartSeq1
double relStartSeq1
relStartSeq2
double relStartSeq2
relStopSeq1
double relStopSeq1
relStopSeq2
double relStopSeq2
relativeCoordinates
int[] relativeCoordinates
LAMBDA
double LAMBDA
K
double K
EFF_M
double EFF_M
EFF_N
double EFF_N
color
java.awt.Color color
lineColor
java.awt.Color lineColor
refSeqRec
java.awt.geom.Rectangle2D refSeqRec
compSeqRec
java.awt.geom.Rectangle2D compSeqRec
line
java.awt.geom.Line2D line
compVisible
boolean compVisible
WIN_SIZE
int WIN_SIZE
MATCH
int MATCH
MISMATCH
int MISMATCH
GAP_CREATE
int GAP_CREATE
GAP_EXT
int GAP_EXT
MIN_SCORE
int MIN_SCORE
START_INDEX_REFSEQ
int START_INDEX_REFSEQ
START_INDEX_COMPSEQ
int START_INDEX_COMPSEQ
LENGTH_REFSEQ
int LENGTH_REFSEQ
LENGTH_COMPSEQ
int LENGTH_COMPSEQ
refSeqFile
java.lang.String refSeqFile
compSeqFile
java.lang.String compSeqFile
NAME_REFSEQ
java.lang.String NAME_REFSEQ
NAME_COMPSEQ
java.lang.String NAME_COMPSEQ
bl2seq
java.lang.String bl2seq
baseName
java.lang.String baseName
PATH_RESULTS
java.lang.String PATH_RESULTS
DUST
boolean DUST
EXTRACT
boolean EXTRACT
compVisible
boolean compVisible
LAMBDA
double LAMBDA
K
double K
H
double H
EFF_M
double EFF_M
EFF_N
double EFF_N
seq1
java.lang.String seq1
startSeq1
int startSeq1
stopSeq1
int stopSeq1
seq2
java.lang.String seq2
startSeq2
int startSeq2
stopSeq2
int stopSeq2
ori
int ori
score
int score
bitScore
double bitScore
expect
java.lang.String expect
oriWord
java.lang.String oriWord
LAMBDA
double LAMBDA
K
double K
EFF_M
double EFF_M
EFF_N
double EFF_N
firstPeakIndex
int firstPeakIndex
leftFlankingIndex
int leftFlankingIndex
rightFlankingIndex
int rightFlankingIndex
peakBP
int peakBP
score
double score
chromosome
java.lang.String chromosome
start1stOligo
int start1stOligo
startLastOligo
int startLastOligo
sizeOfOligoMinusOne
int sizeOfOligoMinusOne
numberOfWindows
int numberOfWindows
bestWindow
Window bestWindow
bestSubWindow
SubWindow bestSubWindow
bindingPeaks
BindingPeak[] bindingPeaks
sortBy
double sortBy
oligos
Oligo[] oligos
celFiles
java.io.File[] celFiles
numberTreatmentIntensities
int numberTreatmentIntensities
numberControlIntensities
int numberControlIntensities
sequence
java.lang.String sequence
numberMotifHits
int numberMotifHits
baseScores
double[] baseScores
maxCluster
int maxCluster
bestWindowScored
boolean bestWindowScored
fractionIntersections
double[] fractionIntersections
regionNames
java.lang.String[] regionNames
index
int index
start
int start
matches
int matches
intensities
java.util.ArrayList intensities
sequence
java.lang.String sequence
smoothedScore
double smoothedScore
skip
boolean skip
inPeak
boolean inPeak
rightSlope
double rightSlope
leftSlope
double leftSlope
oligos
Oligo[] oligos
medianRatio
double medianRatio
index
int index
chromosome
java.lang.String chromosome
start1stOligo
int start1stOligo
startLastOligo
int startLastOligo
numberOligos
int numberOligos
scores
double[] scores
sortBy
double sortBy
width
int width
zoomedWidth
int zoomedWidth
height
int height
A
double A
B
double B
C
double C
D
double D
E
double E
F
double F
pixBtwProtRNA
double pixBtwProtRNA
pixBtwTransGrps
double pixBtwTransGrps
pixBtwTransGrpsGene
double pixBtwTransGrpsGene
pixBtwTransGrpLabel
double pixBtwTransGrpLabel
pixBtwTracks
double pixBtwTracks
pixBtwLabelTrack
double pixBtwLabelTrack
pixBtwDNATracks
double pixBtwDNATracks
pixHeightArrows
double pixHeightArrows
pixThinLineThickness
float pixThinLineThickness
pixFatLineThickness
float pixFatLineThickness
pixNormalLineThickness
float pixNormalLineThickness
backgroundColor
java.awt.Color backgroundColor
labelColor
java.awt.Color labelColor
scaleLineColor
java.awt.Color scaleLineColor
DNAColor
java.awt.Color DNAColor
RNAColor
java.awt.Color RNAColor
proteinColor
java.awt.Color proteinColor
editorPane
javax.swing.JEditorPane editorPane
Class bioroot.Archive extends javax.servlet.http.HttpServlet implements Serializable |
Class bioroot.CellType extends javax.servlet.http.HttpServlet implements Serializable |
Class bioroot.Contact extends javax.servlet.http.HttpServlet implements Serializable |
Class bioroot.Gene extends javax.servlet.http.HttpServlet implements Serializable |
Class bioroot.Login extends javax.servlet.http.HttpServlet implements Serializable |
Class bioroot.Logout extends javax.servlet.http.HttpServlet implements Serializable |
Class bioroot.Marker extends javax.servlet.http.HttpServlet implements Serializable |
Class bioroot.Organism extends javax.servlet.http.HttpServlet implements Serializable |
Class bioroot.Search extends javax.servlet.http.HttpServlet implements Serializable |
Package util.bio.annotation |
start
int start
end
int end
name
java.lang.String name
parent
java.lang.String parent
name
java.lang.String name
chromosome
java.lang.String chromosome
start
int start
end
int end
type
java.lang.String type
transGrps
TransGroup[] transGrps
geneRep
GeneRep geneRep
orientation
int orientation
attributes
java.lang.String attributes
geneGrpRef
GeneGroup geneGrpRef
codingSegments
java.util.ArrayList codingSegments
nonCodingSegments
java.util.ArrayList nonCodingSegments
startATGPosition
int startATGPosition
fivePrimeNonCodingRegion
int[] fivePrimeNonCodingRegion
threePrimeNonCodingRegion
int[] threePrimeNonCodingRegion
translationFlag
boolean translationFlag
start
int start
end
int end
startEnd
int[] startEnd
start
int start
end
int end
name
java.lang.String name
orientation
int orientation
transcript
Transcript transcript
translation
Translation translation
exons
ExonIntron[] exons
extractedStartEndExons
int[][] extractedStartEndExons
start
int start
end
int end
transGrpRef
TransGroup transGrpRef
orientation
int orientation
codingSegments
java.util.ArrayList codingSegments
introns
java.util.ArrayList introns
A
double A
B
double B
C
double C
D
double D
E
double E
ntLenBig
double ntLenBig
ntLenSmall
double ntLenSmall
ntLenRefSeq
double ntLenRefSeq
ntLenCompSeq
double ntLenCompSeq
ntPerPixel
double ntPerPixel
refRealStart
double refRealStart
compRealStart
double compRealStart
windowSize
double windowSize
maxScore
double maxScore
minScore
double minScore
maxScoreColor
double maxScoreColor
minScoreColor
double minScoreColor
alignments
Alignment[] alignments
visableAlignments
Alignment[] visableAlignments
AP
AlignParams AP
params
GATAParams params
refX
double refX
refY
double refY
refW
double refW
refH
double refH
compX
double compX
compY
double compY
compW
double compW
compH
double compH
ref
java.awt.geom.Rectangle2D ref
comp
java.awt.geom.Rectangle2D comp
lineRec
java.awt.geom.Rectangle2D lineRec
selectionRec
java.awt.geom.Rectangle2D selectionRec
shapes
java.util.ArrayList shapes
orientation
int orientation
score
double score
lenAlignments
int lenAlignments
console
Console console
alignFrameWidth
int alignFrameWidth
alignFrameHeight
int alignFrameHeight
tools
ToolsFrame tools
viewPort
javax.swing.JViewport viewPort
widthBuffImage
int widthBuffImage
heightBuffImage
int heightBuffImage
drawCompBox
boolean drawCompBox
refParams
AnnoSpecParams refParams
gffRefPresent
boolean gffRefPresent
compParams
AnnoSpecParams compParams
gffCompPresent
boolean gffCompPresent
mousePressedPoint
java.awt.Point mousePressedPoint
selectRecVis
boolean selectRecVis
lenVisAligns
int lenVisAligns
textArea
javax.swing.JTextArea textArea
AP
AlignParams AP
params
GATAParams params
alignPanel
AlignPanel alignPanel
panel
javax.swing.JPanel panel
ntRefSeq
javax.swing.JLabel ntRefSeq
ntCompSeq
javax.swing.JLabel ntCompSeq
minBit
javax.swing.JTextField minBit
minE
javax.swing.JTextField minE
maxBit
javax.swing.JTextField maxBit
maxE
javax.swing.JTextField maxE
lambdaNats
double lambdaNats
K
double K
effectiveN
double effectiveN
effectiveM
double effectiveM
magicNum
double magicNum
decimalFormat
java.text.DecimalFormat decimalFormat
numberFormat
java.text.NumberFormat numberFormat
panel
FileInputPanel panel
x
int x
y
int y
alignerFile
javax.swing.JTextField alignerFile
gffFileRef
javax.swing.JTextField gffFileRef
gffFileComp
javax.swing.JTextField gffFileComp
frame
javax.swing.JFrame frame
chooser
javax.swing.JFileChooser chooser
maxWidth
int maxWidth
maxHeight
int maxHeight
params
GATAParams params
gataParams
GATAParams gataParams
refAnnotation
Annotation refAnnotation
compAnnotation
Annotation compAnnotation
refParams
AnnoSpecParams refParams
compParams
AnnoSpecParams compParams
gffRefPres
boolean gffRefPres
gffCompPres
boolean gffCompPres
refGenericGlyphs
boolean refGenericGlyphs
compGenericGlyphs
boolean compGenericGlyphs
refGlyphPanel
GlyphPanel refGlyphPanel
compGlyphPanel
GlyphPanel compGlyphPanel
mAnnotation
javax.swing.JMenu mAnnotation
conservedSeqs
ConservedSeqs conservedSeqs
alignPanel
AlignPanel alignPanel
plotterPreferences
PlotterPreferences plotterPreferences
gataFrame
GATAFrame gataFrame
genParams
AnnoSpecParams genParams
documentWindow
TextWindow documentWindow
innerDividerLoc
int innerDividerLoc
panel
SaveImagePanel panel
x
int x
y
int y
saveFolderField
javax.swing.JTextField saveFolderField
nameField
javax.swing.JTextField nameField
widthField
javax.swing.JTextField widthField
frame
javax.swing.JFrame frame
chooser
javax.swing.JFileChooser chooser
maxWidth
int maxWidth
maxHeight
int maxHeight
params
GATAParams params
alignPanel
AlignPanel alignPanel
saveVisible
boolean saveVisible
serialVersionUID: 1l
start
int start
intensity
float intensity
serialVersionUID: 3l
chromosome
java.lang.String chromosome
matches
int matches
start
int start
pmX
int pmX
pmY
int pmY
mmX
int mmX
mmY
int mmY
sequence
java.lang.String sequence
chromosome
java.lang.String chromosome
position
int position
PMX
short PMX
PMY
short PMY
MMX
short MMX
MMY
short MMY
intensity
float intensity
textArea
javax.swing.JTextArea textArea
correlationCoefficient
double correlationCoefficient
parentCluster
Cluster parentCluster
topCluster
Cluster topCluster
bottomCluster
Cluster bottomCluster
totalClusters
double totalClusters
name
java.lang.String name
floatArrayFile
java.io.File floatArrayFile
nameLabel
javax.swing.JLabel nameLabel
line
java.awt.geom.Line2D line
parentPoint
java.awt.geom.Point2D parentPoint
nameLabelCenterYCoordinate
double nameLabelCenterYCoordinate
lines
java.awt.geom.Line2D[] lines
numLines
int numLines
labels
javax.swing.JLabel[] labels
labelIndex
int labelIndex
clusters
Cluster[] clusters
vhc
HierarchicalClustering vhc
fileNameLineSpacer
double fileNameLineSpacer
fileNameSpacer
double fileNameSpacer
startingXCoordinate
double startingXCoordinate
xCoordinateIncrement
double xCoordinateIncrement
failColor
java.awt.Color failColor
labelFont
java.awt.Font labelFont
minimalCCPercent
double minimalCCPercent
panelWidth
double panelWidth
panelHeight
double panelHeight
runningX
double runningX
runningY
double runningY
sequence
java.lang.String sequence
coordinates
int[][] coordinates
intensityArrayLists
java.util.ArrayList intensityArrayLists
lines
java.awt.geom.Line2D[] lines
numLines
int numLines
recs
java.awt.geom.Rectangle2D[] recs
numPts
int numPts
skipZeros
boolean skipZeros
logValues
boolean logValues
serialVersionUID: 0l
stats
double[] stats
names
java.lang.String[] names
value
float value
chromosomeNumber
byte chromosomeNumber
position
int position
panel
IntervalDrawPanel panel
scrollPane
javax.swing.JScrollPane scrollPane
contentPane
java.awt.Container contentPane
font
java.awt.Font font
context
java.awt.font.FontRenderContext context
h
double h
w
double w
x
double x
y
double y
ySpacer
double ySpacer
peakFlanks
int peakFlanks
intGraphs
Graph[] intGraphs
matrixMismatchGraphs
Graph[] matrixMismatchGraphs
boxes
Box[] boxes
bindingPeaks
Box[] bindingPeaks
numIntGraphs
int numIntGraphs
numMatrixMismatchGraphs
int numMatrixMismatchGraphs
numBoxes
int numBoxes
numBindingPeaks
int numBindingPeaks
title
java.lang.String title
chromosome
java.lang.String chromosome
runningY
double runningY
runningX
double runningX
textFrame
TextFrame textFrame
interval
Interval interval
intervalNumber
int intervalNumber
selectionRec
java.awt.geom.Rectangle2D selectionRec
mousePressedPoint
java.awt.Point mousePressedPoint
selectRecVis
boolean selectRecVis
panel
RankedSetDrawPanel panel
scrollPane
javax.swing.JScrollPane scrollPane
contentPane
java.awt.Container contentPane
heightAdjuster
int heightAdjuster
font
java.awt.Font font
context
java.awt.font.FontRenderContext context
textFrame
TextFrame textFrame
maxSideWidth
double maxSideWidth
alignLeftX
double alignLeftX
widthMiddle
double widthMiddle
alignRightX
double alignRightX
spacer
double spacer
glyphHeight
double glyphHeight
baseScalar
double baseScalar
panelWidth
double panelWidth
panelHeight
double panelHeight
one
GenomicRegion[] one
two
GenomicRegion[] two
connectorLines
java.awt.geom.Line2D[] connectorLines
rectangleIntersectingColor
java.awt.Color rectangleIntersectingColor
rectangleNonIntersectingColor
java.awt.Color rectangleNonIntersectingColor
panel
VirtualCelPanel panel
scrollPane
javax.swing.JScrollPane scrollPane
contentPane
java.awt.Container contentPane
celMasker
CelMasker celMasker
frame
VirtualCelFrame frame
colors
java.awt.Color[] colors
colorScalar
double colorScalar
intensities
float[][] intensities
lengthX
int lengthX
lengthY
int lengthY
bufferedImage
java.awt.image.BufferedImage bufferedImage
maskedEllipses
java.awt.geom.Ellipse2D[] maskedEllipses
zoom
double zoom
writePNG
boolean writePNG
pngFile
java.io.File pngFile
maxIntensityValue
int maxIntensityValue
maskValue
float maskValue
selectionEllipse
java.awt.geom.Ellipse2D selectionEllipse
mousePressedPoint
java.awt.Point mousePressedPoint
selectionVisible
boolean selectionVisible