Serialized Form

Package nix.gata.plotter

Class nix.gata.plotter.AlignPanel extends javax.swing.JPanel implements Serializable

Serialized Fields

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

Class nix.gata.plotter.Console extends javax.swing.JFrame implements Serializable

Serialized Fields

textArea

javax.swing.JTextArea textArea

Class nix.gata.plotter.MultiAlignPanel extends javax.swing.JPanel implements Serializable

Class nix.gata.plotter.ToolsFrame extends javax.swing.JFrame implements Serializable

Serialized Fields

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

Package nix.affy.bkgrnd

Class nix.affy.bkgrnd.BackGroundOligo extends java.lang.Object implements Serializable

Serialized Fields

sequence

java.lang.String sequence

coordinates

int[][] coordinates

intensityArrayLists

java.util.ArrayList intensityArrayLists

Package nix.affy.main

Class nix.affy.main.BindingPeak extends java.lang.Object implements Serializable

Serialized Fields

firstPeakIndex

int firstPeakIndex

leftFlankingIndex

int leftFlankingIndex

rightFlankingIndex

int rightFlankingIndex

peakBP

int peakBP

score

double score

Class nix.affy.main.Interval extends java.lang.Object implements Serializable

Serialized Fields

chromosome

java.lang.String chromosome

start1stOligo

int start1stOligo

startLastOligo

int startLastOligo

sizeOfOligo

int sizeOfOligo

numberOfWindows

int numberOfWindows

bestWinIntTest

Window bestWinIntTest

intensityScoreUsed

java.lang.String intensityScoreUsed

bestWinStatTest

Window bestWinStatTest

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

bestAIDWindowScored

boolean bestAIDWindowScored

Class nix.affy.main.Oligo extends java.lang.Object implements Serializable

Serialized Fields

index

int index

start

int start

mismatches

int mismatches

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

Class nix.affy.main.SubWindow extends java.lang.Object implements Serializable

Serialized Fields

oligos

Oligo[] oligos

aveIntDiff

double aveIntDiff

medianIntDiff

double medianIntDiff

aveFoldDiff

double aveFoldDiff

medianFoldDiff

double medianFoldDiff

scoredBy

java.lang.String scoredBy

index

int index

Class nix.affy.main.Window extends java.lang.Object implements Serializable

Serialized Fields

chromosome

java.lang.String chromosome

start1stOligo

int start1stOligo

startLastOligo

int startLastOligo

statisticalScore

double statisticalScore

aveIntValues

double[] aveIntValues

N

int N

sortBy

float sortBy

Package nix.util.gen

Class nix.util.gen.TextFrame extends javax.swing.JFrame implements Serializable

Serialized Fields

textArea

javax.swing.JTextArea textArea

Package nix.affy.graphics

Class nix.affy.graphics.DrawFrame extends javax.swing.JFrame implements Serializable

Serialized Fields

panel

DrawPanel panel

scrollPane

javax.swing.JScrollPane scrollPane

contentPane

java.awt.Container contentPane

Class nix.affy.graphics.DrawPanel extends javax.swing.JPanel implements Serializable

Serialized Fields

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

Class nix.affy.graphics.VirtualCelFrame extends javax.swing.JFrame implements Serializable

Serialized Fields

panel

VirtualCelPanel panel

scrollPane

javax.swing.JScrollPane scrollPane

contentPane

java.awt.Container contentPane

celMasker

CelMasker celMasker

Class nix.affy.graphics.VirtualCelPanel extends javax.swing.JPanel implements Serializable

Serialized Fields

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

selectionEllipse

java.awt.geom.Ellipse2D selectionEllipse

mousePressedPoint

java.awt.Point mousePressedPoint

selectionVisible

boolean selectionVisible

Package nix.gata.main

Class nix.gata.main.PlotterPreferences extends java.lang.Object implements Serializable

Serialized Fields

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

Class nix.gata.main.SimpleTextWindow extends javax.swing.JFrame implements Serializable

Class nix.gata.main.TextWindow extends javax.swing.JFrame implements Serializable

Serialized Fields

editorPane

javax.swing.JEditorPane editorPane

Package nix.util.apps

Class nix.util.apps.ScatterDrawFrame extends javax.swing.JFrame implements Serializable

Class nix.util.apps.ScatterDrawPanel extends javax.swing.JPanel implements Serializable

Serialized Fields

lines

java.awt.geom.Line2D[] lines

numLines

int numLines

recs

java.awt.geom.Rectangle2D[] recs

numPts

int numPts

skipZeros

boolean skipZeros

logValues

boolean logValues

Package nix.affy.bpmap

Class nix.affy.bpmap.BPMapFeature extends java.lang.Object implements Serializable

Serialized Fields

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

Package nix.gata.menu

Class nix.gata.menu.FileInputForm extends javax.swing.JFrame implements Serializable

Serialized Fields

panel

FileInputPanel panel

Class nix.gata.menu.FileInputPanel extends javax.swing.JPanel implements Serializable

Serialized Fields

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

Class nix.gata.menu.GATAFrame extends javax.swing.JFrame implements Serializable

Serialized Fields

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

Class nix.gata.menu.SaveImageForm extends javax.swing.JFrame implements Serializable

Serialized Fields

panel

SaveImagePanel panel

Class nix.gata.menu.SaveImagePanel extends javax.swing.JPanel implements Serializable

Serialized Fields

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

Package nix.util.bio.annotation

Class nix.util.bio.annotation.Exon extends java.lang.Object implements Serializable

Serialized Fields

start

int start

end

int end

name

java.lang.String name

parent

java.lang.String parent

Class nix.util.bio.annotation.GeneGroup extends java.lang.Object implements Serializable

Serialized Fields

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

Class nix.util.bio.annotation.GeneRep extends java.lang.Object implements Serializable

Serialized Fields

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

Class nix.util.bio.annotation.StartEnd extends java.lang.Object implements Serializable

Serialized Fields

start

int start

end

int end

startEnd

int[] startEnd

Class nix.util.bio.annotation.Transcript extends java.lang.Object implements Serializable

Serialized Fields

start

int start

end

int end

name

java.lang.String name

orientation

int orientation

Class nix.util.bio.annotation.TransGroup extends java.lang.Object implements Serializable

Serialized Fields

transcript

Transcript transcript

translation

Translation translation

exons

Exon[] exons

extractedStartEndExons

int[][] extractedStartEndExons

Class nix.util.bio.annotation.Translation extends java.lang.Object implements Serializable

Serialized Fields

start

int start

end

int end

transGrpRef

TransGroup transGrpRef

orientation

int orientation

codingSegments

java.util.ArrayList codingSegments

introns

java.util.ArrayList introns

Package nix.gata.aligner

Class nix.gata.aligner.AlignerInputForm extends javax.swing.JFrame implements Serializable

Serialized Fields

panel

AlignerInputPanel panel

Class nix.gata.aligner.AlignerInputPanel extends javax.swing.JPanel implements Serializable

Serialized Fields

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

Class nix.gata.aligner.AlignerPreferences extends java.lang.Object implements Serializable

Serialized Fields

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

Class nix.gata.aligner.Alignment extends java.lang.Object implements Serializable

Serialized Fields

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

Class nix.gata.aligner.AlignParams extends java.lang.Object implements Serializable

Serialized Fields

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

Class nix.gata.aligner.LocalAlignment extends java.lang.Object implements Serializable

Serialized Fields

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

Package nix.affy.roc

Class nix.affy.roc.RocWindow extends java.lang.Object implements Serializable

Serialized Fields

chromosome

java.lang.String chromosome

start

int start

end

int end

middle

int middle

score

double score

type

int type

Package nix.gata.geneGlyphs

Class nix.gata.geneGlyphs.GlyphPanel extends javax.swing.JPanel implements Serializable

Serialized Fields

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

Package nix.bdtnp.bid

Class nix.bdtnp.bid.Browse extends javax.servlet.http.HttpServlet implements Serializable

Class nix.bdtnp.bid.CascadingImageStackReport extends javax.servlet.http.HttpServlet implements Serializable

Class nix.bdtnp.bid.CascadingStainReport extends javax.servlet.http.HttpServlet implements Serializable

Class nix.bdtnp.bid.Construct extends javax.servlet.http.HttpServlet implements Serializable

Class nix.bdtnp.bid.Embryo extends javax.servlet.http.HttpServlet implements Serializable

Class nix.bdtnp.bid.EmbryoPreparation extends javax.servlet.http.HttpServlet implements Serializable

Class nix.bdtnp.bid.Fluor extends javax.servlet.http.HttpServlet implements Serializable

Class nix.bdtnp.bid.Hybridization extends javax.servlet.http.HttpServlet implements Serializable

Class nix.bdtnp.bid.ImageStack extends javax.servlet.http.HttpServlet implements Serializable

Class nix.bdtnp.bid.Login extends javax.servlet.http.HttpServlet implements Serializable

Class nix.bdtnp.bid.Logout extends javax.servlet.http.HttpServlet implements Serializable

Class nix.bdtnp.bid.Molecule extends javax.servlet.http.HttpServlet implements Serializable

Class nix.bdtnp.bid.NuclearCloud extends javax.servlet.http.HttpServlet implements Serializable

Class nix.bdtnp.bid.Probe extends javax.servlet.http.HttpServlet implements Serializable

Class nix.bdtnp.bid.SecondaryAntibody extends javax.servlet.http.HttpServlet implements Serializable

Class nix.bdtnp.bid.Slide extends javax.servlet.http.HttpServlet implements Serializable

Class nix.bdtnp.bid.Stain extends javax.servlet.http.HttpServlet implements Serializable

Class nix.bdtnp.bid.User extends javax.servlet.http.HttpServlet implements Serializable

Class nix.bdtnp.bid.Vector extends javax.servlet.http.HttpServlet implements Serializable