Serialized Form


Package util

Class util.AAMap extends java.util.HashMap<java.lang.String,java.lang.Character> implements Serializable

serialVersionUID: 1L

Class util.FileDrop.Event extends java.util.EventObject implements Serializable

serialVersionUID: 1L

Serialized Fields

files

java.io.File[] files

Class util.FilterAlignment extends javax.swing.JDialog implements Serializable

serialVersionUID: 1L

Serialized Fields

parent

AlignFrame parent

viewProps

AlignViewProps viewProps

method

java.lang.String method

filterDialog

FilterAlignment filterDialog

paramMttf

javax.swing.JTextField paramMttf

paramRttf

javax.swing.JTextField paramRttf

paramFttf

javax.swing.JTextField paramFttf

paramGttf

javax.swing.JCheckBox paramGttf

presetsCombo

javax.swing.JComboBox presetsCombo

presets

java.util.HashMap<K,V> presets

Class util.RunMethods extends javax.swing.JDialog implements Serializable

serialVersionUID: 1L

Serialized Fields

parent

AlignFrame parent

viewProps

AlignViewProps viewProps

method

java.lang.String method

runDialog

RunMethods runDialog

paramsTtf

javax.swing.JTextField paramsTtf

warningsLabel

javax.swing.JLabel warningsLabel

Class util.SequenceLogo extends javax.swing.JFrame implements Serializable

serialVersionUID: 1L

Serialized Fields

frequencyMatrix

java.util.Vector<E> frequencyMatrix

clusterColors

java.util.Vector<E> clusterColors

currentSelection

java.util.Vector<E> currentSelection

horizontalScrollbar

javax.swing.JScrollBar horizontalScrollbar

verticalScrollbar

javax.swing.JScrollBar verticalScrollbar

logoPanel

javax.swing.JPanel logoPanel

horizontalChange

int horizontalChange

verticalChange

int verticalChange

logoFrame

javax.swing.JFrame logoFrame

startX

int startX

endX

int endX

startY

int startY

endY

int endY

seqOrderer

SequenceOrderer seqOrderer

sequenceLength

int sequenceLength

clusterPanelScale

int clusterPanelScale

logoHeight

int logoHeight

Class util.SequenceLogo.LogoPosition extends javax.swing.JComponent implements Serializable

serialVersionUID: 1L

Serialized Fields

header

java.awt.Image header

fImages

java.util.Vector<E> fImages

imageHeight

int imageHeight

imageWidth

int imageWidth

position

int position

Package view

Class view.AlignFrame extends javax.swing.JFrame implements Serializable

serialVersionUID: 1L

Serialized Fields

viewProps

AlignViewProps viewProps

alignPanel

AlignPanel alignPanel

methods

Methods methods

loadAlignmentItem

javax.swing.JMenuItem loadAlignmentItem

exitMenuItem

javax.swing.JMenuItem exitMenuItem

alignFrame

AlignFrame alignFrame

exportMenuItem

javax.swing.JMenuItem exportMenuItem

saveAlignmentItem

javax.swing.JMenuItem saveAlignmentItem

alObj

AlignObject alObj

loadMethodItem

javax.swing.JMenuItem loadMethodItem

loadS3DetItem

javax.swing.JMenuItem loadS3DetItem

loadStructureItem

javax.swing.JMenuItem loadStructureItem

loadClusterItem

javax.swing.JMenuItem loadClusterItem

loadXDetItem

javax.swing.JMenuItem loadXDetItem

loadMethodMenu

javax.swing.JMenu loadMethodMenu

saveMethodMenu

javax.swing.JMenu saveMethodMenu

saveS3DetItem

javax.swing.JMenuItem saveS3DetItem

saveXDetItem

javax.swing.JMenuItem saveXDetItem

seqPainter

SequencePainter seqPainter

namePainter

NamePainter namePainter

statusPnl

StatusPanel statusPnl

selectMethodItem

javax.swing.JMenu selectMethodItem

selectEntropyItem

javax.swing.JMenuItem selectEntropyItem

selectXDetItem

javax.swing.JMenuItem selectXDetItem

selectS3Item

javax.swing.JMenuItem selectS3Item

filterAlignment

javax.swing.JMenuItem filterAlignment

runMethodMenu

javax.swing.JMenu runMethodMenu

runXDetItem

javax.swing.JMenuItem runXDetItem

runS3DetItem

javax.swing.JMenuItem runS3DetItem

selectUdm

javax.swing.JMenu selectUdm

selectUdmItems

javax.swing.JMenuItem[] selectUdmItems

unselectResiduesItem

javax.swing.JMenuItem unselectResiduesItem

unselectProteinsItem

javax.swing.JMenuItem unselectProteinsItem

exportFastaItem

javax.swing.JMenuItem exportFastaItem

showSelectionItem

javax.swing.JMenuItem showSelectionItem

sequenceLogoItem

javax.swing.JMenuItem sequenceLogoItem

dualLogoItem

javax.swing.JMenuItem dualLogoItem

clusterLogoItem

javax.swing.JMenuItem clusterLogoItem

manualMenuItem

javax.swing.JMenuItem manualMenuItem

tutorialMenuItem

javax.swing.JMenuItem tutorialMenuItem

aboutMenuItem

javax.swing.JMenuItem aboutMenuItem

defaultColorItem

javax.swing.JCheckBoxMenuItem defaultColorItem

mwColorItem

javax.swing.JCheckBoxMenuItem mwColorItem

polgColorItem

javax.swing.JCheckBoxMenuItem polgColorItem

hdfColorItem

javax.swing.JCheckBoxMenuItem hdfColorItem

userDefColorItem

javax.swing.JCheckBoxMenuItem userDefColorItem

paletteRgbItem

javax.swing.JCheckBoxMenuItem paletteRgbItem

paletteRbItem

javax.swing.JCheckBoxMenuItem paletteRbItem

colorSchemeItems

java.util.Vector<E> colorSchemeItems

colorPaletteItems

java.util.Vector<E> colorPaletteItems

buttonBar

javax.swing.JPanel buttonBar

addGapButton

javax.swing.JButton addGapButton

removeGapButton

javax.swing.JButton removeGapButton

gapId

int gapId

Class view.AlignPanel extends javax.swing.JPanel implements Serializable

serialVersionUID: 1L

Serialized Fields

viewProps

AlignViewProps viewProps

indexPanel

IndexPanel indexPanel

namePanel

NamePanel namePanel

seqPanel

SequencePanel seqPanel

alignFrame

AlignFrame alignFrame

wholeSequencePnl

javax.swing.JPanel wholeSequencePnl

horizontalScrollbar

javax.swing.JScrollBar horizontalScrollbar

verticalScrollbar

javax.swing.JScrollBar verticalScrollbar

descriptionPnl

javax.swing.JPanel descriptionPnl

textLabel

javax.swing.JLabel textLabel

descBoxPanel

javax.swing.JPanel descBoxPanel

upperPanel

javax.swing.JPanel upperPanel

methodPanel

MethodPanel methodPanel

upperDescPnl

javax.swing.JPanel upperDescPnl

imageExporter

ImageExporter imageExporter

sliderPanel

SliderPanel sliderPanel

horizontalChange

int horizontalChange

verticalChange

int verticalChange

s3detobj

S3DetObject s3detobj

Class view.Cluster3DFrame extends javax.swing.JFrame implements Serializable

serialVersionUID: 1L

Serialized Fields

selProteinColor

Color3f selProteinColor

selResidueColor

Color3f selResidueColor

highestValue

float highestValue

scaleFactor

float scaleFactor

min_x

float min_x

min_y

float min_y

min_z

float min_z

max_x

float max_x

max_y

float max_y

max_z

float max_z

boxValues

int[] boxValues

s3detobj

S3DetObject s3detobj

clusterPanel

javax.swing.JPanel clusterPanel

optionPanel

javax.swing.JPanel optionPanel

axesBox1

java.awt.Choice axesBox1

axesBox2

java.awt.Choice axesBox2

axesBox3

java.awt.Choice axesBox3

label1

javax.swing.JLabel label1

label2

javax.swing.JLabel label2

label3

javax.swing.JLabel label3

defaultBtn

javax.swing.JButton defaultBtn

canvas3D

Canvas3D canvas3D

simpleUni

SimpleUniverse simpleUni

legendPanel

javax.swing.JPanel legendPanel

subFamiliesLbl

javax.swing.JLabel subFamiliesLbl

residuesLbl

javax.swing.JLabel residuesLbl

clusterCentersLbl

javax.swing.JLabel clusterCentersLbl

branchGroup

BranchGroup branchGroup

seqOrderer

SequenceOrderer seqOrderer

name2ClusterIndex

java.util.HashMap<K,V> name2ClusterIndex

Class view.ColorSchemeInfo extends java.awt.Component implements Serializable

serialVersionUID: 1L

Serialized Fields

minValue

double minValue

maxValue

double maxValue

paletteName

java.lang.String paletteName

Class view.IndexPanel extends javax.swing.JPanel implements Serializable

serialVersionUID: 1L

Serialized Fields

viewProps

AlignViewProps viewProps

seqPainter

SequencePainter seqPainter

isInteractive

boolean isInteractive

Class view.LoadAlignFrame extends javax.swing.JDialog implements Serializable

serialVersionUID: 1L

Serialized Fields

multAlignTtf

javax.swing.JTextField multAlignTtf

browseAlignFileBtn

JXButton browseAlignFileBtn

filename

java.lang.String filename

loadBtn

JXButton loadBtn

closeBtn

JXButton closeBtn

parent

javax.swing.JFrame parent

loadFrame

LoadAlignFrame loadFrame

Class view.LoadAlignFrame.OpenFileAction extends javax.swing.AbstractAction implements Serializable

serialVersionUID: 1L

Serialized Fields

frame

javax.swing.JDialog frame

chooser

javax.swing.JFileChooser chooser

file

java.io.File file

name

java.lang.String name

Class view.LoadMethodFrame extends javax.swing.JDialog implements Serializable

serialVersionUID: 1L

Serialized Fields

filename

java.lang.String filename

otherTtf

javax.swing.JTextField otherTtf

browseOtherFileBtn

JXButton browseOtherFileBtn

loadBtn

JXButton loadBtn

closeBtn

JXButton closeBtn

parent

AlignFrame parent

loadMethodFrame

LoadMethodFrame loadMethodFrame

methods

Methods methods

alignObject

AlignObject alignObject

scorePnl

javax.swing.JPanel scorePnl

scoreCutoffLbl

javax.swing.JLabel scoreCutoffLbl

scoreCutoffTtf

javax.swing.JTextField scoreCutoffTtf

increasingScoreCB

javax.swing.JCheckBox increasingScoreCB

Class view.LoadMethodFrame.OpenFileAction extends javax.swing.AbstractAction implements Serializable

serialVersionUID: 1L

Serialized Fields

frame

javax.swing.JDialog frame

chooser

javax.swing.JFileChooser chooser

file

java.io.File file

name

java.lang.String name

type

java.lang.String type

filter

javax.swing.filechooser.FileFilter filter

Class view.LoadS3DetFrame extends javax.swing.JDialog implements Serializable

serialVersionUID: 1L

Serialized Fields

filename

java.lang.String filename

loadBtn

JXButton loadBtn

closeBtn

JXButton closeBtn

parent

AlignFrame parent

frame

LoadS3DetFrame frame

methods

Methods methods

alignObject

AlignObject alignObject

s3detTtf

javax.swing.JTextField s3detTtf

browseS3DetFileBtn

JXButton browseS3DetFileBtn

avRankPnl

javax.swing.JPanel avRankPnl

avRankCutoffLbl

javax.swing.JLabel avRankCutoffLbl

avRankCutoffTtf

javax.swing.JTextField avRankCutoffTtf

Class view.LoadS3DetFrame.OpenFileAction extends javax.swing.AbstractAction implements Serializable

serialVersionUID: 1L

Serialized Fields

frame

javax.swing.JDialog frame

chooser

javax.swing.JFileChooser chooser

file

java.io.File file

name

java.lang.String name

type

java.lang.String type

filter

javax.swing.filechooser.FileFilter filter

Class view.LoadStructureFrame extends javax.swing.JDialog implements Serializable

serialVersionUID: 1L

Serialized Fields

pdbFileTtf

javax.swing.JTextField pdbFileTtf

frame

LoadStructureFrame frame

filename

java.lang.String filename

browspdbFileBtn

javax.swing.JButton browspdbFileBtn

loadBtn

javax.swing.JButton loadBtn

cancelBtn

javax.swing.JButton cancelBtn

chooseFileLbl

javax.swing.JLabel chooseFileLbl

pdbCodeTtf

javax.swing.JTextField pdbCodeTtf

loadpdbonlineBtn

javax.swing.JButton loadpdbonlineBtn

pdbCodeLbl

javax.swing.JLabel pdbCodeLbl

pdbfileOpener

PdbFileOpener pdbfileOpener

downloadInfoArea

javax.swing.JTextArea downloadInfoArea

pdbCode

java.lang.String pdbCode

statusLbl

javax.swing.JLabel statusLbl

centerPnl

javax.swing.JPanel centerPnl

statusPnl

javax.swing.JPanel statusPnl

chainLbl

javax.swing.JLabel chainLbl

chainTtf

javax.swing.JTextField chainTtf

viewprops

AlignViewProps viewprops

comboBox

javax.swing.JComboBox comboBox

blastPdbOnlineBtn

javax.swing.JButton blastPdbOnlineBtn

pdbFilePnl

javax.swing.JPanel pdbFilePnl

seqPainter

SequencePainter seqPainter

namePainter

NamePainter namePainter

alignPanel

AlignPanel alignPanel

parent

AlignFrame parent

Class view.LoadStructureFrame.OpenFileAction extends javax.swing.AbstractAction implements Serializable

serialVersionUID: 1L

Serialized Fields

frame

javax.swing.JDialog frame

chooser

javax.swing.JFileChooser chooser

filter

view.LoadStructureFrame.InnerPdbFileFilter filter

file

java.io.File file

name

java.lang.String name

Class view.LoadXDetFrame extends javax.swing.JDialog implements Serializable

serialVersionUID: 1L

Serialized Fields

filename

java.lang.String filename

xDetTtf

javax.swing.JTextField xDetTtf

browseXDetFileBtn

JXButton browseXDetFileBtn

loadBtn

JXButton loadBtn

closeBtn

JXButton closeBtn

parent

AlignFrame parent

frame

LoadXDetFrame frame

methods

Methods methods

alignObject

AlignObject alignObject

correlationPnl

javax.swing.JPanel correlationPnl

entropyPnl

javax.swing.JPanel entropyPnl

entropyCutoffLbl

javax.swing.JLabel entropyCutoffLbl

corrCutoffLbl

javax.swing.JLabel corrCutoffLbl

corrCutoffTtf

javax.swing.JTextField corrCutoffTtf

entropyCutoffTtf

javax.swing.JTextField entropyCutoffTtf

Class view.LoadXDetFrame.OpenFileAction extends javax.swing.AbstractAction implements Serializable

serialVersionUID: 1L

Serialized Fields

frame

javax.swing.JDialog frame

chooser

javax.swing.JFileChooser chooser

file

java.io.File file

name

java.lang.String name

type

java.lang.String type

filter

javax.swing.filechooser.FileFilter filter

Class view.MethodPanel extends javax.swing.JPanel implements Serializable

serialVersionUID: 1L

Serialized Fields

xdetObj

XDetObject xdetObj

s3detObj

S3DetObject s3detObj

udmObjs

UDMObject[] udmObjs

viewProps

AlignViewProps viewProps

pos2funcRes

java.util.HashMap<K,V> pos2funcRes

pos2predPos

java.util.HashMap<K,V> pos2predPos

pos2res

java.util.HashMap<K,V> pos2res

xdetThreshold

double xdetThreshold

entropyThreshold

double entropyThreshold

s3detThreshold

double s3detThreshold

scoreThreshold

double[] scoreThreshold

methods

Methods methods

YINDEX_XDET

int YINDEX_XDET

YINDEX_ENTROPY

int YINDEX_ENTROPY

YINDEX_S3DET

int YINDEX_S3DET

YINDEX_UDM

int[] YINDEX_UDM

firstSequence

java.lang.String firstSequence

seqPainter

SequencePainter seqPainter

height

int height

Class view.NamePainter extends javax.swing.JComponent implements Serializable

serialVersionUID: 1L

Serialized Fields

viewProps

AlignViewProps viewProps
Alignment view properties.


graphics2d

java.awt.Graphics2D graphics2d
Graphics2D object.


s3detobj

S3DetObject s3detobj
S3Det object for the cluster groups.


seqPainter

SequencePainter seqPainter
SequencePanel for registering and update.


iWidth

int iWidth
Image width.


iHeight

int iHeight
Image height


isInteractive

boolean isInteractive
Is interactive flag.


startSelection

int startSelection
Marks selection start for multiple sequence selections.

Class view.NamePanel extends javax.swing.JPanel implements Serializable

serialVersionUID: 1L

Serialized Fields

nameRenderer

NamePainter nameRenderer

s3detObj

S3DetObject s3detObj

Class view.SelectionFrame extends javax.swing.JFrame implements Serializable

serialVersionUID: 1L

Serialized Fields

viewProps

AlignViewProps viewProps
Alignment view properties.


seqPanel

SequencePanel seqPanel
Sequence panel


s3detobj

S3DetObject s3detobj
S3Det object for the cluster groups.


indexPanel

IndexPanel indexPanel

namePanel

NamePanel namePanel

wholeSequencePnl

javax.swing.JPanel wholeSequencePnl

descriptionPnl

javax.swing.JPanel descriptionPnl

textLabel

javax.swing.JLabel textLabel

descBoxPanel

javax.swing.JPanel descBoxPanel

upperPanel

javax.swing.JPanel upperPanel

upperDescPnl

javax.swing.JPanel upperDescPnl

horizontalScrollbar

javax.swing.JScrollBar horizontalScrollbar

verticalScrollbar

javax.swing.JScrollBar verticalScrollbar

horizontalChange

int horizontalChange

verticalChange

int verticalChange

Class view.SeparatorPanel extends javax.swing.JPanel implements Serializable

serialVersionUID: 1L

Serialized Fields

leftColor

java.awt.Color leftColor

rightColor

java.awt.Color rightColor

Class view.SequencePainter extends javax.swing.JComponent implements Serializable

serialVersionUID: 1L

Serialized Fields

graphics2d

java.awt.Graphics2D graphics2d
Graphics2D object.


graphics

java.awt.Graphics graphics
Graphics object.


viewProps

AlignViewProps viewProps
Alignment view properties.


fontMetrics

java.awt.FontMetrics fontMetrics
Font Metrics


alignPanel

AlignPanel alignPanel
Alignment panel


colColorMap

java.util.HashMap<K,V> colColorMap
Integer to color hash map


iWidth

int iWidth
Image width.


iHeight

int iHeight
Image height.


s3detobj

S3DetObject s3detobj
s3det object


observersList

java.util.Vector<E> observersList
List of observers.


currentPosition

int currentPosition
Current position in the sequence.


selectedSequence

SequenceImpl selectedSequence
Selected sequence


sumScrollX

int sumScrollX
Sum of the scroll x values.


jmolPanel

view.Structure3DFrame.JmolPanel jmolPanel
The JmolPanel.


isExport

boolean isExport
Is export flag.


isInteractive

boolean isInteractive
Is interactive flag.

Class view.SequencePanel extends javax.swing.JPanel implements Serializable

serialVersionUID: 1L

Serialized Fields

seqPainter

SequencePainter seqPainter

s3detObj

S3DetObject s3detObj

Class view.SliderPanel extends javax.swing.JPanel implements Serializable

serialVersionUID: 1L

Serialized Fields

alignFrame

AlignFrame alignFrame

xDetSlider

javax.swing.JSlider xDetSlider

xDetTtf

javax.swing.JTextField xDetTtf

entropySlider

javax.swing.JSlider entropySlider

entropyTtf

javax.swing.JTextField entropyTtf

s3DetTtf

javax.swing.JTextField s3DetTtf

s3DetSlider

javax.swing.JSlider s3DetSlider

otherTtf

javax.swing.JTextField[] otherTtf

otherSlider

javax.swing.JSlider[] otherSlider

methods

Methods methods

xDetLbl

javax.swing.JLabel xDetLbl

entropyLbl

javax.swing.JLabel entropyLbl

s3DetLbl

javax.swing.JLabel s3DetLbl

otherLbl

javax.swing.JLabel[] otherLbl

udmNumber

int udmNumber

index

int index

xDetCutoff

int xDetCutoff

entropyCutoff

int entropyCutoff

s3DetCutoff

int s3DetCutoff

scoreCutoff

int scoreCutoff

xDetSelectOr

javax.swing.JButton xDetSelectOr

entropySelectOr

javax.swing.JButton entropySelectOr

s3DetSelectOr

javax.swing.JButton s3DetSelectOr

otherSelectOr

javax.swing.JButton[] otherSelectOr

xDetSelectAnd

javax.swing.JButton xDetSelectAnd

entropySelectAnd

javax.swing.JButton entropySelectAnd

s3DetSelectAnd

javax.swing.JButton s3DetSelectAnd

otherSelectAnd

javax.swing.JButton[] otherSelectAnd

Class view.StatusPanel extends javax.swing.JPanel implements Serializable

serialVersionUID: 1L

Serialized Fields

alObj

AlignObject alObj

seqNumberLabel

javax.swing.JLabel seqNumberLabel

alignLengthLabel

javax.swing.JLabel alignLengthLabel

filenameLabel

javax.swing.JLabel filenameLabel

filenameLabel2

javax.swing.JLabel filenameLabel2

alignLengthLabel2

javax.swing.JLabel alignLengthLabel2

seqNumberLabel2

javax.swing.JLabel seqNumberLabel2

contentPanel

javax.swing.JPanel contentPanel

colorLabel

javax.swing.JLabel colorLabel

colorPalette

ColorSchemeInfo colorPalette

Class view.Structure3DFrame extends javax.swing.JFrame implements Serializable

serialVersionUID: 1L

Serialized Fields

jmolPanel

view.Structure3DFrame.JmolPanel jmolPanel

frame

javax.swing.JFrame frame

ribbonMenuItem

javax.swing.JMenuItem ribbonMenuItem

cartoonMenuItem

javax.swing.JMenuItem cartoonMenuItem

spacefillMenuItem

javax.swing.JMenuItem spacefillMenuItem

selectedChain

java.lang.String selectedChain

zoomOutMenuItem

javax.swing.JMenuItem zoomOutMenuItem

zoomInMenuItem

javax.swing.JMenuItem zoomInMenuItem

alignment

Alignment alignment

commandsPanel

javax.swing.JPanel commandsPanel

commandsBox

javax.swing.JTextField commandsBox

execCommand

javax.swing.JButton execCommand