Serialized Form

Package org.emboss.jemboss

Class org.emboss.jemboss.JembossLogo implements Serializable

Serialized Fields

x

int x

y

int y

fontSize

int fontSize

Package org.emboss.jemboss.editor

Class org.emboss.jemboss.editor.AlignApplet implements Serializable

Serialized Fields

gsc

GraphicSequenceCollection gsc

jspSequence

javax.swing.JScrollPane jspSequence

seqs

java.util.Vector seqs

matrix

java.lang.String matrix

cbusy

java.awt.Cursor cbusy

cdone

java.awt.Cursor cdone

Class org.emboss.jemboss.editor.AlignJFrame implements Serializable

Serialized Fields

seqs

java.util.Vector seqs

graphicSequence

java.util.Vector graphicSequence

jspSequence

javax.swing.JScrollPane jspSequence

gsc

GraphicSequenceCollection gsc

mat

Matrix mat

statusField

javax.swing.JTextField statusField

sequenceFile

java.io.File sequenceFile

cbusy

java.awt.Cursor cbusy

cdone

java.awt.Cursor cdone

residueColor

javax.swing.JCheckBoxMenuItem residueColor

currentColour

java.util.Hashtable currentColour

useExitMenu

boolean useExitMenu

Class org.emboss.jemboss.editor.ColourJFrame implements Serializable

Serialized Fields

cbusy

java.awt.Cursor cbusy

cdone

java.awt.Cursor cdone

popup

javax.swing.JPopupMenu popup

YBox

javax.swing.Box YBox

colourTable

java.util.Hashtable colourTable

jspColour

javax.swing.JScrollPane jspColour

align

AlignJFrame align

Class org.emboss.jemboss.editor.GraphicSequenceCollection implements Serializable

Serialized Fields

removedSeqs

java.util.Vector removedSeqs

seqs

java.util.Vector seqs

graphicSequence

java.util.Vector graphicSequence

graphicName

java.util.Vector graphicName

colorScheme

java.util.Hashtable colorScheme

pc

PlotConsensus pc

lenName

int lenName

hgtName

int hgtName

hgt

int hgt

len

int len

MAXSEQLENGTH

int MAXSEQLENGTH

numResiduePerLine

int numResiduePerLine

numberDraw

SequenceJPanel numberDraw

jspSequence

javax.swing.JScrollPane jspSequence

seqNamePanel

javax.swing.JPanel seqNamePanel

seqBox

javax.swing.Box seqBox

seqNameBox

javax.swing.Box seqNameBox

plotconsSeqBox

javax.swing.Box plotconsSeqBox

drawSequence

boolean drawSequence

drawBlackBox

boolean drawBlackBox

drawColorBox

boolean drawColorBox

drawNumber

boolean drawNumber

prettPlot

boolean prettPlot

plotConStrut

int plotConStrut

Class org.emboss.jemboss.editor.MatrixJFrame implements Serializable

Serialized Fields

mScroll

javax.swing.JScrollPane mScroll

cbusy

java.awt.Cursor cbusy

cdone

java.awt.Cursor cdone

mat

Matrix mat

Class org.emboss.jemboss.editor.PatternJFrame implements Serializable

Serialized Fields

gsc

GraphicSequenceCollection gsc

viewResiduePosition

int viewResiduePosition

wrapAround

javax.swing.JCheckBox wrapAround

Class org.emboss.jemboss.editor.PlotConsensus implements Serializable

Serialized Fields

sumscore

float[] sumscore

numbins

int numbins

interval

int interval

ymin

float ymin

ymax

float ymax

viewPane

GraphicSequenceCollection viewPane

Class org.emboss.jemboss.editor.PrintAlignmentImage implements Serializable

Serialized Fields

format

java.awt.print.PageFormat format

pageIndex

int pageIndex

gsc

GraphicSequenceCollection gsc

filePrefix

java.lang.String filePrefix

statusField

javax.swing.JTextField statusField

nResPerLine

int nResPerLine

Class org.emboss.jemboss.editor.SequenceJPanel implements Serializable

Serialized Fields

col

java.awt.Color col

seq

Sequence seq

fontSize

int fontSize

font

java.awt.Font font

boundWidth

int boundWidth

boundWidth2

int boundWidth2

resWidth

int resWidth

seqHeight

int seqHeight

pressedResidue

int pressedResidue

interval

int interval

seqLength

int seqLength

ypad

int ypad

colorTable

java.util.Hashtable colorTable

padChar

java.lang.String padChar

pattern

java.lang.String pattern

drawSequence

boolean drawSequence

drawBlackBox

boolean drawBlackBox

drawColorBox

boolean drawColorBox

drawNumber

boolean drawNumber

prettyPlot

boolean prettyPlot

highlightPattern

boolean highlightPattern

viewPane

javax.swing.JComponent viewPane

popup

javax.swing.JPopupMenu popup

Class org.emboss.jemboss.editor.SequenceNameJButton implements Serializable

Serialized Fields

seq

Sequence seq

boundWidth

int boundWidth

fontSize

int fontSize

nameLabel

java.lang.String nameLabel

ypad

int ypad

font

java.awt.Font font

Package org.emboss.jemboss.gui

Class org.emboss.jemboss.gui.AdvancedOptions implements Serializable

Serialized Fields

saveUserHome

javax.swing.JCheckBox saveUserHome

userHome

javax.swing.JTextField userHome

cwd

java.lang.String cwd

time

java.lang.String[] time

Class org.emboss.jemboss.gui.Browser implements Serializable

Serialized Fields

urlField

MemoryComboBox urlField

htmlPane

javax.swing.JEditorPane htmlPane

initialURL

java.lang.String initialURL

cbusy

java.awt.Cursor cbusy

cdone

java.awt.Cursor cdone

Class org.emboss.jemboss.gui.Browser.JIconButton implements Serializable

Class org.emboss.jemboss.gui.LaunchJalView implements Serializable

Class org.emboss.jemboss.gui.MemoryComboBox implements Serializable

Class org.emboss.jemboss.gui.ResultsMenuBar implements Serializable

Serialized Fields

fileMenuShowres

javax.swing.JMenuItem fileMenuShowres

saveToRemoteFile

javax.swing.JMenuItem saveToRemoteFile

frame

javax.swing.JFrame frame

toolBar

javax.swing.JToolBar toolBar

undo

javax.swing.JMenuItem undo

redo

javax.swing.JMenuItem redo

undoManager

javax.swing.undo.UndoManager undoManager

Class org.emboss.jemboss.gui.ScrollPanel implements Serializable

Class org.emboss.jemboss.gui.SequenceData implements Serializable

Serialization Methods

readObject

private void readObject(java.io.ObjectInputStream in)
                 throws java.io.IOException,
                        java.lang.ClassNotFoundException

writeObject

private void writeObject(java.io.ObjectOutputStream out)
                  throws java.io.IOException

Serialized Fields

s_name

java.lang.String s_name

sequence file/database

s_beg

java.lang.String s_beg

sequence start

s_end

java.lang.String s_end

sequence end

s_default

java.lang.Boolean s_default

use as the default

s_remote

java.lang.Boolean s_remote

file on remote file system

s_listFile

java.lang.Boolean s_listFile

sequence list file

Class org.emboss.jemboss.gui.SequenceList implements Serializable

Serialized Fields

table

DragJTable table

seqModel

SequenceListTableModel seqModel

storeSeqList

javax.swing.JCheckBoxMenuItem storeSeqList

cbusy

java.awt.Cursor cbusy

cdone

java.awt.Cursor cdone

Class org.emboss.jemboss.gui.ShowResultSet implements Serializable

Package org.emboss.jemboss.gui.filetree

Class org.emboss.jemboss.gui.filetree.DragTree implements Serializable

Serialized Fields

mysettings

JembossParams mysettings

root

java.io.File root

openNode

java.util.Vector openNode

fs

java.lang.String fs

popup

javax.swing.JPopupMenu popup

cbusy

java.awt.Cursor cbusy

cdone

java.awt.Cursor cdone

Class org.emboss.jemboss.gui.filetree.FileEditorDisplay implements Serializable

Serialized Fields

pngContent

byte[] pngContent

filename

java.lang.String filename

Class org.emboss.jemboss.gui.filetree.FileNode implements Serializable

Serialization Methods

readObject

private void readObject(java.io.ObjectInputStream in)
                 throws java.io.IOException,
                        java.lang.ClassNotFoundException

writeObject

private void writeObject(java.io.ObjectOutputStream out)
                  throws java.io.IOException

Serialized Fields

explored

boolean explored

Class org.emboss.jemboss.gui.filetree.LocalAndRemoteFileTreeFrame implements Serializable

Serialized Fields

prefClose

javax.swing.JMenuItem prefClose

Class org.emboss.jemboss.gui.filetree.RemoteDragTree implements Serializable

Serialized Fields

mysettings

JembossParams mysettings

popup

javax.swing.JPopupMenu popup

fs

java.lang.String fs

cbusy

java.awt.Cursor cbusy

cdone

java.awt.Cursor cdone

Class org.emboss.jemboss.gui.filetree.RemoteFileNode implements Serializable

Serialization Methods

readObject

private void readObject(java.io.ObjectInputStream in)
                 throws java.io.IOException,
                        java.lang.ClassNotFoundException

writeObject

private void writeObject(java.io.ObjectOutputStream out)
                  throws java.io.IOException

Serialized Fields

explored

boolean explored

isDir

boolean isDir

fullname

java.lang.String fullname

serverPathToFile

java.lang.String serverPathToFile

rootdir

java.lang.String rootdir

fs

java.lang.String fs

Class org.emboss.jemboss.gui.filetree.RemoteFileTreePanel implements Serializable

Serialized Fields

cbusy

java.awt.Cursor cbusy

cdone

java.awt.Cursor cdone

laddCombo

boolean laddCombo

rootSelect

javax.swing.JComboBox rootSelect

Package org.emboss.jemboss.gui.form

Class org.emboss.jemboss.gui.form.ApplicationNamePanel implements Serializable

Serialized Fields

x

int x

y

int y

fontSize

int fontSize

name

java.lang.String name

Class org.emboss.jemboss.gui.form.LabelTextBox implements Serializable

Class org.emboss.jemboss.gui.form.ListFilePanel implements Serializable

Serialized Fields

nFiles

int nFiles

fileChooser

FileChooser[] fileChooser

Class org.emboss.jemboss.gui.form.myComboPopup implements Serializable

Class org.emboss.jemboss.gui.form.Separator implements Serializable

Serialized Fields

light

java.awt.Color light

dark

java.awt.Color dark

d

java.awt.Dimension d

Class org.emboss.jemboss.gui.form.TextFieldFloat implements Serializable

Serialized Fields

toolkit

java.awt.Toolkit toolkit

decimalFormatter

java.text.NumberFormat decimalFormatter

Class org.emboss.jemboss.gui.form.TextFieldFloat.DecimalNumberDocument implements Serializable

Class org.emboss.jemboss.gui.form.TextFieldInt implements Serializable

Serialized Fields

toolkit

java.awt.Toolkit toolkit

integerFormatter

java.text.NumberFormat integerFormatter

Class org.emboss.jemboss.gui.form.TextFieldInt.WholeNumberDocument implements Serializable

Class org.emboss.jemboss.gui.form.TextFieldSink implements Serializable

Package org.emboss.jemboss.gui.sequenceChooser

Class org.emboss.jemboss.gui.sequenceChooser.TextAreaSink implements Serializable

Package org.emboss.jemboss.soap

Class org.emboss.jemboss.soap.AuthPopup implements Serializable

Serialized Fields

splashp

javax.swing.JPanel splashp

iprogress

int iprogress

iprogressmax

int iprogressmax

mysettings

JembossParams mysettings

progressBar

javax.swing.JProgressBar progressBar

progressLabel

javax.swing.JLabel progressLabel

okButton

javax.swing.JButton okButton

ufield

javax.swing.JTextField ufield

pfield

javax.swing.JPasswordField pfield

exitOnDone

boolean exitOnDone

promptPanel

javax.swing.JPanel promptPanel

Class org.emboss.jemboss.soap.FileRoots implements Serializable

Serialization Methods

readObject

private void readObject(java.io.ObjectInputStream in)
                 throws java.io.IOException,
                        java.lang.ClassNotFoundException

writeObject

private void writeObject(java.io.ObjectOutputStream out)
                  throws java.io.IOException

Serialized Fields

fileRoots

java.util.Hashtable fileRoots

currentRoot

java.lang.String currentRoot

currentDir

java.lang.String currentDir

rootVector

java.util.Vector rootVector

defaultRoot

java.lang.String defaultRoot

defaultRootIndex

int defaultRootIndex

Class org.emboss.jemboss.soap.JembossSoapException implements Serializable

Class org.emboss.jemboss.soap.ServerSetup implements Serializable

Serialized Fields

publicURL

MemoryComboBox publicURL

privateURL

MemoryComboBox privateURL

publicName

MemoryComboBox publicName

privateName

MemoryComboBox privateName

proxyName

MemoryComboBox proxyName

proxyPort

MemoryComboBox proxyPort

proxyBrowserName

MemoryComboBox proxyBrowserName

proxyBrowserPort

MemoryComboBox proxyBrowserPort

userAuth

javax.swing.JCheckBox userAuth

useProxy

javax.swing.JCheckBox useProxy

useBrowserProxy

javax.swing.JCheckBox useBrowserProxy

callTFM

javax.swing.JCheckBox callTFM

myset

JembossParams myset