# 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