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Serialized Form

Package org.emboss.jemboss

Class org.emboss.jemboss.JembossLogo extends javax.swing.JPanel implements Serializable

Serialized Fields

x

int x

y

int y

fontSize

int fontSize

Package org.emboss.jemboss.editor

Class org.emboss.jemboss.editor.AlignApplet extends javax.swing.JApplet 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 extends javax.swing.JFrame implements Serializable

Serialized Fields

graphicSequence

java.util.Vector graphicSequence

jspSequence

javax.swing.JScrollPane jspSequence

ppj

PrettyPlotJFrame ppj

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

menuBar

javax.swing.JMenuBar menuBar

Class org.emboss.jemboss.editor.ColourJFrame extends javax.swing.JFrame implements Serializable

Serialized Fields

popup

javax.swing.JPopupMenu popup
Popup menu system

YBox

javax.swing.Box YBox
Container for the all the residue colour

colourTable

java.util.Hashtable colourTable
Colour scheme

jspColour

javax.swing.JScrollPane jspColour
Scroll pane for the colour pallette

align

AlignJFrame align
Associated alignment viewer

Class org.emboss.jemboss.editor.ColourPanel extends javax.swing.JPanel implements Serializable

Serialized Fields

col

java.awt.Color col

xsize

int xsize

ysize

int ysize

popup

javax.swing.JPopupMenu popup

Class org.emboss.jemboss.editor.ConsensusOptions extends javax.swing.JFrame implements Serializable

Serialized Fields

pluralFloat

TextFieldFloat pluralFloat
plurality

idInt

TextFieldInt idInt
identity

caseFloat

TextFieldFloat caseFloat
set the case

gsc

GraphicSequenceCollection gsc
graphic sequence collection

mat

Matrix mat
scoring matrix

cbusy

java.awt.Cursor cbusy

cdone

java.awt.Cursor cdone

jspSequence

javax.swing.JScrollPane jspSequence

Class org.emboss.jemboss.editor.GraphicSequenceCollection extends javax.swing.JPanel implements Serializable

Serialized Fields

removedSeqs

java.util.Vector removedSeqs
Vector of sequences removed from panel

seqs

java.util.Vector seqs
Vector containing Sequence objects

graphicSequence

java.util.Vector graphicSequence
Vector containing graphical sequences

graphicName

java.util.Vector graphicName
Vector containing graphical names of sequences

colorScheme

java.util.Hashtable colorScheme
Colour scheme to use

pc

PlotConsensus pc
Consensus plot

hgt

int hgt

len

int len

MAXSEQLENGTH

int MAXSEQLENGTH
longest sequence length

numResiduePerLine

int numResiduePerLine
number of residues on each line for print

numberDraw

SequenceJPanel numberDraw
panel for sequence numbers

jspSequence

javax.swing.JScrollPane jspSequence
sequence scrollpane

seqNamePanel

javax.swing.JPanel seqNamePanel
sequence name panel

seqBox

javax.swing.Box seqBox
container for sequences

seqNameBox

javax.swing.Box seqNameBox
container for sequence names

plotconsSeqBox

javax.swing.Box plotconsSeqBox
container for consensus plot

drawSequence

boolean drawSequence
draw the sequence

drawBlackBox

boolean drawBlackBox
draw black square around residues

drawColorBox

boolean drawColorBox
colour residues

drawNumber

boolean drawNumber
draw sequence position number

prettPlot

boolean prettPlot
draw as per prettplot

plotConStrut

int plotConStrut
gap between sequences and consensus plot

prettyPlot

PrettyPlotJFrame prettyPlot
pretty plot values

mat

Matrix mat
scoring matrix

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

Serialized Fields

targets

java.util.Vector targets

position

int position

Class org.emboss.jemboss.editor.GroutAlignJFrameEvent extends java.beans.PropertyChangeEvent implements Serializable

Serialized Fields

source

GroutAlignJFrame source

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

Serialized Fields

targets

java.util.Vector targets

Class org.emboss.jemboss.editor.GroutGraphicSequenceCollectionEvent extends java.beans.PropertyChangeEvent implements Serializable

Serialized Fields

source

GroutGraphicSequenceCollection source

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

Serialized Fields

centreMarkerX

int centreMarkerX

indent

int indent

Class org.emboss.jemboss.editor.IDTableJFrame extends javax.swing.JFrame implements Serializable

Serialized Fields

idTable

PrintableJTable idTable

Class org.emboss.jemboss.editor.MatrixJFrame extends javax.swing.JFrame implements Serializable

Serialized Fields

mScroll

javax.swing.JScrollPane mScroll
scroll pane for matrix display

cbusy

java.awt.Cursor cbusy
cursor busy

cdone

java.awt.Cursor cdone
cursor done

mat

Matrix mat
scoring matrix

Class org.emboss.jemboss.editor.Paste extends ScrollPanel implements Serializable

Serialized Fields

cnp

CutNPasteTextArea cnp

Class org.emboss.jemboss.editor.PatternJFrame extends javax.swing.JFrame implements Serializable

Serialized Fields

gsc

GraphicSequenceCollection gsc
graphic sequence panel

viewResiduePosition

int viewResiduePosition
residue position to display

wrapAround

javax.swing.JCheckBox wrapAround
wrap around search check box

Class org.emboss.jemboss.editor.PlotConsensus extends javax.swing.JPanel implements Serializable

Serialized Fields

sumscore

float[] sumscore
sum of scores for each column

numbins

int numbins
number of graph bins making up the seq length

interval

int interval
residue width

ymin

float ymin
minimum y value

ymax

float ymax
maximum y value

viewPane

GraphicSequenceCollection viewPane
associated sequence panel

Class org.emboss.jemboss.editor.PrettyPlotJFrame extends javax.swing.JFrame implements Serializable

Serialized Fields

textInt

TextFieldInt textInt
field to define min number of identities

textFloat

TextFieldFloat textFloat
field to define threshold for positive matches

idColour

javax.swing.JColorChooser idColour
colour panel for identical matches

matchColour

javax.swing.JColorChooser matchColour
colour panel for positive scoring matches

idColourBackground

javax.swing.JColorChooser idColourBackground
colour panel for identical matches background

matchColourBackground

javax.swing.JColorChooser matchColourBackground
colour panel for positive scoring matches background

gsc

GraphicSequenceCollection gsc
graphic sequence panel

prettyBox

javax.swing.JCheckBox prettyBox
define if the identities and matches are to be boxed

Class org.emboss.jemboss.editor.PrintableJTable extends javax.swing.JTable implements Serializable

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

Serialized Fields

format

java.awt.print.PageFormat format
page format

pageIndex

int pageIndex
page number to print

gsc

GraphicSequenceCollection gsc
alignment sequence panel

filePrefix

java.lang.String filePrefix
prefix of file

statusField

javax.swing.JTextField statusField
status field for print preview

nResPerLine

int nResPerLine
number of residues per line

antiAlias

boolean antiAlias
use anti aliasing (default is false)

Class org.emboss.jemboss.editor.SequenceJPanel extends javax.swing.JPanel implements Serializable

Serialized Fields

col

java.awt.Color col

seq

Sequence seq
sequence to display

fontSize

int fontSize
font size

font

java.awt.Font font
font

boundWidth

int boundWidth
boundary width around each residue

boundWidth2

int boundWidth2
half boundary width (boundWidth/2)

resWidth

int resWidth
residue width

seqHeight

int seqHeight
sequence height

pressedResidue

int pressedResidue
residue number when pressed by mouse

interval

int interval
sequence numbering interval

seqLength

int seqLength
sequence length

ypad

int ypad
sequence height pad

colorTable

java.util.Hashtable colorTable
colour scheme

padChar

java.lang.String padChar
pad/gap character

pattern

java.lang.String pattern
pattern to search for

drawSequence

boolean drawSequence
draw the sequence

drawBlackBox

boolean drawBlackBox
draw a black box around residues

drawColorBox

boolean drawColorBox
colour the residues

drawNumber

boolean drawNumber
draw the sequence numbers

prettyPlot

boolean prettyPlot
colour as per prettyplot

highlightPattern

boolean highlightPattern
high light search pattern

viewPane

javax.swing.JComponent viewPane
sequence alignment panel

popup

javax.swing.JPopupMenu popup
pop up menu

observers

java.util.Vector observers
observer panels in this group

Class org.emboss.jemboss.editor.SequenceNameJButton extends javax.swing.JToggleButton implements Serializable

Serialized Fields

seq

Sequence seq
sequence

boundWidth

int boundWidth
boundary width

fontSize

int fontSize
font size

nameLabel

java.lang.String nameLabel
name label

ypad

int ypad
height pad

font

java.awt.Font font
font

Package org.emboss.jemboss.gui

Class org.emboss.jemboss.gui.AdvancedOptions extends javax.swing.JPanel implements Serializable

Serialized Fields

saveUserHome

javax.swing.JCheckBox saveUserHome
save user home directory

userHome

javax.swing.JTextField userHome
user home directory

cwd

java.lang.String cwd
current working directory

time

java.lang.String[] time
times for job manager updates

Class org.emboss.jemboss.gui.Browser extends javax.swing.JFrame implements Serializable

Serialized Fields

urlField

MemoryComboBox urlField
URL cache combo field

htmlPane

javax.swing.JEditorPane htmlPane
HTML pane

initialURL

java.lang.String initialURL
initial URL

cbusy

java.awt.Cursor cbusy
busy cursor

cdone

java.awt.Cursor cdone
done cursor

topics

java.lang.String[] topics
Help topics

spLeft

javax.swing.JList spLeft
JList spLeft

sp

javax.swing.JSplitPane sp
JSplitPane sp

backMenu

javax.swing.JMenuItem backMenu
Back menu option

backBt

javax.swing.JButton backBt
Back button option

fwdMenu

javax.swing.JMenuItem fwdMenu
Forward menu option

fwdBt

javax.swing.JButton fwdBt
Forward button option

Class org.emboss.jemboss.gui.Browser.JIconButton extends javax.swing.JButton implements Serializable

Class org.emboss.jemboss.gui.ImageIconJPanel extends javax.swing.JPanel implements Serializable

Serialized Fields

ii

javax.swing.ImageIcon ii
image icon

Class org.emboss.jemboss.gui.LaunchJalView extends javax.swing.JFrame implements Serializable

Class org.emboss.jemboss.gui.MemoryComboBox extends javax.swing.JComboBox implements Serializable

Serialized Fields

order

java.util.Vector order

Class org.emboss.jemboss.gui.ResultsMenuBar extends javax.swing.JMenuBar implements Serializable

Serialized Fields

saveToLocalFile

javax.swing.JMenuItem saveToLocalFile
menu to save to local file

saveToRemoteFile

javax.swing.JMenuItem saveToRemoteFile
menu to save to remote file

frame

javax.swing.JFrame frame
frame containing the results

toolBar

javax.swing.JToolBar toolBar
tool bar

undo

javax.swing.JMenuItem undo
undo menu item

redo

javax.swing.JMenuItem redo
redo menu item

undoManager

javax.swing.undo.UndoManager undoManager
undo manager

Class org.emboss.jemboss.gui.ScrollPanel extends javax.swing.JPanel implements Serializable

Class org.emboss.jemboss.gui.SequenceData extends java.lang.Object 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 extends javax.swing.JFrame implements Serializable

Serialized Fields

table

DragJTable table
drag and drop table containing the list of sequences

seqModel

SequenceListTableModel seqModel
model for the sequence table

storeSeqList

javax.swing.JCheckBoxMenuItem storeSeqList
select to save the sequence list between sessions

cbusy

java.awt.Cursor cbusy

cdone

java.awt.Cursor cdone

Class org.emboss.jemboss.gui.ShowResultSet extends javax.swing.JFrame implements Serializable

Serialized Fields

menuBar

ResultsMenuBar menuBar
menu bar

rtp

javax.swing.JTabbedPane rtp
tabbed pane

grout

GroutPanel grout
grout panel

Class org.emboss.jemboss.gui.ShowSavedResults extends javax.swing.JFrame implements Serializable

Serialized Fields

cbusy

java.awt.Cursor cbusy
busy cursor

cdone

java.awt.Cursor cdone
done cursor

datasets

javax.swing.DefaultListModel datasets
data list model

sp

ScrollPanel sp
result data list panel

aboutRes

javax.swing.JTextArea aboutRes
text area for initial description of the saved results window and the run information of the results

aboutScroll

javax.swing.JScrollPane aboutScroll
scrollpane for description of the results

ss

javax.swing.JScrollPane ss
scroll panel for result data

resButtonStatus

javax.swing.JPanel resButtonStatus
result status panel

statusField

javax.swing.JTextField statusField
status field

resMenu

javax.swing.JMenuBar resMenu
manu bar for results panel

rfii

javax.swing.ImageIcon rfii
refresh image

Package org.emboss.jemboss.gui.filetree

Class org.emboss.jemboss.gui.filetree.DragTree extends javax.swing.JTree implements Serializable

Serialized Fields

mysettings

JembossParams mysettings
jemboss properties

root

java.io.File root
root directory

openNode

java.util.Vector openNode
store of directories that are opened

fs

java.lang.String fs
file separator

popup

javax.swing.JPopupMenu popup
popup menu

cbusy

java.awt.Cursor cbusy
busy cursor

cdone

java.awt.Cursor cdone
done cursor

autoscrollInsets

java.awt.Insets autoscrollInsets
used by AutoScroll method

Class org.emboss.jemboss.gui.filetree.FileEditorDisplay extends javax.swing.JTextPane implements Serializable

Serialized Fields

pngContent

byte[] pngContent
png file content

filename

java.lang.String filename
file name

Class org.emboss.jemboss.gui.filetree.FileNode extends javax.swing.tree.DefaultMutableTreeNode 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
true if explored

Class org.emboss.jemboss.gui.filetree.LocalAndRemoteFileTreeFrame extends javax.swing.JFrame implements Serializable

Serialized Fields

prefClose

javax.swing.JMenuItem prefClose
close/exit menu item

Class org.emboss.jemboss.gui.filetree.RemoteDragTree extends javax.swing.JTree implements Serializable

Serialized Fields

mysettings

JembossParams mysettings
jemboss properties

popup

javax.swing.JPopupMenu popup
popup menu

fs

java.lang.String fs
file separator

ls

java.lang.String ls
line separator

openNode

java.util.Vector openNode
store of directories that are opened

cbusy

java.awt.Cursor cbusy
busy cursor

cdone

java.awt.Cursor cdone
done cursor

autoscrollInsets

java.awt.Insets autoscrollInsets
used by AutoScroll method

Class org.emboss.jemboss.gui.filetree.RemoteFileNode extends javax.swing.tree.DefaultMutableTreeNode 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
true if node is explored

isDir

boolean isDir
true if node is a directory

fullname

java.lang.String fullname
full name of node

serverPathToFile

java.lang.String serverPathToFile
path to the file on the server

rootdir

java.lang.String rootdir
root directory

fs

java.lang.String fs
file separator for server files

Class org.emboss.jemboss.gui.filetree.RemoteFileTreePanel extends javax.swing.JPanel implements Serializable

Serialized Fields

cbusy

java.awt.Cursor cbusy
busy cursor

cdone

java.awt.Cursor cdone
done cursor

rootSelect

javax.swing.JComboBox rootSelect
combo to select the root directory from

Package org.emboss.jemboss.gui.form

Class org.emboss.jemboss.gui.form.ApplicationNamePanel extends javax.swing.JPanel implements Serializable

Serialized Fields

x

int x
x position for displaying name

y

int y
y position for displaying name

fontSize

int fontSize
font size

name

java.lang.String name
application name

Class org.emboss.jemboss.gui.form.JembossComboPopup extends javax.swing.JComboBox implements Serializable

Class org.emboss.jemboss.gui.form.LabelTextBox extends javax.swing.Box implements Serializable

Class org.emboss.jemboss.gui.form.ListFilePanel extends javax.swing.JPanel implements Serializable

Serialized Fields

nFiles

int nFiles
maximum number of sequences in list

fileChooser

FileChooser[] fileChooser
container for sequences

Class org.emboss.jemboss.gui.form.Separator extends javax.swing.JPanel implements Serializable

Serialized Fields

d

java.awt.Dimension d
size of separator

Class org.emboss.jemboss.gui.form.SetInFileCard extends javax.swing.Box implements Serializable

Serialized Fields

isFile

boolean isFile
selecting sequence file input (default)

isCut

boolean isCut
selecting cut and paste sequence input

isList

boolean isList
selecting list file input

fileChoose

FileChooser fileChoose
sequence file choser

cutnPaste

CutNPasteTextArea cutnPaste
cut and paste text area

listPane

ListFilePanel listPane
list file panel

inSeqAttr

InputSequenceAttributes[] inSeqAttr
input sequence attributes

h

int h
gui handle number

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

Serialized Fields

toolkit

java.awt.Toolkit toolkit

decimalFormatter

java.text.NumberFormat decimalFormatter

Class org.emboss.jemboss.gui.form.TextFieldFloat.DecimalNumberDocument extends javax.swing.text.PlainDocument implements Serializable

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

Serialized Fields

toolkit

java.awt.Toolkit toolkit

integerFormatter

java.text.NumberFormat integerFormatter

Class org.emboss.jemboss.gui.form.TextFieldInt.WholeNumberDocument extends javax.swing.text.PlainDocument implements Serializable

Class org.emboss.jemboss.gui.form.TextFieldSink extends javax.swing.JTextField implements Serializable

Package org.emboss.jemboss.gui.sequenceChooser

Class org.emboss.jemboss.gui.sequenceChooser.TextAreaSink extends javax.swing.JTextArea implements Serializable

Package org.emboss.jemboss.soap

Class org.emboss.jemboss.soap.AuthPopup extends javax.swing.JFrame implements Serializable

Serialized Fields

splashp

javax.swing.JPanel splashp
splash panel

iprogress

int iprogress
progress monitor

iprogressmax

int iprogressmax
max value for the progress monitor

mysettings

JembossParams mysettings
jemboss properties

progressBar

javax.swing.JProgressBar progressBar
progress bar

progressLabel

javax.swing.JLabel progressLabel
progress label

okButton

javax.swing.JButton okButton
OK button

ufield

javax.swing.JTextField ufield
username field

pfield

javax.swing.JPasswordField pfield
passwd field

exitOnDone

boolean exitOnDone
true if window is to be hidden

promptPanel

javax.swing.JPanel promptPanel
prompt for login panel

Class org.emboss.jemboss.soap.FileRoots extends java.lang.Object 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
server directory roots

currentRoot

java.lang.String currentRoot
currently selected root

currentDir

java.lang.String currentDir
currently selected directory

rootVector

java.util.Vector rootVector
file system roots

defaultRoot

java.lang.String defaultRoot
default root

defaultRootIndex

int defaultRootIndex
default root index

Class org.emboss.jemboss.soap.JembossSoapException extends java.lang.Exception implements Serializable

Class org.emboss.jemboss.soap.ServerSetup extends javax.swing.JTabbedPane implements Serializable

Serialized Fields

publicURL

MemoryComboBox publicURL
public server URL

privateURL

MemoryComboBox privateURL
private server URL

publicName

MemoryComboBox publicName
public server name

privateName

MemoryComboBox privateName
private server name

proxyName

MemoryComboBox proxyName
proxy name

proxyPort

MemoryComboBox proxyPort
proxy port

proxyBrowserName

MemoryComboBox proxyBrowserName
proxy name for web browser

proxyBrowserPort

MemoryComboBox proxyBrowserPort
proxy port for web browser

userAuth

javax.swing.JCheckBox userAuth
selected if user authetication required

useProxy

javax.swing.JCheckBox useProxy
selected if using proxy server

useBrowserProxy

javax.swing.JCheckBox useBrowserProxy
selected if using proxy server for web browser

callTFM

javax.swing.JCheckBox callTFM
selected if tfm help is run on the server

myset

JembossParams myset
jemboss properties

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