Index (Jemboss API)

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A B C D E F G H I J K L M N O P Q R S T U V W X Y

## A

about() - Method in class org.emboss.jemboss.server.JembossServer
about() - Method in class org.emboss.jemboss.server.JembossAuthServer
aboutRes - Variable in class org.emboss.jemboss.gui.ShowSavedResults
aboutScroll - Variable in class org.emboss.jemboss.gui.ShowSavedResults
abouturl() - Method in class org.emboss.jemboss.server.JembossServer
abouturl() - Method in class org.emboss.jemboss.server.JembossAuthServer
accelerator_offset - Variable in class org.emboss.jemboss.gui.form.MultiLineToolTipUI
accept(File) - Method in class org.emboss.jemboss.gui.sequenceChooser.SequenceFilter
  Accept all directories and all sequence files (*.fasta, *.msf, *.gcg, *.embl, *.swiss)
acdDirToParse - Variable in class org.emboss.jemboss.JembossParams
acdDirToParse - Variable in class org.emboss.jemboss.server.JembossServer
acdDirToParse - Variable in class org.emboss.jemboss.server.JembossAuthServer
acdDirToParseName - Variable in class org.emboss.jemboss.JembossParams
acdExpAnd(String) - Method in class org.emboss.jemboss.parser.AcdFunResolve
  acdExpAnd Looks for and resolves an expression @( num & num )
acdExpCase(String) - Method in class org.emboss.jemboss.parser.AcdFunResolve
  acdExpCase Looks for and resolves an expression as a switch/case statement
acdExpCond(String) - Method in class org.emboss.jemboss.parser.AcdFunResolve
  acdExpCond Looks for and resolves an expression @( bool ? trueval : falseval )
acdExpDiv(String) - Method in class org.emboss.jemboss.parser.AcdFunResolve
  acdExpDiv Looks for and resolves an expression @( num * num )
acdExpEqual(String) - Method in class org.emboss.jemboss.parser.AcdFunResolve
  acdExpEqual Looks for and resolves an expression @( num == num )
acdExpGreater(String) - Method in class org.emboss.jemboss.parser.AcdFunResolve
  acdExpGreater Looks for and resolves an expression @( num > num )
acdExpLesser(String) - Method in class org.emboss.jemboss.parser.AcdFunResolve
  acdExpLesser Looks for and resolves an expression @( num < num )
acdExpMinus(String) - Method in class org.emboss.jemboss.parser.AcdFunResolve
  acdExpMinus Looks for and resolves an expression @( num - num )
acdExpNot(String) - Method in class org.emboss.jemboss.parser.AcdFunResolve
  acdExpNot Looks for and resolves an expression @(! bool ) or @(NOT bool) or @(not bool).
acdExpNotEqual(String) - Method in class org.emboss.jemboss.parser.AcdFunResolve
  acdExpNotEqual Looks for and resolves an expression @( num != num )
acdExpOr(String) - Method in class org.emboss.jemboss.parser.AcdFunResolve
  acdExpOr Looks for and resolves an expression @( num | num )
acdExpPlus(String) - Method in class org.emboss.jemboss.parser.AcdFunResolve
  Looks for and resolves an expression @( num + num )
acdExpStar(String) - Method in class org.emboss.jemboss.parser.AcdFunResolve
  acdExpStar Looks for and resolves an expression @( num * num )
AcdFunResolve - class org.emboss.jemboss.parser.AcdFunResolve.
  This is a rewrite in Java of the expression functions in ajacd.c of the EMBOSS ajax library, written by Peter Rice.
acdFunResolve(String) - Method in class org.emboss.jemboss.parser.AcdFunResolve
  Looks for and resolves expressions
AcdFunResolve(String) - Constructor for class org.emboss.jemboss.parser.AcdFunResolve
acdStore - Variable in class org.emboss.jemboss.gui.BuildProgramMenu
  acd files cache
acdStore - Static variable in class org.emboss.jemboss.soap.GetACD
AcdVariableResolve - class org.emboss.jemboss.parser.AcdVariableResolve.
  Resolves variable: references.
AcdVariableResolve(String, String, String) - Constructor for class org.emboss.jemboss.parser.AcdVariableResolve
AcdVarResolve - class org.emboss.jemboss.parser.AcdVarResolve.
  Resolves any variable reference in a string.
AcdVarResolve(String, String, String, ParseAcd, int, TextFieldSink[], TextFieldInt[], TextFieldFloat[], myComboPopup[], JCheckBox[]) - Constructor for class org.emboss.jemboss.parser.AcdVarResolve
acidColor - Static variable in class org.emboss.jemboss.editor.SequenceProperties
actionPerformed(ActionEvent) - Method in class org.emboss.jemboss.Jemboss
  Action event to open the file manager
actionPerformed(ActionEvent) - Method in class org.emboss.jemboss.editor.SequenceJPanel
actionPerformed(ActionEvent) - Method in class org.emboss.jemboss.editor.ColourJFrame.ColourPanel
  Popup menu actions
actionPerformed(ActionEvent) - Method in class org.emboss.jemboss.gui.Browser
actionPerformed(ActionEvent) - Method in class org.emboss.jemboss.gui.filetree.RemoteDragTree
  Popup menu actions
actionPerformed(ActionEvent) - Method in class org.emboss.jemboss.gui.filetree.DragTree
  Popup menu actions
actionPerformed(ActionEvent) - Method in class org.emboss.jemboss.gui.form.BuildJembossForm
  Action events Exit, Help, GO, & Show results
activeBorder - Variable in class org.emboss.jemboss.editor.ColourMenu
activeBorder - Variable in class org.emboss.jemboss.gui.ColorMenu
add(String) - Method in class org.emboss.jemboss.gui.MemoryComboBox
addBottomPanel() - Method in class org.emboss.jemboss.soap.AuthPopup
  Buttons across the bottom
addEscapeChars(String) - Method in class org.emboss.jemboss.gui.AdvancedOptions
  Add in escape chars for windows
addFileToList(String, String, Hashtable) - Static method in class org.emboss.jemboss.programs.ListFile
addHashContentsToTab(Hashtable, JTabbedPane) - Method in class org.emboss.jemboss.gui.ShowResultSet
addObject(RemoteFileNode, String, boolean) - Method in class org.emboss.jemboss.gui.filetree.RemoteDragTree
  Adding a file (or directory) to the file tree manager.
addObject(String, String, FileNode) - Method in class org.emboss.jemboss.gui.filetree.DragTree
  Adding a file (or directory) to the file tree manager.
addResult(JembossProcess) - Method in class org.emboss.jemboss.soap.PendingResults
addSequence(Sequence, boolean, int, int) - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection
  Add a sequence to the sequence collection display and to the collection of sequences (seqs) with a specified y-padding.
addSequence(Sequence, boolean, int, int, int) - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection
  Add a sequence at a particular index to the sequence collection display and to the collection of sequences (seqs) with a specified y-padding.
addToScrollPane() - Method in class org.emboss.jemboss.gui.Browser
AdvancedOptions - class org.emboss.jemboss.gui.AdvancedOptions.
AdvancedOptions(JembossParams) - Constructor for class org.emboss.jemboss.gui.AdvancedOptions
advSection - Static variable in class org.emboss.jemboss.gui.form.BuildJembossForm
advSectionBox - Variable in class org.emboss.jemboss.gui.form.BuildJembossForm
af - Variable in class org.emboss.jemboss.gui.form.SectionPanel
af - Variable in class org.emboss.jemboss.gui.form.BuildJembossForm
Ajax - class org.emboss.jemboss.parser.Ajax.
  Used with JNI to access EMBOSS ajax library.
Ajax() - Constructor for class org.emboss.jemboss.parser.Ajax
ajaxLength - Static variable in class org.emboss.jemboss.gui.form.SectionPanel
ajaxProtein - Static variable in class org.emboss.jemboss.gui.form.SectionPanel
AjaxUtil - class org.emboss.jemboss.parser.AjaxUtil.
AjaxUtil() - Constructor for class org.emboss.jemboss.parser.AjaxUtil
ajaxWeight - Static variable in class org.emboss.jemboss.gui.form.SectionPanel
align - Variable in class org.emboss.jemboss.editor.ColourJFrame
align_msf - Static variable in class org.emboss.jemboss.gui.form.AlignFormat
  EMBOSS align formats
align_pairwise - Static variable in class org.emboss.jemboss.gui.form.AlignFormat
AlignApplet - class org.emboss.jemboss.editor.AlignApplet.
AlignApplet() - Constructor for class org.emboss.jemboss.editor.AlignApplet
AlignFormat - class org.emboss.jemboss.gui.form.AlignFormat.
AlignFormat(ParseAcd, int) - Constructor for class org.emboss.jemboss.gui.form.AlignFormat
AlignJFrame - class org.emboss.jemboss.editor.AlignJFrame.
  Displays a grapical representation of a collection of sequences.
AlignJFrame.winExit - class org.emboss.jemboss.editor.AlignJFrame.winExit.
  Extends WindowAdapter to close window
AlignJFrame.winExit() - Constructor for class org.emboss.jemboss.editor.AlignJFrame.winExit
AlignJFrame() - Constructor for class org.emboss.jemboss.editor.AlignJFrame
AlignJFrame(boolean) - Constructor for class org.emboss.jemboss.editor.AlignJFrame
AlignJFrame(File) - Constructor for class org.emboss.jemboss.editor.AlignJFrame
AlignJFrame(String, String) - Constructor for class org.emboss.jemboss.editor.AlignJFrame
AlignJFrame(Vector) - Constructor for class org.emboss.jemboss.editor.AlignJFrame
alignment - Variable in class org.emboss.jemboss.gui.ColumnData
allDescription - Variable in class org.emboss.jemboss.gui.startup.ProgList
  array of program one line descriptions
allProgs - Variable in class org.emboss.jemboss.gui.startup.ProgList
  array of the program names
appendToLogFile(String, String) - Method in class org.emboss.jemboss.server.JembossAuthServer
  Appends a log entry to the log file
appentToSequence(String) - Method in class org.emboss.jemboss.editor.Sequence
appfields - Variable in class org.emboss.jemboss.parser.acd.Application
Application - class org.emboss.jemboss.parser.acd.Application.
Application(String) - Constructor for class org.emboss.jemboss.parser.acd.Application
ApplicationFields - class org.emboss.jemboss.parser.acd.ApplicationFields.
ApplicationFields() - Constructor for class org.emboss.jemboss.parser.acd.ApplicationFields
ApplicationNamePanel - class org.emboss.jemboss.gui.form.ApplicationNamePanel.
ApplicationNamePanel(String, int, int, int) - Constructor for class org.emboss.jemboss.gui.form.ApplicationNamePanel
ApplicationParam - class org.emboss.jemboss.parser.acd.ApplicationParam.
ApplicationParam(String, double) - Constructor for class org.emboss.jemboss.parser.acd.ApplicationParam
ApplicationParam(String, String) - Constructor for class org.emboss.jemboss.parser.acd.ApplicationParam
applName - Variable in class org.emboss.jemboss.gui.form.BuildJembossForm
appName - Variable in class org.emboss.jemboss.gui.form.SectionPanel
appP - Variable in class org.emboss.jemboss.parser.acd.ApplicationFields
appversion() - Method in class org.emboss.jemboss.server.JembossServer
appversion() - Method in class org.emboss.jemboss.server.JembossAuthServer
AQUAMARINE - Static variable in class org.emboss.jemboss.editor.SequenceProperties
aromaticColor - Static variable in class org.emboss.jemboss.editor.SequenceProperties
attach(JPanel, Box, String) - Method in class org.emboss.jemboss.gui.form.BuildJembossForm
attr - Variable in class org.emboss.jemboss.parser.ParseAcd
  parameter data type
attribute - Variable in class org.emboss.jemboss.parser.acd.ApplicationParam
authenticationerror - Variable in class org.emboss.jemboss.soap.PrivateRequest
AuthPopup - class org.emboss.jemboss.soap.AuthPopup.
AuthPopup(JembossParams, int) - Constructor for class org.emboss.jemboss.soap.AuthPopup
  Called on startup to display the login and progress bar.
AuthPopup(JembossParams, JFrame) - Constructor for class org.emboss.jemboss.soap.AuthPopup
  Display a popup asking the user to enter a username and password
autoUpdates - Variable in class org.emboss.jemboss.soap.PendingResults

## B

baseColor - Static variable in class org.emboss.jemboss.editor.SequenceProperties
BatchUpdateTimer - class org.emboss.jemboss.programs.BatchUpdateTimer.
  Simple demo that uses java.util.Timer to schedule a task to execute once 10 seconds have passed.
BatchUpdateTimer.RemindTask - class org.emboss.jemboss.programs.BatchUpdateTimer.RemindTask.
BatchUpdateTimer.RemindTask() - Constructor for class org.emboss.jemboss.programs.BatchUpdateTimer.RemindTask
BatchUpdateTimer(int) - Constructor for class org.emboss.jemboss.programs.BatchUpdateTimer
blankstring - Variable in class org.emboss.jemboss.programs.JembossProcess
BLUEVIOLET - Static variable in class org.emboss.jemboss.editor.SequenceProperties
boundWidth - Variable in class org.emboss.jemboss.editor.SequenceNameJButton
boundWidth - Variable in class org.emboss.jemboss.editor.SequenceJPanel
boundWidth2 - Variable in class org.emboss.jemboss.editor.SequenceJPanel
boxFile - Variable in class org.emboss.jemboss.gui.form.SetInFileCard
breakupLines(String) - Static method in class org.emboss.jemboss.gui.form.PlafMacros
bresults - Variable in class org.emboss.jemboss.gui.form.BuildJembossForm
BROWN - Static variable in class org.emboss.jemboss.editor.SequenceProperties
Browser - class org.emboss.jemboss.gui.Browser.
Browser.JIconButton - class org.emboss.jemboss.gui.Browser.JIconButton.
Browser.JIconButton(ImageIcon) - Constructor for class org.emboss.jemboss.gui.Browser.JIconButton
Browser(String, String, boolean, String, JembossParams) - Constructor for class org.emboss.jemboss.gui.Browser
Browser(String, String, JembossParams) - Constructor for class org.emboss.jemboss.gui.Browser
Browser(URL, String) - Constructor for class org.emboss.jemboss.gui.Browser
browserProxyHost - Variable in class org.emboss.jemboss.JembossParams
browserProxyHostName - Variable in class org.emboss.jemboss.JembossParams
browserProxyPort - Variable in class org.emboss.jemboss.JembossParams
browserProxyPortName - Variable in class org.emboss.jemboss.JembossParams
BuildJembossForm - class org.emboss.jemboss.gui.form.BuildJembossForm.
  Responsible for displaying the graphical representation of the ACD EMBOSS files.
BuildJembossForm(String, String[], String, String[], String, String, String, boolean, ScrollPanel, JembossParams, JFrame) - Constructor for class org.emboss.jemboss.gui.form.BuildJembossForm
BuildProgramMenu - class org.emboss.jemboss.gui.BuildProgramMenu.
  BuildProgramMenu class construct the program menus.
BuildProgramMenu(JPanel, ScrollPanel, JPanel, JScrollPane, String, String[], JembossParams, boolean, String, String, SetUpMenuBar, JFrame, Dimension) - Constructor for class org.emboss.jemboss.gui.BuildProgramMenu
bwdArrow - Variable in class org.emboss.jemboss.Jemboss

## C

calculateCons(Matrix, Vector, float, float, int) - Method in class org.emboss.jemboss.editor.Consensus
call_ajax(String, String) - Method in class org.emboss.jemboss.server.JembossServer
  Uses JNI to calculate sequence attributes using EMBOSS library call.
call_ajax(String, String) - Method in class org.emboss.jemboss.server.JembossAuthServer
  Uses JNI to calculate sequence attributes using EMBOSS library call.
call_ajax(String, String, String) - Method in class org.emboss.jemboss.server.JembossServer
call_ajax(String, String, String, byte[]) - Method in class org.emboss.jemboss.server.JembossAuthServer
  Uses JNI to calculate sequence attributes using EMBOSS library call.
CallAjax - class org.emboss.jemboss.soap.CallAjax.
CallAjax(String, String, JembossParams) - Constructor for class org.emboss.jemboss.soap.CallAjax
callTFM - Variable in class org.emboss.jemboss.soap.ServerSetup
canDo - Variable in class org.emboss.jemboss.gui.filetree.FileSave
cbusy - Variable in class org.emboss.jemboss.editor.PrintAlignment
cbusy - Variable in class org.emboss.jemboss.editor.MatrixJFrame
cbusy - Variable in class org.emboss.jemboss.editor.ColourJFrame
cbusy - Variable in class org.emboss.jemboss.editor.AlignJFrame
cbusy - Variable in class org.emboss.jemboss.editor.AlignApplet
cbusy - Variable in class org.emboss.jemboss.gui.ShowSavedResults
cbusy - Variable in class org.emboss.jemboss.gui.SequenceList
cbusy - Variable in class org.emboss.jemboss.gui.Browser
cbusy - Variable in class org.emboss.jemboss.gui.filetree.RemoteFileTreePanel
cbusy - Variable in class org.emboss.jemboss.gui.filetree.RemoteDragTree
cbusy - Variable in class org.emboss.jemboss.gui.filetree.DragTree
cbusy - Variable in class org.emboss.jemboss.gui.form.BuildJembossForm
cdone - Variable in class org.emboss.jemboss.editor.PrintAlignment
cdone - Variable in class org.emboss.jemboss.editor.MatrixJFrame
cdone - Variable in class org.emboss.jemboss.editor.ColourJFrame
cdone - Variable in class org.emboss.jemboss.editor.AlignJFrame
cdone - Variable in class org.emboss.jemboss.editor.AlignApplet
cdone - Variable in class org.emboss.jemboss.gui.ShowSavedResults
cdone - Variable in class org.emboss.jemboss.gui.SequenceList
cdone - Variable in class org.emboss.jemboss.gui.Browser
cdone - Variable in class org.emboss.jemboss.gui.filetree.RemoteFileTreePanel
cdone - Variable in class org.emboss.jemboss.gui.filetree.RemoteDragTree
cdone - Variable in class org.emboss.jemboss.gui.filetree.DragTree
cdone - Variable in class org.emboss.jemboss.gui.form.BuildJembossForm
chargeColor - Static variable in class org.emboss.jemboss.editor.SequenceProperties
checkBox - Variable in class org.emboss.jemboss.gui.form.SectionPanel
checkBox - Variable in class org.emboss.jemboss.gui.form.BuildJembossForm
checkDependents(Box) - Method in class org.emboss.jemboss.gui.form.SectionPanel
  Checks for dependent variables and adds in action listeners
checkParameters(ParseAcd, int, Hashtable) - Method in class org.emboss.jemboss.gui.form.BuildJembossForm
clear() - Method in class org.emboss.jemboss.gui.SwingWorker.ThreadVar
clone() - Method in class org.emboss.jemboss.server.JembossServer
clone() - Method in class org.emboss.jemboss.server.JembossAuthServer
codons - Static variable in class org.emboss.jemboss.gui.BuildProgramMenu
  codons usage tables
codons - Variable in class org.emboss.jemboss.soap.ShowDB
col - Variable in class org.emboss.jemboss.editor.SequenceJPanel
col - Variable in class org.emboss.jemboss.editor.ColourMenu.ColorPane
col - Variable in class org.emboss.jemboss.editor.ColourJFrame.ColourPanel
col - Variable in class org.emboss.jemboss.gui.ColorMenu.ColorPane
COL_BEG - Static variable in class org.emboss.jemboss.gui.SequenceListTableModel
COL_DEF - Static variable in class org.emboss.jemboss.gui.SequenceListTableModel
COL_END - Static variable in class org.emboss.jemboss.gui.SequenceListTableModel
COL_LIST - Static variable in class org.emboss.jemboss.gui.SequenceListTableModel
COL_NAME - Static variable in class org.emboss.jemboss.gui.SequenceListTableModel
ColorMenu - class org.emboss.jemboss.gui.ColorMenu.
ColorMenu.ColorPane - class org.emboss.jemboss.gui.ColorMenu.ColorPane.
ColorMenu.ColorPane(Color) - Constructor for class org.emboss.jemboss.gui.ColorMenu.ColorPane
ColorMenu(String) - Constructor for class org.emboss.jemboss.gui.ColorMenu
colorScheme - Variable in class org.emboss.jemboss.editor.GraphicSequenceCollection
colorTable - Variable in class org.emboss.jemboss.editor.SequenceJPanel
ColourJFrame - class org.emboss.jemboss.editor.ColourJFrame.
ColourJFrame.ColourPanel - class org.emboss.jemboss.editor.ColourJFrame.ColourPanel.
ColourJFrame.ColourPanel.PopupListener - class org.emboss.jemboss.editor.ColourJFrame.ColourPanel.PopupListener.
ColourJFrame.ColourPanel.PopupListener() - Constructor for class org.emboss.jemboss.editor.ColourJFrame.ColourPanel.PopupListener
ColourJFrame.ColourPanel(String, Color) - Constructor for class org.emboss.jemboss.editor.ColourJFrame.ColourPanel
ColourJFrame(AlignJFrame) - Constructor for class org.emboss.jemboss.editor.ColourJFrame
ColourMenu - class org.emboss.jemboss.editor.ColourMenu.
ColourMenu.ColorPane - class org.emboss.jemboss.editor.ColourMenu.ColorPane.
ColourMenu.ColorPane(Color) - Constructor for class org.emboss.jemboss.editor.ColourMenu.ColorPane
ColourMenu(String) - Constructor for class org.emboss.jemboss.editor.ColourMenu
colourMenus(JMenu) - Method in class org.emboss.jemboss.editor.AlignJFrame
colourScheme(String) - Method in class org.emboss.jemboss.editor.AlignJFrame
  Update the status bar with the selected colour scheme being used.
colourTable - Variable in class org.emboss.jemboss.editor.ColourJFrame
ColumnData - class org.emboss.jemboss.gui.ColumnData.
  Content of each column in the DragJTable
ColumnData(String, int, int) - Constructor for class org.emboss.jemboss.gui.ColumnData
complement(char) - Method in class org.emboss.jemboss.editor.Sequence
complementSequence() - Method in class org.emboss.jemboss.editor.Sequence
complete() - Method in class org.emboss.jemboss.programs.JembossProcess
completed - Variable in class org.emboss.jemboss.programs.JembossProcess
completed_jobs - Variable in class org.emboss.jemboss.soap.PendingResults
cons - Variable in class org.emboss.jemboss.editor.Matrix
cons - Variable in class org.emboss.jemboss.editor.Consensus
Consensus - class org.emboss.jemboss.editor.Consensus.
Consensus(File, Vector, float, float, int) - Constructor for class org.emboss.jemboss.editor.Consensus
Consensus(Matrix, Vector, float, float, int) - Constructor for class org.emboss.jemboss.editor.Consensus
Consensus(String, String, Vector, float, float, int) - Constructor for class org.emboss.jemboss.editor.Consensus
construct() - Method in class org.emboss.jemboss.gui.SwingWorker
  Compute the value to be returned by the `get` method.
convertToOriginal(Object) - Method in class org.emboss.jemboss.gui.ShowSavedResults
convertToPretty(String) - Static method in class org.emboss.jemboss.gui.ShowSavedResults
cp - Variable in class org.emboss.jemboss.gui.form.ReportFormat
cp - Variable in class org.emboss.jemboss.gui.form.AlignFormat
createAlignmentImage(int) - Method in class org.emboss.jemboss.editor.PrintAlignmentImage
  Returns a generated image
createDefaultModel() - Method in class org.emboss.jemboss.gui.form.TextFieldInt
createDefaultModel() - Method in class org.emboss.jemboss.gui.form.TextFieldFloat
createFinishedFile() - Method in class org.emboss.jemboss.server.JembossThread
  Creates a file named "finished" in the project directory, that contains a time stamp.
createFinishedFile(String) - Method in class org.emboss.jemboss.server.JembossServer
  Creates a file named "finished" in the project directory, that contains a time stamp.
createMenu() - Method in class org.emboss.jemboss.editor.AlignApplet
createPlot(Matrix, Vector, int) - Method in class org.emboss.jemboss.editor.PlotConsensus
createPopup() - Method in class org.emboss.jemboss.gui.form.myComboPopup.myComboUI
createTreeModel(File) - Method in class org.emboss.jemboss.gui.filetree.DragTree
  Make the given directory the root and create a new DefaultTreeModel.
createTreeModel(String) - Method in class org.emboss.jemboss.gui.filetree.RemoteDragTree
createUI(JComponent) - Static method in class org.emboss.jemboss.gui.form.MultiLineToolTipUI
currentColour - Variable in class org.emboss.jemboss.editor.AlignJFrame
currentDir - Variable in class org.emboss.jemboss.soap.FileRoots
currentDirectory - Variable in class org.emboss.jemboss.gui.sequenceChooser.FileChooser
currentMode - Variable in class org.emboss.jemboss.JembossParams
currentModeName - Variable in class org.emboss.jemboss.JembossParams
currentRes - Variable in class org.emboss.jemboss.soap.FileList
currentRoot - Variable in class org.emboss.jemboss.soap.FileRoots
cutnPaste - Variable in class org.emboss.jemboss.gui.form.SetInFileCard
CutNPasteTextArea - class org.emboss.jemboss.gui.sequenceChooser.CutNPasteTextArea.
  Makes a cut-and-paste text area.
CutNPasteTextArea(Box, String) - Constructor for class org.emboss.jemboss.gui.sequenceChooser.CutNPasteTextArea
cwd - Variable in class org.emboss.jemboss.gui.AdvancedOptions
cwd - Variable in class org.emboss.jemboss.gui.filetree.FileSaving
cwd - Variable in class org.emboss.jemboss.gui.form.BuildJembossForm

## D

d - Variable in class org.emboss.jemboss.gui.form.Separator
dark - Variable in class org.emboss.jemboss.gui.form.Separator
Database - class org.emboss.jemboss.gui.startup.Database.
  Parses the output from showdb to find the available databases
Database(String) - Constructor for class org.emboss.jemboss.gui.startup.Database
dataFlavor - Variable in class org.emboss.jemboss.gui.sequenceChooser.CutNPasteTextArea
datasets - Variable in class org.emboss.jemboss.gui.ShowSavedResults
datasets - Variable in class org.emboss.jemboss.programs.ResultsUpdateTimer.ResultsTask
db - Static variable in class org.emboss.jemboss.gui.BuildProgramMenu
  database names
db - Variable in class org.emboss.jemboss.gui.form.SectionPanel
db - Variable in class org.emboss.jemboss.gui.form.BuildJembossForm
db - Variable in class org.emboss.jemboss.gui.startup.Database
dbs - Variable in class org.emboss.jemboss.gui.sequenceChooser.InputSequenceAttributes
dbText - Variable in class org.emboss.jemboss.soap.ShowDB
dbText - Variable in class org.emboss.jemboss.soap.GetWossname
debug - Variable in class org.emboss.jemboss.JembossParams
debugName - Variable in class org.emboss.jemboss.JembossParams
decimalFormatter - Variable in class org.emboss.jemboss.gui.form.TextFieldFloat
def - Variable in class org.emboss.jemboss.gui.form.ReportFormat
def - Variable in class org.emboss.jemboss.gui.form.AlignFormat
defaultBorder - Static variable in class org.emboss.jemboss.gui.sequenceChooser.CutNPasteTextArea
defaultRoot - Variable in class org.emboss.jemboss.soap.FileRoots
defaultRootIndex - Variable in class org.emboss.jemboss.soap.FileRoots
delDir(String, byte[], String, String) - Method in class org.emboss.jemboss.parser.Ajax
delDir(String, String, String) - Method in class org.emboss.jemboss.server.JembossFileServer
delDir(String, String, String, byte[]) - Method in class org.emboss.jemboss.server.JembossFileAuthServer
delete_saved_results(String, String) - Method in class org.emboss.jemboss.server.JembossServer
  Private server Deletes a projects saved results.
delete_saved_results(String, String, String) - Method in class org.emboss.jemboss.server.JembossServer
  Private server Deletes a projects saved results.
delete_saved_results(String, String, String, byte[]) - Method in class org.emboss.jemboss.server.JembossAuthServer
  Private server Deletes a projects saved results.
deleteConsensusPlot() - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection
deleteObject(FileNode) - Method in class org.emboss.jemboss.gui.filetree.DragTree
  Delete a node from the JTree
deleteObject(RemoteFileNode, String) - Method in class org.emboss.jemboss.gui.filetree.RemoteDragTree
deleteResidue(int) - Method in class org.emboss.jemboss.editor.Sequence
deleteRow(int) - Method in class org.emboss.jemboss.gui.SequenceListTableModel
  Delete a row from the table
deleteSequence(String) - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection
  Delete a sequence from the sequence collection display and resize the sequence panel display
deleteTmp(File, String) - Method in class org.emboss.jemboss.Jemboss
  Delete temporary files
deleteTmp(File, String) - Method in class org.emboss.jemboss.gui.SetUpMenuBar
  Delete temporary files
delFile(String, byte[], String, String) - Method in class org.emboss.jemboss.parser.Ajax
delFile(String, String, String) - Method in class org.emboss.jemboss.server.JembossFileServer
delFile(String, String, String, byte[]) - Method in class org.emboss.jemboss.server.JembossFileAuthServer
dep - Variable in class org.emboss.jemboss.parser.ParseAcd
  aaray of dependent variables
Dependent - class org.emboss.jemboss.parser.Dependent.
Dependent(int, int, String, String) - Constructor for class org.emboss.jemboss.parser.Dependent
description - Variable in class org.emboss.jemboss.programs.JembossProcess
descriptionHash() - Method in class org.emboss.jemboss.soap.PendingResults
directories - Variable in class org.emboss.jemboss.soap.FileList
directory_shortls(String, String, String) - Method in class org.emboss.jemboss.server.JembossFileServer
directory_shortls(String, String, String, byte[]) - Method in class org.emboss.jemboss.server.JembossFileAuthServer
DISPLAY_ACCELERATOR - Static variable in class org.emboss.jemboss.gui.form.MultiLineToolTipUI
displayAccelerator - Static variable in class org.emboss.jemboss.gui.form.MultiLineToolTipUI
doc - Variable in class org.emboss.jemboss.parser.acd.Application
docurl() - Method in class org.emboss.jemboss.server.JembossServer
docurl() - Method in class org.emboss.jemboss.server.JembossAuthServer
doneEverything(String) - Method in class org.emboss.jemboss.soap.AuthPopup
  Finish the progress bar and label
doneSomething(String) - Method in class org.emboss.jemboss.soap.AuthPopup
  Update the progress bar and label
doReset() - Method in class org.emboss.jemboss.gui.form.SetInFileCard
doReset() - Method in class org.emboss.jemboss.gui.form.ListFilePanel
  Reset the values of the list files
doSelection() - Method in class org.emboss.jemboss.editor.ColourMenu
doSelection() - Method in class org.emboss.jemboss.gui.ColorMenu
doWrite() - Method in class org.emboss.jemboss.gui.filetree.FileSave
dragDropEnd(DragSourceDropEvent) - Method in class org.emboss.jemboss.gui.DragJTable
dragDropEnd(DragSourceDropEvent) - Method in class org.emboss.jemboss.gui.filetree.RemoteDragTree
dragDropEnd(DragSourceDropEvent) - Method in class org.emboss.jemboss.gui.filetree.DragTree
dragEnter(DragSourceDragEvent) - Method in class org.emboss.jemboss.gui.DragJTable
dragEnter(DragSourceDragEvent) - Method in class org.emboss.jemboss.gui.filetree.RemoteDragTree
dragEnter(DragSourceDragEvent) - Method in class org.emboss.jemboss.gui.filetree.DragTree
dragEnter(DropTargetDragEvent) - Method in class org.emboss.jemboss.gui.DragJTable
dragEnter(DropTargetDragEvent) - Method in class org.emboss.jemboss.gui.filetree.RemoteDragTree
dragEnter(DropTargetDragEvent) - Method in class org.emboss.jemboss.gui.filetree.DragTree
dragEnter(DropTargetDragEvent) - Method in class org.emboss.jemboss.gui.form.TextFieldSink
dragEnter(DropTargetDragEvent) - Method in class org.emboss.jemboss.gui.sequenceChooser.TextAreaSink
dragExit(DragSourceEvent) - Method in class org.emboss.jemboss.gui.DragJTable
dragExit(DragSourceEvent) - Method in class org.emboss.jemboss.gui.filetree.RemoteDragTree
dragExit(DragSourceEvent) - Method in class org.emboss.jemboss.gui.filetree.DragTree
dragExit(DropTargetEvent) - Method in class org.emboss.jemboss.gui.DragJTable
dragExit(DropTargetEvent) - Method in class org.emboss.jemboss.gui.filetree.RemoteDragTree
dragExit(DropTargetEvent) - Method in class org.emboss.jemboss.gui.filetree.DragTree
dragExit(DropTargetEvent) - Method in class org.emboss.jemboss.gui.form.TextFieldSink
dragExit(DropTargetEvent) - Method in class org.emboss.jemboss.gui.sequenceChooser.TextAreaSink
dragGestureRecognized(DragGestureEvent) - Method in class org.emboss.jemboss.gui.DragJTable
dragGestureRecognized(DragGestureEvent) - Method in class org.emboss.jemboss.gui.filetree.RemoteDragTree
dragGestureRecognized(DragGestureEvent) - Method in class org.emboss.jemboss.gui.filetree.DragTree
DragJTable - class org.emboss.jemboss.gui.DragJTable.
DragJTable(SequenceListTableModel) - Constructor for class org.emboss.jemboss.gui.DragJTable
dragOver(DragSourceDragEvent) - Method in class org.emboss.jemboss.gui.DragJTable
dragOver(DragSourceDragEvent) - Method in class org.emboss.jemboss.gui.filetree.RemoteDragTree
dragOver(DragSourceDragEvent) - Method in class org.emboss.jemboss.gui.filetree.DragTree
dragOver(DropTargetDragEvent) - Method in class org.emboss.jemboss.gui.DragJTable
dragOver(DropTargetDragEvent) - Method in class org.emboss.jemboss.gui.filetree.RemoteDragTree
  When a suitable DataFlavor is offered over a remote file node the node is highlighted/selected and the drag accepted.
dragOver(DropTargetDragEvent) - Method in class org.emboss.jemboss.gui.filetree.DragTree
  When a suitable DataFlavor is offered over a remote file node the node is highlighted/selected and the drag accepted.
dragOver(DropTargetDragEvent) - Method in class org.emboss.jemboss.gui.form.TextFieldSink
dragOver(DropTargetDragEvent) - Method in class org.emboss.jemboss.gui.sequenceChooser.TextAreaSink
DragTree - class org.emboss.jemboss.gui.filetree.DragTree.
  Creates a local file tree for Jemboss.
DragTree.PopupListener - class org.emboss.jemboss.gui.filetree.DragTree.PopupListener.
DragTree.PopupListener() - Constructor for class org.emboss.jemboss.gui.filetree.DragTree.PopupListener
DragTree(File, JFrame, JembossParams) - Constructor for class org.emboss.jemboss.gui.filetree.DragTree
drawBlackBox - Variable in class org.emboss.jemboss.editor.SequenceJPanel
drawBlackBox - Variable in class org.emboss.jemboss.editor.GraphicSequenceCollection
drawColorBox - Variable in class org.emboss.jemboss.editor.SequenceJPanel
drawColorBox - Variable in class org.emboss.jemboss.editor.GraphicSequenceCollection
drawNumber - Variable in class org.emboss.jemboss.editor.SequenceJPanel
drawNumber - Variable in class org.emboss.jemboss.editor.GraphicSequenceCollection
drawSequence - Variable in class org.emboss.jemboss.editor.SequenceJPanel
drawSequence - Variable in class org.emboss.jemboss.editor.GraphicSequenceCollection
drawSequences(Graphics2D, PageFormat, int) - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection
drawSequences(Graphics2D, PageFormat, int, int) - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection
drop(DropTargetDropEvent) - Method in class org.emboss.jemboss.gui.DragJTable
drop(DropTargetDropEvent) - Method in class org.emboss.jemboss.gui.filetree.RemoteDragTree
drop(DropTargetDropEvent) - Method in class org.emboss.jemboss.gui.filetree.DragTree
drop(DropTargetDropEvent) - Method in class org.emboss.jemboss.gui.form.TextFieldSink
drop(DropTargetDropEvent) - Method in class org.emboss.jemboss.gui.sequenceChooser.TextAreaSink
dropActionChanged(DragSourceDragEvent) - Method in class org.emboss.jemboss.gui.DragJTable
dropActionChanged(DragSourceDragEvent) - Method in class org.emboss.jemboss.gui.filetree.RemoteDragTree
dropActionChanged(DragSourceDragEvent) - Method in class org.emboss.jemboss.gui.filetree.DragTree
dropActionChanged(DropTargetDragEvent) - Method in class org.emboss.jemboss.gui.DragJTable
dropActionChanged(DropTargetDragEvent) - Method in class org.emboss.jemboss.gui.filetree.RemoteDragTree
dropActionChanged(DropTargetDragEvent) - Method in class org.emboss.jemboss.gui.filetree.DragTree
dropActionChanged(DropTargetDragEvent) - Method in class org.emboss.jemboss.gui.form.TextFieldSink
dropActionChanged(DropTargetDragEvent) - Method in class org.emboss.jemboss.gui.sequenceChooser.TextAreaSink
dropBorder - Static variable in class org.emboss.jemboss.gui.form.TextFieldSink
dropBorder - Static variable in class org.emboss.jemboss.gui.sequenceChooser.TextAreaSink

## E

elements() - Method in class org.emboss.jemboss.programs.ResultList
elements() - Method in class org.emboss.jemboss.soap.JembossRun
embl - Static variable in class org.emboss.jemboss.gui.sequenceChooser.SequenceFilter
embossBin - Variable in class org.emboss.jemboss.JembossParams
embossBin - Variable in class org.emboss.jemboss.gui.form.BuildJembossForm
embossBin - Variable in class org.emboss.jemboss.server.JembossServer
embossBin - Variable in class org.emboss.jemboss.server.JembossFileAuthServer
embossBin - Variable in class org.emboss.jemboss.server.JembossAuthServer
embossBinName - Variable in class org.emboss.jemboss.JembossParams
embossCommand - Variable in class org.emboss.jemboss.server.JembossAuthThread
embossData - Variable in class org.emboss.jemboss.JembossParams
embossData - Variable in class org.emboss.jemboss.server.JembossServer
embossData - Variable in class org.emboss.jemboss.server.JembossAuthServer
embossDataName - Variable in class org.emboss.jemboss.JembossParams
embossEnvironment - Variable in class org.emboss.jemboss.JembossParams
embossEnvironmentName - Variable in class org.emboss.jemboss.JembossParams
embossPath - Variable in class org.emboss.jemboss.JembossParams
embossPath - Variable in class org.emboss.jemboss.server.JembossServer
embossPath - Variable in class org.emboss.jemboss.server.JembossFileAuthServer
embossPath - Variable in class org.emboss.jemboss.server.JembossAuthServer
embossPathName - Variable in class org.emboss.jemboss.JembossParams
embossURL - Variable in class org.emboss.jemboss.JembossParams
embreo_roots(String) - Method in class org.emboss.jemboss.server.JembossFileServer
embreo_roots(String, byte[]) - Method in class org.emboss.jemboss.server.JembossFileAuthServer
embURL - Variable in class org.emboss.jemboss.JembossParams
endBorder - Static variable in class org.emboss.jemboss.gui.form.TextFieldSink
env - Variable in class org.emboss.jemboss.server.JembossAuthServer
environ - Variable in class org.emboss.jemboss.server.JembossFileAuthServer
environ - Variable in class org.emboss.jemboss.server.JembossAuthThread
environ - Variable in class org.emboss.jemboss.server.JembossAuthServer
envp - Variable in class org.emboss.jemboss.gui.form.BuildJembossForm
envp - Variable in class org.emboss.jemboss.server.JembossServer
envp_emboss - Variable in class org.emboss.jemboss.server.JembossServer
epr - Variable in class org.emboss.jemboss.soap.GetWossname
epr - Variable in class org.emboss.jemboss.soap.CallAjax
errorLog - Variable in class org.emboss.jemboss.server.JembossAuthServer
errStd - Variable in class org.emboss.jemboss.parser.Ajax
exitOnDone - Variable in class org.emboss.jemboss.soap.AuthPopup
exp - Variable in class org.emboss.jemboss.parser.Dependent
exp - Variable in class org.emboss.jemboss.parser.AcdVariableResolve
exp - Variable in class org.emboss.jemboss.parser.AcdVarResolve
expandWildcards(String) - Static method in class org.emboss.jemboss.programs.ListFile
  Wildcard (*) is allowed in the filelist data types.
explore() - Method in class org.emboss.jemboss.gui.filetree.RemoteFileNode
explore() - Method in class org.emboss.jemboss.gui.filetree.FileNode
explored - Variable in class org.emboss.jemboss.gui.filetree.RemoteFileNode
explored - Variable in class org.emboss.jemboss.gui.filetree.FileNode
extend - Variable in class org.emboss.jemboss.Jemboss

## F

f - Variable in class org.emboss.jemboss.Jemboss
f - Variable in class org.emboss.jemboss.gui.filetree.FileSave
f - Variable in class org.emboss.jemboss.gui.form.SectionPanel
f - Variable in class org.emboss.jemboss.gui.form.BuildJembossForm
fasta - Static variable in class org.emboss.jemboss.gui.sequenceChooser.SequenceFilter
fc - Variable in class org.emboss.jemboss.gui.sequenceChooser.FileChooser
fExists - Variable in class org.emboss.jemboss.gui.filetree.FileSave
ff - Variable in class org.emboss.jemboss.gui.sequenceChooser.OutputSequenceAttributes
ff - Variable in class org.emboss.jemboss.gui.sequenceChooser.InputSequenceAttributes
field - Variable in class org.emboss.jemboss.parser.Dependent
fieldOption - Variable in class org.emboss.jemboss.gui.form.SectionPanel
fieldOption - Variable in class org.emboss.jemboss.gui.form.BuildJembossForm
fileChoose - Variable in class org.emboss.jemboss.gui.form.SetInFileCard
fileChooser - Variable in class org.emboss.jemboss.gui.form.ListFilePanel
FileChooser - class org.emboss.jemboss.gui.sequenceChooser.FileChooser.
  Creates a JFileChooser and add it to the Box.
FileChooser(Box, String, JembossParams) - Constructor for class org.emboss.jemboss.gui.sequenceChooser.FileChooser
FileEditorDisplay - class org.emboss.jemboss.gui.filetree.FileEditorDisplay.
  Display for text, sequence editing, html, gif, png, jpeg.
FileEditorDisplay(JFrame, String) - Constructor for class org.emboss.jemboss.gui.filetree.FileEditorDisplay
FileEditorDisplay(JFrame, String, Object) - Constructor for class org.emboss.jemboss.gui.filetree.FileEditorDisplay
fileExists() - Method in class org.emboss.jemboss.gui.filetree.FileSave
fileFormats - Variable in class org.emboss.jemboss.gui.sequenceChooser.OutputSequenceAttributes
fileFormats - Variable in class org.emboss.jemboss.gui.sequenceChooser.InputSequenceAttributes
filelist - Variable in class org.emboss.jemboss.gui.form.SectionPanel
filelist - Variable in class org.emboss.jemboss.gui.form.BuildJembossForm
FileList - class org.emboss.jemboss.soap.FileList.
FileList(JembossParams, String, String) - Constructor for class org.emboss.jemboss.soap.FileList
  Retrieves a directory listing from an embreo server.
FileManager - class org.emboss.jemboss.FileManager.
FileManager() - Constructor for class org.emboss.jemboss.FileManager
fileMenuShowres - Variable in class org.emboss.jemboss.gui.SetUpMenuBar
fileMenuShowres - Variable in class org.emboss.jemboss.gui.ResultsMenuBar
filename - Variable in class org.emboss.jemboss.gui.filetree.FileEditorDisplay
filename - Static variable in class org.emboss.jemboss.server.TestPrivateServer
fileName - Variable in class org.emboss.jemboss.gui.sequenceChooser.FileChooser
FileNode - class org.emboss.jemboss.gui.filetree.FileNode.
FILENODE - Static variable in class org.emboss.jemboss.gui.filetree.FileNode
FileNode(File) - Constructor for class org.emboss.jemboss.gui.filetree.FileNode
fileok - Variable in class org.emboss.jemboss.parser.Ajax
filePrefix - Variable in class org.emboss.jemboss.editor.PrintAlignmentImage
fileRoots - Variable in class org.emboss.jemboss.soap.FileRoots
FileRoots - class org.emboss.jemboss.soap.FileRoots.
FileRoots(JembossParams) - Constructor for class org.emboss.jemboss.soap.FileRoots
  Retrieve the list of available filesystem roots
FileSave - class org.emboss.jemboss.gui.filetree.FileSave.
FileSave(File) - Constructor for class org.emboss.jemboss.gui.filetree.FileSave
  Check if we can/want to save file to disk.
fileSave(String, String, Object) - Method in class org.emboss.jemboss.gui.ResultsMenuBar
fileSave(String, String, String, Hashtable) - Method in class org.emboss.jemboss.gui.ResultsMenuBar
FileSaving - class org.emboss.jemboss.gui.filetree.FileSaving.
  Saves files
FileSaving(JTextPane, byte[], JembossParams) - Constructor for class org.emboss.jemboss.gui.filetree.FileSaving
fileSaving(Object) - Method in class org.emboss.jemboss.gui.filetree.FileSave
fileSelected - Variable in class org.emboss.jemboss.gui.filetree.FileSaving
fileSelected - Variable in class org.emboss.jemboss.gui.sequenceChooser.FileChooser
filesForSoap(String, String, String, Hashtable) - Method in class org.emboss.jemboss.gui.form.BuildJembossForm
filesForSoap(String, String, String, Hashtable) - Method in class org.emboss.jemboss.server.TestPrivateServer
fileVector() - Method in class org.emboss.jemboss.soap.FileList
  Gets the list of files as a Vector
fileWritten - Variable in class org.emboss.jemboss.gui.filetree.FileSave
finalize() - Method in class org.emboss.jemboss.gui.form.BuildJembossForm
  Ensures garbaged collected when there are no more pointers to this.
findHeader(String) - Method in class org.emboss.jemboss.gui.filetree.FileEditorDisplay
  Sequence header text.
findInt(String) - Method in class org.emboss.jemboss.gui.ShowResultSet
findMiddle(int, int, String) - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection
  Locate the center of a vieport view that contains the defined position to display
findPattern(String, int, boolean) - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection
  Search sequences for a pattern and highlight matches.
finished() - Method in class org.emboss.jemboss.gui.SwingWorker
  Called on the event dispatching thread (not on the worker thread) after the `construct` method has returned.
flavors - Static variable in class org.emboss.jemboss.gui.SequenceData
  available dataflavors
flavors - Static variable in class org.emboss.jemboss.gui.filetree.RemoteFileNode
flavors - Static variable in class org.emboss.jemboss.gui.filetree.FileNode
flist - Variable in class org.emboss.jemboss.soap.FileList
font - Variable in class org.emboss.jemboss.editor.SequenceNameJButton
font - Variable in class org.emboss.jemboss.editor.SequenceJPanel
fontSize - Variable in class org.emboss.jemboss.JembossLogo
fontSize - Variable in class org.emboss.jemboss.editor.SequenceNameJButton
fontSize - Variable in class org.emboss.jemboss.editor.SequenceJPanel
fontSize - Variable in class org.emboss.jemboss.gui.form.ApplicationNamePanel
forkBatch(String, byte[], String, String, String) - Method in class org.emboss.jemboss.parser.Ajax
forkEmboss(String, byte[], String, String, String) - Method in class org.emboss.jemboss.parser.Ajax
format - Variable in class org.emboss.jemboss.editor.PrintAlignmentImage
formatHelpText(String) - Method in class org.emboss.jemboss.parser.ParseAcd
  Limits the length of the line for the help text used in the tool tips.
frame - Variable in class org.emboss.jemboss.gui.ResultsMenuBar
froots - Variable in class org.emboss.jemboss.gui.filetree.RemoteFileNode
froots - Static variable in class org.emboss.jemboss.gui.filetree.RemoteDragTree
fs - Variable in class org.emboss.jemboss.gui.filetree.RemoteFileNode
fs - Variable in class org.emboss.jemboss.gui.filetree.RemoteDragTree
fs - Variable in class org.emboss.jemboss.gui.filetree.DragTree
fs - Variable in class org.emboss.jemboss.server.JembossServer
fs - Variable in class org.emboss.jemboss.server.JembossAuthServer
fullname - Variable in class org.emboss.jemboss.gui.filetree.RemoteFileNode
fvis - Variable in class org.emboss.jemboss.gui.sequenceChooser.InputSequenceAttributes
fwdArrow - Variable in class org.emboss.jemboss.Jemboss

## G

g - Variable in class org.emboss.jemboss.gui.form.MultiLineToolTipUI
gcg - Static variable in class org.emboss.jemboss.gui.sequenceChooser.SequenceFilter
get_file(String, String, String) - Method in class org.emboss.jemboss.server.JembossFileServer
get_file(String, String, String, byte[]) - Method in class org.emboss.jemboss.server.JembossFileAuthServer
get() - Method in class org.emboss.jemboss.gui.SwingWorker
  Return the value created by the `construct` method.
get() - Method in class org.emboss.jemboss.gui.SwingWorker.ThreadVar
get(Object) - Method in class org.emboss.jemboss.programs.ResultList
get(Object) - Method in class org.emboss.jemboss.soap.JembossRun
getAccCheckBox() - Method in class org.emboss.jemboss.gui.form.ReportFormat
getAcceleratorString(JToolTip) - Method in class org.emboss.jemboss.gui.form.MultiLineToolTipUI
GetACD - class org.emboss.jemboss.soap.GetACD.
getAcd() - Method in class org.emboss.jemboss.soap.GetACD
  Return the text of the ACD file
GetACD(String, JembossParams) - Constructor for class org.emboss.jemboss.soap.GetACD
  Retrieve an ACD file using soap
getAcdDirToParse() - Method in class org.emboss.jemboss.JembossParams
getAcdText(String, String, JembossParams, boolean) - Method in class org.emboss.jemboss.gui.BuildProgramMenu
  Get the contents of an ACD file in the form of a String.
getAlignFormat() - Method in class org.emboss.jemboss.gui.form.SectionPanel
getAlignFormat() - Method in class org.emboss.jemboss.gui.form.AlignFormat
getAlignFormats(boolean) - Method in class org.emboss.jemboss.gui.form.AlignFormat
getAllowsChildren() - Method in class org.emboss.jemboss.gui.filetree.RemoteFileNode
getAllowsChildren() - Method in class org.emboss.jemboss.gui.filetree.FileNode
getAnIndex(FileNode, String) - Method in class org.emboss.jemboss.gui.filetree.DragTree
  Finds a new index for adding a new file to the file manager.
getArrayListFile() - Method in class org.emboss.jemboss.gui.form.SetInFileCard
getArrayListFile() - Method in class org.emboss.jemboss.gui.form.ListFilePanel
getAttribute() - Method in class org.emboss.jemboss.parser.acd.ApplicationParam
getBegSeq() - Method in class org.emboss.jemboss.gui.sequenceChooser.InputSequenceAttributes
getBrowserProxyHost() - Method in class org.emboss.jemboss.JembossParams
  The name of the proxy server for the browser
getBrowserProxyPort() - Method in class org.emboss.jemboss.JembossParams
  The port number of the proxy server for the browser
getCodonUsage() - Static method in class org.emboss.jemboss.gui.BuildProgramMenu
getCodonUsage() - Method in class org.emboss.jemboss.soap.ShowDB
  Retrieves the codon tables
getColor() - Method in class org.emboss.jemboss.editor.ColourMenu
getColor() - Method in class org.emboss.jemboss.editor.ColourMenu.ColorPane
getColor() - Method in class org.emboss.jemboss.gui.ColorMenu
getColor() - Method in class org.emboss.jemboss.gui.ColorMenu.ColorPane
getColor(String) - Method in class org.emboss.jemboss.editor.SequenceJPanel
getColor(String, int, String) - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection
getColumnClass(int) - Method in class org.emboss.jemboss.gui.SequenceListTableModel
  DragJTable uses this method to determine the default renderer/ editor for each cell.
getColumnCount() - Method in class org.emboss.jemboss.gui.SequenceListTableModel
  Return the number of columns in the table
getColumnName(int) - Method in class org.emboss.jemboss.gui.SequenceListTableModel
  Return the name columns in the table
getComboPopup() - Method in class org.emboss.jemboss.gui.form.ReportFormat
getComboPopup() - Method in class org.emboss.jemboss.gui.form.AlignFormat
getCommand() - Method in class org.emboss.jemboss.gui.form.BuildJembossForm
  Get the command line for the Standalone version.
getCommand(Hashtable) - Method in class org.emboss.jemboss.gui.form.BuildJembossForm
  Get the command line for the SOAP version.
getConsensusSequence() - Method in class org.emboss.jemboss.editor.Consensus
getCurrentColourScheme() - Method in class org.emboss.jemboss.editor.ColourJFrame
getCurrentDir() - Method in class org.emboss.jemboss.soap.FileRoots
  Get the currently selected directory
getCurrentMatrixName() - Method in class org.emboss.jemboss.editor.Matrix
getCurrentMode() - Method in class org.emboss.jemboss.JembossParams
  The current mode (interactive or batch).
getCurrentRoot() - Method in class org.emboss.jemboss.soap.FileRoots
  Get the currently selected root
getCutNPasteText() - Method in class org.emboss.jemboss.gui.form.SetInFileCard
getDatabaseList() - Static method in class org.emboss.jemboss.gui.BuildProgramMenu
  List of available EMBOSS databases.
getDB() - Method in class org.emboss.jemboss.gui.startup.Database
getDBText() - Method in class org.emboss.jemboss.soap.ShowDB
  The output from showdb
getDBText() - Method in class org.emboss.jemboss.soap.GetWossname
getDebug() - Method in class org.emboss.jemboss.JembossParams
  Whether to show debugging information
getDefaultFormat() - Method in class org.emboss.jemboss.gui.form.ReportFormat
getDefaultFormat() - Method in class org.emboss.jemboss.gui.form.AlignFormat
getDefaultParamValueDbl(int) - Method in class org.emboss.jemboss.parser.ParseAcd
  Return a double default parameter
getDefaultParamValueStr(int) - Method in class org.emboss.jemboss.parser.ParseAcd
  Gets a String default parameter.
getDefaultRoot() - Method in class org.emboss.jemboss.soap.FileRoots
  Get the default root, if defined, else return null
getDefaultRootIndex() - Method in class org.emboss.jemboss.soap.FileRoots
  Get the index of the default root in the Vector, else return -1
getDefaultRow() - Method in class org.emboss.jemboss.gui.SequenceList
  Look for first set to default in the table.
getDefaultSequenceName() - Method in class org.emboss.jemboss.gui.SequenceList
  Get the default Sequence name
getDefaultTab() - Method in class org.emboss.jemboss.gui.TabListCellRenderer
getDependentExp() - Method in class org.emboss.jemboss.parser.Dependent
getDependentField() - Method in class org.emboss.jemboss.parser.Dependent
getDependentParam() - Method in class org.emboss.jemboss.parser.Dependent
getDependents() - Method in class org.emboss.jemboss.parser.ParseAcd
  Gets the dependents associated with the ACD.
getDependentType() - Method in class org.emboss.jemboss.parser.Dependent
getDesCheckBox() - Method in class org.emboss.jemboss.gui.form.ReportFormat
getDescription() - Method in class org.emboss.jemboss.editor.SequenceJPanel
getDescription() - Method in class org.emboss.jemboss.gui.sequenceChooser.SequenceFilter
getDescription() - Method in class org.emboss.jemboss.programs.JembossProcess
getDoc() - Method in class org.emboss.jemboss.parser.acd.Application
getElement(String) - Method in class org.emboss.jemboss.JembossJarUtil
getEmbossBin() - Method in class org.emboss.jemboss.JembossParams
getEmbossData() - Method in class org.emboss.jemboss.JembossParams
getEmbossEnvironment() - Method in class org.emboss.jemboss.JembossParams
getEmbossEnvironmentArray(String[]) - Method in class org.emboss.jemboss.JembossParams
getEmbossPath() - Method in class org.emboss.jemboss.JembossParams
getembURL() - Method in class org.emboss.jemboss.JembossParams
getEndSeq() - Method in class org.emboss.jemboss.gui.sequenceChooser.InputSequenceAttributes
getErrStd() - Method in class org.emboss.jemboss.parser.Ajax
getExpectedCPU() - Method in class org.emboss.jemboss.parser.ParseAcd
  Finds any expected cpu level indicator (low, medium, high)
getExtension(File) - Static method in class org.emboss.jemboss.gui.sequenceChooser.SequenceFilter
getFieldNum() - Method in class org.emboss.jemboss.gui.form.SectionPanel
getFile() - Method in class org.emboss.jemboss.gui.filetree.RemoteFileNode
getFile() - Method in class org.emboss.jemboss.gui.filetree.FileNode
getFile(String, byte[], String, String) - Method in class org.emboss.jemboss.parser.Ajax
getFileChosen() - Method in class org.emboss.jemboss.gui.form.SetInFileCard
getFileChosen() - Method in class org.emboss.jemboss.gui.sequenceChooser.FileChooser
getFilename() - Method in class org.emboss.jemboss.gui.filetree.RemoteDragTree
getFilename() - Method in class org.emboss.jemboss.gui.filetree.DragTree
getFileName() - Method in class org.emboss.jemboss.gui.filetree.FileSaving
getFileName(int) - Method in class org.emboss.jemboss.gui.DragJTable
getFileok() - Method in class org.emboss.jemboss.parser.Ajax
getFileOrDatabaseForAjax(String, String[], JFrame, boolean) - Static method in class org.emboss.jemboss.parser.AjaxUtil
  Returns the sequence file contents or the database entry ready to use in Ajax.
getFont() - Method in class org.emboss.jemboss.editor.SequenceNameJButton
getFontSize() - Method in class org.emboss.jemboss.editor.SequenceJPanel
getFontSize() - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection
getFormat() - Method in class org.emboss.jemboss.editor.PrintAlignmentImage
getFormatChoosen() - Method in class org.emboss.jemboss.gui.sequenceChooser.OutputSequenceAttributes
getFormatChoosen() - Method in class org.emboss.jemboss.gui.sequenceChooser.InputSequenceAttributes
getFormatDialog() - Method in class org.emboss.jemboss.editor.PrintAlignmentImage
  Define a PageFormat
getFullName() - Method in class org.emboss.jemboss.gui.filetree.RemoteFileNode
getGraphicSequence() - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection
getGroups() - Method in class org.emboss.jemboss.parser.acd.Application
getGuiHandleNumber() - Method in class org.emboss.jemboss.parser.acd.ApplicationFields
getGuiHandleNumber(int) - Method in class org.emboss.jemboss.parser.ParseAcd
  Gets the handle for a gui component on the Jemboss form.
getHasBatchMode() - Method in class org.emboss.jemboss.JembossParams
  Whether this service supports batch mode
getHash() - Method in class org.emboss.jemboss.JembossJarUtil
getHash() - Method in class org.emboss.jemboss.soap.PublicRequest
  The hash returned by the embreo call.
getHash() - Method in class org.emboss.jemboss.soap.PrivateRequest
getHashtable(Vector) - Method in class org.emboss.jemboss.server.JembossServer
getHashtable(Vector) - Method in class org.emboss.jemboss.server.JembossAuthServer
getHasInteractiveMode() - Method in class org.emboss.jemboss.JembossParams
  Whether this service supports interactive mode
GetHelp - class org.emboss.jemboss.soap.GetHelp.
GetHelp(String, JembossParams) - Constructor for class org.emboss.jemboss.soap.GetHelp
  Get the help text for an application
getHelpParamValue(int) - Method in class org.emboss.jemboss.parser.ParseAcd
  Finds the help parameter in an ACD field.
getHelpText() - Method in class org.emboss.jemboss.soap.GetHelp
getHomeDirectory() - Method in class org.emboss.jemboss.gui.AdvancedOptions
getID() - Method in class org.emboss.jemboss.editor.Sequence
getIDimension() - Method in class org.emboss.jemboss.editor.Matrix
getInCard() - Method in class org.emboss.jemboss.gui.form.SetInFileCard
getInfoParamValue(int) - Method in class org.emboss.jemboss.parser.ParseAcd
  Finds the prompt, info or help parameter in an ACD field, in that order.
getInputSeqAttr(int) - Method in class org.emboss.jemboss.gui.sequenceChooser.InputSequenceAttributes
getJDimension() - Method in class org.emboss.jemboss.editor.Matrix
getJFileChooser() - Method in class org.emboss.jemboss.gui.sequenceChooser.FileChooser
getJMenuBar() - Method in class org.emboss.jemboss.gui.ResultsMenuBar
getJob() - Method in class org.emboss.jemboss.programs.JembossProcess
getJScrollPane() - Method in class org.emboss.jemboss.gui.sequenceChooser.OutputSequenceAttributes
getJScrollPane() - Method in class org.emboss.jemboss.gui.sequenceChooser.InputSequenceAttributes
getJTextComponentAt(JTabbedPane, int) - Method in class org.emboss.jemboss.gui.ResultsMenuBar
getJTextPane() - Method in class org.emboss.jemboss.gui.filetree.FileEditorDisplay
  Returns instance of JTextPane.
getKeyNames() - Method in class org.emboss.jemboss.editor.Matrix
getKeys() - Method in class org.emboss.jemboss.editor.Matrix
getLength() - Method in class org.emboss.jemboss.editor.Sequence
getLength() - Method in class org.emboss.jemboss.soap.CallAjax
getList(int) - Method in class org.emboss.jemboss.parser.ParseAcd
  Used for a list data type to put the list items in a String array.
getListCellRendererComponent(JList, Object, int, boolean, boolean) - Method in class org.emboss.jemboss.gui.TabListCellRenderer
getListFile() - Method in class org.emboss.jemboss.gui.form.SetInFileCard
getListFile() - Method in class org.emboss.jemboss.gui.form.ListFilePanel
getListLabel(int, int) - Method in class org.emboss.jemboss.parser.ParseAcd
  For a list data type determine the appropriate String entry.
getListOrSelectDefault() - Method in class org.emboss.jemboss.parser.ParseAcd
  Use this after getList or getSelect to retrieve default
getLocalDragTree() - Static method in class org.emboss.jemboss.gui.SetUpMenuBar
getLocalDragTree() - Static method in class org.emboss.jemboss.gui.filetree.LocalAndRemoteFileTreeFrame
getLocalFile(File) - Method in class org.emboss.jemboss.gui.filetree.RemoteDragTree
getLocalFile(File) - Method in class org.emboss.jemboss.gui.form.BuildJembossForm
getLocalFile(File) - Static method in class org.emboss.jemboss.programs.ListFile
  Read file in as a byte array.
getLocalFile(File) - Method in class org.emboss.jemboss.server.TestPrivateServer
getMatrices() - Static method in class org.emboss.jemboss.gui.BuildProgramMenu
getMatrices() - Method in class org.emboss.jemboss.soap.ShowDB
  Retrieves the available matrices
getMatrix() - Method in class org.emboss.jemboss.editor.Matrix
getMatrixIndex(String) - Method in class org.emboss.jemboss.editor.Matrix
getMatrixTable() - Method in class org.emboss.jemboss.editor.Matrix
getMaximumSize() - Method in class org.emboss.jemboss.editor.ColourMenu.ColorPane
getMaximumSize() - Method in class org.emboss.jemboss.gui.ColorMenu.ColorPane
getMaximumSize(JComponent) - Method in class org.emboss.jemboss.gui.form.MultiLineToolTipUI
getMaxParam(int) - Method in class org.emboss.jemboss.parser.ParseAcd
  Locates the max parameter in a field and returns it as a String.
getMaxSeqLength() - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection
getMaxSequenceLength(Vector) - Method in class org.emboss.jemboss.editor.PlotConsensus
  Check all sequences lengths and return length of the longest sequence
getMaxSequenceLength(Vector) - Method in class org.emboss.jemboss.editor.Consensus
  Check all sequences lengths and return length of the longest sequence
getMenuItems() - Method in class org.emboss.jemboss.gui.startup.ProgList
  Returns the program menu items
getMinimumSize() - Method in class org.emboss.jemboss.editor.ColourMenu.ColorPane
getMinimumSize() - Method in class org.emboss.jemboss.gui.ColorMenu.ColorPane
getMinimumSize(JComponent) - Method in class org.emboss.jemboss.gui.form.MultiLineToolTipUI
getMinMaxDefault(String, String, String, int) - Method in class org.emboss.jemboss.gui.form.SectionPanel
getMinParam(int) - Method in class org.emboss.jemboss.parser.ParseAcd
  Locates the min parameter in a field and returns it as a String.
getName() - Method in class org.emboss.jemboss.editor.Sequence
getName() - Method in class org.emboss.jemboss.parser.acd.Application
getNameHeight() - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection
getNamePrintGraphic(Graphics) - Method in class org.emboss.jemboss.editor.SequenceJPanel
getNameViewSize() - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection
  Get the sequence name view size
getNameWidth() - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection
getNode(String) - Method in class org.emboss.jemboss.gui.filetree.DragTree
  Gets the node from the existing explored nodes.
getNodename() - Method in class org.emboss.jemboss.gui.filetree.RemoteDragTree
getNumberMenuItems() - Method in class org.emboss.jemboss.gui.startup.ProgList
  Returns the number of program menu items
getNumberOfParam() - Method in class org.emboss.jemboss.parser.acd.ApplicationFields
getNumberOfSequences() - Method in class org.emboss.jemboss.editor.SequenceReader
  Returns the number of sequences.
getNumberPages(PageFormat) - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection
getNumberPages(PageFormat, int) - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection
getNumBool() - Method in class org.emboss.jemboss.parser.ParseAcd
  Gets the number of boolean data types in the ACD.
getNumFileList() - Method in class org.emboss.jemboss.parser.ParseAcd
  Gets the number of filelist data types in the ACD
getNumList() - Method in class org.emboss.jemboss.parser.ParseAcd
  Gets the number of list & selection data types in the ACD, using single list selection
getNumMList() - Method in class org.emboss.jemboss.parser.ParseAcd
  Gets the number of list & selection data types in the ACD, using multiple list selection
getNumNfloat() - Method in class org.emboss.jemboss.parser.ParseAcd
  Gets the number of float data types in the ACD.
getNumNint() - Method in class org.emboss.jemboss.parser.ParseAcd
  Gets the number of int data types in the ACD.
getNumOfDependents() - Method in class org.emboss.jemboss.parser.ParseAcd
  Gets the number of dependent parameters in the ACD.
getNumofFields() - Method in class org.emboss.jemboss.parser.ParseAcd
  Gets the number of fields in the ACD file.
getNumofParams(int) - Method in class org.emboss.jemboss.parser.ParseAcd
  Gets the number of parameters in a ACD field.
getNumPrimaryGroups() - Method in class org.emboss.jemboss.gui.startup.ProgList
  Returns the number of primary menu groups
getNumProgs() - Method in class org.emboss.jemboss.gui.startup.ProgList
  Returns the number of programs
getNumRange() - Method in class org.emboss.jemboss.parser.ParseAcd
getNumSection() - Method in class org.emboss.jemboss.parser.ParseAcd
  Gets the number of sections in the ACD
getNumSeq() - Method in class org.emboss.jemboss.parser.ParseAcd
  Gets the number of seqset, seqall & sequence data types in the ACD
getNumSubsection() - Method in class org.emboss.jemboss.parser.ParseAcd
  Gets the number of nested sections in the ACD
getNumTextf() - Method in class org.emboss.jemboss.parser.ParseAcd
  Gets the number of float, string, seqout, outfile, infile, regexp, codon & featout data types in the ACD.
getOKButton() - Method in class org.emboss.jemboss.soap.AuthPopup
getOuputSeqAttr() - Method in class org.emboss.jemboss.gui.sequenceChooser.OutputSequenceAttributes
getOutputSequenceFile(int) - Method in class org.emboss.jemboss.parser.ParseAcd
  Gets the name of the output sequence field (seqout).
getOutStd() - Method in class org.emboss.jemboss.parser.Ajax
getPanelHeight() - Method in class org.emboss.jemboss.editor.SequenceNameJButton
getPanelHeight() - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection
getPanelSize() - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection
getPanelWidth() - Method in class org.emboss.jemboss.editor.SequenceNameJButton
getPanelWidth() - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection
getParamAttribute(int) - Method in class org.emboss.jemboss.parser.acd.ApplicationFields
getParameterAttribute(int, int) - Method in class org.emboss.jemboss.parser.ParseAcd
  Get a specified parameter attribute.
getParamValueDbl(int) - Method in class org.emboss.jemboss.parser.acd.ApplicationFields
getParamValueDbl(int, int) - Method in class org.emboss.jemboss.parser.ParseAcd
  Gets the double value of a parameter.
getParamValueStr(int) - Method in class org.emboss.jemboss.parser.acd.ApplicationFields
getParamValueStr(int, int) - Method in class org.emboss.jemboss.parser.ParseAcd
  Gets the String value of a parameter.
getPath() - Method in class org.emboss.jemboss.gui.filetree.FileSaving
getPathName() - Method in class org.emboss.jemboss.gui.filetree.RemoteFileNode
getPatternPositions(int, int, String) - Method in class org.emboss.jemboss.editor.SequenceJPanel
  Find all occurences of the pattern in the sequence between the start and stop positions.
getPatternPositions(int, String) - Method in class org.emboss.jemboss.editor.SequenceJPanel
  Find all occurences of the pattern in the sequence between the start and stop positions.
getPlplot() - Method in class org.emboss.jemboss.JembossParams
getPNGContent() - Method in class org.emboss.jemboss.gui.filetree.FileEditorDisplay
  Returns the content of a png file or null.
getPreferredScrollableViewportSize() - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection
getPreferredScrollableViewportSize() - Method in class org.emboss.jemboss.gui.ScrollPanel
getPreferredSize() - Method in class org.emboss.jemboss.editor.SequenceNameJButton
getPreferredSize() - Method in class org.emboss.jemboss.editor.SequenceJPanel
getPreferredSize() - Method in class org.emboss.jemboss.editor.ColourMenu.ColorPane
getPreferredSize() - Method in class org.emboss.jemboss.gui.ColorMenu.ColorPane
getPreferredSize() - Method in class org.emboss.jemboss.gui.sequenceChooser.FileChooser
getPreferredSize(JComponent) - Method in class org.emboss.jemboss.gui.form.MultiLineToolTipUI
getPrivateServerFailover() - Method in class org.emboss.jemboss.JembossParams
  Return whether we have failover on the private server
getPrivateServers() - Method in class org.emboss.jemboss.JembossParams
  Return a vector containing the list of private servers
getPrivateSoapService() - Method in class org.emboss.jemboss.JembossParams
  Get the name of the private soap service we're using
getPrivateSoapURL() - Method in class org.emboss.jemboss.JembossParams
  Returns the URL of the private soap server
getPrnt() - Method in class org.emboss.jemboss.parser.Ajax
getProcess() - Method in class org.emboss.jemboss.programs.RunEmbossApplication2
getProcess() - Method in class org.emboss.jemboss.programs.RunEmbossApplication
getProcessStdout() - Method in class org.emboss.jemboss.programs.RunEmbossApplication2
getProcessStdout() - Method in class org.emboss.jemboss.programs.RunEmbossApplication
getProgDescription() - Method in class org.emboss.jemboss.gui.startup.ProgList
  Returns the array of the program descriptions
getProgsList() - Method in class org.emboss.jemboss.gui.startup.ProgList
  Returns the array of all the program names
getProject() - Method in class org.emboss.jemboss.programs.JembossProcess
getProxyAuthPasswd() - Method in class org.emboss.jemboss.JembossParams
  password needed to use for the proxy server
getProxyAuthUser() - Method in class org.emboss.jemboss.JembossParams
  username needed to use for the proxy server
getProxyHost() - Method in class org.emboss.jemboss.JembossParams
  The name of the proxy server
getProxyPortNum() - Method in class org.emboss.jemboss.JembossParams
  The port the proxy server listens on
getPublicServerFailover() - Method in class org.emboss.jemboss.JembossParams
  Return whether we have failover on the public server
getPublicServers() - Method in class org.emboss.jemboss.JembossParams
  Return a vector containing the list of public servers
getPublicSoapService() - Method in class org.emboss.jemboss.JembossParams
  Get the name of the public soap service we're using
getPublicSoapURL() - Method in class org.emboss.jemboss.JembossParams
  Returns the URL of the public soap server
getRegularExpression() - Method in class org.emboss.jemboss.editor.Matrix
getReportCheckBox() - Method in class org.emboss.jemboss.gui.form.ReportFormat
getReportFormat() - Method in class org.emboss.jemboss.gui.form.SectionPanel
getReportFormat() - Method in class org.emboss.jemboss.gui.form.ReportFormat
getReportFormats() - Static method in class org.emboss.jemboss.gui.form.ReportFormat
getResidue(int) - Method in class org.emboss.jemboss.editor.Sequence
getResidue(Vector, int, int) - Method in class org.emboss.jemboss.editor.PlotConsensus
  Returns the residue of the sequence i at position k
getResidue(Vector, int, int) - Method in class org.emboss.jemboss.editor.Consensus
getResidueMatrixPosition() - Method in class org.emboss.jemboss.editor.Matrix
getResiduesPerLine(PageFormat) - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection
getResiduesPerPage(PageFormat, int) - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection
getResidueWidth() - Method in class org.emboss.jemboss.editor.SequenceJPanel
getResult() - Method in class org.emboss.jemboss.parser.AcdVariableResolve
getResult() - Method in class org.emboss.jemboss.parser.AcdVarResolve
getResult() - Method in class org.emboss.jemboss.parser.AcdFunResolve
  Returns the value of the result of the expression.
getResult() - Method in class org.emboss.jemboss.soap.PublicRequest
  The result of the embreo call.
getResult() - Method in class org.emboss.jemboss.soap.PrivateRequest
getResult(String) - Method in class org.emboss.jemboss.soap.PendingResults
getResults() - Method in class org.emboss.jemboss.programs.JembossProcess
getRoot(String, String) - Method in class org.emboss.jemboss.server.JembossFileServer
  Given the alias a user root alias e.g.
getRoot(String, String, byte[]) - Method in class org.emboss.jemboss.server.JembossFileAuthServer
  Given the alias a user root alias e.g.
getRootDir() - Method in class org.emboss.jemboss.gui.filetree.RemoteFileNode
getRoots() - Method in class org.emboss.jemboss.soap.FileRoots
  Get the list of filesystem roots
getRootSelect() - Method in class org.emboss.jemboss.gui.filetree.RemoteFileTreePanel
getRootVector() - Method in class org.emboss.jemboss.soap.FileRoots
  Get the list of filesystem roots
getRowCount() - Method in class org.emboss.jemboss.gui.SequenceListTableModel
  Return the number of rows in the table
getRowCount() - Method in class org.emboss.jemboss.gui.SequenceList
  Return the number of rows in the table
getSafeFileName() - Method in class org.emboss.jemboss.soap.MakeFileSafe
getScrollableBlockIncrement(Rectangle, int, int) - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection
getScrollableBlockIncrement(Rectangle, int, int) - Method in class org.emboss.jemboss.gui.ScrollPanel
getScrollableTracksViewportHeight() - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection
getScrollableTracksViewportHeight() - Method in class org.emboss.jemboss.gui.ScrollPanel
getScrollableTracksViewportWidth() - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection
getScrollableTracksViewportWidth() - Method in class org.emboss.jemboss.gui.ScrollPanel
getScrollableTracksViewportWidth() - Method in class org.emboss.jemboss.gui.filetree.FileEditorDisplay
  Override to avoid line wrapping.
getScrollableUnitIncrement(Rectangle, int, int) - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection
getScrollableUnitIncrement(Rectangle, int, int) - Method in class org.emboss.jemboss.gui.ScrollPanel
getSectionBox() - Method in class org.emboss.jemboss.gui.form.SectionPanel
getSectionPanel() - Method in class org.emboss.jemboss.gui.form.SectionPanel
getSelect(int) - Method in class org.emboss.jemboss.parser.ParseAcd
  Used for a selection type to put the list items in a String array.
getSelectedJTextPane(JTabbedPane) - Method in class org.emboss.jemboss.gui.ResultsMenuBar
getSelectedNode() - Method in class org.emboss.jemboss.gui.filetree.DragTree
getSequence() - Method in class org.emboss.jemboss.editor.Sequence
getSequence(int) - Method in class org.emboss.jemboss.editor.SequenceReader
  Returns the sequence at a given position in the Sequence Vector store.
getSequence(int) - Method in class org.emboss.jemboss.gui.form.SetInFileCard
getSequence(int) - Method in class org.emboss.jemboss.gui.form.ListFilePanel
getSequenceCollection() - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection
getSequenceData(int) - Method in class org.emboss.jemboss.gui.SequenceListTableModel
  The `SequenceData` for a given row number.
getSequenceData(int) - Method in class org.emboss.jemboss.gui.SequenceList
  The `SequenceData` for a given row number.
getSequenceFile() - Method in class org.emboss.jemboss.editor.SequenceReader
getSequenceHeight() - Method in class org.emboss.jemboss.editor.SequenceJPanel
getSequenceName() - Method in class org.emboss.jemboss.gui.SequenceData
  Returns the sequence name
getSequencePrintGraphic(Graphics, int, int, int) - Method in class org.emboss.jemboss.editor.SequenceJPanel
getSequenceResidueWidth() - Method in class org.emboss.jemboss.editor.SequenceJPanel
getSequenceVector() - Method in class org.emboss.jemboss.editor.SequenceReader
  Returns the Sequence Vector store
getSequenceWeight(Vector, int) - Method in class org.emboss.jemboss.editor.PlotConsensus
  Returns the weight of sequence i
getSequenceWeight(Vector, int) - Method in class org.emboss.jemboss.editor.Consensus
getSequenceWidth() - Method in class org.emboss.jemboss.editor.SequenceJPanel
getServerName() - Method in class org.emboss.jemboss.gui.filetree.RemoteFileNode
getServicePasswd() - Method in class org.emboss.jemboss.JembossParams
  Return the password needed for the remote service
getServicePasswdByte() - Method in class org.emboss.jemboss.JembossParams
getServiceUserName() - Method in class org.emboss.jemboss.JembossParams
  Return the username needed for the remote service
getSize() - Method in class org.emboss.jemboss.parser.Ajax
getSoapService() - Method in class org.emboss.jemboss.JembossParams
  Get the name of the soap service we're using
getSplashFrame() - Method in class org.emboss.jemboss.soap.AuthPopup
getStatus() - Method in class org.emboss.jemboss.programs.RunEmbossApplication2
getStatus() - Method in class org.emboss.jemboss.programs.RunEmbossApplication
getStatus() - Method in class org.emboss.jemboss.programs.ResultList
  The status of the request
getStatus() - Method in class org.emboss.jemboss.soap.ShowDB
  The status of the request
getStatus() - Method in class org.emboss.jemboss.soap.PendingResults
getStatus() - Method in class org.emboss.jemboss.soap.JembossRun
  The status of the request
getStatus() - Method in class org.emboss.jemboss.soap.GetWossname
getStatus() - Method in class org.emboss.jemboss.soap.GetHelp
  The status of the request
getStatus() - Method in class org.emboss.jemboss.soap.CallAjax
getStatusMsg() - Method in class org.emboss.jemboss.programs.ResultList
  A status message
getStatusMsg() - Method in class org.emboss.jemboss.soap.ShowDB
  A status message
getStatusMsg() - Method in class org.emboss.jemboss.soap.JembossRun
  A status message
getStatusMsg() - Method in class org.emboss.jemboss.soap.GetWossname
getStatusMsg() - Method in class org.emboss.jemboss.soap.GetHelp
  A status message
getStatusMsg() - Method in class org.emboss.jemboss.soap.CallAjax
getTab(int) - Method in class org.emboss.jemboss.gui.TabListCellRenderer
getTabs() - Method in class org.emboss.jemboss.gui.TabListCellRenderer
getText() - Method in class org.emboss.jemboss.gui.sequenceChooser.CutNPasteTextArea
getTextFieldSink() - Method in class org.emboss.jemboss.gui.sequenceChooser.FileChooser
getToolTip() - Static method in class org.emboss.jemboss.gui.form.ReportFormat
getToolTip() - Method in class org.emboss.jemboss.gui.form.AlignFormat
getToolTipLocation(MouseEvent) - Method in class org.emboss.jemboss.editor.SequenceJPanel
getToolTipText(MouseEvent) - Method in class org.emboss.jemboss.editor.SequenceJPanel
getTransferData(DataFlavor) - Method in class org.emboss.jemboss.gui.SequenceData
getTransferData(DataFlavor) - Method in class org.emboss.jemboss.gui.filetree.RemoteFileNode
getTransferData(DataFlavor) - Method in class org.emboss.jemboss.gui.filetree.FileNode
getTransferDataFlavors() - Method in class org.emboss.jemboss.gui.SequenceData
getTransferDataFlavors() - Method in class org.emboss.jemboss.gui.filetree.RemoteFileNode
getTransferDataFlavors() - Method in class org.emboss.jemboss.gui.filetree.FileNode
getUsaDesCheckBox() - Method in class org.emboss.jemboss.gui.form.ReportFormat
getUseAuth() - Method in class org.emboss.jemboss.JembossParams
  Whether the main service requires authentication
getUseProxy() - Method in class org.emboss.jemboss.JembossParams
  If using a proxy server
getUseProxy(String) - Method in class org.emboss.jemboss.JembossParams
  If using a proxy server for a given URL
getUseProxyAuth() - Method in class org.emboss.jemboss.JembossParams
  If using authenticate with the proxy
getUserHome() - Method in class org.emboss.jemboss.JembossParams
getVal(String) - Method in class org.emboss.jemboss.soap.PublicRequest
  Gets an element out of the embreo result hash
getVal(String) - Method in class org.emboss.jemboss.soap.PrivateRequest
  Gets an element out of the embreo result hash
getValue() - Method in class org.emboss.jemboss.gui.SwingWorker
  Get the value produced by the worker thread, or null if it hasn't been constructed yet.
getValue() - Method in class org.emboss.jemboss.gui.form.TextFieldInt
getValue() - Method in class org.emboss.jemboss.gui.form.TextFieldFloat
getValueAt(int, int) - Method in class org.emboss.jemboss.gui.SequenceListTableModel
  Get the Object in a cell in the table
getValueDbl() - Method in class org.emboss.jemboss.parser.acd.ApplicationParam
getValueStr() - Method in class org.emboss.jemboss.parser.acd.ApplicationParam
getVector(Hashtable) - Method in class org.emboss.jemboss.soap.PrivateRequest
getVector(Hashtable) - Method in class org.emboss.jemboss.soap.PendingResults
getViewPosition() - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection
getViewRect() - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection
getViewSize() - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection
  Get the sequence view size
getWeight() - Method in class org.emboss.jemboss.editor.Sequence
getWeight() - Method in class org.emboss.jemboss.soap.CallAjax
GetWossname - class org.emboss.jemboss.soap.GetWossname.
getWossname() - Method in class org.emboss.jemboss.server.JembossServer
  Returns the output of the EMBOSS utility wossname
getWossname() - Method in class org.emboss.jemboss.server.JembossAuthServer
  Returns the output of the EMBOSS utility wossname
GetWossname(JembossParams) - Constructor for class org.emboss.jemboss.soap.GetWossname
graphicName - Variable in class org.emboss.jemboss.editor.GraphicSequenceCollection
graphicSequence - Variable in class org.emboss.jemboss.editor.GraphicSequenceCollection
graphicSequence - Variable in class org.emboss.jemboss.editor.AlignJFrame
GraphicSequenceCollection - class org.emboss.jemboss.editor.GraphicSequenceCollection.
  This class can be used to get a grapical representation of a collection of sequences.
GraphicSequenceCollection(Vector, Hashtable, JScrollPane, boolean, boolean, boolean, boolean, JTextField) - Constructor for class org.emboss.jemboss.editor.GraphicSequenceCollection
GraphicSequenceCollection(Vector, JScrollPane, boolean, boolean, boolean, boolean, JTextField) - Constructor for class org.emboss.jemboss.editor.GraphicSequenceCollection
groupList - Variable in class org.emboss.jemboss.parser.ParseAcd
  String of the groups application belongs to
groups - Variable in class org.emboss.jemboss.parser.acd.Application
gsc - Variable in class org.emboss.jemboss.editor.PrintAlignmentImage
gsc - Variable in class org.emboss.jemboss.editor.PatternJFrame
gsc - Variable in class org.emboss.jemboss.editor.AlignJFrame
gsc - Variable in class org.emboss.jemboss.editor.AlignApplet
guiHandleNumber - Variable in class org.emboss.jemboss.parser.acd.ApplicationFields

## H

h - Variable in class org.emboss.jemboss.gui.form.SetInFileCard
hasBatchMode - Variable in class org.emboss.jemboss.JembossParams
hasBatchModeName - Variable in class org.emboss.jemboss.JembossParams
hash() - Method in class org.emboss.jemboss.programs.ResultList
hash() - Method in class org.emboss.jemboss.soap.JembossRun
hasInteractiveMode - Variable in class org.emboss.jemboss.JembossParams
hasInteractiveModeName - Variable in class org.emboss.jemboss.JembossParams
hasresults - Variable in class org.emboss.jemboss.programs.JembossProcess
hasResults() - Method in class org.emboss.jemboss.programs.JembossProcess
helptext - Variable in class org.emboss.jemboss.gui.form.BuildJembossForm
helpText - Variable in class org.emboss.jemboss.soap.GetHelp
helpText - Variable in class org.emboss.jemboss.soap.GetACD
helpurl() - Method in class org.emboss.jemboss.server.JembossServer
helpurl() - Method in class org.emboss.jemboss.server.JembossAuthServer
hgt - Variable in class org.emboss.jemboss.editor.GraphicSequenceCollection
hgtName - Variable in class org.emboss.jemboss.editor.GraphicSequenceCollection
highlightBorder - Static variable in class org.emboss.jemboss.gui.sequenceChooser.CutNPasteTextArea
highlightPattern - Variable in class org.emboss.jemboss.editor.SequenceJPanel
home - Variable in class org.emboss.jemboss.parser.Ajax
  user home dir
homeDirectory - Variable in class org.emboss.jemboss.server.JembossServer
htmlPane - Variable in class org.emboss.jemboss.gui.Browser
hydrophobicColor - Static variable in class org.emboss.jemboss.editor.SequenceProperties
hyperlinkUpdate(HyperlinkEvent) - Method in class org.emboss.jemboss.gui.Browser
  Method to handle hyper link events.

## I

i - Variable in class org.emboss.jemboss.editor.Matrix
id - Variable in class org.emboss.jemboss.editor.Sequence
idimension - Variable in class org.emboss.jemboss.editor.Matrix
idSort() - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection
init() - Method in class org.emboss.jemboss.editor.SequenceJPanel
init() - Method in class org.emboss.jemboss.editor.AlignApplet
initialize() - Static method in class org.emboss.jemboss.gui.form.MultiLineToolTipUI
initialURL - Variable in class org.emboss.jemboss.gui.Browser
initStylesForTextPane() - Method in class org.emboss.jemboss.gui.filetree.FileEditorDisplay
  Initialise styles for a JTextPane.
inpSection - Static variable in class org.emboss.jemboss.gui.form.BuildJembossForm
InputSequenceAttributes - class org.emboss.jemboss.gui.sequenceChooser.InputSequenceAttributes.
  Creates the input sequence attibutes window
InputSequenceAttributes(String[], FileChooser) - Constructor for class org.emboss.jemboss.gui.sequenceChooser.InputSequenceAttributes
inSeq - Variable in class org.emboss.jemboss.gui.form.SectionPanel
inSeq - Variable in class org.emboss.jemboss.gui.form.BuildJembossForm
inSeqAttr - Variable in class org.emboss.jemboss.gui.form.SetInFileCard
inSeqAttr - Variable in class org.emboss.jemboss.gui.form.SectionPanel
inSeqAttr - Variable in class org.emboss.jemboss.gui.form.BuildJembossForm
insertData(SequenceListTableModel, Point, String, String, String, Boolean, Boolean, Boolean) - Method in class org.emboss.jemboss.gui.DragJTable
insertResidue(String, int) - Method in class org.emboss.jemboss.editor.Sequence
insertRow(int) - Method in class org.emboss.jemboss.gui.SequenceListTableModel
  Insert a blank row
insertString(int, String, AttributeSet) - Method in class org.emboss.jemboss.gui.form.TextFieldInt.WholeNumberDocument
insertString(int, String, AttributeSet) - Method in class org.emboss.jemboss.gui.form.TextFieldFloat.DecimalNumberDocument
inset - Variable in class org.emboss.jemboss.gui.form.MultiLineToolTipUI
installUI(JComponent) - Method in class org.emboss.jemboss.gui.form.MultiLineToolTipUI
integerFormatter - Variable in class org.emboss.jemboss.gui.form.TextFieldInt
interrupt() - Method in class org.emboss.jemboss.gui.SwingWorker
  A new method that interrupts the worker thread.
interval - Variable in class org.emboss.jemboss.editor.SequenceJPanel
interval - Variable in class org.emboss.jemboss.editor.PlotConsensus
interval - Variable in class org.emboss.jemboss.gui.SplashThread
iprogress - Variable in class org.emboss.jemboss.soap.AuthPopup
iprogressmax - Variable in class org.emboss.jemboss.soap.AuthPopup
isAdv - Variable in class org.emboss.jemboss.gui.form.SectionPanel
isAdvancedSection() - Method in class org.emboss.jemboss.gui.form.SectionPanel
isAlignFormat() - Method in class org.emboss.jemboss.gui.form.SectionPanel
isAutoUpdate() - Method in class org.emboss.jemboss.soap.PendingResults
isBatchable() - Method in class org.emboss.jemboss.parser.ParseAcd
  Finds if the program is identifies as being able to run in a batch queue
isBeginSeqDefault() - Method in class org.emboss.jemboss.gui.sequenceChooser.InputSequenceAttributes
isBrowserProxy() - Method in class org.emboss.jemboss.JembossParams
  True is using a proxy server for the browser
isCellEditable(int, int) - Method in class org.emboss.jemboss.gui.SequenceListTableModel
  Define if a cell is editable by the user
isCompleted() - Method in class org.emboss.jemboss.programs.JembossProcess
isCut - Variable in class org.emboss.jemboss.gui.form.SetInFileCard
isCutNPase() - Method in class org.emboss.jemboss.gui.form.SetInFileCard
isDataFlavorSupported(DataFlavor) - Method in class org.emboss.jemboss.gui.SequenceData
isDataFlavorSupported(DataFlavor) - Method in class org.emboss.jemboss.gui.filetree.RemoteFileNode
isDataFlavorSupported(DataFlavor) - Method in class org.emboss.jemboss.gui.filetree.FileNode
isDBNameDefault() - Method in class org.emboss.jemboss.gui.sequenceChooser.OutputSequenceAttributes
isDBNameDefault() - Method in class org.emboss.jemboss.gui.sequenceChooser.InputSequenceAttributes
isDefaultParamValueStr(int) - Method in class org.emboss.jemboss.parser.ParseAcd
  Determine if there is a default parameter in a field of the ACD.
isDependents(String, int, int) - Method in class org.emboss.jemboss.parser.ParseAcd
  Always start by calling isDependents(), which calculates the number of dependents and construct the Dependent array.
isDir - Variable in class org.emboss.jemboss.gui.filetree.RemoteFileNode
isDirectory() - Method in class org.emboss.jemboss.gui.filetree.RemoteFileNode
isDirectory() - Method in class org.emboss.jemboss.gui.filetree.FileNode
isDirectory(String) - Method in class org.emboss.jemboss.soap.FileList
  Gets whether this name is a directory
isEndSeqDefault() - Method in class org.emboss.jemboss.gui.sequenceChooser.InputSequenceAttributes
isEqualSequenceLength(Vector) - Method in class org.emboss.jemboss.editor.Consensus
  Check all sequences are the same length
isExplored() - Method in class org.emboss.jemboss.gui.filetree.RemoteFileNode
isExplored() - Method in class org.emboss.jemboss.gui.filetree.FileNode
isExtensionDefault() - Method in class org.emboss.jemboss.gui.sequenceChooser.OutputSequenceAttributes
isFile - Variable in class org.emboss.jemboss.gui.form.SetInFileCard
isFileName() - Method in class org.emboss.jemboss.gui.form.SetInFileCard
isFileSelection() - Method in class org.emboss.jemboss.gui.filetree.RemoteDragTree
isFileSelection() - Method in class org.emboss.jemboss.gui.filetree.DragTree
isFNameDefault() - Method in class org.emboss.jemboss.gui.sequenceChooser.OutputSequenceAttributes
isInp - Variable in class org.emboss.jemboss.gui.form.SectionPanel
isInputSection() - Method in class org.emboss.jemboss.gui.form.SectionPanel
isJembossServer() - Static method in class org.emboss.jemboss.JembossParams
isLeaf() - Method in class org.emboss.jemboss.gui.filetree.RemoteFileNode
isLeaf() - Method in class org.emboss.jemboss.gui.filetree.FileNode
isList - Variable in class org.emboss.jemboss.gui.form.SetInFileCard
isListFile() - Method in class org.emboss.jemboss.gui.form.SetInFileCard
isListFile(int) - Method in class org.emboss.jemboss.gui.DragJTable
isMaxParamValue(int) - Method in class org.emboss.jemboss.parser.ParseAcd
  Determine if there is a max parameter in a field of the ACD.
isMinParamValue(int) - Method in class org.emboss.jemboss.parser.ParseAcd
  Determine if there is a min parameter in a field of the ACD.
isNameDefault() - Method in class org.emboss.jemboss.gui.sequenceChooser.OutputSequenceAttributes
isOpenFileDefault() - Method in class org.emboss.jemboss.gui.sequenceChooser.InputSequenceAttributes
isOptionalParam() - Method in class org.emboss.jemboss.parser.ParseAcd
  Determine if there is a optional parameter in any field of the ACD.
isOptionalParamValue(int) - Method in class org.emboss.jemboss.parser.ParseAcd
  Determine if there is a optional parameter in a field of the ACD.
isOut - Variable in class org.emboss.jemboss.gui.form.SectionPanel
isOutputFile(int) - Method in class org.emboss.jemboss.parser.ParseAcd
  Determine if a field is data type outfile.
isOutputGraph(int) - Method in class org.emboss.jemboss.parser.ParseAcd
  Determine if a field is data type graph or xygraph.
isOutputSection() - Method in class org.emboss.jemboss.gui.form.SectionPanel
isOutputSequence(int) - Method in class org.emboss.jemboss.parser.ParseAcd
  Determine if data type of a field is seqout.
isPairWise(ParseAcd, int) - Method in class org.emboss.jemboss.gui.form.AlignFormat
  Method to determine whether this is a pairwise (returning true) or multiple sequence alignment format.
isParamValueStr(int) - Method in class org.emboss.jemboss.parser.acd.ApplicationFields
isParamValueStr(int, int) - Method in class org.emboss.jemboss.parser.ParseAcd
  Determine if the value of the parameter is a String.
isParamValueString() - Method in class org.emboss.jemboss.parser.acd.ApplicationParam
isPrimaryGp - Variable in class org.emboss.jemboss.parser.ParseAcd
  true if primary group is defined
isProcessStdout() - Method in class org.emboss.jemboss.programs.RunEmbossApplication2
isProcessStdout() - Method in class org.emboss.jemboss.programs.RunEmbossApplication
isProtein() - Method in class org.emboss.jemboss.editor.Sequence
isProtein() - Method in class org.emboss.jemboss.soap.CallAjax
isReading() - Method in class org.emboss.jemboss.editor.SequenceReader
isReportFormat() - Method in class org.emboss.jemboss.gui.form.SectionPanel
isReq - Variable in class org.emboss.jemboss.gui.form.SectionPanel
isRequiredSection() - Method in class org.emboss.jemboss.gui.form.SectionPanel
isRunning() - Method in class org.emboss.jemboss.programs.JembossProcess
isSaveUserHomeSelected() - Method in class org.emboss.jemboss.gui.AdvancedOptions
isSecondaryGp - Variable in class org.emboss.jemboss.parser.ParseAcd
  true if secondary group is defined
isSelected() - Method in class org.emboss.jemboss.editor.ColourMenu.ColorPane
isSelected() - Method in class org.emboss.jemboss.gui.ColorMenu.ColorPane
isShadedGUI - Variable in class org.emboss.jemboss.gui.form.SectionPanel
isSIDDefault() - Method in class org.emboss.jemboss.gui.sequenceChooser.InputSequenceAttributes
isStoreSequenceList() - Method in class org.emboss.jemboss.gui.SequenceList
  Determines if a sequence list has been stored ("~/.jembossSeqList")
isUFODefault() - Method in class org.emboss.jemboss.gui.sequenceChooser.OutputSequenceAttributes
isUFODefault() - Method in class org.emboss.jemboss.gui.sequenceChooser.InputSequenceAttributes
isUseTFM() - Method in class org.emboss.jemboss.JembossParams

## J

jarStore - Variable in class org.emboss.jemboss.JembossJarUtil
javaNoProxy - Variable in class org.emboss.jemboss.JembossParams
javaNoProxyEntries - Variable in class org.emboss.jemboss.JembossParams
javaProxyHost - Variable in class org.emboss.jemboss.JembossParams
javaProxyPort - Variable in class org.emboss.jemboss.JembossParams
javaProxyPortNum - Variable in class org.emboss.jemboss.JembossParams
jdim - Static variable in class org.emboss.jemboss.Jemboss
  Jemboss window dimension
jdimension - Variable in class org.emboss.jemboss.editor.Matrix
jdimExtend - Static variable in class org.emboss.jemboss.Jemboss
Jemboss - class org.emboss.jemboss.Jemboss.
  Java interface to EMBOSS (http://www.emboss.org/) (i) standalone - with a locally installation of EMBOSS.
Jemboss.winExit - class org.emboss.jemboss.Jemboss.winExit.
  Extends WindowAdapter to close window
Jemboss.winExit() - Constructor for class org.emboss.jemboss.Jemboss.winExit
Jemboss() - Constructor for class org.emboss.jemboss.Jemboss
JembossAuthServer - class org.emboss.jemboss.server.JembossAuthServer.
  Jemboss Authenticated Server for SOAP
JembossAuthServer() - Constructor for class org.emboss.jemboss.server.JembossAuthServer
JembossAuthThread - class org.emboss.jemboss.server.JembossAuthThread.
JembossAuthThread(String, byte[], String, String, String) - Constructor for class org.emboss.jemboss.server.JembossAuthThread
JembossFileAuthServer - class org.emboss.jemboss.server.JembossFileAuthServer.
JembossFileAuthServer() - Constructor for class org.emboss.jemboss.server.JembossFileAuthServer
JembossFileServer - class org.emboss.jemboss.server.JembossFileServer.
JembossFileServer() - Constructor for class org.emboss.jemboss.server.JembossFileServer
JembossJarUtil - class org.emboss.jemboss.JembossJarUtil.
  Unpacks a Jar file into a Hashtable
JembossJarUtil(String) - Constructor for class org.emboss.jemboss.JembossJarUtil
JembossLogo - class org.emboss.jemboss.JembossLogo.
JembossLogo(int, int, int) - Constructor for class org.emboss.jemboss.JembossLogo
JembossParams - class org.emboss.jemboss.JembossParams.
JembossParams() - Constructor for class org.emboss.jemboss.JembossParams
  Loads and holds the properties
JembossProcess - class org.emboss.jemboss.programs.JembossProcess.
JembossProcess(String) - Constructor for class org.emboss.jemboss.programs.JembossProcess
JembossProcess(String, String) - Constructor for class org.emboss.jemboss.programs.JembossProcess
JembossProcess(String, String, String) - Constructor for class org.emboss.jemboss.programs.JembossProcess
JembossRun - class org.emboss.jemboss.soap.JembossRun.
JembossRun(String, String, Hashtable, JembossParams) - Constructor for class org.emboss.jemboss.soap.JembossRun
  Executes an application on a server
jembossServer - Static variable in class org.emboss.jemboss.JembossParams
  Jemboss java server
JembossServer - class org.emboss.jemboss.server.JembossServer.
  Jemboss Non-authenticating Server for SOAP
JembossServer() - Constructor for class org.emboss.jemboss.server.JembossServer
jembossServerName - Variable in class org.emboss.jemboss.JembossParams
jembossSettings - Variable in class org.emboss.jemboss.JembossParams
JembossSoapException - exception org.emboss.jemboss.soap.JembossSoapException.
JembossSoapException() - Constructor for class org.emboss.jemboss.soap.JembossSoapException
  When trown indicates a communication error with the server.
JembossSoapException(String) - Constructor for class org.emboss.jemboss.soap.JembossSoapException
JembossThread - class org.emboss.jemboss.server.JembossThread.
JembossThread(RunEmbossApplication2, String) - Constructor for class org.emboss.jemboss.server.JembossThread
jobButton - Variable in class org.emboss.jemboss.soap.PendingResults
jobComboBox - Variable in class org.emboss.jemboss.soap.PendingResults
jobid - Variable in class org.emboss.jemboss.programs.JembossProcess
jobMgr - Static variable in class org.emboss.jemboss.gui.AdvancedOptions
jobStatus() - Method in class org.emboss.jemboss.soap.PendingResults
  Report the status of completed and running processes.
jp - Variable in class org.emboss.jemboss.server.JembossServer
jp - Variable in class org.emboss.jemboss.server.JembossFileAuthServer
jp - Variable in class org.emboss.jemboss.server.JembossAuthServer
jspColour - Variable in class org.emboss.jemboss.editor.ColourJFrame
jspSequence - Variable in class org.emboss.jemboss.editor.GraphicSequenceCollection
jspSequence - Variable in class org.emboss.jemboss.editor.AlignJFrame
jspSequence - Variable in class org.emboss.jemboss.editor.AlignApplet

## K

k - Variable in class org.emboss.jemboss.editor.Matrix
keys - Variable in class org.emboss.jemboss.editor.Matrix
keys() - Method in class org.emboss.jemboss.programs.ResultList
keys() - Method in class org.emboss.jemboss.soap.JembossRun

## L

lab - Variable in class org.emboss.jemboss.gui.form.SectionPanel
labelColor - Static variable in class org.emboss.jemboss.gui.form.SectionPanel
LabelTextBox - class org.emboss.jemboss.gui.form.LabelTextBox.
LabelTextBox(String, String) - Constructor for class org.emboss.jemboss.gui.form.LabelTextBox
labfont - Static variable in class org.emboss.jemboss.gui.form.SectionPanel
labfont2 - Static variable in class org.emboss.jemboss.gui.form.SectionPanel
laddCombo - Variable in class org.emboss.jemboss.gui.filetree.RemoteFileTreePanel
LaunchJalView - class org.emboss.jemboss.gui.LaunchJalView.
LaunchJalView() - Constructor for class org.emboss.jemboss.gui.LaunchJalView
len - Variable in class org.emboss.jemboss.editor.GraphicSequenceCollection
length - Variable in class org.emboss.jemboss.editor.Sequence
length - Static variable in class org.emboss.jemboss.parser.Ajax
  sequence length
length - Variable in class org.emboss.jemboss.soap.CallAjax
length_soap - Variable in class org.emboss.jemboss.parser.Ajax
  sequence length
lenName - Variable in class org.emboss.jemboss.editor.GraphicSequenceCollection
light - Variable in class org.emboss.jemboss.gui.form.Separator
LINE_SEPARATOR - Static variable in class org.emboss.jemboss.gui.form.PlafMacros
LINE_SEPARATOR_LEN - Static variable in class org.emboss.jemboss.gui.form.PlafMacros
list_saved_results() - Method in class org.emboss.jemboss.server.JembossServer
  Private Server List of the saved results on the server.
list_saved_results(String) - Method in class org.emboss.jemboss.server.JembossServer
  Private Server List of the saved results on the server.
list_saved_results(String, byte[]) - Method in class org.emboss.jemboss.server.JembossAuthServer
  Private Server List of the saved results on the server.
listByDateRun(ResultList, boolean) - Method in class org.emboss.jemboss.gui.ShowSavedResults
listByProgramName() - Method in class org.emboss.jemboss.gui.ShowSavedResults
listdefault - Variable in class org.emboss.jemboss.parser.ParseAcd
  default for list or select data type
listDirs(String, byte[], String, String) - Method in class org.emboss.jemboss.parser.Ajax
ListFile - class org.emboss.jemboss.programs.ListFile.
ListFile() - Constructor for class org.emboss.jemboss.programs.ListFile
ListFilePanel - class org.emboss.jemboss.gui.form.ListFilePanel.
ListFilePanel(int, JembossParams) - Constructor for class org.emboss.jemboss.gui.form.ListFilePanel
listFiles(String, byte[], String, String) - Method in class org.emboss.jemboss.parser.Ajax
listPane - Variable in class org.emboss.jemboss.gui.form.SetInFileCard
lname - Variable in class org.emboss.jemboss.gui.sequenceChooser.FileChooser
loadFilesContent(Ajax, String, byte[], File, String, Vector, Hashtable) - Method in class org.emboss.jemboss.server.JembossAuthServer
  Reads in files from EMBOSS output
loadFilesContent(File, String, Vector, Hashtable) - Method in class org.emboss.jemboss.server.JembossServer
  Reads in files from EMBOSS output
loadIn(String) - Method in class org.emboss.jemboss.JembossParams
loadPNGContent(File, String, Vector) - Method in class org.emboss.jemboss.server.JembossServer
  Reads in png files from EMBOSS output
loadPNGContent(String) - Method in class org.emboss.jemboss.gui.filetree.FileEditorDisplay
  Need to read png in, in case it is saved out
loadStoredSeqList(File) - Method in class org.emboss.jemboss.gui.SequenceListTableModel
  Load from stored file the SequenceList created from a previous session.
LocalAndRemoteFileTreeFrame - class org.emboss.jemboss.gui.filetree.LocalAndRemoteFileTreeFrame.
LocalAndRemoteFileTreeFrame(JembossParams) - Constructor for class org.emboss.jemboss.gui.filetree.LocalAndRemoteFileTreeFrame
  Displays the remote and local file managers in the same frame.
localAndRemoteTree - Static variable in class org.emboss.jemboss.gui.SetUpMenuBar
logFile - Variable in class org.emboss.jemboss.server.JembossAuthServer
lower - Variable in class org.emboss.jemboss.gui.sequenceChooser.InputSequenceAttributes
lpair - Variable in class org.emboss.jemboss.gui.form.AlignFormat
lsaved - Variable in class org.emboss.jemboss.gui.filetree.FileSaving
ltree - Static variable in class org.emboss.jemboss.gui.filetree.LocalAndRemoteFileTreeFrame

## M

m_defaultTab - Variable in class org.emboss.jemboss.gui.TabListCellRenderer
m_fm - Variable in class org.emboss.jemboss.gui.TabListCellRenderer
m_insets - Variable in class org.emboss.jemboss.gui.TabListCellRenderer
m_noFocusBorder - Static variable in class org.emboss.jemboss.gui.TabListCellRenderer
m_tabs - Variable in class org.emboss.jemboss.gui.TabListCellRenderer
MAGENTA - Static variable in class org.emboss.jemboss.editor.SequenceProperties
mailServer - Static variable in class org.emboss.jemboss.gui.AdvancedOptions
main(String[]) - Static method in class org.emboss.jemboss.Jemboss
  Launches Jemboss in standalone or client-server mode.
main(String[]) - Static method in class org.emboss.jemboss.FileManager
main(String[]) - Static method in class org.emboss.jemboss.editor.Sequence
main(String[]) - Static method in class org.emboss.jemboss.editor.PlotConsensus
main(String[]) - Static method in class org.emboss.jemboss.editor.GraphicSequenceCollection
main(String[]) - Static method in class org.emboss.jemboss.editor.Consensus
main(String[]) - Static method in class org.emboss.jemboss.editor.AlignJFrame
main(String[]) - Static method in class org.emboss.jemboss.server.TestPublicServer
main(String[]) - Static method in class org.emboss.jemboss.server.TestPrivateServer
makeDir(String, byte[], String, String) - Method in class org.emboss.jemboss.parser.Ajax
MakeFileSafe - class org.emboss.jemboss.soap.MakeFileSafe.
MakeFileSafe(String) - Constructor for class org.emboss.jemboss.soap.MakeFileSafe
  Create a sanitised filename.
mat - Variable in class org.emboss.jemboss.editor.MatrixJFrame
mat - Variable in class org.emboss.jemboss.editor.AlignJFrame
matrices - Static variable in class org.emboss.jemboss.gui.BuildProgramMenu
  matrices
matrices - Variable in class org.emboss.jemboss.soap.ShowDB
matrix - Variable in class org.emboss.jemboss.editor.Matrix
matrix - Variable in class org.emboss.jemboss.editor.Consensus
matrix - Variable in class org.emboss.jemboss.editor.AlignApplet
Matrix - class org.emboss.jemboss.editor.Matrix.
Matrix(File) - Constructor for class org.emboss.jemboss.editor.Matrix
Matrix(String, String) - Constructor for class org.emboss.jemboss.editor.Matrix
matrixFileName - Variable in class org.emboss.jemboss.editor.Matrix
MatrixJFrame - class org.emboss.jemboss.editor.MatrixJFrame.
MatrixJFrame(Matrix, JTextField, AlignJFrame) - Constructor for class org.emboss.jemboss.editor.MatrixJFrame
matrixLineCount(String, RE) - Method in class org.emboss.jemboss.editor.Matrix
matrixLineParse(String, RE) - Method in class org.emboss.jemboss.editor.Matrix
matrixRead(File) - Method in class org.emboss.jemboss.editor.Matrix
matrixReadString(String) - Method in class org.emboss.jemboss.editor.Matrix
matrixString - Variable in class org.emboss.jemboss.editor.Matrix
MAX_MEM_LEN - Static variable in class org.emboss.jemboss.gui.MemoryComboBox
maxSectionWidth - Variable in class org.emboss.jemboss.gui.form.SectionPanel
MAXSEQLENGTH - Variable in class org.emboss.jemboss.editor.GraphicSequenceCollection
maybeShowPopup(MouseEvent) - Method in class org.emboss.jemboss.editor.SequenceJPanel.PopupListener
maybeShowPopup(MouseEvent) - Method in class org.emboss.jemboss.editor.ColourJFrame.ColourPanel.PopupListener
maybeShowPopup(MouseEvent) - Method in class org.emboss.jemboss.gui.filetree.RemoteDragTree.PopupListener
maybeShowPopup(MouseEvent) - Method in class org.emboss.jemboss.gui.filetree.DragTree.PopupListener
MemoryComboBox - class org.emboss.jemboss.gui.MemoryComboBox.
MemoryComboBox(Vector) - Constructor for class org.emboss.jemboss.gui.MemoryComboBox
menuFont - Variable in class org.emboss.jemboss.gui.startup.ProgList
  font used for the menu items
mItem - Variable in class org.emboss.jemboss.gui.startup.ProgList
  used to create the program menus
mkdir(String, String, String) - Method in class org.emboss.jemboss.server.JembossFileServer
mkdir(String, String, String, byte[]) - Method in class org.emboss.jemboss.server.JembossFileAuthServer
mlist - Variable in class org.emboss.jemboss.parser.ParseAcd
  number of list & selection fields - multiple selection
modelColumns - Static variable in class org.emboss.jemboss.gui.SequenceListTableModel
modelVector - Static variable in class org.emboss.jemboss.gui.SequenceListTableModel
modeVector() - Method in class org.emboss.jemboss.JembossParams
  Return the mode list as a vector, suitable for loading into a combobox.
mouseClicked(MouseEvent) - Method in class org.emboss.jemboss.editor.ColourMenu.ColorPane
mouseClicked(MouseEvent) - Method in class org.emboss.jemboss.gui.ColorMenu.ColorPane
mouseEntered(MouseEvent) - Method in class org.emboss.jemboss.editor.ColourMenu.ColorPane
mouseEntered(MouseEvent) - Method in class org.emboss.jemboss.gui.ColorMenu.ColorPane
mouseExited(MouseEvent) - Method in class org.emboss.jemboss.editor.ColourMenu.ColorPane
mouseExited(MouseEvent) - Method in class org.emboss.jemboss.gui.ColorMenu.ColorPane
mousePressed(MouseEvent) - Method in class org.emboss.jemboss.editor.SequenceJPanel.PopupListener
mousePressed(MouseEvent) - Method in class org.emboss.jemboss.editor.ColourMenu.ColorPane
mousePressed(MouseEvent) - Method in class org.emboss.jemboss.editor.ColourJFrame.ColourPanel.PopupListener
mousePressed(MouseEvent) - Method in class org.emboss.jemboss.gui.ColorMenu.ColorPane
mousePressed(MouseEvent) - Method in class org.emboss.jemboss.gui.filetree.RemoteDragTree.PopupListener
mousePressed(MouseEvent) - Method in class org.emboss.jemboss.gui.filetree.DragTree.PopupListener
mouseReleased(MouseEvent) - Method in class org.emboss.jemboss.editor.SequenceJPanel.PopupListener
mouseReleased(MouseEvent) - Method in class org.emboss.jemboss.editor.ColourMenu.ColorPane
mouseReleased(MouseEvent) - Method in class org.emboss.jemboss.editor.ColourJFrame.ColourPanel.PopupListener
mouseReleased(MouseEvent) - Method in class org.emboss.jemboss.gui.ColorMenu.ColorPane
mouseReleased(MouseEvent) - Method in class org.emboss.jemboss.gui.filetree.RemoteDragTree.PopupListener
mouseReleased(MouseEvent) - Method in class org.emboss.jemboss.gui.filetree.DragTree.PopupListener
moveSequence(String, int) - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection
mScroll - Variable in class org.emboss.jemboss.editor.MatrixJFrame
msf - Static variable in class org.emboss.jemboss.gui.sequenceChooser.SequenceFilter
MultiLineToolTipUI - class org.emboss.jemboss.gui.form.MultiLineToolTipUI.
MultiLineToolTipUI.MyToolTip - class org.emboss.jemboss.gui.form.MultiLineToolTipUI.MyToolTip.
  Use this to getFontMetrics
MultiLineToolTipUI.MyToolTip() - Constructor for class org.emboss.jemboss.gui.form.MultiLineToolTipUI.MyToolTip
MultiLineToolTipUI() - Constructor for class org.emboss.jemboss.gui.form.MultiLineToolTipUI
multiOption - Variable in class org.emboss.jemboss.gui.form.SectionPanel
multiOption - Variable in class org.emboss.jemboss.gui.form.BuildJembossForm
myComboPopup - class org.emboss.jemboss.gui.form.myComboPopup.
myComboPopup.myComboUI - class org.emboss.jemboss.gui.form.myComboPopup.myComboUI.
  Create scroller
myComboPopup.myComboUI() - Constructor for class org.emboss.jemboss.gui.form.myComboPopup.myComboUI
myComboPopup(Object[]) - Constructor for class org.emboss.jemboss.gui.form.myComboPopup
  Creates a JComboBox that contains the elements in the specified array.
myComboPopup(Vector) - Constructor for class org.emboss.jemboss.gui.form.myComboPopup
myset - Variable in class org.emboss.jemboss.soap.ServerSetup
mysettings - Variable in class org.emboss.jemboss.gui.filetree.RemoteFileNode
mysettings - Variable in class org.emboss.jemboss.gui.filetree.RemoteDragTree
mysettings - Variable in class org.emboss.jemboss.gui.filetree.DragTree
mysettings - Variable in class org.emboss.jemboss.gui.form.SectionPanel
mysettings - Variable in class org.emboss.jemboss.gui.form.BuildJembossForm
mysettings - Static variable in class org.emboss.jemboss.server.TestPublicServer
mysettings - Static variable in class org.emboss.jemboss.server.TestPrivateServer
mysettings - Variable in class org.emboss.jemboss.soap.PendingResults
mysettings - Variable in class org.emboss.jemboss.soap.AuthPopup

## N

name - Variable in class org.emboss.jemboss.editor.Sequence
name - Variable in class org.emboss.jemboss.gui.form.ApplicationNamePanel
name - Variable in class org.emboss.jemboss.parser.acd.Application
name() - Method in class org.emboss.jemboss.server.JembossServer
name() - Method in class org.emboss.jemboss.server.JembossAuthServer
nameLabel - Variable in class org.emboss.jemboss.editor.SequenceNameJButton
nbool - Variable in class org.emboss.jemboss.parser.ParseAcd
  number of checkbox fields
newRoot(String) - Method in class org.emboss.jemboss.gui.filetree.DragTree
nf - Variable in class org.emboss.jemboss.gui.form.SectionPanel
nFiles - Variable in class org.emboss.jemboss.gui.form.ListFilePanel
nflist - Variable in class org.emboss.jemboss.parser.ParseAcd
  number of filelist fields
nfloat - Variable in class org.emboss.jemboss.parser.ParseAcd
  number of float fields
nint - Variable in class org.emboss.jemboss.parser.ParseAcd
  number of integer fields
nlist - Variable in class org.emboss.jemboss.parser.ParseAcd
  number of list & selection fields - single selection
nm - Variable in class org.emboss.jemboss.gui.startup.ProgList
  number of JMenuItem created
npG - Variable in class org.emboss.jemboss.gui.startup.ProgList
  number of primary group programs
nrange - Variable in class org.emboss.jemboss.parser.ParseAcd
  number of range fields
nResPerLine - Variable in class org.emboss.jemboss.editor.PrintAlignmentImage
nsection - Variable in class org.emboss.jemboss.parser.ParseAcd
  number of sections
nseqs - Variable in class org.emboss.jemboss.parser.ParseAcd
  number of sequence fields
nsplash - Variable in class org.emboss.jemboss.gui.SplashThread
nsubsection - Variable in class org.emboss.jemboss.parser.ParseAcd
  number of subsections
ntextf - Variable in class org.emboss.jemboss.parser.ParseAcd
  number of text fields
nucleotide - Variable in class org.emboss.jemboss.gui.sequenceChooser.InputSequenceAttributes
numberDraw - Variable in class org.emboss.jemboss.editor.GraphicSequenceCollection
numbins - Variable in class org.emboss.jemboss.editor.PlotConsensus
numdb - Variable in class org.emboss.jemboss.gui.startup.Database
numOfDependents - Variable in class org.emboss.jemboss.parser.ParseAcd
  number of dependent variables
numofFields - Variable in class org.emboss.jemboss.gui.form.SectionPanel
numofFields - Variable in class org.emboss.jemboss.gui.form.BuildJembossForm
numofFields - Variable in class org.emboss.jemboss.parser.ParseAcd
  number of ACD fields
numofParams - Variable in class org.emboss.jemboss.parser.ParseAcd
  number of parameters in a field
numofParams - Variable in class org.emboss.jemboss.parser.acd.ApplicationFields
numProgs - Variable in class org.emboss.jemboss.gui.startup.ProgList
  number of programs
numResiduePerLine - Variable in class org.emboss.jemboss.editor.GraphicSequenceCollection
nvalue - Variable in class org.emboss.jemboss.parser.ParseAcd
  double value of a parameter
nvalue - Variable in class org.emboss.jemboss.parser.acd.ApplicationParam

## O

oext - Variable in class org.emboss.jemboss.gui.sequenceChooser.OutputSequenceAttributes
offormat - Variable in class org.emboss.jemboss.gui.sequenceChooser.OutputSequenceAttributes
ofname - Variable in class org.emboss.jemboss.gui.sequenceChooser.OutputSequenceAttributes
okButton - Variable in class org.emboss.jemboss.soap.AuthPopup
openMethod(Vector) - Method in class org.emboss.jemboss.editor.AlignJFrame
openNode - Variable in class org.emboss.jemboss.gui.filetree.DragTree
org.emboss.jemboss - package org.emboss.jemboss
org.emboss.jemboss.editor - package org.emboss.jemboss.editor
org.emboss.jemboss.gui - package org.emboss.jemboss.gui
org.emboss.jemboss.gui.filetree - package org.emboss.jemboss.gui.filetree
org.emboss.jemboss.gui.form - package org.emboss.jemboss.gui.form
org.emboss.jemboss.gui.sequenceChooser - package org.emboss.jemboss.gui.sequenceChooser
org.emboss.jemboss.gui.startup - package org.emboss.jemboss.gui.startup
org.emboss.jemboss.parser - package org.emboss.jemboss.parser
org.emboss.jemboss.parser.acd - package org.emboss.jemboss.parser.acd
org.emboss.jemboss.programs - package org.emboss.jemboss.programs
org.emboss.jemboss.server - package org.emboss.jemboss.server
org.emboss.jemboss.soap - package org.emboss.jemboss.soap
osdbname - Variable in class org.emboss.jemboss.gui.sequenceChooser.OutputSequenceAttributes
osextension - Variable in class org.emboss.jemboss.gui.sequenceChooser.OutputSequenceAttributes
osname - Variable in class org.emboss.jemboss.gui.sequenceChooser.OutputSequenceAttributes
ossingle - Variable in class org.emboss.jemboss.gui.sequenceChooser.OutputSequenceAttributes
outfileResult - Variable in class org.emboss.jemboss.gui.form.BuildJembossForm
OutputSequenceAttributes - class org.emboss.jemboss.gui.sequenceChooser.OutputSequenceAttributes.
  Creates the output sequence attibutes window
OutputSequenceAttributes() - Constructor for class org.emboss.jemboss.gui.sequenceChooser.OutputSequenceAttributes
outSection - Static variable in class org.emboss.jemboss.gui.form.BuildJembossForm
outSeqAttr - Static variable in class org.emboss.jemboss.gui.form.BuildJembossForm
outStd - Variable in class org.emboss.jemboss.parser.Ajax
  stdout & stderr from fork

## P

p - Variable in class org.emboss.jemboss.programs.RunEmbossApplication2
p - Variable in class org.emboss.jemboss.programs.RunEmbossApplication
p2 - Variable in class org.emboss.jemboss.gui.form.BuildJembossForm
p3 - Variable in class org.emboss.jemboss.Jemboss
p3 - Variable in class org.emboss.jemboss.gui.form.SectionPanel
padChar - Variable in class org.emboss.jemboss.editor.SequenceJPanel
pageIndex - Variable in class org.emboss.jemboss.editor.PrintAlignmentImage
paint(Graphics) - Method in class org.emboss.jemboss.gui.TabListCellRenderer
paint(Graphics) - Method in class org.emboss.jemboss.gui.form.Separator
paint(Graphics, JComponent) - Method in class org.emboss.jemboss.gui.form.MultiLineToolTipUI
paintComponent(Graphics) - Method in class org.emboss.jemboss.JembossLogo
paintComponent(Graphics) - Method in class org.emboss.jemboss.editor.SequenceJPanel
paintComponent(Graphics) - Method in class org.emboss.jemboss.editor.PrintAlignmentImage
  Override this method to draw the sequences
paintComponent(Graphics) - Method in class org.emboss.jemboss.editor.PlotConsensus
paintComponent(Graphics) - Method in class org.emboss.jemboss.editor.ColourJFrame.ColourPanel
paintComponent(Graphics) - Method in class org.emboss.jemboss.gui.form.ApplicationNamePanel
panes - Variable in class org.emboss.jemboss.editor.ColourMenu
panes - Variable in class org.emboss.jemboss.gui.ColorMenu
param - Variable in class org.emboss.jemboss.parser.Dependent
parentList - Variable in class org.emboss.jemboss.gui.filetree.RemoteFileNode
parse(String, Hashtable) - Static method in class org.emboss.jemboss.programs.ListFile
  Parse a list file, reading it in line by line, loading other list files recursively if necessary, and loading any files referred to into the filesToMove hash
parseAcd - Variable in class org.emboss.jemboss.gui.form.SectionPanel
parseAcd - Variable in class org.emboss.jemboss.gui.form.BuildJembossForm
ParseAcd - class org.emboss.jemboss.parser.ParseAcd.
  ACD (Ajax command line definition) file parser.
ParseAcd(String, boolean) - Constructor for class org.emboss.jemboss.parser.ParseAcd
  The constructor takes the ACD as a string.
parseParam(BufferedReader, StreamTokenizer) - Method in class org.emboss.jemboss.parser.ParseAcd
  Parses a parameter in a ACD field
passwd - Variable in class org.emboss.jemboss.server.JembossAuthThread
pasteText() - Method in class org.emboss.jemboss.gui.form.TextFieldSink
pasteText() - Method in class org.emboss.jemboss.gui.sequenceChooser.TextAreaSink
pattern - Variable in class org.emboss.jemboss.editor.SequenceJPanel
PatternJFrame - class org.emboss.jemboss.editor.PatternJFrame.
PatternJFrame() - Constructor for class org.emboss.jemboss.editor.PatternJFrame
pc - Variable in class org.emboss.jemboss.editor.GraphicSequenceCollection
pendingResults - Variable in class org.emboss.jemboss.soap.PendingResults
PendingResults - class org.emboss.jemboss.soap.PendingResults.
PendingResults(JembossParams) - Constructor for class org.emboss.jemboss.soap.PendingResults
pfield - Variable in class org.emboss.jemboss.soap.AuthPopup
PINK - Static variable in class org.emboss.jemboss.editor.SequenceProperties
PlafMacros - class org.emboss.jemboss.gui.form.PlafMacros.
PlafMacros() - Constructor for class org.emboss.jemboss.gui.form.PlafMacros
PlotConsensus - class org.emboss.jemboss.editor.PlotConsensus.
PlotConsensus(File, Vector, int, int) - Constructor for class org.emboss.jemboss.editor.PlotConsensus
PlotConsensus(File, Vector, int, int, GraphicSequenceCollection) - Constructor for class org.emboss.jemboss.editor.PlotConsensus
PlotConsensus(Matrix, Vector, int, int) - Constructor for class org.emboss.jemboss.editor.PlotConsensus
PlotConsensus(Matrix, Vector, int, int, GraphicSequenceCollection) - Constructor for class org.emboss.jemboss.editor.PlotConsensus
PlotConsensus(String, String, Vector, int, int) - Constructor for class org.emboss.jemboss.editor.PlotConsensus
plotconsSeqBox - Variable in class org.emboss.jemboss.editor.GraphicSequenceCollection
plotConStrut - Variable in class org.emboss.jemboss.editor.GraphicSequenceCollection
plplot - Variable in class org.emboss.jemboss.JembossParams
plplot - Variable in class org.emboss.jemboss.server.JembossServer
plplot - Variable in class org.emboss.jemboss.server.JembossAuthServer
plplotName - Variable in class org.emboss.jemboss.JembossParams
pmain - Variable in class org.emboss.jemboss.Jemboss
pngContent - Variable in class org.emboss.jemboss.gui.filetree.FileEditorDisplay
polarColor - Static variable in class org.emboss.jemboss.editor.SequenceProperties
popup - Variable in class org.emboss.jemboss.editor.SequenceJPanel
popup - Variable in class org.emboss.jemboss.editor.ColourJFrame
popup - Variable in class org.emboss.jemboss.editor.ColourJFrame.ColourPanel
popup - Variable in class org.emboss.jemboss.gui.filetree.RemoteDragTree
popup - Variable in class org.emboss.jemboss.gui.filetree.DragTree
prefClose - Variable in class org.emboss.jemboss.gui.filetree.LocalAndRemoteFileTreeFrame
prefjni - Static variable in class org.emboss.jemboss.gui.AdvancedOptions
prefShadeGUI - Static variable in class org.emboss.jemboss.gui.AdvancedOptions
pressedResidue - Variable in class org.emboss.jemboss.editor.SequenceJPanel
prettPlot - Variable in class org.emboss.jemboss.editor.GraphicSequenceCollection
prettyPlot - Variable in class org.emboss.jemboss.editor.SequenceJPanel
primaryGp - Variable in class org.emboss.jemboss.parser.ParseAcd
  primary group
print() - Method in class org.emboss.jemboss.editor.PrintAlignmentImage
  Print to a jpeg or png file
print(Graphics, PageFormat, int) - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection
PrintAlignment - class org.emboss.jemboss.editor.PrintAlignment.
PrintAlignment(GraphicSequenceCollection) - Constructor for class org.emboss.jemboss.editor.PrintAlignment
PrintAlignmentImage - class org.emboss.jemboss.editor.PrintAlignmentImage.
PrintAlignmentImage(GraphicSequenceCollection) - Constructor for class org.emboss.jemboss.editor.PrintAlignmentImage
  Java 1.4 or higher is required for the imageio package which is used here to create jpeg and png images of the multiple alignment.
PrintAlignmentImage(GraphicSequenceCollection, PageFormat) - Constructor for class org.emboss.jemboss.editor.PrintAlignmentImage
  Java 1.4 or higher is required for the imageio package which is used here to create jpeg and png images of the multiple alignment.
printPreview() - Method in class org.emboss.jemboss.editor.PrintAlignmentImage
  Display a print preview page
privateName - Variable in class org.emboss.jemboss.soap.ServerSetup
PrivateRequest - class org.emboss.jemboss.soap.PrivateRequest.
PrivateRequest(JembossParams, String, String) - Constructor for class org.emboss.jemboss.soap.PrivateRequest
  Make a soap call to a private server
PrivateRequest(JembossParams, String, String, Vector) - Constructor for class org.emboss.jemboss.soap.PrivateRequest
  Make a soap call to a private server
PrivateRequest(JembossParams, String, Vector) - Constructor for class org.emboss.jemboss.soap.PrivateRequest
  Make a soap call to a private server, using the default service
privateServerFailOver - Variable in class org.emboss.jemboss.JembossParams
privateServers - Variable in class org.emboss.jemboss.JembossParams
privateSoapService - Variable in class org.emboss.jemboss.JembossParams
privateSoapServiceName - Variable in class org.emboss.jemboss.JembossParams
privateSoapURL - Variable in class org.emboss.jemboss.JembossParams
privateSoapURLName - Variable in class org.emboss.jemboss.JembossParams
privateURL - Variable in class org.emboss.jemboss.soap.ServerSetup
prnt - Variable in class org.emboss.jemboss.parser.Ajax
prog - Static variable in class org.emboss.jemboss.server.TestPrivateServer
proganswer - Variable in class org.emboss.jemboss.programs.ResultList
proganswer - Variable in class org.emboss.jemboss.soap.PublicRequest
proganswer - Variable in class org.emboss.jemboss.soap.PrivateRequest
proganswer - Variable in class org.emboss.jemboss.soap.JembossRun
proganswer - Variable in class org.emboss.jemboss.soap.FileList
ProgList - class org.emboss.jemboss.gui.startup.ProgList.
  Used on startup of Jemboss to retrieve the alphabetical list of programs and uses the programs groups to create the menu structure based on the program type.
ProgList.HorizontalMenu - class org.emboss.jemboss.gui.startup.ProgList.HorizontalMenu.
  HorizontalMenu extends JMenu to produces horizontal menus.
ProgList.HorizontalMenu(String) - Constructor for class org.emboss.jemboss.gui.startup.ProgList.HorizontalMenu
ProgList(String, String, JMenuBar) - Constructor for class org.emboss.jemboss.gui.startup.ProgList
progressBar - Variable in class org.emboss.jemboss.soap.AuthPopup
progressLabel - Variable in class org.emboss.jemboss.soap.AuthPopup
project - Variable in class org.emboss.jemboss.programs.RunEmbossApplication2
project - Variable in class org.emboss.jemboss.programs.RunEmbossApplication
project - Variable in class org.emboss.jemboss.programs.JembossProcess
project - Variable in class org.emboss.jemboss.server.JembossThread
project - Variable in class org.emboss.jemboss.server.JembossAuthThread
promptPanel - Variable in class org.emboss.jemboss.soap.AuthPopup
protein - Variable in class org.emboss.jemboss.editor.Sequence
protein - Variable in class org.emboss.jemboss.gui.sequenceChooser.InputSequenceAttributes
protein - Static variable in class org.emboss.jemboss.parser.Ajax
  true if the sequence is protein
protein - Variable in class org.emboss.jemboss.soap.CallAjax
protein_soap - Variable in class org.emboss.jemboss.parser.Ajax
  true if the sequence is protein
proxyAuthPasswd - Variable in class org.emboss.jemboss.JembossParams
proxyAuthPasswdName - Variable in class org.emboss.jemboss.JembossParams
proxyAuthUser - Variable in class org.emboss.jemboss.JembossParams
proxyAuthUserName - Variable in class org.emboss.jemboss.JembossParams
proxyBrowserName - Variable in class org.emboss.jemboss.soap.ServerSetup
proxyBrowserPort - Variable in class org.emboss.jemboss.soap.ServerSetup
proxyDescription() - Method in class org.emboss.jemboss.JembossParams
  A description of the proxy settings
proxyHost - Variable in class org.emboss.jemboss.JembossParams
proxyHostName - Variable in class org.emboss.jemboss.JembossParams
proxyName - Variable in class org.emboss.jemboss.soap.ServerSetup
proxyOverride - Variable in class org.emboss.jemboss.JembossParams
proxyOverrideName - Variable in class org.emboss.jemboss.JembossParams
proxyPort - Variable in class org.emboss.jemboss.soap.ServerSetup
proxyPortNum - Variable in class org.emboss.jemboss.JembossParams
proxyPortNumName - Variable in class org.emboss.jemboss.JembossParams
ps - Variable in class org.emboss.jemboss.server.JembossFileAuthServer
ps - Variable in class org.emboss.jemboss.server.JembossAuthServer
publicName - Variable in class org.emboss.jemboss.soap.ServerSetup
PublicRequest - class org.emboss.jemboss.soap.PublicRequest.
PublicRequest(JembossParams, String) - Constructor for class org.emboss.jemboss.soap.PublicRequest
  Makes a soap call to a public server, using the default service
PublicRequest(JembossParams, String, String) - Constructor for class org.emboss.jemboss.soap.PublicRequest
  Makes a soap call to a public server
PublicRequest(JembossParams, String, String, Vector) - Constructor for class org.emboss.jemboss.soap.PublicRequest
  Makes a soap call to a public server
PublicRequest(JembossParams, String, Vector) - Constructor for class org.emboss.jemboss.soap.PublicRequest
  Makes a soap call to a public server, using the default service
publicServerFailOver - Variable in class org.emboss.jemboss.JembossParams
publicServers - Variable in class org.emboss.jemboss.JembossParams
publicSoapService - Variable in class org.emboss.jemboss.JembossParams
publicSoapServiceName - Variable in class org.emboss.jemboss.JembossParams
publicSoapURL - Variable in class org.emboss.jemboss.JembossParams
publicSoapURLName - Variable in class org.emboss.jemboss.JembossParams
publicURL - Variable in class org.emboss.jemboss.soap.ServerSetup
put_file(String, String, byte[], String) - Method in class org.emboss.jemboss.server.JembossFileServer
put_file(String, String, byte[], String, byte[]) - Method in class org.emboss.jemboss.server.JembossFileAuthServer
putFile(String, byte[], String, String, byte[]) - Method in class org.emboss.jemboss.parser.Ajax

## Q

quoteMe(String) - Method in class org.emboss.jemboss.server.JembossAuthServer
  Quote all tokens ready for shell scripts

## R

raccshow - Variable in class org.emboss.jemboss.gui.form.ReportFormat
rangeField - Variable in class org.emboss.jemboss.gui.form.SectionPanel
rangeField - Variable in class org.emboss.jemboss.gui.form.BuildJembossForm
rasmolColor - Static variable in class org.emboss.jemboss.editor.SequenceProperties
rdesshow - Variable in class org.emboss.jemboss.gui.form.ReportFormat
rea - Variable in class org.emboss.jemboss.programs.RunEmbossApplication2.StdoutHandler
rea - Variable in class org.emboss.jemboss.programs.RunEmbossApplication2.StderrHandler
rea - Variable in class org.emboss.jemboss.server.JembossThread
readByteFile(String) - Static method in class org.emboss.jemboss.server.JembossServer
  Read a file into a byte array.
readFastaFile(BufferedReader) - Method in class org.emboss.jemboss.editor.SequenceReader
  Reads in the FASTA sequence file and creates a Vector containing the sequence(s).
reading - Variable in class org.emboss.jemboss.editor.SequenceReader
readMSFFile(BufferedReader) - Method in class org.emboss.jemboss.editor.SequenceReader
  Reads in the MSF sequence file and creates a Vector containing the sequence(s).
readObject(ObjectInputStream) - Method in class org.emboss.jemboss.gui.SequenceData
readObject(ObjectInputStream) - Method in class org.emboss.jemboss.gui.filetree.RemoteFileNode
readObject(ObjectInputStream) - Method in class org.emboss.jemboss.gui.filetree.FileNode
readObject(ObjectInputStream) - Method in class org.emboss.jemboss.soap.FileRoots
readProcessStderr() - Method in class org.emboss.jemboss.programs.RunEmbossApplication2
  Read in the process stderr.
readProcessStdout() - Method in class org.emboss.jemboss.programs.RunEmbossApplication2
  Read in the process stdout.
readSequenceFile() - Method in class org.emboss.jemboss.editor.SequenceReader
readSequenceString(String) - Method in class org.emboss.jemboss.editor.SequenceReader
redo - Variable in class org.emboss.jemboss.gui.ResultsMenuBar
reExplore() - Method in class org.emboss.jemboss.gui.filetree.FileNode
refresh(FileNode) - Method in class org.emboss.jemboss.gui.filetree.DragTree
refreshRoot() - Method in class org.emboss.jemboss.gui.filetree.RemoteDragTree
  This is used to refresh the file manager
RemoteDragTree - class org.emboss.jemboss.gui.filetree.RemoteDragTree.
  Creates a remote file tree which is a drag source & sink
RemoteDragTree.PopupListener - class org.emboss.jemboss.gui.filetree.RemoteDragTree.PopupListener.
RemoteDragTree.PopupListener() - Constructor for class org.emboss.jemboss.gui.filetree.RemoteDragTree.PopupListener
RemoteDragTree(JembossParams, FileRoots, JPanel) - Constructor for class org.emboss.jemboss.gui.filetree.RemoteDragTree
RemoteFileNode - class org.emboss.jemboss.gui.filetree.RemoteFileNode.
REMOTEFILENODE - Static variable in class org.emboss.jemboss.gui.filetree.RemoteFileNode
RemoteFileNode(JembossParams, FileRoots, String, FileList, String) - Constructor for class org.emboss.jemboss.gui.filetree.RemoteFileNode
RemoteFileNode(JembossParams, FileRoots, String, FileList, String, boolean) - Constructor for class org.emboss.jemboss.gui.filetree.RemoteFileNode
RemoteFileTreePanel - class org.emboss.jemboss.gui.filetree.RemoteFileTreePanel.
RemoteFileTreePanel(JembossParams) - Constructor for class org.emboss.jemboss.gui.filetree.RemoteFileTreePanel
RemoteFileTreePanel(JembossParams, boolean) - Constructor for class org.emboss.jemboss.gui.filetree.RemoteFileTreePanel
  Creates a panel to contain the directory trees on an embreo server.
removedSeqs - Variable in class org.emboss.jemboss.editor.GraphicSequenceCollection
removeResult(JembossProcess) - Method in class org.emboss.jemboss.soap.PendingResults
removeSequence(String) - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection
rename(String, String, String, String) - Method in class org.emboss.jemboss.server.JembossFileServer
rename(String, String, String, String, byte[]) - Method in class org.emboss.jemboss.server.JembossFileAuthServer
renameFile(File, FileNode, String) - Method in class org.emboss.jemboss.gui.filetree.DragTree
  Method to rename a file and update the filenode's.
renameFile(String, byte[], String, String, String) - Method in class org.emboss.jemboss.parser.Ajax
repaintSequences(Hashtable) - Method in class org.emboss.jemboss.editor.AlignJFrame
ReportFormat - class org.emboss.jemboss.gui.form.ReportFormat.
ReportFormat(ParseAcd, int) - Constructor for class org.emboss.jemboss.gui.form.ReportFormat
reqdSection - Static variable in class org.emboss.jemboss.gui.form.BuildJembossForm
res - Variable in class org.emboss.jemboss.editor.ColourJFrame.ColourPanel
resButtonStatus - Variable in class org.emboss.jemboss.gui.ShowSavedResults
reset(double) - Method in class org.emboss.jemboss.parser.acd.ApplicationParam
reset(String) - Method in class org.emboss.jemboss.parser.acd.ApplicationParam
resetCount() - Method in class org.emboss.jemboss.soap.PendingResults
resetParam(int, double) - Method in class org.emboss.jemboss.parser.acd.ApplicationFields
resetParam(int, String) - Method in class org.emboss.jemboss.parser.acd.ApplicationFields
residueColor - Static variable in class org.emboss.jemboss.editor.SequenceProperties
residueColor - Variable in class org.emboss.jemboss.editor.AlignJFrame
residueMatrixPosition - Variable in class org.emboss.jemboss.editor.Matrix
resMenu - Variable in class org.emboss.jemboss.gui.ShowSavedResults
resolveDependents(int, Dependent[], String, String) - Method in class org.emboss.jemboss.gui.form.SectionPanel
  Given an ACD variable and the value it takes, resolve any dependent attribute values.
resolveVariables(ApplicationFields[], int, String) - Method in class org.emboss.jemboss.parser.ParseAcd
  Used to replace the "variable:" or "var:" shorthand notation in the ACD to the full expression it represent
result - Variable in class org.emboss.jemboss.parser.AcdFunResolve
  result as a String of the expression used in constructor
result - Variable in class org.emboss.jemboss.soap.PublicRequest
result - Variable in class org.emboss.jemboss.soap.PrivateRequest
ResultList - class org.emboss.jemboss.programs.ResultList.
  Used by ShowSavedResults to show (show_saved_results), delete (delete_saved_results) & list results (list_saved_results).
ResultList(JembossParams) - Constructor for class org.emboss.jemboss.programs.ResultList
  Holds the list of stored results
ResultList(JembossParams, String, String) - Constructor for class org.emboss.jemboss.programs.ResultList
ResultList(JembossParams, String, String, String) - Constructor for class org.emboss.jemboss.programs.ResultList
  Manipulate a dataset.
results - Variable in class org.emboss.jemboss.programs.JembossProcess
resultsManager - Static variable in class org.emboss.jemboss.Jemboss
  to manage the pending results
ResultsMenuBar - class org.emboss.jemboss.gui.ResultsMenuBar.
  Sets up a results menu bar with save and close
ResultsMenuBar(JFrame, FileEditorDisplay, JembossParams) - Constructor for class org.emboss.jemboss.gui.ResultsMenuBar
  Adds action listener to save contents of a JTextPane.
ResultsMenuBar(JFrame, JTabbedPane, Hashtable, Hashtable) - Constructor for class org.emboss.jemboss.gui.ResultsMenuBar
ResultsMenuBar(JFrame, JTabbedPane, Hashtable, Hashtable, String, JembossParams) - Constructor for class org.emboss.jemboss.gui.ResultsMenuBar
  Adds action listener to save contents of contents of a tabbed pane.
ResultsMenuBar(JFrame, JTabbedPane, Hashtable, JembossParams) - Constructor for class org.emboss.jemboss.gui.ResultsMenuBar
ResultsUpdateTimer - class org.emboss.jemboss.programs.ResultsUpdateTimer.
  Simple demo that uses java.util.Timer to schedule a task to execute once 10 seconds have passed.
ResultsUpdateTimer.ResultsTask - class org.emboss.jemboss.programs.ResultsUpdateTimer.ResultsTask.
ResultsUpdateTimer.ResultsTask() - Constructor for class org.emboss.jemboss.programs.ResultsUpdateTimer.ResultsTask
ResultsUpdateTimer.ResultsTask(DefaultListModel, JFrame) - Constructor for class org.emboss.jemboss.programs.ResultsUpdateTimer.ResultsTask
ResultsUpdateTimer(int, DefaultListModel, JFrame) - Constructor for class org.emboss.jemboss.programs.ResultsUpdateTimer
resWidth - Variable in class org.emboss.jemboss.editor.SequenceJPanel
returnError(Ajax, String) - Method in class org.emboss.jemboss.server.JembossAuthServer
  Report the stderr and stdout to error logs
rev - Variable in class org.emboss.jemboss.gui.sequenceChooser.InputSequenceAttributes
reverseComplementSequence() - Method in class org.emboss.jemboss.editor.Sequence
reverseSequence() - Method in class org.emboss.jemboss.editor.Sequence
rewriteProperties(String, String) - Method in class org.emboss.jemboss.gui.AdvancedOptions
rf - Variable in class org.emboss.jemboss.gui.form.SectionPanel
rf - Variable in class org.emboss.jemboss.gui.form.BuildJembossForm
rfii - Variable in class org.emboss.jemboss.gui.ShowSavedResults
root - Variable in class org.emboss.jemboss.gui.filetree.DragTree
rootdir - Variable in class org.emboss.jemboss.gui.filetree.RemoteFileNode
rootSelect - Variable in class org.emboss.jemboss.gui.filetree.RemoteFileTreePanel
rootVector - Variable in class org.emboss.jemboss.soap.FileRoots
rpt - Static variable in class org.emboss.jemboss.gui.form.ReportFormat
  EMBOSS Report formats
rscroll - Variable in class org.emboss.jemboss.gui.sequenceChooser.OutputSequenceAttributes
rscroll - Variable in class org.emboss.jemboss.gui.sequenceChooser.InputSequenceAttributes
run_prog(String, String, Hashtable) - Method in class org.emboss.jemboss.server.JembossServer
  Run an EMBOSS application
run_prog(String, String, Hashtable, String, byte[]) - Method in class org.emboss.jemboss.server.JembossAuthServer
  Private Authenticated Server Run an EMBOSS application
run_prog(String, String, String[]) - Method in class org.emboss.jemboss.server.JembossServer
  Private Server Run an EMBOSS application
run_prog(String, String, Vector, String) - Method in class org.emboss.jemboss.server.JembossServer
run_prog(String, String, Vector, String, byte[]) - Method in class org.emboss.jemboss.server.JembossAuthServer
run() - Method in class org.emboss.jemboss.gui.SplashThread
run() - Method in class org.emboss.jemboss.programs.RunEmbossApplication2.StdoutHandler
run() - Method in class org.emboss.jemboss.programs.RunEmbossApplication2.StderrHandler
run() - Method in class org.emboss.jemboss.programs.ResultsUpdateTimer.ResultsTask
run() - Method in class org.emboss.jemboss.programs.BatchUpdateTimer.RemindTask
run() - Method in class org.emboss.jemboss.server.JembossThread
run() - Method in class org.emboss.jemboss.server.JembossAuthThread
runAsBatch(Ajax, String, byte[], String, String) - Method in class org.emboss.jemboss.server.JembossAuthServer
runAsGNQSBatch(Ajax, String, byte[], String, String) - Method in class org.emboss.jemboss.server.JembossAuthServer
  Submit to a Generic NQS batch queue.
runAsPBSBatch(Ajax, String, byte[], String, String) - Method in class org.emboss.jemboss.server.JembossAuthServer
  Submit to a OpenPBS batch queue.
RunEmbossApplication - class org.emboss.jemboss.programs.RunEmbossApplication.
  RunEmbossApplication class used to run an EMBOSS process
RunEmbossApplication(String, String[], File) - Constructor for class org.emboss.jemboss.programs.RunEmbossApplication
RunEmbossApplication2 - class org.emboss.jemboss.programs.RunEmbossApplication2.
  RunEmbossApplication2 class used to run an EMBOSS process this reads stdout and stderr in separate threads.
RunEmbossApplication2.StderrHandler - class org.emboss.jemboss.programs.RunEmbossApplication2.StderrHandler.
RunEmbossApplication2.StderrHandler(RunEmbossApplication2) - Constructor for class org.emboss.jemboss.programs.RunEmbossApplication2.StderrHandler
RunEmbossApplication2.StdoutHandler - class org.emboss.jemboss.programs.RunEmbossApplication2.StdoutHandler.
RunEmbossApplication2.StdoutHandler(RunEmbossApplication2) - Constructor for class org.emboss.jemboss.programs.RunEmbossApplication2.StdoutHandler
RunEmbossApplication2(String, String[], File) - Constructor for class org.emboss.jemboss.programs.RunEmbossApplication2
running - Variable in class org.emboss.jemboss.programs.JembossProcess
running_jobs - Variable in class org.emboss.jemboss.soap.PendingResults
rusashow - Variable in class org.emboss.jemboss.gui.form.ReportFormat

## S

s_beg - Variable in class org.emboss.jemboss.gui.SequenceData
  sequence start
s_default - Variable in class org.emboss.jemboss.gui.SequenceData
  use as the default
s_end - Variable in class org.emboss.jemboss.gui.SequenceData
  sequence end
s_listFile - Variable in class org.emboss.jemboss.gui.SequenceData
  sequence list file
s_name - Variable in class org.emboss.jemboss.gui.SequenceData
  sequence file/database
s_remote - Variable in class org.emboss.jemboss.gui.SequenceData
  file on remote file system
safeFileName - Variable in class org.emboss.jemboss.soap.MakeFileSafe
SALMON - Static variable in class org.emboss.jemboss.editor.SequenceProperties
save_project_file(String, String, String, String) - Method in class org.emboss.jemboss.server.JembossServer
  Private server Save a file to a project directory on the server.
save_project_file(String, String, String, String, byte[]) - Method in class org.emboss.jemboss.server.JembossAuthServer
  Private server Save a file to a project directory on the server.
savedResFrame - Variable in class org.emboss.jemboss.gui.ShowSavedResults
savedResFrame - Variable in class org.emboss.jemboss.programs.ResultsUpdateTimer.ResultsTask
saveFile(File, Vector) - Method in class org.emboss.jemboss.editor.SequenceSaver
saveSequenceList() - Static method in class org.emboss.jemboss.gui.SetUpMenuBar
  Save the sequence list for a future session.
saveToRemoteFile - Variable in class org.emboss.jemboss.gui.ResultsMenuBar
saveUserHome - Variable in class org.emboss.jemboss.gui.AdvancedOptions
sbeg - Variable in class org.emboss.jemboss.gui.sequenceChooser.InputSequenceAttributes
ScrollPanel - class org.emboss.jemboss.gui.ScrollPanel.
ScrollPanel() - Constructor for class org.emboss.jemboss.gui.ScrollPanel
ScrollPanel(LayoutManager) - Constructor for class org.emboss.jemboss.gui.ScrollPanel
scrollTree - Variable in class org.emboss.jemboss.Jemboss
sdbName - Variable in class org.emboss.jemboss.gui.sequenceChooser.InputSequenceAttributes
searchSequences(int, String) - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection
  Search the sequences for the position in that matches the given pattern to search for.
secondaryGp - Variable in class org.emboss.jemboss.parser.ParseAcd
  secondary group
sectionBox - Variable in class org.emboss.jemboss.gui.form.SectionPanel
sectionPane - Variable in class org.emboss.jemboss.gui.form.SectionPanel
SectionPanel - class org.emboss.jemboss.gui.form.SectionPanel.
  Responsible for displaying the graphical representation of an ACD section.
SectionPanel(JFrame, JPanel, Box, ParseAcd, int, TextFieldSink[], TextFieldInt[], TextFieldFloat[], JTextField[], JCheckBox[], InputSequenceAttributes[], myComboPopup[], JList[], SetInFileCard[], ListFilePanel[], String[], String, Box[], int, JembossParams, boolean) - Constructor for class org.emboss.jemboss.gui.form.SectionPanel
sectionResize(JPanel) - Method in class org.emboss.jemboss.gui.form.SectionPanel
selected - Variable in class org.emboss.jemboss.editor.ColourMenu
selected - Variable in class org.emboss.jemboss.editor.ColourMenu.ColorPane
selected - Variable in class org.emboss.jemboss.gui.ColorMenu
selected - Variable in class org.emboss.jemboss.gui.ColorMenu.ColorPane
selectedBorder - Variable in class org.emboss.jemboss.editor.ColourMenu
selectedBorder - Variable in class org.emboss.jemboss.gui.ColorMenu
send - Variable in class org.emboss.jemboss.gui.sequenceChooser.InputSequenceAttributes
Separator - class org.emboss.jemboss.gui.form.Separator.
Separator(Dimension) - Constructor for class org.emboss.jemboss.gui.form.Separator
seq - Variable in class org.emboss.jemboss.editor.SequenceNameJButton
seq - Variable in class org.emboss.jemboss.editor.SequenceJPanel
seq - Variable in class org.emboss.jemboss.editor.Sequence
seqAttrib(String, byte[], String, String) - Method in class org.emboss.jemboss.parser.Ajax
  determine sequence attributes as the user
seqBox - Variable in class org.emboss.jemboss.editor.GraphicSequenceCollection
seqFile - Variable in class org.emboss.jemboss.editor.SequenceReader
seqHeight - Variable in class org.emboss.jemboss.editor.SequenceJPanel
seqLength - Variable in class org.emboss.jemboss.editor.SequenceJPanel
seqList - Static variable in class org.emboss.jemboss.gui.SetUpMenuBar
seqModel - Variable in class org.emboss.jemboss.gui.DragJTable
seqModel - Variable in class org.emboss.jemboss.gui.SequenceList
seqNameBox - Variable in class org.emboss.jemboss.editor.GraphicSequenceCollection
seqNamePanel - Variable in class org.emboss.jemboss.editor.GraphicSequenceCollection
seqoutResult - Variable in class org.emboss.jemboss.gui.form.BuildJembossForm
seqPaste - Variable in class org.emboss.jemboss.gui.sequenceChooser.CutNPasteTextArea
seqs - Variable in class org.emboss.jemboss.editor.SequenceReader
seqs - Variable in class org.emboss.jemboss.editor.GraphicSequenceCollection
seqs - Variable in class org.emboss.jemboss.editor.AlignJFrame
seqs - Variable in class org.emboss.jemboss.editor.AlignApplet
seqScroll - Variable in class org.emboss.jemboss.gui.sequenceChooser.CutNPasteTextArea
seqsetAttrib(String, byte[], String, String) - Method in class org.emboss.jemboss.parser.Ajax
seqsetType(String) - Method in class org.emboss.jemboss.parser.Ajax
seqType(String) - Method in class org.emboss.jemboss.parser.Ajax
  determine sequence attributes
Sequence - class org.emboss.jemboss.editor.Sequence.
  Sequence object
Sequence(String) - Constructor for class org.emboss.jemboss.editor.Sequence
Sequence(String, float) - Constructor for class org.emboss.jemboss.editor.Sequence
Sequence(String, String) - Constructor for class org.emboss.jemboss.editor.Sequence
Sequence(String, String, int) - Constructor for class org.emboss.jemboss.editor.Sequence
Sequence(String, String, int, float) - Constructor for class org.emboss.jemboss.editor.Sequence
SequenceData - class org.emboss.jemboss.gui.SequenceData.
  Object to represent the content of each row in the DragJTable of a SequenceList.
SEQUENCEDATA - Static variable in class org.emboss.jemboss.gui.SequenceData
  dataflavor for drag and drop transfers
SequenceData() - Constructor for class org.emboss.jemboss.gui.SequenceData
SequenceData(String, String, String, Boolean, Boolean, Boolean) - Constructor for class org.emboss.jemboss.gui.SequenceData
sequenceFile - Variable in class org.emboss.jemboss.editor.AlignJFrame
SequenceFilter - class org.emboss.jemboss.gui.sequenceChooser.SequenceFilter.
SequenceFilter() - Constructor for class org.emboss.jemboss.gui.sequenceChooser.SequenceFilter
SequenceJPanel - class org.emboss.jemboss.editor.SequenceJPanel.
  Applet for drawing sequence
SequenceJPanel.PopupListener - class org.emboss.jemboss.editor.SequenceJPanel.PopupListener.
SequenceJPanel.PopupListener() - Constructor for class org.emboss.jemboss.editor.SequenceJPanel.PopupListener
SequenceJPanel(int, int) - Constructor for class org.emboss.jemboss.editor.SequenceJPanel
SequenceJPanel(Sequence, JComponent, boolean, boolean, boolean, Hashtable, int) - Constructor for class org.emboss.jemboss.editor.SequenceJPanel
  Constructor with default font size.
SequenceJPanel(Sequence, JComponent, boolean, boolean, boolean, Hashtable, int, int) - Constructor for class org.emboss.jemboss.editor.SequenceJPanel
SequenceList - class org.emboss.jemboss.gui.SequenceList.
  SequenceList extends JFrame to display a set of sequences that the user is working on in a session.
SequenceList(boolean, JembossParams) - Constructor for class org.emboss.jemboss.gui.SequenceList
SequenceListTableModel - class org.emboss.jemboss.gui.SequenceListTableModel.
SequenceListTableModel() - Constructor for class org.emboss.jemboss.gui.SequenceListTableModel
SequenceNameJButton - class org.emboss.jemboss.editor.SequenceNameJButton.
  Draw sequence name
SequenceNameJButton(Sequence, int) - Constructor for class org.emboss.jemboss.editor.SequenceNameJButton
SequenceProperties - class org.emboss.jemboss.editor.SequenceProperties.
SequenceProperties() - Constructor for class org.emboss.jemboss.editor.SequenceProperties
SequenceReader - class org.emboss.jemboss.editor.SequenceReader.
  This class reads sequences in FASTA and MSF format.
SequenceReader() - Constructor for class org.emboss.jemboss.editor.SequenceReader
SequenceReader(File) - Constructor for class org.emboss.jemboss.editor.SequenceReader
SequenceReader(String) - Constructor for class org.emboss.jemboss.editor.SequenceReader
SequenceSaver - class org.emboss.jemboss.editor.SequenceSaver.
  This class saves sequences in FASTA format.
SequenceSaver(Vector) - Constructor for class org.emboss.jemboss.editor.SequenceSaver
SequenceSaver(Vector, File) - Constructor for class org.emboss.jemboss.editor.SequenceSaver
SERVER_DOWN - Static variable in class org.emboss.jemboss.JembossParams
SERVER_ERR - Static variable in class org.emboss.jemboss.JembossParams
SERVER_OK - Static variable in class org.emboss.jemboss.JembossParams
serverDescription() - Method in class org.emboss.jemboss.JembossParams
  A description of the server settings
serverPathToFile - Variable in class org.emboss.jemboss.gui.filetree.RemoteFileNode
serverPrivateList - Variable in class org.emboss.jemboss.JembossParams
serverPrivateListName - Variable in class org.emboss.jemboss.JembossParams
serverPublicList - Variable in class org.emboss.jemboss.JembossParams
serverPublicListName - Variable in class org.emboss.jemboss.JembossParams
ServerSetup - class org.emboss.jemboss.soap.ServerSetup.
ServerSetup(JembossParams) - Constructor for class org.emboss.jemboss.soap.ServerSetup
  Setting for public and private settings panel.
serverStatusHash - Variable in class org.emboss.jemboss.JembossParams
servicedesc() - Method in class org.emboss.jemboss.server.JembossServer
servicedesc() - Method in class org.emboss.jemboss.server.JembossAuthServer
servicePasswd - Variable in class org.emboss.jemboss.JembossParams
servicePasswdByte - Variable in class org.emboss.jemboss.JembossParams
serviceUserName - Variable in class org.emboss.jemboss.JembossParams
serviceUserNameName - Variable in class org.emboss.jemboss.JembossParams
setAppTitle(String, JPanel) - Method in class org.emboss.jemboss.gui.form.SectionPanel
setAttribute(String) - Method in class org.emboss.jemboss.parser.acd.ApplicationParam
setAutoUpdate(boolean) - Method in class org.emboss.jemboss.soap.PendingResults
setBegSeq(int) - Method in class org.emboss.jemboss.gui.sequenceChooser.InputSequenceAttributes
setBegSeq(String) - Method in class org.emboss.jemboss.gui.sequenceChooser.InputSequenceAttributes
setBottomPanel() - Method in class org.emboss.jemboss.soap.AuthPopup
  Buttons across the bottom
setBrowserSize() - Method in class org.emboss.jemboss.gui.Browser
setColor(Color) - Method in class org.emboss.jemboss.editor.ColourMenu
setColor(Color) - Method in class org.emboss.jemboss.gui.ColorMenu
setColorScheme(Hashtable) - Method in class org.emboss.jemboss.editor.SequenceJPanel
setColorScheme(Hashtable) - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection
setCurrentColour(Hashtable) - Method in class org.emboss.jemboss.editor.ColourJFrame
setCurrentDir(String) - Method in class org.emboss.jemboss.soap.FileRoots
  Set the current directory
setCurrentMode(String) - Method in class org.emboss.jemboss.JembossParams
  Set the current mode (interactive or batch).
setCurrentRoot(String) - Method in class org.emboss.jemboss.soap.FileRoots
  Set the current root
setDefaultColorHashtable() - Method in class org.emboss.jemboss.editor.SequenceJPanel
setDefaultData() - Method in class org.emboss.jemboss.gui.SequenceListTableModel
  Setup a blank square table
setDefaultTab(int) - Method in class org.emboss.jemboss.gui.TabListCellRenderer
setDependentExp(String) - Method in class org.emboss.jemboss.parser.Dependent
setDescription(String) - Method in class org.emboss.jemboss.programs.JembossProcess
setDisplayAcceleratorKey(boolean) - Static method in class org.emboss.jemboss.gui.form.MultiLineToolTipUI
setDoc(String) - Method in class org.emboss.jemboss.parser.acd.Application
setDrawBoxes(boolean) - Method in class org.emboss.jemboss.editor.SequenceJPanel
setDrawBoxes(boolean) - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection
setDrawColor(boolean) - Method in class org.emboss.jemboss.editor.SequenceJPanel
setDrawColor(boolean) - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection
setEnableFileManagers(boolean) - Method in class org.emboss.jemboss.gui.SetUpMenuBar
setEnableShowResults(boolean) - Method in class org.emboss.jemboss.gui.SetUpMenuBar
setEndSeq(int) - Method in class org.emboss.jemboss.gui.sequenceChooser.InputSequenceAttributes
setEndSeq(String) - Method in class org.emboss.jemboss.gui.sequenceChooser.InputSequenceAttributes
setErrStd() - Method in class org.emboss.jemboss.parser.Ajax
setExit() - Method in class org.emboss.jemboss.gui.filetree.LocalAndRemoteFileTreeFrame
setFontSize(int) - Method in class org.emboss.jemboss.editor.SequenceNameJButton
setFontSize(int) - Method in class org.emboss.jemboss.editor.SequenceJPanel
setFontSizeForCollection(int) - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection
setForeground(Color) - Method in class org.emboss.jemboss.gui.sequenceChooser.FileChooser
setFormat(PageFormat) - Method in class org.emboss.jemboss.editor.PrintAlignmentImage
  Set the page format
setGraphic(GraphicSequenceCollection) - Method in class org.emboss.jemboss.editor.PatternJFrame
setGroups(String) - Method in class org.emboss.jemboss.parser.acd.Application
setGuiHandleNumber(int) - Method in class org.emboss.jemboss.parser.acd.ApplicationFields
setGuiHandleNumber(String, ApplicationFields) - Method in class org.emboss.jemboss.parser.ParseAcd
  Sets the gui handle depending on the data type.
SetInFileCard - class org.emboss.jemboss.gui.form.SetInFileCard.
SetInFileCard(JPanel, int, String[], String, String, InputSequenceAttributes[], boolean, JembossParams) - Constructor for class org.emboss.jemboss.gui.form.SetInFileCard
  Build the GUI components for an input sequence(s).
setInterval(int) - Method in class org.emboss.jemboss.editor.PlotConsensus
setInterval(int) - Method in class org.emboss.jemboss.gui.SplashThread
setJScrollPaneViewportView() - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection
setLength(int) - Method in class org.emboss.jemboss.parser.Ajax
  Sets the sequence length
setMatrix(Matrix) - Method in class org.emboss.jemboss.editor.MatrixJFrame
setMatrix(Matrix) - Method in class org.emboss.jemboss.editor.AlignJFrame
setMaxSeqLength() - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection
setMaxSequenceLength(int) - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection
setName(String) - Method in class org.emboss.jemboss.parser.acd.Application
setNamePanelWidth(int) - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection
setNewSettings() - Method in class org.emboss.jemboss.soap.ServerSetup
setNumberOfParam(int) - Method in class org.emboss.jemboss.parser.acd.ApplicationFields
setNumberOfResiduesPerLine(int) - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection
setNumberSize() - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection
SetOutFileCard - class org.emboss.jemboss.gui.form.SetOutFileCard.
  Creates an output file Box
SetOutFileCard(Box, TextFieldSink, Color, JPanel) - Constructor for class org.emboss.jemboss.gui.form.SetOutFileCard
setPageIndex(int) - Method in class org.emboss.jemboss.editor.PrintAlignmentImage
  Set the page number to create an image of
setParam(int, String, double) - Method in class org.emboss.jemboss.parser.acd.ApplicationFields
setParam(int, String, String) - Method in class org.emboss.jemboss.parser.acd.ApplicationFields
setPlotSize() - Method in class org.emboss.jemboss.editor.PlotConsensus
setPopupMenuVisible(boolean) - Method in class org.emboss.jemboss.gui.startup.ProgList.HorizontalMenu
setPreferredSize(Dimension) - Method in class org.emboss.jemboss.gui.sequenceChooser.FileChooser
setPrettyPlot(boolean) - Method in class org.emboss.jemboss.editor.SequenceJPanel
setPrettyPlot(boolean) - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection
setPrivateSoapService(String) - Method in class org.emboss.jemboss.JembossParams
  Set the name of the private soap service we're using
setPrivateSoapURL(String) - Method in class org.emboss.jemboss.JembossParams
  Set the URL of the private soap server
setProtein(boolean) - Method in class org.emboss.jemboss.parser.Ajax
  Sets whether sequence is protein (true)
setPublicSoapService(String) - Method in class org.emboss.jemboss.JembossParams
  Set the name of the public soap service we're using
setPublicSoapURL(String) - Method in class org.emboss.jemboss.JembossParams
  Set the URL of the public soap server
setResults(Hashtable) - Method in class org.emboss.jemboss.programs.JembossProcess
setResultsMenuBar(JFrame, boolean) - Method in class org.emboss.jemboss.gui.ResultsMenuBar
  Sets up a results menu bar with save and close
setSelected(boolean) - Method in class org.emboss.jemboss.editor.ColourMenu.ColorPane
setSelected(boolean) - Method in class org.emboss.jemboss.gui.ColorMenu.ColorPane
setSequenceLength(int) - Method in class org.emboss.jemboss.editor.SequenceJPanel
setSequenceSelection(boolean) - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection
setServerStatus(String, int) - Method in class org.emboss.jemboss.JembossParams
  Mark a server as bad
setServicePasswd(char[]) - Method in class org.emboss.jemboss.JembossParams
  Save the password needed for the remote service
setServiceUserName(String) - Method in class org.emboss.jemboss.JembossParams
  Save the username needed for the remote service
setShadingAndVisibility(Component, boolean, int) - Method in class org.emboss.jemboss.gui.form.SectionPanel
setSize(Dimension) - Method in class org.emboss.jemboss.gui.filetree.FileEditorDisplay
  Override to avoid line wrapping.
setSize(Dimension) - Method in class org.emboss.jemboss.gui.sequenceChooser.FileChooser
setTabs(int[]) - Method in class org.emboss.jemboss.gui.TabListCellRenderer
setText(String) - Method in class org.emboss.jemboss.gui.sequenceChooser.FileChooser
setText(String) - Method in class org.emboss.jemboss.gui.sequenceChooser.CutNPasteTextArea
setText(String, String) - Method in class org.emboss.jemboss.gui.filetree.FileEditorDisplay
  Set the text & style in the JTextPane.
setType(boolean) - Method in class org.emboss.jemboss.editor.Sequence
setUpJMenuBar(Vector) - Method in class org.emboss.jemboss.gui.Browser
  Method to create the frames menu and tool bar.
SetUpMenuBar - class org.emboss.jemboss.gui.SetUpMenuBar.
  Sets the top menu bar for Jemboss main window
SetUpMenuBar(JembossParams, JFrame, String[], String, boolean) - Constructor for class org.emboss.jemboss.gui.SetUpMenuBar
setupServerRedundancy() - Method in class org.emboss.jemboss.JembossParams
  Initialize the server redundancy data.
setUserHome(String) - Method in class org.emboss.jemboss.JembossParams
setValue(double) - Method in class org.emboss.jemboss.gui.form.TextFieldFloat
setValue(double) - Method in class org.emboss.jemboss.parser.acd.ApplicationParam
setValue(int) - Method in class org.emboss.jemboss.gui.form.TextFieldInt
setValue(Object) - Method in class org.emboss.jemboss.gui.SwingWorker
  Set the value produced by worker thread
setValue(String) - Method in class org.emboss.jemboss.parser.acd.ApplicationParam
setValueAt(Object, int, int) - Method in class org.emboss.jemboss.gui.SequenceListTableModel
  Set the Object in a cell in the table
setWeight(float) - Method in class org.emboss.jemboss.parser.Ajax
  Sets the sequence weight
ShiftEast(int, int) - Method in class org.emboss.jemboss.JembossLogo
ShiftNorth(int, int) - Method in class org.emboss.jemboss.JembossLogo
ShiftSouth(int, int) - Method in class org.emboss.jemboss.JembossLogo
ShiftWest(int, int) - Method in class org.emboss.jemboss.JembossLogo
show_acd(String) - Method in class org.emboss.jemboss.server.JembossServer
  Retrieves the ACD file of an application.
show_acd(String) - Method in class org.emboss.jemboss.server.JembossAuthServer
  Retrieves the ACD file of an application.
show_db() - Method in class org.emboss.jemboss.server.JembossServer
  Returns the databases held on the server
show_db() - Method in class org.emboss.jemboss.server.JembossAuthServer
  Returns the databases held on the server
show_help(String) - Method in class org.emboss.jemboss.server.JembossServer
  Returns the help for an application as given by 'tfm'
show_help(String) - Method in class org.emboss.jemboss.server.JembossAuthServer
  Returns the help for an application as given by 'tfm'
show_saved_results(String, String) - Method in class org.emboss.jemboss.server.JembossServer
  Private Server Returns the results for a saved project.
show_saved_results(String, String, String) - Method in class org.emboss.jemboss.server.JembossServer
  Private Server Returns the results for a saved project.
show_saved_results(String, String, String, byte[]) - Method in class org.emboss.jemboss.server.JembossAuthServer
  Private Server Returns the results for a saved project.
showConsensusPlot(File, int) - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection
showConsensusPlot(Matrix, int) - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection
ShowDB - class org.emboss.jemboss.soap.ShowDB.
ShowDB(JembossParams) - Constructor for class org.emboss.jemboss.soap.ShowDB
  Makes a soap call to retrieve the showdb output
showFilePane(String, JembossParams) - Static method in class org.emboss.jemboss.gui.filetree.RemoteDragTree
  Opens a JFrame with the file contents displayed.
showFilePane(String, JembossParams) - Static method in class org.emboss.jemboss.gui.filetree.DragTree
  Opens a JFrame with the file contents displayed.
showLocalRemoteFile - Variable in class org.emboss.jemboss.gui.SetUpMenuBar
showOptions(boolean) - Method in class org.emboss.jemboss.editor.PrintAlignmentImage
  Provide some options for the image created
showOptions(GraphicSequenceCollection, PageFormat) - Method in class org.emboss.jemboss.editor.PrintAlignment
  Provide some options for the image created
showPattern(String) - Method in class org.emboss.jemboss.editor.SequenceJPanel
showPendingResults(JFrame) - Method in class org.emboss.jemboss.soap.PendingResults
ShowResultSet - class org.emboss.jemboss.gui.ShowResultSet.
  Displays JTabbedPane of the contents of the Hashtable
ShowResultSet(Hashtable, Hashtable) - Constructor for class org.emboss.jemboss.gui.ShowResultSet
ShowResultSet(Hashtable, Hashtable, JembossParams) - Constructor for class org.emboss.jemboss.gui.ShowResultSet
ShowResultSet(Hashtable, Hashtable, String, JembossParams) - Constructor for class org.emboss.jemboss.gui.ShowResultSet
ShowResultSet(Hashtable, String, JembossParams) - Constructor for class org.emboss.jemboss.gui.ShowResultSet
ShowSavedResults - class org.emboss.jemboss.gui.ShowSavedResults.
  Shows a list of results from the SOAP server and displays individual result sets
ShowSavedResults(JembossParams, JFrame) - Constructor for class org.emboss.jemboss.gui.ShowSavedResults
  Show the saved results on the server.
ShowSavedResults(JembossParams, PendingResults) - Constructor for class org.emboss.jemboss.gui.ShowSavedResults
  Show the results sent to a batch queue.
ShowSavedResults(String) - Constructor for class org.emboss.jemboss.gui.ShowSavedResults
sID - Variable in class org.emboss.jemboss.gui.sequenceChooser.InputSequenceAttributes
SINGLETON - Static variable in class org.emboss.jemboss.gui.form.MultiLineToolTipUI
size - Variable in class org.emboss.jemboss.parser.Ajax
sizeColor - Static variable in class org.emboss.jemboss.editor.SequenceProperties
soapService - Variable in class org.emboss.jemboss.JembossParams
soapServiceName - Variable in class org.emboss.jemboss.JembossParams
sopenFile - Variable in class org.emboss.jemboss.gui.sequenceChooser.InputSequenceAttributes
sp - Variable in class org.emboss.jemboss.gui.ShowSavedResults
splashing - Variable in class org.emboss.jemboss.gui.SplashThread
splashing - Variable in class org.emboss.jemboss.gui.BuildProgramMenu
splashp - Variable in class org.emboss.jemboss.soap.AuthPopup
splashThread - Variable in class org.emboss.jemboss.gui.BuildProgramMenu
SplashThread - class org.emboss.jemboss.gui.SplashThread.
SplashThread(AuthPopup, int) - Constructor for class org.emboss.jemboss.gui.SplashThread
ss - Variable in class org.emboss.jemboss.gui.ShowSavedResults
ss - Variable in class org.emboss.jemboss.gui.SetUpMenuBar
start() - Method in class org.emboss.jemboss.editor.AlignApplet
start() - Method in class org.emboss.jemboss.gui.SwingWorker
  Start the worker thread.
status - Variable in class org.emboss.jemboss.programs.RunEmbossApplication2
status - Variable in class org.emboss.jemboss.programs.RunEmbossApplication
status - Variable in class org.emboss.jemboss.programs.ResultList
status - Variable in class org.emboss.jemboss.soap.ShowDB
status - Variable in class org.emboss.jemboss.soap.JembossRun
status - Variable in class org.emboss.jemboss.soap.GetWossname
status - Variable in class org.emboss.jemboss.soap.GetHelp
status - Variable in class org.emboss.jemboss.soap.FileList
status - Variable in class org.emboss.jemboss.soap.CallAjax
statusField - Variable in class org.emboss.jemboss.editor.PrintAlignmentImage
statusField - Variable in class org.emboss.jemboss.editor.AlignJFrame
statusField - Variable in class org.emboss.jemboss.gui.ShowSavedResults
statusHash() - Method in class org.emboss.jemboss.soap.PendingResults
statusmsg - Variable in class org.emboss.jemboss.programs.ResultList
statusmsg - Variable in class org.emboss.jemboss.soap.ShowDB
statusmsg - Variable in class org.emboss.jemboss.soap.JembossRun
statusmsg - Variable in class org.emboss.jemboss.soap.GetWossname
statusmsg - Variable in class org.emboss.jemboss.soap.GetHelp
statusmsg - Variable in class org.emboss.jemboss.soap.FileList
statusmsg - Variable in class org.emboss.jemboss.soap.CallAjax
statusPanel(JFrame) - Method in class org.emboss.jemboss.soap.PendingResults
  A panel with appropriate gadgets to show the status of any jobs and to view them, and to set the mode.
stderr - Variable in class org.emboss.jemboss.programs.RunEmbossApplication2
stdout - Variable in class org.emboss.jemboss.gui.form.BuildJembossForm
stdout - Variable in class org.emboss.jemboss.programs.RunEmbossApplication2
stdout - Variable in class org.emboss.jemboss.programs.RunEmbossApplication
storeSeqList - Variable in class org.emboss.jemboss.gui.SequenceList
succeeded() - Method in class org.emboss.jemboss.soap.PublicRequest
  Whether the call succeeded (eventually) or not
succeeded() - Method in class org.emboss.jemboss.soap.PrivateRequest
successful - Variable in class org.emboss.jemboss.soap.PublicRequest
successful - Variable in class org.emboss.jemboss.soap.PrivateRequest
sumscore - Variable in class org.emboss.jemboss.editor.PlotConsensus
surfaceColor - Static variable in class org.emboss.jemboss.editor.SequenceProperties
svalue - Variable in class org.emboss.jemboss.parser.ParseAcd
  string value of a parameter
svalue - Variable in class org.emboss.jemboss.parser.acd.ApplicationParam
SwingWorker - class org.emboss.jemboss.gui.SwingWorker.
  This is the 3rd version of SwingWorker (also known as SwingWorker 3), an abstract class that you subclass to perform GUI-related work in a dedicated thread.
SwingWorker.ThreadVar - class org.emboss.jemboss.gui.SwingWorker.ThreadVar.
  Class to maintain reference to current worker thread under separate synchronization control.
SwingWorker.ThreadVar(Thread) - Constructor for class org.emboss.jemboss.gui.SwingWorker.ThreadVar
SwingWorker() - Constructor for class org.emboss.jemboss.gui.SwingWorker
  Start a thread that will call the `construct` method and then exit.
swiss - Static variable in class org.emboss.jemboss.gui.sequenceChooser.SequenceFilter

## T

table - Variable in class org.emboss.jemboss.gui.SequenceList
TabListCellRenderer - class org.emboss.jemboss.gui.TabListCellRenderer.
  Adapted from an example at http://www.spindoczine.com/sbe/
TabListCellRenderer() - Constructor for class org.emboss.jemboss.gui.TabListCellRenderer
taylorColor - Static variable in class org.emboss.jemboss.editor.SequenceProperties
TestPrivateServer - class org.emboss.jemboss.server.TestPrivateServer.
  This can be used to test the private server.
TestPrivateServer() - Constructor for class org.emboss.jemboss.server.TestPrivateServer
TestPublicServer - class org.emboss.jemboss.server.TestPublicServer.
TestPublicServer() - Constructor for class org.emboss.jemboss.server.TestPublicServer
TextAreaSink - class org.emboss.jemboss.gui.sequenceChooser.TextAreaSink.
  Extends JTextArea so that is becomes a sink for pasting into.
TextAreaSink() - Constructor for class org.emboss.jemboss.gui.sequenceChooser.TextAreaSink
textf - Variable in class org.emboss.jemboss.gui.form.SectionPanel
textf - Variable in class org.emboss.jemboss.gui.form.BuildJembossForm
TextFieldFloat - class org.emboss.jemboss.gui.form.TextFieldFloat.
TextFieldFloat.DecimalNumberDocument - class org.emboss.jemboss.gui.form.TextFieldFloat.DecimalNumberDocument.
TextFieldFloat.DecimalNumberDocument() - Constructor for class org.emboss.jemboss.gui.form.TextFieldFloat.DecimalNumberDocument
TextFieldFloat() - Constructor for class org.emboss.jemboss.gui.form.TextFieldFloat
TextFieldInt - class org.emboss.jemboss.gui.form.TextFieldInt.
TextFieldInt.WholeNumberDocument - class org.emboss.jemboss.gui.form.TextFieldInt.WholeNumberDocument.
TextFieldInt.WholeNumberDocument() - Constructor for class org.emboss.jemboss.gui.form.TextFieldInt.WholeNumberDocument
TextFieldInt() - Constructor for class org.emboss.jemboss.gui.form.TextFieldInt
TextFieldSink - class org.emboss.jemboss.gui.form.TextFieldSink.
  Extends JTextField to enable pasting & drag and drop into it.
TextFieldSink() - Constructor for class org.emboss.jemboss.gui.form.TextFieldSink
textFloat - Variable in class org.emboss.jemboss.gui.form.SectionPanel
textFloat - Variable in class org.emboss.jemboss.gui.form.BuildJembossForm
textInt - Variable in class org.emboss.jemboss.gui.form.SectionPanel
textInt - Variable in class org.emboss.jemboss.gui.form.BuildJembossForm
thread - Variable in class org.emboss.jemboss.gui.SwingWorker
thread - Variable in class org.emboss.jemboss.gui.SwingWorker.ThreadVar
threadVar - Variable in class org.emboss.jemboss.gui.SwingWorker
time - Variable in class org.emboss.jemboss.gui.AdvancedOptions
timer - Static variable in class org.emboss.jemboss.programs.ResultsUpdateTimer
timer - Static variable in class org.emboss.jemboss.programs.BatchUpdateTimer
title - Variable in class org.emboss.jemboss.gui.ColumnData
tmproot - Variable in class org.emboss.jemboss.server.JembossServer
tmproot - Variable in class org.emboss.jemboss.server.JembossAuthServer
tmprootDir - Variable in class org.emboss.jemboss.server.JembossServer
toByteArr(char[]) - Static method in class org.emboss.jemboss.JembossParams
  Return the password as byte array
toolBar - Variable in class org.emboss.jemboss.gui.ResultsMenuBar
toolkit - Variable in class org.emboss.jemboss.gui.form.TextFieldInt
toolkit - Variable in class org.emboss.jemboss.gui.form.TextFieldFloat
toolTipFontMetrics(Font) - Method in class org.emboss.jemboss.gui.form.MultiLineToolTipUI.MyToolTip
toString() - Method in class org.emboss.jemboss.gui.filetree.FileNode
tree - Static variable in class org.emboss.jemboss.Jemboss
trim(String) - Static method in class org.emboss.jemboss.programs.ListFile
  Given a list file @file or list::file return just the file name
TURQUOISE - Static variable in class org.emboss.jemboss.editor.SequenceProperties
type - Variable in class org.emboss.jemboss.parser.Dependent

## U

ufield - Variable in class org.emboss.jemboss.soap.AuthPopup
UFO - Variable in class org.emboss.jemboss.gui.sequenceChooser.OutputSequenceAttributes
UFO - Variable in class org.emboss.jemboss.gui.sequenceChooser.InputSequenceAttributes
undo - Variable in class org.emboss.jemboss.gui.ResultsMenuBar
undoManager - Variable in class org.emboss.jemboss.gui.ResultsMenuBar
uninstallUI(JComponent) - Method in class org.emboss.jemboss.gui.form.MultiLineToolTipUI
unselectedBorder - Variable in class org.emboss.jemboss.editor.ColourMenu
unselectedBorder - Variable in class org.emboss.jemboss.gui.ColorMenu
update_result_status(String, String, Hashtable) - Method in class org.emboss.jemboss.server.JembossServer
  Used to provide information on the batch/background processes.
update_result_status(String, String, Hashtable, String) - Method in class org.emboss.jemboss.server.JembossServer
update_result_status(String, String, Hashtable, String, byte[]) - Method in class org.emboss.jemboss.server.JembossAuthServer
update_result_status(String, String, Vector, String) - Method in class org.emboss.jemboss.server.JembossServer
  Used to provide information on the batch/background processes.
update_result_status(String, String, Vector, String, byte[]) - Method in class org.emboss.jemboss.server.JembossAuthServer
  Used to provide information on the batch/background processes.
updateBeginEnd(String, String) - Method in class org.emboss.jemboss.gui.form.SectionPanel
updateJembossProperty(String, String) - Method in class org.emboss.jemboss.JembossParams
  Update the properties structure.
updateJembossPropHash(Hashtable) - Method in class org.emboss.jemboss.JembossParams
  Update properties from a Hashtable
updateJembossPropString(String) - Method in class org.emboss.jemboss.JembossParams
  Parse a key=value string to update the properties structure
updateJembossPropStrings(String[]) - Method in class org.emboss.jemboss.JembossParams
  Parse an array of key=value strings to update the properties structure
updateJobStats() - Method in class org.emboss.jemboss.soap.PendingResults
updateMenu() - Method in class org.emboss.jemboss.gui.ResultsMenuBar
  Update the undo and redo menus and enable or disable dependent on the editing event that proceeded.
updateMode() - Method in class org.emboss.jemboss.soap.PendingResults
  Updates the mode on the combo box to reflect the current state
updateMode(String) - Method in class org.emboss.jemboss.soap.PendingResults
  Updates the mode on the combo box to reflect the requested value
updateRes(Hashtable) - Method in class org.emboss.jemboss.programs.ResultList
  Replace the current results hash
updateSettingsFromProperties() - Method in class org.emboss.jemboss.JembossParams
updateStatus() - Method in class org.emboss.jemboss.soap.PendingResults
  Connect to the embreo server, and update the status of the jobs in the list.
upper - Variable in class org.emboss.jemboss.gui.sequenceChooser.InputSequenceAttributes
urlField - Variable in class org.emboss.jemboss.gui.Browser
useAuth - Variable in class org.emboss.jemboss.JembossParams
useAuthName - Variable in class org.emboss.jemboss.JembossParams
useBrowserProxy - Variable in class org.emboss.jemboss.JembossParams
useBrowserProxy - Variable in class org.emboss.jemboss.soap.ServerSetup
useBrowserProxyName - Variable in class org.emboss.jemboss.JembossParams
useExitMenu - Variable in class org.emboss.jemboss.editor.AlignJFrame
useJavaNoProxy - Variable in class org.emboss.jemboss.JembossParams
useJavaProxy - Variable in class org.emboss.jemboss.JembossParams
useProxy - Variable in class org.emboss.jemboss.JembossParams
useProxy - Variable in class org.emboss.jemboss.soap.ServerSetup
useProxyAuth - Variable in class org.emboss.jemboss.JembossParams
useProxyAuthName - Variable in class org.emboss.jemboss.JembossParams
useProxyName - Variable in class org.emboss.jemboss.JembossParams
userAuth - Variable in class org.emboss.jemboss.soap.ServerSetup
userAuth(String, byte[], String) - Method in class org.emboss.jemboss.parser.Ajax
  authentication methods
userHome - Variable in class org.emboss.jemboss.JembossParams
userHome - Variable in class org.emboss.jemboss.gui.AdvancedOptions
userHomeName - Variable in class org.emboss.jemboss.JembossParams
userHomeSave() - Method in class org.emboss.jemboss.gui.AdvancedOptions
username - Variable in class org.emboss.jemboss.server.JembossServer
userName - Variable in class org.emboss.jemboss.server.JembossAuthThread
useTFM - Variable in class org.emboss.jemboss.JembossParams
useTFMName - Variable in class org.emboss.jemboss.JembossParams

## V

value - Variable in class org.emboss.jemboss.gui.SwingWorker
vappF - Variable in class org.emboss.jemboss.parser.ParseAcd
  vector containing the application fields
vdir - Variable in class org.emboss.jemboss.soap.FileList
verifyUser(Ajax, String, byte[], Vector) - Method in class org.emboss.jemboss.server.JembossFileAuthServer
verifyUser(Ajax, String, byte[], Vector) - Method in class org.emboss.jemboss.server.JembossAuthServer
version() - Method in class org.emboss.jemboss.server.JembossServer
version() - Method in class org.emboss.jemboss.server.JembossAuthServer
viewPane - Variable in class org.emboss.jemboss.editor.SequenceJPanel
viewPane - Variable in class org.emboss.jemboss.editor.PlotConsensus
viewPaneResize() - Method in class org.emboss.jemboss.editor.SequenceJPanel
viewResiduePosition - Variable in class org.emboss.jemboss.editor.PatternJFrame

## W

warnUser(String) - Method in class org.emboss.jemboss.gui.Browser
weight - Static variable in class org.emboss.jemboss.parser.Ajax
  sequence weight
weight - Variable in class org.emboss.jemboss.soap.CallAjax
weight_soap - Variable in class org.emboss.jemboss.parser.Ajax
  sequence weight
WHEAT - Static variable in class org.emboss.jemboss.editor.SequenceProperties
width - Variable in class org.emboss.jemboss.gui.ColumnData
windowClosing(WindowEvent) - Method in class org.emboss.jemboss.Jemboss.winExit
windowClosing(WindowEvent) - Method in class org.emboss.jemboss.editor.AlignJFrame.winExit
withSoap - Static variable in class org.emboss.jemboss.Jemboss
  true if in client-server mode (using SOAP)
withSoap - Variable in class org.emboss.jemboss.gui.form.SectionPanel
withSoap - Variable in class org.emboss.jemboss.gui.form.BuildJembossForm
wrapAround - Variable in class org.emboss.jemboss.editor.PatternJFrame
writeByteFile(String, String) - Method in class org.emboss.jemboss.JembossJarUtil
writeImageToFile(RenderedImage, File, String) - Method in class org.emboss.jemboss.editor.PrintAlignmentImage
  Write out the image
writeList() - Method in class org.emboss.jemboss.gui.startup.ProgList
  Writes to screen the program names
writeObject(ObjectOutputStream) - Method in class org.emboss.jemboss.gui.SequenceData
writeObject(ObjectOutputStream) - Method in class org.emboss.jemboss.gui.filetree.RemoteFileNode
writeObject(ObjectOutputStream) - Method in class org.emboss.jemboss.gui.filetree.FileNode
writeObject(ObjectOutputStream) - Method in class org.emboss.jemboss.soap.FileRoots
writeOK() - Method in class org.emboss.jemboss.gui.filetree.FileSaving
writeOK() - Method in class org.emboss.jemboss.gui.filetree.FileSave
  Whether the fileSaving() operation was successful
writeStdout() - Method in class org.emboss.jemboss.programs.RunEmbossApplication2
  This method can be called after the process has completed to write the stdout to the project directory.
wt - Variable in class org.emboss.jemboss.editor.Sequence

## X

x - Variable in class org.emboss.jemboss.JembossLogo
x - Variable in class org.emboss.jemboss.gui.form.ApplicationNamePanel
xsize - Variable in class org.emboss.jemboss.editor.ColourJFrame.ColourPanel

## Y

y - Variable in class org.emboss.jemboss.JembossLogo
y - Variable in class org.emboss.jemboss.gui.form.ApplicationNamePanel
YBox - Variable in class org.emboss.jemboss.editor.ColourJFrame
ymax - Variable in class org.emboss.jemboss.editor.PlotConsensus
ymin - Variable in class org.emboss.jemboss.editor.PlotConsensus
ypad - Variable in class org.emboss.jemboss.editor.SequenceNameJButton
ypad - Variable in class org.emboss.jemboss.editor.SequenceJPanel
ysize - Variable in class org.emboss.jemboss.editor.ColourJFrame.ColourPanel

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