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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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