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A

AQUAMARINE - Static variable in class org.emboss.jemboss.editor.SequenceProperties: AQUAMARINE from EMBOSS data Ecolour.map
AUTOSCROLL_MARGIN - Static variable in class org.emboss.jemboss.gui.filetree.DragTree: AutoScroll margin
AUTOSCROLL_MARGIN - Static variable in class org.emboss.jemboss.gui.filetree.RemoteDragTree: AutoScroll margin
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) - Constructor for class org.emboss.jemboss.parser.AcdFunResolve
AcdVarResolve - class org.emboss.jemboss.parser.AcdVarResolve.: Resolves any variable reference in a string.
AcdVarResolve(String, String, String, ParseAcd, int, TextFieldSink[], TextFieldInt[], TextFieldFloat[], JembossComboPopup[], JCheckBox[]) - Constructor for class org.emboss.jemboss.parser.AcdVarResolve
AcdVariableResolve - class org.emboss.jemboss.parser.AcdVariableResolve.: Resolves variable references.
AcdVariableResolve(String, String, String) - Constructor for class org.emboss.jemboss.parser.AcdVariableResolve: Given an expression this is searched for occurences of a variable name for which the value is known.
AdvancedOptions - class org.emboss.jemboss.gui.AdvancedOptions.: Jemboss advanced options and settings.
AdvancedOptions(JembossParams) - Constructor for class org.emboss.jemboss.gui.AdvancedOptions
Ajax - class org.emboss.jemboss.parser.Ajax.: Used with JNI to access EMBOSS ajax library.
Ajax() - Constructor for class org.emboss.jemboss.parser.Ajax
AjaxUtil - class org.emboss.jemboss.parser.AjaxUtil.: Utility to get the sequence file contents or the database entry ready to use in Ajax
AjaxUtil() - Constructor for class org.emboss.jemboss.parser.AjaxUtil
AlignApplet - class org.emboss.jemboss.editor.AlignApplet.
AlignApplet() - Constructor for class org.emboss.jemboss.editor.AlignApplet
AlignFormat - class org.emboss.jemboss.gui.form.AlignFormat.: Handles emboss alignment formats http://www.hgmp.mrc.ac.uk/Software/EMBOSS/Themes/AlignFormats.html
AlignFormat(ParseAcd, int) - Constructor for class org.emboss.jemboss.gui.form.AlignFormat
AlignFormat(String, boolean) - 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(Vector) - 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() - Constructor for class org.emboss.jemboss.editor.AlignJFrame
AlignJFrame(boolean) - Constructor for class org.emboss.jemboss.editor.AlignJFrame
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
AppendToLogFileThread - class org.emboss.jemboss.server.AppendToLogFileThread.: Write to a log file in a separate thread
AppendToLogFileThread(String, String, boolean) - Constructor for class org.emboss.jemboss.server.AppendToLogFileThread
ApplicationFields - class org.emboss.jemboss.parser.acd.ApplicationFields.: Object for an field in the ACD file.
ApplicationFields() - Constructor for class org.emboss.jemboss.parser.acd.ApplicationFields
ApplicationNamePanel - class org.emboss.jemboss.gui.form.ApplicationNamePanel.: Panel to display the EMBOSS application name on
ApplicationNamePanel(String, int, int, int) - Constructor for class org.emboss.jemboss.gui.form.ApplicationNamePanel
ApplicationParam - class org.emboss.jemboss.parser.acd.ApplicationParam.: Object for a parameter of a field in the EMBOSS ACD file
ApplicationParam(String, String) - Constructor for class org.emboss.jemboss.parser.acd.ApplicationParam
ApplicationParam(String, double) - Constructor for class org.emboss.jemboss.parser.acd.ApplicationParam
AuthPopup - class org.emboss.jemboss.soap.AuthPopup.: Display a popup asking the user to enter a username and password
AuthPopup(JembossParams, JFrame) - Constructor for 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.
about() - Method in class org.emboss.jemboss.server.JembossServer
aboutRes - Variable in class org.emboss.jemboss.gui.ShowSavedResults: text area for initial description of the saved results window and the run information of the results
aboutScroll - Variable in class org.emboss.jemboss.gui.ShowSavedResults: scrollpane for description of the results
abouturl() - Method in class org.emboss.jemboss.server.JembossServer
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: acd file location
acdDirToParse - Variable in class org.emboss.jemboss.server.JembossServer: acd directory
acdDirToParseName - Variable in class org.emboss.jemboss.JembossParams: property name for acd file location
acdExpAnd(String) - Method in class org.emboss.jemboss.parser.AcdFunResolve: Looks for and resolves an expression @( num & num )
acdExpCase(String) - Method in class org.emboss.jemboss.parser.AcdFunResolve: Looks for and resolves an expression as a switch/case statement @( var = casea : vala, caseb: valb else: val )
acdExpCond(String) - Method in class org.emboss.jemboss.parser.AcdFunResolve: Looks for and resolves an expression @( bool ? trueval : falseval )
acdExpDiv(String) - Method in class org.emboss.jemboss.parser.AcdFunResolve: Looks for and resolves an expression @( num * num )
acdExpEqual(String) - Method in class org.emboss.jemboss.parser.AcdFunResolve: Looks for and resolves an expression @( num == num )
acdExpGreater(String) - Method in class org.emboss.jemboss.parser.AcdFunResolve: Looks for and resolves an expression @( num > num )
acdExpLesser(String) - Method in class org.emboss.jemboss.parser.AcdFunResolve: Looks for and resolves an expression @( num < num )
acdExpMinus(String) - Method in class org.emboss.jemboss.parser.AcdFunResolve: Looks for and resolves an expression @( num - num )
acdExpNot(String) - Method in class org.emboss.jemboss.parser.AcdFunResolve: Looks for and resolves an expression @(! bool ) or @(NOT bool) or @(not bool).
acdExpNotEqual(String) - Method in class org.emboss.jemboss.parser.AcdFunResolve: Looks for and resolves an expression @( num != num )
acdExpOr(String) - Method in class org.emboss.jemboss.parser.AcdFunResolve: 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: Looks for and resolves an expression @( num * num )
acdFunResolve(String) - Method in class org.emboss.jemboss.parser.AcdFunResolve: Looks for and resolves expressions
acdStore - Variable in class org.emboss.jemboss.gui.BuildProgramMenu: acd files cache
acdStore - Static variable in class org.emboss.jemboss.soap.GetACD: acd store
acidColor - Static variable in class org.emboss.jemboss.editor.SequenceProperties: Acidic/Basic (Red=acidic, Blue=basic)
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.ColourJFrame.ResidueColourPanel: Popup menu actions
actionPerformed(ActionEvent) - Method in class org.emboss.jemboss.editor.ColourPanel: Popup menu actions
actionPerformed(ActionEvent) - Method in class org.emboss.jemboss.editor.PrettyPlotJFrame
actionPerformed(ActionEvent) - Method in class org.emboss.jemboss.editor.SequenceJPanel: Override actionPerformed for popup menu actions
actionPerformed(ActionEvent) - Method in class org.emboss.jemboss.gui.Browser: Override actionPerformed
actionPerformed(ActionEvent) - Method in class org.emboss.jemboss.gui.ShowResultSet.GroutPanelListener
actionPerformed(ActionEvent) - Method in class org.emboss.jemboss.gui.filetree.DragTree: Popup menu actions
actionPerformed(ActionEvent) - Method in class org.emboss.jemboss.gui.filetree.RemoteDragTree: 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: active border
activeBorder - Variable in class org.emboss.jemboss.gui.ColorMenu
addAnnotationSequence(Sequence) - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection
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) to the backslash chars
addFileToList(String, String, Hashtable) - Static method in class org.emboss.jemboss.programs.ListFile: Add a file to the list
addGroutAlignJFrameListener(GroutAlignJFrameListener) - Method in class org.emboss.jemboss.editor.GroutAlignJFrame
addGroutGraphicSequenceCollectionListener(GroutGraphicSequenceCollectionListener) - Method in class org.emboss.jemboss.editor.GroutGraphicSequenceCollection
addHashContentsToTab(Hashtable, JTabbedPane) - Method in class org.emboss.jemboss.gui.ShowResultSet: Add the contents of a hash table to the tabbed pane
addMenuItems() - Method in class org.emboss.jemboss.editor.GroutAlignJFrame
addObject(String, String, FileNode) - Method in class org.emboss.jemboss.gui.filetree.DragTree: Adding a file (or directory) to the file tree manager.
addObject(RemoteFileNode, String, boolean) - Method in class org.emboss.jemboss.gui.filetree.RemoteDragTree: Adding a file (or directory) to the file tree manager.
addResidue() - Method in class org.emboss.jemboss.editor.GroutGraphicSequenceCollection
addResult(JembossProcess) - Method in class org.emboss.jemboss.soap.PendingResults: Add a pending process to the list
addSection - Static variable in class org.emboss.jemboss.gui.form.BuildJembossForm
addSectionBox - Variable in class org.emboss.jemboss.gui.form.BuildJembossForm
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.
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.GroutGraphicSequenceCollection: Add a sequence at a particular index to the sequence collection display and to the collection of sequences (seqs) with a specified y-padding.
addSequence(Sequence, boolean, int, int) - Method in class org.emboss.jemboss.editor.GroutGraphicSequenceCollection: Add a sequence 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: Add the html pane to a scrollpane, list and splitpane and set the size of the html pane
addURL(Object) - Method in class org.emboss.jemboss.gui.MemoryComboBox: Add an element to the combobox
addWindowCloser() - Method in class org.emboss.jemboss.editor.GroutAlignJFrame: when you close the window, should remove lines from Grout
adjustmentValueChanged(AdjustmentEvent) - Method in class org.emboss.jemboss.editor.GroutGraphicSequenceCollection
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.BuildJembossForm
af - Variable in class org.emboss.jemboss.gui.form.SectionPanel: alignment format
ajaxLength - Static variable in class org.emboss.jemboss.gui.form.SectionPanel: sequence length
ajaxProtein - Static variable in class org.emboss.jemboss.gui.form.SectionPanel: sequence type
ajaxWeight - Static variable in class org.emboss.jemboss.gui.form.SectionPanel: sequence weight
align - Variable in class org.emboss.jemboss.editor.ColourJFrame: Associated alignment viewer
align_msf - Static variable in class org.emboss.jemboss.gui.form.AlignFormat: EMBOSS alignment formats
align_pairwise - Static variable in class org.emboss.jemboss.gui.form.AlignFormat: EMBOSS pairwise alignment formats
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
antiAlias - Variable in class org.emboss.jemboss.editor.PrintAlignmentImage: use anti aliasing (default is false)
ao - Variable in class org.emboss.jemboss.gui.SetUpMenuBar: advanced options
appName - Variable in class org.emboss.jemboss.gui.form.SectionPanel: application name
appP - Variable in class org.emboss.jemboss.parser.acd.ApplicationFields: parameters for this field
appendToLogFile(String, String) - Method in class org.emboss.jemboss.server.JembossAuthServer: Appends a log entry to the log file
appendToSequence(String) - Method in class org.emboss.jemboss.editor.Sequence: Append to a sequence
applName - Variable in class org.emboss.jemboss.gui.form.BuildJembossForm
appversion() - Method in class org.emboss.jemboss.server.JembossServer
aromaticColor - Static variable in class org.emboss.jemboss.editor.SequenceProperties: Aromatic/Aliphatic (Red=Aromatic, Blue=Aliphatic)
attach(SequenceJPanel) - Method in class org.emboss.jemboss.editor.SequenceJPanel: Attach sequence display to the same group
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: parameter/attribute type
autoUpdates - Variable in class org.emboss.jemboss.soap.PendingResults: automatic job status updates
autoscroll(Point) - Method in class org.emboss.jemboss.gui.filetree.DragTree: Handles the auto scrolling of the JTree.
autoscroll(Point) - Method in class org.emboss.jemboss.gui.filetree.RemoteDragTree: Handles the auto scrolling of the JTree.
autoscrollInsets - Variable in class org.emboss.jemboss.gui.filetree.DragTree: used by AutoScroll method
autoscrollInsets - Variable in class org.emboss.jemboss.gui.filetree.RemoteDragTree: used by AutoScroll method

B

BLUEVIOLET - Static variable in class org.emboss.jemboss.editor.SequenceProperties: BLUEVIOLET from EMBOSS data Ecolour.map
BROWN - Static variable in class org.emboss.jemboss.editor.SequenceProperties: BROWN from EMBOSS data Ecolour.map
BatchUpdateTimer - class org.emboss.jemboss.programs.BatchUpdateTimer.: Timer for updating the Jemboss job manager for batch jobs submitted
BatchUpdateTimer(int) - Constructor for class org.emboss.jemboss.programs.BatchUpdateTimer
BatchUpdateTimer.RemindTask - class org.emboss.jemboss.programs.BatchUpdateTimer.RemindTask.: Timer task to update the Jemboss job manager
BatchUpdateTimer.RemindTask() - Constructor for class org.emboss.jemboss.programs.BatchUpdateTimer.RemindTask
Browser - class org.emboss.jemboss.gui.Browser.: Jemboss web browser
Browser(String, String, JembossParams) - Constructor for class org.emboss.jemboss.gui.Browser
Browser(String, String, boolean, String, JembossParams) - Constructor for class org.emboss.jemboss.gui.Browser
Browser(URL, String) - Constructor for class org.emboss.jemboss.gui.Browser
Browser.JIconButton - class org.emboss.jemboss.gui.Browser.JIconButton.: Jemboss icon button
Browser.JIconButton(ImageIcon) - Constructor for class org.emboss.jemboss.gui.Browser.JIconButton
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, 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, JembossParams, boolean, SetUpMenuBar, JFrame, Dimension) - Constructor for class org.emboss.jemboss.gui.BuildProgramMenu
backBt - Variable in class org.emboss.jemboss.gui.Browser: Back button option
backMenu - Variable in class org.emboss.jemboss.gui.Browser: Back menu option
baseColor - Static variable in class org.emboss.jemboss.editor.SequenceProperties: nucletide colour scheme
boundWidth - Variable in class org.emboss.jemboss.editor.SequenceJPanel: boundary width around each residue
boundWidth - Variable in class org.emboss.jemboss.editor.SequenceNameJButton: boundary width
boundWidth2 - Variable in class org.emboss.jemboss.editor.SequenceJPanel: half boundary width (boundWidth/2)
breakupLines(String) - Static method in class org.emboss.jemboss.gui.form.PlafMacros: Break text into separate lines
bresults - Variable in class org.emboss.jemboss.gui.form.BuildJembossForm
browserProxyHost - Variable in class org.emboss.jemboss.JembossParams: browser proxy host
browserProxyHostName - Variable in class org.emboss.jemboss.JembossParams: property name for browser proxy host
browserProxyPort - Variable in class org.emboss.jemboss.JembossParams: browser proxy port
browserProxyPortName - Variable in class org.emboss.jemboss.JembossParams: property name for browser proxy port
bwdArrow - Variable in class org.emboss.jemboss.Jemboss: Image for hiding the local filemanager

C

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
CallAjax - class org.emboss.jemboss.soap.CallAjax.: Calls the EMBOSS ajax library
CallAjax(String, String, JembossParams) - Constructor for class org.emboss.jemboss.soap.CallAjax
ColorMenu - class org.emboss.jemboss.gui.ColorMenu.: Colour pallette menu
ColorMenu(String) - Constructor for 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
ColourJFrame - class org.emboss.jemboss.editor.ColourJFrame.: Colour pallette display and editor.
ColourJFrame(AlignJFrame) - Constructor for class org.emboss.jemboss.editor.ColourJFrame
ColourJFrame.ResidueColourPanel - class org.emboss.jemboss.editor.ColourJFrame.ResidueColourPanel.: Colour panel for each individual residue in the pallette
ColourJFrame.ResidueColourPanel(String, Color) - Constructor for class org.emboss.jemboss.editor.ColourJFrame.ResidueColourPanel
ColourMenu - class org.emboss.jemboss.editor.ColourMenu.: Colour menu displayed in a popup menu from the colour display pallette (ColourJFrame).
ColourMenu(String) - Constructor for 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
ColourPanel - class org.emboss.jemboss.editor.ColourPanel.: Colour panel for each individual residue in the pallette
ColourPanel(String, Color) - Constructor for class org.emboss.jemboss.editor.ColourPanel
ColourPanel.PopupListener - class org.emboss.jemboss.editor.ColourPanel.PopupListener.: Popup listener
ColourPanel.PopupListener() - Constructor for class org.emboss.jemboss.editor.ColourPanel.PopupListener
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
Consensus - class org.emboss.jemboss.editor.Consensus.: Calculate a consensus using the same method as 'cons' in the EMBOSS suite.
Consensus(File, 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
Consensus(Matrix, Vector, float, float, int) - Constructor for class org.emboss.jemboss.editor.Consensus
ConsensusOptions - class org.emboss.jemboss.editor.ConsensusOptions.: Defines the options to be used in calculating a consensus
ConsensusOptions(JScrollPane) - Constructor for class org.emboss.jemboss.editor.ConsensusOptions
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
calculateCons(Matrix, Vector, float, float, int) - Method in class org.emboss.jemboss.editor.Consensus: Routine to calculate the consensus of a set of sequences
callTFM - Variable in class org.emboss.jemboss.soap.ServerSetup: selected if tfm help is run on the server
call_ajax(String, String, String, byte[]) - Method in class org.emboss.jemboss.server.JembossAuthServer: 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: Uses JNI to calculate sequence attributes using EMBOSS library call.
call_ajax(String, String) - Method in class org.emboss.jemboss.server.JembossServer: Uses JNI to calculate sequence attributes using EMBOSS library call.
canDo - Variable in class org.emboss.jemboss.gui.filetree.FileSave: true if it is possible to write to this file
caseFloat - Variable in class org.emboss.jemboss.editor.ConsensusOptions: set the case
cbusy - Variable in class org.emboss.jemboss.editor.AlignApplet
cbusy - Variable in class org.emboss.jemboss.editor.AlignJFrame
cbusy - Variable in class org.emboss.jemboss.editor.ConsensusOptions
cbusy - Variable in class org.emboss.jemboss.editor.MatrixJFrame: cursor busy
cbusy - Variable in class org.emboss.jemboss.gui.Browser: busy cursor
cbusy - Variable in class org.emboss.jemboss.gui.SequenceList
cbusy - Variable in class org.emboss.jemboss.gui.ShowSavedResults: busy cursor
cbusy - Variable in class org.emboss.jemboss.gui.filetree.DragTree: busy cursor
cbusy - Variable in class org.emboss.jemboss.gui.filetree.RemoteDragTree: busy cursor
cbusy - Variable in class org.emboss.jemboss.gui.filetree.RemoteFileTreePanel: busy cursor
cbusy - Variable in class org.emboss.jemboss.gui.form.BuildJembossForm
cdone - Variable in class org.emboss.jemboss.editor.AlignApplet
cdone - Variable in class org.emboss.jemboss.editor.AlignJFrame
cdone - Variable in class org.emboss.jemboss.editor.ConsensusOptions
cdone - Variable in class org.emboss.jemboss.editor.MatrixJFrame: cursor done
cdone - Variable in class org.emboss.jemboss.gui.Browser: done cursor
cdone - Variable in class org.emboss.jemboss.gui.SequenceList
cdone - Variable in class org.emboss.jemboss.gui.ShowSavedResults: done cursor
cdone - Variable in class org.emboss.jemboss.gui.filetree.DragTree: done cursor
cdone - Variable in class org.emboss.jemboss.gui.filetree.RemoteDragTree: done cursor
cdone - Variable in class org.emboss.jemboss.gui.filetree.RemoteFileTreePanel: done cursor
cdone - Variable in class org.emboss.jemboss.gui.form.BuildJembossForm
centreMarkerX - Variable in class org.emboss.jemboss.editor.GroutSequenceJPanel
chargeColor - Static variable in class org.emboss.jemboss.editor.SequenceProperties: Positive/Negative charge (Red=Positive, Blue=Negative)
checkBox - Variable in class org.emboss.jemboss.gui.form.BuildJembossForm
checkBox - Variable in class org.emboss.jemboss.gui.form.SectionPanel: boolean fields
checkDependents(Box, String[]) - 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.JembossAuthServer
clone() - Method in class org.emboss.jemboss.server.JembossServer
cnp - Variable in class org.emboss.jemboss.editor.Paste
codons - Static variable in class org.emboss.jemboss.gui.BuildProgramMenu: codons usage tables
codons - Variable in class org.emboss.jemboss.soap.ShowDB: codon usage tables
col - Variable in class org.emboss.jemboss.editor.ColourMenu.ColorPane
col - Variable in class org.emboss.jemboss.editor.ColourPanel
col - Variable in class org.emboss.jemboss.editor.SequenceJPanel
col - Variable in class org.emboss.jemboss.gui.ColorMenu.ColorPane
colorScheme - Variable in class org.emboss.jemboss.editor.GraphicSequenceCollection: Colour scheme to use
colorTable - Variable in class org.emboss.jemboss.editor.SequenceJPanel: colour scheme
colourMenus(JMenu) - Method in class org.emboss.jemboss.editor.AlignJFrame: Constructs the colour menus
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: Colour scheme
complement(char) - Method in class org.emboss.jemboss.editor.Sequence: Complement a residue
complementSequence() - Method in class org.emboss.jemboss.editor.Sequence: Complement the sequence
complete() - Method in class org.emboss.jemboss.programs.JembossProcess: Called when a process has completed
completed - Variable in class org.emboss.jemboss.programs.JembossProcess: true when process is complete
completed_jobs - Variable in class org.emboss.jemboss.soap.PendingResults: number of completed processes
cons - Variable in class org.emboss.jemboss.editor.Consensus
cons - Variable in class org.emboss.jemboss.editor.Matrix
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: Convert back to the original project names replace blank spaces with underscores ('_')
convertToPretty(String) - Static method in class org.emboss.jemboss.gui.ShowSavedResults: Convert the project names to remove the underscores ('_') with blank spaces
cp - Variable in class org.emboss.jemboss.gui.form.AlignFormat: component to display formats
cp - Variable in class org.emboss.jemboss.gui.form.ReportFormat: container for report formats
createAlignmentImage(int) - Method in class org.emboss.jemboss.editor.PrintAlignmentImage: Returns a generated image
createDefaultModel() - Method in class org.emboss.jemboss.gui.form.TextFieldFloat
createDefaultModel() - Method in class org.emboss.jemboss.gui.form.TextFieldInt
createFinishedFile(String) - Method in class org.emboss.jemboss.server.JembossServer: Creates a file named "finished" in the project directory, that contains a time stamp.
createFinishedFile() - Method in class org.emboss.jemboss.server.JembossThread: 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: Create the consensus plot
createPopup() - Method in class org.emboss.jemboss.gui.form.JembossComboPopup.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: Creates the tree model for the given root
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: currently selected directory
currentMode - Variable in class org.emboss.jemboss.JembossParams: current mode for running an application
currentModeName - Variable in class org.emboss.jemboss.JembossParams: property name for current mode
currentRoot - Variable in class org.emboss.jemboss.soap.FileRoots: currently selected root
cutnPaste - Variable in class org.emboss.jemboss.gui.form.SetInFileCard: cut and paste text area
cwd - Variable in class org.emboss.jemboss.gui.AdvancedOptions: current working directory
cwd - Variable in class org.emboss.jemboss.gui.filetree.FileSaving: path to saved file
cwd - Variable in class org.emboss.jemboss.gui.form.BuildJembossForm
cygwin - Static variable in class org.emboss.jemboss.JembossParams: cygwin
cygwinName - Variable in class org.emboss.jemboss.JembossParams: property name for Jemboss java server
cygwinSeqAttr(String, JembossParams) - Method in class org.emboss.jemboss.gui.SequenceList: Cygwin uses infoseq to get sequence length and type and uses infoalign to get the sequence weight.
cygwinSeqAttr(String, String[], String) - Method in class org.emboss.jemboss.gui.form.SectionPanel: Cygwin uses infoseq to get sequence length and type and uses infoalign to get the sequence weight.

D

DISPLAY_ACCELERATOR - Static variable in class org.emboss.jemboss.gui.form.MultiLineToolTipUI
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
Dependent - class org.emboss.jemboss.parser.Dependent.: Variable that is dependent on the value of another variable
Dependent(int, int, String, String) - Constructor for class org.emboss.jemboss.parser.Dependent
DragJTable - class org.emboss.jemboss.gui.DragJTable.: Extend JTable to implement a drag and drop table for storing sequence lists (SequenceList)
DragJTable(SequenceListTableModel) - Constructor for class org.emboss.jemboss.gui.DragJTable
DragTree - class org.emboss.jemboss.gui.filetree.DragTree.: Creates a local file tree manager for Jemboss.
DragTree(File, JFrame, JembossParams) - Constructor for class org.emboss.jemboss.gui.filetree.DragTree
DragTree.PopupListener - class org.emboss.jemboss.gui.filetree.DragTree.PopupListener.: Popup menu listener
DragTree.PopupListener() - Constructor for class org.emboss.jemboss.gui.filetree.DragTree.PopupListener
d - Variable in class org.emboss.jemboss.gui.form.Separator: size of separator
datasets - Variable in class org.emboss.jemboss.gui.ShowSavedResults: data list model
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.BuildJembossForm
db - Variable in class org.emboss.jemboss.gui.form.SectionPanel: available databases
db - Variable in class org.emboss.jemboss.gui.startup.Database: available databases
dbText - Variable in class org.emboss.jemboss.soap.ShowDB: showdb output
dbs - Variable in class org.emboss.jemboss.gui.sequenceChooser.InputSequenceAttributes: available databases
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.AlignFormat: default format
def - Variable in class org.emboss.jemboss.gui.form.ReportFormat: default report format
defaultBorder - Static variable in class org.emboss.jemboss.gui.sequenceChooser.CutNPasteTextArea: default border for field
defaultRoot - Variable in class org.emboss.jemboss.soap.FileRoots: default root
defaultRootIndex - Variable in class org.emboss.jemboss.soap.FileRoots: default root index
delDir(String, byte[], String, String) - Method in class org.emboss.jemboss.parser.Ajax: delete a directory
delDir(String, String, String, byte[]) - Method in class org.emboss.jemboss.server.JembossFileAuthServer: Delete a directory
delDir(String, String, String) - Method in class org.emboss.jemboss.server.JembossFileServer: Delete a directory
delFile(String, byte[], String, String) - Method in class org.emboss.jemboss.parser.Ajax: delete a file
delFile(String, String, String, byte[]) - Method in class org.emboss.jemboss.server.JembossFileAuthServer: Delete a file
delFile(String, String, String) - Method in class org.emboss.jemboss.server.JembossFileServer: Delete a file
deleteConsensusPlot() - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection: Remove the consensus plot from the sequence editor
deleteFile(FileNode) - Method in class org.emboss.jemboss.gui.filetree.DragTree: Delete a file from the tree
deleteNode(RemoteFileNode) - Method in class org.emboss.jemboss.gui.filetree.RemoteDragTree: Delete a node (file or directory) from the tree and from the server
deleteObject(FileNode) - Method in class org.emboss.jemboss.gui.filetree.DragTree: Delete a node from the JTree
deleteObject(RemoteFileNode) - Method in class org.emboss.jemboss.gui.filetree.RemoteDragTree: Delete a node from the tree
deleteResidue(int) - Method in class org.emboss.jemboss.editor.Sequence: Delete a residue from the 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.gui.SetUpMenuBar: Delete temporary files
delete_saved_results(String, String, String, byte[]) - Method in class org.emboss.jemboss.server.JembossAuthServer: Deletes a projects saved results.
delete_saved_results(String, String, String) - Method in class org.emboss.jemboss.server.JembossServer: Deletes a projects saved results.
delete_saved_results(String, String) - Method in class org.emboss.jemboss.server.JembossServer: Deletes a projects saved results.
dep - Variable in class org.emboss.jemboss.parser.ParseAcd: array of dependent variables
description - Variable in class org.emboss.jemboss.programs.JembossProcess: project description
descriptionHash() - Method in class org.emboss.jemboss.soap.PendingResults: Get the processes description
detach(SequenceJPanel) - Method in class org.emboss.jemboss.editor.SequenceJPanel: Detach sequence display from this group
detachAll() - Method in class org.emboss.jemboss.editor.SequenceJPanel: Detach all sequence displays from this group
directories - Variable in class org.emboss.jemboss.soap.FileList: directory list
directory_shortls(String, String, String, byte[]) - Method in class org.emboss.jemboss.server.JembossFileAuthServer: Get a directory listing
directory_shortls(String, String, String) - Method in class org.emboss.jemboss.server.JembossFileServer: Get a directory listing
displayAccelerator - Static variable in class org.emboss.jemboss.gui.form.MultiLineToolTipUI
doDrawNumber(int, FontMetrics, Graphics) - Method in class org.emboss.jemboss.editor.GroutSequenceJPanel
doIndent(Vector) - Method in class org.emboss.jemboss.editor.GroutGraphicSequenceCollection
doPrintActions() - Method in class org.emboss.jemboss.editor.PrintableJTable
doReset() - Method in class org.emboss.jemboss.gui.form.ListFilePanel: Reset the values of the list files
doReset() - Method in class org.emboss.jemboss.gui.form.SetInFileCard: Reset all text areas for sequence entering
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
docurl() - Method in class org.emboss.jemboss.server.JembossServer
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
dragDropEnd(DragSourceDropEvent) - Method in class org.emboss.jemboss.gui.DragJTable
dragDropEnd(DragSourceDropEvent) - Method in class org.emboss.jemboss.gui.filetree.DragTree
dragDropEnd(DragSourceDropEvent) - Method in class org.emboss.jemboss.gui.filetree.RemoteDragTree
dragEnter(DragSourceDragEvent) - Method in class org.emboss.jemboss.gui.DragJTable
dragEnter(DropTargetDragEvent) - Method in class org.emboss.jemboss.gui.DragJTable
dragEnter(DragSourceDragEvent) - Method in class org.emboss.jemboss.gui.filetree.DragTree
dragEnter(DropTargetDragEvent) - Method in class org.emboss.jemboss.gui.filetree.DragTree
dragEnter(DragSourceDragEvent) - Method in class org.emboss.jemboss.gui.filetree.RemoteDragTree
dragEnter(DropTargetDragEvent) - Method in class org.emboss.jemboss.gui.filetree.RemoteDragTree
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(DropTargetEvent) - Method in class org.emboss.jemboss.gui.DragJTable
dragExit(DragSourceEvent) - Method in class org.emboss.jemboss.gui.filetree.DragTree
dragExit(DropTargetEvent) - Method in class org.emboss.jemboss.gui.filetree.DragTree
dragExit(DragSourceEvent) - Method in class org.emboss.jemboss.gui.filetree.RemoteDragTree
dragExit(DropTargetEvent) - Method in class org.emboss.jemboss.gui.filetree.RemoteDragTree
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.DragTree
dragGestureRecognized(DragGestureEvent) - Method in class org.emboss.jemboss.gui.filetree.RemoteDragTree
dragOver(DragSourceDragEvent) - Method in class org.emboss.jemboss.gui.DragJTable
dragOver(DropTargetDragEvent) - Method in class org.emboss.jemboss.gui.DragJTable
dragOver(DragSourceDragEvent) - Method in class org.emboss.jemboss.gui.filetree.DragTree
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(DragSourceDragEvent) - Method in class org.emboss.jemboss.gui.filetree.RemoteDragTree
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.form.TextFieldSink
dragOver(DropTargetDragEvent) - Method in class org.emboss.jemboss.gui.sequenceChooser.TextAreaSink
drawBlackBox - Variable in class org.emboss.jemboss.editor.GraphicSequenceCollection: draw black square around residues
drawBlackBox - Variable in class org.emboss.jemboss.editor.SequenceJPanel: draw a black box around residues
drawCentreMarker(Graphics) - Method in class org.emboss.jemboss.editor.GroutSequenceJPanel
drawColorBox - Variable in class org.emboss.jemboss.editor.GraphicSequenceCollection: colour residues
drawColorBox - Variable in class org.emboss.jemboss.editor.SequenceJPanel: colour the residues
drawNumber - Variable in class org.emboss.jemboss.editor.GraphicSequenceCollection: draw sequence position number
drawNumber() - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection
drawNumber() - Method in class org.emboss.jemboss.editor.GroutGraphicSequenceCollection
drawNumber - Variable in class org.emboss.jemboss.editor.SequenceJPanel: draw the sequence numbers
drawSequence - Variable in class org.emboss.jemboss.editor.GraphicSequenceCollection: draw the sequence
drawSequence - Variable in class org.emboss.jemboss.editor.SequenceJPanel: draw the sequence
drawSequences(Graphics2D, PageFormat, int) - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection: Draws the sequences for printing
drawSequences(Graphics2D, PageFormat, int, int) - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection: Draws the sequences for printing
drop(DropTargetDropEvent) - Method in class org.emboss.jemboss.gui.DragJTable
drop(DropTargetDropEvent) - Method in class org.emboss.jemboss.gui.filetree.DragTree
drop(DropTargetDropEvent) - Method in class org.emboss.jemboss.gui.filetree.RemoteDragTree
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(DropTargetDragEvent) - Method in class org.emboss.jemboss.gui.DragJTable
dropActionChanged(DragSourceDragEvent) - Method in class org.emboss.jemboss.gui.filetree.DragTree
dropActionChanged(DropTargetDragEvent) - Method in class org.emboss.jemboss.gui.filetree.DragTree
dropActionChanged(DragSourceDragEvent) - Method in class org.emboss.jemboss.gui.filetree.RemoteDragTree
dropActionChanged(DropTargetDragEvent) - Method in class org.emboss.jemboss.gui.filetree.RemoteDragTree
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
embURL - Variable in class org.emboss.jemboss.JembossParams: documentation URL
embl - Static variable in class org.emboss.jemboss.gui.sequenceChooser.SequenceFilter
embossBin - Variable in class org.emboss.jemboss.JembossParams: emboss binary location
embossBin - Variable in class org.emboss.jemboss.gui.form.BuildJembossForm
embossBin - Variable in class org.emboss.jemboss.server.JembossAuthServer: emboss binary path
embossBin - Variable in class org.emboss.jemboss.server.JembossFileAuthServer: emboss binary directory
embossBin - Variable in class org.emboss.jemboss.server.JembossServer: emboss binary directory
embossBinName - Variable in class org.emboss.jemboss.JembossParams: property name for emboss binary location
embossData - Variable in class org.emboss.jemboss.JembossParams: emboss data location
embossData - Variable in class org.emboss.jemboss.server.JembossAuthServer: emboss data path
embossData - Variable in class org.emboss.jemboss.server.JembossServer: emboss data directory
embossDataName - Variable in class org.emboss.jemboss.JembossParams: property name for emboss data location
embossEnvironment - Variable in class org.emboss.jemboss.JembossParams: emboss environment
embossEnvironmentName - Variable in class org.emboss.jemboss.JembossParams: property name for emboss environment
embossPath - Variable in class org.emboss.jemboss.JembossParams: emboss path environment variable
embossPath - Variable in class org.emboss.jemboss.server.JembossAuthServer: path environment variable
embossPath - Variable in class org.emboss.jemboss.server.JembossFileAuthServer: emboss path
embossPath - Variable in class org.emboss.jemboss.server.JembossServer: emboss path
embossPathName - Variable in class org.emboss.jemboss.JembossParams: property name for emboss path environment variable
embossURL - Variable in class org.emboss.jemboss.JembossParams: property name for documentation URL
embreo_roots(String, byte[]) - Method in class org.emboss.jemboss.server.JembossFileAuthServer: Retrieves the file manager roots on the server
embreo_roots(String) - Method in class org.emboss.jemboss.server.JembossFileServer: Retrieves the file manager roots on the server
endBorder - Static variable in class org.emboss.jemboss.gui.form.TextFieldSink
env - Variable in class org.emboss.jemboss.server.JembossAuthServer: emboss run environment
environ - Variable in class org.emboss.jemboss.server.JembossAuthServer: emboss run environment as a string
environ - Variable in class org.emboss.jemboss.server.JembossFileAuthServer: emboss run environment
envp - Variable in class org.emboss.jemboss.gui.BuildProgramMenu: environment vars
envp - Variable in class org.emboss.jemboss.gui.form.BuildJembossForm
envp - Variable in class org.emboss.jemboss.server.JembossServer: emboss run environment
envp_emboss - Variable in class org.emboss.jemboss.server.JembossServer: emboss run environment
epr - Variable in class org.emboss.jemboss.soap.CallAjax: request to private server
epr - Variable in class org.emboss.jemboss.soap.GetWossname: request to Jemboss public server
errStd - Variable in class org.emboss.jemboss.parser.Ajax: stderr
errorLog - Variable in class org.emboss.jemboss.server.JembossAuthServer: Jemboss error log file
exitJemboss() - Method in class org.emboss.jemboss.gui.SetUpMenuBar
exitOnDone - Variable in class org.emboss.jemboss.soap.AuthPopup: true if window is to be hidden
exp - Variable in class org.emboss.jemboss.parser.AcdVarResolve: expression
exp - Variable in class org.emboss.jemboss.parser.AcdVariableResolve: expression to resolve
exp - Variable in class org.emboss.jemboss.parser.Dependent: expression
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.FileNode: Explores a directory adding a FileNode for each child
explore() - Method in class org.emboss.jemboss.gui.filetree.RemoteFileNode: Explore the node and add new child nodes
exploreNode(FileNode) - Method in class org.emboss.jemboss.gui.filetree.DragTree: Explore a directory node
exploreNode(RemoteFileNode) - Method in class org.emboss.jemboss.gui.filetree.RemoteDragTree: Explore a directory node
explored - Variable in class org.emboss.jemboss.gui.filetree.FileNode: true if explored
explored - Variable in class org.emboss.jemboss.gui.filetree.RemoteFileNode: true if node is explored
extend - Variable in class org.emboss.jemboss.Jemboss: Button to open local filemanager

F

FILENODE - Static variable in class org.emboss.jemboss.gui.filetree.FileNode: data flavour of a file node
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(String) - Constructor for class org.emboss.jemboss.gui.filetree.FileEditorDisplay
FileEditorDisplay(String, Object) - Constructor for class org.emboss.jemboss.gui.filetree.FileEditorDisplay
FileList - class org.emboss.jemboss.soap.FileList.: Retrieves a directory listing from an Jemboss server.
FileList(JembossParams, String, String) - Constructor for class org.emboss.jemboss.soap.FileList
FileManager - class org.emboss.jemboss.FileManager.: Display the local and remote file managers
FileManager() - Constructor for class org.emboss.jemboss.FileManager
FileNode - class org.emboss.jemboss.gui.filetree.FileNode.: File node for local file tree manager
FileNode(File) - Constructor for class org.emboss.jemboss.gui.filetree.FileNode
FileRoots - class org.emboss.jemboss.soap.FileRoots.: Retrieve the list of available filesystem roots
FileRoots(JembossParams) - Constructor for class org.emboss.jemboss.soap.FileRoots
FileSave - class org.emboss.jemboss.gui.filetree.FileSave.: Saving files locally
FileSave(File) - Constructor for class org.emboss.jemboss.gui.filetree.FileSave: Check if we can/want to save file to disk.
FileSaving - class org.emboss.jemboss.gui.filetree.FileSaving.: Saves to local files from a text pane
FileSaving(JTextPane, byte[], JembossParams) - Constructor for class org.emboss.jemboss.gui.filetree.FileSaving
f - Variable in class org.emboss.jemboss.Jemboss: Jemboss frame
f - Variable in class org.emboss.jemboss.gui.filetree.FileSave: file to save
f - Variable in class org.emboss.jemboss.gui.form.BuildJembossForm
f - Variable in class org.emboss.jemboss.gui.form.SectionPanel: Jemboss frame
fExists - Variable in class org.emboss.jemboss.gui.filetree.FileSave: true if the file exists
fasta - Static variable in class org.emboss.jemboss.gui.sequenceChooser.SequenceFilter
fc - Variable in class org.emboss.jemboss.gui.sequenceChooser.FileChooser: file chooser
ff - Variable in class org.emboss.jemboss.gui.sequenceChooser.InputSequenceAttributes: input format types
ff - Variable in class org.emboss.jemboss.gui.sequenceChooser.OutputSequenceAttributes: output format types
field - Variable in class org.emboss.jemboss.parser.Dependent: field number in the ACD file
fieldOption - Variable in class org.emboss.jemboss.gui.form.BuildJembossForm
fieldOption - Variable in class org.emboss.jemboss.gui.form.SectionPanel: checkbox popup field for list and select
fileChoose - Variable in class org.emboss.jemboss.gui.form.SetInFileCard: sequence file choser
fileChooser - Variable in class org.emboss.jemboss.gui.form.ListFilePanel: container for sequences
fileExists() - Method in class org.emboss.jemboss.gui.filetree.FileSave
fileFormats - Variable in class org.emboss.jemboss.gui.sequenceChooser.InputSequenceAttributes: combobox for file formats
fileFormats - Variable in class org.emboss.jemboss.gui.sequenceChooser.OutputSequenceAttributes: combobox for file formats
fileMenuShowres - Variable in class org.emboss.jemboss.gui.SetUpMenuBar: show saved results menu item
fileName - Variable in class org.emboss.jemboss.gui.sequenceChooser.FileChooser: file name text field
filePrefix - Variable in class org.emboss.jemboss.editor.PrintAlignmentImage: prefix of file
fileRoots - Variable in class org.emboss.jemboss.soap.FileRoots: server directory roots
fileSave(String, String, String, Hashtable) - Method in class org.emboss.jemboss.gui.ResultsMenuBar: Save to a local file
fileSave(String, String, Object) - Method in class org.emboss.jemboss.gui.ResultsMenuBar: Save to a local file
fileSaving(Object) - Method in class org.emboss.jemboss.gui.filetree.FileSave
fileSelected - Variable in class org.emboss.jemboss.gui.filetree.FileSaving: file to save to
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: true if the file has been written
filelist - Variable in class org.emboss.jemboss.gui.form.BuildJembossForm
filelist - Variable in class org.emboss.jemboss.gui.form.SectionPanel: list file panel
filename - Variable in class org.emboss.jemboss.gui.filetree.FileEditorDisplay: file name
filename - Static variable in class org.emboss.jemboss.server.TestPrivateServer
fileok - Variable in class org.emboss.jemboss.parser.Ajax
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
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: Find the number in a string expression
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.FileNode: flavours file node and string
flist - Variable in class org.emboss.jemboss.soap.FileList: file list
font - Variable in class org.emboss.jemboss.editor.SequenceJPanel: font
font - Variable in class org.emboss.jemboss.editor.SequenceNameJButton: font
fontSize - Variable in class org.emboss.jemboss.JembossLogo
fontSize - Variable in class org.emboss.jemboss.editor.SequenceJPanel: font size
fontSize - Variable in class org.emboss.jemboss.editor.SequenceNameJButton: font size
fontSize - Variable in class org.emboss.jemboss.gui.form.ApplicationNamePanel: font size
forkBatch(String, byte[], String, String, String) - Method in class org.emboss.jemboss.parser.Ajax: fork emboss batch proceess
forkEmboss(String, byte[], String, String, String) - Method in class org.emboss.jemboss.parser.Ajax: fork emboss proceess
format - Variable in class org.emboss.jemboss.editor.PrintAlignmentImage: page format
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: frame containing the results
froots - Static variable in class org.emboss.jemboss.gui.filetree.RemoteDragTree: remote directory roots
froots - Variable in class org.emboss.jemboss.gui.filetree.RemoteFileNode: remote server file roots
fs - Variable in class org.emboss.jemboss.gui.filetree.DragTree: file separator
fs - Variable in class org.emboss.jemboss.gui.filetree.RemoteDragTree: file separator
fs - Variable in class org.emboss.jemboss.gui.filetree.RemoteFileNode: file separator for server files
fs - Variable in class org.emboss.jemboss.server.JembossAuthServer: file separator
fs - Variable in class org.emboss.jemboss.server.JembossServer: file separator
fullname - Variable in class org.emboss.jemboss.gui.filetree.RemoteFileNode: full name of node
fwdArrow - Variable in class org.emboss.jemboss.Jemboss: Image for displaying the local filemanager
fwdBt - Variable in class org.emboss.jemboss.gui.Browser: Forward button option
fwdMenu - Variable in class org.emboss.jemboss.gui.Browser: Forward menu option

G

GetACD - class org.emboss.jemboss.soap.GetACD.: Retrieve an ACD file using soap
GetACD(String, JembossParams) - Constructor for class org.emboss.jemboss.soap.GetACD
GetHelp - class org.emboss.jemboss.soap.GetHelp.: Get the help text for an application
GetHelp(String, JembossParams) - Constructor for class org.emboss.jemboss.soap.GetHelp
GetWossname - class org.emboss.jemboss.soap.GetWossname.: Run wossname of a Jemboss server
GetWossname(JembossParams) - Constructor for class org.emboss.jemboss.soap.GetWossname
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
GroutAlignJFrame - class org.emboss.jemboss.editor.GroutAlignJFrame.: Displays a grapical representation of a collection of sequences.
GroutAlignJFrame(Vector, Vector) - Constructor for class org.emboss.jemboss.editor.GroutAlignJFrame: This constructor is for Grout.
GroutAlignJFrame(Vector) - Constructor for class org.emboss.jemboss.editor.GroutAlignJFrame
GroutAlignJFrame(File) - Constructor for class org.emboss.jemboss.editor.GroutAlignJFrame
GroutAlignJFrame(String, String) - Constructor for class org.emboss.jemboss.editor.GroutAlignJFrame
GroutAlignJFrame() - Constructor for class org.emboss.jemboss.editor.GroutAlignJFrame
GroutAlignJFrame(boolean) - Constructor for class org.emboss.jemboss.editor.GroutAlignJFrame
GroutAlignJFrame.winExit - class org.emboss.jemboss.editor.GroutAlignJFrame.winExit.: Extends WindowAdapter to handle disposal of the occurance
GroutAlignJFrame.winExit() - Constructor for class org.emboss.jemboss.editor.GroutAlignJFrame.winExit
GroutAlignJFrameEvent - class org.emboss.jemboss.editor.GroutAlignJFrameEvent.
GroutAlignJFrameEvent(Object, String, Object, Object) - Constructor for class org.emboss.jemboss.editor.GroutAlignJFrameEvent: Creates a new instance of GroutAlignJFrameEvent with source set
GroutAlignJFrameListener - interface org.emboss.jemboss.editor.GroutAlignJFrameListener.: GroutAlignJFrameListener.java Created: 10th June 2003
GroutGraphicSequenceCollection - class org.emboss.jemboss.editor.GroutGraphicSequenceCollection.: This class can be used to get a grapical representation of a collection of sequences.
GroutGraphicSequenceCollection(Vector, Hashtable, JScrollPane, boolean, boolean, boolean, boolean, JTextField) - Constructor for class org.emboss.jemboss.editor.GroutGraphicSequenceCollection
GroutGraphicSequenceCollection(Vector, JScrollPane, boolean, boolean, boolean, boolean, JTextField) - Constructor for class org.emboss.jemboss.editor.GroutGraphicSequenceCollection
GroutGraphicSequenceCollection(Vector, Vector, Hashtable, JScrollPane, boolean, boolean, boolean, boolean, JTextField) - Constructor for class org.emboss.jemboss.editor.GroutGraphicSequenceCollection
GroutGraphicSequenceCollection(Vector, Vector, JScrollPane, boolean, boolean, boolean, boolean, JTextField) - Constructor for class org.emboss.jemboss.editor.GroutGraphicSequenceCollection
GroutGraphicSequenceCollectionEvent - class org.emboss.jemboss.editor.GroutGraphicSequenceCollectionEvent.
GroutGraphicSequenceCollectionEvent(Object, String, Object, Object) - Constructor for class org.emboss.jemboss.editor.GroutGraphicSequenceCollectionEvent: Creates a new instance of GroutGraphicSequenceCollectionEvent with source set
GroutGraphicSequenceCollectionListener - interface org.emboss.jemboss.editor.GroutGraphicSequenceCollectionListener.: GroutGraphicSequenceCollectionListener.java Created: Thu Mar 13 14:42:13 2003
GroutSequence - class org.emboss.jemboss.editor.GroutSequence.: Sequence object
GroutSequence(String, String, int, float) - Constructor for class org.emboss.jemboss.editor.GroutSequence
GroutSequence(String, String, int) - Constructor for class org.emboss.jemboss.editor.GroutSequence
GroutSequence(String, String) - Constructor for class org.emboss.jemboss.editor.GroutSequence
GroutSequence(String) - Constructor for class org.emboss.jemboss.editor.GroutSequence
GroutSequence(String, float) - Constructor for class org.emboss.jemboss.editor.GroutSequence
GroutSequenceJPanel - class org.emboss.jemboss.editor.GroutSequenceJPanel.: Sequence panel for drawing a sequence or the sequence numbers
GroutSequenceJPanel(int, Sequence, JComponent, boolean, boolean, boolean, Hashtable, int, int) - Constructor for class org.emboss.jemboss.editor.GroutSequenceJPanel: Constructor for indenting the sequence
GroutSequenceJPanel(int, Sequence, JComponent, boolean, boolean, boolean, Hashtable, int) - Constructor for class org.emboss.jemboss.editor.GroutSequenceJPanel: Constructor with default font size and indenting the sequence
GroutSequenceJPanel(int, int, int) - Constructor for class org.emboss.jemboss.editor.GroutSequenceJPanel: Constructor for sequence numbering and indenting the sequence
GroutSequenceJPanel(Sequence, JComponent, boolean, boolean, boolean, Hashtable, int, int) - Constructor for class org.emboss.jemboss.editor.GroutSequenceJPanel
GroutSequenceJPanel(Sequence, JComponent, boolean, boolean, boolean, Hashtable, int) - Constructor for class org.emboss.jemboss.editor.GroutSequenceJPanel: Constructor with default font size
GroutSequenceJPanel(int, int) - Constructor for class org.emboss.jemboss.editor.GroutSequenceJPanel: Constructor for sequence numbering
g - Variable in class org.emboss.jemboss.gui.form.MultiLineToolTipUI
gcg - Static variable in class org.emboss.jemboss.gui.sequenceChooser.SequenceFilter
get() - Method in class org.emboss.jemboss.gui.SwingWorker.ThreadVar
get() - Method in class org.emboss.jemboss.gui.SwingWorker: Return the value created by the construct method.
get(Object) - Method in class org.emboss.jemboss.programs.ResultList
get(Object) - Method in class org.emboss.jemboss.soap.JembossRun: Get a result from the result Hashtable
getAccCheckBox() - Method in class org.emboss.jemboss.gui.form.ReportFormat: Get the check box for accession number display
getAcceleratorString(JToolTip) - Method in class org.emboss.jemboss.gui.form.MultiLineToolTipUI
getAcd() - Method in class org.emboss.jemboss.soap.GetACD: Return the text of the ACD file
getAcdDirToParse() - Method in class org.emboss.jemboss.JembossParams: Acd file location
getAcdText(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.AlignFormat: Get the alignment format to add to the EMBOSS command line
getAlignFormat() - Method in class org.emboss.jemboss.gui.form.SectionPanel: Get the alignment format
getAlignFormats(boolean) - Method in class org.emboss.jemboss.gui.form.AlignFormat: Get the alignment formats as a string array
getAllowsChildren() - Method in class org.emboss.jemboss.gui.filetree.FileNode: Determine if this is a directory
getAllowsChildren() - Method in class org.emboss.jemboss.gui.filetree.RemoteFileNode
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.ListFilePanel
getArrayListFile() - Method in class org.emboss.jemboss.gui.form.SetInFileCard
getAttribute() - Method in class org.emboss.jemboss.parser.acd.ApplicationParam: Get the parameter/attribute type
getAutoscrollInsets() - Method in class org.emboss.jemboss.gui.filetree.DragTree: Gets the insets used for the autoscroll.
getAutoscrollInsets() - Method in class org.emboss.jemboss.gui.filetree.RemoteDragTree: Gets the insets used for the autoscroll.
getBegSeq() - Method in class org.emboss.jemboss.gui.sequenceChooser.InputSequenceAttributes: Get the -sbegin flag
getBrowserProxyHost() - Method in class org.emboss.jemboss.JembossParams: Get 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
getCase() - Method in class org.emboss.jemboss.editor.ConsensusOptions: Get the minimum positive matches for a site to be made upper case in the consensus.
getChildNode(FileNode, String) - Method in class org.emboss.jemboss.gui.filetree.DragTree: Gets the child node of a parent node
getChildNode(RemoteFileNode, String) - Method in class org.emboss.jemboss.gui.filetree.RemoteDragTree: Gets the child node of a parent node
getCodonUsage() - Static method in class org.emboss.jemboss.gui.BuildProgramMenu: Contains all codon usage tables
getCodonUsage() - Method in class org.emboss.jemboss.soap.ShowDB: Get the codon usage tables
getColor() - Method in class org.emboss.jemboss.editor.ColourMenu.ColorPane
getColor() - Method in class org.emboss.jemboss.editor.ColourMenu
getColor(String, int, String) - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection: Determine the colour of a residue at a given position.
getColor(String) - Method in class org.emboss.jemboss.editor.SequenceJPanel: Get a residue colour
getColor() - Method in class org.emboss.jemboss.gui.ColorMenu.ColorPane
getColor() - Method in class org.emboss.jemboss.gui.ColorMenu
getColour() - Method in class org.emboss.jemboss.editor.ColourPanel: Return current colour selection
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.AlignFormat: Get the combo-popup component for alignment formats
getComboPopup() - Method in class org.emboss.jemboss.gui.form.ReportFormat: Get the combo popup box containing the report formats
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: Get the consensus sequence
getConsensusSequence() - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection: Get the consensus sequence
getCurrentColourScheme() - Method in class org.emboss.jemboss.editor.ColourJFrame: Get the colour scheme as a hashtable
getCurrentDir() - Method in class org.emboss.jemboss.soap.FileRoots: Get the currently selected directory
getCurrentMatrixName() - Method in class org.emboss.jemboss.editor.Matrix: Get the current scoring matrix name
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
getCygwinRoot() - Method in class org.emboss.jemboss.JembossParams: Get the cygwin root
getDB() - Method in class org.emboss.jemboss.gui.startup.Database: Get the available databases
getDBText() - Method in class org.emboss.jemboss.soap.ShowDB: Get the output from showdb
getDatabaseList() - Static method in class org.emboss.jemboss.gui.BuildProgramMenu: List of available EMBOSS databases
getDebug() - Method in class org.emboss.jemboss.JembossParams: Whether to show debugging information
getDefaultFormat() - Method in class org.emboss.jemboss.gui.form.AlignFormat
getDefaultFormat() - Method in class org.emboss.jemboss.gui.form.ReportFormat: Get the default report format
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: Get the expression
getDependentField() - Method in class org.emboss.jemboss.parser.Dependent: Get the field
getDependentParam() - Method in class org.emboss.jemboss.parser.Dependent: Get the parameter number
getDependentType() - Method in class org.emboss.jemboss.parser.Dependent: Get type of parameter
getDependents() - Method in class org.emboss.jemboss.parser.ParseAcd: Gets the dependents associated with the ACD.
getDesCheckBox() - Method in class org.emboss.jemboss.gui.form.ReportFormat: Get the check box for description display
getDescription() - Method in class org.emboss.jemboss.gui.sequenceChooser.SequenceFilter
getDescription() - Method in class org.emboss.jemboss.programs.JembossProcess: Get the project description
getElement(String) - Method in class org.emboss.jemboss.JembossJarUtil: Return an element of the hashtable
getEmbossBin() - Method in class org.emboss.jemboss.JembossParams
getEmbossData() - Method in class org.emboss.jemboss.JembossParams
getEmbossEnvironment() - Method in class org.emboss.jemboss.JembossParams: Get the environment for emboss
getEmbossEnvironmentArray(String[]) - Method in class org.emboss.jemboss.JembossParams: Get the emboss environment as a String array
getEmbossPath() - Method in class org.emboss.jemboss.JembossParams: Get the path for emboss
getEndSeq() - Method in class org.emboss.jemboss.gui.sequenceChooser.InputSequenceAttributes: Get the -send flag
getErrStd() - Method in class org.emboss.jemboss.parser.Ajax: Get the stderr
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: Get the extension of a file
getFieldNum() - Method in class org.emboss.jemboss.gui.form.SectionPanel: Get the current field
getFile() - Method in class org.emboss.jemboss.gui.filetree.FileNode: Get the File this node represents
getFile() - Method in class org.emboss.jemboss.gui.filetree.RemoteFileNode
getFile(String, byte[], String, String) - Method in class org.emboss.jemboss.parser.Ajax: get the contents of a file
getFileChosen() - Method in class org.emboss.jemboss.gui.form.SetInFileCard
getFileChosen() - Method in class org.emboss.jemboss.gui.sequenceChooser.FileChooser: Get the selected file
getFileName(int) - Method in class org.emboss.jemboss.gui.DragJTable
getFileName() - Method in class org.emboss.jemboss.gui.filetree.FileSaving
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.
getFilename() - Method in class org.emboss.jemboss.gui.filetree.RemoteDragTree: Get the selected node file name
getFileok() - Method in class org.emboss.jemboss.parser.Ajax
getFont() - Method in class org.emboss.jemboss.editor.SequenceNameJButton: Get the font
getFontSize() - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection: Get the font size used to display the sequences in the editor return font size
getFontSize() - Method in class org.emboss.jemboss.editor.SequenceJPanel: Get the font size
getFormat() - Method in class org.emboss.jemboss.editor.PrintAlignmentImage: Get the page format
getFormatChoosen() - Method in class org.emboss.jemboss.gui.sequenceChooser.InputSequenceAttributes: Get the file format selected
getFormatChoosen() - Method in class org.emboss.jemboss.gui.sequenceChooser.OutputSequenceAttributes: Get the format selected
getFormatDialog() - Method in class org.emboss.jemboss.editor.PrintAlignmentImage: Get a default page format
getFullName() - Method in class org.emboss.jemboss.gui.filetree.RemoteFileNode
getGraphicSequence() - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection: Get the vector containing the SequenceJPanel objects
getGuiHandleNumber(int) - Method in class org.emboss.jemboss.parser.ParseAcd: Gets the handle for a gui component on the Jemboss form.
getGuiHandleNumber() - Method in class org.emboss.jemboss.parser.acd.ApplicationFields: Get the gui handle
getHasBatchMode() - Method in class org.emboss.jemboss.JembossParams: Whether this service supports batch mode
getHasInteractiveMode() - Method in class org.emboss.jemboss.JembossParams: Whether this service supports interactive mode
getHash() - Method in class org.emboss.jemboss.JembossJarUtil: Return the hashtable
getHash() - Method in class org.emboss.jemboss.soap.PrivateRequest: Get the results returned by the server call
getHash() - Method in class org.emboss.jemboss.soap.PublicRequest: The hash returned by the Jemboss call.
getHashtable(Vector) - Method in class org.emboss.jemboss.server.JembossServer: Convert contents from a Vector to a Hashtable
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: Get the help text
getHomeDirectory() - Method in class org.emboss.jemboss.gui.AdvancedOptions: Get the user home/working directory
getID() - Method in class org.emboss.jemboss.editor.Sequence: Get the sequence id
getIDBackgroundColour() - Method in class org.emboss.jemboss.editor.PrettyPlotJFrame: Get the users defined background colour to draw identical residues
getIDColour() - Method in class org.emboss.jemboss.editor.PrettyPlotJFrame: Get the users defined colour to draw identical residues
getIDimension() - Method in class org.emboss.jemboss.editor.Matrix: Get number of rows in the scoring table
getIdentity() - Method in class org.emboss.jemboss.editor.ConsensusOptions: Get the minimum identical matches for a site to be included in the consensus.
getImageableSize(int) - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection: Get the imageable size.
getIndexOf(Object) - Method in class org.emboss.jemboss.gui.MemoryComboBox
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: Get the EMBOSS command line for the values selected for the input sequence attributes
getJDimension() - Method in class org.emboss.jemboss.editor.Matrix: Get number of columns in the scoring table
getJFileChooser() - Method in class org.emboss.jemboss.gui.sequenceChooser.FileChooser: Get the JFileChooser
getJScrollPane() - Method in class org.emboss.jemboss.gui.sequenceChooser.InputSequenceAttributes: Get the scroll panel
getJScrollPane() - Method in class org.emboss.jemboss.gui.sequenceChooser.OutputSequenceAttributes: Get the scoll panel
getJTextComponentAt(JTabbedPane, int) - Method in class org.emboss.jemboss.gui.ResultsMenuBar: Get text component from a tabbed pane
getJob() - Method in class org.emboss.jemboss.programs.JembossProcess: Get the project id
getKeyNames() - Method in class org.emboss.jemboss.editor.Matrix: Scoring matrix names available
getKeyNamesString() - Method in class org.emboss.jemboss.editor.Matrix: Scoring matrix names available
getKeys() - Method in class org.emboss.jemboss.editor.Matrix: Scoring matrix filenames in jar file
getLength() - Method in class org.emboss.jemboss.editor.Sequence: Get the sequence length
getLength() - Method in class org.emboss.jemboss.soap.CallAjax: Get the sequence length
getLineSeparator() - Static method in class org.emboss.jemboss.gui.form.PlafMacros: Get the line separator string
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.ListFilePanel
getListFile() - Method in class org.emboss.jemboss.gui.form.SetInFileCard
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: Get local file manager
getLocalDragTree() - Static method in class org.emboss.jemboss.gui.filetree.LocalAndRemoteFileTreeFrame: Returns the local file tree
getLocalFile(File) - Method in class org.emboss.jemboss.gui.filetree.RemoteDragTree: Get the contents of a local file as a byte array
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
getMatchBackgroundColour() - Method in class org.emboss.jemboss.editor.PrettyPlotJFrame: Get the users defined background colour to draw positive match residues
getMatchColour() - Method in class org.emboss.jemboss.editor.PrettyPlotJFrame: Get the users defined colour to draw positive match residues
getMatchThreshold() - Method in class org.emboss.jemboss.editor.PrettyPlotJFrame: Get the match threshold value
getMatrices() - Static method in class org.emboss.jemboss.gui.BuildProgramMenu: Contains all scoring matrix files
getMatrices() - Method in class org.emboss.jemboss.soap.ShowDB: Get the available matrices
getMatrix() - Method in class org.emboss.jemboss.editor.Matrix: Get the scoring matrix as a 2 dimensional integer array
getMatrixIndex(String) - Method in class org.emboss.jemboss.editor.Matrix: Get the residue position in the scoring table
getMatrixTable() - Method in class org.emboss.jemboss.editor.Matrix: Get the scoring matrix as text
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: Get the longest sequence length
getMaxSequenceLength(Vector) - Method in class org.emboss.jemboss.editor.Consensus: Check all sequences lengths and return length of the longest sequence
getMaxSequenceLength(Vector) - Method in class org.emboss.jemboss.editor.PlotConsensus: Check all sequences lengths and return length of the longest sequence
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
getMenuItems() - Method in class org.emboss.jemboss.gui.startup.ProgList: Returns the program menu items
getMinMaxDefault(String, String, String, int) - Method in class org.emboss.jemboss.gui.form.SectionPanel: Get the min, max and default values for a field in the ACD as a string representation in the form (min: max: default:)
getMinParam(int) - Method in class org.emboss.jemboss.parser.ParseAcd: Locates the min parameter in a field and returns it as a String.
getMinimumIdentity(int) - Method in class org.emboss.jemboss.editor.PrettyPlotJFrame: Get the users defined identity limit
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
getName(int) - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection
getName() - Method in class org.emboss.jemboss.editor.Sequence: Get the sequence name
getName() - Method in class org.emboss.jemboss.editor.SequenceJPanel: Get the sequence name associated with this display
getNameHeight() - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection: Get the sequence name panel height
getNamePrintGraphic(Graphics) - Method in class org.emboss.jemboss.editor.SequenceJPanel: Render the sequence name graphic
getNameViewSize() - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection: Get the sequence name view size
getNameWidth() - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection: Get the sequence name panel width
getNode(String) - Method in class org.emboss.jemboss.gui.filetree.DragTree: Gets the node from the existing explored nodes and their children.
getNode(String) - Method in class org.emboss.jemboss.gui.filetree.RemoteDragTree: Gets the node from the existing explored nodes and their children.
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.
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.
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: Get the number of parameters in this field
getNumberOfSequences() - Method in class org.emboss.jemboss.editor.SequenceReader: Returns the number of sequences.
getNumberPages(PageFormat) - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection: Get the number of pages to print the alignment in a given format
getNumberPages(PageFormat, int) - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection: Get the number of pages to print the alignment in a given format and with a given number of residues per line
getNumberSequences() - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection: Get the number of sequences
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.
getOuputSeqAttr() - Method in class org.emboss.jemboss.gui.sequenceChooser.OutputSequenceAttributes: Get the EMBOSS command line for the output sequence attributes
getOutStd() - Method in class org.emboss.jemboss.parser.Ajax: Get the stdout
getOutputSequenceFile(int) - Method in class org.emboss.jemboss.parser.ParseAcd: Gets the name of the output sequence field (seqout).
getPNGContent() - Method in class org.emboss.jemboss.gui.filetree.FileEditorDisplay: Returns the content of a png file or null.
getPanelHeight() - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection: Get the sequence panel height
getPanelHeight() - Method in class org.emboss.jemboss.editor.SequenceNameJButton: Get the button height
getPanelSize() - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection: Get the sequence view size
getPanelWidth() - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection: Get the sequence panel width
getPanelWidth() - Method in class org.emboss.jemboss.editor.SequenceNameJButton: Get the button width
getParamAttribute(int) - Method in class org.emboss.jemboss.parser.acd.ApplicationFields: Get a parameter attribute, given the parameter number in the field
getParamValueDbl(int, int) - Method in class org.emboss.jemboss.parser.ParseAcd: Gets the double value of a parameter.
getParamValueDbl(int) - Method in class org.emboss.jemboss.parser.acd.ApplicationFields: Get a parameter value, given the parameter number in the field
getParamValueStr(int, int) - Method in class org.emboss.jemboss.parser.ParseAcd: Gets the String value of a parameter.
getParamValueStr(int) - Method in class org.emboss.jemboss.parser.acd.ApplicationFields: Get a parameter value, given the parameter number in the field
getParameterAttribute(int, int) - Method in class org.emboss.jemboss.parser.ParseAcd: Get a specified parameter attribute.
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: Get the location of plplot
getPlurality() - Method in class org.emboss.jemboss.editor.ConsensusOptions: Get the minimum positive match score for a site to be included in the consensus.
getPreferredScrollableViewportSize() - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection: Override for scrollable interface
getPreferredScrollableViewportSize() - Method in class org.emboss.jemboss.gui.ImageIconJPanel
getPreferredScrollableViewportSize() - Method in class org.emboss.jemboss.gui.ScrollPanel
getPreferredSize() - Method in class org.emboss.jemboss.editor.ColourMenu.ColorPane
getPreferredSize() - Method in class org.emboss.jemboss.editor.SequenceJPanel: Get the preferred size dimension
getPreferredSize() - Method in class org.emboss.jemboss.editor.SequenceNameJButton: Get the preferred size of this component
getPreferredSize() - Method in class org.emboss.jemboss.gui.ColorMenu.ColorPane
getPreferredSize() - Method in class org.emboss.jemboss.gui.ImageIconJPanel: Override getPreferredSize to return the dimensions of the ImageIcon
getPreferredSize(JComponent) - Method in class org.emboss.jemboss.gui.form.MultiLineToolTipUI
getPreferredSize() - Method in class org.emboss.jemboss.gui.sequenceChooser.FileChooser: Get the preferred size of the text field
getPrettyBackground(Color) - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection: Determine the colour of a residue background
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
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.RunEmbossApplication
getProcess() - Method in class org.emboss.jemboss.programs.RunEmbossApplication2
getProcessStderr() - Method in class org.emboss.jemboss.programs.RunEmbossApplication2
getProcessStdout() - Method in class org.emboss.jemboss.programs.RunEmbossApplication
getProcessStdout() - Method in class org.emboss.jemboss.programs.RunEmbossApplication2
getProgDescription() - Method in class org.emboss.jemboss.gui.startup.ProgList: Returns the array of the program descriptions
getProgramGroup(String) - Method in class org.emboss.jemboss.gui.startup.ProgList: Returns the groups for the given application
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: Get the project name
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: Get regular expression for values in the scoring table
getReportCheckBox() - Method in class org.emboss.jemboss.gui.form.ReportFormat: Get the container box for the report format display on the Jemboss application form
getReportFormat() - Method in class org.emboss.jemboss.gui.form.ReportFormat: Return the EMBOSS command line string depending on what has been selected
getReportFormat() - Method in class org.emboss.jemboss.gui.form.SectionPanel: Get the report format
getReportFormats() - Static method in class org.emboss.jemboss.gui.form.ReportFormat: Get the available report formats
getResidue(Vector, int, int) - Method in class org.emboss.jemboss.editor.Consensus: Get the residue at a given position from a given sequence
getResidue(Vector, int, int) - Method in class org.emboss.jemboss.editor.PlotConsensus: Returns the residue of the sequence i at position k
getResidue(int) - Method in class org.emboss.jemboss.editor.Sequence: Get a residue in the sequence at a given position
getResidueAt(int) - Method in class org.emboss.jemboss.editor.Sequence: Get the residue at a position
getResidueMatrixPosition() - Method in class org.emboss.jemboss.editor.Matrix: Get the hashtable of the residue positions in the scoring table
getResidueWidth() - Method in class org.emboss.jemboss.editor.SequenceJPanel: Get the width of a residue
getResiduesPerLine(PageFormat) - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection: Get the number residues per line
getResiduesPerPage(PageFormat, int) - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection: Get the number residues per page
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.parser.AcdVarResolve: Get the resolved expression
getResult() - Method in class org.emboss.jemboss.parser.AcdVariableResolve: Get the resolved expression
getResult(String) - Method in class org.emboss.jemboss.soap.PendingResults: Get the processes result
getRoot(String, String, byte[]) - Method in class org.emboss.jemboss.server.JembossFileAuthServer: Given a file manager root alias e.g.
getRoot(String, String) - Method in class org.emboss.jemboss.server.JembossFileServer: Given the alias a user root alias e.g.
getRootDir() - Method in class org.emboss.jemboss.gui.filetree.RemoteFileNode
getRootSelect() - Method in class org.emboss.jemboss.gui.filetree.RemoteFileTreePanel: Get the root selection JComboBox
getRootVector() - Method in class org.emboss.jemboss.soap.FileRoots: Get the list of file manager roots
getRoots() - Method in class org.emboss.jemboss.soap.FileRoots: Get the list of file manager roots
getRowCount() - Method in class org.emboss.jemboss.gui.SequenceList: Return the number of rows in the table
getRowCount() - Method in class org.emboss.jemboss.gui.SequenceListTableModel: Return the number of rows in the table
getSafeFileName() - Method in class org.emboss.jemboss.soap.MakeFileSafe: Get the safe/sanitised file name
getScrollableBlockIncrement(Rectangle, int, int) - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection: Override for scrollable interface
getScrollableBlockIncrement(Rectangle, int, int) - Method in class org.emboss.jemboss.editor.GroutGraphicSequenceCollection: Override for scrollable interface
getScrollableBlockIncrement(Rectangle, int, int) - Method in class org.emboss.jemboss.gui.ImageIconJPanel
getScrollableBlockIncrement(Rectangle, int, int) - Method in class org.emboss.jemboss.gui.ScrollPanel
getScrollableTracksViewportHeight() - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection: Override for scrollable interface
getScrollableTracksViewportHeight() - Method in class org.emboss.jemboss.gui.ImageIconJPanel
getScrollableTracksViewportHeight() - Method in class org.emboss.jemboss.gui.ScrollPanel
getScrollableTracksViewportWidth() - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection: Override for scrollable interface
getScrollableTracksViewportWidth() - Method in class org.emboss.jemboss.gui.ImageIconJPanel
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: Override for scrollable interface
getScrollableUnitIncrement(Rectangle, int, int) - Method in class org.emboss.jemboss.editor.GroutGraphicSequenceCollection: Override for scrollable interface
getScrollableUnitIncrement(Rectangle, int, int) - Method in class org.emboss.jemboss.gui.ImageIconJPanel
getScrollableUnitIncrement(Rectangle, int, int) - Method in class org.emboss.jemboss.gui.ScrollPanel
getSectionBox() - Method in class org.emboss.jemboss.gui.form.SectionPanel: get the box or this section
getSectionPanel() - Method in class org.emboss.jemboss.gui.form.SectionPanel: get the panel for this section
getSelect(int) - Method in class org.emboss.jemboss.parser.ParseAcd: Used for a selection type to put the list items in a String array.
getSelectedFiles() - Method in class org.emboss.jemboss.gui.filetree.DragTree: Get selected files
getSelectedJTextPane(JTabbedPane) - Method in class org.emboss.jemboss.gui.ResultsMenuBar: Get selected text pane from tabbed pane
getSelectedNode() - Method in class org.emboss.jemboss.gui.filetree.DragTree: Get FileNode of selected node
getSelectedNode() - Method in class org.emboss.jemboss.gui.filetree.RemoteDragTree: Get RemoteFileNode of selected node
getSelectedNodes() - Method in class org.emboss.jemboss.gui.filetree.DragTree: Get FileNodes of selected nodes
getSelectedNodes() - Method in class org.emboss.jemboss.gui.filetree.RemoteDragTree: Get RemoteFileNodes of selected nodes
getSequence() - Method in class org.emboss.jemboss.editor.Paste
getSequence() - Method in class org.emboss.jemboss.editor.Sequence: Get the 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.ListFilePanel: Get a sequence form the list using its number in the list
getSequence(int) - Method in class org.emboss.jemboss.gui.form.SetInFileCard: Return a sequence from a list of sequences
getSequenceCollection() - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection: Get the vector of Sequences
getSequenceData(int) - Method in class org.emboss.jemboss.gui.SequenceList: The SequenceData for a given row number.
getSequenceData(int) - Method in class org.emboss.jemboss.gui.SequenceListTableModel: The SequenceData for a given row number.
getSequenceFile() - Method in class org.emboss.jemboss.editor.SequenceReader: Get the sequence file
getSequenceHeight() - Method in class org.emboss.jemboss.editor.SequenceJPanel: Get the sequence panel height
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: Render the sequence graphic
getSequenceResidueWidth() - Method in class org.emboss.jemboss.editor.SequenceJPanel: Get the width of a residue
getSequenceVector() - Method in class org.emboss.jemboss.editor.SequenceReader: Returns the Sequence Vector store
getSequenceWeight(Vector, int) - Method in class org.emboss.jemboss.editor.Consensus: Get the sequence weight
getSequenceWeight(Vector, int) - Method in class org.emboss.jemboss.editor.PlotConsensus: Returns the weight of sequence i
getSequenceWidth() - Method in class org.emboss.jemboss.editor.SequenceJPanel: Get the sequence panel width
getServerName() - Method in class org.emboss.jemboss.gui.filetree.RemoteFileNode: Get the server name
getServicePasswd() - Method in class org.emboss.jemboss.JembossParams: Return the password needed for the remote service
getServicePasswdByte() - Method in class org.emboss.jemboss.JembossParams: Return the password needed for the remote service
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
getSplashFrame() - Method in class org.emboss.jemboss.soap.AuthPopup
getStatus() - Method in class org.emboss.jemboss.programs.ResultList: The status of the request
getStatus() - Method in class org.emboss.jemboss.programs.RunEmbossApplication
getStatus() - Method in class org.emboss.jemboss.programs.RunEmbossApplication2
getStatus() - Method in class org.emboss.jemboss.soap.CallAjax: Get the status
getStatus() - Method in class org.emboss.jemboss.soap.GetHelp: The status of the request
getStatus() - Method in class org.emboss.jemboss.soap.JembossRun: The status of the request
getStatus() - Method in class org.emboss.jemboss.soap.PendingResults
getStatus() - Method in class org.emboss.jemboss.soap.ShowDB: Get the status of the request
getStatusMsg() - Method in class org.emboss.jemboss.programs.ResultList: A status message.
getStatusMsg() - Method in class org.emboss.jemboss.soap.CallAjax: Get the message
getStatusMsg() - Method in class org.emboss.jemboss.soap.GetHelp: A status message .
getStatusMsg() - Method in class org.emboss.jemboss.soap.JembossRun: A status message or description of a error
getStatusMsg() - Method in class org.emboss.jemboss.soap.ShowDB: Get the status message
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: Get the text field
getToolBar() - Method in class org.emboss.jemboss.gui.ResultsMenuBar: Get the tool bar
getToolTip() - Method in class org.emboss.jemboss.gui.form.AlignFormat
getToolTip() - Static method in class org.emboss.jemboss.gui.form.ReportFormat
getToolTipLocation(MouseEvent) - Method in class org.emboss.jemboss.editor.SequenceJPanel: Get the tool tip location
getToolTipText(MouseEvent) - Method in class org.emboss.jemboss.editor.SequenceJPanel: Determine the tool tip to display
getTotalWeight(Vector) - Static method in class org.emboss.jemboss.editor.AlignJFrame
getTransferData(DataFlavor) - Method in class org.emboss.jemboss.gui.SequenceData
getTransferData(DataFlavor) - Method in class org.emboss.jemboss.gui.filetree.FileNode
getTransferData(DataFlavor) - Method in class org.emboss.jemboss.gui.filetree.RemoteFileNode
getTransferDataFlavors() - Method in class org.emboss.jemboss.gui.SequenceData
getTransferDataFlavors() - Method in class org.emboss.jemboss.gui.filetree.FileNode
getTransferDataFlavors() - Method in class org.emboss.jemboss.gui.filetree.RemoteFileNode
getURLAt(int) - Method in class org.emboss.jemboss.gui.MemoryComboBox
getUsaDesCheckBox() - Method in class org.emboss.jemboss.gui.form.ReportFormat: Get the check box for USA display
getUseAuth() - Method in class org.emboss.jemboss.JembossParams: Whether the main service requires authentication
getUseHTTPSProxy() - Method in class org.emboss.jemboss.JembossParams: If using an https proxy server
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: Get the user home directory
getVal(String) - Method in class org.emboss.jemboss.soap.PrivateRequest: Gets an element out of the embreo result hash
getVal(String) - Method in class org.emboss.jemboss.soap.PublicRequest: Gets an element out of the Jemboss 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.TextFieldFloat
getValue() - Method in class org.emboss.jemboss.gui.form.TextFieldInt
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: Get the parameter value
getValueStr() - Method in class org.emboss.jemboss.parser.acd.ApplicationParam: Get the parameter value
getVector(Hashtable) - Method in class org.emboss.jemboss.soap.PendingResults: Change a hashtable to a vector
getVector(Hashtable) - Method in class org.emboss.jemboss.soap.PrivateRequest: Change the contents of a hashtable to a vector
getViewPosition() - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection: Get the position of the sequence JViewPort
getViewRect() - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection: Get the Rectangle being displayed by the sequence JViewPort
getViewSize() - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection: Get the sequence view size
getWeight() - Method in class org.emboss.jemboss.editor.Sequence: Get the sequence weight
getWeight() - Method in class org.emboss.jemboss.soap.CallAjax: Get the sequence weight
getWossname() - Method in class org.emboss.jemboss.server.JembossAuthServer: Returns the output of the EMBOSS utility wossname
getWossname() - Method in class org.emboss.jemboss.server.JembossServer: Returns the output of the EMBOSS utility wossname
getWossnameText() - Method in class org.emboss.jemboss.soap.GetWossname: Get wossname output
get_file(String, String, String, byte[]) - Method in class org.emboss.jemboss.server.JembossFileAuthServer: Get the contents of a file
get_file(String, String, String) - Method in class org.emboss.jemboss.server.JembossFileServer: Get the contents of a file
getembURL() - Method in class org.emboss.jemboss.JembossParams
graphicName - Variable in class org.emboss.jemboss.editor.GraphicSequenceCollection: Vector containing graphical names of sequences
graphicSequence - Variable in class org.emboss.jemboss.editor.AlignJFrame
graphicSequence - Variable in class org.emboss.jemboss.editor.GraphicSequenceCollection: Vector containing graphical sequences
groupList - Variable in class org.emboss.jemboss.parser.ParseAcd: String of the groups application belongs to
grout - Variable in class org.emboss.jemboss.gui.ShowResultSet: grout panel
groutAlignJFrameChanged(GroutAlignJFrameEvent) - Method in interface org.emboss.jemboss.editor.GroutAlignJFrameListener
groutGraphicSequenceCollectionChanged(GroutGraphicSequenceCollectionEvent) - Method in class org.emboss.jemboss.editor.GroutAlignJFrame: Responds to the groutGraphicSequenceCollectionChanged event
groutGraphicSequenceCollectionChanged(GroutGraphicSequenceCollectionEvent) - Method in interface org.emboss.jemboss.editor.GroutGraphicSequenceCollectionListener
groutGraphicSequenceCollectionChanged(GroutGraphicSequenceCollectionEvent) - Method in class org.emboss.jemboss.editor.GroutSequenceJPanel
gsc - Variable in class org.emboss.jemboss.editor.AlignApplet
gsc - Static variable in class org.emboss.jemboss.editor.AlignJFrame
gsc - Variable in class org.emboss.jemboss.editor.ConsensusOptions: graphic sequence collection
gsc - Variable in class org.emboss.jemboss.editor.PatternJFrame: graphic sequence panel
gsc - Variable in class org.emboss.jemboss.editor.PrettyPlotJFrame: graphic sequence panel
gsc - Variable in class org.emboss.jemboss.editor.PrintAlignmentImage: alignment sequence panel
guiHandleNumber - Variable in class org.emboss.jemboss.parser.acd.ApplicationFields: the gui handle

H

h - Variable in class org.emboss.jemboss.gui.form.SetInFileCard: gui handle number
hasBatchMode - Variable in class org.emboss.jemboss.JembossParams: batch mode support
hasBatchModeName - Variable in class org.emboss.jemboss.JembossParams: property name for batch mode support
hasInteractiveMode - Variable in class org.emboss.jemboss.JembossParams: interactive mode support
hasInteractiveModeName - Variable in class org.emboss.jemboss.JembossParams: property name for interactive mode support
hash() - Method in class org.emboss.jemboss.programs.ResultList
hash() - Method in class org.emboss.jemboss.soap.JembossRun: Get a Hashtable of filenames and their contents generated by running the application
helpText - Variable in class org.emboss.jemboss.soap.GetACD: acd text
helpText - Variable in class org.emboss.jemboss.soap.GetHelp
helptext - Variable in class org.emboss.jemboss.gui.form.BuildJembossForm
helpurl() - Method in class org.emboss.jemboss.server.JembossServer
hgt - Variable in class org.emboss.jemboss.editor.GraphicSequenceCollection
highlightPattern - Variable in class org.emboss.jemboss.editor.SequenceJPanel: high light search pattern
home - Variable in class org.emboss.jemboss.parser.Ajax: user home dir
homeDirectory - Variable in class org.emboss.jemboss.server.JembossServer: user home directory
htmlPane - Variable in class org.emboss.jemboss.gui.Browser: HTML pane
hydrophobicColor - Static variable in class org.emboss.jemboss.editor.SequenceProperties: Hydrophobic (Red=Hydrophobic)
hyperlinkUpdate(HyperlinkEvent) - Method in class org.emboss.jemboss.gui.Browser: Method to handle hyper link events.

I

IDTableJFrame - class org.emboss.jemboss.editor.IDTableJFrame.: Use to display the identical matches table for each pair of sequences
IDTableJFrame(Vector) - Constructor for class org.emboss.jemboss.editor.IDTableJFrame
ImageIconJPanel - class org.emboss.jemboss.gui.ImageIconJPanel.: Use to display ImageIcons on a JPanel
ImageIconJPanel(ImageIcon) - Constructor for class org.emboss.jemboss.gui.ImageIconJPanel
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
i - Variable in class org.emboss.jemboss.editor.Matrix
id - Variable in class org.emboss.jemboss.editor.Sequence: sequence id
idColour - Variable in class org.emboss.jemboss.editor.PrettyPlotJFrame: colour panel for identical matches
idColourBackground - Variable in class org.emboss.jemboss.editor.PrettyPlotJFrame: colour panel for identical matches background
idInt - Variable in class org.emboss.jemboss.editor.ConsensusOptions: identity
idSort() - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection: Sorts the sequences and displays them by their id's
idTable - Variable in class org.emboss.jemboss.editor.IDTableJFrame
idimension - Variable in class org.emboss.jemboss.editor.Matrix
ii - Variable in class org.emboss.jemboss.gui.ImageIconJPanel: image icon
inSeq - Variable in class org.emboss.jemboss.gui.form.BuildJembossForm
inSeq - Variable in class org.emboss.jemboss.gui.form.SectionPanel: input sequence field
inSeqAttr - Variable in class org.emboss.jemboss.gui.form.BuildJembossForm
inSeqAttr - Variable in class org.emboss.jemboss.gui.form.SectionPanel: input sequence attributes
inSeqAttr - Variable in class org.emboss.jemboss.gui.form.SetInFileCard: input sequence attributes
indent - Variable in class org.emboss.jemboss.editor.GroutSequence
indent - Variable in class org.emboss.jemboss.editor.GroutSequenceJPanel
init() - Method in class org.emboss.jemboss.editor.AlignApplet
init() - Method in class org.emboss.jemboss.editor.GroutSequenceJPanel: Add the mouse listener's
init() - Method in class org.emboss.jemboss.editor.SequenceJPanel: Add the mouse listener's
initStylesForTextPane() - Method in class org.emboss.jemboss.gui.filetree.FileEditorDisplay: Initialise styles for a JTextPane.
initialURL - Variable in class org.emboss.jemboss.gui.Browser: initial URL
initialize() - Static method in class org.emboss.jemboss.gui.form.MultiLineToolTipUI
inpSection - Static 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: Inser sequence data into the sequence table
insertResidue(String, int) - Method in class org.emboss.jemboss.editor.Sequence: Insert a residue into the 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.TextFieldFloat.DecimalNumberDocument
insertString(int, String, AttributeSet) - Method in class org.emboss.jemboss.gui.form.TextFieldInt.WholeNumberDocument
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.PlotConsensus: residue width
interval - Variable in class org.emboss.jemboss.editor.SequenceJPanel: sequence numbering interval
interval - Variable in class org.emboss.jemboss.gui.SplashThread
iprogress - Variable in class org.emboss.jemboss.soap.AuthPopup: progress monitor
iprogressmax - Variable in class org.emboss.jemboss.soap.AuthPopup: max value for the progress monitor
isAdd - Variable in class org.emboss.jemboss.gui.form.SectionPanel: true if the additional section
isAdditionalSection() - Method in class org.emboss.jemboss.gui.form.SectionPanel
isAdv - Variable in class org.emboss.jemboss.gui.form.SectionPanel: true if the advanced section
isAdvancedSection() - Method in class org.emboss.jemboss.gui.form.SectionPanel
isAlignFormat() - Method in class org.emboss.jemboss.gui.form.SectionPanel: Determine if alignment formats are used in the EMBOSS program
isAutoUpdate() - Method in class org.emboss.jemboss.soap.PendingResults: Automatically updating status manager with BatchUpdateTimer thread
isBackPage() - Method in class org.emboss.jemboss.gui.MemoryComboBox: Determine if a return page is stored
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: Determine if there is a default -sbeg value
isBrowserProxy() - Method in class org.emboss.jemboss.JembossParams: Determine if the a proxy server is being used for web browsing
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: Determine if a job has completed
isCut - Variable in class org.emboss.jemboss.gui.form.SetInFileCard: selecting cut and paste sequence input
isCutNPase() - Method in class org.emboss.jemboss.gui.form.SetInFileCard
isCygwin() - Static method in class org.emboss.jemboss.JembossParams
isDataFlavorSupported(DataFlavor) - Method in class org.emboss.jemboss.gui.SequenceData
isDataFlavorSupported(DataFlavor) - Method in class org.emboss.jemboss.gui.filetree.FileNode
isDataFlavorSupported(DataFlavor) - Method in class org.emboss.jemboss.gui.filetree.RemoteFileNode
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: true if node is a directory
isDirectory() - Method in class org.emboss.jemboss.gui.filetree.FileNode: Determine if this is a directory
isDirectory() - Method in class org.emboss.jemboss.gui.filetree.RemoteFileNode
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: Determine if there is a default -send value
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.FileNode: Determine if this node has been explored
isExplored() - Method in class org.emboss.jemboss.gui.filetree.RemoteFileNode
isExtensionDefault() - Method in class org.emboss.jemboss.gui.sequenceChooser.OutputSequenceAttributes: Determine if an extension has been selected
isFNameDefault() - Method in class org.emboss.jemboss.gui.sequenceChooser.OutputSequenceAttributes: Determine if a feature name is set
isFile - Variable in class org.emboss.jemboss.gui.form.SetInFileCard: selecting sequence file input (default)
isFileName() - Method in class org.emboss.jemboss.gui.form.SetInFileCard
isFileSelection() - Method in class org.emboss.jemboss.gui.filetree.DragTree: Return true if selected node is a file
isFileSelection() - Method in class org.emboss.jemboss.gui.filetree.RemoteDragTree: Determine if selected node is a file
isForwardPage() - Method in class org.emboss.jemboss.gui.MemoryComboBox: Determine if a forward page is stored
isInp - Variable in class org.emboss.jemboss.gui.form.SectionPanel: true if the input section
isInputSection() - Method in class org.emboss.jemboss.gui.form.SectionPanel
isItem(Object) - Method in class org.emboss.jemboss.gui.MemoryComboBox: Determine if item is in the JComboBox
isJembossServer() - Static method in class org.emboss.jemboss.JembossParams
isLeaf() - Method in class org.emboss.jemboss.gui.filetree.FileNode: Determine if this is a file
isLeaf() - Method in class org.emboss.jemboss.gui.filetree.RemoteFileNode
isList - Variable in class org.emboss.jemboss.gui.form.SetInFileCard: selecting list file input
isListFile(int) - Method in class org.emboss.jemboss.gui.DragJTable: Determine if a row in the table contains a list file
isListFile() - Method in class org.emboss.jemboss.gui.form.SetInFileCard
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: Determine if a output file name is set
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: true if the output section
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, int) - Method in class org.emboss.jemboss.parser.ParseAcd: Determine if the value of the parameter is a String.
isParamValueStr(int) - Method in class org.emboss.jemboss.parser.acd.ApplicationFields: Determine if the parameter value is a string
isParamValueString() - Method in class org.emboss.jemboss.parser.acd.ApplicationParam: Determine if the parameter has a string value
isPrettyBox() - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection: Determine if the identities are to be boxed
isPrettyBox() - Method in class org.emboss.jemboss.editor.PrettyPlotJFrame: Determine if boxes are to be drawn around the identical matches
isPrettyPlot() - Method in class org.emboss.jemboss.editor.SequenceJPanel: Determine if using prettyplot display
isPrimaryGp - Variable in class org.emboss.jemboss.parser.ParseAcd: true if primary group is defined
isProcessStdout() - Method in class org.emboss.jemboss.programs.RunEmbossApplication
isProtein() - Method in class org.emboss.jemboss.editor.Sequence: Get the sequence type
isProtein() - Method in class org.emboss.jemboss.soap.CallAjax: Deternmine the sequence type
isReading() - Method in class org.emboss.jemboss.editor.SequenceReader
isReportFormat() - Method in class org.emboss.jemboss.gui.form.SectionPanel: Determine if report formats are used in the EMBOSS program
isReq - Variable in class org.emboss.jemboss.gui.form.SectionPanel: true if the required section
isRequiredSection() - Method in class org.emboss.jemboss.gui.form.SectionPanel
isRunning() - Method in class org.emboss.jemboss.programs.JembossProcess: Determine if a job is running
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: true if shading disabled fields, otherwise they are removed from the form
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.InputSequenceAttributes: Determine if there is a default -sufo value
isUFODefault() - Method in class org.emboss.jemboss.gui.sequenceChooser.OutputSequenceAttributes: Determine if UFO has a value
isUseTFM() - Method in class org.emboss.jemboss.JembossParams

J

Jemboss - class org.emboss.jemboss.Jemboss.: Java interface to EMBOSS (http://www.emboss.org/).
Jemboss() - Constructor for class org.emboss.jemboss.Jemboss: Display the Jemboss GUI.
Jemboss.winExit - class org.emboss.jemboss.Jemboss.winExit.: Extends WindowAdapter to close window and save any session properties and clean up
Jemboss.winExit() - Constructor for class org.emboss.jemboss.Jemboss.winExit
JembossAuthServer - class org.emboss.jemboss.server.JembossAuthServer.: Jemboss Authenticated Server for Apache Axis (SOAP) web services
JembossAuthServer() - Constructor for class org.emboss.jemboss.server.JembossAuthServer
JembossComboPopup - class org.emboss.jemboss.gui.form.JembossComboPopup.: Creates a scrolling JComboBox
JembossComboPopup(Object[]) - Constructor for class org.emboss.jemboss.gui.form.JembossComboPopup: Creates a JComboBox that contains the elements in the specified array.
JembossComboPopup(Vector) - Constructor for class org.emboss.jemboss.gui.form.JembossComboPopup: Creates a JComboBox that contains the elements in the vextor
JembossComboPopup.myComboUI - class org.emboss.jemboss.gui.form.JembossComboPopup.myComboUI.: Create scroller
JembossComboPopup.myComboUI() - Constructor for class org.emboss.jemboss.gui.form.JembossComboPopup.myComboUI
JembossFileAuthServer - class org.emboss.jemboss.server.JembossFileAuthServer.: File manager methods
JembossFileAuthServer() - Constructor for class org.emboss.jemboss.server.JembossFileAuthServer
JembossFileServer - class org.emboss.jemboss.server.JembossFileServer.: File manager methods - for a non-authenticating server
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: Given the path to a jar file unpack to a hashtable
JembossLogo - class org.emboss.jemboss.JembossLogo.
JembossLogo(int, int, int) - Constructor for class org.emboss.jemboss.JembossLogo
JembossParams - class org.emboss.jemboss.JembossParams.: Contains all property information about the client and the server.
JembossParams() - Constructor for class org.emboss.jemboss.JembossParams: Loads and holds the properties
JembossProcess - class org.emboss.jemboss.programs.JembossProcess.: Monitor for Jemboss batch processes
JembossProcess(String, String, String) - Constructor for class org.emboss.jemboss.programs.JembossProcess
JembossProcess(String, String) - Constructor for class org.emboss.jemboss.programs.JembossProcess
JembossProcess(String) - Constructor for class org.emboss.jemboss.programs.JembossProcess
JembossRun - class org.emboss.jemboss.soap.JembossRun.: Executes an application on a server
JembossRun(String, String, Hashtable, JembossParams) - Constructor for class org.emboss.jemboss.soap.JembossRun
JembossServer - class org.emboss.jemboss.server.JembossServer.: Jemboss Non-authenticated Server for Apache Axis (SOAP) web services
JembossServer() - Constructor for class org.emboss.jemboss.server.JembossServer
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.: Use to run an EMBOSS application in batch mode by running the process in a separate thread
JembossThread(RunEmbossApplication2, String) - Constructor for class org.emboss.jemboss.server.JembossThread
jarStore - Variable in class org.emboss.jemboss.JembossJarUtil: Hashtable containing the unpacked contents of the jar file
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
jdimExtend - Static variable in class org.emboss.jemboss.Jemboss: Jemboss window dimension with local filemanager displayed
jdimension - Variable in class org.emboss.jemboss.editor.Matrix
jembossServer - Static variable in class org.emboss.jemboss.JembossParams: Jemboss java server
jembossServerName - Variable in class org.emboss.jemboss.JembossParams: property name for Jemboss java server
jembossSettings - Variable in class org.emboss.jemboss.JembossParams
jobButton - Variable in class org.emboss.jemboss.soap.PendingResults: job manager button
jobComboBox - Variable in class org.emboss.jemboss.soap.PendingResults: job manager interactive/batch selection
jobMgr - Static variable in class org.emboss.jemboss.gui.AdvancedOptions: job manager update times
jobStatus() - Method in class org.emboss.jemboss.soap.PendingResults: Report the status of completed and running processes.
jobid - Variable in class org.emboss.jemboss.programs.JembossProcess: project id
jp - Variable in class org.emboss.jemboss.server.JembossAuthServer: jemboss properties
jp - Variable in class org.emboss.jemboss.server.JembossFileAuthServer: jemboss properties
jp - Variable in class org.emboss.jemboss.server.JembossServer: jemboss properties
jspColour - Variable in class org.emboss.jemboss.editor.ColourJFrame: Scroll pane for the colour pallette
jspSequence - Variable in class org.emboss.jemboss.editor.AlignApplet
jspSequence - Variable in class org.emboss.jemboss.editor.AlignJFrame
jspSequence - Variable in class org.emboss.jemboss.editor.ConsensusOptions
jspSequence - Variable in class org.emboss.jemboss.editor.GraphicSequenceCollection: sequence scrollpane

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

L

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
LabelTextBox - class org.emboss.jemboss.gui.form.LabelTextBox.: Container for Jemboss form label this will also wrap the text
LabelTextBox(String, String) - Constructor for class org.emboss.jemboss.gui.form.LabelTextBox
LaunchJalView - class org.emboss.jemboss.gui.LaunchJalView.: Launch Jalview (M.Clamp )
LaunchJalView() - Constructor for class org.emboss.jemboss.gui.LaunchJalView
ListFile - class org.emboss.jemboss.programs.ListFile.: Parse an EMBOSS 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
ListFile() - Constructor for class org.emboss.jemboss.programs.ListFile
ListFilePanel - class org.emboss.jemboss.gui.form.ListFilePanel.: List file panel, enabling the user to generate a list of sequence in the GUI which can be used to generate an EMBOSS list file to be used in the command line.
ListFilePanel(int, JembossParams) - Constructor for class org.emboss.jemboss.gui.form.ListFilePanel
LocalAndRemoteFileTreeFrame - class org.emboss.jemboss.gui.filetree.LocalAndRemoteFileTreeFrame.: Local and remote combo file manager
LocalAndRemoteFileTreeFrame(JembossParams) - Constructor for class org.emboss.jemboss.gui.filetree.LocalAndRemoteFileTreeFrame: Displays the remote and local file managers in the same frame.
lab - Variable in class org.emboss.jemboss.gui.form.SectionPanel: field label container
labelColor - Static variable in class org.emboss.jemboss.gui.form.SectionPanel: label colour
labfont - Static variable in class org.emboss.jemboss.gui.form.SectionPanel: label font
labfont2 - Static variable in class org.emboss.jemboss.gui.form.SectionPanel: small label font
len - Variable in class org.emboss.jemboss.editor.GraphicSequenceCollection
length - Variable in class org.emboss.jemboss.editor.Sequence: sequence length
length - Static variable in class org.emboss.jemboss.parser.Ajax: sequence length
length - Variable in class org.emboss.jemboss.soap.CallAjax: sequence length
length_soap - Variable in class org.emboss.jemboss.parser.Ajax: sequence length
listByDateRun(ResultList, boolean) - Method in class org.emboss.jemboss.gui.ShowSavedResults: List results by date
listByProgramName() - Method in class org.emboss.jemboss.gui.ShowSavedResults: List results by alphabetical name
listDirs(String, byte[], String, String) - Method in class org.emboss.jemboss.parser.Ajax: list directorys
listFiles(String, byte[], String, String) - Method in class org.emboss.jemboss.parser.Ajax: list files in a directory
listPane - Variable in class org.emboss.jemboss.gui.form.SetInFileCard: list file panel
list_saved_results(String, byte[]) - Method in class org.emboss.jemboss.server.JembossAuthServer: List of the saved results on the server.
list_saved_results(String) - Method in class org.emboss.jemboss.server.JembossServer: List of the saved results on the server.
list_saved_results() - Method in class org.emboss.jemboss.server.JembossServer: List of the saved results on the server.
listdefault - Variable in class org.emboss.jemboss.parser.ParseAcd: default for list or select data type
lname - Variable in class org.emboss.jemboss.gui.sequenceChooser.FileChooser: label for text field
loadFilesContent(Ajax, String, byte[], File, String, Vector, Vector) - 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: Load a property from the jemboss.property file.
loadPNGContent(String) - Method in class org.emboss.jemboss.gui.filetree.FileEditorDisplay: Need to read png in, in case it is saved out
loadPNGContent(File, String, Vector) - Method in class org.emboss.jemboss.server.JembossServer: Reads in png files from EMBOSS output
loadStoredSeqList(File) - Method in class org.emboss.jemboss.gui.SequenceListTableModel: Load from stored file the SequenceList created from a previous session.
localAndRemoteTree - Static variable in class org.emboss.jemboss.gui.SetUpMenuBar: local and remote file manager window
logEntry - Variable in class org.emboss.jemboss.server.AppendToLogFileThread
logFile - Variable in class org.emboss.jemboss.server.JembossAuthServer: Jemboss log file
logFileName - Variable in class org.emboss.jemboss.server.AppendToLogFileThread
lower - Variable in class org.emboss.jemboss.gui.sequenceChooser.InputSequenceAttributes: select to specify lower case
lpair - Variable in class org.emboss.jemboss.gui.form.AlignFormat: true if pairwise alignment format
ls - Variable in class org.emboss.jemboss.gui.filetree.RemoteDragTree: line separator
ls - Variable in class org.emboss.jemboss.server.JembossAuthServer: line seperator
lsaved - Variable in class org.emboss.jemboss.gui.filetree.FileSaving: true if the file is saved ok
ltree - Static variable in class org.emboss.jemboss.gui.filetree.LocalAndRemoteFileTreeFrame: local file tree

M

MAGENTA - Static variable in class org.emboss.jemboss.editor.SequenceProperties: MAGENTA from EMBOSS data Ecolour.map
MAXSEQLENGTH - Variable in class org.emboss.jemboss.editor.GraphicSequenceCollection: longest sequence length
MAX_MEM_LEN - Static variable in class org.emboss.jemboss.gui.MemoryComboBox
MakeFileSafe - class org.emboss.jemboss.soap.MakeFileSafe.: Create a sanitised filename.
MakeFileSafe(String) - Constructor for class org.emboss.jemboss.soap.MakeFileSafe
Matrix - class org.emboss.jemboss.editor.Matrix.: Reads and hold a sequence scoring matrix
Matrix(File) - Constructor for class org.emboss.jemboss.editor.Matrix
Matrix(String, String) - Constructor for class org.emboss.jemboss.editor.Matrix
MatrixJFrame - class org.emboss.jemboss.editor.MatrixJFrame.: Display a matrix and list of available scoring matrix files
MatrixJFrame(Matrix, JTextField, AlignJFrame) - Constructor for class org.emboss.jemboss.editor.MatrixJFrame
MemoryComboBox - class org.emboss.jemboss.gui.MemoryComboBox.: Extends JComboBox to add and store new elements
MemoryComboBox(Vector) - Constructor for class org.emboss.jemboss.gui.MemoryComboBox
MultiLineToolTipUI - class org.emboss.jemboss.gui.form.MultiLineToolTipUI.: UI for multiple line tooltips
MultiLineToolTipUI() - Constructor for 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
mItem - Variable in class org.emboss.jemboss.gui.startup.ProgList: used to create the program menus
mScroll - Variable in class org.emboss.jemboss.editor.MatrixJFrame: scroll pane for matrix display
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
main(String[]) - Static method in class org.emboss.jemboss.FileManager
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.editor.AlignJFrame
main(String[]) - Static method in class org.emboss.jemboss.editor.Consensus
main(String[]) - Static method in class org.emboss.jemboss.editor.GraphicSequenceCollection
main(String[]) - Static method in class org.emboss.jemboss.editor.GroutAlignJFrame: Test main really
main(String[]) - Static method in class org.emboss.jemboss.editor.PlotConsensus
main(String[]) - Static method in class org.emboss.jemboss.editor.Sequence
main(String[]) - Static method in class org.emboss.jemboss.gui.Browser
main(String[]) - Static method in class org.emboss.jemboss.gui.ImageIconJPanel
main(String[]) - Static method in class org.emboss.jemboss.server.TestPrivateServer
main(String[]) - Static method in class org.emboss.jemboss.server.TestPublicServer
mainMenu - Variable in class org.emboss.jemboss.Jemboss: Jemboss main menu
makeDir(String, byte[], String, String) - Method in class org.emboss.jemboss.parser.Ajax: make a directory
makeShape(float, float, float, float, float, float, float, float, float, float) - Static method in class org.emboss.jemboss.gui.Browser: Use to draw a Shape.
mat - Static variable in class org.emboss.jemboss.editor.AlignJFrame
mat - Variable in class org.emboss.jemboss.editor.ConsensusOptions: scoring matrix
mat - Variable in class org.emboss.jemboss.editor.GraphicSequenceCollection: scoring matrix
mat - Variable in class org.emboss.jemboss.editor.MatrixJFrame: scoring matrix
matchColour - Variable in class org.emboss.jemboss.editor.PrettyPlotJFrame: colour panel for positive scoring matches
matchColourBackground - Variable in class org.emboss.jemboss.editor.PrettyPlotJFrame: colour panel for positive scoring matches background
matrices - Static variable in class org.emboss.jemboss.gui.BuildProgramMenu: matrices
matrices - Variable in class org.emboss.jemboss.soap.ShowDB: scoring matrices
matrix - Variable in class org.emboss.jemboss.editor.AlignApplet
matrix - Variable in class org.emboss.jemboss.editor.Consensus
matrix - Variable in class org.emboss.jemboss.editor.Matrix
matrixFileName - Variable in class org.emboss.jemboss.editor.Matrix
matrixLineCount(String, RE) - Method in class org.emboss.jemboss.editor.Matrix: Count as a matrix row and number of columns
matrixLineParse(String, RE) - Method in class org.emboss.jemboss.editor.Matrix: Parse a line from a scoring matrix file.
matrixRead(File) - Method in class org.emboss.jemboss.editor.Matrix: Read and parse a scoring matrix file
matrixReadString(String) - Method in class org.emboss.jemboss.editor.Matrix: Read and parse a scoring matrix
matrixString - Variable in class org.emboss.jemboss.editor.Matrix
maxSectionWidth - Variable in class org.emboss.jemboss.gui.form.SectionPanel: maximum width of the form
maybeShowPopup(MouseEvent) - Method in class org.emboss.jemboss.editor.ColourPanel.PopupListener
maybeShowPopup(MouseEvent) - Method in class org.emboss.jemboss.editor.SequenceJPanel.PopupListener
maybeShowPopup(MouseEvent) - Method in class org.emboss.jemboss.gui.filetree.DragTree.PopupListener
maybeShowPopup(MouseEvent) - Method in class org.emboss.jemboss.gui.filetree.RemoteDragTree.PopupListener
memLog - Variable in class org.emboss.jemboss.server.AppendToLogFileThread
menuBar - Variable in class org.emboss.jemboss.editor.AlignJFrame
menuBar - Variable in class org.emboss.jemboss.gui.ShowResultSet: menu bar
menuFont - Variable in class org.emboss.jemboss.gui.startup.ProgList: font used for the menu items
mkdir(String, String, String, byte[]) - Method in class org.emboss.jemboss.server.JembossFileAuthServer: Make a directory
mkdir(String, String, String) - Method in class org.emboss.jemboss.server.JembossFileServer: Make a directory
mlist - Variable in class org.emboss.jemboss.parser.ParseAcd: number of list & selection fields - multiple selection
modeVector() - Method in class org.emboss.jemboss.JembossParams: Return the mode list as a vector, suitable for loading into a combobox.
modelColumns - Static variable in class org.emboss.jemboss.gui.SequenceListTableModel: Define the columns as file/start/end/list and default
modelVector - Static variable in class org.emboss.jemboss.gui.SequenceListTableModel
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.ColourMenu.ColorPane
mousePressed(MouseEvent) - Method in class org.emboss.jemboss.editor.ColourPanel.PopupListener
mousePressed(MouseEvent) - Method in class org.emboss.jemboss.editor.SequenceJPanel.PopupListener
mousePressed(MouseEvent) - Method in class org.emboss.jemboss.gui.ColorMenu.ColorPane
mousePressed(MouseEvent) - Method in class org.emboss.jemboss.gui.filetree.DragTree.PopupListener
mousePressed(MouseEvent) - Method in class org.emboss.jemboss.gui.filetree.RemoteDragTree.PopupListener
mouseReleased(MouseEvent) - Method in class org.emboss.jemboss.editor.ColourMenu.ColorPane
mouseReleased(MouseEvent) - Method in class org.emboss.jemboss.editor.ColourPanel.PopupListener
mouseReleased(MouseEvent) - Method in class org.emboss.jemboss.editor.SequenceJPanel.PopupListener
mouseReleased(MouseEvent) - Method in class org.emboss.jemboss.gui.ColorMenu.ColorPane
mouseReleased(MouseEvent) - Method in class org.emboss.jemboss.gui.filetree.DragTree.PopupListener
mouseReleased(MouseEvent) - Method in class org.emboss.jemboss.gui.filetree.RemoteDragTree.PopupListener
moveSequence(String, int) - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection: Move a sequence to a new position
msf - Static variable in class org.emboss.jemboss.gui.sequenceChooser.SequenceFilter
multiOption - Variable in class org.emboss.jemboss.gui.form.BuildJembossForm
multiOption - Variable in class org.emboss.jemboss.gui.form.SectionPanel: multiple option field for list and select
myset - Variable in class org.emboss.jemboss.soap.ServerSetup: jemboss properties
mysettings - Variable in class org.emboss.jemboss.gui.filetree.DragTree: jemboss properties
mysettings - Variable in class org.emboss.jemboss.gui.filetree.RemoteDragTree: jemboss properties
mysettings - Variable in class org.emboss.jemboss.gui.filetree.RemoteFileNode: jemboss properties
mysettings - Variable in class org.emboss.jemboss.gui.form.BuildJembossForm
mysettings - Variable in class org.emboss.jemboss.gui.form.SectionPanel: jemboss properties
mysettings - Static variable in class org.emboss.jemboss.server.TestPrivateServer
mysettings - Static variable in class org.emboss.jemboss.server.TestPublicServer
mysettings - Variable in class org.emboss.jemboss.soap.AuthPopup: jemboss properties
mysettings - Variable in class org.emboss.jemboss.soap.PendingResults: jemboss properties




N

nFiles - 
Variable in class org.emboss.jemboss.gui.form.ListFilePanel
maximum number of sequences in list
nResPerLine - 
Variable in class org.emboss.jemboss.editor.PrintAlignmentImage
number of residues per line
name - 
Variable in class org.emboss.jemboss.editor.Sequence
sequence name
name - 
Variable in class org.emboss.jemboss.gui.form.ApplicationNamePanel
application name
name() - 
Method in class org.emboss.jemboss.server.JembossServer
 
nameLabel - 
Variable in class org.emboss.jemboss.editor.SequenceNameJButton
name label
nbool - 
Variable in class org.emboss.jemboss.parser.ParseAcd
number of checkbox fields
newRoot(String) - 
Method in class org.emboss.jemboss.gui.filetree.DragTree
Define a directory root for the file tree
nf - 
Variable in class org.emboss.jemboss.gui.form.SectionPanel
field number to start from
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
nodeExists(RemoteFileNode, String) - 
Method in class org.emboss.jemboss.gui.filetree.RemoteDragTree
Test if a child node exists
notifyGroup(int, int) - 
Method in class org.emboss.jemboss.editor.SequenceJPanel
Update all observers
notifyTargets(String, Object, Object) - 
Method in class org.emboss.jemboss.editor.GroutAlignJFrame
 
notifyTargets(String, Object, Object) - 
Method in class org.emboss.jemboss.editor.GroutGraphicSequenceCollection
 
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
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
select to specify a nucleotide sequence
numOfDependents - 
Variable in class org.emboss.jemboss.parser.ParseAcd
number of dependent variables
numProgs - 
Variable in class org.emboss.jemboss.gui.startup.ProgList
number of programs
numResiduePerLine - 
Variable in class org.emboss.jemboss.editor.GraphicSequenceCollection
number of residues on each line for print
numberDraw - 
Variable in class org.emboss.jemboss.editor.GraphicSequenceCollection
panel for sequence numbers
numbins - 
Variable in class org.emboss.jemboss.editor.PlotConsensus
number of graph bins making up the seq length
numofFields - 
Variable in class org.emboss.jemboss.gui.form.BuildJembossForm
 
numofFields - 
Variable in class org.emboss.jemboss.gui.form.SectionPanel
number of fields in the ACD
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
number of parameters for this field
nvalue - 
Variable in class org.emboss.jemboss.parser.ParseAcd
double value of a parameter
nvalue - 
Variable in class org.emboss.jemboss.parser.acd.ApplicationParam
parameter number value



O

OutputSequenceAttributes - class org.emboss.jemboss.gui.sequenceChooser.OutputSequenceAttributes.
Creates the output sequence attibutes window
OutputSequenceAttributes() - 
Constructor for class org.emboss.jemboss.gui.sequenceChooser.OutputSequenceAttributes
 
observers - 
Variable in class org.emboss.jemboss.editor.SequenceJPanel
observer panels in this group
offormat - 
Variable in class org.emboss.jemboss.gui.sequenceChooser.OutputSequenceAttributes
feature format
ofname - 
Variable in class org.emboss.jemboss.gui.sequenceChooser.OutputSequenceAttributes
features filename
okButton - 
Variable in class org.emboss.jemboss.soap.AuthPopup
OK button
openMethod(Vector) - 
Method in class org.emboss.jemboss.editor.AlignJFrame
Given a Vector of Sequence display them in the editor
openMethod(Vector) - 
Method in class org.emboss.jemboss.editor.GroutAlignJFrame
Given a Vector of Sequence display them in the editor
openMethod(Vector, Vector) - 
Method in class org.emboss.jemboss.editor.GroutAlignJFrame
Given a Vector of Sequence and the indent for each
 display them in the editor
openNode - 
Variable in class org.emboss.jemboss.gui.filetree.DragTree
store of directories that are opened
openNode - 
Variable in class org.emboss.jemboss.gui.filetree.RemoteDragTree
store of directories that are opened
order - 
Variable in class org.emboss.jemboss.gui.MemoryComboBox
 
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
 
osextension - 
Variable in class org.emboss.jemboss.gui.sequenceChooser.OutputSequenceAttributes
ouput file extension to use
osname - 
Variable in class org.emboss.jemboss.gui.sequenceChooser.OutputSequenceAttributes
output base name
ossingle - 
Variable in class org.emboss.jemboss.gui.sequenceChooser.OutputSequenceAttributes
separate file for each entry
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
outfileResult - 
Variable in class org.emboss.jemboss.gui.form.BuildJembossForm
 



P

PINK - 
Static variable in class org.emboss.jemboss.editor.SequenceProperties
PINK from EMBOSS data Ecolour.map
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.
Paste - class org.emboss.jemboss.editor.Paste.
 
Paste() - 
Constructor for class org.emboss.jemboss.editor.Paste
 
PatternJFrame - class org.emboss.jemboss.editor.PatternJFrame.
Frame for searching for patterns in the sequences
PatternJFrame() - 
Constructor for class org.emboss.jemboss.editor.PatternJFrame
 
PendingResults - class org.emboss.jemboss.soap.PendingResults.
Record the batch job status (pending/completed)
PendingResults(JembossParams) - 
Constructor for class org.emboss.jemboss.soap.PendingResults
 
PlafMacros - class org.emboss.jemboss.gui.form.PlafMacros.
Macros class
PlafMacros() - 
Constructor for class org.emboss.jemboss.gui.form.PlafMacros
 
PlotConsensus - class org.emboss.jemboss.editor.PlotConsensus.
Plot the average similarity.
PlotConsensus(File, Vector, int, int, GraphicSequenceCollection) - 
Constructor for class org.emboss.jemboss.editor.PlotConsensus
 
PlotConsensus(File, Vector, int, int) - 
Constructor for class org.emboss.jemboss.editor.PlotConsensus
 
PlotConsensus(String, String, 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(Matrix, Vector, int, int) - 
Constructor for class org.emboss.jemboss.editor.PlotConsensus
 
PrettyPlotJFrame - class org.emboss.jemboss.editor.PrettyPlotJFrame.
JFrame to define the colour of residue if identical or 
 a positive match.
PrettyPlotJFrame(int, float, Color, Color, Color, Color, boolean) - 
Constructor for class org.emboss.jemboss.editor.PrettyPlotJFrame
 
PrettyPlotJFrame(GraphicSequenceCollection) - 
Constructor for class org.emboss.jemboss.editor.PrettyPlotJFrame
 
PrintAlignment - class org.emboss.jemboss.editor.PrintAlignment.
Class for printing the alignment
PrintAlignment(GraphicSequenceCollection) - 
Constructor for class org.emboss.jemboss.editor.PrintAlignment
 
PrintAlignmentImage - class org.emboss.jemboss.editor.PrintAlignmentImage.
Print png/jpeg image and print preview.
PrintAlignmentImage(GraphicSequenceCollection, PageFormat) - 
Constructor for class org.emboss.jemboss.editor.PrintAlignmentImage
 
PrintAlignmentImage(GraphicSequenceCollection) - 
Constructor for class org.emboss.jemboss.editor.PrintAlignmentImage
 
PrintableJTable - class org.emboss.jemboss.editor.PrintableJTable.
 
PrintableJTable() - 
Constructor for class org.emboss.jemboss.editor.PrintableJTable
 
PrintableJTable(Object[][], String[]) - 
Constructor for class org.emboss.jemboss.editor.PrintableJTable
 
PrivateRequest - class org.emboss.jemboss.soap.PrivateRequest.
Make a axis call to a private server, using the default service
PrivateRequest(JembossParams, String, Vector) - 
Constructor for class org.emboss.jemboss.soap.PrivateRequest
 
PrivateRequest(JembossParams, String, String) - 
Constructor for class org.emboss.jemboss.soap.PrivateRequest
 
PrivateRequest(JembossParams, String, String, Vector) - 
Constructor for class org.emboss.jemboss.soap.PrivateRequest
 
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(String, JMenuBar) - 
Constructor for class org.emboss.jemboss.gui.startup.ProgList
 
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
 
PublicRequest - class org.emboss.jemboss.soap.PublicRequest.
Make a axis call to a public server, using the default service
PublicRequest(JembossParams, String) - 
Constructor for class org.emboss.jemboss.soap.PublicRequest
 
PublicRequest(JembossParams, String, Vector) - 
Constructor for class org.emboss.jemboss.soap.PublicRequest
 
PublicRequest(JembossParams, String, String) - 
Constructor for class org.emboss.jemboss.soap.PublicRequest
 
PublicRequest(JembossParams, String, String, Vector) - 
Constructor for class org.emboss.jemboss.soap.PublicRequest
 
p - 
Variable in class org.emboss.jemboss.programs.RunEmbossApplication
running process
p - 
Variable in class org.emboss.jemboss.programs.RunEmbossApplication2
running process
p2 - 
Variable in class org.emboss.jemboss.gui.form.BuildJembossForm
 
p3 - 
Variable in class org.emboss.jemboss.Jemboss
Local filemanager panel
p3 - 
Variable in class org.emboss.jemboss.gui.form.SectionPanel
Jemboss form panel
padChar - 
Variable in class org.emboss.jemboss.editor.SequenceJPanel
pad/gap character
pageIndex - 
Variable in class org.emboss.jemboss.editor.PrintAlignmentImage
page number to print
paint(Graphics) - 
Method in class org.emboss.jemboss.gui.TabListCellRenderer
 
paint(Graphics, JComponent) - 
Method in class org.emboss.jemboss.gui.form.MultiLineToolTipUI
 
paint(Graphics) - 
Method in class org.emboss.jemboss.gui.form.Separator
Override paint to draw separator
paintComponent(Graphics) - 
Method in class org.emboss.jemboss.JembossLogo
 
paintComponent(Graphics) - 
Method in class org.emboss.jemboss.editor.ColourPanel
Override paintComponent
paintComponent(Graphics) - 
Method in class org.emboss.jemboss.editor.PlotConsensus
Override paintComponent to draw consensus plot
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.SequenceJPanel
Override paintComponent
paintComponent(Graphics) - 
Method in class org.emboss.jemboss.gui.ImageIconJPanel
Override the paintComponent
paintComponent(Graphics) - 
Method in class org.emboss.jemboss.gui.form.ApplicationNamePanel
Override paintComponent
panes - 
Variable in class org.emboss.jemboss.editor.ColourMenu
hashtable of the colour panes
panes - 
Variable in class org.emboss.jemboss.gui.ColorMenu
 
param - 
Variable in class org.emboss.jemboss.parser.Dependent
parameter number
parentList - 
Variable in class org.emboss.jemboss.gui.filetree.RemoteFileNode
parent directory listing
parse(String, Hashtable) - 
Static method in class org.emboss.jemboss.programs.ListFile
 
parseAcd - 
Variable in class org.emboss.jemboss.gui.form.BuildJembossForm
 
parseAcd - 
Variable in class org.emboss.jemboss.gui.form.SectionPanel
ACD parser for the application selected
parseParam(BufferedReader, StreamTokenizer) - 
Method in class org.emboss.jemboss.parser.ParseAcd
Parses a parameter in a ACD field
pasteText() - 
Method in class org.emboss.jemboss.gui.form.TextFieldSink
 
pasteText() - 
Method in class org.emboss.jemboss.gui.sequenceChooser.TextAreaSink
Add text from the system clipboard into the text area
pattern - 
Variable in class org.emboss.jemboss.editor.SequenceJPanel
pattern to search for
pc - 
Variable in class org.emboss.jemboss.editor.GraphicSequenceCollection
Consensus plot
pendingResults - 
Variable in class org.emboss.jemboss.soap.PendingResults
pending results
pfield - 
Variable in class org.emboss.jemboss.soap.AuthPopup
passwd field
plotConStrut - 
Variable in class org.emboss.jemboss.editor.GraphicSequenceCollection
gap between sequences and consensus plot
plotconsSeqBox - 
Variable in class org.emboss.jemboss.editor.GraphicSequenceCollection
container for consensus plot
plplot - 
Variable in class org.emboss.jemboss.JembossParams
plplot library location
plplot - 
Variable in class org.emboss.jemboss.server.JembossAuthServer
plplot path
plplot - 
Variable in class org.emboss.jemboss.server.JembossServer
plplot path
plplotName - 
Variable in class org.emboss.jemboss.JembossParams
property name for plplot library location
pluralFloat - 
Variable in class org.emboss.jemboss.editor.ConsensusOptions
plurality
pmain - 
Variable in class org.emboss.jemboss.Jemboss
Jemboss split pain
pngContent - 
Variable in class org.emboss.jemboss.gui.filetree.FileEditorDisplay
png file content
polarColor - 
Static variable in class org.emboss.jemboss.editor.SequenceProperties
Polar (Red=Polar)
popup - 
Variable in class org.emboss.jemboss.editor.ColourJFrame
Popup menu system
popup - 
Variable in class org.emboss.jemboss.editor.ColourPanel
 
popup - 
Variable in class org.emboss.jemboss.editor.SequenceJPanel
pop up menu
popup - 
Variable in class org.emboss.jemboss.gui.filetree.DragTree
popup menu
popup - 
Variable in class org.emboss.jemboss.gui.filetree.RemoteDragTree
popup menu
position - 
Variable in class org.emboss.jemboss.editor.GroutAlignJFrame
 
ppj - 
Variable in class org.emboss.jemboss.editor.AlignJFrame
 
prefClose - 
Variable in class org.emboss.jemboss.gui.filetree.LocalAndRemoteFileTreeFrame
close/exit menu item
prefShadeGUI - 
Static variable in class org.emboss.jemboss.gui.AdvancedOptions
shade or remove unused parameters
prefjni - 
Static variable in class org.emboss.jemboss.gui.AdvancedOptions
use JNI to calculate parameter dependencies
pressedResidue - 
Variable in class org.emboss.jemboss.editor.SequenceJPanel
residue number when pressed by mouse
prettPlot - 
Variable in class org.emboss.jemboss.editor.GraphicSequenceCollection
draw as per prettplot
prettyBox - 
Variable in class org.emboss.jemboss.editor.PrettyPlotJFrame
define if the identities and matches are to be boxed
prettyDraw(int, int, int, String, int, int, boolean, Graphics) - 
Method in class org.emboss.jemboss.editor.SequenceJPanel
 
prettyPlot - 
Variable in class org.emboss.jemboss.editor.GraphicSequenceCollection
pretty plot values
prettyPlot - 
Variable in class org.emboss.jemboss.editor.SequenceJPanel
colour as per prettyplot
primaryGp - 
Variable in class org.emboss.jemboss.parser.ParseAcd
primary group
print(Graphics, PageFormat, int) - 
Method in class org.emboss.jemboss.editor.GraphicSequenceCollection
Used to print the sequence alignment
print() - 
Method in class org.emboss.jemboss.editor.PrintAlignmentImage
Print to a jpeg or png file
print(int, String, String, boolean, double, double, double, double) - 
Method in class org.emboss.jemboss.editor.PrintAlignmentImage
Print to a jpeg or png file
print(String, double, double, double, double) - 
Method in class org.emboss.jemboss.editor.PrintAlignmentImage
Print to one jpeg or png file
print(int, String, String, double, double, double, double) - 
Method in class org.emboss.jemboss.editor.PrintAlignmentImage
Print to one jpeg or png file
print(Graphics, PageFormat, int) - 
Method in class org.emboss.jemboss.editor.PrintableJTable
The method @print@ must be implemented for @Printable@ interface.
printPreview() - 
Method in class org.emboss.jemboss.editor.PrintAlignmentImage
Display a print preview page
printSinglePagePreview() - 
Method in class org.emboss.jemboss.editor.PrintAlignmentImage
Display a single page print preview page
printTable() - 
Method in class org.emboss.jemboss.editor.IDTableJFrame
 
privateName - 
Variable in class org.emboss.jemboss.soap.ServerSetup
private server name
privateServerFailOver - 
Variable in class org.emboss.jemboss.JembossParams
 
privateServers - 
Variable in class org.emboss.jemboss.JembossParams
 
privateSoapService - 
Variable in class org.emboss.jemboss.JembossParams
private service name
privateSoapServiceName - 
Variable in class org.emboss.jemboss.JembossParams
property name for private service name
privateSoapURL - 
Variable in class org.emboss.jemboss.JembossParams
private services URL
privateSoapURLName - 
Variable in class org.emboss.jemboss.JembossParams
property name for private services URL
privateURL - 
Variable in class org.emboss.jemboss.soap.ServerSetup
private server URL
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.JembossRun
program result
proganswer - 
Variable in class org.emboss.jemboss.soap.PrivateRequest
results from calling the web service
proganswer - 
Variable in class org.emboss.jemboss.soap.PublicRequest
 
programGroup - 
Variable in class org.emboss.jemboss.gui.startup.ProgList
program group
progressBar - 
Variable in class org.emboss.jemboss.soap.AuthPopup
progress bar
progressLabel - 
Variable in class org.emboss.jemboss.soap.AuthPopup
progress label
project - 
Variable in class org.emboss.jemboss.programs.JembossProcess
project name
project - 
Variable in class org.emboss.jemboss.programs.RunEmbossApplication
running directory
project - 
Variable in class org.emboss.jemboss.programs.RunEmbossApplication2
running directory
project - 
Variable in class org.emboss.jemboss.server.JembossThread
project directory
promptPanel - 
Variable in class org.emboss.jemboss.soap.AuthPopup
prompt for login panel
protein - 
Variable in class org.emboss.jemboss.editor.Sequence
sequence type
protein - 
Variable in class org.emboss.jemboss.gui.sequenceChooser.InputSequenceAttributes
select to specify a protein sequence
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
type of sequence protein or nucleotide
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
proxy name for web browser
proxyBrowserPort - 
Variable in class org.emboss.jemboss.soap.ServerSetup
proxy port for web browser
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
proxy name
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
proxy port
proxyPortNum - 
Variable in class org.emboss.jemboss.JembossParams
 
proxyPortNumName - 
Variable in class org.emboss.jemboss.JembossParams
 
ps - 
Variable in class org.emboss.jemboss.server.JembossAuthServer
path separator
ps - 
Variable in class org.emboss.jemboss.server.JembossFileAuthServer
path separator
publicName - 
Variable in class org.emboss.jemboss.soap.ServerSetup
public server name
publicServerFailOver - 
Variable in class org.emboss.jemboss.JembossParams
 
publicServers - 
Variable in class org.emboss.jemboss.JembossParams
 
publicSoapService - 
Variable in class org.emboss.jemboss.JembossParams
public service name
publicSoapServiceName - 
Variable in class org.emboss.jemboss.JembossParams
property name for public service name
publicSoapURL - 
Variable in class org.emboss.jemboss.JembossParams
public services URL
publicSoapURLName - 
Variable in class org.emboss.jemboss.JembossParams
property name for public services URL
publicURL - 
Variable in class org.emboss.jemboss.soap.ServerSetup
public server URL
putFile(String, byte[], String, String, byte[]) - 
Method in class org.emboss.jemboss.parser.Ajax
create a file
put_file(String, String, byte[], String, byte[]) - 
Method in class org.emboss.jemboss.server.JembossFileAuthServer
Put a file on the server file system
put_file(String, String, byte[], String) - 
Method in class org.emboss.jemboss.server.JembossFileServer
Put a file on the server file system



Q

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



R

REMOTEFILENODE - 
Static variable in class org.emboss.jemboss.gui.filetree.RemoteFileNode
 
RemoteDragTree - class org.emboss.jemboss.gui.filetree.RemoteDragTree.
Creates a remote file tree which is a drag source & sink
RemoteDragTree(JembossParams, FileRoots) - 
Constructor for class org.emboss.jemboss.gui.filetree.RemoteDragTree
 
RemoteDragTree.PopupListener - class org.emboss.jemboss.gui.filetree.RemoteDragTree.PopupListener.
Popup menu listener
RemoteDragTree.PopupListener() - 
Constructor for class org.emboss.jemboss.gui.filetree.RemoteDragTree.PopupListener
 
RemoteFileNode - class org.emboss.jemboss.gui.filetree.RemoteFileNode.
File node for remote file tree manager
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.
Panel for the remote file tree manager
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.
ReportFormat - class org.emboss.jemboss.gui.form.ReportFormat.
EMBOSS Report formats
 http://www.hgmp.mrc.ac.uk/Software/EMBOSS/Themes/ReportFormats.html
ReportFormat(ParseAcd, int) - 
Constructor for class org.emboss.jemboss.gui.form.ReportFormat
 
ResultList - class org.emboss.jemboss.programs.ResultList.
Holds the list of stored 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
Holds the list of stored results
ResultList(JembossParams, String, String, String) - 
Constructor for class org.emboss.jemboss.programs.ResultList
Manipulate a dataset.
ResultsMenuBar - class org.emboss.jemboss.gui.ResultsMenuBar.
Sets up a results menu bar with save and close
ResultsMenuBar(JFrame, JTabbedPane, Hashtable, JembossParams) - 
Constructor for class org.emboss.jemboss.gui.ResultsMenuBar
Sets up a results menu bar with save and close
ResultsMenuBar(JFrame, JTabbedPane, Hashtable, Hashtable) - 
Constructor for 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, String, JembossParams) - 
Constructor for class org.emboss.jemboss.gui.ResultsMenuBar
Adds action listener to save contents of contents of a
 tabbed pane.
ResultsUpdateTimer - class org.emboss.jemboss.programs.ResultsUpdateTimer.
Timer for updating saved results window for
 batch jobs submitted
ResultsUpdateTimer(int, DefaultListModel, JFrame) - 
Constructor for class org.emboss.jemboss.programs.ResultsUpdateTimer
 
ResultsUpdateTimer.ResultsTask - class org.emboss.jemboss.programs.ResultsUpdateTimer.ResultsTask.
Timer task to update the results window
ResultsUpdateTimer.ResultsTask() - 
Constructor for class org.emboss.jemboss.programs.ResultsUpdateTimer.ResultsTask
 
ResultsUpdateTimer.ResultsTask(DefaultListModel, JFrame) - 
Constructor for class org.emboss.jemboss.programs.ResultsUpdateTimer.ResultsTask
 
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(String, String[], File) - 
Constructor for class org.emboss.jemboss.programs.RunEmbossApplication2
 
RunEmbossApplication2(String, String[], File, JTextArea) - 
Constructor for class org.emboss.jemboss.programs.RunEmbossApplication2
 
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
 
raccshow - 
Variable in class org.emboss.jemboss.gui.form.ReportFormat
select to show the accession number
rangeField - 
Variable in class org.emboss.jemboss.gui.form.BuildJembossForm
 
rangeField - 
Variable in class org.emboss.jemboss.gui.form.SectionPanel
range field
rasmolColor - 
Static variable in class org.emboss.jemboss.editor.SequenceProperties
rasmol colour scheme
rdesshow - 
Variable in class org.emboss.jemboss.gui.form.ReportFormat
select to show the description
reExplore() - 
Method in class org.emboss.jemboss.gui.filetree.FileNode
Forces the directory to be re-explored
rea - 
Variable in class org.emboss.jemboss.programs.RunEmbossApplication2.StderrHandler
 
rea - 
Variable in class org.emboss.jemboss.programs.RunEmbossApplication2.StdoutHandler
 
rea - 
Variable in class org.emboss.jemboss.server.JembossThread
runs the emboss process
readByteFile(String) - 
Static method in class org.emboss.jemboss.gui.filetree.DragTree
Read a file into a byte array.
readByteFile(String) - 
Static method in class org.emboss.jemboss.server.JembossServer
Read a file into a byte array.
readClustalFile(BufferedReader) - 
Method in class org.emboss.jemboss.editor.SequenceReader
Reads in the CLUSTAL sequence file and creates a Vector
 containing the sequence(s).
readFastaFile(BufferedReader) - 
Method in class org.emboss.jemboss.editor.SequenceReader
Reads in the FASTA sequence file and creates a Vector 
 containing the sequence(s).
readJPredFile(BufferedReader) - 
Method in class org.emboss.jemboss.editor.SequenceReader
Reads in the JPred sequence file and creates a Vector
 containing the sequence(s).
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.FileNode
 
readObject(ObjectInputStream) - 
Method in class org.emboss.jemboss.gui.filetree.RemoteFileNode
 
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
Read a sequence file and create a vector of sequences
readSequenceString(String) - 
Method in class org.emboss.jemboss.editor.SequenceReader
Read a formatted sequence string (e.g msf) and create a vector
 of sequences
reading - 
Variable in class org.emboss.jemboss.editor.SequenceReader
true if read ok
redo - 
Variable in class org.emboss.jemboss.gui.ResultsMenuBar
redo menu item
refresh(FileNode) - 
Method in class org.emboss.jemboss.gui.filetree.DragTree
Refresh
refreshRoot() - 
Method in class org.emboss.jemboss.gui.filetree.RemoteDragTree
This is used to refresh the file manager
remoteFlavors - 
Static variable in class org.emboss.jemboss.gui.filetree.RemoteFileNode
 
removeGroutAlignJFrameListener(GroutAlignJFrameListener) - 
Method in class org.emboss.jemboss.editor.GroutAlignJFrame
 
removeGroutGraphicSequenceCollectionListener(GroutGraphicSequenceCollectionListener) - 
Method in class org.emboss.jemboss.editor.GroutGraphicSequenceCollection
 
removeResult(JembossProcess) - 
Method in class org.emboss.jemboss.soap.PendingResults
Remove a pending process from the list
removeSequence(String) - 
Method in class org.emboss.jemboss.editor.GraphicSequenceCollection
Remove a sequence from the editor display
removedSeqs - 
Variable in class org.emboss.jemboss.editor.GraphicSequenceCollection
Vector of sequences removed from panel
rename(String, String, String, String, RemoteFileNode, RemoteFileNode) - 
Method in class org.emboss.jemboss.gui.filetree.RemoteDragTree
Rename a node from the tree
rename(String, String, String, String, byte[]) - 
Method in class org.emboss.jemboss.server.JembossFileAuthServer
Rename a file
rename(String, String, String, String) - 
Method in class org.emboss.jemboss.server.JembossFileServer
Rename a file
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
rename a file
repaintSequences(Hashtable) - 
Method in class org.emboss.jemboss.editor.AlignJFrame
Force a re-display of the sequences with a new colour
 scheme.
reqdSection - 
Static variable in class org.emboss.jemboss.gui.form.BuildJembossForm
 
res - 
Variable in class org.emboss.jemboss.editor.ColourJFrame.ResidueColourPanel
 
resButtonStatus - 
Variable in class org.emboss.jemboss.gui.ShowSavedResults
result status panel
resMenu - 
Variable in class org.emboss.jemboss.gui.ShowSavedResults
manu bar for results panel
resWidth - 
Variable in class org.emboss.jemboss.editor.SequenceJPanel
residue width
resetCount() - 
Method in class org.emboss.jemboss.soap.PendingResults
Reset the pending and completed job status
residueColor - 
Variable in class org.emboss.jemboss.editor.AlignJFrame
 
residueColor - 
Static variable in class org.emboss.jemboss.editor.SequenceProperties
 
residueMatrixPosition - 
Variable in class org.emboss.jemboss.editor.Matrix
hashtable of the residue positions in the table
resolveColor(String[], int) - 
Static method in class org.emboss.jemboss.editor.AlignJFrame
red, blue, cyan, darkGray, gray , green, lightGray,
  magenta , orange, pink, white, yellow, black
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(Vector, 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
resultsManager - 
Static variable in class org.emboss.jemboss.Jemboss
to manage the pending results
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
select to reverse sequence
reverseComplementSequence() - 
Method in class org.emboss.jemboss.editor.Sequence
Reverse and complement the sequence
reverseSequence() - 
Method in class org.emboss.jemboss.editor.Sequence
Reverse the sequence order
rewriteProperties(String, String) - 
Method in class org.emboss.jemboss.gui.AdvancedOptions
Re-write jemboss.properties when there is an existing jemboss,properties
 and insert/update the user.home property
rf - 
Variable in class org.emboss.jemboss.gui.form.BuildJembossForm
 
rf - 
Variable in class org.emboss.jemboss.gui.form.SectionPanel
report format
rfii - 
Variable in class org.emboss.jemboss.gui.ShowSavedResults
refresh image
root - 
Variable in class org.emboss.jemboss.gui.filetree.DragTree
root directory
rootSelect - 
Variable in class org.emboss.jemboss.gui.filetree.RemoteFileTreePanel
combo to select the root directory from
rootVector - 
Variable in class org.emboss.jemboss.soap.FileRoots
file system roots
rootdir - 
Variable in class org.emboss.jemboss.gui.filetree.RemoteFileNode
root directory
rpt - 
Static variable in class org.emboss.jemboss.gui.form.ReportFormat
EMBOSS Report formats
rscroll - 
Variable in class org.emboss.jemboss.gui.sequenceChooser.InputSequenceAttributes
scroll panel for attibute panel
rscroll - 
Variable in class org.emboss.jemboss.gui.sequenceChooser.OutputSequenceAttributes
scroll pane for output attributes
rtp - 
Variable in class org.emboss.jemboss.gui.ShowResultSet
tabbed pane
run() - 
Method in class org.emboss.jemboss.gui.SplashThread
 
run() - 
Method in class org.emboss.jemboss.programs.BatchUpdateTimer.RemindTask
 
run() - 
Method in class org.emboss.jemboss.programs.ResultsUpdateTimer.ResultsTask
 
run() - 
Method in class org.emboss.jemboss.programs.RunEmbossApplication2.StderrHandler
 
run() - 
Method in class org.emboss.jemboss.programs.RunEmbossApplication2.StdoutHandler
 
run() - 
Method in class org.emboss.jemboss.server.AppendToLogFileThread
Override Thread run() method
run() - 
Method in class org.emboss.jemboss.server.JembossThread
 
runAsBatch(Ajax, String, byte[], String, String) - 
Method in class org.emboss.jemboss.server.JembossAuthServer
Submit to a batch queue
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.
run_prog(String, String, Vector, String, byte[]) - 
Method in class org.emboss.jemboss.server.JembossAuthServer
Run an emboss application
run_prog(String, String, String[]) - 
Method in class org.emboss.jemboss.server.JembossServer
Run an EMBOSS application
run_prog(String, String, Vector, String) - 
Method in class org.emboss.jemboss.server.JembossServer
Run an EMBOSS application
run_prog(String, String, Hashtable) - 
Method in class org.emboss.jemboss.server.JembossServer
Run an EMBOSS application
running - 
Variable in class org.emboss.jemboss.programs.JembossProcess
true when process is running
running_jobs - 
Variable in class org.emboss.jemboss.soap.PendingResults
number of peding processes
rusashow - 
Variable in class org.emboss.jemboss.gui.form.ReportFormat
select to show the USA



S

SALMON - 
Static variable in class org.emboss.jemboss.editor.SequenceProperties
SALMON from EMBOSS data Ecolour.map
SEQUENCEDATA - 
Static variable in class org.emboss.jemboss.gui.SequenceData
dataflavor for drag and drop transfers
SERVER_DOWN - 
Static variable in class org.emboss.jemboss.JembossParams
denotes a server is not responding
SERVER_ERR - 
Static variable in class org.emboss.jemboss.JembossParams
denotes a server is giving errors
SERVER_OK - 
Static variable in class org.emboss.jemboss.JembossParams
denotes a server is OK
SINGLETON - 
Static variable in class org.emboss.jemboss.gui.form.MultiLineToolTipUI
 
ScrollPanel - class org.emboss.jemboss.gui.ScrollPanel.
Extends JPanel to implement Scrollable to speed scroll pane
 scrolling
ScrollPanel() - 
Constructor for class org.emboss.jemboss.gui.ScrollPanel
 
ScrollPanel(LayoutManager) - 
Constructor for class org.emboss.jemboss.gui.ScrollPanel
 
SectionPanel - class org.emboss.jemboss.gui.form.SectionPanel.
Responsible for displaying the Jemboss application form
 generated from the ACD file.
SectionPanel(JFrame, JPanel, Box, ParseAcd, int, TextFieldSink[], TextFieldInt[], TextFieldFloat[], JTextField[], JCheckBox[], InputSequenceAttributes[], JembossComboPopup[], JList[], SetInFileCard[], ListFilePanel[], String[], String, Box[], int, JembossParams, boolean, String[]) - 
Constructor for class org.emboss.jemboss.gui.form.SectionPanel
 
Separator - class org.emboss.jemboss.gui.form.Separator.
Panel separator
Separator(Dimension) - 
Constructor for class org.emboss.jemboss.gui.form.Separator
 
Sequence - class org.emboss.jemboss.editor.Sequence.
Sequence object
Sequence(String, String, int, float) - 
Constructor for class org.emboss.jemboss.editor.Sequence
 
Sequence(String, String, int) - 
Constructor for class org.emboss.jemboss.editor.Sequence
 
Sequence(String, String) - 
Constructor for class org.emboss.jemboss.editor.Sequence
 
Sequence(String) - 
Constructor for class org.emboss.jemboss.editor.Sequence
 
Sequence(String, 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() - 
Constructor for class org.emboss.jemboss.gui.SequenceData
 
SequenceData(String, String, String, Boolean, Boolean, Boolean) - 
Constructor for class org.emboss.jemboss.gui.SequenceData
 
SequenceFilter - class org.emboss.jemboss.gui.sequenceChooser.SequenceFilter.
Sequence format file name suffix filter
SequenceFilter() - 
Constructor for class org.emboss.jemboss.gui.sequenceChooser.SequenceFilter
 
SequenceJPanel - class org.emboss.jemboss.editor.SequenceJPanel.
Sequence panel for drawing a sequence or the 
 sequence numbers
SequenceJPanel(Sequence, JComponent, boolean, boolean, boolean, Hashtable, 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(int, int) - 
Constructor for class org.emboss.jemboss.editor.SequenceJPanel
Constructor for sequence numbering
SequenceJPanel.PopupListener - class org.emboss.jemboss.editor.SequenceJPanel.PopupListener.
Popup listener
SequenceJPanel.PopupListener() - 
Constructor for class org.emboss.jemboss.editor.SequenceJPanel.PopupListener
 
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.
Model for the sequence table
SequenceListTableModel() - 
Constructor for class org.emboss.jemboss.gui.SequenceListTableModel
 
SequenceNameJButton - class org.emboss.jemboss.editor.SequenceNameJButton.
Draw sequence name toggle button
SequenceNameJButton(Sequence, int) - 
Constructor for class org.emboss.jemboss.editor.SequenceNameJButton
 
SequenceProperties - class org.emboss.jemboss.editor.SequenceProperties.
General sequence properties
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, File) - 
Constructor for class org.emboss.jemboss.editor.SequenceSaver
 
SequenceSaver(Vector) - 
Constructor for class org.emboss.jemboss.editor.SequenceSaver
 
ServerSetup - class org.emboss.jemboss.soap.ServerSetup.
Jemboss properties for the server setup
ServerSetup(JembossParams) - 
Constructor for class org.emboss.jemboss.soap.ServerSetup
 
SetInFileCard - class org.emboss.jemboss.gui.form.SetInFileCard.
Input sequence file card
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).
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
 
SetUpMenuBar - class org.emboss.jemboss.gui.SetUpMenuBar.
Sets the top menu bar for Jemboss main window
SetUpMenuBar(JembossParams, JFrame, boolean) - 
Constructor for class org.emboss.jemboss.gui.SetUpMenuBar
 
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
 
ShowDB - class org.emboss.jemboss.soap.ShowDB.
Run showdb and find the available scoring matrices
 and codon usage tables on the Jemboss server
ShowDB(JembossParams) - 
Constructor for class org.emboss.jemboss.soap.ShowDB
 
ShowResultSet - class org.emboss.jemboss.gui.ShowResultSet.
Displays JTabbedPane of the contents of the Hashtable
ShowResultSet(Hashtable, String, JembossParams) - 
Constructor for class org.emboss.jemboss.gui.ShowResultSet
 
ShowResultSet(Hashtable, Hashtable) - 
Constructor for class org.emboss.jemboss.gui.ShowResultSet
 
ShowResultSet(Hashtable, JembossParams) - 
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.GroutPanelListener - class org.emboss.jemboss.gui.ShowResultSet.GroutPanelListener.
 
ShowResultSet.GroutPanelListener() - 
Constructor for class org.emboss.jemboss.gui.ShowResultSet.GroutPanelListener
 
ShowSavedResults - class org.emboss.jemboss.gui.ShowSavedResults.
Shows a list of results from the SOAP server
 and displays individual result sets
ShowSavedResults(String) - 
Constructor for class org.emboss.jemboss.gui.ShowSavedResults
 
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.
SplashThread - class org.emboss.jemboss.gui.SplashThread.
Extends Thread to update the progress bar
 in the login window
SplashThread(AuthPopup, int) - 
Constructor for class org.emboss.jemboss.gui.SplashThread
 
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() - 
Constructor for class org.emboss.jemboss.gui.SwingWorker
Start a thread that will call the construct method
 and then exit.
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
 
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
 
saveFile(File, Vector) - 
Method in class org.emboss.jemboss.editor.SequenceSaver
Save the sequences out
saveSequenceList() - 
Static method in class org.emboss.jemboss.gui.SetUpMenuBar
Save the sequence list for a future session.
saveToLocalFile - 
Variable in class org.emboss.jemboss.gui.ResultsMenuBar
menu to save to local file
saveToRemoteFile - 
Variable in class org.emboss.jemboss.gui.ResultsMenuBar
menu to save to remote file
saveUserHome - 
Variable in class org.emboss.jemboss.gui.AdvancedOptions
save user home directory
save_project_file(String, String, String, String, byte[]) - 
Method in class org.emboss.jemboss.server.JembossAuthServer
Save a file to a project directory on the server.
save_project_file(String, String, String, String) - 
Method in class org.emboss.jemboss.server.JembossServer
Save a file to a project directory on the server.
savedResFrame - 
Variable in class org.emboss.jemboss.programs.ResultsUpdateTimer.ResultsTask
 
sbeg - 
Variable in class org.emboss.jemboss.gui.sequenceChooser.InputSequenceAttributes
-sbegin flag
scrollTree - 
Variable in class org.emboss.jemboss.Jemboss
Scroll pane for local filemanager
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
container for this ACD section
sectionPane - 
Variable in class org.emboss.jemboss.gui.form.SectionPanel
container for this ACD section
sectionResize(JPanel) - 
Method in class org.emboss.jemboss.gui.form.SectionPanel
Resize the section panel
selected - 
Variable in class org.emboss.jemboss.editor.ColourMenu.ColorPane
 
selected - 
Variable in class org.emboss.jemboss.editor.ColourMenu
selected colour pane
selected - 
Variable in class org.emboss.jemboss.gui.ColorMenu.ColorPane
 
selected - 
Variable in class org.emboss.jemboss.gui.ColorMenu
 
selectedBorder - 
Variable in class org.emboss.jemboss.editor.ColourMenu
selected border
selectedBorder - 
Variable in class org.emboss.jemboss.gui.ColorMenu
 
send - 
Variable in class org.emboss.jemboss.gui.sequenceChooser.InputSequenceAttributes
-send flag
seq - 
Variable in class org.emboss.jemboss.editor.Sequence
sequence as a string
seq - 
Variable in class org.emboss.jemboss.editor.SequenceJPanel
sequence to display
seq - 
Variable in class org.emboss.jemboss.editor.SequenceNameJButton
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
container for sequences
seqFile - 
Variable in class org.emboss.jemboss.editor.SequenceReader
sequence file
seqHeight - 
Variable in class org.emboss.jemboss.editor.SequenceJPanel
sequence height
seqLength - 
Variable in class org.emboss.jemboss.editor.SequenceJPanel
sequence length
seqList - 
Static variable in class org.emboss.jemboss.gui.SetUpMenuBar
sequence store list
seqModel - 
Variable in class org.emboss.jemboss.gui.DragJTable
model for the sequence table
seqModel - 
Variable in class org.emboss.jemboss.gui.SequenceList
model for the sequence table
seqNameBox - 
Variable in class org.emboss.jemboss.editor.GraphicSequenceCollection
container for sequence names
seqNamePanel - 
Variable in class org.emboss.jemboss.editor.GraphicSequenceCollection
sequence name panel
seqPaste - 
Variable in class org.emboss.jemboss.gui.sequenceChooser.CutNPasteTextArea
sequence paste field
seqType(String) - 
Method in class org.emboss.jemboss.parser.Ajax
determine sequence attributes
seqoutResult - 
Variable in class org.emboss.jemboss.gui.form.BuildJembossForm
 
seqs - 
Variable in class org.emboss.jemboss.editor.AlignApplet
 
seqs - 
Variable in class org.emboss.jemboss.editor.GraphicSequenceCollection
Vector containing Sequence objects
seqs - 
Variable in class org.emboss.jemboss.editor.SequenceReader
sequence store
seqsetAttrib(String, byte[], String, String) - 
Method in class org.emboss.jemboss.parser.Ajax
determine sequence set attributes as the user
seqsetType(String) - 
Method in class org.emboss.jemboss.parser.Ajax
determine sequence set attributes
sequenceFile - 
Variable in class org.emboss.jemboss.editor.AlignJFrame
 
serverDescription() - 
Method in class org.emboss.jemboss.JembossParams
A description of the server settings
serverPathToFile - 
Variable in class org.emboss.jemboss.gui.filetree.RemoteFileNode
path to the file on the server
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
 
serverStatusHash - 
Variable in class org.emboss.jemboss.JembossParams
 
servicePasswd - 
Variable in class org.emboss.jemboss.JembossParams
 
servicePasswdByte - 
Variable in class org.emboss.jemboss.JembossParams
services password
serviceUserName - 
Variable in class org.emboss.jemboss.JembossParams
 
serviceUserNameName - 
Variable in class org.emboss.jemboss.JembossParams
 
servicedesc() - 
Method in class org.emboss.jemboss.server.JembossServer
 
setAntiAlias(boolean) - 
Method in class org.emboss.jemboss.editor.PrintAlignmentImage
 
setAppTitle(String, JPanel) - 
Method in class org.emboss.jemboss.gui.form.SectionPanel
Set the application title panel
setAttribute(String) - 
Method in class org.emboss.jemboss.parser.acd.ApplicationParam
Set the attribute/parameter type
setAutoUpdate(boolean) - 
Method in class org.emboss.jemboss.soap.PendingResults
Automatically updating status manager with
 BatchUpdateTimer thread
setBegSeq(int) - 
Method in class org.emboss.jemboss.gui.sequenceChooser.InputSequenceAttributes
Set the -sbegin flag
setBegSeq(String) - 
Method in class org.emboss.jemboss.gui.sequenceChooser.InputSequenceAttributes
Set the -sbegin flag
setBottomPanel() - 
Method in class org.emboss.jemboss.soap.AuthPopup
Buttons across the bottom
setBrowserSize() - 
Method in class org.emboss.jemboss.gui.Browser
Set the Jemboss web browser size
setCase(float) - 
Method in class org.emboss.jemboss.editor.ConsensusOptions
Set the minimum positive matches for a
 site to be made upper case in the consensus.
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.GraphicSequenceCollection
Set the colour scheme to use
setColorScheme(Hashtable) - 
Method in class org.emboss.jemboss.editor.SequenceJPanel
Set the colour scheme
setCurrentColour(Hashtable) - 
Method in class org.emboss.jemboss.editor.ColourJFrame
Set the colour scheme to display
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
Set a default colour scheme
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
Set the value of the expression
setDescription(String) - 
Method in class org.emboss.jemboss.programs.JembossProcess
Set the description of a project
setDisplayAcceleratorKey(boolean) - 
Static method in class org.emboss.jemboss.gui.form.MultiLineToolTipUI
 
setDrawBoxes(boolean) - 
Method in class org.emboss.jemboss.editor.GraphicSequenceCollection
Draw the boxes around the residues of each sequence
setDrawBoxes(boolean) - 
Method in class org.emboss.jemboss.editor.SequenceJPanel
Set whether to draw boxes around residues
setDrawColor(boolean) - 
Method in class org.emboss.jemboss.editor.GraphicSequenceCollection
Draw the residue colours in each sequence
setDrawColor(boolean) - 
Method in class org.emboss.jemboss.editor.SequenceJPanel
Set whether to colour residues
setEnableFileManagers(boolean) - 
Method in class org.emboss.jemboss.gui.SetUpMenuBar
Enable/disable file manager menu item
setEnableShowResults(boolean) - 
Method in class org.emboss.jemboss.gui.SetUpMenuBar
Enable/disable show results menu item
setEndSeq(int) - 
Method in class org.emboss.jemboss.gui.sequenceChooser.InputSequenceAttributes
Set the -send flag
setEndSeq(String) - 
Method in class org.emboss.jemboss.gui.sequenceChooser.InputSequenceAttributes
Set the -send flag
setErrStd() - 
Method in class org.emboss.jemboss.parser.Ajax
Clear the stderr
setExit() - 
Method in class org.emboss.jemboss.gui.filetree.LocalAndRemoteFileTreeFrame
Set the closing menu item to exit (for standalone
 file manager)
setFontSize(int) - 
Method in class org.emboss.jemboss.editor.SequenceJPanel
Set the font size and set the size
setFontSize(int) - 
Method in class org.emboss.jemboss.editor.SequenceNameJButton
Set the font size
setFontSizeForCollection(int) - 
Method in class org.emboss.jemboss.editor.GraphicSequenceCollection
Set the font size of the sequences in the editor
setForeground(Color) - 
Method in class org.emboss.jemboss.gui.sequenceChooser.FileChooser
Set the label colour
setFormat(PageFormat) - 
Method in class org.emboss.jemboss.editor.PrintAlignmentImage
Set the page format
setGraphic(GraphicSequenceCollection) - 
Method in class org.emboss.jemboss.editor.PatternJFrame
Set the graphic sequence panel
setGraphicSequenceCollection(GraphicSequenceCollection) - 
Method in class org.emboss.jemboss.editor.ConsensusOptions
Set the graphic sequence collection
setGraphicSequenceCollection(GraphicSequenceCollection) - 
Method in class org.emboss.jemboss.editor.PrettyPlotJFrame
Set the current graphic display
setGuiHandleNumber(String, ApplicationFields) - 
Method in class org.emboss.jemboss.parser.ParseAcd
Sets the gui handle depending on the data type.
setGuiHandleNumber(int) - 
Method in class org.emboss.jemboss.parser.acd.ApplicationFields
Set the gui handle
setIndent(int) - 
Method in class org.emboss.jemboss.editor.GroutSequence
Insert a residue into the sequence
setIndent(int) - 
Method in class org.emboss.jemboss.editor.GroutSequenceJPanel
indents the sequence by specifed amount
setIndents(Vector) - 
Method in class org.emboss.jemboss.editor.GroutAlignJFrame
Sets the indents to these values
setInterval(int) - 
Method in class org.emboss.jemboss.editor.PlotConsensus
Set the interval
setInterval(int) - 
Method in class org.emboss.jemboss.gui.SplashThread
 
setJMenuBar() - 
Method in class org.emboss.jemboss.gui.ShowResultSet
Set the menu bar based on the title of the
 tabbed pane
setJScrollPaneViewportView() - 
Method in class org.emboss.jemboss.editor.GraphicSequenceCollection
Force display in the viewport
setLastIndex(Object) - 
Method in class org.emboss.jemboss.gui.MemoryComboBox
Ensure order is changed
setLength(int) - 
Method in class org.emboss.jemboss.parser.Ajax
Sets the sequence length
setMatrix(Matrix) - 
Method in class org.emboss.jemboss.editor.AlignJFrame
Set the scoring matrix
setMatrix(Matrix) - 
Method in class org.emboss.jemboss.editor.ConsensusOptions
Set the matrix to use
setMatrix(Matrix) - 
Method in class org.emboss.jemboss.editor.GraphicSequenceCollection
 
setMatrix(Matrix) - 
Method in class org.emboss.jemboss.editor.MatrixJFrame
Set the matrix to display
setMaxSeqLength() - 
Method in class org.emboss.jemboss.editor.GraphicSequenceCollection
Calculate the longest sequence length
setMaxSequenceLength(int) - 
Method in class org.emboss.jemboss.editor.GraphicSequenceCollection
Set the longest sequence length
setNamePanelWidth(int) - 
Method in class org.emboss.jemboss.editor.GraphicSequenceCollection
Set the sequence name panel width
setNewSettings() - 
Method in class org.emboss.jemboss.soap.ServerSetup
Set the new settings in the server settings window
setNumberOfParam(int) - 
Method in class org.emboss.jemboss.parser.acd.ApplicationFields
Set the number of parmeters in this field
setNumberOfResiduesPerLine(int) - 
Method in class org.emboss.jemboss.editor.GraphicSequenceCollection
Set the number of residues per line to user setting
setNumberSize() - 
Method in class org.emboss.jemboss.editor.GraphicSequenceCollection
Set the size of the sequence number panel
setPageIndex(int) - 
Method in class org.emboss.jemboss.editor.PrintAlignmentImage
Set the page number to create an image of
setParam(int, String, String) - 
Method in class org.emboss.jemboss.parser.acd.ApplicationFields
Set the value of a parameter
setParam(int, String, double) - 
Method in class org.emboss.jemboss.parser.acd.ApplicationFields
Set the value of a parameter
setPlotSize() - 
Method in class org.emboss.jemboss.editor.PlotConsensus
Set the consensus plot preferred size using the
 graph dimensions
setPlurality(float) - 
Method in class org.emboss.jemboss.editor.ConsensusOptions
Set the minimum positive match score for a
 site to be included in the consensus.
setPopupMenuVisible(boolean) - 
Method in class org.emboss.jemboss.gui.startup.ProgList.HorizontalMenu
 
setPosition(int) - 
Method in class org.emboss.jemboss.editor.GroutAlignJFrame
Moves the view position to this point
setPosition(int) - 
Method in class org.emboss.jemboss.editor.GroutGraphicSequenceCollection
Moves the view position to this residue
setPreferredSize(Dimension) - 
Method in class org.emboss.jemboss.gui.sequenceChooser.FileChooser
Set the preferred size of the text field
setPrettyPlot(boolean, PrettyPlotJFrame) - 
Method in class org.emboss.jemboss.editor.GraphicSequenceCollection
Display the sequences as per emboss prettyplot colours
setPrettyPlot(boolean) - 
Method in class org.emboss.jemboss.editor.SequenceJPanel
Set prettyplot display
setPrivateSoapService(String) - 
Method in class org.emboss.jemboss.JembossParams
Set the name of the private soap service
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
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
Set the sequence length
setSequenceLock(boolean) - 
Method in class org.emboss.jemboss.editor.GraphicSequenceCollection
Lock/group the sequences
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
Set the shading or visibility of a component
setSize() - 
Method in class org.emboss.jemboss.editor.GroutGraphicSequenceCollection
 
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
Set the size of the text field
setTabs(int[]) - 
Method in class org.emboss.jemboss.gui.TabListCellRenderer
 
setText(String, String) - 
Method in class org.emboss.jemboss.gui.filetree.FileEditorDisplay
Set the text & style in the JTextPane.
setText(String) - 
Method in class org.emboss.jemboss.gui.sequenceChooser.CutNPasteTextArea
Set contents of the text area
setText(String) - 
Method in class org.emboss.jemboss.gui.sequenceChooser.FileChooser
Set the text field
setType(boolean) - 
Method in class org.emboss.jemboss.editor.Sequence
Set the sequence type
setURL(URL, String) - 
Method in class org.emboss.jemboss.gui.Browser
Set the URL in the browser
setUpJMenuBar(Vector) - 
Method in class org.emboss.jemboss.gui.Browser
Method to create the frames menu and tool bar.
setUserHome(String) - 
Method in class org.emboss.jemboss.JembossParams
Set the user home directory property
setValue(Object) - 
Method in class org.emboss.jemboss.gui.SwingWorker
Set the value produced by worker thread
setValue(double) - 
Method in class org.emboss.jemboss.gui.form.TextFieldFloat
 
setValue(int) - 
Method in class org.emboss.jemboss.gui.form.TextFieldInt
 
setValue(String) - 
Method in class org.emboss.jemboss.parser.acd.ApplicationParam
Set the parameter string value
setValue(double) - 
Method in class org.emboss.jemboss.parser.acd.ApplicationParam
Set the parameter number value
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.editor.Sequence
Set the sequence weight
setWeight(float) - 
Method in class org.emboss.jemboss.parser.Ajax
Sets the sequence weight
setupServerRedundancy() - 
Method in class org.emboss.jemboss.JembossParams
Initialize the server redundancy data.
showConsensusPlot(File, int) - 
Method in class org.emboss.jemboss.editor.GraphicSequenceCollection
Calculate and display the consensus plot
showConsensusPlot(Matrix, int) - 
Method in class org.emboss.jemboss.editor.GraphicSequenceCollection
Calculate and display the consensus plot
showFilePane(String, JembossParams) - 
Static method in class org.emboss.jemboss.gui.filetree.DragTree
Opens a JFrame with the file contents displayed.
showFilePane(String, JembossParams) - 
Static method in class org.emboss.jemboss.gui.filetree.RemoteDragTree
Opens a JFrame with the file contents displayed.
showLocalRemoteFile - 
Variable in class org.emboss.jemboss.gui.SetUpMenuBar
local and remote file manager menu item
showOptions(GraphicSequenceCollection, PageFormat) - 
Method in class org.emboss.jemboss.editor.PrintAlignment
Provide some options for the image created
showOptions(boolean) - 
Method in class org.emboss.jemboss.editor.PrintAlignmentImage
Provide some options for the image created
showPattern(String) - 
Method in class org.emboss.jemboss.editor.SequenceJPanel
Set pattern to high light
showPendingResults(JFrame) - 
Method in class org.emboss.jemboss.soap.PendingResults
Display the list of pending and completed batch results
 window
show_acd(String) - 
Method in class org.emboss.jemboss.server.JembossAuthServer
Retrieves the ACD file of an application.
show_acd(String) - 
Method in class org.emboss.jemboss.server.JembossServer
Retrieves the ACD file of an application.
show_db() - 
Method in class org.emboss.jemboss.server.JembossAuthServer
Returns the databases held on the server
show_db() - 
Method in class org.emboss.jemboss.server.JembossServer
Returns the databases held on the server
show_help(String) - 
Method in class org.emboss.jemboss.server.JembossAuthServer
Returns the help for an application as given by 'tfm'
show_help(String) - 
Method in class org.emboss.jemboss.server.JembossServer
Returns the help for an application as given by 'tfm'
show_saved_results(String, String, String, byte[]) - 
Method in class org.emboss.jemboss.server.JembossAuthServer
Returns the results for a saved project.
show_saved_results(String, String, String) - 
Method in class org.emboss.jemboss.server.JembossServer
Returns the results for a saved project.
show_saved_results(String, String) - 
Method in class org.emboss.jemboss.server.JembossServer
Returns the results for a saved project.
size - 
Variable in class org.emboss.jemboss.parser.Ajax
 
sizeColor - 
Static variable in class org.emboss.jemboss.editor.SequenceProperties
Tiny/Small/Large (Red=Tiny, Green=Small, Blue=Large)
soapService - 
Variable in class org.emboss.jemboss.JembossParams
service name
soapServiceName - 
Variable in class org.emboss.jemboss.JembossParams
property name for service name
source - 
Variable in class org.emboss.jemboss.editor.GroutAlignJFrameEvent
 
source - 
Variable in class org.emboss.jemboss.editor.GroutGraphicSequenceCollectionEvent
 
sp - 
Variable in class org.emboss.jemboss.gui.Browser
JSplitPane sp
sp - 
Variable in class org.emboss.jemboss.gui.ShowSavedResults
result data list panel
spLeft - 
Variable in class org.emboss.jemboss.gui.Browser
JList spLeft
splashThread - 
Variable in class org.emboss.jemboss.gui.BuildProgramMenu
thread for progress monitor on the login window
splashing - 
Variable in class org.emboss.jemboss.gui.BuildProgramMenu
login window
splashing - 
Variable in class org.emboss.jemboss.gui.SplashThread
 
splashp - 
Variable in class org.emboss.jemboss.soap.AuthPopup
splash panel
ss - 
Variable in class org.emboss.jemboss.gui.SetUpMenuBar
server settings
ss - 
Variable in class org.emboss.jemboss.gui.ShowSavedResults
scroll panel for result data
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.ResultList
 
status - 
Variable in class org.emboss.jemboss.programs.RunEmbossApplication
status of the process
status - 
Variable in class org.emboss.jemboss.programs.RunEmbossApplication2
process status
status - 
Variable in class org.emboss.jemboss.soap.GetHelp
 
status - 
Variable in class org.emboss.jemboss.soap.JembossRun
status of the request
status - 
Variable in class org.emboss.jemboss.soap.ShowDB
status
statusField - 
Static variable in class org.emboss.jemboss.editor.AlignJFrame
 
statusField - 
Variable in class org.emboss.jemboss.editor.PrintAlignmentImage
status field for print preview
statusField - 
Variable in class org.emboss.jemboss.gui.ShowSavedResults
status field
statusPanel(JFrame) - 
Method in class org.emboss.jemboss.soap.PendingResults
A panel to show the status of any jobs and to view them,
 and to set the mode.
statusmsg - 
Variable in class org.emboss.jemboss.programs.ResultList
 
statusmsg - 
Variable in class org.emboss.jemboss.soap.GetHelp
 
statusmsg - 
Variable in class org.emboss.jemboss.soap.JembossRun
status message
statusmsg - 
Variable in class org.emboss.jemboss.soap.ShowDB
status message
stderr - 
Variable in class org.emboss.jemboss.programs.RunEmbossApplication2
standard error
stderrh - 
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.RunEmbossApplication
standard out
stdout - 
Variable in class org.emboss.jemboss.programs.RunEmbossApplication2
standard out
stdouth - 
Variable in class org.emboss.jemboss.programs.RunEmbossApplication2
 
storeSeqList - 
Variable in class org.emboss.jemboss.gui.SequenceList
select to save the sequence list between sessions
sumscore - 
Variable in class org.emboss.jemboss.editor.PlotConsensus
sum of scores for each column
surfaceColor - 
Static variable in class org.emboss.jemboss.editor.SequenceProperties
Surface/Buried (Red=Surface, Blue=Buried)
svalue - 
Variable in class org.emboss.jemboss.parser.ParseAcd
string value of a parameter
svalue - 
Variable in class org.emboss.jemboss.parser.acd.ApplicationParam
parameter string value
swiss - 
Static variable in class org.emboss.jemboss.gui.sequenceChooser.SequenceFilter
 



T

TURQUOISE - 
Static variable in class org.emboss.jemboss.editor.SequenceProperties
TURQUOISE from EMBOSS data Ecolour.map
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
 
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.
This can be used to test the public server.
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
 or drag and dropping to
TextAreaSink() - 
Constructor for class org.emboss.jemboss.gui.sequenceChooser.TextAreaSink
 
TextFieldFloat - class org.emboss.jemboss.gui.form.TextFieldFloat.
JTextfield for float fields in the EMBOSS form
TextFieldFloat() - 
Constructor for 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
 
TextFieldInt - class org.emboss.jemboss.gui.form.TextFieldInt.
JTextfield for int fields in the EMBOSS form
TextFieldInt() - 
Constructor for 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
 
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
 
table - 
Variable in class org.emboss.jemboss.gui.SequenceList
drag and drop table containing the list of sequences
targets - 
Variable in class org.emboss.jemboss.editor.GroutAlignJFrame
 
targets - 
Variable in class org.emboss.jemboss.editor.GroutGraphicSequenceCollection
 
taylorColor - 
Static variable in class org.emboss.jemboss.editor.SequenceProperties
Taylor colour scheme, W.R.Taylor Protein 
            Eng vol.10,  7 pp743-746, 1997
testUpAndDown(int, Sequence) - 
Method in class org.emboss.jemboss.editor.GraphicSequenceCollection
 
textArea - 
Variable in class org.emboss.jemboss.programs.RunEmbossApplication2
 
textFloat - 
Variable in class org.emboss.jemboss.editor.PrettyPlotJFrame
field to define threshold for positive matches
textFloat - 
Variable in class org.emboss.jemboss.gui.form.BuildJembossForm
 
textFloat - 
Variable in class org.emboss.jemboss.gui.form.SectionPanel
float field sink
textInt - 
Variable in class org.emboss.jemboss.editor.PrettyPlotJFrame
field to define min number of identities
textInt - 
Variable in class org.emboss.jemboss.gui.form.BuildJembossForm
 
textInt - 
Variable in class org.emboss.jemboss.gui.form.SectionPanel
integer field sink
textf - 
Variable in class org.emboss.jemboss.gui.form.BuildJembossForm
 
textf - 
Variable in class org.emboss.jemboss.gui.form.SectionPanel
text field sink
thread - 
Variable in class org.emboss.jemboss.gui.SwingWorker.ThreadVar
 
thread - 
Variable in class org.emboss.jemboss.gui.SwingWorker
 
threadVar - 
Variable in class org.emboss.jemboss.gui.SwingWorker
 
time - 
Variable in class org.emboss.jemboss.gui.AdvancedOptions
times for job manager updates
timer - 
Static variable in class org.emboss.jemboss.programs.BatchUpdateTimer
timer
timer - 
Static variable in class org.emboss.jemboss.programs.ResultsUpdateTimer
timer
title - 
Variable in class org.emboss.jemboss.gui.ColumnData
 
tmproot - 
Variable in class org.emboss.jemboss.server.JembossAuthServer
SOAP results directory
tmproot - 
Variable in class org.emboss.jemboss.server.JembossServer
results directory
tmprootDir - 
Variable in class org.emboss.jemboss.server.JembossServer
results directory
toByteArr(char[]) - 
Static method in class org.emboss.jemboss.JembossParams
Return the password as byte array
toString() - 
Method in class org.emboss.jemboss.gui.filetree.FileNode
Returns the name of the file
toolBar - 
Variable in class org.emboss.jemboss.gui.ResultsMenuBar
tool bar
toolTipFontMetrics(Font) - 
Method in class org.emboss.jemboss.gui.form.MultiLineToolTipUI.MyToolTip
 
toolkit - 
Variable in class org.emboss.jemboss.gui.form.TextFieldFloat
 
toolkit - 
Variable in class org.emboss.jemboss.gui.form.TextFieldInt
 
topics - 
Variable in class org.emboss.jemboss.gui.Browser
Help topics
tree - 
Static variable in class org.emboss.jemboss.Jemboss
Local filemanager
trim(int, int) - 
Method in class org.emboss.jemboss.editor.Sequence
Trim a sequence
trim(String) - 
Static method in class org.emboss.jemboss.programs.ListFile
Given a list file @file or list::file return just the file name
type - 
Variable in class org.emboss.jemboss.parser.Dependent
parameter type



U

UFO - 
Variable in class org.emboss.jemboss.gui.sequenceChooser.InputSequenceAttributes
uniform feature object
UFO - 
Variable in class org.emboss.jemboss.gui.sequenceChooser.OutputSequenceAttributes
uniform feature object
ufield - 
Variable in class org.emboss.jemboss.soap.AuthPopup
username field
undo - 
Variable in class org.emboss.jemboss.gui.ResultsMenuBar
undo menu item
undoManager - 
Variable in class org.emboss.jemboss.gui.ResultsMenuBar
undo manager
uninstallUI(JComponent) - 
Method in class org.emboss.jemboss.gui.form.MultiLineToolTipUI
 
unselectedBorder - 
Variable in class org.emboss.jemboss.editor.ColourMenu
unselected border
unselectedBorder - 
Variable in class org.emboss.jemboss.gui.ColorMenu
 
update(int, int) - 
Method in class org.emboss.jemboss.editor.SequenceJPanel
Implement update() for observers i.e.
updateBeginEnd(String, String) - 
Method in class org.emboss.jemboss.gui.form.SectionPanel
Check sbeg and send values before updating in the
 panel to avoid overriding user selection
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
updateJembossProperty(String, String) - 
Method in class org.emboss.jemboss.JembossParams
Update the properties structure.
updateJobStats() - 
Method in class org.emboss.jemboss.soap.PendingResults
Update the number of completed and pending
 processes
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
Update the property settings for jembossSettings.
updateStatus() - 
Method in class org.emboss.jemboss.soap.PendingResults
Connect to the Jemboss server, and update the status of the jobs
 in the list.
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.
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, Hashtable, String) - 
Method in class org.emboss.jemboss.server.JembossServer
Used to provide information on the batch/background
 processes.
update_result_status(String, String, Hashtable) - 
Method in class org.emboss.jemboss.server.JembossServer
Used to provide information on the batch/background
 processes.
upper - 
Variable in class org.emboss.jemboss.gui.sequenceChooser.InputSequenceAttributes
select to specify upper case
urlField - 
Variable in class org.emboss.jemboss.gui.Browser
URL cache combo field
useAuth - 
Variable in class org.emboss.jemboss.JembossParams
use unix authentication to run applications on the server
useAuthName - 
Variable in class org.emboss.jemboss.JembossParams
property name for using unix authentication
useBrowserProxy - 
Variable in class org.emboss.jemboss.JembossParams
use a separate proxy for browsing the web
useBrowserProxy - 
Variable in class org.emboss.jemboss.soap.ServerSetup
selected if using proxy server for web browser
useBrowserProxyName - 
Variable in class org.emboss.jemboss.JembossParams
property name for using separate proxy for browsing the web
useExitMenu - 
Variable in class org.emboss.jemboss.editor.AlignJFrame
 
useHTTPSProxy - 
Variable in class org.emboss.jemboss.JembossParams
 
useHTTPSProxyName - 
Variable in class org.emboss.jemboss.JembossParams
 
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
selected if using proxy server
useProxyAuth - 
Variable in class org.emboss.jemboss.JembossParams
use proxy authentication
useProxyAuthName - 
Variable in class org.emboss.jemboss.JembossParams
property name for using proxy authentication
useProxyName - 
Variable in class org.emboss.jemboss.JembossParams
 
useTFM - 
Variable in class org.emboss.jemboss.JembossParams
 
useTFMName - 
Variable in class org.emboss.jemboss.JembossParams
 
userAuth(String, byte[], String) - 
Method in class org.emboss.jemboss.parser.Ajax
authentication method
userAuth - 
Variable in class org.emboss.jemboss.soap.ServerSetup
selected if user authetication required
userHome - 
Variable in class org.emboss.jemboss.JembossParams
user home directory
userHome - 
Variable in class org.emboss.jemboss.gui.AdvancedOptions
user home directory
userHomeName - 
Variable in class org.emboss.jemboss.JembossParams
property name for user home directory
userHomeSave() - 
Method in class org.emboss.jemboss.gui.AdvancedOptions
Save the user home/working directory to jemboss.properties
username - 
Variable in class org.emboss.jemboss.server.JembossServer
user name



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
vector containing directories
verifyUser(Ajax, String, byte[], Vector) - 
Method in class org.emboss.jemboss.server.JembossAuthServer
Verify the username/passwd
verifyUser(Ajax, String, byte[], Vector) - 
Method in class org.emboss.jemboss.server.JembossFileAuthServer
Verify the username/passwd
version() - 
Method in class org.emboss.jemboss.server.JembossServer
 
viewPane - 
Variable in class org.emboss.jemboss.editor.PlotConsensus
associated sequence panel
viewPane - 
Variable in class org.emboss.jemboss.editor.SequenceJPanel
sequence alignment panel
viewPaneResize() - 
Method in class org.emboss.jemboss.editor.SequenceJPanel
Re-size the sequence alignment panel if the width of 
 this sequence pane increases
viewResiduePosition - 
Variable in class org.emboss.jemboss.editor.PatternJFrame
residue position to display



W

WHEAT - 
Static variable in class org.emboss.jemboss.editor.SequenceProperties
WHEAT from EMBOSS data Ecolour.map
waitFor() - 
Method in class org.emboss.jemboss.programs.RunEmbossApplication2
Wait for the process to end
warnUser(String) - 
Method in class org.emboss.jemboss.gui.Browser
Display a warning message
weight - 
Static variable in class org.emboss.jemboss.parser.Ajax
sequence weight
weight - 
Variable in class org.emboss.jemboss.soap.CallAjax
sequence weight
weight_soap - 
Variable in class org.emboss.jemboss.parser.Ajax
sequence weight
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
 
windowClosing(WindowEvent) - 
Method in class org.emboss.jemboss.editor.GroutAlignJFrame.winExit
 
windowDeiconified(WindowEvent) - 
Method in class org.emboss.jemboss.editor.GroutAlignJFrame.winExit
 
windowOpened(WindowEvent) - 
Method in class org.emboss.jemboss.editor.GroutAlignJFrame.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.BuildJembossForm
 
withSoap - 
Variable in class org.emboss.jemboss.gui.form.SectionPanel
true if in client-server mode
wrapAround - 
Variable in class org.emboss.jemboss.editor.PatternJFrame
wrap around search check box
writeByteFile(String, String) - 
Method in class org.emboss.jemboss.JembossJarUtil
Write contents of an element in the hashtable
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
writeListFile(String) - 
Method in class org.emboss.jemboss.gui.form.ListFilePanel
 
writeListFile(String) - 
Method in class org.emboss.jemboss.gui.form.SetInFileCard
 
writeOK() - 
Method in class org.emboss.jemboss.gui.filetree.FileSave
Whether the fileSaving() operation was successful
writeOK() - 
Method in class org.emboss.jemboss.gui.filetree.FileSaving
 
writeObject(ObjectOutputStream) - 
Method in class org.emboss.jemboss.gui.SequenceData
 
writeObject(ObjectOutputStream) - 
Method in class org.emboss.jemboss.gui.filetree.FileNode
 
writeObject(ObjectOutputStream) - 
Method in class org.emboss.jemboss.gui.filetree.RemoteFileNode
 
writeObject(ObjectOutputStream) - 
Method in class org.emboss.jemboss.soap.FileRoots
 
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
sequence weight



X

x - 
Variable in class org.emboss.jemboss.JembossLogo
 
x - 
Variable in class org.emboss.jemboss.gui.form.ApplicationNamePanel
x position for displaying name
xsize - 
Variable in class org.emboss.jemboss.editor.ColourPanel
 



Y

YBox - 
Variable in class org.emboss.jemboss.editor.ColourJFrame
Container for the all the residue colour
y - 
Variable in class org.emboss.jemboss.JembossLogo
 
y - 
Variable in class org.emboss.jemboss.gui.form.ApplicationNamePanel
y position for displaying name
ymax - 
Variable in class org.emboss.jemboss.editor.PlotConsensus
maximum y value
ymin - 
Variable in class org.emboss.jemboss.editor.PlotConsensus
minimum y value
ypad - 
Variable in class org.emboss.jemboss.editor.SequenceJPanel
sequence height pad
ypad - 
Variable in class org.emboss.jemboss.editor.SequenceNameJButton
height pad
ysize - 
Variable in class org.emboss.jemboss.editor.ColourPanel
 


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