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

## <

() - Static method in class org.emboss.jemboss.parser.Ajax

## A

about() - Method in class org.emboss.jemboss.server.JembossServer
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.server.JembossServer
AcdFunResolve - class org.emboss.jemboss.parser.AcdFunResolve.
  This is a rewrite in Java of the expression functions in ajacd.c of the EMBOSS ajax library, written by Peter Rice.
acdFunResolve(String) - Method in class org.emboss.jemboss.parser.AcdFunResolve
  Looks for and resolves expressions
AcdFunResolve(String) - Constructor for class org.emboss.jemboss.parser.AcdFunResolve
AcdVariableResolve - class org.emboss.jemboss.parser.AcdVariableResolve.
  Resolves variable: references.
AcdVariableResolve(String, String, String) - Constructor for class org.emboss.jemboss.parser.AcdVariableResolve
AcdVarResolve - class org.emboss.jemboss.parser.AcdVarResolve.
  Resolves any variable reference in a string.
AcdVarResolve(String, String, String, ParseAcd, int, TextFieldSink[], TextFieldInt[], TextFieldFloat[], myComboPopup[], JCheckBox[]) - Constructor for class org.emboss.jemboss.parser.AcdVarResolve
actionPerformed(ActionEvent) - Method in class org.emboss.jemboss.Jemboss
  Action event to open the file manager
actionPerformed(ActionEvent) - Method in class org.emboss.jemboss.gui.form.BuildJembossForm
  Action events Exit, Help, GO, & Show results
add(String) - Method in class org.emboss.jemboss.gui.MemoryComboBox
addObject(String, String) - Method in class org.emboss.jemboss.gui.filetree.DragTree
  Adding a file (or directory) to the file tree manager.
addResult(JembossProcess) - Method in class org.emboss.jemboss.soap.PendingResults
AdvancedOptions - class org.emboss.jemboss.gui.AdvancedOptions.
AdvancedOptions() - Constructor for class org.emboss.jemboss.gui.AdvancedOptions
advSection - Static variable in class org.emboss.jemboss.gui.form.BuildJembossForm
Ajax - class org.emboss.jemboss.parser.Ajax.
  Used with JNI to EMBOSS ajax library to determine sequence attributes.
Ajax() - Constructor for class org.emboss.jemboss.parser.Ajax
ajaxLength - Static variable in class org.emboss.jemboss.gui.form.SectionPanel
ajaxProtein - Static variable in class org.emboss.jemboss.gui.form.SectionPanel
AjaxUtil - class org.emboss.jemboss.parser.AjaxUtil.
AjaxUtil() - Constructor for class org.emboss.jemboss.parser.AjaxUtil
ajaxWeight - Static variable in class org.emboss.jemboss.gui.form.SectionPanel
alignment - Variable in class org.emboss.jemboss.gui.ColumnData
Application - class org.emboss.jemboss.parser.acd.Application.
Application(String) - Constructor for class org.emboss.jemboss.parser.acd.Application
ApplicationFields - class org.emboss.jemboss.parser.acd.ApplicationFields.
ApplicationFields() - Constructor for class org.emboss.jemboss.parser.acd.ApplicationFields
ApplicationParam - class org.emboss.jemboss.parser.acd.ApplicationParam.
ApplicationParam(String, double) - Constructor for class org.emboss.jemboss.parser.acd.ApplicationParam
ApplicationParam(String, String) - Constructor for class org.emboss.jemboss.parser.acd.ApplicationParam
appversion() - Method in class org.emboss.jemboss.server.JembossServer
attach(int, JPanel, Box) - Method in class org.emboss.jemboss.gui.form.BuildJembossForm
AuthPopup - class org.emboss.jemboss.soap.AuthPopup.
AuthPopup(EmbreoParams, int) - Constructor for class org.emboss.jemboss.soap.AuthPopup
  Called on startup to display the login and progress bar.
AuthPopup(EmbreoParams, JFrame) - Constructor for class org.emboss.jemboss.soap.AuthPopup
  Display a popup asking the user to enter their username and password

## B

BatchUpdateTimer - class org.emboss.jemboss.programs.BatchUpdateTimer.
  Simple demo that uses java.util.Timer to schedule a task to execute once 10 seconds have passed.
BatchUpdateTimer.RemindTask - class org.emboss.jemboss.programs.BatchUpdateTimer.RemindTask.
BatchUpdateTimer.RemindTask(BatchUpdateTimer) - Constructor for class org.emboss.jemboss.programs.BatchUpdateTimer.RemindTask
BatchUpdateTimer(int) - Constructor for class org.emboss.jemboss.programs.BatchUpdateTimer
breakupLines(String) - Static method in class org.emboss.jemboss.gui.form.PlafMacros
BuildJembossForm - class org.emboss.jemboss.gui.form.BuildJembossForm.
  Responsible for displaying the graphical representation of the ACD EMBOSS files.
BuildJembossForm(int, String[], String[], String[], String[], String, String, String, boolean, JPanel, EmbreoParams, Hashtable, 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, JPanel, JPanel, JScrollPane, String, String[], EmbreoParams, boolean, String, String, JFrame, AuthPopup) - Constructor for class org.emboss.jemboss.gui.BuildProgramMenu

## C

call_ajax(String, String) - Method in class org.emboss.jemboss.server.JembossServer
  Uses JNI to calculate sequence attributes using EMBOSS library call.
CallAjax - class org.emboss.jemboss.soap.CallAjax.
CallAjax(String, String, EmbreoParams) - Constructor for class org.emboss.jemboss.soap.CallAjax
cbusy - Variable in class org.emboss.jemboss.gui.BuildProgramMenu
cbusy - Variable in class org.emboss.jemboss.gui.ResultsMenuBar
cbusy - Variable in class org.emboss.jemboss.gui.SequenceList
cbusy - Variable in class org.emboss.jemboss.gui.filetree.DragTree
cbusy - Variable in class org.emboss.jemboss.gui.filetree.FileSaving
cbusy - Variable in class org.emboss.jemboss.gui.filetree.RemoteDragTree
cbusy - Variable in class org.emboss.jemboss.gui.filetree.RemoteFileTreePanel
cbusy - Variable in class org.emboss.jemboss.soap.PendingResults
cdone - Variable in class org.emboss.jemboss.gui.BuildProgramMenu
cdone - Variable in class org.emboss.jemboss.gui.ResultsMenuBar
cdone - Variable in class org.emboss.jemboss.gui.SequenceList
cdone - Variable in class org.emboss.jemboss.gui.filetree.DragTree
cdone - Variable in class org.emboss.jemboss.gui.filetree.FileSaving
cdone - Variable in class org.emboss.jemboss.gui.filetree.RemoteDragTree
cdone - Variable in class org.emboss.jemboss.gui.filetree.RemoteFileTreePanel
cdone - Variable in class org.emboss.jemboss.soap.PendingResults
checkParameters(ParseAcd, int, Hashtable) - Method in class org.emboss.jemboss.gui.form.BuildJembossForm
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
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
complete() - Method in class org.emboss.jemboss.programs.JembossProcess
construct() - Method in class org.emboss.jemboss.gui.SwingWorker
  Compute the value to be returned by the `get` method.
createDefaultModel() - Method in class org.emboss.jemboss.gui.form.TextFieldFloat
createDefaultModel() - Method in class org.emboss.jemboss.gui.form.TextFieldInt
createPopup() - Method in class org.emboss.jemboss.gui.form.myComboPopup.myComboUI
createUI(JComponent) - Static method in class org.emboss.jemboss.gui.form.MultiLineToolTipUI
CutNPasteTextArea - class org.emboss.jemboss.gui.sequenceChooser.CutNPasteTextArea.
  Makes a cut-and-paste text area.
CutNPasteTextArea(Box, String) - Constructor for class org.emboss.jemboss.gui.sequenceChooser.CutNPasteTextArea
cwd - Static variable in class org.emboss.jemboss.gui.AdvancedOptions

## D

Database - class org.emboss.jemboss.gui.startup.Database.
  Parses the output from showdb to find the available databases
Database(String) - Constructor for class org.emboss.jemboss.gui.startup.Database
dataFlavor - Variable in class org.emboss.jemboss.gui.sequenceChooser.CutNPasteTextArea
defaultBorder - Static variable in class org.emboss.jemboss.gui.sequenceChooser.CutNPasteTextArea
delete_saved_results(String, String) - Method in class org.emboss.jemboss.server.JembossServer
  Private server Deletes a projects saved results.
delete_saved_results(String, String, String) - Method in class org.emboss.jemboss.server.JembossServer
  Private server Deletes a projects saved results.
deleteRow(int) - Method in class org.emboss.jemboss.gui.SequenceListTableModel
  Delete a row from the table
deleteTmp(File, String) - Method in class org.emboss.jemboss.gui.SetUpMenuBar
  Delete temporary files
Dependent - class org.emboss.jemboss.parser.Dependent.
Dependent(int, int, String, String) - Constructor for class org.emboss.jemboss.parser.Dependent
descriptionHash() - Method in class org.emboss.jemboss.soap.PendingResults
directory_shortls(String, String) - Method in class org.emboss.jemboss.server.JembossFileServer
DISPLAY_ACCELERATOR - Static variable in class org.emboss.jemboss.gui.form.MultiLineToolTipUI
displayAccelerator - Static variable in class org.emboss.jemboss.gui.form.MultiLineToolTipUI
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
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
doWrite() - Method in class org.emboss.jemboss.gui.filetree.FileSave
dragDropEnd(DragSourceDropEvent) - Method in class org.emboss.jemboss.gui.DragJTable
dragDropEnd(DragSourceDropEvent) - Method in class org.emboss.jemboss.gui.filetree.DragTree
dragDropEnd(DragSourceDropEvent) - Method in class org.emboss.jemboss.gui.filetree.RemoteDragTree
dragEnter(DragSourceDragEvent) - Method in class org.emboss.jemboss.gui.DragJTable
dragEnter(DragSourceDragEvent) - 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.DragJTable
dragEnter(DropTargetDragEvent) - Method in class org.emboss.jemboss.gui.filetree.DragTree
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(DragSourceEvent) - 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.DragJTable
dragExit(DropTargetEvent) - Method in class org.emboss.jemboss.gui.filetree.DragTree
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
DragJTable - class org.emboss.jemboss.gui.DragJTable.
DragJTable(SequenceListTableModel) - Constructor for class org.emboss.jemboss.gui.DragJTable
dragOver(DragSourceDragEvent) - Method in class org.emboss.jemboss.gui.DragJTable
dragOver(DragSourceDragEvent) - Method in class org.emboss.jemboss.gui.filetree.DragTree
dragOver(DragSourceDragEvent) - Method in class org.emboss.jemboss.gui.filetree.RemoteDragTree
dragOver(DropTargetDragEvent) - Method in class org.emboss.jemboss.gui.DragJTable
dragOver(DropTargetDragEvent) - Method in class org.emboss.jemboss.gui.filetree.DragTree
  When a suitable DataFlavor is offered over a remote file node the node is highlighted/selected and the drag accepted.
dragOver(DropTargetDragEvent) - Method in class org.emboss.jemboss.gui.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
DragTree - class org.emboss.jemboss.gui.filetree.DragTree.
  Creates a local file tree for Jemboss.
DragTree(File, JFrame, EmbreoParams) - Constructor for class org.emboss.jemboss.gui.filetree.DragTree
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(DragSourceDragEvent) - 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.DragJTable
dropActionChanged(DropTargetDragEvent) - Method in class org.emboss.jemboss.gui.filetree.DragTree
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
elements() - Method in class org.emboss.jemboss.soap.JembossRun
embl - Static variable in class org.emboss.jemboss.gui.sequenceChooser.SequenceFilter
embossBin - Variable in class org.emboss.jemboss.server.JembossServer
embossData - Variable in class org.emboss.jemboss.server.JembossServer
embossPath - Variable in class org.emboss.jemboss.server.JembossServer
embreo_roots() - Method in class org.emboss.jemboss.server.JembossFileServer
endBorder - Static variable in class org.emboss.jemboss.gui.form.TextFieldSink
explore() - Method in class org.emboss.jemboss.gui.filetree.RemoteFileNode
explore(Hashtable) - Method in class org.emboss.jemboss.gui.filetree.FileNode

## F

fasta - Static variable in class org.emboss.jemboss.gui.sequenceChooser.SequenceFilter
FileChooser - class org.emboss.jemboss.gui.sequenceChooser.FileChooser.
  Creates a JFileChooser and add it to the Box.
FileChooser(Box, String) - 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.PopupListener - class org.emboss.jemboss.gui.filetree.FileEditorDisplay.PopupListener.
FileEditorDisplay.PopupListener(FileEditorDisplay) - Constructor for class org.emboss.jemboss.gui.filetree.FileEditorDisplay.PopupListener
FileEditorDisplay(JFrame, String) - Constructor for class org.emboss.jemboss.gui.filetree.FileEditorDisplay
FileEditorDisplay(JFrame, String, Object) - Constructor for class org.emboss.jemboss.gui.filetree.FileEditorDisplay
FileEditorDisplay(String) - Constructor for class org.emboss.jemboss.gui.filetree.FileEditorDisplay
fileExists() - Method in class org.emboss.jemboss.gui.filetree.FileSave
FileNode - class org.emboss.jemboss.gui.filetree.FileNode.
FILENODE - Static variable in class org.emboss.jemboss.gui.filetree.FileNode
FileNode(File, Hashtable) - Constructor for class org.emboss.jemboss.gui.filetree.FileNode
FileSave - class org.emboss.jemboss.gui.filetree.FileSave.
FileSave(File) - Constructor for class org.emboss.jemboss.gui.filetree.FileSave
  Check if we can/want to save file to disk.
FileSaving - class org.emboss.jemboss.gui.filetree.FileSaving.
  Saves files
FileSaving(JTextPane, byte[]) - Constructor for class org.emboss.jemboss.gui.filetree.FileSaving
fileSaving(Object) - Method in class org.emboss.jemboss.gui.filetree.FileSave
filesForSoap(String, String, String, Hashtable) - Method in class org.emboss.jemboss.gui.form.BuildJembossForm
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
flavors - Static variable in class org.emboss.jemboss.gui.filetree.RemoteFileNode
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.

## G

g - Variable in class org.emboss.jemboss.gui.form.MultiLineToolTipUI
gcg - Static variable in class org.emboss.jemboss.gui.sequenceChooser.SequenceFilter
get_file(String, String) - Method in class org.emboss.jemboss.server.JembossFileServer
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
getAcceleratorString(JToolTip) - Method in class org.emboss.jemboss.gui.form.MultiLineToolTipUI
getAcdDirToParse() - Method in class org.emboss.jemboss.JembossParams
getacdStore() - Method in class org.emboss.jemboss.gui.form.BuildJembossForm
getAcdText() - Method in class org.emboss.jemboss.gui.form.BuildJembossForm
  Get the contents of an ACD file in the form of a String.
getAllowsChildren() - Method in class org.emboss.jemboss.gui.filetree.FileNode
getAllowsChildren() - Method in class org.emboss.jemboss.gui.filetree.RemoteFileNode
getAnIndex(String) - Method in class org.emboss.jemboss.gui.filetree.FileNode
getApplicationFields() - Method in class org.emboss.jemboss.parser.ParseAcd
  Gets the application field.
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
getBegSeq() - Method in class org.emboss.jemboss.gui.sequenceChooser.InputSequenceAttributes
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
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.
getCurrent() - Method in class org.emboss.jemboss.programs.ResultList
getCurrent() - Method in class org.emboss.jemboss.soap.PendingResults
  Gives which of the available datasets is currently being looked at by the gui
getCutNPasteText() - Method in class org.emboss.jemboss.gui.form.SetInFileCard
getDatabaseList() - Static method in class org.emboss.jemboss.gui.BuildProgramMenu
getDB() - Method in class org.emboss.jemboss.gui.startup.Database
getDBText() - Method in class org.emboss.jemboss.soap.GetWossname
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.
getDefaultSequenceName() - Method in class org.emboss.jemboss.gui.SequenceList
  Get the default Sequence name
getDependentExp() - Method in class org.emboss.jemboss.parser.Dependent
getDependentField() - Method in class org.emboss.jemboss.parser.Dependent
getDependentParam() - Method in class org.emboss.jemboss.parser.Dependent
getDependents() - Method in class org.emboss.jemboss.parser.ParseAcd
  Gets the dependents associated with the ACD.
getDependentType() - Method in class org.emboss.jemboss.parser.Dependent
getDescription() - Method in class org.emboss.jemboss.gui.sequenceChooser.SequenceFilter
getDescription() - Method in class org.emboss.jemboss.programs.JembossProcess
getDoc() - Method in class org.emboss.jemboss.parser.acd.Application
getEmbossBin() - Method in class org.emboss.jemboss.JembossParams
getEmbossData() - Method in class org.emboss.jemboss.JembossParams
getEmbossPath() - Method in class org.emboss.jemboss.JembossParams
getEndSeq() - Method in class org.emboss.jemboss.gui.sequenceChooser.InputSequenceAttributes
getExpectedCPU() - Method in class org.emboss.jemboss.parser.ParseAcd
  Finds any expected cpu level indicator (low, medium, high)
getExtension(File) - Static method in class org.emboss.jemboss.gui.sequenceChooser.SequenceFilter
getFieldNum() - Method in class org.emboss.jemboss.gui.form.SectionPanel
getFile() - Method in class org.emboss.jemboss.gui.filetree.FileNode
getFile() - Method in class org.emboss.jemboss.gui.filetree.RemoteFileNode
getFileChosen() - Method in class org.emboss.jemboss.gui.form.SetInFileCard
getFileChosen() - Method in class org.emboss.jemboss.gui.sequenceChooser.FileChooser
getFilename() - Method in class org.emboss.jemboss.gui.filetree.DragTree
getFilename() - Method in class org.emboss.jemboss.gui.filetree.RemoteDragTree
getFileName(int) - Method in class org.emboss.jemboss.gui.DragJTable
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.
getFormatChoosen() - Method in class org.emboss.jemboss.gui.sequenceChooser.InputSequenceAttributes
getFormatChoosen() - Method in class org.emboss.jemboss.gui.sequenceChooser.OutputSequenceAttributes
getFullName() - Method in class org.emboss.jemboss.gui.filetree.RemoteFileNode
getGroups() - Method in class org.emboss.jemboss.parser.ParseAcd
  Gets the list of groups defined by setGroups.
getGroups() - Method in class org.emboss.jemboss.parser.acd.Application
getGuiHandleNumber() - Method in class org.emboss.jemboss.parser.acd.ApplicationFields
getGuiHandleNumber(int) - Method in class org.emboss.jemboss.parser.ParseAcd
  Gets the handle for a gui component on the Jemboss form.
getHash() - Method in class org.emboss.jemboss.soap.PrivateRequest
getHelpParamValue(int) - Method in class org.emboss.jemboss.parser.ParseAcd
  Finds the help parameter in an ACD field.
getInCard() - Method in class org.emboss.jemboss.gui.form.SetInFileCard
getInfoParamValue(int) - Method in class org.emboss.jemboss.parser.ParseAcd
  Finds the prompt, info or help parameter in an ACD field, in that order.
getInputSeqAttr(int) - Method in class org.emboss.jemboss.gui.sequenceChooser.InputSequenceAttributes
getJFileChooser() - Method in class org.emboss.jemboss.gui.sequenceChooser.FileChooser
getJMenuBar() - Method in class org.emboss.jemboss.gui.ResultsMenuBar
getJob() - Method in class org.emboss.jemboss.programs.JembossProcess
getJScrollPane() - Method in class org.emboss.jemboss.gui.sequenceChooser.InputSequenceAttributes
getJScrollPane() - Method in class org.emboss.jemboss.gui.sequenceChooser.OutputSequenceAttributes
getJTextPane() - Method in class org.emboss.jemboss.gui.filetree.FileEditorDisplay
  Returns instance of JTextPane.
getLength() - Method in class org.emboss.jemboss.soap.CallAjax
getList(int) - Method in class org.emboss.jemboss.parser.ParseAcd
  Used for a list data type to put the list items in a String array.
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
getLocalFile(File) - Method in class org.emboss.jemboss.gui.filetree.RemoteDragTree
getMaximumSize(JComponent) - Method in class org.emboss.jemboss.gui.form.MultiLineToolTipUI
getMaxParam(int) - Method in class org.emboss.jemboss.parser.ParseAcd
  Locates the max parameter in a field and returns it as a String.
getMenuItems() - Method in class org.emboss.jemboss.gui.startup.ProgList
getMinimumSize(JComponent) - Method in class org.emboss.jemboss.gui.form.MultiLineToolTipUI
getMinParam(int) - Method in class org.emboss.jemboss.parser.ParseAcd
  Locates the min parameter in a field and returns it as a String.
getName() - Method in class org.emboss.jemboss.parser.acd.Application
getNodename() - Method in class org.emboss.jemboss.gui.filetree.DragTree
getNodename() - Method in class org.emboss.jemboss.gui.filetree.RemoteDragTree
getNumberMenuItems() - Method in class org.emboss.jemboss.gui.startup.ProgList
getNumberOfParam() - Method in class org.emboss.jemboss.parser.acd.ApplicationFields
getNumBool() - Method in class org.emboss.jemboss.parser.ParseAcd
  Gets the number of boolean data types in the ACD.
getNumList() - Method in class org.emboss.jemboss.parser.ParseAcd
  Gets the number of list & selection data types in the ACD, using single list selection
getNumMList() - Method in class org.emboss.jemboss.parser.ParseAcd
  Gets the number of list & selection data types in the ACD, using multiple list selection
getNumNfloat() - Method in class org.emboss.jemboss.parser.ParseAcd
  Gets the number of float data types in the ACD.
getNumNint() - Method in class org.emboss.jemboss.parser.ParseAcd
  Gets the number of int data types in the ACD.
getNumOfDependents() - Method in class org.emboss.jemboss.parser.ParseAcd
  Gets the number of dependent parameters in the ACD.
getNumofFields() - Method in class org.emboss.jemboss.parser.ParseAcd
  Gets the number of fields in the ACD file.
getNumofParams(int) - Method in class org.emboss.jemboss.parser.ParseAcd
  Gets the number of parameters in a ACD field.
getNumPrimaryGroups() - Method in class org.emboss.jemboss.gui.startup.ProgList
getNumProgs() - Method in class org.emboss.jemboss.gui.startup.ProgList
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.
getOuputSeqAttr() - Method in class org.emboss.jemboss.gui.sequenceChooser.OutputSequenceAttributes
getOutputSequenceFile(int) - Method in class org.emboss.jemboss.parser.ParseAcd
  Gets the name of the output sequence field (seqout).
getParamAttribute(int) - Method in class org.emboss.jemboss.parser.acd.ApplicationFields
getParameterAttribute(int, int) - Method in class org.emboss.jemboss.parser.ParseAcd
  Get a specified parameter attribute.
getParamValueDbl(int) - Method in class org.emboss.jemboss.parser.acd.ApplicationFields
getParamValueDbl(int, int) - Method in class org.emboss.jemboss.parser.ParseAcd
  Gets the double value of a parameter.
getParamValueStr(int) - Method in class org.emboss.jemboss.parser.acd.ApplicationFields
getParamValueStr(int, int) - Method in class org.emboss.jemboss.parser.ParseAcd
  Gets the String value of a parameter.
getPathName() - Method in class org.emboss.jemboss.gui.filetree.RemoteFileNode
getPlplot() - Method in class org.emboss.jemboss.JembossParams
getPNGByte(String) - Method in class org.emboss.jemboss.gui.form.BuildJembossForm
getPNGContent() - Method in class org.emboss.jemboss.gui.filetree.FileEditorDisplay
  Returns the content of a png file or null.
getPreferredSize(JComponent) - Method in class org.emboss.jemboss.gui.form.MultiLineToolTipUI
getPrimaryGroup() - Method in class org.emboss.jemboss.parser.ParseAcd
  Gets the primary groups the application is a member of.
getPrimaryGroups() - Method in class org.emboss.jemboss.gui.startup.ProgList
getProcess() - Method in class org.emboss.jemboss.programs.RunEmbossApplication
getProcessStdout() - Method in class org.emboss.jemboss.programs.RunEmbossApplication
getProgDescription() - Method in class org.emboss.jemboss.gui.startup.ProgList
getProgsList() - Method in class org.emboss.jemboss.gui.startup.ProgList
getProject() - Method in class org.emboss.jemboss.programs.JembossProcess
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
getResult() - Method in class org.emboss.jemboss.parser.AcdVariableResolve
getResult() - Method in class org.emboss.jemboss.soap.PrivateRequest
getResult(String) - Method in class org.emboss.jemboss.soap.PendingResults
getResults() - Method in class org.emboss.jemboss.programs.JembossProcess
getRootDir() - Method in class org.emboss.jemboss.gui.filetree.RemoteFileNode
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
getSecondaryGroup() - Method in class org.emboss.jemboss.parser.ParseAcd
  Gets the secondary groups the application is a member of.
getSectionBox() - Method in class org.emboss.jemboss.gui.form.SectionPanel
getSectionPanel() - Method in class org.emboss.jemboss.gui.form.SectionPanel
getSelect(int) - Method in class org.emboss.jemboss.parser.ParseAcd
  Used for a selection type to put the list items in a String array.
getSequence(int) - Method in class org.emboss.jemboss.gui.form.ListFilePanel
getSequence(int) - Method in class org.emboss.jemboss.gui.form.SetInFileCard
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.
getSequenceName() - Method in class org.emboss.jemboss.gui.SequenceData
  Returns the sequence name
getServerName() - Method in class org.emboss.jemboss.gui.filetree.RemoteFileNode
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.soap.CallAjax
getStatus() - Method in class org.emboss.jemboss.soap.GetWossname
getStatus() - Method in class org.emboss.jemboss.soap.JembossRun
  The status of the request
getStatus() - Method in class org.emboss.jemboss.soap.PendingResults
getStatusMsg() - Method in class org.emboss.jemboss.programs.ResultList
  A status message
getStatusMsg() - Method in class org.emboss.jemboss.soap.CallAjax
getStatusMsg() - Method in class org.emboss.jemboss.soap.GetWossname
getStatusMsg() - Method in class org.emboss.jemboss.soap.JembossRun
  A status message
getText() - Method in class org.emboss.jemboss.gui.sequenceChooser.CutNPasteTextArea
getTextFieldSink() - Method in class org.emboss.jemboss.gui.sequenceChooser.FileChooser
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
getTreeModel() - Method in class org.emboss.jemboss.gui.filetree.DragTree
getTreeModel() - Method in class org.emboss.jemboss.gui.filetree.RemoteDragTree
getVal(String) - Method in class org.emboss.jemboss.soap.PrivateRequest
  Gets an element out of the embreo result hash
getValue() - Method in class org.emboss.jemboss.gui.SwingWorker
  Get the value produced by the worker thread, or null if it hasn't been constructed yet.
getValue() - Method in class org.emboss.jemboss.gui.form.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
getValueStr() - Method in class org.emboss.jemboss.parser.acd.ApplicationParam
getWeight() - Method in class org.emboss.jemboss.soap.CallAjax
GetWossname - class org.emboss.jemboss.soap.GetWossname.
getWossname() - Method in class org.emboss.jemboss.server.JembossServer
  Returns the output of the EMBOSS utility wossname
GetWossname(EmbreoParams) - Constructor for class org.emboss.jemboss.soap.GetWossname

## H

hash() - Method in class org.emboss.jemboss.programs.ResultList
hash() - Method in class org.emboss.jemboss.soap.JembossRun
hasResults() - Method in class org.emboss.jemboss.programs.JembossProcess
helpurl() - Method in class org.emboss.jemboss.server.JembossServer
highlightBorder - Static variable in class org.emboss.jemboss.gui.sequenceChooser.CutNPasteTextArea

## I

initialize() - Static method in class org.emboss.jemboss.gui.form.MultiLineToolTipUI
initStylesForTextPane(JTextPane) - Method in class org.emboss.jemboss.gui.filetree.FileEditorDisplay
  Initialise styles for a JTextPane.
inpSection - Static variable in class org.emboss.jemboss.gui.form.BuildJembossForm
InputSequenceAttributes - class org.emboss.jemboss.gui.sequenceChooser.InputSequenceAttributes.
  Creates the input sequence attibutes window
InputSequenceAttributes(String[], FileChooser) - Constructor for class org.emboss.jemboss.gui.sequenceChooser.InputSequenceAttributes
insertData(SequenceListTableModel, Point, String, String, String, Boolean, Boolean, Boolean) - Method in class org.emboss.jemboss.gui.DragJTable
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
interrupt() - Method in class org.emboss.jemboss.gui.SwingWorker
  A new method that interrupts the worker thread.
isAdvancedSection() - Method in class org.emboss.jemboss.gui.form.SectionPanel
isAutoUpdate() - Method in class org.emboss.jemboss.soap.PendingResults
isBatchable() - Method in class org.emboss.jemboss.parser.ParseAcd
  Finds if the program is identifies as being able to run in a batch queue
isBeginSeqDefault() - Method in class org.emboss.jemboss.gui.sequenceChooser.InputSequenceAttributes
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
isCutNPase() - Method in class org.emboss.jemboss.gui.form.SetInFileCard
isDataFlavorSupported(DataFlavor) - Method in class org.emboss.jemboss.gui.SequenceData
isDataFlavorSupported(DataFlavor) - Method in class org.emboss.jemboss.gui.filetree.FileNode
isDataFlavorSupported(DataFlavor) - Method in class org.emboss.jemboss.gui.filetree.RemoteFileNode
isDBNameDefault() - Method in class org.emboss.jemboss.gui.sequenceChooser.InputSequenceAttributes
isDBNameDefault() - Method in class org.emboss.jemboss.gui.sequenceChooser.OutputSequenceAttributes
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.
isDirectory() - Method in class org.emboss.jemboss.gui.filetree.FileNode
isDirectory() - Method in class org.emboss.jemboss.gui.filetree.RemoteFileNode
isEndSeqDefault() - Method in class org.emboss.jemboss.gui.sequenceChooser.InputSequenceAttributes
isExplored() - Method in class org.emboss.jemboss.gui.filetree.FileNode
isExplored() - Method in class org.emboss.jemboss.gui.filetree.RemoteFileNode
isExtensionDefault() - Method in class org.emboss.jemboss.gui.sequenceChooser.OutputSequenceAttributes
isFileName() - Method in class org.emboss.jemboss.gui.form.SetInFileCard
isFileSelection() - Method in class org.emboss.jemboss.gui.filetree.DragTree
isFileSelection() - Method in class org.emboss.jemboss.gui.filetree.RemoteDragTree
isFNameDefault() - Method in class org.emboss.jemboss.gui.sequenceChooser.OutputSequenceAttributes
isInputSection() - Method in class org.emboss.jemboss.gui.form.SectionPanel
isLeaf() - Method in class org.emboss.jemboss.gui.filetree.FileNode
isLeaf() - Method in class org.emboss.jemboss.gui.filetree.RemoteFileNode
isListFile() - Method in class org.emboss.jemboss.gui.form.SetInFileCard
isListFile(int) - Method in class org.emboss.jemboss.gui.DragJTable
isMaxParamValue(int) - Method in class org.emboss.jemboss.parser.ParseAcd
  Determine if there is a max parameter in a field of the ACD.
isMinParamValue(int) - Method in class org.emboss.jemboss.parser.ParseAcd
  Determine if there is a min parameter in a field of the ACD.
isNameDefault() - Method in class org.emboss.jemboss.gui.sequenceChooser.OutputSequenceAttributes
isOpenFileDefault() - Method in class org.emboss.jemboss.gui.sequenceChooser.InputSequenceAttributes
isOptionalParam() - Method in class org.emboss.jemboss.parser.ParseAcd
  Determine if there is a optional parameter in any field of the ACD.
isOptionalParamValue(int) - Method in class org.emboss.jemboss.parser.ParseAcd
  Determine if there is a optional parameter in a field of the ACD.
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.
isParamValueStr(int) - Method in class org.emboss.jemboss.parser.acd.ApplicationFields
isParamValueStr(int, int) - Method in class org.emboss.jemboss.parser.ParseAcd
  Determine if the value of the parameter is a String.
isParamValueString() - Method in class org.emboss.jemboss.parser.acd.ApplicationParam
isPrimaryGroup() - Method in class org.emboss.jemboss.parser.ParseAcd
  True if a primary group is defined.
isProcessStdout() - Method in class org.emboss.jemboss.programs.RunEmbossApplication
isProtein() - Method in class org.emboss.jemboss.soap.CallAjax
isRequiredSection() - Method in class org.emboss.jemboss.gui.form.SectionPanel
isRunning() - Method in class org.emboss.jemboss.programs.JembossProcess
isSecondaryGroup() - Method in class org.emboss.jemboss.parser.ParseAcd
  True if a secondary group is defined.
isSIDDefault() - Method in class org.emboss.jemboss.gui.sequenceChooser.InputSequenceAttributes
isStoreSequenceList() - Method in class org.emboss.jemboss.gui.SequenceList
  Determines if a sequence list has been stored ("~/.jembossSeqList")
isUFODefault() - Method in class org.emboss.jemboss.gui.sequenceChooser.InputSequenceAttributes
isUFODefault() - Method in class org.emboss.jemboss.gui.sequenceChooser.OutputSequenceAttributes

## J

jdim - Static variable in class org.emboss.jemboss.Jemboss
  Jemboss window dimension
jdimExtend - Static variable in class org.emboss.jemboss.Jemboss
Jemboss - class org.emboss.jemboss.Jemboss.
  Java interface to EMBOSS (http://www.emboss.org/) (i) standalone - with a locally installation of EMBOSS.
Jemboss.winExit - class org.emboss.jemboss.Jemboss.winExit.
  Extends WindowAdapter to close window
Jemboss.winExit(Jemboss) - Constructor for class org.emboss.jemboss.Jemboss.winExit
Jemboss() - Constructor for class org.emboss.jemboss.Jemboss
JembossFileServer - class org.emboss.jemboss.server.JembossFileServer.
JembossFileServer() - Constructor for class org.emboss.jemboss.server.JembossFileServer
JembossLogo - class org.emboss.jemboss.JembossLogo.
JembossLogo(int, int, int) - Constructor for class org.emboss.jemboss.JembossLogo
JembossParams - class org.emboss.jemboss.JembossParams.
JembossParams() - Constructor for class org.emboss.jemboss.JembossParams
JembossProcess - class org.emboss.jemboss.programs.JembossProcess.
JembossProcess(String) - Constructor for class org.emboss.jemboss.programs.JembossProcess
JembossProcess(String, String) - Constructor for class org.emboss.jemboss.programs.JembossProcess
JembossProcess(String, String, String) - Constructor for class org.emboss.jemboss.programs.JembossProcess
JembossRun - class org.emboss.jemboss.soap.JembossRun.
JembossRun(String, String, Hashtable, EmbreoParams) - Constructor for class org.emboss.jemboss.soap.JembossRun
  Executes an application on a server
JembossServer - class org.emboss.jemboss.server.JembossServer.
  Jemboss Server for SOAP
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.
JembossThread(Process, String) - Constructor for class org.emboss.jemboss.server.JembossThread
jobMgr - Static variable in class org.emboss.jemboss.gui.AdvancedOptions
jobStatus() - Method in class org.emboss.jemboss.soap.PendingResults
jp - Variable in class org.emboss.jemboss.server.JembossServer

## K

keys() - Method in class org.emboss.jemboss.programs.ResultList
keys() - Method in class org.emboss.jemboss.soap.JembossRun

## L

labelColor - Static variable in class org.emboss.jemboss.gui.form.SectionPanel
labfont - Static variable in class org.emboss.jemboss.gui.form.SectionPanel
labfont2 - Static variable in class org.emboss.jemboss.gui.form.SectionPanel
LaunchJalView - class org.emboss.jemboss.gui.LaunchJalView.
LaunchJalView() - Constructor for class org.emboss.jemboss.gui.LaunchJalView
length - Static variable in class org.emboss.jemboss.parser.Ajax
  sequence length
list_saved_results() - Method in class org.emboss.jemboss.server.JembossServer
  Private Server List of the saved results on the server.
list_saved_results(String) - Method in class org.emboss.jemboss.server.JembossServer
  Private Server List of the saved results on the server.
ListFile - class org.emboss.jemboss.programs.ListFile.
ListFile() - Constructor for class org.emboss.jemboss.programs.ListFile
ListFilePanel - class org.emboss.jemboss.gui.form.ListFilePanel.
ListFilePanel(int) - Constructor for class org.emboss.jemboss.gui.form.ListFilePanel
loadStoredSeqList(File) - Method in class org.emboss.jemboss.gui.SequenceListTableModel
  Load from stored file the SequenceList created from a previous session.

## M

mailServer - Static variable in class org.emboss.jemboss.gui.AdvancedOptions
main(String[]) - Static method in class org.emboss.jemboss.Jemboss
  Launches Jemboss in standalone or client-server mode.
MAX_MEM_LEN - Static variable in class org.emboss.jemboss.gui.MemoryComboBox
MemoryComboBox - class org.emboss.jemboss.gui.MemoryComboBox.
MemoryComboBox(Vector) - Constructor for class org.emboss.jemboss.gui.MemoryComboBox
model - Static variable in class org.emboss.jemboss.gui.filetree.DragTree
model - Static variable in class org.emboss.jemboss.gui.filetree.RemoteDragTree
modelColumns - Static variable in class org.emboss.jemboss.gui.SequenceListTableModel
modelVector - Static variable in class org.emboss.jemboss.gui.SequenceListTableModel
mousePressed(MouseEvent) - Method in class org.emboss.jemboss.gui.filetree.FileEditorDisplay.PopupListener
mouseReleased(MouseEvent) - Method in class org.emboss.jemboss.gui.filetree.FileEditorDisplay.PopupListener
msf - Static variable in class org.emboss.jemboss.gui.sequenceChooser.SequenceFilter
MultiLineToolTipUI - class org.emboss.jemboss.gui.form.MultiLineToolTipUI.
myComboPopup - class org.emboss.jemboss.gui.form.myComboPopup.
myComboPopup.myComboUI - class org.emboss.jemboss.gui.form.myComboPopup.myComboUI.
  Create scroller
myComboPopup.myComboUI(myComboPopup) - Constructor for class org.emboss.jemboss.gui.form.myComboPopup.myComboUI
myComboPopup(Object[]) - Constructor for class org.emboss.jemboss.gui.form.myComboPopup
  Creates a JComboBox that contains the elements in the specified array.
mysettings - Static variable in class org.emboss.jemboss.Jemboss
  SOAP settings

## N

name() - Method in class org.emboss.jemboss.server.JembossServer
newRoot(String) - Method in class org.emboss.jemboss.gui.filetree.DragTree
numCompleted() - Method in class org.emboss.jemboss.soap.PendingResults
numRunning() - Method in class org.emboss.jemboss.soap.PendingResults

## 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
outSection - Static variable in class org.emboss.jemboss.gui.form.BuildJembossForm
outSeqAttr - Static variable in class org.emboss.jemboss.gui.form.BuildJembossForm

## P

p - Variable in class org.emboss.jemboss.server.JembossThread
paint(Graphics) - Method in class org.emboss.jemboss.gui.form.Separator
paint(Graphics, JComponent) - Method in class org.emboss.jemboss.gui.form.MultiLineToolTipUI
paintComponent(Graphics) - Method in class org.emboss.jemboss.JembossLogo
parse(String, Hashtable) - Static method in class org.emboss.jemboss.programs.ListFile
  Parse a list file, reading it in line by line, loading other list files recursively if necessary, and loading any files referred to into the filesToMove hash
ParseAcd - class org.emboss.jemboss.parser.ParseAcd.
  ACD (Ajax command line definition) file parser.
ParseAcd(String, boolean) - Constructor for class org.emboss.jemboss.parser.ParseAcd
  The constructor takes the ACD as a string.
parseParam(BufferedReader, StreamTokenizer) - Method in class org.emboss.jemboss.parser.ParseAcd
  Parses each parameter in a field
pasteText() - Method in class org.emboss.jemboss.gui.form.TextFieldSink
pasteText() - Method in class org.emboss.jemboss.gui.sequenceChooser.TextAreaSink
PendingResults - class org.emboss.jemboss.soap.PendingResults.
PendingResults(EmbreoParams) - Constructor for class org.emboss.jemboss.soap.PendingResults
PlafMacros - class org.emboss.jemboss.gui.form.PlafMacros.
PlafMacros() - Constructor for class org.emboss.jemboss.gui.form.PlafMacros
plplot - Variable in class org.emboss.jemboss.server.JembossServer
prefjni - Static variable in class org.emboss.jemboss.gui.AdvancedOptions
prefShadeGUI - Static variable in class org.emboss.jemboss.gui.AdvancedOptions
PrivateRequest - class org.emboss.jemboss.soap.PrivateRequest.
PrivateRequest(EmbreoParams, String, String) - Constructor for class org.emboss.jemboss.soap.PrivateRequest
  Make a soap call to a private server
PrivateRequest(EmbreoParams, String, String, Vector) - Constructor for class org.emboss.jemboss.soap.PrivateRequest
  Make a soap call to a private server
PrivateRequest(EmbreoParams, String, Vector) - Constructor for class org.emboss.jemboss.soap.PrivateRequest
  Make a soap call to a private server, using the default service
ProgList - class org.emboss.jemboss.gui.startup.ProgList.
ProgList.HorizontalMenu - class org.emboss.jemboss.gui.startup.ProgList.HorizontalMenu.
ProgList.HorizontalMenu(ProgList, String) - Constructor for class org.emboss.jemboss.gui.startup.ProgList.HorizontalMenu
ProgList(String, String, JMenuBar) - Constructor for class org.emboss.jemboss.gui.startup.ProgList
progressBar - Variable in class org.emboss.jemboss.soap.AuthPopup
progressLabel - Variable in class org.emboss.jemboss.soap.AuthPopup
project - Variable in class org.emboss.jemboss.server.JembossThread
protein - Static variable in class org.emboss.jemboss.parser.Ajax
  true if the sequence is protein
put_file(String, String, byte[]) - Method in class org.emboss.jemboss.server.JembossFileServer

## R

raisedBorder - Static variable in class org.emboss.jemboss.gui.startup.ProgList
RemoteDragTree - class org.emboss.jemboss.gui.filetree.RemoteDragTree.
  Creates a remote file tree which is a drag source & sink
RemoteDragTree(EmbreoParams, EmbreoFileRoots, JPanel) - Constructor for class org.emboss.jemboss.gui.filetree.RemoteDragTree
RemoteFileNode - class org.emboss.jemboss.gui.filetree.RemoteFileNode.
REMOTEFILENODE - Static variable in class org.emboss.jemboss.gui.filetree.RemoteFileNode
RemoteFileNode(EmbreoParams, EmbreoFileRoots, String, EmbreoFileList, String) - Constructor for class org.emboss.jemboss.gui.filetree.RemoteFileNode
RemoteFileTreePanel - class org.emboss.jemboss.gui.filetree.RemoteFileTreePanel.
RemoteFileTreePanel(EmbreoParams) - Constructor for class org.emboss.jemboss.gui.filetree.RemoteFileTreePanel
  Creates a panel to contain the directory trees on an embreo server.
removeResult(JembossProcess) - Method in class org.emboss.jemboss.soap.PendingResults
reqdSection - Static variable in class org.emboss.jemboss.gui.form.BuildJembossForm
reset(double) - Method in class org.emboss.jemboss.parser.acd.ApplicationParam
reset(String) - Method in class org.emboss.jemboss.parser.acd.ApplicationParam
resetCount() - Method in class org.emboss.jemboss.soap.PendingResults
resetParam(int, double) - Method in class org.emboss.jemboss.parser.acd.ApplicationFields
resetParam(int, String) - Method in class org.emboss.jemboss.parser.acd.ApplicationFields
result - Variable in class org.emboss.jemboss.parser.AcdFunResolve
  result as a String of the expression used in constructor
ResultList - class org.emboss.jemboss.programs.ResultList.
ResultList(EmbreoParams) - Constructor for class org.emboss.jemboss.programs.ResultList
  Holds the list of stored results
ResultList(EmbreoParams, String, String) - Constructor for class org.emboss.jemboss.programs.ResultList
  Manipulate a dataset.
resultsManager - Static variable in class org.emboss.jemboss.Jemboss
  to manage the pending results
ResultsMenuBar - class org.emboss.jemboss.gui.ResultsMenuBar.
  Sets up a results menu bar with save and close
ResultsMenuBar(JFrame) - Constructor for class org.emboss.jemboss.gui.ResultsMenuBar
  Sets up a results menu bar with save and close
ResultsMenuBar(JFrame, FileEditorDisplay) - Constructor for class org.emboss.jemboss.gui.ResultsMenuBar
  Adds action listener to save contents of a JTextPane.
ResultsMenuBar(JFrame, JTabbedPane, Hashtable) - 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.
  Simple demo that uses java.util.Timer to schedule a task to execute once 10 seconds have passed.
ResultsUpdateTimer.ResultsTask - class org.emboss.jemboss.programs.ResultsUpdateTimer.ResultsTask.
ResultsUpdateTimer.ResultsTask(ResultsUpdateTimer) - Constructor for class org.emboss.jemboss.programs.ResultsUpdateTimer.ResultsTask
ResultsUpdateTimer.ResultsTask(ResultsUpdateTimer, DefaultListModel, JFrame) - Constructor for class org.emboss.jemboss.programs.ResultsUpdateTimer.ResultsTask
ResultsUpdateTimer(int, DefaultListModel, JFrame) - Constructor for class org.emboss.jemboss.programs.ResultsUpdateTimer
run_prog(String, String, Hashtable) - Method in class org.emboss.jemboss.server.JembossServer
  Run an EMBOSS application
run_prog(String, String, Hashtable, String) - Method in class org.emboss.jemboss.server.JembossServer
  Run an EMBOSS application
run_prog(String, String, String[]) - Method in class org.emboss.jemboss.server.JembossServer
  Private Server Run an EMBOSS application
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.server.JembossThread
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

## S

s_beg - Variable in class org.emboss.jemboss.gui.SequenceData
  sequence start
s_default - Variable in class org.emboss.jemboss.gui.SequenceData
  use as the default
s_end - Variable in class org.emboss.jemboss.gui.SequenceData
  sequence end
s_listFile - Variable in class org.emboss.jemboss.gui.SequenceData
  sequence list file
s_name - Variable in class org.emboss.jemboss.gui.SequenceData
  sequence file/database
s_remote - Variable in class org.emboss.jemboss.gui.SequenceData
  file on remote file system
saveSequenceList() - Static method in class org.emboss.jemboss.gui.SetUpMenuBar
  Save the sequence list for a future session.
SectionPanel - class org.emboss.jemboss.gui.form.SectionPanel.
  Responsible for displaying the graphical representation of an ACD section.
SectionPanel(JFrame, JPanel, Box, ParseAcd, int, TextFieldSink[], TextFieldInt[], TextFieldFloat[], JTextField[], JCheckBox[], InputSequenceAttributes[], myComboPopup[], JList[], SetInFileCard[], String[], String, Box[], int, EmbreoParams, boolean) - Constructor for class org.emboss.jemboss.gui.form.SectionPanel
Separator - class org.emboss.jemboss.gui.form.Separator.
Separator(Dimension) - Constructor for class org.emboss.jemboss.gui.form.Separator
seqList - Static variable in class org.emboss.jemboss.gui.SetUpMenuBar
seqPaste - Variable in class org.emboss.jemboss.gui.sequenceChooser.CutNPasteTextArea
seqScroll - Variable in class org.emboss.jemboss.gui.sequenceChooser.CutNPasteTextArea
seqsetType(String) - Method in class org.emboss.jemboss.parser.Ajax
seqType(String) - Method in class org.emboss.jemboss.parser.Ajax
  determine sequence attributes
SequenceData - class org.emboss.jemboss.gui.SequenceData.
  Object to represent the content of each row in the DragJTable of a SequenceList.
SEQUENCEDATA - Static variable in class org.emboss.jemboss.gui.SequenceData
  dataflavor for drag and drop transfers
SequenceData() - Constructor for class org.emboss.jemboss.gui.SequenceData
SequenceData(String, String, String, Boolean, Boolean, Boolean) - Constructor for class org.emboss.jemboss.gui.SequenceData
SequenceFilter - class org.emboss.jemboss.gui.sequenceChooser.SequenceFilter.
SequenceFilter() - Constructor for class org.emboss.jemboss.gui.sequenceChooser.SequenceFilter
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, EmbreoParams) - Constructor for class org.emboss.jemboss.gui.SequenceList
SequenceListTableModel - class org.emboss.jemboss.gui.SequenceListTableModel.
SequenceListTableModel() - Constructor for class org.emboss.jemboss.gui.SequenceListTableModel
ServerSetup - class org.emboss.jemboss.soap.ServerSetup.
ServerSetup(EmbreoParams) - Constructor for class org.emboss.jemboss.soap.ServerSetup
  Setting for public and private settings panel.
servicedesc() - Method in class org.emboss.jemboss.server.JembossServer
setAttribute(String) - Method in class org.emboss.jemboss.parser.acd.ApplicationParam
setAutoUpdate(boolean) - Method in class org.emboss.jemboss.soap.PendingResults
setBegSeq(int) - Method in class org.emboss.jemboss.gui.sequenceChooser.InputSequenceAttributes
setBegSeq(String) - Method in class org.emboss.jemboss.gui.sequenceChooser.InputSequenceAttributes
setCurrent(String) - Method in class org.emboss.jemboss.programs.ResultList
  Save the name of a dataset, marking it as the current dataset
setCurrent(String) - Method in class org.emboss.jemboss.soap.PendingResults
  Save the name of a dataset, marking it as the current dataset
setDefaultData() - Method in class org.emboss.jemboss.gui.SequenceListTableModel
  Setup a blank square table
setDependentExp(String) - Method in class org.emboss.jemboss.parser.Dependent
setDescription(String) - Method in class org.emboss.jemboss.programs.JembossProcess
setDisplayAcceleratorKey(boolean) - Static method in class org.emboss.jemboss.gui.form.MultiLineToolTipUI
setDoc(String) - Method in class org.emboss.jemboss.parser.acd.Application
setEndSeq(int) - Method in class org.emboss.jemboss.gui.sequenceChooser.InputSequenceAttributes
setEndSeq(String) - Method in class org.emboss.jemboss.gui.sequenceChooser.InputSequenceAttributes
setForeground(Color) - Method in class org.emboss.jemboss.gui.sequenceChooser.FileChooser
setGroups(int) - Method in class org.emboss.jemboss.parser.ParseAcd
  Finds the primary and secondary groups, defined in the ACD file.
setGroups(String) - Method in class org.emboss.jemboss.parser.acd.Application
setGuiHandleNumber(int) - Method in class org.emboss.jemboss.parser.acd.ApplicationFields
SetInFileCard - class org.emboss.jemboss.gui.form.SetInFileCard.
SetInFileCard(JPanel, int, String[], String, String, InputSequenceAttributes[], boolean) - Constructor for class org.emboss.jemboss.gui.form.SetInFileCard
  Build the GUI components for an input sequence(s).
setLabelText(String, String) - Method in class org.emboss.jemboss.gui.form.SectionPanel
setLength(int) - Method in class org.emboss.jemboss.parser.Ajax
  Sets the sequence length
setName(String) - Method in class org.emboss.jemboss.parser.acd.Application
setNewSettings() - Method in class org.emboss.jemboss.soap.ServerSetup
setNumberOfParam(int) - Method in class org.emboss.jemboss.parser.acd.ApplicationFields
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
setParam(int, String, double) - Method in class org.emboss.jemboss.parser.acd.ApplicationFields
setParam(int, String, String) - Method in class org.emboss.jemboss.parser.acd.ApplicationFields
setParamValueStr(int, int, String) - Method in class org.emboss.jemboss.parser.ParseAcd
setPopupMenuVisible(boolean) - Method in class org.emboss.jemboss.gui.startup.ProgList.HorizontalMenu
setProtein(boolean) - Method in class org.emboss.jemboss.parser.Ajax
  Sets whether sequence is protein (true)
setResults(Hashtable) - Method in class org.emboss.jemboss.programs.JembossProcess
setSize(Dimension) - Method in class org.emboss.jemboss.gui.sequenceChooser.FileChooser
setText(String) - Method in class org.emboss.jemboss.gui.sequenceChooser.CutNPasteTextArea
setText(String) - Method in class org.emboss.jemboss.gui.sequenceChooser.FileChooser
setText(String, String, JTextPane) - Method in class org.emboss.jemboss.gui.filetree.FileEditorDisplay
  Set the text & style in the JTextPane.
SetUpMenuBar - class org.emboss.jemboss.gui.SetUpMenuBar.
  Sets the top menu bar for Jemboss main window
SetUpMenuBar(EmbreoParams, JFrame, String[], String, boolean) - Constructor for class org.emboss.jemboss.gui.SetUpMenuBar
setValue(double) - Method in class org.emboss.jemboss.gui.form.TextFieldFloat
setValue(double) - Method in class org.emboss.jemboss.parser.acd.ApplicationParam
setValue(int) - Method in class org.emboss.jemboss.gui.form.TextFieldInt
setValue(String) - Method in class org.emboss.jemboss.parser.acd.ApplicationParam
setValueAt(Object, int, int) - Method in class org.emboss.jemboss.gui.SequenceListTableModel
  Set the Object in a cell in the table
setWeight(float) - Method in class org.emboss.jemboss.parser.Ajax
  Sets the sequence weight
ShiftEast(int, int) - Method in class org.emboss.jemboss.JembossLogo
ShiftNorth(int, int) - Method in class org.emboss.jemboss.JembossLogo
ShiftSouth(int, int) - Method in class org.emboss.jemboss.JembossLogo
ShiftWest(int, int) - Method in class org.emboss.jemboss.JembossLogo
show_acd(String) - Method in class org.emboss.jemboss.server.JembossServer
  Retrieves the ACD file of an application.
show_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.JembossServer
  Returns the help for an application as given by 'tfm'
show_saved_results(String, String) - Method in class org.emboss.jemboss.server.JembossServer
  Private Server Returns the results for a saved project.
show_saved_results(String, String, String) - Method in class org.emboss.jemboss.server.JembossServer
  Private Server Returns the results for a saved project.
showFilePane(String) - Static method in class org.emboss.jemboss.gui.filetree.DragTree
  Opens a JFrame with the file contents displayed.
showFilePane(String) - Static method in class org.emboss.jemboss.gui.filetree.RemoteDragTree
  Opens a JFrame with the file contents displayed.
showPendingResults(JFrame) - Method in class org.emboss.jemboss.soap.PendingResults
ShowResultSet - class org.emboss.jemboss.gui.ShowResultSet.
  Displays JTabbedPane of the contents of the Hashtable
ShowResultSet(Hashtable) - Constructor for class org.emboss.jemboss.gui.ShowResultSet
ShowSavedResults - class org.emboss.jemboss.gui.ShowSavedResults.
  Shows a list of results from the SOAP server and displays individual result sets
ShowSavedResults(EmbreoParams, JFrame) - Constructor for class org.emboss.jemboss.gui.ShowSavedResults
  Show the saved results on the server.
ShowSavedResults(EmbreoParams, PendingResults) - Constructor for class org.emboss.jemboss.gui.ShowSavedResults
  Show the results sent to a batch queue.
ShowSavedResults(String) - Constructor for class org.emboss.jemboss.gui.ShowSavedResults
SINGLETON - Static variable in class org.emboss.jemboss.gui.form.MultiLineToolTipUI
start() - Method in class org.emboss.jemboss.gui.SwingWorker
  Start the worker thread.
startupFailed() - Method in class org.emboss.jemboss.soap.AuthPopup
  Called if something went wrong in startup.
statusHash() - Method in class org.emboss.jemboss.soap.PendingResults
statusPanel(JFrame) - Method in class org.emboss.jemboss.soap.PendingResults
  A panel with appropriate gadgets to show the status of any jobs and to view them, and to set the mode.
succeeded() - Method in class org.emboss.jemboss.soap.PrivateRequest
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.
swiss - Static variable in class org.emboss.jemboss.gui.sequenceChooser.SequenceFilter

## T

TextAreaSink - class org.emboss.jemboss.gui.sequenceChooser.TextAreaSink.
  Extends JTextArea so that is becomes a sink for pasting into.
TextAreaSink() - Constructor for class org.emboss.jemboss.gui.sequenceChooser.TextAreaSink
TextFieldFloat - class org.emboss.jemboss.gui.form.TextFieldFloat.
TextFieldFloat.DecimalNumberDocument - class org.emboss.jemboss.gui.form.TextFieldFloat.DecimalNumberDocument.
TextFieldFloat.DecimalNumberDocument(TextFieldFloat) - Constructor for class org.emboss.jemboss.gui.form.TextFieldFloat.DecimalNumberDocument
TextFieldFloat() - Constructor for class org.emboss.jemboss.gui.form.TextFieldFloat
TextFieldInt - class org.emboss.jemboss.gui.form.TextFieldInt.
TextFieldInt.WholeNumberDocument - class org.emboss.jemboss.gui.form.TextFieldInt.WholeNumberDocument.
TextFieldInt.WholeNumberDocument(TextFieldInt) - Constructor for class org.emboss.jemboss.gui.form.TextFieldInt.WholeNumberDocument
TextFieldInt() - Constructor for class org.emboss.jemboss.gui.form.TextFieldInt
TextFieldSink - class org.emboss.jemboss.gui.form.TextFieldSink.
  Extends JTextField to enable pasting & drag and drop into it.
TextFieldSink() - Constructor for class org.emboss.jemboss.gui.form.TextFieldSink
title - Variable in class org.emboss.jemboss.gui.ColumnData
toString() - Method in class org.emboss.jemboss.gui.filetree.FileNode
tree - Static variable in class org.emboss.jemboss.Jemboss

## U

uninstallUI(JComponent) - Method in class org.emboss.jemboss.gui.form.MultiLineToolTipUI
update_result_status(String, String, Hashtable) - Method in class org.emboss.jemboss.server.JembossServer
  Used to provide information on the batch/background processes.
update_result_status(String, String, Hashtable, String) - Method in class org.emboss.jemboss.server.JembossServer
  Used to provide information on the batch/background processes.
updateJobStats() - Method in class org.emboss.jemboss.soap.PendingResults
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
updateStatus() - Method in class org.emboss.jemboss.soap.PendingResults
  Connect to the embreo server, and update the status of the jobs in the list.

## V

version() - Method in class org.emboss.jemboss.server.JembossServer

## W

weight - Static 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
withSoap - Static variable in class org.emboss.jemboss.Jemboss
  true if in client-server mode (using SOAP)
writeList() - Method in class org.emboss.jemboss.gui.startup.ProgList
writeOK() - Method in class org.emboss.jemboss.gui.filetree.FileSave
  Whether the fileSaving() operation was successful

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