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

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() - 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
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
 
ajaxWeight - Static variable in class org.emboss.jemboss.gui.form.SectionPanel
 
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.SetUpMenuBar
 
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.SetUpMenuBar
 
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
 
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
Deletes a projects saved results.
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.JembossServer
 
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
doWrite() - Method in class org.emboss.jemboss.gui.filetree.FileSave
 
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.filetree.DragTree
 
dragEnter(DragSourceDragEvent) - Method in class org.emboss.jemboss.gui.filetree.RemoteDragTree
 
dragEnter(DropTargetDragEvent) - Method in class org.emboss.jemboss.gui.filetree.DragTree
 
dragEnter(DropTargetDragEvent) - Method in class org.emboss.jemboss.gui.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.filetree.DragTree
 
dragExit(DragSourceEvent) - Method in class org.emboss.jemboss.gui.filetree.RemoteDragTree
 
dragExit(DropTargetEvent) - Method in class org.emboss.jemboss.gui.filetree.DragTree
 
dragExit(DropTargetEvent) - Method in class org.emboss.jemboss.gui.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.filetree.DragTree
 
dragGestureRecognized(DragGestureEvent) - Method in class org.emboss.jemboss.gui.filetree.RemoteDragTree
 
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.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.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.filetree.DragTree
 
dropActionChanged(DragSourceDragEvent) - Method in class org.emboss.jemboss.gui.filetree.RemoteDragTree
 
dropActionChanged(DropTargetDragEvent) - Method in class org.emboss.jemboss.gui.filetree.DragTree
 
dropActionChanged(DropTargetDragEvent) - Method in class org.emboss.jemboss.gui.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.JembossServer
 
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.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() - 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
 
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
 
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.
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
 
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.
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
 
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
 
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.filetree.FileNode
 
getTransferData(DataFlavor) - Method in class org.emboss.jemboss.gui.filetree.RemoteFileNode
 
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
 
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
 
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
 
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.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
 
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
 
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
 
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.
HGMP 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
 
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
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
 

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.
model - Static variable in class org.emboss.jemboss.gui.filetree.DragTree
 
model - Static variable in class org.emboss.jemboss.gui.filetree.RemoteDragTree
 
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

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
 
protein - Static variable in class org.emboss.jemboss.parser.Ajax
true if the sequence is protein

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, String[]) - Method in class org.emboss.jemboss.server.JembossServer
Run an EMBOSS application
run() - Method in class org.emboss.jemboss.programs.BatchUpdateTimer.RemindTask
 
run() - Method in 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
 

S

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
 
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
SequenceFilter - class org.emboss.jemboss.gui.sequenceChooser.SequenceFilter.
 
SequenceFilter() - Constructor for class org.emboss.jemboss.gui.sequenceChooser.SequenceFilter
 
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
 
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
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
 
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
 
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.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
 
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
Returns the results for a saved project.
showFilePane(String) - Method in class org.emboss.jemboss.gui.filetree.DragTree
Opens a JFrame with the file contents displayed.
showFilePane(String) - 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
 
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
 
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
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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