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

A

AQUAMARINE - Static variable in class org.emboss.jemboss.editor.SequenceProperties

AQUAMARINE from EMBOSS data Ecolour.map

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

AutoScroll margin

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

AutoScroll margin

AcdFunResolve - class org.emboss.jemboss.parser.AcdFunResolve.

This is a rewrite in Java of the expression functions in ajacd.c of the EMBOSS ajax library, written by Peter Rice.

AcdFunResolve(String) - Constructor for class org.emboss.jemboss.parser.AcdFunResolve

AcdVarResolve - class org.emboss.jemboss.parser.AcdVarResolve.

Resolves any variable reference in a string.

AcdVarResolve(String, String, String, ParseAcd, int, TextFieldSink[], TextFieldInt[], TextFieldFloat[], JembossComboPopup[], JCheckBox[]) - Constructor for class org.emboss.jemboss.parser.AcdVarResolve

AcdVariableResolve - class org.emboss.jemboss.parser.AcdVariableResolve.

Resolves variable references.

AcdVariableResolve(String, String, String) - Constructor for class org.emboss.jemboss.parser.AcdVariableResolve

Given an expression this is searched for occurences of a variable name for which the value is known.

AdvancedOptions - class org.emboss.jemboss.gui.AdvancedOptions.

Jemboss advanced options and settings.

AdvancedOptions(JembossParams) - Constructor for class org.emboss.jemboss.gui.AdvancedOptions

Ajax - class org.emboss.jemboss.parser.Ajax.

Used with JNI to access EMBOSS ajax library.

Ajax() - Constructor for class org.emboss.jemboss.parser.Ajax

AjaxUtil - class org.emboss.jemboss.parser.AjaxUtil.

Utility to get the sequence file contents or the database entry ready to use in Ajax

AjaxUtil() - Constructor for class org.emboss.jemboss.parser.AjaxUtil

AlignApplet - class org.emboss.jemboss.editor.AlignApplet.

AlignApplet() - Constructor for class org.emboss.jemboss.editor.AlignApplet

AlignFormat - class org.emboss.jemboss.gui.form.AlignFormat.

Handles emboss alignment formats http://www.hgmp.mrc.ac.uk/Software/EMBOSS/Themes/AlignFormats.html

AlignFormat(ParseAcd, int) - Constructor for class org.emboss.jemboss.gui.form.AlignFormat

AlignFormat(String, boolean) - Constructor for class org.emboss.jemboss.gui.form.AlignFormat

AlignJFrame - class org.emboss.jemboss.editor.AlignJFrame.

Displays a grapical representation of a collection of sequences.

AlignJFrame(Vector) - Constructor for class org.emboss.jemboss.editor.AlignJFrame

AlignJFrame(File) - Constructor for class org.emboss.jemboss.editor.AlignJFrame

AlignJFrame(String, String) - Constructor for class org.emboss.jemboss.editor.AlignJFrame

AlignJFrame() - Constructor for class org.emboss.jemboss.editor.AlignJFrame

AlignJFrame(boolean) - Constructor for class org.emboss.jemboss.editor.AlignJFrame

AlignJFrame.winExit - class org.emboss.jemboss.editor.AlignJFrame.winExit.

Extends WindowAdapter to close window

AlignJFrame.winExit() - Constructor for class org.emboss.jemboss.editor.AlignJFrame.winExit

AppendToLogFileThread - class org.emboss.jemboss.server.AppendToLogFileThread.

Write to a log file in a separate thread

AppendToLogFileThread(String, String, boolean) - Constructor for class org.emboss.jemboss.server.AppendToLogFileThread

ApplicationFields - class org.emboss.jemboss.parser.acd.ApplicationFields.

Object for an field in the ACD file.

ApplicationFields() - Constructor for class org.emboss.jemboss.parser.acd.ApplicationFields

ApplicationNamePanel - class org.emboss.jemboss.gui.form.ApplicationNamePanel.

Panel to display the EMBOSS application name on

ApplicationNamePanel(String, int, int, int) - Constructor for class org.emboss.jemboss.gui.form.ApplicationNamePanel

ApplicationParam - class org.emboss.jemboss.parser.acd.ApplicationParam.

Object for a parameter of a field in the EMBOSS ACD file

ApplicationParam(String, String) - Constructor for class org.emboss.jemboss.parser.acd.ApplicationParam

ApplicationParam(String, double) - Constructor for class org.emboss.jemboss.parser.acd.ApplicationParam

AuthPopup - class org.emboss.jemboss.soap.AuthPopup.

Display a popup asking the user to enter a username and password

AuthPopup(JembossParams, JFrame) - Constructor for class org.emboss.jemboss.soap.AuthPopup

AuthPopup(JembossParams, int) - Constructor for class org.emboss.jemboss.soap.AuthPopup

Called on startup to display the login and progress bar.

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

aboutRes - Variable in class org.emboss.jemboss.gui.ShowSavedResults

text area for initial description of the saved results window and the run information of the results

aboutScroll - Variable in class org.emboss.jemboss.gui.ShowSavedResults

scrollpane for description of the results

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

accelerator_offset - Variable in class org.emboss.jemboss.gui.form.MultiLineToolTipUI

accept(File) - Method in class org.emboss.jemboss.gui.sequenceChooser.SequenceFilter

Accept all directories and all sequence files (*.fasta, *.msf, *.gcg, *.embl, *.swiss)

acdDirToParse - Variable in class org.emboss.jemboss.JembossParams

acd file location

acdDirToParse - Variable in class org.emboss.jemboss.server.JembossServer

acd directory

acdDirToParseName - Variable in class org.emboss.jemboss.JembossParams

property name for acd file location

acdExpAnd(String) - Method in class org.emboss.jemboss.parser.AcdFunResolve

Looks for and resolves an expression @( num & num )

acdExpCase(String) - Method in class org.emboss.jemboss.parser.AcdFunResolve

Looks for and resolves an expression as a switch/case statement @( var = casea : vala, caseb: valb else: val )

acdExpCond(String) - Method in class org.emboss.jemboss.parser.AcdFunResolve

Looks for and resolves an expression @( bool ? trueval : falseval )

acdExpDiv(String) - Method in class org.emboss.jemboss.parser.AcdFunResolve

Looks for and resolves an expression @( num * num )

acdExpEqual(String) - Method in class org.emboss.jemboss.parser.AcdFunResolve

Looks for and resolves an expression @( num == num )

acdExpGreater(String) - Method in class org.emboss.jemboss.parser.AcdFunResolve

Looks for and resolves an expression @( num > num )

acdExpLesser(String) - Method in class org.emboss.jemboss.parser.AcdFunResolve

Looks for and resolves an expression @( num < num )

acdExpMinus(String) - Method in class org.emboss.jemboss.parser.AcdFunResolve

Looks for and resolves an expression @( num - num )

acdExpNot(String) - Method in class org.emboss.jemboss.parser.AcdFunResolve

Looks for and resolves an expression @(! bool ) or @(NOT bool) or @(not bool).

acdExpNotEqual(String) - Method in class org.emboss.jemboss.parser.AcdFunResolve

Looks for and resolves an expression @( num != num )

acdExpOr(String) - Method in class org.emboss.jemboss.parser.AcdFunResolve

Looks for and resolves an expression @( num | num )

acdExpPlus(String) - Method in class org.emboss.jemboss.parser.AcdFunResolve

Looks for and resolves an expression @( num + num )

acdExpStar(String) - Method in class org.emboss.jemboss.parser.AcdFunResolve

Looks for and resolves an expression @( num * num )

acdFunResolve(String) - Method in class org.emboss.jemboss.parser.AcdFunResolve

Looks for and resolves expressions

acdStore - Variable in class org.emboss.jemboss.gui.BuildProgramMenu

acd files cache

acdStore - Static variable in class org.emboss.jemboss.soap.GetACD

acd store

acidColor - Static variable in class org.emboss.jemboss.editor.SequenceProperties

Acidic/Basic (Red=acidic, Blue=basic)

actionPerformed(ActionEvent) - Method in class org.emboss.jemboss.Jemboss

Action event to open the file manager

actionPerformed(ActionEvent) - Method in class org.emboss.jemboss.editor.ColourJFrame.ResidueColourPanel

Popup menu actions

actionPerformed(ActionEvent) - Method in class org.emboss.jemboss.editor.ColourPanel

Popup menu actions

actionPerformed(ActionEvent) - Method in class org.emboss.jemboss.editor.PrettyPlotJFrame

actionPerformed(ActionEvent) - Method in class org.emboss.jemboss.editor.SequenceJPanel

Override actionPerformed for popup menu actions

actionPerformed(ActionEvent) - Method in class org.emboss.jemboss.gui.Browser

Override actionPerformed

actionPerformed(ActionEvent) - Method in class org.emboss.jemboss.gui.ShowResultSet.GroutPanelListener

actionPerformed(ActionEvent) - Method in class org.emboss.jemboss.gui.filetree.DragTree

Popup menu actions

actionPerformed(ActionEvent) - Method in class org.emboss.jemboss.gui.filetree.RemoteDragTree

Popup menu actions

actionPerformed(ActionEvent) - Method in class org.emboss.jemboss.gui.form.BuildJembossForm

Action events Exit, Help, GO, & Show results

activeBorder - Variable in class org.emboss.jemboss.editor.ColourMenu

active border

activeBorder - Variable in class org.emboss.jemboss.gui.ColorMenu

addAnnotationSequence(Sequence) - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection

addBottomPanel() - Method in class org.emboss.jemboss.soap.AuthPopup

Buttons across the bottom

addEscapeChars(String) - Method in class org.emboss.jemboss.gui.AdvancedOptions

Add in escape chars (for windows) to the backslash chars

addFileToList(String, String, Hashtable) - Static method in class org.emboss.jemboss.programs.ListFile

Add a file to the list

addGroutAlignJFrameListener(GroutAlignJFrameListener) - Method in class org.emboss.jemboss.editor.GroutAlignJFrame

addGroutGraphicSequenceCollectionListener(GroutGraphicSequenceCollectionListener) - Method in class org.emboss.jemboss.editor.GroutGraphicSequenceCollection

addHashContentsToTab(Hashtable, JTabbedPane) - Method in class org.emboss.jemboss.gui.ShowResultSet

Add the contents of a hash table to the tabbed pane

addMenuItems() - Method in class org.emboss.jemboss.editor.GroutAlignJFrame

addObject(String, String, FileNode) - Method in class org.emboss.jemboss.gui.filetree.DragTree

Adding a file (or directory) to the file tree manager.

addObject(RemoteFileNode, String, boolean) - Method in class org.emboss.jemboss.gui.filetree.RemoteDragTree

Adding a file (or directory) to the file tree manager.

addResidue() - Method in class org.emboss.jemboss.editor.GroutGraphicSequenceCollection

addResult(JembossProcess) - Method in class org.emboss.jemboss.soap.PendingResults

Add a pending process to the list

addSection - Static variable in class org.emboss.jemboss.gui.form.BuildJembossForm

addSectionBox - Variable in class org.emboss.jemboss.gui.form.BuildJembossForm

addSequence(Sequence, boolean, int, int, int) - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection

Add a sequence at a particular index to the sequence collection display and to the collection of sequences (seqs) with a specified y-padding.

addSequence(Sequence, boolean, int, int) - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection

Add a sequence to the sequence collection display and to the collection of sequences (seqs) with a specified y-padding.

addSequence(Sequence, boolean, int, int, int) - Method in class org.emboss.jemboss.editor.GroutGraphicSequenceCollection

Add a sequence at a particular index to the sequence collection display and to the collection of sequences (seqs) with a specified y-padding.

addSequence(Sequence, boolean, int, int) - Method in class org.emboss.jemboss.editor.GroutGraphicSequenceCollection

Add a sequence to the sequence collection display and to the collection of sequences (seqs) with a specified y-padding.

addToScrollPane() - Method in class org.emboss.jemboss.gui.Browser

Add the html pane to a scrollpane, list and splitpane and set the size of the html pane

addURL(Object) - Method in class org.emboss.jemboss.gui.MemoryComboBox

Add an element to the combobox

addWindowCloser() - Method in class org.emboss.jemboss.editor.GroutAlignJFrame

when you close the window, should remove lines from Grout

adjustmentValueChanged(AdjustmentEvent) - Method in class org.emboss.jemboss.editor.GroutGraphicSequenceCollection

advSection - Static variable in class org.emboss.jemboss.gui.form.BuildJembossForm

advSectionBox - Variable in class org.emboss.jemboss.gui.form.BuildJembossForm

af - Variable in class org.emboss.jemboss.gui.form.BuildJembossForm

af - Variable in class org.emboss.jemboss.gui.form.SectionPanel

alignment format

ajaxLength - Static variable in class org.emboss.jemboss.gui.form.SectionPanel

sequence length

ajaxProtein - Static variable in class org.emboss.jemboss.gui.form.SectionPanel

sequence type

ajaxWeight - Static variable in class org.emboss.jemboss.gui.form.SectionPanel

sequence weight

align - Variable in class org.emboss.jemboss.editor.ColourJFrame

Associated alignment viewer

align_msf - Static variable in class org.emboss.jemboss.gui.form.AlignFormat

EMBOSS alignment formats

align_pairwise - Static variable in class org.emboss.jemboss.gui.form.AlignFormat

EMBOSS pairwise alignment formats

alignment - Variable in class org.emboss.jemboss.gui.ColumnData

allDescription - Variable in class org.emboss.jemboss.gui.startup.ProgList

array of program one line descriptions

allProgs - Variable in class org.emboss.jemboss.gui.startup.ProgList

array of the program names

antiAlias - Variable in class org.emboss.jemboss.editor.PrintAlignmentImage

use anti aliasing (default is false)

ao - Variable in class org.emboss.jemboss.gui.SetUpMenuBar

advanced options

appName - Variable in class org.emboss.jemboss.gui.form.SectionPanel

application name

appP - Variable in class org.emboss.jemboss.parser.acd.ApplicationFields

parameters for this field

appendToLogFile(String, String) - Method in class org.emboss.jemboss.server.JembossAuthServer

Appends a log entry to the log file

appendToSequence(String) - Method in class org.emboss.jemboss.editor.Sequence

Append to a sequence

applName - Variable in class org.emboss.jemboss.gui.form.BuildJembossForm

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

aromaticColor - Static variable in class org.emboss.jemboss.editor.SequenceProperties

Aromatic/Aliphatic (Red=Aromatic, Blue=Aliphatic)

attach(SequenceJPanel) - Method in class org.emboss.jemboss.editor.SequenceJPanel

Attach sequence display to the same group

attach(JPanel, Box, String) - Method in class org.emboss.jemboss.gui.form.BuildJembossForm

attr - Variable in class org.emboss.jemboss.parser.ParseAcd

parameter data type

attribute - Variable in class org.emboss.jemboss.parser.acd.ApplicationParam

parameter/attribute type

autoUpdates - Variable in class org.emboss.jemboss.soap.PendingResults

automatic job status updates

autoscroll(Point) - Method in class org.emboss.jemboss.gui.filetree.DragTree

Handles the auto scrolling of the JTree.

autoscroll(Point) - Method in class org.emboss.jemboss.gui.filetree.RemoteDragTree

Handles the auto scrolling of the JTree.

autoscrollInsets - Variable in class org.emboss.jemboss.gui.filetree.DragTree

used by AutoScroll method

autoscrollInsets - Variable in class org.emboss.jemboss.gui.filetree.RemoteDragTree

used by AutoScroll method

B

BLUEVIOLET - Static variable in class org.emboss.jemboss.editor.SequenceProperties

BLUEVIOLET from EMBOSS data Ecolour.map

BROWN - Static variable in class org.emboss.jemboss.editor.SequenceProperties

BROWN from EMBOSS data Ecolour.map

BatchUpdateTimer - class org.emboss.jemboss.programs.BatchUpdateTimer.

Timer for updating the Jemboss job manager for batch jobs submitted

BatchUpdateTimer(int) - Constructor for class org.emboss.jemboss.programs.BatchUpdateTimer

BatchUpdateTimer.RemindTask - class org.emboss.jemboss.programs.BatchUpdateTimer.RemindTask.

Timer task to update the Jemboss job manager

BatchUpdateTimer.RemindTask() - Constructor for class org.emboss.jemboss.programs.BatchUpdateTimer.RemindTask

Browser - class org.emboss.jemboss.gui.Browser.

Jemboss web browser

Browser(String, String, JembossParams) - Constructor for class org.emboss.jemboss.gui.Browser

Browser(String, String, boolean, String, JembossParams) - Constructor for class org.emboss.jemboss.gui.Browser

Browser(URL, String) - Constructor for class org.emboss.jemboss.gui.Browser

Browser.JIconButton - class org.emboss.jemboss.gui.Browser.JIconButton.

Jemboss icon button

Browser.JIconButton(ImageIcon) - Constructor for class org.emboss.jemboss.gui.Browser.JIconButton

BuildJembossForm - class org.emboss.jemboss.gui.form.BuildJembossForm.

Responsible for displaying the graphical representation of the ACD EMBOSS files.

BuildJembossForm(String, String[], String, String[], String, String, boolean, ScrollPanel, JembossParams, JFrame) - Constructor for class org.emboss.jemboss.gui.form.BuildJembossForm

BuildProgramMenu - class org.emboss.jemboss.gui.BuildProgramMenu.

BuildProgramMenu class construct the program menus.

BuildProgramMenu(JPanel, ScrollPanel, JPanel, JScrollPane, JembossParams, boolean, SetUpMenuBar, JFrame, Dimension) - Constructor for class org.emboss.jemboss.gui.BuildProgramMenu

backBt - Variable in class org.emboss.jemboss.gui.Browser

Back button option

backMenu - Variable in class org.emboss.jemboss.gui.Browser

Back menu option

baseColor - Static variable in class org.emboss.jemboss.editor.SequenceProperties

nucletide colour scheme

boundWidth - Variable in class org.emboss.jemboss.editor.SequenceJPanel

boundary width around each residue

boundWidth - Variable in class org.emboss.jemboss.editor.SequenceNameJButton

boundary width

boundWidth2 - Variable in class org.emboss.jemboss.editor.SequenceJPanel

half boundary width (boundWidth/2)

breakupLines(String) - Static method in class org.emboss.jemboss.gui.form.PlafMacros

Break text into separate lines

bresults - Variable in class org.emboss.jemboss.gui.form.BuildJembossForm

browserProxyHost - Variable in class org.emboss.jemboss.JembossParams

browser proxy host

browserProxyHostName - Variable in class org.emboss.jemboss.JembossParams

property name for browser proxy host

browserProxyPort - Variable in class org.emboss.jemboss.JembossParams

browser proxy port

browserProxyPortName - Variable in class org.emboss.jemboss.JembossParams

property name for browser proxy port

bwdArrow - Variable in class org.emboss.jemboss.Jemboss

Image for hiding the local filemanager

C

COL_BEG - Static variable in class org.emboss.jemboss.gui.SequenceListTableModel

COL_DEF - Static variable in class org.emboss.jemboss.gui.SequenceListTableModel

COL_END - Static variable in class org.emboss.jemboss.gui.SequenceListTableModel

COL_LIST - Static variable in class org.emboss.jemboss.gui.SequenceListTableModel

COL_NAME - Static variable in class org.emboss.jemboss.gui.SequenceListTableModel

CallAjax - class org.emboss.jemboss.soap.CallAjax.

Calls the EMBOSS ajax library

CallAjax(String, String, JembossParams) - Constructor for class org.emboss.jemboss.soap.CallAjax

ColorMenu - class org.emboss.jemboss.gui.ColorMenu.

Colour pallette menu

ColorMenu(String) - Constructor for class org.emboss.jemboss.gui.ColorMenu

ColorMenu.ColorPane - class org.emboss.jemboss.gui.ColorMenu.ColorPane.

ColorMenu.ColorPane(Color) - Constructor for class org.emboss.jemboss.gui.ColorMenu.ColorPane

ColourJFrame - class org.emboss.jemboss.editor.ColourJFrame.

Colour pallette display and editor.

ColourJFrame(AlignJFrame) - Constructor for class org.emboss.jemboss.editor.ColourJFrame

ColourJFrame.ResidueColourPanel - class org.emboss.jemboss.editor.ColourJFrame.ResidueColourPanel.

Colour panel for each individual residue in the pallette

ColourJFrame.ResidueColourPanel(String, Color) - Constructor for class org.emboss.jemboss.editor.ColourJFrame.ResidueColourPanel

ColourMenu - class org.emboss.jemboss.editor.ColourMenu.

Colour menu displayed in a popup menu from the colour display pallette (ColourJFrame).

ColourMenu(String) - Constructor for class org.emboss.jemboss.editor.ColourMenu

ColourMenu.ColorPane - class org.emboss.jemboss.editor.ColourMenu.ColorPane.

ColourMenu.ColorPane(Color) - Constructor for class org.emboss.jemboss.editor.ColourMenu.ColorPane

ColourPanel - class org.emboss.jemboss.editor.ColourPanel.

Colour panel for each individual residue in the pallette

ColourPanel(String, Color) - Constructor for class org.emboss.jemboss.editor.ColourPanel

ColourPanel.PopupListener - class org.emboss.jemboss.editor.ColourPanel.PopupListener.

Popup listener

ColourPanel.PopupListener() - Constructor for class org.emboss.jemboss.editor.ColourPanel.PopupListener

ColumnData - class org.emboss.jemboss.gui.ColumnData.

Content of each column in the DragJTable

ColumnData(String, int, int) - Constructor for class org.emboss.jemboss.gui.ColumnData

Consensus - class org.emboss.jemboss.editor.Consensus.

Calculate a consensus using the same method as 'cons' in the EMBOSS suite.

Consensus(File, Vector, float, float, int) - Constructor for class org.emboss.jemboss.editor.Consensus

Consensus(String, String, Vector, float, float, int) - Constructor for class org.emboss.jemboss.editor.Consensus

Consensus(Matrix, Vector, float, float, int) - Constructor for class org.emboss.jemboss.editor.Consensus

ConsensusOptions - class org.emboss.jemboss.editor.ConsensusOptions.

Defines the options to be used in calculating a consensus

ConsensusOptions(JScrollPane) - Constructor for class org.emboss.jemboss.editor.ConsensusOptions

CutNPasteTextArea - class org.emboss.jemboss.gui.sequenceChooser.CutNPasteTextArea.

Makes a cut-and-paste text area.

CutNPasteTextArea(Box, String) - Constructor for class org.emboss.jemboss.gui.sequenceChooser.CutNPasteTextArea

calculateCons(Matrix, Vector, float, float, int) - Method in class org.emboss.jemboss.editor.Consensus

Routine to calculate the consensus of a set of sequences

callTFM - Variable in class org.emboss.jemboss.soap.ServerSetup

selected if tfm help is run on the server

call_ajax(String, String, String, byte[]) - Method in class org.emboss.jemboss.server.JembossAuthServer

Uses JNI to calculate sequence attributes using EMBOSS library call.

call_ajax(String, String) - Method in class org.emboss.jemboss.server.JembossAuthServer

Uses JNI to calculate sequence attributes using EMBOSS library call.

call_ajax(String, String, String) - Method in class org.emboss.jemboss.server.JembossServer

Uses JNI to calculate sequence attributes using EMBOSS library call.

call_ajax(String, String) - Method in class org.emboss.jemboss.server.JembossServer

Uses JNI to calculate sequence attributes using EMBOSS library call.

canDo - Variable in class org.emboss.jemboss.gui.filetree.FileSave

true if it is possible to write to this file

caseFloat - Variable in class org.emboss.jemboss.editor.ConsensusOptions

set the case

cbusy - Variable in class org.emboss.jemboss.editor.AlignApplet

cbusy - Variable in class org.emboss.jemboss.editor.AlignJFrame

cbusy - Variable in class org.emboss.jemboss.editor.ConsensusOptions

cbusy - Variable in class org.emboss.jemboss.editor.MatrixJFrame

cursor busy

cbusy - Variable in class org.emboss.jemboss.gui.Browser

busy cursor

cbusy - Variable in class org.emboss.jemboss.gui.SequenceList

cbusy - Variable in class org.emboss.jemboss.gui.ShowSavedResults

busy cursor

cbusy - Variable in class org.emboss.jemboss.gui.filetree.DragTree

busy cursor

cbusy - Variable in class org.emboss.jemboss.gui.filetree.RemoteDragTree

busy cursor

cbusy - Variable in class org.emboss.jemboss.gui.filetree.RemoteFileTreePanel

busy cursor

cbusy - Variable in class org.emboss.jemboss.gui.form.BuildJembossForm

cdone - Variable in class org.emboss.jemboss.editor.AlignApplet

cdone - Variable in class org.emboss.jemboss.editor.AlignJFrame

cdone - Variable in class org.emboss.jemboss.editor.ConsensusOptions

cdone - Variable in class org.emboss.jemboss.editor.MatrixJFrame

cursor done

cdone - Variable in class org.emboss.jemboss.gui.Browser

done cursor

cdone - Variable in class org.emboss.jemboss.gui.SequenceList

cdone - Variable in class org.emboss.jemboss.gui.ShowSavedResults

done cursor

cdone - Variable in class org.emboss.jemboss.gui.filetree.DragTree

done cursor

cdone - Variable in class org.emboss.jemboss.gui.filetree.RemoteDragTree

done cursor

cdone - Variable in class org.emboss.jemboss.gui.filetree.RemoteFileTreePanel

done cursor

cdone - Variable in class org.emboss.jemboss.gui.form.BuildJembossForm

centreMarkerX - Variable in class org.emboss.jemboss.editor.GroutSequenceJPanel

chargeColor - Static variable in class org.emboss.jemboss.editor.SequenceProperties

Positive/Negative charge (Red=Positive, Blue=Negative)

checkBox - Variable in class org.emboss.jemboss.gui.form.BuildJembossForm

checkBox - Variable in class org.emboss.jemboss.gui.form.SectionPanel

boolean fields

checkDependents(Box, String[]) - Method in class org.emboss.jemboss.gui.form.SectionPanel

Checks for dependent variables and adds in action listeners

checkParameters(ParseAcd, int, Hashtable) - Method in class org.emboss.jemboss.gui.form.BuildJembossForm

clear() - Method in class org.emboss.jemboss.gui.SwingWorker.ThreadVar

clone() - Method in class org.emboss.jemboss.server.JembossAuthServer

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

cnp - Variable in class org.emboss.jemboss.editor.Paste

codons - Static variable in class org.emboss.jemboss.gui.BuildProgramMenu

codons usage tables

codons - Variable in class org.emboss.jemboss.soap.ShowDB

codon usage tables

col - Variable in class org.emboss.jemboss.editor.ColourMenu.ColorPane

col - Variable in class org.emboss.jemboss.editor.ColourPanel

col - Variable in class org.emboss.jemboss.editor.SequenceJPanel

col - Variable in class org.emboss.jemboss.gui.ColorMenu.ColorPane

colorScheme - Variable in class org.emboss.jemboss.editor.GraphicSequenceCollection

Colour scheme to use

colorTable - Variable in class org.emboss.jemboss.editor.SequenceJPanel

colour scheme

colourMenus(JMenu) - Method in class org.emboss.jemboss.editor.AlignJFrame

Constructs the colour menus

colourScheme(String) - Method in class org.emboss.jemboss.editor.AlignJFrame

Update the status bar with the selected colour scheme being used.

colourTable - Variable in class org.emboss.jemboss.editor.ColourJFrame

Colour scheme

complement(char) - Method in class org.emboss.jemboss.editor.Sequence

Complement a residue

complementSequence() - Method in class org.emboss.jemboss.editor.Sequence

Complement the sequence

complete() - Method in class org.emboss.jemboss.programs.JembossProcess

Called when a process has completed

completed - Variable in class org.emboss.jemboss.programs.JembossProcess

true when process is complete

completed_jobs - Variable in class org.emboss.jemboss.soap.PendingResults

number of completed processes

cons - Variable in class org.emboss.jemboss.editor.Consensus

cons - Variable in class org.emboss.jemboss.editor.Matrix

construct() - Method in class org.emboss.jemboss.gui.SwingWorker

Compute the value to be returned by the get method.

convertToOriginal(Object) - Method in class org.emboss.jemboss.gui.ShowSavedResults

Convert back to the original project names replace blank spaces with underscores ('_')

convertToPretty(String) - Static method in class org.emboss.jemboss.gui.ShowSavedResults

Convert the project names to remove the underscores ('_') with blank spaces

cp - Variable in class org.emboss.jemboss.gui.form.AlignFormat

component to display formats

cp - Variable in class org.emboss.jemboss.gui.form.ReportFormat

container for report formats

createAlignmentImage(int) - Method in class org.emboss.jemboss.editor.PrintAlignmentImage

Returns a generated image

createDefaultModel() - Method in class org.emboss.jemboss.gui.form.TextFieldFloat

createDefaultModel() - Method in class org.emboss.jemboss.gui.form.TextFieldInt

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

Creates a file named "finished" in the project directory, that contains a time stamp.

createFinishedFile() - Method in class org.emboss.jemboss.server.JembossThread

Creates a file named "finished" in the project directory, that contains a time stamp.

createMenu() - Method in class org.emboss.jemboss.editor.AlignApplet

createPlot(Matrix, Vector, int) - Method in class org.emboss.jemboss.editor.PlotConsensus

Create the consensus plot

createPopup() - Method in class org.emboss.jemboss.gui.form.JembossComboPopup.myComboUI

createTreeModel(File) - Method in class org.emboss.jemboss.gui.filetree.DragTree

Make the given directory the root and create a new DefaultTreeModel.

createTreeModel(String) - Method in class org.emboss.jemboss.gui.filetree.RemoteDragTree

Creates the tree model for the given root

createUI(JComponent) - Static method in class org.emboss.jemboss.gui.form.MultiLineToolTipUI

currentColour - Variable in class org.emboss.jemboss.editor.AlignJFrame

currentDir - Variable in class org.emboss.jemboss.soap.FileRoots

currently selected directory

currentMode - Variable in class org.emboss.jemboss.JembossParams

current mode for running an application

currentModeName - Variable in class org.emboss.jemboss.JembossParams

property name for current mode

currentRoot - Variable in class org.emboss.jemboss.soap.FileRoots

currently selected root

cutnPaste - Variable in class org.emboss.jemboss.gui.form.SetInFileCard

cut and paste text area

cwd - Variable in class org.emboss.jemboss.gui.AdvancedOptions

current working directory

cwd - Variable in class org.emboss.jemboss.gui.filetree.FileSaving

path to saved file

cwd - Variable in class org.emboss.jemboss.gui.form.BuildJembossForm

cygwin - Static variable in class org.emboss.jemboss.JembossParams

cygwin

cygwinName - Variable in class org.emboss.jemboss.JembossParams

property name for Jemboss java server

cygwinSeqAttr(String, JembossParams) - Method in class org.emboss.jemboss.gui.SequenceList

Cygwin uses infoseq to get sequence length and type and uses infoalign to get the sequence weight.

cygwinSeqAttr(String, String[], String) - Method in class org.emboss.jemboss.gui.form.SectionPanel

Cygwin uses infoseq to get sequence length and type and uses infoalign to get the sequence weight.

D

DISPLAY_ACCELERATOR - Static variable in class org.emboss.jemboss.gui.form.MultiLineToolTipUI

Database - class org.emboss.jemboss.gui.startup.Database.

Parses the output from showdb to find the available databases

Database(String) - Constructor for class org.emboss.jemboss.gui.startup.Database

Dependent - class org.emboss.jemboss.parser.Dependent.

Variable that is dependent on the value of another variable

Dependent(int, int, String, String) - Constructor for class org.emboss.jemboss.parser.Dependent

DragJTable - class org.emboss.jemboss.gui.DragJTable.

Extend JTable to implement a drag and drop table for storing sequence lists (SequenceList)

DragJTable(SequenceListTableModel) - Constructor for class org.emboss.jemboss.gui.DragJTable

DragTree - class org.emboss.jemboss.gui.filetree.DragTree.

Creates a local file tree manager for Jemboss.

DragTree(File, JFrame, JembossParams) - Constructor for class org.emboss.jemboss.gui.filetree.DragTree

DragTree.PopupListener - class org.emboss.jemboss.gui.filetree.DragTree.PopupListener.

Popup menu listener

DragTree.PopupListener() - Constructor for class org.emboss.jemboss.gui.filetree.DragTree.PopupListener

d - Variable in class org.emboss.jemboss.gui.form.Separator

size of separator

datasets - Variable in class org.emboss.jemboss.gui.ShowSavedResults

data list model

datasets - Variable in class org.emboss.jemboss.programs.ResultsUpdateTimer.ResultsTask

db - Static variable in class org.emboss.jemboss.gui.BuildProgramMenu

database names

db - Variable in class org.emboss.jemboss.gui.form.BuildJembossForm

db - Variable in class org.emboss.jemboss.gui.form.SectionPanel

available databases

db - Variable in class org.emboss.jemboss.gui.startup.Database

available databases

dbText - Variable in class org.emboss.jemboss.soap.ShowDB

showdb output

dbs - Variable in class org.emboss.jemboss.gui.sequenceChooser.InputSequenceAttributes

available databases

debug - Variable in class org.emboss.jemboss.JembossParams

debugName - Variable in class org.emboss.jemboss.JembossParams

decimalFormatter - Variable in class org.emboss.jemboss.gui.form.TextFieldFloat

def - Variable in class org.emboss.jemboss.gui.form.AlignFormat

default format

def - Variable in class org.emboss.jemboss.gui.form.ReportFormat

default report format

defaultBorder - Static variable in class org.emboss.jemboss.gui.sequenceChooser.CutNPasteTextArea

default border for field

defaultRoot - Variable in class org.emboss.jemboss.soap.FileRoots

default root

defaultRootIndex - Variable in class org.emboss.jemboss.soap.FileRoots

default root index

delDir(String, byte[], String, String) - Method in class org.emboss.jemboss.parser.Ajax

delete a directory

delDir(String, String, String, byte[]) - Method in class org.emboss.jemboss.server.JembossFileAuthServer

Delete a directory

delDir(String, String, String) - Method in class org.emboss.jemboss.server.JembossFileServer

Delete a directory

delFile(String, byte[], String, String) - Method in class org.emboss.jemboss.parser.Ajax

delete a file

delFile(String, String, String, byte[]) - Method in class org.emboss.jemboss.server.JembossFileAuthServer

Delete a file

delFile(String, String, String) - Method in class org.emboss.jemboss.server.JembossFileServer

Delete a file

deleteConsensusPlot() - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection

Remove the consensus plot from the sequence editor

deleteFile(FileNode) - Method in class org.emboss.jemboss.gui.filetree.DragTree

Delete a file from the tree

deleteNode(RemoteFileNode) - Method in class org.emboss.jemboss.gui.filetree.RemoteDragTree

Delete a node (file or directory) from the tree and from the server

deleteObject(FileNode) - Method in class org.emboss.jemboss.gui.filetree.DragTree

Delete a node from the JTree

deleteObject(RemoteFileNode) - Method in class org.emboss.jemboss.gui.filetree.RemoteDragTree

Delete a node from the tree

deleteResidue(int) - Method in class org.emboss.jemboss.editor.Sequence

Delete a residue from the sequence

deleteRow(int) - Method in class org.emboss.jemboss.gui.SequenceListTableModel

Delete a row from the table

deleteSequence(String) - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection

Delete a sequence from the sequence collection display and resize the sequence panel display

deleteTmp(File, String) - Method in class org.emboss.jemboss.gui.SetUpMenuBar

Delete temporary files

delete_saved_results(String, String, String, byte[]) - Method in class org.emboss.jemboss.server.JembossAuthServer

Deletes a projects saved results.

delete_saved_results(String, String, String) - Method in class org.emboss.jemboss.server.JembossServer

Deletes a projects saved results.

delete_saved_results(String, String) - Method in class org.emboss.jemboss.server.JembossServer

Deletes a projects saved results.

dep - Variable in class org.emboss.jemboss.parser.ParseAcd

array of dependent variables

description - Variable in class org.emboss.jemboss.programs.JembossProcess

project description

descriptionHash() - Method in class org.emboss.jemboss.soap.PendingResults

Get the processes description

detach(SequenceJPanel) - Method in class org.emboss.jemboss.editor.SequenceJPanel

Detach sequence display from this group

detachAll() - Method in class org.emboss.jemboss.editor.SequenceJPanel

Detach all sequence displays from this group

directories - Variable in class org.emboss.jemboss.soap.FileList

directory list

directory_shortls(String, String, String, byte[]) - Method in class org.emboss.jemboss.server.JembossFileAuthServer

Get a directory listing

directory_shortls(String, String, String) - Method in class org.emboss.jemboss.server.JembossFileServer

Get a directory listing

displayAccelerator - Static variable in class org.emboss.jemboss.gui.form.MultiLineToolTipUI

doDrawNumber(int, FontMetrics, Graphics) - Method in class org.emboss.jemboss.editor.GroutSequenceJPanel

doIndent(Vector) - Method in class org.emboss.jemboss.editor.GroutGraphicSequenceCollection

doPrintActions() - Method in class org.emboss.jemboss.editor.PrintableJTable

doReset() - Method in class org.emboss.jemboss.gui.form.ListFilePanel

Reset the values of the list files

doReset() - Method in class org.emboss.jemboss.gui.form.SetInFileCard

Reset all text areas for sequence entering

doSelection() - Method in class org.emboss.jemboss.editor.ColourMenu

doSelection() - Method in class org.emboss.jemboss.gui.ColorMenu

doWrite() - Method in class org.emboss.jemboss.gui.filetree.FileSave

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

doneEverything(String) - Method in class org.emboss.jemboss.soap.AuthPopup

Finish the progress bar and label

doneSomething(String) - Method in class org.emboss.jemboss.soap.AuthPopup

Update the progress bar and label

dragDropEnd(DragSourceDropEvent) - Method in class org.emboss.jemboss.gui.DragJTable

dragDropEnd(DragSourceDropEvent) - Method in class org.emboss.jemboss.gui.filetree.DragTree

dragDropEnd(DragSourceDropEvent) - Method in class org.emboss.jemboss.gui.filetree.RemoteDragTree

dragEnter(DragSourceDragEvent) - Method in class org.emboss.jemboss.gui.DragJTable

dragEnter(DropTargetDragEvent) - Method in class org.emboss.jemboss.gui.DragJTable

dragEnter(DragSourceDragEvent) - Method in class org.emboss.jemboss.gui.filetree.DragTree

dragEnter(DropTargetDragEvent) - Method in class org.emboss.jemboss.gui.filetree.DragTree

dragEnter(DragSourceDragEvent) - Method in class org.emboss.jemboss.gui.filetree.RemoteDragTree

dragEnter(DropTargetDragEvent) - Method in class org.emboss.jemboss.gui.filetree.RemoteDragTree

dragEnter(DropTargetDragEvent) - Method in class org.emboss.jemboss.gui.form.TextFieldSink

dragEnter(DropTargetDragEvent) - Method in class org.emboss.jemboss.gui.sequenceChooser.TextAreaSink

dragExit(DragSourceEvent) - Method in class org.emboss.jemboss.gui.DragJTable

dragExit(DropTargetEvent) - Method in class org.emboss.jemboss.gui.DragJTable

dragExit(DragSourceEvent) - Method in class org.emboss.jemboss.gui.filetree.DragTree

dragExit(DropTargetEvent) - Method in class org.emboss.jemboss.gui.filetree.DragTree

dragExit(DragSourceEvent) - Method in class org.emboss.jemboss.gui.filetree.RemoteDragTree

dragExit(DropTargetEvent) - Method in class org.emboss.jemboss.gui.filetree.RemoteDragTree

dragExit(DropTargetEvent) - Method in class org.emboss.jemboss.gui.form.TextFieldSink

dragExit(DropTargetEvent) - Method in class org.emboss.jemboss.gui.sequenceChooser.TextAreaSink

dragGestureRecognized(DragGestureEvent) - Method in class org.emboss.jemboss.gui.DragJTable

dragGestureRecognized(DragGestureEvent) - Method in class org.emboss.jemboss.gui.filetree.DragTree

dragGestureRecognized(DragGestureEvent) - Method in class org.emboss.jemboss.gui.filetree.RemoteDragTree

dragOver(DragSourceDragEvent) - Method in class org.emboss.jemboss.gui.DragJTable

dragOver(DropTargetDragEvent) - Method in class org.emboss.jemboss.gui.DragJTable

dragOver(DragSourceDragEvent) - Method in class org.emboss.jemboss.gui.filetree.DragTree

dragOver(DropTargetDragEvent) - Method in class org.emboss.jemboss.gui.filetree.DragTree

When a suitable DataFlavor is offered over a remote file node the node is highlighted/selected and the drag accepted.

dragOver(DragSourceDragEvent) - Method in class org.emboss.jemboss.gui.filetree.RemoteDragTree

dragOver(DropTargetDragEvent) - Method in class org.emboss.jemboss.gui.filetree.RemoteDragTree

When a suitable DataFlavor is offered over a remote file node the node is highlighted/selected and the drag accepted.

dragOver(DropTargetDragEvent) - Method in class org.emboss.jemboss.gui.form.TextFieldSink

dragOver(DropTargetDragEvent) - Method in class org.emboss.jemboss.gui.sequenceChooser.TextAreaSink

drawBlackBox - Variable in class org.emboss.jemboss.editor.GraphicSequenceCollection

draw black square around residues

drawBlackBox - Variable in class org.emboss.jemboss.editor.SequenceJPanel

draw a black box around residues

drawCentreMarker(Graphics) - Method in class org.emboss.jemboss.editor.GroutSequenceJPanel

drawColorBox - Variable in class org.emboss.jemboss.editor.GraphicSequenceCollection

colour residues

drawColorBox - Variable in class org.emboss.jemboss.editor.SequenceJPanel

colour the residues

drawNumber - Variable in class org.emboss.jemboss.editor.GraphicSequenceCollection

draw sequence position number

drawNumber() - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection

drawNumber() - Method in class org.emboss.jemboss.editor.GroutGraphicSequenceCollection

drawNumber - Variable in class org.emboss.jemboss.editor.SequenceJPanel

draw the sequence numbers

drawSequence - Variable in class org.emboss.jemboss.editor.GraphicSequenceCollection

draw the sequence

drawSequence - Variable in class org.emboss.jemboss.editor.SequenceJPanel

draw the sequence

drawSequences(Graphics2D, PageFormat, int) - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection

Draws the sequences for printing

drawSequences(Graphics2D, PageFormat, int, int) - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection

Draws the sequences for printing

drop(DropTargetDropEvent) - Method in class org.emboss.jemboss.gui.DragJTable

drop(DropTargetDropEvent) - Method in class org.emboss.jemboss.gui.filetree.DragTree

drop(DropTargetDropEvent) - Method in class org.emboss.jemboss.gui.filetree.RemoteDragTree

drop(DropTargetDropEvent) - Method in class org.emboss.jemboss.gui.form.TextFieldSink

drop(DropTargetDropEvent) - Method in class org.emboss.jemboss.gui.sequenceChooser.TextAreaSink

dropActionChanged(DragSourceDragEvent) - Method in class org.emboss.jemboss.gui.DragJTable

dropActionChanged(DropTargetDragEvent) - Method in class org.emboss.jemboss.gui.DragJTable

dropActionChanged(DragSourceDragEvent) - Method in class org.emboss.jemboss.gui.filetree.DragTree

dropActionChanged(DropTargetDragEvent) - Method in class org.emboss.jemboss.gui.filetree.DragTree

dropActionChanged(DragSourceDragEvent) - Method in class org.emboss.jemboss.gui.filetree.RemoteDragTree

dropActionChanged(DropTargetDragEvent) - Method in class org.emboss.jemboss.gui.filetree.RemoteDragTree

dropActionChanged(DropTargetDragEvent) - Method in class org.emboss.jemboss.gui.form.TextFieldSink

dropActionChanged(DropTargetDragEvent) - Method in class org.emboss.jemboss.gui.sequenceChooser.TextAreaSink

dropBorder - Static variable in class org.emboss.jemboss.gui.form.TextFieldSink

dropBorder - Static variable in class org.emboss.jemboss.gui.sequenceChooser.TextAreaSink

E

elements() - Method in class org.emboss.jemboss.programs.ResultList

embURL - Variable in class org.emboss.jemboss.JembossParams

documentation URL

embl - Static variable in class org.emboss.jemboss.gui.sequenceChooser.SequenceFilter

embossBin - Variable in class org.emboss.jemboss.JembossParams

emboss binary location

embossBin - Variable in class org.emboss.jemboss.gui.form.BuildJembossForm

embossBin - Variable in class org.emboss.jemboss.server.JembossAuthServer

emboss binary path

embossBin - Variable in class org.emboss.jemboss.server.JembossFileAuthServer

emboss binary directory

embossBin - Variable in class org.emboss.jemboss.server.JembossServer

emboss binary directory

embossBinName - Variable in class org.emboss.jemboss.JembossParams

property name for emboss binary location

embossData - Variable in class org.emboss.jemboss.JembossParams

emboss data location

embossData - Variable in class org.emboss.jemboss.server.JembossAuthServer

emboss data path

embossData - Variable in class org.emboss.jemboss.server.JembossServer

emboss data directory

embossDataName - Variable in class org.emboss.jemboss.JembossParams

property name for emboss data location

embossEnvironment - Variable in class org.emboss.jemboss.JembossParams

emboss environment

embossEnvironmentName - Variable in class org.emboss.jemboss.JembossParams

property name for emboss environment

embossPath - Variable in class org.emboss.jemboss.JembossParams

emboss path environment variable

embossPath - Variable in class org.emboss.jemboss.server.JembossAuthServer

path environment variable

embossPath - Variable in class org.emboss.jemboss.server.JembossFileAuthServer

emboss path

embossPath - Variable in class org.emboss.jemboss.server.JembossServer

emboss path

embossPathName - Variable in class org.emboss.jemboss.JembossParams

property name for emboss path environment variable

embossURL - Variable in class org.emboss.jemboss.JembossParams

property name for documentation URL

embreo_roots(String, byte[]) - Method in class org.emboss.jemboss.server.JembossFileAuthServer

Retrieves the file manager roots on the server

embreo_roots(String) - Method in class org.emboss.jemboss.server.JembossFileServer

Retrieves the file manager roots on the server

endBorder - Static variable in class org.emboss.jemboss.gui.form.TextFieldSink

env - Variable in class org.emboss.jemboss.server.JembossAuthServer

emboss run environment

environ - Variable in class org.emboss.jemboss.server.JembossAuthServer

emboss run environment as a string

environ - Variable in class org.emboss.jemboss.server.JembossFileAuthServer

emboss run environment

envp - Variable in class org.emboss.jemboss.gui.BuildProgramMenu

environment vars

envp - Variable in class org.emboss.jemboss.gui.form.BuildJembossForm

envp - Variable in class org.emboss.jemboss.server.JembossServer

emboss run environment

envp_emboss - Variable in class org.emboss.jemboss.server.JembossServer

emboss run environment

epr - Variable in class org.emboss.jemboss.soap.CallAjax

request to private server

epr - Variable in class org.emboss.jemboss.soap.GetWossname

request to Jemboss public server

errStd - Variable in class org.emboss.jemboss.parser.Ajax

stderr

errorLog - Variable in class org.emboss.jemboss.server.JembossAuthServer

Jemboss error log file

exitJemboss() - Method in class org.emboss.jemboss.gui.SetUpMenuBar

exitOnDone - Variable in class org.emboss.jemboss.soap.AuthPopup

true if window is to be hidden

exp - Variable in class org.emboss.jemboss.parser.AcdVarResolve

expression

exp - Variable in class org.emboss.jemboss.parser.AcdVariableResolve

expression to resolve

exp - Variable in class org.emboss.jemboss.parser.Dependent

expression

expandWildcards(String) - Static method in class org.emboss.jemboss.programs.ListFile

Wildcard (*) is allowed in the filelist data types.

explore() - Method in class org.emboss.jemboss.gui.filetree.FileNode

Explores a directory adding a FileNode for each child

explore() - Method in class org.emboss.jemboss.gui.filetree.RemoteFileNode

Explore the node and add new child nodes

exploreNode(FileNode) - Method in class org.emboss.jemboss.gui.filetree.DragTree

Explore a directory node

exploreNode(RemoteFileNode) - Method in class org.emboss.jemboss.gui.filetree.RemoteDragTree

Explore a directory node

explored - Variable in class org.emboss.jemboss.gui.filetree.FileNode

true if explored

explored - Variable in class org.emboss.jemboss.gui.filetree.RemoteFileNode

true if node is explored

extend - Variable in class org.emboss.jemboss.Jemboss

Button to open local filemanager

F

FILENODE - Static variable in class org.emboss.jemboss.gui.filetree.FileNode

data flavour of a file node

FileChooser - class org.emboss.jemboss.gui.sequenceChooser.FileChooser.

Creates a JFileChooser and add it to the Box.

FileChooser(Box, String, JembossParams) - Constructor for class org.emboss.jemboss.gui.sequenceChooser.FileChooser

FileEditorDisplay - class org.emboss.jemboss.gui.filetree.FileEditorDisplay.

Display for text, sequence editing, html, gif, png, jpeg.

FileEditorDisplay(String) - Constructor for class org.emboss.jemboss.gui.filetree.FileEditorDisplay

FileEditorDisplay(String, Object) - Constructor for class org.emboss.jemboss.gui.filetree.FileEditorDisplay

FileList - class org.emboss.jemboss.soap.FileList.

Retrieves a directory listing from an Jemboss server.

FileList(JembossParams, String, String) - Constructor for class org.emboss.jemboss.soap.FileList

FileManager - class org.emboss.jemboss.FileManager.

Display the local and remote file managers

FileManager() - Constructor for class org.emboss.jemboss.FileManager

FileNode - class org.emboss.jemboss.gui.filetree.FileNode.

File node for local file tree manager

FileNode(File) - Constructor for class org.emboss.jemboss.gui.filetree.FileNode

FileRoots - class org.emboss.jemboss.soap.FileRoots.

Retrieve the list of available filesystem roots

FileRoots(JembossParams) - Constructor for class org.emboss.jemboss.soap.FileRoots

FileSave - class org.emboss.jemboss.gui.filetree.FileSave.

Saving files locally

FileSave(File) - Constructor for class org.emboss.jemboss.gui.filetree.FileSave

Check if we can/want to save file to disk.

FileSaving - class org.emboss.jemboss.gui.filetree.FileSaving.

Saves to local files from a text pane

FileSaving(JTextPane, byte[], JembossParams) - Constructor for class org.emboss.jemboss.gui.filetree.FileSaving

f - Variable in class org.emboss.jemboss.Jemboss

Jemboss frame

f - Variable in class org.emboss.jemboss.gui.filetree.FileSave

file to save

f - Variable in class org.emboss.jemboss.gui.form.BuildJembossForm

f - Variable in class org.emboss.jemboss.gui.form.SectionPanel

Jemboss frame

fExists - Variable in class org.emboss.jemboss.gui.filetree.FileSave

true if the file exists

fasta - Static variable in class org.emboss.jemboss.gui.sequenceChooser.SequenceFilter

fc - Variable in class org.emboss.jemboss.gui.sequenceChooser.FileChooser

file chooser

ff - Variable in class org.emboss.jemboss.gui.sequenceChooser.InputSequenceAttributes

input format types

ff - Variable in class org.emboss.jemboss.gui.sequenceChooser.OutputSequenceAttributes

output format types

field - Variable in class org.emboss.jemboss.parser.Dependent

field number in the ACD file

fieldOption - Variable in class org.emboss.jemboss.gui.form.BuildJembossForm

fieldOption - Variable in class org.emboss.jemboss.gui.form.SectionPanel

checkbox popup field for list and select

fileChoose - Variable in class org.emboss.jemboss.gui.form.SetInFileCard

sequence file choser

fileChooser - Variable in class org.emboss.jemboss.gui.form.ListFilePanel

container for sequences

fileExists() - Method in class org.emboss.jemboss.gui.filetree.FileSave

fileFormats - Variable in class org.emboss.jemboss.gui.sequenceChooser.InputSequenceAttributes

combobox for file formats

fileFormats - Variable in class org.emboss.jemboss.gui.sequenceChooser.OutputSequenceAttributes

combobox for file formats

fileMenuShowres - Variable in class org.emboss.jemboss.gui.SetUpMenuBar

show saved results menu item

fileName - Variable in class org.emboss.jemboss.gui.sequenceChooser.FileChooser

file name text field

filePrefix - Variable in class org.emboss.jemboss.editor.PrintAlignmentImage

prefix of file

fileRoots - Variable in class org.emboss.jemboss.soap.FileRoots

server directory roots

fileSave(String, String, String, Hashtable) - Method in class org.emboss.jemboss.gui.ResultsMenuBar

Save to a local file

fileSave(String, String, Object) - Method in class org.emboss.jemboss.gui.ResultsMenuBar

Save to a local file

fileSaving(Object) - Method in class org.emboss.jemboss.gui.filetree.FileSave

fileSelected - Variable in class org.emboss.jemboss.gui.filetree.FileSaving

file to save to

fileVector() - Method in class org.emboss.jemboss.soap.FileList

Gets the list of files as a Vector

fileWritten - Variable in class org.emboss.jemboss.gui.filetree.FileSave

true if the file has been written

filelist - Variable in class org.emboss.jemboss.gui.form.BuildJembossForm

filelist - Variable in class org.emboss.jemboss.gui.form.SectionPanel

list file panel

filename - Variable in class org.emboss.jemboss.gui.filetree.FileEditorDisplay

file name

filename - Static variable in class org.emboss.jemboss.server.TestPrivateServer

fileok - Variable in class org.emboss.jemboss.parser.Ajax

filesForSoap(String, String, String, Hashtable) - Method in class org.emboss.jemboss.gui.form.BuildJembossForm

filesForSoap(String, String, String, Hashtable) - Method in class org.emboss.jemboss.server.TestPrivateServer

finalize() - Method in class org.emboss.jemboss.gui.form.BuildJembossForm

Ensures garbaged collected when there are no more pointers to this.

findHeader(String) - Method in class org.emboss.jemboss.gui.filetree.FileEditorDisplay

Sequence header text.

findInt(String) - Method in class org.emboss.jemboss.gui.ShowResultSet

Find the number in a string expression

findMiddle(int, int, String) - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection

Locate the center of a vieport view that contains the defined position to display

findPattern(String, int, boolean) - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection

Search sequences for a pattern and highlight matches.

finished() - Method in class org.emboss.jemboss.gui.SwingWorker

Called on the event dispatching thread (not on the worker thread) after the construct method has returned.

flavors - Static variable in class org.emboss.jemboss.gui.SequenceData

available dataflavors

flavors - Static variable in class org.emboss.jemboss.gui.filetree.FileNode

flavours file node and string

flist - Variable in class org.emboss.jemboss.soap.FileList

file list

font - Variable in class org.emboss.jemboss.editor.SequenceJPanel

font

font - Variable in class org.emboss.jemboss.editor.SequenceNameJButton

font

fontSize - Variable in class org.emboss.jemboss.JembossLogo

fontSize - Variable in class org.emboss.jemboss.editor.SequenceJPanel

font size

fontSize - Variable in class org.emboss.jemboss.editor.SequenceNameJButton

font size

fontSize - Variable in class org.emboss.jemboss.gui.form.ApplicationNamePanel

font size

forkBatch(String, byte[], String, String, String) - Method in class org.emboss.jemboss.parser.Ajax

fork emboss batch proceess

forkEmboss(String, byte[], String, String, String) - Method in class org.emboss.jemboss.parser.Ajax

fork emboss proceess

format - Variable in class org.emboss.jemboss.editor.PrintAlignmentImage

page format

formatHelpText(String) - Method in class org.emboss.jemboss.parser.ParseAcd

Limits the length of the line for the help text used in the tool tips.

frame - Variable in class org.emboss.jemboss.gui.ResultsMenuBar

frame containing the results

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

remote directory roots

froots - Variable in class org.emboss.jemboss.gui.filetree.RemoteFileNode

remote server file roots

fs - Variable in class org.emboss.jemboss.gui.filetree.DragTree

file separator

fs - Variable in class org.emboss.jemboss.gui.filetree.RemoteDragTree

file separator

fs - Variable in class org.emboss.jemboss.gui.filetree.RemoteFileNode

file separator for server files

fs - Variable in class org.emboss.jemboss.server.JembossAuthServer

file separator

fs - Variable in class org.emboss.jemboss.server.JembossServer

file separator

fullname - Variable in class org.emboss.jemboss.gui.filetree.RemoteFileNode

full name of node

fwdArrow - Variable in class org.emboss.jemboss.Jemboss

Image for displaying the local filemanager

fwdBt - Variable in class org.emboss.jemboss.gui.Browser

Forward button option

fwdMenu - Variable in class org.emboss.jemboss.gui.Browser

Forward menu option

G

GetACD - class org.emboss.jemboss.soap.GetACD.

Retrieve an ACD file using soap

GetACD(String, JembossParams) - Constructor for class org.emboss.jemboss.soap.GetACD

GetHelp - class org.emboss.jemboss.soap.GetHelp.

Get the help text for an application

GetHelp(String, JembossParams) - Constructor for class org.emboss.jemboss.soap.GetHelp

GetWossname - class org.emboss.jemboss.soap.GetWossname.

Run wossname of a Jemboss server

GetWossname(JembossParams) - Constructor for class org.emboss.jemboss.soap.GetWossname

GraphicSequenceCollection - class org.emboss.jemboss.editor.GraphicSequenceCollection.

This class can be used to get a grapical representation of a collection of sequences.

GraphicSequenceCollection(Vector, Hashtable, JScrollPane, boolean, boolean, boolean, boolean, JTextField) - Constructor for class org.emboss.jemboss.editor.GraphicSequenceCollection

GraphicSequenceCollection(Vector, JScrollPane, boolean, boolean, boolean, boolean, JTextField) - Constructor for class org.emboss.jemboss.editor.GraphicSequenceCollection

GroutAlignJFrame - class org.emboss.jemboss.editor.GroutAlignJFrame.

Displays a grapical representation of a collection of sequences.

GroutAlignJFrame(Vector, Vector) - Constructor for class org.emboss.jemboss.editor.GroutAlignJFrame

This constructor is for Grout.

GroutAlignJFrame(Vector) - Constructor for class org.emboss.jemboss.editor.GroutAlignJFrame

GroutAlignJFrame(File) - Constructor for class org.emboss.jemboss.editor.GroutAlignJFrame

GroutAlignJFrame(String, String) - Constructor for class org.emboss.jemboss.editor.GroutAlignJFrame

GroutAlignJFrame() - Constructor for class org.emboss.jemboss.editor.GroutAlignJFrame

GroutAlignJFrame(boolean) - Constructor for class org.emboss.jemboss.editor.GroutAlignJFrame

GroutAlignJFrame.winExit - class org.emboss.jemboss.editor.GroutAlignJFrame.winExit.

Extends WindowAdapter to handle disposal of the occurance

GroutAlignJFrame.winExit() - Constructor for class org.emboss.jemboss.editor.GroutAlignJFrame.winExit

GroutAlignJFrameEvent - class org.emboss.jemboss.editor.GroutAlignJFrameEvent.

GroutAlignJFrameEvent(Object, String, Object, Object) - Constructor for class org.emboss.jemboss.editor.GroutAlignJFrameEvent

Creates a new instance of GroutAlignJFrameEvent with source set

GroutAlignJFrameListener - interface org.emboss.jemboss.editor.GroutAlignJFrameListener.

GroutAlignJFrameListener.java Created: 10th June 2003

GroutGraphicSequenceCollection - class org.emboss.jemboss.editor.GroutGraphicSequenceCollection.

This class can be used to get a grapical representation of a collection of sequences.

GroutGraphicSequenceCollection(Vector, Hashtable, JScrollPane, boolean, boolean, boolean, boolean, JTextField) - Constructor for class org.emboss.jemboss.editor.GroutGraphicSequenceCollection

GroutGraphicSequenceCollection(Vector, JScrollPane, boolean, boolean, boolean, boolean, JTextField) - Constructor for class org.emboss.jemboss.editor.GroutGraphicSequenceCollection

GroutGraphicSequenceCollection(Vector, Vector, Hashtable, JScrollPane, boolean, boolean, boolean, boolean, JTextField) - Constructor for class org.emboss.jemboss.editor.GroutGraphicSequenceCollection

GroutGraphicSequenceCollection(Vector, Vector, JScrollPane, boolean, boolean, boolean, boolean, JTextField) - Constructor for class org.emboss.jemboss.editor.GroutGraphicSequenceCollection

GroutGraphicSequenceCollectionEvent - class org.emboss.jemboss.editor.GroutGraphicSequenceCollectionEvent.

GroutGraphicSequenceCollectionEvent(Object, String, Object, Object) - Constructor for class org.emboss.jemboss.editor.GroutGraphicSequenceCollectionEvent

Creates a new instance of GroutGraphicSequenceCollectionEvent with source set

GroutGraphicSequenceCollectionListener - interface org.emboss.jemboss.editor.GroutGraphicSequenceCollectionListener.

GroutGraphicSequenceCollectionListener.java Created: Thu Mar 13 14:42:13 2003

GroutSequence - class org.emboss.jemboss.editor.GroutSequence.

Sequence object

GroutSequence(String, String, int, float) - Constructor for class org.emboss.jemboss.editor.GroutSequence

GroutSequence(String, String, int) - Constructor for class org.emboss.jemboss.editor.GroutSequence

GroutSequence(String, String) - Constructor for class org.emboss.jemboss.editor.GroutSequence

GroutSequence(String) - Constructor for class org.emboss.jemboss.editor.GroutSequence

GroutSequence(String, float) - Constructor for class org.emboss.jemboss.editor.GroutSequence

GroutSequenceJPanel - class org.emboss.jemboss.editor.GroutSequenceJPanel.

Sequence panel for drawing a sequence or the sequence numbers

GroutSequenceJPanel(int, Sequence, JComponent, boolean, boolean, boolean, Hashtable, int, int) - Constructor for class org.emboss.jemboss.editor.GroutSequenceJPanel

Constructor for indenting the sequence

GroutSequenceJPanel(int, Sequence, JComponent, boolean, boolean, boolean, Hashtable, int) - Constructor for class org.emboss.jemboss.editor.GroutSequenceJPanel

Constructor with default font size and indenting the sequence

GroutSequenceJPanel(int, int, int) - Constructor for class org.emboss.jemboss.editor.GroutSequenceJPanel

Constructor for sequence numbering and indenting the sequence

GroutSequenceJPanel(Sequence, JComponent, boolean, boolean, boolean, Hashtable, int, int) - Constructor for class org.emboss.jemboss.editor.GroutSequenceJPanel

GroutSequenceJPanel(Sequence, JComponent, boolean, boolean, boolean, Hashtable, int) - Constructor for class org.emboss.jemboss.editor.GroutSequenceJPanel

Constructor with default font size

GroutSequenceJPanel(int, int) - Constructor for class org.emboss.jemboss.editor.GroutSequenceJPanel

Constructor for sequence numbering

g - Variable in class org.emboss.jemboss.gui.form.MultiLineToolTipUI

gcg - Static variable in class org.emboss.jemboss.gui.sequenceChooser.SequenceFilter

get() - Method in class org.emboss.jemboss.gui.SwingWorker.ThreadVar

get() - Method in class org.emboss.jemboss.gui.SwingWorker

Return the value created by the construct method.

get(Object) - Method in class org.emboss.jemboss.programs.ResultList

get(Object) - Method in class org.emboss.jemboss.soap.JembossRun

Get a result from the result Hashtable

getAccCheckBox() - Method in class org.emboss.jemboss.gui.form.ReportFormat

Get the check box for accession number display

getAcceleratorString(JToolTip) - Method in class org.emboss.jemboss.gui.form.MultiLineToolTipUI

getAcd() - Method in class org.emboss.jemboss.soap.GetACD

Return the text of the ACD file

getAcdDirToParse() - Method in class org.emboss.jemboss.JembossParams

Acd file location

getAcdText(String, JembossParams, boolean) - Method in class org.emboss.jemboss.gui.BuildProgramMenu

Get the contents of an ACD file in the form of a String

getAlignFormat() - Method in class org.emboss.jemboss.gui.form.AlignFormat

Get the alignment format to add to the EMBOSS command line

getAlignFormat() - Method in class org.emboss.jemboss.gui.form.SectionPanel

Get the alignment format

getAlignFormats(boolean) - Method in class org.emboss.jemboss.gui.form.AlignFormat

Get the alignment formats as a string array

getAllowsChildren() - Method in class org.emboss.jemboss.gui.filetree.FileNode

Determine if this is a directory

getAllowsChildren() - Method in class org.emboss.jemboss.gui.filetree.RemoteFileNode

getAnIndex(FileNode, String) - Method in class org.emboss.jemboss.gui.filetree.DragTree

Finds a new index for adding a new file to the file manager.

getArrayListFile() - Method in class org.emboss.jemboss.gui.form.ListFilePanel

getArrayListFile() - Method in class org.emboss.jemboss.gui.form.SetInFileCard

getAttribute() - Method in class org.emboss.jemboss.parser.acd.ApplicationParam

Get the parameter/attribute type

getAutoscrollInsets() - Method in class org.emboss.jemboss.gui.filetree.DragTree

Gets the insets used for the autoscroll.

getAutoscrollInsets() - Method in class org.emboss.jemboss.gui.filetree.RemoteDragTree

Gets the insets used for the autoscroll.

getBegSeq() - Method in class org.emboss.jemboss.gui.sequenceChooser.InputSequenceAttributes

Get the -sbegin flag

getBrowserProxyHost() - Method in class org.emboss.jemboss.JembossParams

Get the name of the proxy server for the browser

getBrowserProxyPort() - Method in class org.emboss.jemboss.JembossParams

The port number of the proxy server for the browser

getCase() - Method in class org.emboss.jemboss.editor.ConsensusOptions

Get the minimum positive matches for a site to be made upper case in the consensus.

getChildNode(FileNode, String) - Method in class org.emboss.jemboss.gui.filetree.DragTree

Gets the child node of a parent node

getChildNode(RemoteFileNode, String) - Method in class org.emboss.jemboss.gui.filetree.RemoteDragTree

Gets the child node of a parent node

getCodonUsage() - Static method in class org.emboss.jemboss.gui.BuildProgramMenu

Contains all codon usage tables

getCodonUsage() - Method in class org.emboss.jemboss.soap.ShowDB

Get the codon usage tables

getColor() - Method in class org.emboss.jemboss.editor.ColourMenu.ColorPane

getColor() - Method in class org.emboss.jemboss.editor.ColourMenu

getColor(String, int, String) - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection

Determine the colour of a residue at a given position.

getColor(String) - Method in class org.emboss.jemboss.editor.SequenceJPanel

Get a residue colour

getColor() - Method in class org.emboss.jemboss.gui.ColorMenu.ColorPane

getColor() - Method in class org.emboss.jemboss.gui.ColorMenu

getColour() - Method in class org.emboss.jemboss.editor.ColourPanel

Return current colour selection

getColumnClass(int) - Method in class org.emboss.jemboss.gui.SequenceListTableModel

DragJTable uses this method to determine the default renderer/ editor for each cell.

getColumnCount() - Method in class org.emboss.jemboss.gui.SequenceListTableModel

Return the number of columns in the table

getColumnName(int) - Method in class org.emboss.jemboss.gui.SequenceListTableModel

Return the name columns in the table

getComboPopup() - Method in class org.emboss.jemboss.gui.form.AlignFormat

Get the combo-popup component for alignment formats

getComboPopup() - Method in class org.emboss.jemboss.gui.form.ReportFormat

Get the combo popup box containing the report formats

getCommand() - Method in class org.emboss.jemboss.gui.form.BuildJembossForm

Get the command line for the Standalone version.

getCommand(Hashtable) - Method in class org.emboss.jemboss.gui.form.BuildJembossForm

Get the command line for the SOAP version.

getConsensusSequence() - Method in class org.emboss.jemboss.editor.Consensus

Get the consensus sequence

getConsensusSequence() - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection

Get the consensus sequence

getCurrentColourScheme() - Method in class org.emboss.jemboss.editor.ColourJFrame

Get the colour scheme as a hashtable

getCurrentDir() - Method in class org.emboss.jemboss.soap.FileRoots

Get the currently selected directory

getCurrentMatrixName() - Method in class org.emboss.jemboss.editor.Matrix

Get the current scoring matrix name

getCurrentMode() - Method in class org.emboss.jemboss.JembossParams

The current mode (interactive or batch).

getCurrentRoot() - Method in class org.emboss.jemboss.soap.FileRoots

Get the currently selected root

getCutNPasteText() - Method in class org.emboss.jemboss.gui.form.SetInFileCard

getCygwinRoot() - Method in class org.emboss.jemboss.JembossParams

Get the cygwin root

getDB() - Method in class org.emboss.jemboss.gui.startup.Database

Get the available databases

getDBText() - Method in class org.emboss.jemboss.soap.ShowDB

Get the output from showdb

getDatabaseList() - Static method in class org.emboss.jemboss.gui.BuildProgramMenu

List of available EMBOSS databases

getDebug() - Method in class org.emboss.jemboss.JembossParams

Whether to show debugging information

getDefaultFormat() - Method in class org.emboss.jemboss.gui.form.AlignFormat

getDefaultFormat() - Method in class org.emboss.jemboss.gui.form.ReportFormat

Get the default report format

getDefaultParamValueDbl(int) - Method in class org.emboss.jemboss.parser.ParseAcd

Return a double default parameter

getDefaultParamValueStr(int) - Method in class org.emboss.jemboss.parser.ParseAcd

Gets a String default parameter.

getDefaultRoot() - Method in class org.emboss.jemboss.soap.FileRoots

Get the default root, if defined, else return null

getDefaultRootIndex() - Method in class org.emboss.jemboss.soap.FileRoots

Get the index of the default root in the Vector, else return -1

getDefaultRow() - Method in class org.emboss.jemboss.gui.SequenceList

Look for first set to default in the table.

getDefaultSequenceName() - Method in class org.emboss.jemboss.gui.SequenceList

Get the default Sequence name

getDefaultTab() - Method in class org.emboss.jemboss.gui.TabListCellRenderer

getDependentExp() - Method in class org.emboss.jemboss.parser.Dependent

Get the expression

getDependentField() - Method in class org.emboss.jemboss.parser.Dependent

Get the field

getDependentParam() - Method in class org.emboss.jemboss.parser.Dependent

Get the parameter number

getDependentType() - Method in class org.emboss.jemboss.parser.Dependent

Get type of parameter

getDependents() - Method in class org.emboss.jemboss.parser.ParseAcd

Gets the dependents associated with the ACD.

getDesCheckBox() - Method in class org.emboss.jemboss.gui.form.ReportFormat

Get the check box for description display

getDescription() - Method in class org.emboss.jemboss.gui.sequenceChooser.SequenceFilter

getDescription() - Method in class org.emboss.jemboss.programs.JembossProcess

Get the project description

getElement(String) - Method in class org.emboss.jemboss.JembossJarUtil

Return an element of the hashtable

getEmbossBin() - Method in class org.emboss.jemboss.JembossParams

getEmbossData() - Method in class org.emboss.jemboss.JembossParams

getEmbossEnvironment() - Method in class org.emboss.jemboss.JembossParams

Get the environment for emboss

getEmbossEnvironmentArray(String[]) - Method in class org.emboss.jemboss.JembossParams

Get the emboss environment as a String array

getEmbossPath() - Method in class org.emboss.jemboss.JembossParams

Get the path for emboss

getEndSeq() - Method in class org.emboss.jemboss.gui.sequenceChooser.InputSequenceAttributes

Get the -send flag

getErrStd() - Method in class org.emboss.jemboss.parser.Ajax

Get the stderr

getExpectedCPU() - Method in class org.emboss.jemboss.parser.ParseAcd

Finds any expected cpu level indicator (low, medium, high)

getExtension(File) - Static method in class org.emboss.jemboss.gui.sequenceChooser.SequenceFilter

Get the extension of a file

getFieldNum() - Method in class org.emboss.jemboss.gui.form.SectionPanel

Get the current field

getFile() - Method in class org.emboss.jemboss.gui.filetree.FileNode

Get the File this node represents

getFile() - Method in class org.emboss.jemboss.gui.filetree.RemoteFileNode

getFile(String, byte[], String, String) - Method in class org.emboss.jemboss.parser.Ajax

get the contents of a file

getFileChosen() - Method in class org.emboss.jemboss.gui.form.SetInFileCard

getFileChosen() - Method in class org.emboss.jemboss.gui.sequenceChooser.FileChooser

Get the selected file

getFileName(int) - Method in class org.emboss.jemboss.gui.DragJTable

getFileName() - Method in class org.emboss.jemboss.gui.filetree.FileSaving

getFileOrDatabaseForAjax(String, String[], JFrame, boolean) - Static method in class org.emboss.jemboss.parser.AjaxUtil

Returns the sequence file contents or the database entry ready to use in Ajax.

getFilename() - Method in class org.emboss.jemboss.gui.filetree.RemoteDragTree

Get the selected node file name

getFileok() - Method in class org.emboss.jemboss.parser.Ajax

getFont() - Method in class org.emboss.jemboss.editor.SequenceNameJButton

Get the font

getFontSize() - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection

Get the font size used to display the sequences in the editor return font size

getFontSize() - Method in class org.emboss.jemboss.editor.SequenceJPanel

Get the font size

getFormat() - Method in class org.emboss.jemboss.editor.PrintAlignmentImage

Get the page format

getFormatChoosen() - Method in class org.emboss.jemboss.gui.sequenceChooser.InputSequenceAttributes

Get the file format selected

getFormatChoosen() - Method in class org.emboss.jemboss.gui.sequenceChooser.OutputSequenceAttributes

Get the format selected

getFormatDialog() - Method in class org.emboss.jemboss.editor.PrintAlignmentImage

Get a default page format

getFullName() - Method in class org.emboss.jemboss.gui.filetree.RemoteFileNode

getGraphicSequence() - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection

Get the vector containing the SequenceJPanel objects

getGuiHandleNumber(int) - Method in class org.emboss.jemboss.parser.ParseAcd

Gets the handle for a gui component on the Jemboss form.

getGuiHandleNumber() - Method in class org.emboss.jemboss.parser.acd.ApplicationFields

Get the gui handle

getHasBatchMode() - Method in class org.emboss.jemboss.JembossParams

Whether this service supports batch mode

getHasInteractiveMode() - Method in class org.emboss.jemboss.JembossParams

Whether this service supports interactive mode

getHash() - Method in class org.emboss.jemboss.JembossJarUtil

Return the hashtable

getHash() - Method in class org.emboss.jemboss.soap.PrivateRequest

Get the results returned by the server call

getHash() - Method in class org.emboss.jemboss.soap.PublicRequest

The hash returned by the Jemboss call.

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

Convert contents from a Vector to a Hashtable

getHelpParamValue(int) - Method in class org.emboss.jemboss.parser.ParseAcd

Finds the help parameter in an ACD field.

getHelpText() - Method in class org.emboss.jemboss.soap.GetHelp

Get the help text

getHomeDirectory() - Method in class org.emboss.jemboss.gui.AdvancedOptions

Get the user home/working directory

getID() - Method in class org.emboss.jemboss.editor.Sequence

Get the sequence id

getIDBackgroundColour() - Method in class org.emboss.jemboss.editor.PrettyPlotJFrame

Get the users defined background colour to draw identical residues

getIDColour() - Method in class org.emboss.jemboss.editor.PrettyPlotJFrame

Get the users defined colour to draw identical residues

getIDimension() - Method in class org.emboss.jemboss.editor.Matrix

Get number of rows in the scoring table

getIdentity() - Method in class org.emboss.jemboss.editor.ConsensusOptions

Get the minimum identical matches for a site to be included in the consensus.

getImageableSize(int) - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection

Get the imageable size.

getIndexOf(Object) - Method in class org.emboss.jemboss.gui.MemoryComboBox

getInfoParamValue(int) - Method in class org.emboss.jemboss.parser.ParseAcd

Finds the prompt, info or help parameter in an ACD field, in that order.

getInputSeqAttr(int) - Method in class org.emboss.jemboss.gui.sequenceChooser.InputSequenceAttributes

Get the EMBOSS command line for the values selected for the input sequence attributes

getJDimension() - Method in class org.emboss.jemboss.editor.Matrix

Get number of columns in the scoring table

getJFileChooser() - Method in class org.emboss.jemboss.gui.sequenceChooser.FileChooser

Get the JFileChooser

getJScrollPane() - Method in class org.emboss.jemboss.gui.sequenceChooser.InputSequenceAttributes

Get the scroll panel

getJScrollPane() - Method in class org.emboss.jemboss.gui.sequenceChooser.OutputSequenceAttributes

Get the scoll panel

getJTextComponentAt(JTabbedPane, int) - Method in class org.emboss.jemboss.gui.ResultsMenuBar

Get text component from a tabbed pane

getJob() - Method in class org.emboss.jemboss.programs.JembossProcess

Get the project id

getKeyNames() - Method in class org.emboss.jemboss.editor.Matrix

Scoring matrix names available

getKeyNamesString() - Method in class org.emboss.jemboss.editor.Matrix

Scoring matrix names available

getKeys() - Method in class org.emboss.jemboss.editor.Matrix

Scoring matrix filenames in jar file

getLength() - Method in class org.emboss.jemboss.editor.Sequence

Get the sequence length

getLength() - Method in class org.emboss.jemboss.soap.CallAjax

Get the sequence length

getLineSeparator() - Static method in class org.emboss.jemboss.gui.form.PlafMacros

Get the line separator string

getList(int) - Method in class org.emboss.jemboss.parser.ParseAcd

Used for a list data type to put the list items in a String array.

getListCellRendererComponent(JList, Object, int, boolean, boolean) - Method in class org.emboss.jemboss.gui.TabListCellRenderer

getListFile() - Method in class org.emboss.jemboss.gui.form.ListFilePanel

getListFile() - Method in class org.emboss.jemboss.gui.form.SetInFileCard

getListLabel(int, int) - Method in class org.emboss.jemboss.parser.ParseAcd

For a list data type determine the appropriate String entry.

getListOrSelectDefault() - Method in class org.emboss.jemboss.parser.ParseAcd

Use this after getList or getSelect to retrieve default

getLocalDragTree() - Static method in class org.emboss.jemboss.gui.SetUpMenuBar

Get local file manager

getLocalDragTree() - Static method in class org.emboss.jemboss.gui.filetree.LocalAndRemoteFileTreeFrame

Returns the local file tree

getLocalFile(File) - Method in class org.emboss.jemboss.gui.filetree.RemoteDragTree

Get the contents of a local file as a byte array

getLocalFile(File) - Method in class org.emboss.jemboss.gui.form.BuildJembossForm

getLocalFile(File) - Static method in class org.emboss.jemboss.programs.ListFile

Read file in as a byte array.

getLocalFile(File) - Method in class org.emboss.jemboss.server.TestPrivateServer

getMatchBackgroundColour() - Method in class org.emboss.jemboss.editor.PrettyPlotJFrame

Get the users defined background colour to draw positive match residues

getMatchColour() - Method in class org.emboss.jemboss.editor.PrettyPlotJFrame

Get the users defined colour to draw positive match residues

getMatchThreshold() - Method in class org.emboss.jemboss.editor.PrettyPlotJFrame

Get the match threshold value

getMatrices() - Static method in class org.emboss.jemboss.gui.BuildProgramMenu

Contains all scoring matrix files

getMatrices() - Method in class org.emboss.jemboss.soap.ShowDB

Get the available matrices

getMatrix() - Method in class org.emboss.jemboss.editor.Matrix

Get the scoring matrix as a 2 dimensional integer array

getMatrixIndex(String) - Method in class org.emboss.jemboss.editor.Matrix

Get the residue position in the scoring table

getMatrixTable() - Method in class org.emboss.jemboss.editor.Matrix

Get the scoring matrix as text

getMaxParam(int) - Method in class org.emboss.jemboss.parser.ParseAcd

Locates the max parameter in a field and returns it as a String.

getMaxSeqLength() - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection

Get the longest sequence length

getMaxSequenceLength(Vector) - Method in class org.emboss.jemboss.editor.Consensus

Check all sequences lengths and return length of the longest sequence

getMaxSequenceLength(Vector) - Method in class org.emboss.jemboss.editor.PlotConsensus

Check all sequences lengths and return length of the longest sequence

getMaximumSize() - Method in class org.emboss.jemboss.editor.ColourMenu.ColorPane

getMaximumSize() - Method in class org.emboss.jemboss.gui.ColorMenu.ColorPane

getMaximumSize(JComponent) - Method in class org.emboss.jemboss.gui.form.MultiLineToolTipUI

getMenuItems() - Method in class org.emboss.jemboss.gui.startup.ProgList

Returns the program menu items

getMinMaxDefault(String, String, String, int) - Method in class org.emboss.jemboss.gui.form.SectionPanel

Get the min, max and default values for a field in the ACD as a string representation in the form (min: max: default:)

getMinParam(int) - Method in class org.emboss.jemboss.parser.ParseAcd

Locates the min parameter in a field and returns it as a String.

getMinimumIdentity(int) - Method in class org.emboss.jemboss.editor.PrettyPlotJFrame

Get the users defined identity limit

getMinimumSize() - Method in class org.emboss.jemboss.editor.ColourMenu.ColorPane

getMinimumSize() - Method in class org.emboss.jemboss.gui.ColorMenu.ColorPane

getMinimumSize(JComponent) - Method in class org.emboss.jemboss.gui.form.MultiLineToolTipUI

getName(int) - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection

getName() - Method in class org.emboss.jemboss.editor.Sequence

Get the sequence name

getName() - Method in class org.emboss.jemboss.editor.SequenceJPanel

Get the sequence name associated with this display

getNameHeight() - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection

Get the sequence name panel height

getNamePrintGraphic(Graphics) - Method in class org.emboss.jemboss.editor.SequenceJPanel

Render the sequence name graphic

getNameViewSize() - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection

Get the sequence name view size

getNameWidth() - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection

Get the sequence name panel width

getNode(String) - Method in class org.emboss.jemboss.gui.filetree.DragTree

Gets the node from the existing explored nodes and their children.

getNode(String) - Method in class org.emboss.jemboss.gui.filetree.RemoteDragTree

Gets the node from the existing explored nodes and their children.

getNumBool() - Method in class org.emboss.jemboss.parser.ParseAcd

Gets the number of boolean data types in the ACD.

getNumFileList() - Method in class org.emboss.jemboss.parser.ParseAcd

Gets the number of filelist data types in the ACD

getNumList() - Method in class org.emboss.jemboss.parser.ParseAcd

Gets the number of list & selection data types in the ACD, using single list selection

getNumMList() - Method in class org.emboss.jemboss.parser.ParseAcd

Gets the number of list & selection data types in the ACD, using multiple list selection

getNumNfloat() - Method in class org.emboss.jemboss.parser.ParseAcd

Gets the number of float data types in the ACD.

getNumNint() - Method in class org.emboss.jemboss.parser.ParseAcd

Gets the number of int data types in the ACD.

getNumOfDependents() - Method in class org.emboss.jemboss.parser.ParseAcd

Gets the number of dependent parameters in the ACD.

getNumPrimaryGroups() - Method in class org.emboss.jemboss.gui.startup.ProgList

Returns the number of primary menu groups

getNumProgs() - Method in class org.emboss.jemboss.gui.startup.ProgList

Returns the number of programs

getNumRange() - Method in class org.emboss.jemboss.parser.ParseAcd

getNumSection() - Method in class org.emboss.jemboss.parser.ParseAcd

Gets the number of sections in the ACD

getNumSeq() - Method in class org.emboss.jemboss.parser.ParseAcd

Gets the number of seqset, seqall & sequence data types in the ACD

getNumSubsection() - Method in class org.emboss.jemboss.parser.ParseAcd

Gets the number of nested sections in the ACD

getNumTextf() - Method in class org.emboss.jemboss.parser.ParseAcd

Gets the number of float, string, seqout, outfile, infile, regexp, codon & featout data types in the ACD.

getNumberMenuItems() - Method in class org.emboss.jemboss.gui.startup.ProgList

Returns the number of program menu items

getNumberOfParam() - Method in class org.emboss.jemboss.parser.acd.ApplicationFields

Get the number of parameters in this field

getNumberOfSequences() - Method in class org.emboss.jemboss.editor.SequenceReader

Returns the number of sequences.

getNumberPages(PageFormat) - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection

Get the number of pages to print the alignment in a given format

getNumberPages(PageFormat, int) - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection

Get the number of pages to print the alignment in a given format and with a given number of residues per line

getNumberSequences() - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection

Get the number of sequences

getNumofFields() - Method in class org.emboss.jemboss.parser.ParseAcd

Gets the number of fields in the ACD file.

getNumofParams(int) - Method in class org.emboss.jemboss.parser.ParseAcd

Gets the number of parameters in a ACD field.

getOuputSeqAttr() - Method in class org.emboss.jemboss.gui.sequenceChooser.OutputSequenceAttributes

Get the EMBOSS command line for the output sequence attributes

getOutStd() - Method in class org.emboss.jemboss.parser.Ajax

Get the stdout

getOutputSequenceFile(int) - Method in class org.emboss.jemboss.parser.ParseAcd

Gets the name of the output sequence field (seqout).

getPNGContent() - Method in class org.emboss.jemboss.gui.filetree.FileEditorDisplay

Returns the content of a png file or null.

getPanelHeight() - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection

Get the sequence panel height

getPanelHeight() - Method in class org.emboss.jemboss.editor.SequenceNameJButton

Get the button height

getPanelSize() - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection

Get the sequence view size

getPanelWidth() - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection

Get the sequence panel width

getPanelWidth() - Method in class org.emboss.jemboss.editor.SequenceNameJButton

Get the button width

getParamAttribute(int) - Method in class org.emboss.jemboss.parser.acd.ApplicationFields

Get a parameter attribute, given the parameter number in the field

getParamValueDbl(int, int) - Method in class org.emboss.jemboss.parser.ParseAcd

Gets the double value of a parameter.

getParamValueDbl(int) - Method in class org.emboss.jemboss.parser.acd.ApplicationFields

Get a parameter value, given the parameter number in the field

getParamValueStr(int, int) - Method in class org.emboss.jemboss.parser.ParseAcd

Gets the String value of a parameter.

getParamValueStr(int) - Method in class org.emboss.jemboss.parser.acd.ApplicationFields

Get a parameter value, given the parameter number in the field

getParameterAttribute(int, int) - Method in class org.emboss.jemboss.parser.ParseAcd

Get a specified parameter attribute.

getPath() - Method in class org.emboss.jemboss.gui.filetree.FileSaving

getPathName() - Method in class org.emboss.jemboss.gui.filetree.RemoteFileNode

getPatternPositions(int, int, String) - Method in class org.emboss.jemboss.editor.SequenceJPanel

Find all occurences of the pattern in the sequence between the start and stop positions.

getPatternPositions(int, String) - Method in class org.emboss.jemboss.editor.SequenceJPanel

Find all occurences of the pattern in the sequence between the start and stop positions.

getPlplot() - Method in class org.emboss.jemboss.JembossParams

Get the location of plplot

getPlurality() - Method in class org.emboss.jemboss.editor.ConsensusOptions

Get the minimum positive match score for a site to be included in the consensus.

getPreferredScrollableViewportSize() - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection

Override for scrollable interface

getPreferredScrollableViewportSize() - Method in class org.emboss.jemboss.gui.ImageIconJPanel

getPreferredScrollableViewportSize() - Method in class org.emboss.jemboss.gui.ScrollPanel

getPreferredSize() - Method in class org.emboss.jemboss.editor.ColourMenu.ColorPane

getPreferredSize() - Method in class org.emboss.jemboss.editor.SequenceJPanel

Get the preferred size dimension

getPreferredSize() - Method in class org.emboss.jemboss.editor.SequenceNameJButton

Get the preferred size of this component

getPreferredSize() - Method in class org.emboss.jemboss.gui.ColorMenu.ColorPane

getPreferredSize() - Method in class org.emboss.jemboss.gui.ImageIconJPanel

Override getPreferredSize to return the dimensions of the ImageIcon

getPreferredSize(JComponent) - Method in class org.emboss.jemboss.gui.form.MultiLineToolTipUI

getPreferredSize() - Method in class org.emboss.jemboss.gui.sequenceChooser.FileChooser

Get the preferred size of the text field

getPrettyBackground(Color) - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection

Determine the colour of a residue background

getPrivateServerFailover() - Method in class org.emboss.jemboss.JembossParams

Return whether we have failover on the private server

getPrivateServers() - Method in class org.emboss.jemboss.JembossParams

Return a vector containing the list of private servers

getPrivateSoapService() - Method in class org.emboss.jemboss.JembossParams

Get the name of the private soap service

getPrivateSoapURL() - Method in class org.emboss.jemboss.JembossParams

Returns the URL of the private soap server

getPrnt() - Method in class org.emboss.jemboss.parser.Ajax

getProcess() - Method in class org.emboss.jemboss.programs.RunEmbossApplication

getProcess() - Method in class org.emboss.jemboss.programs.RunEmbossApplication2

getProcessStderr() - Method in class org.emboss.jemboss.programs.RunEmbossApplication2

getProcessStdout() - Method in class org.emboss.jemboss.programs.RunEmbossApplication

getProcessStdout() - Method in class org.emboss.jemboss.programs.RunEmbossApplication2

getProgDescription() - Method in class org.emboss.jemboss.gui.startup.ProgList

Returns the array of the program descriptions

getProgramGroup(String) - Method in class org.emboss.jemboss.gui.startup.ProgList

Returns the groups for the given application

getProgsList() - Method in class org.emboss.jemboss.gui.startup.ProgList

Returns the array of all the program names

getProject() - Method in class org.emboss.jemboss.programs.JembossProcess

Get the project name

getProxyAuthPasswd() - Method in class org.emboss.jemboss.JembossParams

Password needed to use for the proxy server

getProxyAuthUser() - Method in class org.emboss.jemboss.JembossParams

Username needed to use for the proxy server

getProxyHost() - Method in class org.emboss.jemboss.JembossParams

The name of the proxy server

getProxyPortNum() - Method in class org.emboss.jemboss.JembossParams

The port the proxy server listens on

getPublicServerFailover() - Method in class org.emboss.jemboss.JembossParams

Return whether we have failover on the public server

getPublicServers() - Method in class org.emboss.jemboss.JembossParams

Return a vector containing the list of public servers

getPublicSoapService() - Method in class org.emboss.jemboss.JembossParams

Get the name of the public soap service we're using

getPublicSoapURL() - Method in class org.emboss.jemboss.JembossParams

Returns the URL of the public soap server

getRegularExpression() - Method in class org.emboss.jemboss.editor.Matrix

Get regular expression for values in the scoring table

getReportCheckBox() - Method in class org.emboss.jemboss.gui.form.ReportFormat

Get the container box for the report format display on the Jemboss application form

getReportFormat() - Method in class org.emboss.jemboss.gui.form.ReportFormat

Return the EMBOSS command line string depending on what has been selected

getReportFormat() - Method in class org.emboss.jemboss.gui.form.SectionPanel

Get the report format

getReportFormats() - Static method in class org.emboss.jemboss.gui.form.ReportFormat

Get the available report formats

getResidue(Vector, int, int) - Method in class org.emboss.jemboss.editor.Consensus

Get the residue at a given position from a given sequence

getResidue(Vector, int, int) - Method in class org.emboss.jemboss.editor.PlotConsensus

Returns the residue of the sequence i at position k

getResidue(int) - Method in class org.emboss.jemboss.editor.Sequence

Get a residue in the sequence at a given position

getResidueAt(int) - Method in class org.emboss.jemboss.editor.Sequence

Get the residue at a position

getResidueMatrixPosition() - Method in class org.emboss.jemboss.editor.Matrix

Get the hashtable of the residue positions in the scoring table

getResidueWidth() - Method in class org.emboss.jemboss.editor.SequenceJPanel

Get the width of a residue

getResiduesPerLine(PageFormat) - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection

Get the number residues per line

getResiduesPerPage(PageFormat, int) - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection

Get the number residues per page

getResult() - Method in class org.emboss.jemboss.parser.AcdFunResolve

Returns the value of the result of the expression.

getResult() - Method in class org.emboss.jemboss.parser.AcdVarResolve

Get the resolved expression

getResult() - Method in class org.emboss.jemboss.parser.AcdVariableResolve

Get the resolved expression

getResult(String) - Method in class org.emboss.jemboss.soap.PendingResults

Get the processes result

getRoot(String, String, byte[]) - Method in class org.emboss.jemboss.server.JembossFileAuthServer

Given a file manager root alias e.g.

getRoot(String, String) - Method in class org.emboss.jemboss.server.JembossFileServer

Given the alias a user root alias e.g.

getRootDir() - Method in class org.emboss.jemboss.gui.filetree.RemoteFileNode

getRootSelect() - Method in class org.emboss.jemboss.gui.filetree.RemoteFileTreePanel

Get the root selection JComboBox

getRootVector() - Method in class org.emboss.jemboss.soap.FileRoots

Get the list of file manager roots

getRoots() - Method in class org.emboss.jemboss.soap.FileRoots

Get the list of file manager roots

getRowCount() - Method in class org.emboss.jemboss.gui.SequenceList

Return the number of rows in the table

getRowCount() - Method in class org.emboss.jemboss.gui.SequenceListTableModel

Return the number of rows in the table

getSafeFileName() - Method in class org.emboss.jemboss.soap.MakeFileSafe

Get the safe/sanitised file name

getScrollableBlockIncrement(Rectangle, int, int) - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection

Override for scrollable interface

getScrollableBlockIncrement(Rectangle, int, int) - Method in class org.emboss.jemboss.editor.GroutGraphicSequenceCollection

Override for scrollable interface

getScrollableBlockIncrement(Rectangle, int, int) - Method in class org.emboss.jemboss.gui.ImageIconJPanel

getScrollableBlockIncrement(Rectangle, int, int) - Method in class org.emboss.jemboss.gui.ScrollPanel

getScrollableTracksViewportHeight() - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection

Override for scrollable interface

getScrollableTracksViewportHeight() - Method in class org.emboss.jemboss.gui.ImageIconJPanel

getScrollableTracksViewportHeight() - Method in class org.emboss.jemboss.gui.ScrollPanel

getScrollableTracksViewportWidth() - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection

Override for scrollable interface

getScrollableTracksViewportWidth() - Method in class org.emboss.jemboss.gui.ImageIconJPanel

getScrollableTracksViewportWidth() - Method in class org.emboss.jemboss.gui.ScrollPanel

getScrollableTracksViewportWidth() - Method in class org.emboss.jemboss.gui.filetree.FileEditorDisplay

Override to avoid line wrapping.

getScrollableUnitIncrement(Rectangle, int, int) - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection

Override for scrollable interface

getScrollableUnitIncrement(Rectangle, int, int) - Method in class org.emboss.jemboss.editor.GroutGraphicSequenceCollection

Override for scrollable interface

getScrollableUnitIncrement(Rectangle, int, int) - Method in class org.emboss.jemboss.gui.ImageIconJPanel

getScrollableUnitIncrement(Rectangle, int, int) - Method in class org.emboss.jemboss.gui.ScrollPanel

getSectionBox() - Method in class org.emboss.jemboss.gui.form.SectionPanel

get the box or this section

getSectionPanel() - Method in class org.emboss.jemboss.gui.form.SectionPanel

get the panel for this section

getSelect(int) - Method in class org.emboss.jemboss.parser.ParseAcd

Used for a selection type to put the list items in a String array.

getSelectedFiles() - Method in class org.emboss.jemboss.gui.filetree.DragTree

Get selected files

getSelectedJTextPane(JTabbedPane) - Method in class org.emboss.jemboss.gui.ResultsMenuBar

Get selected text pane from tabbed pane

getSelectedNode() - Method in class org.emboss.jemboss.gui.filetree.DragTree

Get FileNode of selected node

getSelectedNode() - Method in class org.emboss.jemboss.gui.filetree.RemoteDragTree

Get RemoteFileNode of selected node

getSelectedNodes() - Method in class org.emboss.jemboss.gui.filetree.DragTree

Get FileNodes of selected nodes

getSelectedNodes() - Method in class org.emboss.jemboss.gui.filetree.RemoteDragTree

Get RemoteFileNodes of selected nodes

getSequence() - Method in class org.emboss.jemboss.editor.Paste

getSequence() - Method in class org.emboss.jemboss.editor.Sequence

Get the sequence

getSequence(int) - Method in class org.emboss.jemboss.editor.SequenceReader

Returns the sequence at a given position in the Sequence Vector store.

getSequence(int) - Method in class org.emboss.jemboss.gui.form.ListFilePanel

Get a sequence form the list using its number in the list

getSequence(int) - Method in class org.emboss.jemboss.gui.form.SetInFileCard

Return a sequence from a list of sequences

getSequenceCollection() - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection

Get the vector of Sequences

getSequenceData(int) - Method in class org.emboss.jemboss.gui.SequenceList

The SequenceData for a given row number.

getSequenceData(int) - Method in class org.emboss.jemboss.gui.SequenceListTableModel

The SequenceData for a given row number.

getSequenceFile() - Method in class org.emboss.jemboss.editor.SequenceReader

Get the sequence file

getSequenceHeight() - Method in class org.emboss.jemboss.editor.SequenceJPanel

Get the sequence panel height

getSequenceName() - Method in class org.emboss.jemboss.gui.SequenceData

Returns the sequence name

getSequencePrintGraphic(Graphics, int, int, int) - Method in class org.emboss.jemboss.editor.SequenceJPanel

Render the sequence graphic

getSequenceResidueWidth() - Method in class org.emboss.jemboss.editor.SequenceJPanel

Get the width of a residue

getSequenceVector() - Method in class org.emboss.jemboss.editor.SequenceReader

Returns the Sequence Vector store

getSequenceWeight(Vector, int) - Method in class org.emboss.jemboss.editor.Consensus

Get the sequence weight

getSequenceWeight(Vector, int) - Method in class org.emboss.jemboss.editor.PlotConsensus

Returns the weight of sequence i

getSequenceWidth() - Method in class org.emboss.jemboss.editor.SequenceJPanel

Get the sequence panel width

getServerName() - Method in class org.emboss.jemboss.gui.filetree.RemoteFileNode

Get the server name

getServicePasswd() - Method in class org.emboss.jemboss.JembossParams

Return the password needed for the remote service

getServicePasswdByte() - Method in class org.emboss.jemboss.JembossParams

Return the password needed for the remote service

getServiceUserName() - Method in class org.emboss.jemboss.JembossParams

Return the username needed for the remote service

getSize() - Method in class org.emboss.jemboss.parser.Ajax

getSoapService() - Method in class org.emboss.jemboss.JembossParams

Get the name of the soap service

getSplashFrame() - Method in class org.emboss.jemboss.soap.AuthPopup

getStatus() - Method in class org.emboss.jemboss.programs.ResultList

The status of the request

getStatus() - Method in class org.emboss.jemboss.programs.RunEmbossApplication

getStatus() - Method in class org.emboss.jemboss.programs.RunEmbossApplication2

getStatus() - Method in class org.emboss.jemboss.soap.CallAjax

Get the status

getStatus() - Method in class org.emboss.jemboss.soap.GetHelp

The status of the request

getStatus() - Method in class org.emboss.jemboss.soap.JembossRun

The status of the request

getStatus() - Method in class org.emboss.jemboss.soap.PendingResults

getStatus() - Method in class org.emboss.jemboss.soap.ShowDB

Get the status of the request

getStatusMsg() - Method in class org.emboss.jemboss.programs.ResultList

A status message.

getStatusMsg() - Method in class org.emboss.jemboss.soap.CallAjax

Get the message

getStatusMsg() - Method in class org.emboss.jemboss.soap.GetHelp

A status message .

getStatusMsg() - Method in class org.emboss.jemboss.soap.JembossRun

A status message or description of a error

getStatusMsg() - Method in class org.emboss.jemboss.soap.ShowDB

Get the status message

getTab(int) - Method in class org.emboss.jemboss.gui.TabListCellRenderer

getTabs() - Method in class org.emboss.jemboss.gui.TabListCellRenderer

getText() - Method in class org.emboss.jemboss.gui.sequenceChooser.CutNPasteTextArea

getTextFieldSink() - Method in class org.emboss.jemboss.gui.sequenceChooser.FileChooser

Get the text field

getToolBar() - Method in class org.emboss.jemboss.gui.ResultsMenuBar

Get the tool bar

getToolTip() - Method in class org.emboss.jemboss.gui.form.AlignFormat

getToolTip() - Static method in class org.emboss.jemboss.gui.form.ReportFormat

getToolTipLocation(MouseEvent) - Method in class org.emboss.jemboss.editor.SequenceJPanel

Get the tool tip location

getToolTipText(MouseEvent) - Method in class org.emboss.jemboss.editor.SequenceJPanel

Determine the tool tip to display

getTotalWeight(Vector) - Static method in class org.emboss.jemboss.editor.AlignJFrame

getTransferData(DataFlavor) - Method in class org.emboss.jemboss.gui.SequenceData

getTransferData(DataFlavor) - Method in class org.emboss.jemboss.gui.filetree.FileNode

getTransferData(DataFlavor) - Method in class org.emboss.jemboss.gui.filetree.RemoteFileNode

getTransferDataFlavors() - Method in class org.emboss.jemboss.gui.SequenceData

getTransferDataFlavors() - Method in class org.emboss.jemboss.gui.filetree.FileNode

getTransferDataFlavors() - Method in class org.emboss.jemboss.gui.filetree.RemoteFileNode

getURLAt(int) - Method in class org.emboss.jemboss.gui.MemoryComboBox

getUsaDesCheckBox() - Method in class org.emboss.jemboss.gui.form.ReportFormat

Get the check box for USA display

getUseAuth() - Method in class org.emboss.jemboss.JembossParams

Whether the main service requires authentication

getUseHTTPSProxy() - Method in class org.emboss.jemboss.JembossParams

If using an https proxy server

getUseProxy() - Method in class org.emboss.jemboss.JembossParams

If using a proxy server

getUseProxy(String) - Method in class org.emboss.jemboss.JembossParams

If using a proxy server for a given URL

getUseProxyAuth() - Method in class org.emboss.jemboss.JembossParams

If using authenticate with the proxy

getUserHome() - Method in class org.emboss.jemboss.JembossParams

Get the user home directory

getVal(String) - Method in class org.emboss.jemboss.soap.PrivateRequest

Gets an element out of the embreo result hash

getVal(String) - Method in class org.emboss.jemboss.soap.PublicRequest

Gets an element out of the Jemboss result hash

getValue() - Method in class org.emboss.jemboss.gui.SwingWorker

Get the value produced by the worker thread, or null if it hasn't been constructed yet.

getValue() - Method in class org.emboss.jemboss.gui.form.TextFieldFloat

getValue() - Method in class org.emboss.jemboss.gui.form.TextFieldInt

getValueAt(int, int) - Method in class org.emboss.jemboss.gui.SequenceListTableModel

Get the Object in a cell in the table

getValueDbl() - Method in class org.emboss.jemboss.parser.acd.ApplicationParam

Get the parameter value

getValueStr() - Method in class org.emboss.jemboss.parser.acd.ApplicationParam

Get the parameter value

getVector(Hashtable) - Method in class org.emboss.jemboss.soap.PendingResults

Change a hashtable to a vector

getVector(Hashtable) - Method in class org.emboss.jemboss.soap.PrivateRequest

Change the contents of a hashtable to a vector

getViewPosition() - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection

Get the position of the sequence JViewPort

getViewRect() - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection

Get the Rectangle being displayed by the sequence JViewPort

getViewSize() - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection

Get the sequence view size

getWeight() - Method in class org.emboss.jemboss.editor.Sequence

Get the sequence weight

getWeight() - Method in class org.emboss.jemboss.soap.CallAjax

Get the sequence weight

getWossname() - Method in class org.emboss.jemboss.server.JembossAuthServer

Returns the output of the EMBOSS utility wossname

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

Returns the output of the EMBOSS utility wossname

getWossnameText() - Method in class org.emboss.jemboss.soap.GetWossname

Get wossname output

get_file(String, String, String, byte[]) - Method in class org.emboss.jemboss.server.JembossFileAuthServer

Get the contents of a file

get_file(String, String, String) - Method in class org.emboss.jemboss.server.JembossFileServer

Get the contents of a file

getembURL() - Method in class org.emboss.jemboss.JembossParams

graphicName - Variable in class org.emboss.jemboss.editor.GraphicSequenceCollection

Vector containing graphical names of sequences

graphicSequence - Variable in class org.emboss.jemboss.editor.AlignJFrame

graphicSequence - Variable in class org.emboss.jemboss.editor.GraphicSequenceCollection

Vector containing graphical sequences

groupList - Variable in class org.emboss.jemboss.parser.ParseAcd

String of the groups application belongs to

grout - Variable in class org.emboss.jemboss.gui.ShowResultSet

grout panel

groutAlignJFrameChanged(GroutAlignJFrameEvent) - Method in interface org.emboss.jemboss.editor.GroutAlignJFrameListener

groutGraphicSequenceCollectionChanged(GroutGraphicSequenceCollectionEvent) - Method in class org.emboss.jemboss.editor.GroutAlignJFrame

Responds to the groutGraphicSequenceCollectionChanged event

groutGraphicSequenceCollectionChanged(GroutGraphicSequenceCollectionEvent) - Method in interface org.emboss.jemboss.editor.GroutGraphicSequenceCollectionListener

groutGraphicSequenceCollectionChanged(GroutGraphicSequenceCollectionEvent) - Method in class org.emboss.jemboss.editor.GroutSequenceJPanel

gsc - Variable in class org.emboss.jemboss.editor.AlignApplet

gsc - Static variable in class org.emboss.jemboss.editor.AlignJFrame

gsc - Variable in class org.emboss.jemboss.editor.ConsensusOptions

graphic sequence collection

gsc - Variable in class org.emboss.jemboss.editor.PatternJFrame

graphic sequence panel

gsc - Variable in class org.emboss.jemboss.editor.PrettyPlotJFrame

graphic sequence panel

gsc - Variable in class org.emboss.jemboss.editor.PrintAlignmentImage

alignment sequence panel

guiHandleNumber - Variable in class org.emboss.jemboss.parser.acd.ApplicationFields

the gui handle

H

h - Variable in class org.emboss.jemboss.gui.form.SetInFileCard

gui handle number

hasBatchMode - Variable in class org.emboss.jemboss.JembossParams

batch mode support

hasBatchModeName - Variable in class org.emboss.jemboss.JembossParams

property name for batch mode support

hasInteractiveMode - Variable in class org.emboss.jemboss.JembossParams

interactive mode support

hasInteractiveModeName - Variable in class org.emboss.jemboss.JembossParams

property name for interactive mode support

hash() - Method in class org.emboss.jemboss.programs.ResultList

hash() - Method in class org.emboss.jemboss.soap.JembossRun

Get a Hashtable of filenames and their contents generated by running the application

helpText - Variable in class org.emboss.jemboss.soap.GetACD

acd text

helpText - Variable in class org.emboss.jemboss.soap.GetHelp

helptext - Variable in class org.emboss.jemboss.gui.form.BuildJembossForm

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

hgt - Variable in class org.emboss.jemboss.editor.GraphicSequenceCollection

highlightPattern - Variable in class org.emboss.jemboss.editor.SequenceJPanel

high light search pattern

home - Variable in class org.emboss.jemboss.parser.Ajax

user home dir

homeDirectory - Variable in class org.emboss.jemboss.server.JembossServer

user home directory

htmlPane - Variable in class org.emboss.jemboss.gui.Browser

HTML pane

hydrophobicColor - Static variable in class org.emboss.jemboss.editor.SequenceProperties

Hydrophobic (Red=Hydrophobic)

hyperlinkUpdate(HyperlinkEvent) - Method in class org.emboss.jemboss.gui.Browser

Method to handle hyper link events.

I

IDTableJFrame - class org.emboss.jemboss.editor.IDTableJFrame.

Use to display the identical matches table for each pair of sequences

IDTableJFrame(Vector) - Constructor for class org.emboss.jemboss.editor.IDTableJFrame

ImageIconJPanel - class org.emboss.jemboss.gui.ImageIconJPanel.

Use to display ImageIcons on a JPanel

ImageIconJPanel(ImageIcon) - Constructor for class org.emboss.jemboss.gui.ImageIconJPanel

InputSequenceAttributes - class org.emboss.jemboss.gui.sequenceChooser.InputSequenceAttributes.

Creates the input sequence attibutes window

InputSequenceAttributes(String[], FileChooser) - Constructor for class org.emboss.jemboss.gui.sequenceChooser.InputSequenceAttributes

i - Variable in class org.emboss.jemboss.editor.Matrix

id - Variable in class org.emboss.jemboss.editor.Sequence

sequence id

idColour - Variable in class org.emboss.jemboss.editor.PrettyPlotJFrame

colour panel for identical matches

idColourBackground - Variable in class org.emboss.jemboss.editor.PrettyPlotJFrame

colour panel for identical matches background

idInt - Variable in class org.emboss.jemboss.editor.ConsensusOptions

identity

idSort() - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection

Sorts the sequences and displays them by their id's

idTable - Variable in class org.emboss.jemboss.editor.IDTableJFrame

idimension - Variable in class org.emboss.jemboss.editor.Matrix

ii - Variable in class org.emboss.jemboss.gui.ImageIconJPanel

image icon

inSeq - Variable in class org.emboss.jemboss.gui.form.BuildJembossForm

inSeq - Variable in class org.emboss.jemboss.gui.form.SectionPanel

input sequence field

inSeqAttr - Variable in class org.emboss.jemboss.gui.form.BuildJembossForm

inSeqAttr - Variable in class org.emboss.jemboss.gui.form.SectionPanel

input sequence attributes

inSeqAttr - Variable in class org.emboss.jemboss.gui.form.SetInFileCard

input sequence attributes

indent - Variable in class org.emboss.jemboss.editor.GroutSequence

indent - Variable in class org.emboss.jemboss.editor.GroutSequenceJPanel

init() - Method in class org.emboss.jemboss.editor.AlignApplet

init() - Method in class org.emboss.jemboss.editor.GroutSequenceJPanel

Add the mouse listener's

init() - Method in class org.emboss.jemboss.editor.SequenceJPanel

Add the mouse listener's

initStylesForTextPane() - Method in class org.emboss.jemboss.gui.filetree.FileEditorDisplay

Initialise styles for a JTextPane.

initialURL - Variable in class org.emboss.jemboss.gui.Browser

initial URL

initialize() - Static method in class org.emboss.jemboss.gui.form.MultiLineToolTipUI

inpSection - Static variable in class org.emboss.jemboss.gui.form.BuildJembossForm

insertData(SequenceListTableModel, Point, String, String, String, Boolean, Boolean, Boolean) - Method in class org.emboss.jemboss.gui.DragJTable

Inser sequence data into the sequence table

insertResidue(String, int) - Method in class org.emboss.jemboss.editor.Sequence

Insert a residue into the sequence

insertRow(int) - Method in class org.emboss.jemboss.gui.SequenceListTableModel

Insert a blank row

insertString(int, String, AttributeSet) - Method in class org.emboss.jemboss.gui.form.TextFieldFloat.DecimalNumberDocument

insertString(int, String, AttributeSet) - Method in class org.emboss.jemboss.gui.form.TextFieldInt.WholeNumberDocument

inset - Variable in class org.emboss.jemboss.gui.form.MultiLineToolTipUI

installUI(JComponent) - Method in class org.emboss.jemboss.gui.form.MultiLineToolTipUI

integerFormatter - Variable in class org.emboss.jemboss.gui.form.TextFieldInt

interrupt() - Method in class org.emboss.jemboss.gui.SwingWorker

A new method that interrupts the worker thread.

interval - Variable in class org.emboss.jemboss.editor.PlotConsensus

residue width

interval - Variable in class org.emboss.jemboss.editor.SequenceJPanel

sequence numbering interval

interval - Variable in class org.emboss.jemboss.gui.SplashThread

iprogress - Variable in class org.emboss.jemboss.soap.AuthPopup

progress monitor

iprogressmax - Variable in class org.emboss.jemboss.soap.AuthPopup

max value for the progress monitor

isAdd - Variable in class org.emboss.jemboss.gui.form.SectionPanel

true if the additional section

isAdditionalSection() - Method in class org.emboss.jemboss.gui.form.SectionPanel

isAdv - Variable in class org.emboss.jemboss.gui.form.SectionPanel

true if the advanced section

isAdvancedSection() - Method in class org.emboss.jemboss.gui.form.SectionPanel

isAlignFormat() - Method in class org.emboss.jemboss.gui.form.SectionPanel

Determine if alignment formats are used in the EMBOSS program

isAutoUpdate() - Method in class org.emboss.jemboss.soap.PendingResults

Automatically updating status manager with BatchUpdateTimer thread

isBackPage() - Method in class org.emboss.jemboss.gui.MemoryComboBox

Determine if a return page is stored

isBatchable() - Method in class org.emboss.jemboss.parser.ParseAcd

Finds if the program is identifies as being able to run in a batch queue

isBeginSeqDefault() - Method in class org.emboss.jemboss.gui.sequenceChooser.InputSequenceAttributes

Determine if there is a default -sbeg value

isBrowserProxy() - Method in class org.emboss.jemboss.JembossParams

Determine if the a proxy server is being used for web browsing

isCellEditable(int, int) - Method in class org.emboss.jemboss.gui.SequenceListTableModel

Define if a cell is editable by the user

isCompleted() - Method in class org.emboss.jemboss.programs.JembossProcess

Determine if a job has completed

isCut - Variable in class org.emboss.jemboss.gui.form.SetInFileCard

selecting cut and paste sequence input

isCutNPase() - Method in class org.emboss.jemboss.gui.form.SetInFileCard

isCygwin() - Static method in class org.emboss.jemboss.JembossParams

isDataFlavorSupported(DataFlavor) - Method in class org.emboss.jemboss.gui.SequenceData

isDataFlavorSupported(DataFlavor) - Method in class org.emboss.jemboss.gui.filetree.FileNode

isDataFlavorSupported(DataFlavor) - Method in class org.emboss.jemboss.gui.filetree.RemoteFileNode

isDefaultParamValueStr(int) - Method in class org.emboss.jemboss.parser.ParseAcd

Determine if there is a default parameter in a field of the ACD.

isDependents(String, int, int) - Method in class org.emboss.jemboss.parser.ParseAcd

Always start by calling isDependents(), which calculates the number of dependents and construct the Dependent array.

isDir - Variable in class org.emboss.jemboss.gui.filetree.RemoteFileNode

true if node is a directory

isDirectory() - Method in class org.emboss.jemboss.gui.filetree.FileNode

Determine if this is a directory

isDirectory() - Method in class org.emboss.jemboss.gui.filetree.RemoteFileNode

isDirectory(String) - Method in class org.emboss.jemboss.soap.FileList

Gets whether this name is a directory

isEndSeqDefault() - Method in class org.emboss.jemboss.gui.sequenceChooser.InputSequenceAttributes

Determine if there is a default -send value

isEqualSequenceLength(Vector) - Method in class org.emboss.jemboss.editor.Consensus

Check all sequences are the same length

isExplored() - Method in class org.emboss.jemboss.gui.filetree.FileNode

Determine if this node has been explored

isExplored() - Method in class org.emboss.jemboss.gui.filetree.RemoteFileNode

isExtensionDefault() - Method in class org.emboss.jemboss.gui.sequenceChooser.OutputSequenceAttributes

Determine if an extension has been selected

isFNameDefault() - Method in class org.emboss.jemboss.gui.sequenceChooser.OutputSequenceAttributes

Determine if a feature name is set

isFile - Variable in class org.emboss.jemboss.gui.form.SetInFileCard

selecting sequence file input (default)

isFileName() - Method in class org.emboss.jemboss.gui.form.SetInFileCard

isFileSelection() - Method in class org.emboss.jemboss.gui.filetree.DragTree

Return true if selected node is a file

isFileSelection() - Method in class org.emboss.jemboss.gui.filetree.RemoteDragTree

Determine if selected node is a file

isForwardPage() - Method in class org.emboss.jemboss.gui.MemoryComboBox

Determine if a forward page is stored

isInp - Variable in class org.emboss.jemboss.gui.form.SectionPanel

true if the input section

isInputSection() - Method in class org.emboss.jemboss.gui.form.SectionPanel

isItem(Object) - Method in class org.emboss.jemboss.gui.MemoryComboBox

Determine if item is in the JComboBox

isJembossServer() - Static method in class org.emboss.jemboss.JembossParams

isLeaf() - Method in class org.emboss.jemboss.gui.filetree.FileNode

Determine if this is a file

isLeaf() - Method in class org.emboss.jemboss.gui.filetree.RemoteFileNode

isList - Variable in class org.emboss.jemboss.gui.form.SetInFileCard

selecting list file input

isListFile(int) - Method in class org.emboss.jemboss.gui.DragJTable

Determine if a row in the table contains a list file

isListFile() - Method in class org.emboss.jemboss.gui.form.SetInFileCard

isMaxParamValue(int) - Method in class org.emboss.jemboss.parser.ParseAcd

Determine if there is a max parameter in a field of the ACD.

isMinParamValue(int) - Method in class org.emboss.jemboss.parser.ParseAcd

Determine if there is a min parameter in a field of the ACD.

isNameDefault() - Method in class org.emboss.jemboss.gui.sequenceChooser.OutputSequenceAttributes

Determine if a output file name is set

isOptionalParam() - Method in class org.emboss.jemboss.parser.ParseAcd

Determine if there is a optional parameter in any field of the ACD.

isOptionalParamValue(int) - Method in class org.emboss.jemboss.parser.ParseAcd

Determine if there is a optional parameter in a field of the ACD.

isOut - Variable in class org.emboss.jemboss.gui.form.SectionPanel

true if the output section

isOutputFile(int) - Method in class org.emboss.jemboss.parser.ParseAcd

Determine if a field is data type outfile.

isOutputGraph(int) - Method in class org.emboss.jemboss.parser.ParseAcd

Determine if a field is data type graph or xygraph.

isOutputSection() - Method in class org.emboss.jemboss.gui.form.SectionPanel

isOutputSequence(int) - Method in class org.emboss.jemboss.parser.ParseAcd

Determine if data type of a field is seqout.

isPairWise(ParseAcd, int) - Method in class org.emboss.jemboss.gui.form.AlignFormat

Method to determine whether this is a pairwise (returning true) or multiple sequence alignment format.

isParamValueStr(int, int) - Method in class org.emboss.jemboss.parser.ParseAcd

Determine if the value of the parameter is a String.

isParamValueStr(int) - Method in class org.emboss.jemboss.parser.acd.ApplicationFields

Determine if the parameter value is a string

isParamValueString() - Method in class org.emboss.jemboss.parser.acd.ApplicationParam

Determine if the parameter has a string value

isPrettyBox() - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection

Determine if the identities are to be boxed

isPrettyBox() - Method in class org.emboss.jemboss.editor.PrettyPlotJFrame

Determine if boxes are to be drawn around the identical matches

isPrettyPlot() - Method in class org.emboss.jemboss.editor.SequenceJPanel

Determine if using prettyplot display

isPrimaryGp - Variable in class org.emboss.jemboss.parser.ParseAcd

true if primary group is defined

isProcessStdout() - Method in class org.emboss.jemboss.programs.RunEmbossApplication

isProtein() - Method in class org.emboss.jemboss.editor.Sequence

Get the sequence type

isProtein() - Method in class org.emboss.jemboss.soap.CallAjax

Deternmine the sequence type

isReading() - Method in class org.emboss.jemboss.editor.SequenceReader

isReportFormat() - Method in class org.emboss.jemboss.gui.form.SectionPanel

Determine if report formats are used in the EMBOSS program

isReq - Variable in class org.emboss.jemboss.gui.form.SectionPanel

true if the required section

isRequiredSection() - Method in class org.emboss.jemboss.gui.form.SectionPanel

isRunning() - Method in class org.emboss.jemboss.programs.JembossProcess

Determine if a job is running

isSaveUserHomeSelected() - Method in class org.emboss.jemboss.gui.AdvancedOptions

isSecondaryGp - Variable in class org.emboss.jemboss.parser.ParseAcd

true if secondary group is defined

isSelected() - Method in class org.emboss.jemboss.editor.ColourMenu.ColorPane

isSelected() - Method in class org.emboss.jemboss.gui.ColorMenu.ColorPane

isShadedGUI - Variable in class org.emboss.jemboss.gui.form.SectionPanel

true if shading disabled fields, otherwise they are removed from the form

isStoreSequenceList() - Method in class org.emboss.jemboss.gui.SequenceList

Determines if a sequence list has been stored ("~/.jembossSeqList")

isUFODefault() - Method in class org.emboss.jemboss.gui.sequenceChooser.InputSequenceAttributes

Determine if there is a default -sufo value

isUFODefault() - Method in class org.emboss.jemboss.gui.sequenceChooser.OutputSequenceAttributes

Determine if UFO has a value

isUseTFM() - Method in class org.emboss.jemboss.JembossParams

J

Jemboss - class org.emboss.jemboss.Jemboss.

Java interface to EMBOSS (http://www.emboss.org/).

Jemboss() - Constructor for class org.emboss.jemboss.Jemboss

Display the Jemboss GUI.

Jemboss.winExit - class org.emboss.jemboss.Jemboss.winExit.

Extends WindowAdapter to close window and save any session properties and clean up

Jemboss.winExit() - Constructor for class org.emboss.jemboss.Jemboss.winExit

JembossAuthServer - class org.emboss.jemboss.server.JembossAuthServer.

Jemboss Authenticated Server for Apache Axis (SOAP) web services

JembossAuthServer() - Constructor for class org.emboss.jemboss.server.JembossAuthServer

JembossComboPopup - class org.emboss.jemboss.gui.form.JembossComboPopup.

Creates a scrolling JComboBox

JembossComboPopup(Object[]) - Constructor for class org.emboss.jemboss.gui.form.JembossComboPopup

Creates a JComboBox that contains the elements in the specified array.

JembossComboPopup(Vector) - Constructor for class org.emboss.jemboss.gui.form.JembossComboPopup

Creates a JComboBox that contains the elements in the vextor

JembossComboPopup.myComboUI - class org.emboss.jemboss.gui.form.JembossComboPopup.myComboUI.

Create scroller

JembossComboPopup.myComboUI() - Constructor for class org.emboss.jemboss.gui.form.JembossComboPopup.myComboUI

JembossFileAuthServer - class org.emboss.jemboss.server.JembossFileAuthServer.

File manager methods

JembossFileAuthServer() - Constructor for class org.emboss.jemboss.server.JembossFileAuthServer

JembossFileServer - class org.emboss.jemboss.server.JembossFileServer.

File manager methods - for a non-authenticating server

JembossFileServer() - Constructor for class org.emboss.jemboss.server.JembossFileServer

JembossJarUtil - class org.emboss.jemboss.JembossJarUtil.

Unpacks a Jar file into a Hashtable

JembossJarUtil(String) - Constructor for class org.emboss.jemboss.JembossJarUtil

Given the path to a jar file unpack to a hashtable

JembossLogo - class org.emboss.jemboss.JembossLogo.

JembossLogo(int, int, int) - Constructor for class org.emboss.jemboss.JembossLogo

JembossParams - class org.emboss.jemboss.JembossParams.

Contains all property information about the client and the server.

JembossParams() - Constructor for class org.emboss.jemboss.JembossParams

Loads and holds the properties

JembossProcess - class org.emboss.jemboss.programs.JembossProcess.

Monitor for Jemboss batch processes

JembossProcess(String, String, String) - Constructor for class org.emboss.jemboss.programs.JembossProcess

JembossProcess(String, String) - Constructor for class org.emboss.jemboss.programs.JembossProcess

JembossProcess(String) - Constructor for class org.emboss.jemboss.programs.JembossProcess

JembossRun - class org.emboss.jemboss.soap.JembossRun.

Executes an application on a server

JembossRun(String, String, Hashtable, JembossParams) - Constructor for class org.emboss.jemboss.soap.JembossRun

JembossServer - class org.emboss.jemboss.server.JembossServer.

Jemboss Non-authenticated Server for Apache Axis (SOAP) web services

JembossServer() - Constructor for class org.emboss.jemboss.server.JembossServer

JembossSoapException - exception org.emboss.jemboss.soap.JembossSoapException.

JembossSoapException() - Constructor for class org.emboss.jemboss.soap.JembossSoapException

When trown indicates a communication error with the server.

JembossSoapException(String) - Constructor for class org.emboss.jemboss.soap.JembossSoapException

JembossThread - class org.emboss.jemboss.server.JembossThread.

Use to run an EMBOSS application in batch mode by running the process in a separate thread

JembossThread(RunEmbossApplication2, String) - Constructor for class org.emboss.jemboss.server.JembossThread

jarStore - Variable in class org.emboss.jemboss.JembossJarUtil

Hashtable containing the unpacked contents of the jar file

javaNoProxy - Variable in class org.emboss.jemboss.JembossParams

javaNoProxyEntries - Variable in class org.emboss.jemboss.JembossParams

javaProxyHost - Variable in class org.emboss.jemboss.JembossParams

javaProxyPort - Variable in class org.emboss.jemboss.JembossParams

javaProxyPortNum - Variable in class org.emboss.jemboss.JembossParams

jdim - Static variable in class org.emboss.jemboss.Jemboss

Jemboss window dimension

jdimExtend - Static variable in class org.emboss.jemboss.Jemboss

Jemboss window dimension with local filemanager displayed

jdimension - Variable in class org.emboss.jemboss.editor.Matrix

jembossServer - Static variable in class org.emboss.jemboss.JembossParams

Jemboss java server

jembossServerName - Variable in class org.emboss.jemboss.JembossParams

property name for Jemboss java server

jembossSettings - Variable in class org.emboss.jemboss.JembossParams

jobButton - Variable in class org.emboss.jemboss.soap.PendingResults

job manager button

jobComboBox - Variable in class org.emboss.jemboss.soap.PendingResults

job manager interactive/batch selection

jobMgr - Static variable in class org.emboss.jemboss.gui.AdvancedOptions

job manager update times

jobStatus() - Method in class org.emboss.jemboss.soap.PendingResults

Report the status of completed and running processes.

jobid - Variable in class org.emboss.jemboss.programs.JembossProcess

project id

jp - Variable in class org.emboss.jemboss.server.JembossAuthServer

jemboss properties

jp - Variable in class org.emboss.jemboss.server.JembossFileAuthServer

jemboss properties

jp - Variable in class org.emboss.jemboss.server.JembossServer

jemboss properties

jspColour - Variable in class org.emboss.jemboss.editor.ColourJFrame

Scroll pane for the colour pallette

jspSequence - Variable in class org.emboss.jemboss.editor.AlignApplet

jspSequence - Variable in class org.emboss.jemboss.editor.AlignJFrame

jspSequence - Variable in class org.emboss.jemboss.editor.ConsensusOptions

jspSequence - Variable in class org.emboss.jemboss.editor.GraphicSequenceCollection

sequence scrollpane

K

k - Variable in class org.emboss.jemboss.editor.Matrix

keys - Variable in class org.emboss.jemboss.editor.Matrix

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

L

LINE_SEPARATOR - Static variable in class org.emboss.jemboss.gui.form.PlafMacros

LINE_SEPARATOR_LEN - Static variable in class org.emboss.jemboss.gui.form.PlafMacros

LabelTextBox - class org.emboss.jemboss.gui.form.LabelTextBox.

Container for Jemboss form label this will also wrap the text

LabelTextBox(String, String) - Constructor for class org.emboss.jemboss.gui.form.LabelTextBox

LaunchJalView - class org.emboss.jemboss.gui.LaunchJalView.

Launch Jalview (M.Clamp )

LaunchJalView() - Constructor for class org.emboss.jemboss.gui.LaunchJalView

ListFile - class org.emboss.jemboss.programs.ListFile.

Parse an EMBOSS list file, reading it in line by line, loading other list files recursively if necessary, and loading any files referred to into the filesToMove hash

ListFile() - Constructor for class org.emboss.jemboss.programs.ListFile

ListFilePanel - class org.emboss.jemboss.gui.form.ListFilePanel.

List file panel, enabling the user to generate a list of sequence in the GUI which can be used to generate an EMBOSS list file to be used in the command line.

ListFilePanel(int, JembossParams) - Constructor for class org.emboss.jemboss.gui.form.ListFilePanel

LocalAndRemoteFileTreeFrame - class org.emboss.jemboss.gui.filetree.LocalAndRemoteFileTreeFrame.

Local and remote combo file manager

LocalAndRemoteFileTreeFrame(JembossParams) - Constructor for class org.emboss.jemboss.gui.filetree.LocalAndRemoteFileTreeFrame

Displays the remote and local file managers in the same frame.

lab - Variable in class org.emboss.jemboss.gui.form.SectionPanel

field label container

labelColor - Static variable in class org.emboss.jemboss.gui.form.SectionPanel

label colour

labfont - Static variable in class org.emboss.jemboss.gui.form.SectionPanel

label font

labfont2 - Static variable in class org.emboss.jemboss.gui.form.SectionPanel

small label font

len - Variable in class org.emboss.jemboss.editor.GraphicSequenceCollection

length - Variable in class org.emboss.jemboss.editor.Sequence

sequence length

length - Static variable in class org.emboss.jemboss.parser.Ajax

sequence length

length - Variable in class org.emboss.jemboss.soap.CallAjax

sequence length

length_soap - Variable in class org.emboss.jemboss.parser.Ajax

sequence length

listByDateRun(ResultList, boolean) - Method in class org.emboss.jemboss.gui.ShowSavedResults

List results by date

listByProgramName() - Method in class org.emboss.jemboss.gui.ShowSavedResults

List results by alphabetical name

listDirs(String, byte[], String, String) - Method in class org.emboss.jemboss.parser.Ajax

list directorys

listFiles(String, byte[], String, String) - Method in class org.emboss.jemboss.parser.Ajax

list files in a directory

listPane - Variable in class org.emboss.jemboss.gui.form.SetInFileCard

list file panel

list_saved_results(String, byte[]) - Method in class org.emboss.jemboss.server.JembossAuthServer

List of the saved results on the server.

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

List of the saved results on the server.

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

List of the saved results on the server.

listdefault - Variable in class org.emboss.jemboss.parser.ParseAcd

default for list or select data type

lname - Variable in class org.emboss.jemboss.gui.sequenceChooser.FileChooser

label for text field

loadFilesContent(Ajax, String, byte[], File, String, Vector, Vector) - Method in class org.emboss.jemboss.server.JembossAuthServer

Reads in files from EMBOSS output

loadFilesContent(File, String, Vector, Hashtable) - Method in class org.emboss.jemboss.server.JembossServer

Reads in files from EMBOSS output

loadIn(String) - Method in class org.emboss.jemboss.JembossParams

Load a property from the jemboss.property file.

loadPNGContent(String) - Method in class org.emboss.jemboss.gui.filetree.FileEditorDisplay

Need to read png in, in case it is saved out

loadPNGContent(File, String, Vector) - Method in class org.emboss.jemboss.server.JembossServer

Reads in png files from EMBOSS output

loadStoredSeqList(File) - Method in class org.emboss.jemboss.gui.SequenceListTableModel

Load from stored file the SequenceList created from a previous session.

localAndRemoteTree - Static variable in class org.emboss.jemboss.gui.SetUpMenuBar

local and remote file manager window

logEntry - Variable in class org.emboss.jemboss.server.AppendToLogFileThread

logFile - Variable in class org.emboss.jemboss.server.JembossAuthServer

Jemboss log file

logFileName - Variable in class org.emboss.jemboss.server.AppendToLogFileThread

lower - Variable in class org.emboss.jemboss.gui.sequenceChooser.InputSequenceAttributes

select to specify lower case

lpair - Variable in class org.emboss.jemboss.gui.form.AlignFormat

true if pairwise alignment format

ls - Variable in class org.emboss.jemboss.gui.filetree.RemoteDragTree

line separator

ls - Variable in class org.emboss.jemboss.server.JembossAuthServer

line seperator

lsaved - Variable in class org.emboss.jemboss.gui.filetree.FileSaving

true if the file is saved ok

ltree - Static variable in class org.emboss.jemboss.gui.filetree.LocalAndRemoteFileTreeFrame

local file tree

M

MAGENTA - Static variable in class org.emboss.jemboss.editor.SequenceProperties

MAGENTA from EMBOSS data Ecolour.map

MAXSEQLENGTH - Variable in class org.emboss.jemboss.editor.GraphicSequenceCollection

longest sequence length

MAX_MEM_LEN - Static variable in class org.emboss.jemboss.gui.MemoryComboBox

MakeFileSafe - class org.emboss.jemboss.soap.MakeFileSafe.

Create a sanitised filename.

MakeFileSafe(String) - Constructor for class org.emboss.jemboss.soap.MakeFileSafe

Matrix - class org.emboss.jemboss.editor.Matrix.

Reads and hold a sequence scoring matrix

Matrix(File) - Constructor for class org.emboss.jemboss.editor.Matrix

Matrix(String, String) - Constructor for class org.emboss.jemboss.editor.Matrix

MatrixJFrame - class org.emboss.jemboss.editor.MatrixJFrame.

Display a matrix and list of available scoring matrix files

MatrixJFrame(Matrix, JTextField, AlignJFrame) - Constructor for class org.emboss.jemboss.editor.MatrixJFrame

MemoryComboBox - class org.emboss.jemboss.gui.MemoryComboBox.

Extends JComboBox to add and store new elements

MemoryComboBox(Vector) - Constructor for class org.emboss.jemboss.gui.MemoryComboBox

MultiLineToolTipUI - class org.emboss.jemboss.gui.form.MultiLineToolTipUI.

UI for multiple line tooltips

MultiLineToolTipUI() - Constructor for class org.emboss.jemboss.gui.form.MultiLineToolTipUI

MultiLineToolTipUI.MyToolTip - class org.emboss.jemboss.gui.form.MultiLineToolTipUI.MyToolTip.

Use this to getFontMetrics

MultiLineToolTipUI.MyToolTip() - Constructor for class org.emboss.jemboss.gui.form.MultiLineToolTipUI.MyToolTip

mItem - Variable in class org.emboss.jemboss.gui.startup.ProgList

used to create the program menus

mScroll - Variable in class org.emboss.jemboss.editor.MatrixJFrame

scroll pane for matrix display

m_defaultTab - Variable in class org.emboss.jemboss.gui.TabListCellRenderer

m_fm - Variable in class org.emboss.jemboss.gui.TabListCellRenderer

m_insets - Variable in class org.emboss.jemboss.gui.TabListCellRenderer

m_noFocusBorder - Static variable in class org.emboss.jemboss.gui.TabListCellRenderer

m_tabs - Variable in class org.emboss.jemboss.gui.TabListCellRenderer

main(String[]) - Static method in class org.emboss.jemboss.FileManager

main(String[]) - Static method in class org.emboss.jemboss.Jemboss

Launches Jemboss in standalone or client-server mode.

main(String[]) - Static method in class org.emboss.jemboss.editor.AlignJFrame

main(String[]) - Static method in class org.emboss.jemboss.editor.Consensus

main(String[]) - Static method in class org.emboss.jemboss.editor.GraphicSequenceCollection

main(String[]) - Static method in class org.emboss.jemboss.editor.GroutAlignJFrame

Test main really

main(String[]) - Static method in class org.emboss.jemboss.editor.PlotConsensus

main(String[]) - Static method in class org.emboss.jemboss.editor.Sequence

main(String[]) - Static method in class org.emboss.jemboss.gui.Browser

main(String[]) - Static method in class org.emboss.jemboss.gui.ImageIconJPanel

main(String[]) - Static method in class org.emboss.jemboss.server.TestPrivateServer

main(String[]) - Static method in class org.emboss.jemboss.server.TestPublicServer

mainMenu - Variable in class org.emboss.jemboss.Jemboss

Jemboss main menu

makeDir(String, byte[], String, String) - Method in class org.emboss.jemboss.parser.Ajax

make a directory

makeShape(float, float, float, float, float, float, float, float, float, float) - Static method in class org.emboss.jemboss.gui.Browser

Use to draw a Shape.

mat - Static variable in class org.emboss.jemboss.editor.AlignJFrame

mat - Variable in class org.emboss.jemboss.editor.ConsensusOptions

scoring matrix

mat - Variable in class org.emboss.jemboss.editor.GraphicSequenceCollection

scoring matrix

mat - Variable in class org.emboss.jemboss.editor.MatrixJFrame

scoring matrix

matchColour - Variable in class org.emboss.jemboss.editor.PrettyPlotJFrame

colour panel for positive scoring matches

matchColourBackground - Variable in class org.emboss.jemboss.editor.PrettyPlotJFrame

colour panel for positive scoring matches background

matrices - Static variable in class org.emboss.jemboss.gui.BuildProgramMenu

matrices

matrices - Variable in class org.emboss.jemboss.soap.ShowDB

scoring matrices

matrix - Variable in class org.emboss.jemboss.editor.AlignApplet

matrix - Variable in class org.emboss.jemboss.editor.Consensus

matrix - Variable in class org.emboss.jemboss.editor.Matrix

matrixFileName - Variable in class org.emboss.jemboss.editor.Matrix

matrixLineCount(String, RE) - Method in class org.emboss.jemboss.editor.Matrix

Count as a matrix row and number of columns

matrixLineParse(String, RE) - Method in class org.emboss.jemboss.editor.Matrix

Parse a line from a scoring matrix file.

matrixRead(File) - Method in class org.emboss.jemboss.editor.Matrix

Read and parse a scoring matrix file

matrixReadString(String) - Method in class org.emboss.jemboss.editor.Matrix

Read and parse a scoring matrix

matrixString - Variable in class org.emboss.jemboss.editor.Matrix

maxSectionWidth - Variable in class org.emboss.jemboss.gui.form.SectionPanel

maximum width of the form

maybeShowPopup(MouseEvent) - Method in class org.emboss.jemboss.editor.ColourPanel.PopupListener

maybeShowPopup(MouseEvent) - Method in class org.emboss.jemboss.editor.SequenceJPanel.PopupListener

maybeShowPopup(MouseEvent) - Method in class org.emboss.jemboss.gui.filetree.DragTree.PopupListener

maybeShowPopup(MouseEvent) - Method in class org.emboss.jemboss.gui.filetree.RemoteDragTree.PopupListener

memLog - Variable in class org.emboss.jemboss.server.AppendToLogFileThread

menuBar - Variable in class org.emboss.jemboss.editor.AlignJFrame

menuBar - Variable in class org.emboss.jemboss.gui.ShowResultSet

menu bar

menuFont - Variable in class org.emboss.jemboss.gui.startup.ProgList

font used for the menu items

mkdir(String, String, String, byte[]) - Method in class org.emboss.jemboss.server.JembossFileAuthServer

Make a directory

mkdir(String, String, String) - Method in class org.emboss.jemboss.server.JembossFileServer

Make a directory

mlist - Variable in class org.emboss.jemboss.parser.ParseAcd

number of list & selection fields - multiple selection

modeVector() - Method in class org.emboss.jemboss.JembossParams

Return the mode list as a vector, suitable for loading into a combobox.

modelColumns - Static variable in class org.emboss.jemboss.gui.SequenceListTableModel

Define the columns as file/start/end/list and default

modelVector - Static variable in class org.emboss.jemboss.gui.SequenceListTableModel

mouseClicked(MouseEvent) - Method in class org.emboss.jemboss.editor.ColourMenu.ColorPane

mouseClicked(MouseEvent) - Method in class org.emboss.jemboss.gui.ColorMenu.ColorPane

mouseEntered(MouseEvent) - Method in class org.emboss.jemboss.editor.ColourMenu.ColorPane

mouseEntered(MouseEvent) - Method in class org.emboss.jemboss.gui.ColorMenu.ColorPane

mouseExited(MouseEvent) - Method in class org.emboss.jemboss.editor.ColourMenu.ColorPane

mouseExited(MouseEvent) - Method in class org.emboss.jemboss.gui.ColorMenu.ColorPane

mousePressed(MouseEvent) - Method in class org.emboss.jemboss.editor.ColourMenu.ColorPane

mousePressed(MouseEvent) - Method in class org.emboss.jemboss.editor.ColourPanel.PopupListener

mousePressed(MouseEvent) - Method in class org.emboss.jemboss.editor.SequenceJPanel.PopupListener

mousePressed(MouseEvent) - Method in class org.emboss.jemboss.gui.ColorMenu.ColorPane

mousePressed(MouseEvent) - Method in class org.emboss.jemboss.gui.filetree.DragTree.PopupListener

mousePressed(MouseEvent) - Method in class org.emboss.jemboss.gui.filetree.RemoteDragTree.PopupListener

mouseReleased(MouseEvent) - Method in class org.emboss.jemboss.editor.ColourMenu.ColorPane

mouseReleased(MouseEvent) - Method in class org.emboss.jemboss.editor.ColourPanel.PopupListener

mouseReleased(MouseEvent) - Method in class org.emboss.jemboss.editor.SequenceJPanel.PopupListener

mouseReleased(MouseEvent) - Method in class org.emboss.jemboss.gui.ColorMenu.ColorPane

mouseReleased(MouseEvent) - Method in class org.emboss.jemboss.gui.filetree.DragTree.PopupListener

mouseReleased(MouseEvent) - Method in class org.emboss.jemboss.gui.filetree.RemoteDragTree.PopupListener

moveSequence(String, int) - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection

Move a sequence to a new position

msf - Static variable in class org.emboss.jemboss.gui.sequenceChooser.SequenceFilter

multiOption - Variable in class org.emboss.jemboss.gui.form.BuildJembossForm

multiOption - Variable in class org.emboss.jemboss.gui.form.SectionPanel

multiple option field for list and select

myset - Variable in class org.emboss.jemboss.soap.ServerSetup

jemboss properties

mysettings - Variable in class org.emboss.jemboss.gui.filetree.DragTree

jemboss properties

mysettings - Variable in class org.emboss.jemboss.gui.filetree.RemoteDragTree

jemboss properties

mysettings - Variable in class org.emboss.jemboss.gui.filetree.RemoteFileNode

jemboss properties

mysettings - Variable in class org.emboss.jemboss.gui.form.BuildJembossForm

mysettings - Variable in class org.emboss.jemboss.gui.form.SectionPanel

jemboss properties

mysettings - Static variable in class org.emboss.jemboss.server.TestPrivateServer

mysettings - Static variable in class org.emboss.jemboss.server.TestPublicServer

mysettings - Variable in class org.emboss.jemboss.soap.AuthPopup

jemboss properties

mysettings - Variable in class org.emboss.jemboss.soap.PendingResults

jemboss properties

N

nFiles - Variable in class org.emboss.jemboss.gui.form.ListFilePanel

maximum number of sequences in list

nResPerLine - Variable in class org.emboss.jemboss.editor.PrintAlignmentImage

number of residues per line

name - Variable in class org.emboss.jemboss.editor.Sequence

sequence name

name - Variable in class org.emboss.jemboss.gui.form.ApplicationNamePanel

application name

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

nameLabel - Variable in class org.emboss.jemboss.editor.SequenceNameJButton

name label

nbool - Variable in class org.emboss.jemboss.parser.ParseAcd

number of checkbox fields

newRoot(String) - Method in class org.emboss.jemboss.gui.filetree.DragTree

Define a directory root for the file tree

nf - Variable in class org.emboss.jemboss.gui.form.SectionPanel

field number to start from

nflist - Variable in class org.emboss.jemboss.parser.ParseAcd

number of filelist fields

nfloat - Variable in class org.emboss.jemboss.parser.ParseAcd

number of float fields

nint - Variable in class org.emboss.jemboss.parser.ParseAcd

number of integer fields

nlist - Variable in class org.emboss.jemboss.parser.ParseAcd

number of list & selection fields - single selection

nm - Variable in class org.emboss.jemboss.gui.startup.ProgList

number of JMenuItem created

nodeExists(RemoteFileNode, String) - Method in class org.emboss.jemboss.gui.filetree.RemoteDragTree

Test if a child node exists

notifyGroup(int, int) - Method in class org.emboss.jemboss.editor.SequenceJPanel

Update all observers

notifyTargets(String, Object, Object) - Method in class org.emboss.jemboss.editor.GroutAlignJFrame

notifyTargets(String, Object, Object) - Method in class org.emboss.jemboss.editor.GroutGraphicSequenceCollection

npG - Variable in class org.emboss.jemboss.gui.startup.ProgList

number of primary group programs

nrange - Variable in class org.emboss.jemboss.parser.ParseAcd

number of range fields

nsection - Variable in class org.emboss.jemboss.parser.ParseAcd

number of sections

nseqs - Variable in class org.emboss.jemboss.parser.ParseAcd

number of sequence fields

nsplash - Variable in class org.emboss.jemboss.gui.SplashThread

nsubsection - Variable in class org.emboss.jemboss.parser.ParseAcd

number of subsections

ntextf - Variable in class org.emboss.jemboss.parser.ParseAcd

number of text fields

nucleotide - Variable in class org.emboss.jemboss.gui.sequenceChooser.InputSequenceAttributes

select to specify a nucleotide sequence

numOfDependents - Variable in class org.emboss.jemboss.parser.ParseAcd

number of dependent variables

numProgs - Variable in class org.emboss.jemboss.gui.startup.ProgList

number of programs

numResiduePerLine - Variable in class org.emboss.jemboss.editor.GraphicSequenceCollection

number of residues on each line for print

numberDraw - Variable in class org.emboss.jemboss.editor.GraphicSequenceCollection

panel for sequence numbers

numbins - Variable in class org.emboss.jemboss.editor.PlotConsensus

number of graph bins making up the seq length

numofFields - Variable in class org.emboss.jemboss.gui.form.BuildJembossForm

numofFields - Variable in class org.emboss.jemboss.gui.form.SectionPanel

number of fields in the ACD

numofFields - Variable in class org.emboss.jemboss.parser.ParseAcd

number of ACD fields

numofParams - Variable in class org.emboss.jemboss.parser.ParseAcd

number of parameters in a field

numofParams - Variable in class org.emboss.jemboss.parser.acd.ApplicationFields

number of parameters for this field

nvalue - Variable in class org.emboss.jemboss.parser.ParseAcd

double value of a parameter

nvalue - Variable in class org.emboss.jemboss.parser.acd.ApplicationParam

parameter number value

O

OutputSequenceAttributes - class org.emboss.jemboss.gui.sequenceChooser.OutputSequenceAttributes.

Creates the output sequence attibutes window

OutputSequenceAttributes() - Constructor for class org.emboss.jemboss.gui.sequenceChooser.OutputSequenceAttributes

observers - Variable in class org.emboss.jemboss.editor.SequenceJPanel

observer panels in this group

offormat - Variable in class org.emboss.jemboss.gui.sequenceChooser.OutputSequenceAttributes

feature format

ofname - Variable in class org.emboss.jemboss.gui.sequenceChooser.OutputSequenceAttributes

features filename

okButton - Variable in class org.emboss.jemboss.soap.AuthPopup

OK button

openMethod(Vector) - Method in class org.emboss.jemboss.editor.AlignJFrame

Given a Vector of Sequence display them in the editor

openMethod(Vector) - Method in class org.emboss.jemboss.editor.GroutAlignJFrame

Given a Vector of Sequence display them in the editor

openMethod(Vector, Vector) - Method in class org.emboss.jemboss.editor.GroutAlignJFrame

Given a Vector of Sequence and the indent for each display them in the editor

openNode - Variable in class org.emboss.jemboss.gui.filetree.DragTree

store of directories that are opened

openNode - Variable in class org.emboss.jemboss.gui.filetree.RemoteDragTree

store of directories that are opened

order - Variable in class org.emboss.jemboss.gui.MemoryComboBox

org.emboss.jemboss - package org.emboss.jemboss

org.emboss.jemboss.editor - package org.emboss.jemboss.editor

org.emboss.jemboss.gui - package org.emboss.jemboss.gui

org.emboss.jemboss.gui.filetree - package org.emboss.jemboss.gui.filetree

org.emboss.jemboss.gui.form - package org.emboss.jemboss.gui.form

org.emboss.jemboss.gui.sequenceChooser - package org.emboss.jemboss.gui.sequenceChooser

org.emboss.jemboss.gui.startup - package org.emboss.jemboss.gui.startup

org.emboss.jemboss.parser - package org.emboss.jemboss.parser

org.emboss.jemboss.parser.acd - package org.emboss.jemboss.parser.acd

org.emboss.jemboss.programs - package org.emboss.jemboss.programs

org.emboss.jemboss.server - package org.emboss.jemboss.server

org.emboss.jemboss.soap - package org.emboss.jemboss.soap

osextension - Variable in class org.emboss.jemboss.gui.sequenceChooser.OutputSequenceAttributes

ouput file extension to use

osname - Variable in class org.emboss.jemboss.gui.sequenceChooser.OutputSequenceAttributes

output base name

ossingle - Variable in class org.emboss.jemboss.gui.sequenceChooser.OutputSequenceAttributes

separate file for each entry

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

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

outStd - Variable in class org.emboss.jemboss.parser.Ajax

stdout

outfileResult - Variable in class org.emboss.jemboss.gui.form.BuildJembossForm

P

PINK - Static variable in class org.emboss.jemboss.editor.SequenceProperties

PINK from EMBOSS data Ecolour.map

ParseAcd - class org.emboss.jemboss.parser.ParseAcd.

ACD (Ajax command line definition) file parser.

ParseAcd(String, boolean) - Constructor for class org.emboss.jemboss.parser.ParseAcd

The constructor takes the ACD as a string.

Paste - class org.emboss.jemboss.editor.Paste.

Paste() - Constructor for class org.emboss.jemboss.editor.Paste

PatternJFrame - class org.emboss.jemboss.editor.PatternJFrame.

Frame for searching for patterns in the sequences

PatternJFrame() - Constructor for class org.emboss.jemboss.editor.PatternJFrame

PendingResults - class org.emboss.jemboss.soap.PendingResults.

Record the batch job status (pending/completed)

PendingResults(JembossParams) - Constructor for class org.emboss.jemboss.soap.PendingResults

PlafMacros - class org.emboss.jemboss.gui.form.PlafMacros.

Macros class

PlafMacros() - Constructor for class org.emboss.jemboss.gui.form.PlafMacros

PlotConsensus - class org.emboss.jemboss.editor.PlotConsensus.

Plot the average similarity.

PlotConsensus(File, Vector, int, int, GraphicSequenceCollection) - Constructor for class org.emboss.jemboss.editor.PlotConsensus

PlotConsensus(File, Vector, int, int) - Constructor for class org.emboss.jemboss.editor.PlotConsensus

PlotConsensus(String, String, Vector, int, int) - Constructor for class org.emboss.jemboss.editor.PlotConsensus

PlotConsensus(Matrix, Vector, int, int, GraphicSequenceCollection) - Constructor for class org.emboss.jemboss.editor.PlotConsensus

PlotConsensus(Matrix, Vector, int, int) - Constructor for class org.emboss.jemboss.editor.PlotConsensus

PrettyPlotJFrame - class org.emboss.jemboss.editor.PrettyPlotJFrame.

JFrame to define the colour of residue if identical or a positive match.

PrettyPlotJFrame(int, float, Color, Color, Color, Color, boolean) - Constructor for class org.emboss.jemboss.editor.PrettyPlotJFrame

PrettyPlotJFrame(GraphicSequenceCollection) - Constructor for class org.emboss.jemboss.editor.PrettyPlotJFrame

PrintAlignment - class org.emboss.jemboss.editor.PrintAlignment.

Class for printing the alignment

PrintAlignment(GraphicSequenceCollection) - Constructor for class org.emboss.jemboss.editor.PrintAlignment

PrintAlignmentImage - class org.emboss.jemboss.editor.PrintAlignmentImage.

Print png/jpeg image and print preview.

PrintAlignmentImage(GraphicSequenceCollection, PageFormat) - Constructor for class org.emboss.jemboss.editor.PrintAlignmentImage

PrintAlignmentImage(GraphicSequenceCollection) - Constructor for class org.emboss.jemboss.editor.PrintAlignmentImage

PrintableJTable - class org.emboss.jemboss.editor.PrintableJTable.

PrintableJTable() - Constructor for class org.emboss.jemboss.editor.PrintableJTable

PrintableJTable(Object[][], String[]) - Constructor for class org.emboss.jemboss.editor.PrintableJTable

PrivateRequest - class org.emboss.jemboss.soap.PrivateRequest.

Make a axis call to a private server, using the default service

PrivateRequest(JembossParams, String, Vector) - Constructor for class org.emboss.jemboss.soap.PrivateRequest

PrivateRequest(JembossParams, String, String) - Constructor for class org.emboss.jemboss.soap.PrivateRequest

PrivateRequest(JembossParams, String, String, Vector) - Constructor for class org.emboss.jemboss.soap.PrivateRequest

ProgList - class org.emboss.jemboss.gui.startup.ProgList.

Used on startup of Jemboss to retrieve the alphabetical list of programs and uses the programs groups to create the menu structure based on the program type.

ProgList(String, JMenuBar) - Constructor for class org.emboss.jemboss.gui.startup.ProgList

ProgList.HorizontalMenu - class org.emboss.jemboss.gui.startup.ProgList.HorizontalMenu.

HorizontalMenu extends JMenu to produces horizontal menus.

ProgList.HorizontalMenu(String) - Constructor for class org.emboss.jemboss.gui.startup.ProgList.HorizontalMenu

PublicRequest - class org.emboss.jemboss.soap.PublicRequest.

Make a axis call to a public server, using the default service

PublicRequest(JembossParams, String) - Constructor for class org.emboss.jemboss.soap.PublicRequest

PublicRequest(JembossParams, String, Vector) - Constructor for class org.emboss.jemboss.soap.PublicRequest

PublicRequest(JembossParams, String, String) - Constructor for class org.emboss.jemboss.soap.PublicRequest

PublicRequest(JembossParams, String, String, Vector) - Constructor for class org.emboss.jemboss.soap.PublicRequest

p - Variable in class org.emboss.jemboss.programs.RunEmbossApplication

running process

p - Variable in class org.emboss.jemboss.programs.RunEmbossApplication2

running process

p2 - Variable in class org.emboss.jemboss.gui.form.BuildJembossForm

p3 - Variable in class org.emboss.jemboss.Jemboss

Local filemanager panel

p3 - Variable in class org.emboss.jemboss.gui.form.SectionPanel

Jemboss form panel

padChar - Variable in class org.emboss.jemboss.editor.SequenceJPanel

pad/gap character

pageIndex - Variable in class org.emboss.jemboss.editor.PrintAlignmentImage

page number to print

paint(Graphics) - Method in class org.emboss.jemboss.gui.TabListCellRenderer

paint(Graphics, JComponent) - Method in class org.emboss.jemboss.gui.form.MultiLineToolTipUI

paint(Graphics) - Method in class org.emboss.jemboss.gui.form.Separator

Override paint to draw separator

paintComponent(Graphics) - Method in class org.emboss.jemboss.JembossLogo

paintComponent(Graphics) - Method in class org.emboss.jemboss.editor.ColourPanel

Override paintComponent

paintComponent(Graphics) - Method in class org.emboss.jemboss.editor.PlotConsensus

Override paintComponent to draw consensus plot

paintComponent(Graphics) - Method in class org.emboss.jemboss.editor.PrintAlignmentImage

Override this method to draw the sequences

paintComponent(Graphics) - Method in class org.emboss.jemboss.editor.SequenceJPanel

Override paintComponent

paintComponent(Graphics) - Method in class org.emboss.jemboss.gui.ImageIconJPanel

Override the paintComponent

paintComponent(Graphics) - Method in class org.emboss.jemboss.gui.form.ApplicationNamePanel

Override paintComponent

panes - Variable in class org.emboss.jemboss.editor.ColourMenu

hashtable of the colour panes

panes - Variable in class org.emboss.jemboss.gui.ColorMenu

param - Variable in class org.emboss.jemboss.parser.Dependent

parameter number

parentList - Variable in class org.emboss.jemboss.gui.filetree.RemoteFileNode

parent directory listing

parse(String, Hashtable) - Static method in class org.emboss.jemboss.programs.ListFile

parseAcd - Variable in class org.emboss.jemboss.gui.form.BuildJembossForm

parseAcd - Variable in class org.emboss.jemboss.gui.form.SectionPanel

ACD parser for the application selected

parseParam(BufferedReader, StreamTokenizer) - Method in class org.emboss.jemboss.parser.ParseAcd

Parses a parameter in a ACD field

pasteText() - Method in class org.emboss.jemboss.gui.form.TextFieldSink

pasteText() - Method in class org.emboss.jemboss.gui.sequenceChooser.TextAreaSink

Add text from the system clipboard into the text area

pattern - Variable in class org.emboss.jemboss.editor.SequenceJPanel

pattern to search for

pc - Variable in class org.emboss.jemboss.editor.GraphicSequenceCollection

Consensus plot

pendingResults - Variable in class org.emboss.jemboss.soap.PendingResults

pending results

pfield - Variable in class org.emboss.jemboss.soap.AuthPopup

passwd field

plotConStrut - Variable in class org.emboss.jemboss.editor.GraphicSequenceCollection

gap between sequences and consensus plot

plotconsSeqBox - Variable in class org.emboss.jemboss.editor.GraphicSequenceCollection

container for consensus plot

plplot - Variable in class org.emboss.jemboss.JembossParams

plplot library location

plplot - Variable in class org.emboss.jemboss.server.JembossAuthServer

plplot path

plplot - Variable in class org.emboss.jemboss.server.JembossServer

plplot path

plplotName - Variable in class org.emboss.jemboss.JembossParams

property name for plplot library location

pluralFloat - Variable in class org.emboss.jemboss.editor.ConsensusOptions

plurality

pmain - Variable in class org.emboss.jemboss.Jemboss

Jemboss split pain

pngContent - Variable in class org.emboss.jemboss.gui.filetree.FileEditorDisplay

png file content

polarColor - Static variable in class org.emboss.jemboss.editor.SequenceProperties

Polar (Red=Polar)

popup - Variable in class org.emboss.jemboss.editor.ColourJFrame

Popup menu system

popup - Variable in class org.emboss.jemboss.editor.ColourPanel

popup - Variable in class org.emboss.jemboss.editor.SequenceJPanel

pop up menu

popup - Variable in class org.emboss.jemboss.gui.filetree.DragTree

popup menu

popup - Variable in class org.emboss.jemboss.gui.filetree.RemoteDragTree

popup menu

position - Variable in class org.emboss.jemboss.editor.GroutAlignJFrame

ppj - Variable in class org.emboss.jemboss.editor.AlignJFrame

prefClose - Variable in class org.emboss.jemboss.gui.filetree.LocalAndRemoteFileTreeFrame

close/exit menu item

prefShadeGUI - Static variable in class org.emboss.jemboss.gui.AdvancedOptions

shade or remove unused parameters

prefjni - Static variable in class org.emboss.jemboss.gui.AdvancedOptions

use JNI to calculate parameter dependencies

pressedResidue - Variable in class org.emboss.jemboss.editor.SequenceJPanel

residue number when pressed by mouse

prettPlot - Variable in class org.emboss.jemboss.editor.GraphicSequenceCollection

draw as per prettplot

prettyBox - Variable in class org.emboss.jemboss.editor.PrettyPlotJFrame

define if the identities and matches are to be boxed

prettyDraw(int, int, int, String, int, int, boolean, Graphics) - Method in class org.emboss.jemboss.editor.SequenceJPanel

prettyPlot - Variable in class org.emboss.jemboss.editor.GraphicSequenceCollection

pretty plot values

prettyPlot - Variable in class org.emboss.jemboss.editor.SequenceJPanel

colour as per prettyplot

primaryGp - Variable in class org.emboss.jemboss.parser.ParseAcd

primary group

print(Graphics, PageFormat, int) - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection

Used to print the sequence alignment

print() - Method in class org.emboss.jemboss.editor.PrintAlignmentImage

Print to a jpeg or png file

print(int, String, String, boolean, double, double, double, double) - Method in class org.emboss.jemboss.editor.PrintAlignmentImage

Print to a jpeg or png file

print(String, double, double, double, double) - Method in class org.emboss.jemboss.editor.PrintAlignmentImage

Print to one jpeg or png file

print(int, String, String, double, double, double, double) - Method in class org.emboss.jemboss.editor.PrintAlignmentImage

Print to one jpeg or png file

print(Graphics, PageFormat, int) - Method in class org.emboss.jemboss.editor.PrintableJTable

The method @print@ must be implemented for @Printable@ interface.

printPreview() - Method in class org.emboss.jemboss.editor.PrintAlignmentImage

Display a print preview page

printSinglePagePreview() - Method in class org.emboss.jemboss.editor.PrintAlignmentImage

Display a single page print preview page

printTable() - Method in class org.emboss.jemboss.editor.IDTableJFrame

privateName - Variable in class org.emboss.jemboss.soap.ServerSetup

private server name

privateServerFailOver - Variable in class org.emboss.jemboss.JembossParams

privateServers - Variable in class org.emboss.jemboss.JembossParams

privateSoapService - Variable in class org.emboss.jemboss.JembossParams

private service name

privateSoapServiceName - Variable in class org.emboss.jemboss.JembossParams

property name for private service name

privateSoapURL - Variable in class org.emboss.jemboss.JembossParams

private services URL

privateSoapURLName - Variable in class org.emboss.jemboss.JembossParams

property name for private services URL

privateURL - Variable in class org.emboss.jemboss.soap.ServerSetup

private server URL

prnt - Variable in class org.emboss.jemboss.parser.Ajax

prog - Static variable in class org.emboss.jemboss.server.TestPrivateServer

proganswer - Variable in class org.emboss.jemboss.programs.ResultList

proganswer - Variable in class org.emboss.jemboss.soap.JembossRun

program result

proganswer - Variable in class org.emboss.jemboss.soap.PrivateRequest

results from calling the web service

proganswer - Variable in class org.emboss.jemboss.soap.PublicRequest

programGroup - Variable in class org.emboss.jemboss.gui.startup.ProgList

program group

progressBar - Variable in class org.emboss.jemboss.soap.AuthPopup

progress bar

progressLabel - Variable in class org.emboss.jemboss.soap.AuthPopup

progress label

project - Variable in class org.emboss.jemboss.programs.JembossProcess

project name

project - Variable in class org.emboss.jemboss.programs.RunEmbossApplication

running directory

project - Variable in class org.emboss.jemboss.programs.RunEmbossApplication2

running directory

project - Variable in class org.emboss.jemboss.server.JembossThread

project directory

promptPanel - Variable in class org.emboss.jemboss.soap.AuthPopup

prompt for login panel

protein - Variable in class org.emboss.jemboss.editor.Sequence

sequence type

protein - Variable in class org.emboss.jemboss.gui.sequenceChooser.InputSequenceAttributes

select to specify a protein sequence

protein - Static variable in class org.emboss.jemboss.parser.Ajax

true if the sequence is protein

protein - Variable in class org.emboss.jemboss.soap.CallAjax

type of sequence protein or nucleotide

protein_soap - Variable in class org.emboss.jemboss.parser.Ajax

true if the sequence is protein

proxyAuthPasswd - Variable in class org.emboss.jemboss.JembossParams

proxyAuthPasswdName - Variable in class org.emboss.jemboss.JembossParams

proxyAuthUser - Variable in class org.emboss.jemboss.JembossParams

proxyAuthUserName - Variable in class org.emboss.jemboss.JembossParams

proxyBrowserName - Variable in class org.emboss.jemboss.soap.ServerSetup

proxy name for web browser

proxyBrowserPort - Variable in class org.emboss.jemboss.soap.ServerSetup

proxy port for web browser

proxyDescription() - Method in class org.emboss.jemboss.JembossParams

A description of the proxy settings

proxyHost - Variable in class org.emboss.jemboss.JembossParams

proxyHostName - Variable in class org.emboss.jemboss.JembossParams

proxyName - Variable in class org.emboss.jemboss.soap.ServerSetup

proxy name

proxyOverride - Variable in class org.emboss.jemboss.JembossParams

proxyOverrideName - Variable in class org.emboss.jemboss.JembossParams

proxyPort - Variable in class org.emboss.jemboss.soap.ServerSetup

proxy port

proxyPortNum - Variable in class org.emboss.jemboss.JembossParams

proxyPortNumName - Variable in class org.emboss.jemboss.JembossParams

ps - Variable in class org.emboss.jemboss.server.JembossAuthServer

path separator

ps - Variable in class org.emboss.jemboss.server.JembossFileAuthServer

path separator

publicName - Variable in class org.emboss.jemboss.soap.ServerSetup

public server name

publicServerFailOver - Variable in class org.emboss.jemboss.JembossParams

publicServers - Variable in class org.emboss.jemboss.JembossParams

publicSoapService - Variable in class org.emboss.jemboss.JembossParams

public service name

publicSoapServiceName - Variable in class org.emboss.jemboss.JembossParams

property name for public service name

publicSoapURL - Variable in class org.emboss.jemboss.JembossParams

public services URL

publicSoapURLName - Variable in class org.emboss.jemboss.JembossParams

property name for public services URL

publicURL - Variable in class org.emboss.jemboss.soap.ServerSetup

public server URL

putFile(String, byte[], String, String, byte[]) - Method in class org.emboss.jemboss.parser.Ajax

create a file

put_file(String, String, byte[], String, byte[]) - Method in class org.emboss.jemboss.server.JembossFileAuthServer

Put a file on the server file system

put_file(String, String, byte[], String) - Method in class org.emboss.jemboss.server.JembossFileServer

Put a file on the server file system

Q

quoteMe(String) - Method in class org.emboss.jemboss.server.JembossAuthServer

Quote all tokens ready for shell scripts

R

REMOTEFILENODE - Static variable in class org.emboss.jemboss.gui.filetree.RemoteFileNode

RemoteDragTree - class org.emboss.jemboss.gui.filetree.RemoteDragTree.

Creates a remote file tree which is a drag source & sink

RemoteDragTree(JembossParams, FileRoots) - Constructor for class org.emboss.jemboss.gui.filetree.RemoteDragTree

RemoteDragTree.PopupListener - class org.emboss.jemboss.gui.filetree.RemoteDragTree.PopupListener.

Popup menu listener

RemoteDragTree.PopupListener() - Constructor for class org.emboss.jemboss.gui.filetree.RemoteDragTree.PopupListener

RemoteFileNode - class org.emboss.jemboss.gui.filetree.RemoteFileNode.

File node for remote file tree manager

RemoteFileNode(JembossParams, FileRoots, String, FileList, String) - Constructor for class org.emboss.jemboss.gui.filetree.RemoteFileNode

RemoteFileNode(JembossParams, FileRoots, String, FileList, String, boolean) - Constructor for class org.emboss.jemboss.gui.filetree.RemoteFileNode

RemoteFileTreePanel - class org.emboss.jemboss.gui.filetree.RemoteFileTreePanel.

Panel for the remote file tree manager

RemoteFileTreePanel(JembossParams) - Constructor for class org.emboss.jemboss.gui.filetree.RemoteFileTreePanel

RemoteFileTreePanel(JembossParams, boolean) - Constructor for class org.emboss.jemboss.gui.filetree.RemoteFileTreePanel

Creates a panel to contain the directory trees on an embreo server.

ReportFormat - class org.emboss.jemboss.gui.form.ReportFormat.

EMBOSS Report formats http://www.hgmp.mrc.ac.uk/Software/EMBOSS/Themes/ReportFormats.html

ReportFormat(ParseAcd, int) - Constructor for class org.emboss.jemboss.gui.form.ReportFormat

ResultList - class org.emboss.jemboss.programs.ResultList.

Holds the list of stored results.

ResultList(JembossParams) - Constructor for class org.emboss.jemboss.programs.ResultList

Holds the list of stored results

ResultList(JembossParams, String, String) - Constructor for class org.emboss.jemboss.programs.ResultList

Holds the list of stored results

ResultList(JembossParams, String, String, String) - Constructor for class org.emboss.jemboss.programs.ResultList

Manipulate a dataset.

ResultsMenuBar - class org.emboss.jemboss.gui.ResultsMenuBar.

Sets up a results menu bar with save and close

ResultsMenuBar(JFrame, JTabbedPane, Hashtable, JembossParams) - Constructor for class org.emboss.jemboss.gui.ResultsMenuBar

Sets up a results menu bar with save and close

ResultsMenuBar(JFrame, JTabbedPane, Hashtable, Hashtable) - Constructor for class org.emboss.jemboss.gui.ResultsMenuBar

Sets up a results menu bar with save and close

ResultsMenuBar(JFrame, FileEditorDisplay, JembossParams) - Constructor for class org.emboss.jemboss.gui.ResultsMenuBar

Adds action listener to save contents of a JTextPane.

ResultsMenuBar(JFrame, JTabbedPane, Hashtable, Hashtable, String, JembossParams) - Constructor for class org.emboss.jemboss.gui.ResultsMenuBar

Adds action listener to save contents of contents of a tabbed pane.

ResultsUpdateTimer - class org.emboss.jemboss.programs.ResultsUpdateTimer.

Timer for updating saved results window for batch jobs submitted

ResultsUpdateTimer(int, DefaultListModel, JFrame) - Constructor for class org.emboss.jemboss.programs.ResultsUpdateTimer

ResultsUpdateTimer.ResultsTask - class org.emboss.jemboss.programs.ResultsUpdateTimer.ResultsTask.

Timer task to update the results window

ResultsUpdateTimer.ResultsTask() - Constructor for class org.emboss.jemboss.programs.ResultsUpdateTimer.ResultsTask

ResultsUpdateTimer.ResultsTask(DefaultListModel, JFrame) - Constructor for class org.emboss.jemboss.programs.ResultsUpdateTimer.ResultsTask

RunEmbossApplication - class org.emboss.jemboss.programs.RunEmbossApplication.

RunEmbossApplication class used to run an EMBOSS process

RunEmbossApplication(String, String[], File) - Constructor for class org.emboss.jemboss.programs.RunEmbossApplication

RunEmbossApplication2 - class org.emboss.jemboss.programs.RunEmbossApplication2.

RunEmbossApplication2 class used to run an EMBOSS process this reads stdout and stderr in separate threads.

RunEmbossApplication2(String, String[], File) - Constructor for class org.emboss.jemboss.programs.RunEmbossApplication2

RunEmbossApplication2(String, String[], File, JTextArea) - Constructor for class org.emboss.jemboss.programs.RunEmbossApplication2

RunEmbossApplication2.StderrHandler - class org.emboss.jemboss.programs.RunEmbossApplication2.StderrHandler.

RunEmbossApplication2.StderrHandler(RunEmbossApplication2) - Constructor for class org.emboss.jemboss.programs.RunEmbossApplication2.StderrHandler

RunEmbossApplication2.StdoutHandler - class org.emboss.jemboss.programs.RunEmbossApplication2.StdoutHandler.

RunEmbossApplication2.StdoutHandler(RunEmbossApplication2) - Constructor for class org.emboss.jemboss.programs.RunEmbossApplication2.StdoutHandler

raccshow - Variable in class org.emboss.jemboss.gui.form.ReportFormat

select to show the accession number

rangeField - Variable in class org.emboss.jemboss.gui.form.BuildJembossForm

rangeField - Variable in class org.emboss.jemboss.gui.form.SectionPanel

range field

rasmolColor - Static variable in class org.emboss.jemboss.editor.SequenceProperties

rasmol colour scheme

rdesshow - Variable in class org.emboss.jemboss.gui.form.ReportFormat

select to show the description

reExplore() - Method in class org.emboss.jemboss.gui.filetree.FileNode

Forces the directory to be re-explored

rea - Variable in class org.emboss.jemboss.programs.RunEmbossApplication2.StderrHandler

rea - Variable in class org.emboss.jemboss.programs.RunEmbossApplication2.StdoutHandler

rea - Variable in class org.emboss.jemboss.server.JembossThread

runs the emboss process

readByteFile(String) - Static method in class org.emboss.jemboss.gui.filetree.DragTree

Read a file into a byte array.

readByteFile(String) - Static method in class org.emboss.jemboss.server.JembossServer

Read a file into a byte array.

readClustalFile(BufferedReader) - Method in class org.emboss.jemboss.editor.SequenceReader

Reads in the CLUSTAL sequence file and creates a Vector containing the sequence(s).

readFastaFile(BufferedReader) - Method in class org.emboss.jemboss.editor.SequenceReader

Reads in the FASTA sequence file and creates a Vector containing the sequence(s).

readJPredFile(BufferedReader) - Method in class org.emboss.jemboss.editor.SequenceReader

Reads in the JPred sequence file and creates a Vector containing the sequence(s).

readMSFFile(BufferedReader) - Method in class org.emboss.jemboss.editor.SequenceReader

Reads in the MSF sequence file and creates a Vector containing the sequence(s).

readObject(ObjectInputStream) - Method in class org.emboss.jemboss.gui.SequenceData

readObject(ObjectInputStream) - Method in class org.emboss.jemboss.gui.filetree.FileNode

readObject(ObjectInputStream) - Method in class org.emboss.jemboss.gui.filetree.RemoteFileNode

readObject(ObjectInputStream) - Method in class org.emboss.jemboss.soap.FileRoots

readProcessStderr() - Method in class org.emboss.jemboss.programs.RunEmbossApplication2

Read in the process stderr.

readProcessStdout() - Method in class org.emboss.jemboss.programs.RunEmbossApplication2

Read in the process stdout.

readSequenceFile() - Method in class org.emboss.jemboss.editor.SequenceReader

Read a sequence file and create a vector of sequences

readSequenceString(String) - Method in class org.emboss.jemboss.editor.SequenceReader

Read a formatted sequence string (e.g msf) and create a vector of sequences

reading - Variable in class org.emboss.jemboss.editor.SequenceReader

true if read ok

redo - Variable in class org.emboss.jemboss.gui.ResultsMenuBar

redo menu item

refresh(FileNode) - Method in class org.emboss.jemboss.gui.filetree.DragTree

Refresh

refreshRoot() - Method in class org.emboss.jemboss.gui.filetree.RemoteDragTree

This is used to refresh the file manager

remoteFlavors - Static variable in class org.emboss.jemboss.gui.filetree.RemoteFileNode

removeGroutAlignJFrameListener(GroutAlignJFrameListener) - Method in class org.emboss.jemboss.editor.GroutAlignJFrame

removeGroutGraphicSequenceCollectionListener(GroutGraphicSequenceCollectionListener) - Method in class org.emboss.jemboss.editor.GroutGraphicSequenceCollection

removeResult(JembossProcess) - Method in class org.emboss.jemboss.soap.PendingResults

Remove a pending process from the list

removeSequence(String) - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection

Remove a sequence from the editor display

removedSeqs - Variable in class org.emboss.jemboss.editor.GraphicSequenceCollection

Vector of sequences removed from panel

rename(String, String, String, String, RemoteFileNode, RemoteFileNode) - Method in class org.emboss.jemboss.gui.filetree.RemoteDragTree

Rename a node from the tree

rename(String, String, String, String, byte[]) - Method in class org.emboss.jemboss.server.JembossFileAuthServer

Rename a file

rename(String, String, String, String) - Method in class org.emboss.jemboss.server.JembossFileServer

Rename a file

renameFile(File, FileNode, String) - Method in class org.emboss.jemboss.gui.filetree.DragTree

Method to rename a file and update the filenode's.

renameFile(String, byte[], String, String, String) - Method in class org.emboss.jemboss.parser.Ajax

rename a file

repaintSequences(Hashtable) - Method in class org.emboss.jemboss.editor.AlignJFrame

Force a re-display of the sequences with a new colour scheme.

reqdSection - Static variable in class org.emboss.jemboss.gui.form.BuildJembossForm

res - Variable in class org.emboss.jemboss.editor.ColourJFrame.ResidueColourPanel

resButtonStatus - Variable in class org.emboss.jemboss.gui.ShowSavedResults

result status panel

resMenu - Variable in class org.emboss.jemboss.gui.ShowSavedResults

manu bar for results panel

resWidth - Variable in class org.emboss.jemboss.editor.SequenceJPanel

residue width

resetCount() - Method in class org.emboss.jemboss.soap.PendingResults

Reset the pending and completed job status

residueColor - Variable in class org.emboss.jemboss.editor.AlignJFrame

residueColor - Static variable in class org.emboss.jemboss.editor.SequenceProperties

residueMatrixPosition - Variable in class org.emboss.jemboss.editor.Matrix

hashtable of the residue positions in the table

resolveColor(String[], int) - Static method in class org.emboss.jemboss.editor.AlignJFrame

red, blue, cyan, darkGray, gray , green, lightGray, magenta , orange, pink, white, yellow, black

resolveDependents(int, Dependent[], String, String) - Method in class org.emboss.jemboss.gui.form.SectionPanel

Given an ACD variable and the value it takes, resolve any dependent attribute values.

resolveVariables(Vector, String) - Method in class org.emboss.jemboss.parser.ParseAcd

Used to replace the "variable:" or "var:" shorthand notation in the ACD to the full expression it represent

result - Variable in class org.emboss.jemboss.parser.AcdFunResolve

result as a String of the expression used in constructor

resultsManager - Static variable in class org.emboss.jemboss.Jemboss

to manage the pending results

returnError(Ajax, String) - Method in class org.emboss.jemboss.server.JembossAuthServer

Report the stderr and stdout to error logs

rev - Variable in class org.emboss.jemboss.gui.sequenceChooser.InputSequenceAttributes

select to reverse sequence

reverseComplementSequence() - Method in class org.emboss.jemboss.editor.Sequence

Reverse and complement the sequence

reverseSequence() - Method in class org.emboss.jemboss.editor.Sequence

Reverse the sequence order

rewriteProperties(String, String) - Method in class org.emboss.jemboss.gui.AdvancedOptions

Re-write jemboss.properties when there is an existing jemboss,properties and insert/update the user.home property

rf - Variable in class org.emboss.jemboss.gui.form.BuildJembossForm

rf - Variable in class org.emboss.jemboss.gui.form.SectionPanel

report format

rfii - Variable in class org.emboss.jemboss.gui.ShowSavedResults

refresh image

root - Variable in class org.emboss.jemboss.gui.filetree.DragTree

root directory

rootSelect - Variable in class org.emboss.jemboss.gui.filetree.RemoteFileTreePanel

combo to select the root directory from

rootVector - Variable in class org.emboss.jemboss.soap.FileRoots

file system roots

rootdir - Variable in class org.emboss.jemboss.gui.filetree.RemoteFileNode

root directory

rpt - Static variable in class org.emboss.jemboss.gui.form.ReportFormat

EMBOSS Report formats

rscroll - Variable in class org.emboss.jemboss.gui.sequenceChooser.InputSequenceAttributes

scroll panel for attibute panel

rscroll - Variable in class org.emboss.jemboss.gui.sequenceChooser.OutputSequenceAttributes

scroll pane for output attributes

rtp - Variable in class org.emboss.jemboss.gui.ShowResultSet

tabbed pane

run() - Method in class org.emboss.jemboss.gui.SplashThread

run() - Method in class org.emboss.jemboss.programs.BatchUpdateTimer.RemindTask

run() - Method in class org.emboss.jemboss.programs.ResultsUpdateTimer.ResultsTask

run() - Method in class org.emboss.jemboss.programs.RunEmbossApplication2.StderrHandler

run() - Method in class org.emboss.jemboss.programs.RunEmbossApplication2.StdoutHandler

run() - Method in class org.emboss.jemboss.server.AppendToLogFileThread

Override Thread run() method

run() - Method in class org.emboss.jemboss.server.JembossThread

runAsBatch(Ajax, String, byte[], String, String) - Method in class org.emboss.jemboss.server.JembossAuthServer

Submit to a batch queue

runAsGNQSBatch(Ajax, String, byte[], String, String) - Method in class org.emboss.jemboss.server.JembossAuthServer

Submit to a Generic NQS batch queue.

runAsPBSBatch(Ajax, String, byte[], String, String) - Method in class org.emboss.jemboss.server.JembossAuthServer

Submit to a OpenPBS batch queue.

run_prog(String, String, Vector, String, byte[]) - Method in class org.emboss.jemboss.server.JembossAuthServer

Run an emboss application

run_prog(String, String, String[]) - Method in class org.emboss.jemboss.server.JembossServer

Run an EMBOSS application

run_prog(String, String, Vector, String) - Method in class org.emboss.jemboss.server.JembossServer

Run an EMBOSS application

run_prog(String, String, Hashtable) - Method in class org.emboss.jemboss.server.JembossServer

Run an EMBOSS application

running - Variable in class org.emboss.jemboss.programs.JembossProcess

true when process is running

running_jobs - Variable in class org.emboss.jemboss.soap.PendingResults

number of peding processes

rusashow - Variable in class org.emboss.jemboss.gui.form.ReportFormat

select to show the USA

S

SALMON - Static variable in class org.emboss.jemboss.editor.SequenceProperties

SALMON from EMBOSS data Ecolour.map

SEQUENCEDATA - Static variable in class org.emboss.jemboss.gui.SequenceData

dataflavor for drag and drop transfers

SERVER_DOWN - Static variable in class org.emboss.jemboss.JembossParams

denotes a server is not responding

SERVER_ERR - Static variable in class org.emboss.jemboss.JembossParams

denotes a server is giving errors

SERVER_OK - Static variable in class org.emboss.jemboss.JembossParams

denotes a server is OK

SINGLETON - Static variable in class org.emboss.jemboss.gui.form.MultiLineToolTipUI

ScrollPanel - class org.emboss.jemboss.gui.ScrollPanel.

Extends JPanel to implement Scrollable to speed scroll pane scrolling

ScrollPanel() - Constructor for class org.emboss.jemboss.gui.ScrollPanel

ScrollPanel(LayoutManager) - Constructor for class org.emboss.jemboss.gui.ScrollPanel

SectionPanel - class org.emboss.jemboss.gui.form.SectionPanel.

Responsible for displaying the Jemboss application form generated from the ACD file.

SectionPanel(JFrame, JPanel, Box, ParseAcd, int, TextFieldSink[], TextFieldInt[], TextFieldFloat[], JTextField[], JCheckBox[], InputSequenceAttributes[], JembossComboPopup[], JList[], SetInFileCard[], ListFilePanel[], String[], String, Box[], int, JembossParams, boolean, String[]) - Constructor for class org.emboss.jemboss.gui.form.SectionPanel

Separator - class org.emboss.jemboss.gui.form.Separator.

Panel separator

Separator(Dimension) - Constructor for class org.emboss.jemboss.gui.form.Separator

Sequence - class org.emboss.jemboss.editor.Sequence.

Sequence object

Sequence(String, String, int, float) - Constructor for class org.emboss.jemboss.editor.Sequence

Sequence(String, String, int) - Constructor for class org.emboss.jemboss.editor.Sequence

Sequence(String, String) - Constructor for class org.emboss.jemboss.editor.Sequence

Sequence(String) - Constructor for class org.emboss.jemboss.editor.Sequence

Sequence(String, float) - Constructor for class org.emboss.jemboss.editor.Sequence

SequenceData - class org.emboss.jemboss.gui.SequenceData.

Object to represent the content of each row in the DragJTable of a SequenceList.

SequenceData() - Constructor for class org.emboss.jemboss.gui.SequenceData

SequenceData(String, String, String, Boolean, Boolean, Boolean) - Constructor for class org.emboss.jemboss.gui.SequenceData

SequenceFilter - class org.emboss.jemboss.gui.sequenceChooser.SequenceFilter.

Sequence format file name suffix filter

SequenceFilter() - Constructor for class org.emboss.jemboss.gui.sequenceChooser.SequenceFilter

SequenceJPanel - class org.emboss.jemboss.editor.SequenceJPanel.

Sequence panel for drawing a sequence or the sequence numbers

SequenceJPanel(Sequence, JComponent, boolean, boolean, boolean, Hashtable, int, int) - Constructor for class org.emboss.jemboss.editor.SequenceJPanel

SequenceJPanel(Sequence, JComponent, boolean, boolean, boolean, Hashtable, int) - Constructor for class org.emboss.jemboss.editor.SequenceJPanel

Constructor with default font size.

SequenceJPanel(int, int) - Constructor for class org.emboss.jemboss.editor.SequenceJPanel

Constructor for sequence numbering

SequenceJPanel.PopupListener - class org.emboss.jemboss.editor.SequenceJPanel.PopupListener.

Popup listener

SequenceJPanel.PopupListener() - Constructor for class org.emboss.jemboss.editor.SequenceJPanel.PopupListener

SequenceList - class org.emboss.jemboss.gui.SequenceList.

SequenceList extends JFrame to display a set of sequences that the user is working on in a session.

SequenceList(boolean, JembossParams) - Constructor for class org.emboss.jemboss.gui.SequenceList

SequenceListTableModel - class org.emboss.jemboss.gui.SequenceListTableModel.

Model for the sequence table

SequenceListTableModel() - Constructor for class org.emboss.jemboss.gui.SequenceListTableModel

SequenceNameJButton - class org.emboss.jemboss.editor.SequenceNameJButton.

Draw sequence name toggle button

SequenceNameJButton(Sequence, int) - Constructor for class org.emboss.jemboss.editor.SequenceNameJButton

SequenceProperties - class org.emboss.jemboss.editor.SequenceProperties.

General sequence properties

SequenceProperties() - Constructor for class org.emboss.jemboss.editor.SequenceProperties

SequenceReader - class org.emboss.jemboss.editor.SequenceReader.

This class reads sequences in FASTA and MSF format.

SequenceReader() - Constructor for class org.emboss.jemboss.editor.SequenceReader

SequenceReader(File) - Constructor for class org.emboss.jemboss.editor.SequenceReader

SequenceReader(String) - Constructor for class org.emboss.jemboss.editor.SequenceReader

SequenceSaver - class org.emboss.jemboss.editor.SequenceSaver.

This class saves sequences in FASTA format.

SequenceSaver(Vector, File) - Constructor for class org.emboss.jemboss.editor.SequenceSaver

SequenceSaver(Vector) - Constructor for class org.emboss.jemboss.editor.SequenceSaver

ServerSetup - class org.emboss.jemboss.soap.ServerSetup.

Jemboss properties for the server setup

ServerSetup(JembossParams) - Constructor for class org.emboss.jemboss.soap.ServerSetup

SetInFileCard - class org.emboss.jemboss.gui.form.SetInFileCard.

Input sequence file card

SetInFileCard(JPanel, int, String[], String, String, InputSequenceAttributes[], boolean, JembossParams) - Constructor for class org.emboss.jemboss.gui.form.SetInFileCard

Build the GUI components for an input sequence(s).

SetOutFileCard - class org.emboss.jemboss.gui.form.SetOutFileCard.

Creates an output file Box

SetOutFileCard(Box, TextFieldSink, Color, JPanel) - Constructor for class org.emboss.jemboss.gui.form.SetOutFileCard

SetUpMenuBar - class org.emboss.jemboss.gui.SetUpMenuBar.

Sets the top menu bar for Jemboss main window

SetUpMenuBar(JembossParams, JFrame, boolean) - Constructor for class org.emboss.jemboss.gui.SetUpMenuBar

ShiftEast(int, int) - Method in class org.emboss.jemboss.JembossLogo

ShiftNorth(int, int) - Method in class org.emboss.jemboss.JembossLogo

ShiftSouth(int, int) - Method in class org.emboss.jemboss.JembossLogo

ShiftWest(int, int) - Method in class org.emboss.jemboss.JembossLogo

ShowDB - class org.emboss.jemboss.soap.ShowDB.

Run showdb and find the available scoring matrices and codon usage tables on the Jemboss server

ShowDB(JembossParams) - Constructor for class org.emboss.jemboss.soap.ShowDB

ShowResultSet - class org.emboss.jemboss.gui.ShowResultSet.

Displays JTabbedPane of the contents of the Hashtable

ShowResultSet(Hashtable, String, JembossParams) - Constructor for class org.emboss.jemboss.gui.ShowResultSet

ShowResultSet(Hashtable, Hashtable) - Constructor for class org.emboss.jemboss.gui.ShowResultSet

ShowResultSet(Hashtable, JembossParams) - Constructor for class org.emboss.jemboss.gui.ShowResultSet

ShowResultSet(Hashtable, Hashtable, JembossParams) - Constructor for class org.emboss.jemboss.gui.ShowResultSet

ShowResultSet(Hashtable, Hashtable, String, JembossParams) - Constructor for class org.emboss.jemboss.gui.ShowResultSet

ShowResultSet.GroutPanelListener - class org.emboss.jemboss.gui.ShowResultSet.GroutPanelListener.

ShowResultSet.GroutPanelListener() - Constructor for class org.emboss.jemboss.gui.ShowResultSet.GroutPanelListener

ShowSavedResults - class org.emboss.jemboss.gui.ShowSavedResults.

Shows a list of results from the SOAP server and displays individual result sets

ShowSavedResults(String) - Constructor for class org.emboss.jemboss.gui.ShowSavedResults

ShowSavedResults(JembossParams, JFrame) - Constructor for class org.emboss.jemboss.gui.ShowSavedResults

Show the saved results on the server.

ShowSavedResults(JembossParams, PendingResults) - Constructor for class org.emboss.jemboss.gui.ShowSavedResults

Show the results sent to a batch queue.

SplashThread - class org.emboss.jemboss.gui.SplashThread.

Extends Thread to update the progress bar in the login window

SplashThread(AuthPopup, int) - Constructor for class org.emboss.jemboss.gui.SplashThread

SwingWorker - class org.emboss.jemboss.gui.SwingWorker.

This is the 3rd version of SwingWorker (also known as SwingWorker 3), an abstract class that you subclass to perform GUI-related work in a dedicated thread.

SwingWorker() - Constructor for class org.emboss.jemboss.gui.SwingWorker

Start a thread that will call the construct method and then exit.

SwingWorker.ThreadVar - class org.emboss.jemboss.gui.SwingWorker.ThreadVar.

Class to maintain reference to current worker thread under separate synchronization control.

SwingWorker.ThreadVar(Thread) - Constructor for class org.emboss.jemboss.gui.SwingWorker.ThreadVar

s_beg - Variable in class org.emboss.jemboss.gui.SequenceData

sequence start

s_default - Variable in class org.emboss.jemboss.gui.SequenceData

use as the default

s_end - Variable in class org.emboss.jemboss.gui.SequenceData

sequence end

s_listFile - Variable in class org.emboss.jemboss.gui.SequenceData

sequence list file

s_name - Variable in class org.emboss.jemboss.gui.SequenceData

sequence file/database

s_remote - Variable in class org.emboss.jemboss.gui.SequenceData

file on remote file system

safeFileName - Variable in class org.emboss.jemboss.soap.MakeFileSafe

saveFile(File, Vector) - Method in class org.emboss.jemboss.editor.SequenceSaver

Save the sequences out

saveSequenceList() - Static method in class org.emboss.jemboss.gui.SetUpMenuBar

Save the sequence list for a future session.

saveToLocalFile - Variable in class org.emboss.jemboss.gui.ResultsMenuBar

menu to save to local file

saveToRemoteFile - Variable in class org.emboss.jemboss.gui.ResultsMenuBar

menu to save to remote file

saveUserHome - Variable in class org.emboss.jemboss.gui.AdvancedOptions

save user home directory

save_project_file(String, String, String, String, byte[]) - Method in class org.emboss.jemboss.server.JembossAuthServer

Save a file to a project directory on the server.

save_project_file(String, String, String, String) - Method in class org.emboss.jemboss.server.JembossServer

Save a file to a project directory on the server.

savedResFrame - Variable in class org.emboss.jemboss.programs.ResultsUpdateTimer.ResultsTask

sbeg - Variable in class org.emboss.jemboss.gui.sequenceChooser.InputSequenceAttributes

-sbegin flag

scrollTree - Variable in class org.emboss.jemboss.Jemboss

Scroll pane for local filemanager

searchSequences(int, String) - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection

Search the sequences for the position in that matches the given pattern to search for.

secondaryGp - Variable in class org.emboss.jemboss.parser.ParseAcd

secondary group

sectionBox - Variable in class org.emboss.jemboss.gui.form.SectionPanel

container for this ACD section

sectionPane - Variable in class org.emboss.jemboss.gui.form.SectionPanel

container for this ACD section

sectionResize(JPanel) - Method in class org.emboss.jemboss.gui.form.SectionPanel

Resize the section panel

selected - Variable in class org.emboss.jemboss.editor.ColourMenu.ColorPane

selected - Variable in class org.emboss.jemboss.editor.ColourMenu

selected colour pane

selected - Variable in class org.emboss.jemboss.gui.ColorMenu.ColorPane

selected - Variable in class org.emboss.jemboss.gui.ColorMenu

selectedBorder - Variable in class org.emboss.jemboss.editor.ColourMenu

selected border

selectedBorder - Variable in class org.emboss.jemboss.gui.ColorMenu

send - Variable in class org.emboss.jemboss.gui.sequenceChooser.InputSequenceAttributes

-send flag

seq - Variable in class org.emboss.jemboss.editor.Sequence

sequence as a string

seq - Variable in class org.emboss.jemboss.editor.SequenceJPanel

sequence to display

seq - Variable in class org.emboss.jemboss.editor.SequenceNameJButton

sequence

seqAttrib(String, byte[], String, String) - Method in class org.emboss.jemboss.parser.Ajax

determine sequence attributes as the user

seqBox - Variable in class org.emboss.jemboss.editor.GraphicSequenceCollection

container for sequences

seqFile - Variable in class org.emboss.jemboss.editor.SequenceReader

sequence file

seqHeight - Variable in class org.emboss.jemboss.editor.SequenceJPanel

sequence height

seqLength - Variable in class org.emboss.jemboss.editor.SequenceJPanel

sequence length

seqList - Static variable in class org.emboss.jemboss.gui.SetUpMenuBar

sequence store list

seqModel - Variable in class org.emboss.jemboss.gui.DragJTable

model for the sequence table

seqModel - Variable in class org.emboss.jemboss.gui.SequenceList

model for the sequence table

seqNameBox - Variable in class org.emboss.jemboss.editor.GraphicSequenceCollection

container for sequence names

seqNamePanel - Variable in class org.emboss.jemboss.editor.GraphicSequenceCollection

sequence name panel

seqPaste - Variable in class org.emboss.jemboss.gui.sequenceChooser.CutNPasteTextArea

sequence paste field

seqType(String) - Method in class org.emboss.jemboss.parser.Ajax

determine sequence attributes

seqoutResult - Variable in class org.emboss.jemboss.gui.form.BuildJembossForm

seqs - Variable in class org.emboss.jemboss.editor.AlignApplet

seqs - Variable in class org.emboss.jemboss.editor.GraphicSequenceCollection

Vector containing Sequence objects

seqs - Variable in class org.emboss.jemboss.editor.SequenceReader

sequence store

seqsetAttrib(String, byte[], String, String) - Method in class org.emboss.jemboss.parser.Ajax

determine sequence set attributes as the user

seqsetType(String) - Method in class org.emboss.jemboss.parser.Ajax

determine sequence set attributes

sequenceFile - Variable in class org.emboss.jemboss.editor.AlignJFrame

serverDescription() - Method in class org.emboss.jemboss.JembossParams

A description of the server settings

serverPathToFile - Variable in class org.emboss.jemboss.gui.filetree.RemoteFileNode

path to the file on the server

serverPrivateList - Variable in class org.emboss.jemboss.JembossParams

serverPrivateListName - Variable in class org.emboss.jemboss.JembossParams

serverPublicList - Variable in class org.emboss.jemboss.JembossParams

serverPublicListName - Variable in class org.emboss.jemboss.JembossParams

serverStatusHash - Variable in class org.emboss.jemboss.JembossParams

servicePasswd - Variable in class org.emboss.jemboss.JembossParams

servicePasswdByte - Variable in class org.emboss.jemboss.JembossParams

services password

serviceUserName - Variable in class org.emboss.jemboss.JembossParams

serviceUserNameName - Variable in class org.emboss.jemboss.JembossParams

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

setAntiAlias(boolean) - Method in class org.emboss.jemboss.editor.PrintAlignmentImage

setAppTitle(String, JPanel) - Method in class org.emboss.jemboss.gui.form.SectionPanel

Set the application title panel

setAttribute(String) - Method in class org.emboss.jemboss.parser.acd.ApplicationParam

Set the attribute/parameter type

setAutoUpdate(boolean) - Method in class org.emboss.jemboss.soap.PendingResults

Automatically updating status manager with BatchUpdateTimer thread

setBegSeq(int) - Method in class org.emboss.jemboss.gui.sequenceChooser.InputSequenceAttributes

Set the -sbegin flag

setBegSeq(String) - Method in class org.emboss.jemboss.gui.sequenceChooser.InputSequenceAttributes

Set the -sbegin flag

setBottomPanel() - Method in class org.emboss.jemboss.soap.AuthPopup

Buttons across the bottom

setBrowserSize() - Method in class org.emboss.jemboss.gui.Browser

Set the Jemboss web browser size

setCase(float) - Method in class org.emboss.jemboss.editor.ConsensusOptions

Set the minimum positive matches for a site to be made upper case in the consensus.

setColor(Color) - Method in class org.emboss.jemboss.editor.ColourMenu

setColor(Color) - Method in class org.emboss.jemboss.gui.ColorMenu

setColorScheme(Hashtable) - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection

Set the colour scheme to use

setColorScheme(Hashtable) - Method in class org.emboss.jemboss.editor.SequenceJPanel

Set the colour scheme

setCurrentColour(Hashtable) - Method in class org.emboss.jemboss.editor.ColourJFrame

Set the colour scheme to display

setCurrentDir(String) - Method in class org.emboss.jemboss.soap.FileRoots

Set the current directory

setCurrentMode(String) - Method in class org.emboss.jemboss.JembossParams

Set the current mode (interactive or batch).

setCurrentRoot(String) - Method in class org.emboss.jemboss.soap.FileRoots

Set the current root

setDefaultColorHashtable() - Method in class org.emboss.jemboss.editor.SequenceJPanel

Set a default colour scheme

setDefaultData() - Method in class org.emboss.jemboss.gui.SequenceListTableModel

Setup a blank square table

setDefaultTab(int) - Method in class org.emboss.jemboss.gui.TabListCellRenderer

setDependentExp(String) - Method in class org.emboss.jemboss.parser.Dependent

Set the value of the expression

setDescription(String) - Method in class org.emboss.jemboss.programs.JembossProcess

Set the description of a project

setDisplayAcceleratorKey(boolean) - Static method in class org.emboss.jemboss.gui.form.MultiLineToolTipUI

setDrawBoxes(boolean) - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection

Draw the boxes around the residues of each sequence

setDrawBoxes(boolean) - Method in class org.emboss.jemboss.editor.SequenceJPanel

Set whether to draw boxes around residues

setDrawColor(boolean) - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection

Draw the residue colours in each sequence

setDrawColor(boolean) - Method in class org.emboss.jemboss.editor.SequenceJPanel

Set whether to colour residues

setEnableFileManagers(boolean) - Method in class org.emboss.jemboss.gui.SetUpMenuBar

Enable/disable file manager menu item

setEnableShowResults(boolean) - Method in class org.emboss.jemboss.gui.SetUpMenuBar

Enable/disable show results menu item

setEndSeq(int) - Method in class org.emboss.jemboss.gui.sequenceChooser.InputSequenceAttributes

Set the -send flag

setEndSeq(String) - Method in class org.emboss.jemboss.gui.sequenceChooser.InputSequenceAttributes

Set the -send flag

setErrStd() - Method in class org.emboss.jemboss.parser.Ajax

Clear the stderr

setExit() - Method in class org.emboss.jemboss.gui.filetree.LocalAndRemoteFileTreeFrame

Set the closing menu item to exit (for standalone file manager)

setFontSize(int) - Method in class org.emboss.jemboss.editor.SequenceJPanel

Set the font size and set the size

setFontSize(int) - Method in class org.emboss.jemboss.editor.SequenceNameJButton

Set the font size

setFontSizeForCollection(int) - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection

Set the font size of the sequences in the editor

setForeground(Color) - Method in class org.emboss.jemboss.gui.sequenceChooser.FileChooser

Set the label colour

setFormat(PageFormat) - Method in class org.emboss.jemboss.editor.PrintAlignmentImage

Set the page format

setGraphic(GraphicSequenceCollection) - Method in class org.emboss.jemboss.editor.PatternJFrame

Set the graphic sequence panel

setGraphicSequenceCollection(GraphicSequenceCollection) - Method in class org.emboss.jemboss.editor.ConsensusOptions

Set the graphic sequence collection

setGraphicSequenceCollection(GraphicSequenceCollection) - Method in class org.emboss.jemboss.editor.PrettyPlotJFrame

Set the current graphic display

setGuiHandleNumber(String, ApplicationFields) - Method in class org.emboss.jemboss.parser.ParseAcd

Sets the gui handle depending on the data type.

setGuiHandleNumber(int) - Method in class org.emboss.jemboss.parser.acd.ApplicationFields

Set the gui handle

setIndent(int) - Method in class org.emboss.jemboss.editor.GroutSequence

Insert a residue into the sequence

setIndent(int) - Method in class org.emboss.jemboss.editor.GroutSequenceJPanel

indents the sequence by specifed amount

setIndents(Vector) - Method in class org.emboss.jemboss.editor.GroutAlignJFrame

Sets the indents to these values

setInterval(int) - Method in class org.emboss.jemboss.editor.PlotConsensus

Set the interval

setInterval(int) - Method in class org.emboss.jemboss.gui.SplashThread

setJMenuBar() - Method in class org.emboss.jemboss.gui.ShowResultSet

Set the menu bar based on the title of the tabbed pane

setJScrollPaneViewportView() - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection

Force display in the viewport

setLastIndex(Object) - Method in class org.emboss.jemboss.gui.MemoryComboBox

Ensure order is changed

setLength(int) - Method in class org.emboss.jemboss.parser.Ajax

Sets the sequence length

setMatrix(Matrix) - Method in class org.emboss.jemboss.editor.AlignJFrame

Set the scoring matrix

setMatrix(Matrix) - Method in class org.emboss.jemboss.editor.ConsensusOptions

Set the matrix to use

setMatrix(Matrix) - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection

setMatrix(Matrix) - Method in class org.emboss.jemboss.editor.MatrixJFrame

Set the matrix to display

setMaxSeqLength() - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection

Calculate the longest sequence length

setMaxSequenceLength(int) - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection

Set the longest sequence length

setNamePanelWidth(int) - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection

Set the sequence name panel width

setNewSettings() - Method in class org.emboss.jemboss.soap.ServerSetup

Set the new settings in the server settings window

setNumberOfParam(int) - Method in class org.emboss.jemboss.parser.acd.ApplicationFields

Set the number of parmeters in this field

setNumberOfResiduesPerLine(int) - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection

Set the number of residues per line to user setting

setNumberSize() - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection

Set the size of the sequence number panel

setPageIndex(int) - Method in class org.emboss.jemboss.editor.PrintAlignmentImage

Set the page number to create an image of

setParam(int, String, String) - Method in class org.emboss.jemboss.parser.acd.ApplicationFields

Set the value of a parameter

setParam(int, String, double) - Method in class org.emboss.jemboss.parser.acd.ApplicationFields

Set the value of a parameter

setPlotSize() - Method in class org.emboss.jemboss.editor.PlotConsensus

Set the consensus plot preferred size using the graph dimensions

setPlurality(float) - Method in class org.emboss.jemboss.editor.ConsensusOptions

Set the minimum positive match score for a site to be included in the consensus.

setPopupMenuVisible(boolean) - Method in class org.emboss.jemboss.gui.startup.ProgList.HorizontalMenu

setPosition(int) - Method in class org.emboss.jemboss.editor.GroutAlignJFrame

Moves the view position to this point

setPosition(int) - Method in class org.emboss.jemboss.editor.GroutGraphicSequenceCollection

Moves the view position to this residue

setPreferredSize(Dimension) - Method in class org.emboss.jemboss.gui.sequenceChooser.FileChooser

Set the preferred size of the text field

setPrettyPlot(boolean, PrettyPlotJFrame) - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection

Display the sequences as per emboss prettyplot colours

setPrettyPlot(boolean) - Method in class org.emboss.jemboss.editor.SequenceJPanel

Set prettyplot display

setPrivateSoapService(String) - Method in class org.emboss.jemboss.JembossParams

Set the name of the private soap service

setPrivateSoapURL(String) - Method in class org.emboss.jemboss.JembossParams

Set the URL of the private soap server

setProtein(boolean) - Method in class org.emboss.jemboss.parser.Ajax

Sets whether sequence is protein (true)

setPublicSoapService(String) - Method in class org.emboss.jemboss.JembossParams

Set the name of the public soap service we're using

setPublicSoapURL(String) - Method in class org.emboss.jemboss.JembossParams

Set the URL of the public soap server

setResultsMenuBar(JFrame, boolean) - Method in class org.emboss.jemboss.gui.ResultsMenuBar

Sets up a results menu bar with save and close

setSelected(boolean) - Method in class org.emboss.jemboss.editor.ColourMenu.ColorPane

setSelected(boolean) - Method in class org.emboss.jemboss.gui.ColorMenu.ColorPane

setSequenceLength(int) - Method in class org.emboss.jemboss.editor.SequenceJPanel

Set the sequence length

setSequenceLock(boolean) - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection

Lock/group the sequences

setServerStatus(String, int) - Method in class org.emboss.jemboss.JembossParams

Mark a server as bad

setServicePasswd(char[]) - Method in class org.emboss.jemboss.JembossParams

Save the password needed for the remote service

setServiceUserName(String) - Method in class org.emboss.jemboss.JembossParams

Save the username needed for the remote service

setShadingAndVisibility(Component, boolean, int) - Method in class org.emboss.jemboss.gui.form.SectionPanel

Set the shading or visibility of a component

setSize() - Method in class org.emboss.jemboss.editor.GroutGraphicSequenceCollection

setSize(Dimension) - Method in class org.emboss.jemboss.gui.filetree.FileEditorDisplay

Override to avoid line wrapping.

setSize(Dimension) - Method in class org.emboss.jemboss.gui.sequenceChooser.FileChooser

Set the size of the text field

setTabs(int[]) - Method in class org.emboss.jemboss.gui.TabListCellRenderer

setText(String, String) - Method in class org.emboss.jemboss.gui.filetree.FileEditorDisplay

Set the text & style in the JTextPane.

setText(String) - Method in class org.emboss.jemboss.gui.sequenceChooser.CutNPasteTextArea

Set contents of the text area

setText(String) - Method in class org.emboss.jemboss.gui.sequenceChooser.FileChooser

Set the text field

setType(boolean) - Method in class org.emboss.jemboss.editor.Sequence

Set the sequence type

setURL(URL, String) - Method in class org.emboss.jemboss.gui.Browser

Set the URL in the browser

setUpJMenuBar(Vector) - Method in class org.emboss.jemboss.gui.Browser

Method to create the frames menu and tool bar.

setUserHome(String) - Method in class org.emboss.jemboss.JembossParams

Set the user home directory property

setValue(Object) - Method in class org.emboss.jemboss.gui.SwingWorker

Set the value produced by worker thread

setValue(double) - Method in class org.emboss.jemboss.gui.form.TextFieldFloat

setValue(int) - Method in class org.emboss.jemboss.gui.form.TextFieldInt

setValue(String) - Method in class org.emboss.jemboss.parser.acd.ApplicationParam

Set the parameter string value

setValue(double) - Method in class org.emboss.jemboss.parser.acd.ApplicationParam

Set the parameter number value

setValueAt(Object, int, int) - Method in class org.emboss.jemboss.gui.SequenceListTableModel

Set the Object in a cell in the table

setWeight(float) - Method in class org.emboss.jemboss.editor.Sequence

Set the sequence weight

setWeight(float) - Method in class org.emboss.jemboss.parser.Ajax

Sets the sequence weight

setupServerRedundancy() - Method in class org.emboss.jemboss.JembossParams

Initialize the server redundancy data.

showConsensusPlot(File, int) - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection

Calculate and display the consensus plot

showConsensusPlot(Matrix, int) - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection

Calculate and display the consensus plot

showFilePane(String, JembossParams) - Static method in class org.emboss.jemboss.gui.filetree.DragTree

Opens a JFrame with the file contents displayed.

showFilePane(String, JembossParams) - Static method in class org.emboss.jemboss.gui.filetree.RemoteDragTree

Opens a JFrame with the file contents displayed.

showLocalRemoteFile - Variable in class org.emboss.jemboss.gui.SetUpMenuBar

local and remote file manager menu item

showOptions(GraphicSequenceCollection, PageFormat) - Method in class org.emboss.jemboss.editor.PrintAlignment

Provide some options for the image created

showOptions(boolean) - Method in class org.emboss.jemboss.editor.PrintAlignmentImage

Provide some options for the image created

showPattern(String) - Method in class org.emboss.jemboss.editor.SequenceJPanel

Set pattern to high light

showPendingResults(JFrame) - Method in class org.emboss.jemboss.soap.PendingResults

Display the list of pending and completed batch results window

show_acd(String) - Method in class org.emboss.jemboss.server.JembossAuthServer

Retrieves the ACD file of an application.

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

Retrieves the ACD file of an application.

show_db() - Method in class org.emboss.jemboss.server.JembossAuthServer

Returns the databases held on the server

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

Returns the databases held on the server

show_help(String) - Method in class org.emboss.jemboss.server.JembossAuthServer

Returns the help for an application as given by 'tfm'

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

Returns the help for an application as given by 'tfm'

show_saved_results(String, String, String, byte[]) - Method in class org.emboss.jemboss.server.JembossAuthServer

Returns the results for a saved project.

show_saved_results(String, String, String) - Method in class org.emboss.jemboss.server.JembossServer

Returns the results for a saved project.

show_saved_results(String, String) - Method in class org.emboss.jemboss.server.JembossServer

Returns the results for a saved project.

size - Variable in class org.emboss.jemboss.parser.Ajax

sizeColor - Static variable in class org.emboss.jemboss.editor.SequenceProperties

Tiny/Small/Large (Red=Tiny, Green=Small, Blue=Large)

soapService - Variable in class org.emboss.jemboss.JembossParams

service name

soapServiceName - Variable in class org.emboss.jemboss.JembossParams

property name for service name

source - Variable in class org.emboss.jemboss.editor.GroutAlignJFrameEvent

source - Variable in class org.emboss.jemboss.editor.GroutGraphicSequenceCollectionEvent

sp - Variable in class org.emboss.jemboss.gui.Browser

JSplitPane sp

sp - Variable in class org.emboss.jemboss.gui.ShowSavedResults

result data list panel

spLeft - Variable in class org.emboss.jemboss.gui.Browser

JList spLeft

splashThread - Variable in class org.emboss.jemboss.gui.BuildProgramMenu

thread for progress monitor on the login window

splashing - Variable in class org.emboss.jemboss.gui.BuildProgramMenu

login window

splashing - Variable in class org.emboss.jemboss.gui.SplashThread

splashp - Variable in class org.emboss.jemboss.soap.AuthPopup

splash panel

ss - Variable in class org.emboss.jemboss.gui.SetUpMenuBar

server settings

ss - Variable in class org.emboss.jemboss.gui.ShowSavedResults

scroll panel for result data

start() - Method in class org.emboss.jemboss.editor.AlignApplet

start() - Method in class org.emboss.jemboss.gui.SwingWorker

Start the worker thread.

status - Variable in class org.emboss.jemboss.programs.ResultList

status - Variable in class org.emboss.jemboss.programs.RunEmbossApplication

status of the process

status - Variable in class org.emboss.jemboss.programs.RunEmbossApplication2

process status

status - Variable in class org.emboss.jemboss.soap.GetHelp

status - Variable in class org.emboss.jemboss.soap.JembossRun

status of the request

status - Variable in class org.emboss.jemboss.soap.ShowDB

status

statusField - Static variable in class org.emboss.jemboss.editor.AlignJFrame

statusField - Variable in class org.emboss.jemboss.editor.PrintAlignmentImage

status field for print preview

statusField - Variable in class org.emboss.jemboss.gui.ShowSavedResults

status field

statusPanel(JFrame) - Method in class org.emboss.jemboss.soap.PendingResults

A panel to show the status of any jobs and to view them, and to set the mode.

statusmsg - Variable in class org.emboss.jemboss.programs.ResultList

statusmsg - Variable in class org.emboss.jemboss.soap.GetHelp

statusmsg - Variable in class org.emboss.jemboss.soap.JembossRun

status message

statusmsg - Variable in class org.emboss.jemboss.soap.ShowDB

status message

stderr - Variable in class org.emboss.jemboss.programs.RunEmbossApplication2

standard error

stderrh - Variable in class org.emboss.jemboss.programs.RunEmbossApplication2

stdout - Variable in class org.emboss.jemboss.gui.form.BuildJembossForm

stdout - Variable in class org.emboss.jemboss.programs.RunEmbossApplication

standard out

stdout - Variable in class org.emboss.jemboss.programs.RunEmbossApplication2

standard out

stdouth - Variable in class org.emboss.jemboss.programs.RunEmbossApplication2

storeSeqList - Variable in class org.emboss.jemboss.gui.SequenceList

select to save the sequence list between sessions

sumscore - Variable in class org.emboss.jemboss.editor.PlotConsensus

sum of scores for each column

surfaceColor - Static variable in class org.emboss.jemboss.editor.SequenceProperties

Surface/Buried (Red=Surface, Blue=Buried)

svalue - Variable in class org.emboss.jemboss.parser.ParseAcd

string value of a parameter

svalue - Variable in class org.emboss.jemboss.parser.acd.ApplicationParam

parameter string value

swiss - Static variable in class org.emboss.jemboss.gui.sequenceChooser.SequenceFilter

T

TURQUOISE - Static variable in class org.emboss.jemboss.editor.SequenceProperties

TURQUOISE from EMBOSS data Ecolour.map

TabListCellRenderer - class org.emboss.jemboss.gui.TabListCellRenderer.

Adapted from an example at http://www.spindoczine.com/sbe/

TabListCellRenderer() - Constructor for class org.emboss.jemboss.gui.TabListCellRenderer

TestPrivateServer - class org.emboss.jemboss.server.TestPrivateServer.

This can be used to test the private server.

TestPrivateServer() - Constructor for class org.emboss.jemboss.server.TestPrivateServer

TestPublicServer - class org.emboss.jemboss.server.TestPublicServer.

This can be used to test the public server.

TestPublicServer() - Constructor for class org.emboss.jemboss.server.TestPublicServer

TextAreaSink - class org.emboss.jemboss.gui.sequenceChooser.TextAreaSink.

Extends JTextArea so that is becomes a sink for pasting into or drag and dropping to

TextAreaSink() - Constructor for class org.emboss.jemboss.gui.sequenceChooser.TextAreaSink

TextFieldFloat - class org.emboss.jemboss.gui.form.TextFieldFloat.

JTextfield for float fields in the EMBOSS form

TextFieldFloat() - Constructor for class org.emboss.jemboss.gui.form.TextFieldFloat

TextFieldFloat.DecimalNumberDocument - class org.emboss.jemboss.gui.form.TextFieldFloat.DecimalNumberDocument.

TextFieldFloat.DecimalNumberDocument() - Constructor for class org.emboss.jemboss.gui.form.TextFieldFloat.DecimalNumberDocument

TextFieldInt - class org.emboss.jemboss.gui.form.TextFieldInt.

JTextfield for int fields in the EMBOSS form

TextFieldInt() - Constructor for class org.emboss.jemboss.gui.form.TextFieldInt

TextFieldInt.WholeNumberDocument - class org.emboss.jemboss.gui.form.TextFieldInt.WholeNumberDocument.

TextFieldInt.WholeNumberDocument() - Constructor for class org.emboss.jemboss.gui.form.TextFieldInt.WholeNumberDocument

TextFieldSink - class org.emboss.jemboss.gui.form.TextFieldSink.

Extends JTextField to enable pasting & drag and drop into it.

TextFieldSink() - Constructor for class org.emboss.jemboss.gui.form.TextFieldSink

table - Variable in class org.emboss.jemboss.gui.SequenceList

drag and drop table containing the list of sequences

targets - Variable in class org.emboss.jemboss.editor.GroutAlignJFrame

targets - Variable in class org.emboss.jemboss.editor.GroutGraphicSequenceCollection

taylorColor - Static variable in class org.emboss.jemboss.editor.SequenceProperties

Taylor colour scheme, W.R.Taylor Protein Eng vol.10, 7 pp743-746, 1997

testUpAndDown(int, Sequence) - Method in class org.emboss.jemboss.editor.GraphicSequenceCollection

textArea - Variable in class org.emboss.jemboss.programs.RunEmbossApplication2

textFloat - Variable in class org.emboss.jemboss.editor.PrettyPlotJFrame

field to define threshold for positive matches

textFloat - Variable in class org.emboss.jemboss.gui.form.BuildJembossForm

textFloat - Variable in class org.emboss.jemboss.gui.form.SectionPanel

float field sink

textInt - Variable in class org.emboss.jemboss.editor.PrettyPlotJFrame

field to define min number of identities

textInt - Variable in class org.emboss.jemboss.gui.form.BuildJembossForm

textInt - Variable in class org.emboss.jemboss.gui.form.SectionPanel

integer field sink

textf - Variable in class org.emboss.jemboss.gui.form.BuildJembossForm

textf - Variable in class org.emboss.jemboss.gui.form.SectionPanel

text field sink

thread - Variable in class org.emboss.jemboss.gui.SwingWorker.ThreadVar

thread - Variable in class org.emboss.jemboss.gui.SwingWorker

threadVar - Variable in class org.emboss.jemboss.gui.SwingWorker

time - Variable in class org.emboss.jemboss.gui.AdvancedOptions

times for job manager updates

timer - Static variable in class org.emboss.jemboss.programs.BatchUpdateTimer

timer

timer - Static variable in class org.emboss.jemboss.programs.ResultsUpdateTimer

timer

title - Variable in class org.emboss.jemboss.gui.ColumnData

tmproot - Variable in class org.emboss.jemboss.server.JembossAuthServer

SOAP results directory

tmproot - Variable in class org.emboss.jemboss.server.JembossServer

results directory

tmprootDir - Variable in class org.emboss.jemboss.server.JembossServer

results directory

toByteArr(char[]) - Static method in class org.emboss.jemboss.JembossParams

Return the password as byte array

toString() - Method in class org.emboss.jemboss.gui.filetree.FileNode

Returns the name of the file

toolBar - Variable in class org.emboss.jemboss.gui.ResultsMenuBar

tool bar

toolTipFontMetrics(Font) - Method in class org.emboss.jemboss.gui.form.MultiLineToolTipUI.MyToolTip

toolkit - Variable in class org.emboss.jemboss.gui.form.TextFieldFloat

toolkit - Variable in class org.emboss.jemboss.gui.form.TextFieldInt

topics - Variable in class org.emboss.jemboss.gui.Browser

Help topics

tree - Static variable in class org.emboss.jemboss.Jemboss

Local filemanager

trim(int, int) - Method in class org.emboss.jemboss.editor.Sequence

Trim a sequence

trim(String) - Static method in class org.emboss.jemboss.programs.ListFile

Given a list file @file or list::file return just the file name

type - Variable in class org.emboss.jemboss.parser.Dependent

parameter type

U

UFO - Variable in class org.emboss.jemboss.gui.sequenceChooser.InputSequenceAttributes

uniform feature object

UFO - Variable in class org.emboss.jemboss.gui.sequenceChooser.OutputSequenceAttributes

uniform feature object

ufield - Variable in class org.emboss.jemboss.soap.AuthPopup

username field

undo - Variable in class org.emboss.jemboss.gui.ResultsMenuBar

undo menu item

undoManager - Variable in class org.emboss.jemboss.gui.ResultsMenuBar

undo manager

uninstallUI(JComponent) - Method in class org.emboss.jemboss.gui.form.MultiLineToolTipUI

unselectedBorder - Variable in class org.emboss.jemboss.editor.ColourMenu

unselected border

unselectedBorder - Variable in class org.emboss.jemboss.gui.ColorMenu

update(int, int) - Method in class org.emboss.jemboss.editor.SequenceJPanel

Implement update() for observers i.e.

updateBeginEnd(String, String) - Method in class org.emboss.jemboss.gui.form.SectionPanel

Check sbeg and send values before updating in the panel to avoid overriding user selection

updateJembossPropHash(Hashtable) - Method in class org.emboss.jemboss.JembossParams

Update properties from a Hashtable

updateJembossPropString(String) - Method in class org.emboss.jemboss.JembossParams

Parse a key=value string to update the properties structure

updateJembossPropStrings(String[]) - Method in class org.emboss.jemboss.JembossParams

Parse an array of key=value strings to update the properties structure

updateJembossProperty(String, String) - Method in class org.emboss.jemboss.JembossParams

Update the properties structure.

updateJobStats() - Method in class org.emboss.jemboss.soap.PendingResults

Update the number of completed and pending processes

updateMenu() - Method in class org.emboss.jemboss.gui.ResultsMenuBar

Update the undo and redo menus and enable or disable dependent on the editing event that proceeded.

updateMode() - Method in class org.emboss.jemboss.soap.PendingResults

Updates the mode on the combo box to reflect the current state

updateMode(String) - Method in class org.emboss.jemboss.soap.PendingResults

Updates the mode on the combo box to reflect the requested value

updateRes(Hashtable) - Method in class org.emboss.jemboss.programs.ResultList

Replace the current results hash

updateSettingsFromProperties() - Method in class org.emboss.jemboss.JembossParams

Update the property settings for jembossSettings.

updateStatus() - Method in class org.emboss.jemboss.soap.PendingResults

Connect to the Jemboss server, and update the status of the jobs in the list.

update_result_status(String, String, Vector, String, byte[]) - Method in class org.emboss.jemboss.server.JembossAuthServer

Used to provide information on the batch/background processes.

update_result_status(String, String, Vector, String) - Method in class org.emboss.jemboss.server.JembossServer

Used to provide information on the batch/background processes.

update_result_status(String, String, Hashtable, String) - Method in class org.emboss.jemboss.server.JembossServer

Used to provide information on the batch/background processes.

update_result_status(String, String, Hashtable) - Method in class org.emboss.jemboss.server.JembossServer

Used to provide information on the batch/background processes.

upper - Variable in class org.emboss.jemboss.gui.sequenceChooser.InputSequenceAttributes

select to specify upper case

urlField - Variable in class org.emboss.jemboss.gui.Browser

URL cache combo field

useAuth - Variable in class org.emboss.jemboss.JembossParams

use unix authentication to run applications on the server

useAuthName - Variable in class org.emboss.jemboss.JembossParams

property name for using unix authentication

useBrowserProxy - Variable in class org.emboss.jemboss.JembossParams

use a separate proxy for browsing the web

useBrowserProxy - Variable in class org.emboss.jemboss.soap.ServerSetup

selected if using proxy server for web browser

useBrowserProxyName - Variable in class org.emboss.jemboss.JembossParams

property name for using separate proxy for browsing the web

useExitMenu - Variable in class org.emboss.jemboss.editor.AlignJFrame

useHTTPSProxy - Variable in class org.emboss.jemboss.JembossParams

useHTTPSProxyName - Variable in class org.emboss.jemboss.JembossParams

useJavaNoProxy - Variable in class org.emboss.jemboss.JembossParams

useJavaProxy - Variable in class org.emboss.jemboss.JembossParams

useProxy - Variable in class org.emboss.jemboss.JembossParams

useProxy - Variable in class org.emboss.jemboss.soap.ServerSetup

selected if using proxy server

useProxyAuth - Variable in class org.emboss.jemboss.JembossParams

use proxy authentication

useProxyAuthName - Variable in class org.emboss.jemboss.JembossParams

property name for using proxy authentication

useProxyName - Variable in class org.emboss.jemboss.JembossParams

useTFM - Variable in class org.emboss.jemboss.JembossParams

useTFMName - Variable in class org.emboss.jemboss.JembossParams

userAuth(String, byte[], String) - Method in class org.emboss.jemboss.parser.Ajax

authentication method

userAuth - Variable in class org.emboss.jemboss.soap.ServerSetup

selected if user authetication required

userHome - Variable in class org.emboss.jemboss.JembossParams

user home directory

userHome - Variable in class org.emboss.jemboss.gui.AdvancedOptions

user home directory

userHomeName - Variable in class org.emboss.jemboss.JembossParams

property name for user home directory

userHomeSave() - Method in class org.emboss.jemboss.gui.AdvancedOptions

Save the user home/working directory to jemboss.properties

username - Variable in class org.emboss.jemboss.server.JembossServer

user name

V

value - Variable in class org.emboss.jemboss.gui.SwingWorker

vappF - Variable in class org.emboss.jemboss.parser.ParseAcd

vector containing the application fields

vdir - Variable in class org.emboss.jemboss.soap.FileList

vector containing directories

verifyUser(Ajax, String, byte[], Vector) - Method in class org.emboss.jemboss.server.JembossAuthServer

Verify the username/passwd

verifyUser(Ajax, String, byte[], Vector) - Method in class org.emboss.jemboss.server.JembossFileAuthServer

Verify the username/passwd

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

viewPane - Variable in class org.emboss.jemboss.editor.PlotConsensus

associated sequence panel

viewPane - Variable in class org.emboss.jemboss.editor.SequenceJPanel

sequence alignment panel

viewPaneResize() - Method in class org.emboss.jemboss.editor.SequenceJPanel

Re-size the sequence alignment panel if the width of this sequence pane increases

viewResiduePosition - Variable in class org.emboss.jemboss.editor.PatternJFrame

residue position to display

W

WHEAT - Static variable in class org.emboss.jemboss.editor.SequenceProperties

WHEAT from EMBOSS data Ecolour.map

waitFor() - Method in class org.emboss.jemboss.programs.RunEmbossApplication2

Wait for the process to end

warnUser(String) - Method in class org.emboss.jemboss.gui.Browser

Display a warning message

weight - Static variable in class org.emboss.jemboss.parser.Ajax

sequence weight

weight - Variable in class org.emboss.jemboss.soap.CallAjax

sequence weight

weight_soap - Variable in class org.emboss.jemboss.parser.Ajax

sequence weight

width - Variable in class org.emboss.jemboss.gui.ColumnData

windowClosing(WindowEvent) - Method in class org.emboss.jemboss.Jemboss.winExit

windowClosing(WindowEvent) - Method in class org.emboss.jemboss.editor.AlignJFrame.winExit

windowClosing(WindowEvent) - Method in class org.emboss.jemboss.editor.GroutAlignJFrame.winExit

windowDeiconified(WindowEvent) - Method in class org.emboss.jemboss.editor.GroutAlignJFrame.winExit

windowOpened(WindowEvent) - Method in class org.emboss.jemboss.editor.GroutAlignJFrame.winExit

withSoap - Static variable in class org.emboss.jemboss.Jemboss

true if in client-server mode (using SOAP)

withSoap - Variable in class org.emboss.jemboss.gui.form.BuildJembossForm

withSoap - Variable in class org.emboss.jemboss.gui.form.SectionPanel

true if in client-server mode

wrapAround - Variable in class org.emboss.jemboss.editor.PatternJFrame

wrap around search check box

writeByteFile(String, String) - Method in class org.emboss.jemboss.JembossJarUtil

Write contents of an element in the hashtable

writeImageToFile(RenderedImage, File, String) - Method in class org.emboss.jemboss.editor.PrintAlignmentImage

Write out the image

writeList() - Method in class org.emboss.jemboss.gui.startup.ProgList

Writes to screen the program names

writeListFile(String) - Method in class org.emboss.jemboss.gui.form.ListFilePanel

writeListFile(String) - Method in class org.emboss.jemboss.gui.form.SetInFileCard

writeOK() - Method in class org.emboss.jemboss.gui.filetree.FileSave

Whether the fileSaving() operation was successful

writeOK() - Method in class org.emboss.jemboss.gui.filetree.FileSaving

writeObject(ObjectOutputStream) - Method in class org.emboss.jemboss.gui.SequenceData

writeObject(ObjectOutputStream) - Method in class org.emboss.jemboss.gui.filetree.FileNode

writeObject(ObjectOutputStream) - Method in class org.emboss.jemboss.gui.filetree.RemoteFileNode

writeObject(ObjectOutputStream) - Method in class org.emboss.jemboss.soap.FileRoots

writeStdout() - Method in class org.emboss.jemboss.programs.RunEmbossApplication2

This method can be called after the process has completed to write the stdout to the project directory.

wt - Variable in class org.emboss.jemboss.editor.Sequence

sequence weight

X

x - Variable in class org.emboss.jemboss.JembossLogo

x - Variable in class org.emboss.jemboss.gui.form.ApplicationNamePanel

x position for displaying name

xsize - Variable in class org.emboss.jemboss.editor.ColourPanel

Y

YBox - Variable in class org.emboss.jemboss.editor.ColourJFrame

Container for the all the residue colour

y - Variable in class org.emboss.jemboss.JembossLogo

y - Variable in class org.emboss.jemboss.gui.form.ApplicationNamePanel

y position for displaying name

ymax - Variable in class org.emboss.jemboss.editor.PlotConsensus

maximum y value

ymin - Variable in class org.emboss.jemboss.editor.PlotConsensus

minimum y value

ypad - Variable in class org.emboss.jemboss.editor.SequenceJPanel

sequence height pad

ypad - Variable in class org.emboss.jemboss.editor.SequenceNameJButton

height pad

ysize - Variable in class org.emboss.jemboss.editor.ColourPanel

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