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@( num & num )
@( var = casea : vala, caseb: valb else: val )
@( bool ? trueval : falseval )
@( num * num )
@( num == num )
@( num > num )
@( num < num )
@( num - num )
@(! bool )
or @(NOT bool)
or @(not bool)
.
@( num != num )
@( num | num )
@( num + num )
@( num * num )
get
method.
construct
method has returned.
construct
method.
SequenceData
for a given row
number.
SequenceData
for a given row
number.
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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