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Public Member Functions | Public Attributes | Protected Member Functions | Protected Attributes | Package Functions | Package Attributes | Static Package Attributes | Private Member Functions

jalview::appletgui::AlignFrame Class Reference

Inheritance diagram for jalview::appletgui::AlignFrame:
Inheritance graph
Collaboration diagram for jalview::appletgui::AlignFrame:
Collaboration graph

List of all members.

Public Member Functions

void abovePIDThreshold_actionPerformed ()
void actionPerformed (ActionEvent evt)
void addHistoryItem (CommandI command)
boolean addPdbFile (String sequenceId, String pdbEntryString, String pdbFile)
SequenceStructureBinding addStructureViewInstance (Object jmolviewer, String[] sequenceIds)
void alignedStructureView (JalviewLite applet, PDBEntry[] pdb, SequenceI[][] seqs, String[][] chains, String[] protocols)
 AlignFrame (AlignmentI al, jalview.bin.JalviewLite applet, String title, boolean embedded)
void averageDistanceTreeMenuItem_actionPerformed ()
void closeMenuItem_actionPerformed ()
void createAlignFrameWindow (boolean reallyEmbedded, String title)
void deselectAllSequenceMenuItem_actionPerformed ()
void destroyMenus ()
void finalize () throws Throwable
void findMenuItem_actionPerformed ()
AlignViewport getAlignViewport ()
String[] getFeatureGroups ()
String[] getFeatureGroupsOfState (boolean visible)
SeqCanvas getSeqcanvas ()
String getSequenceSetId ()
void inputText_actionPerformed ()
void invertColSel_actionPerformed ()
void invertSequenceMenuItem_actionPerformed ()
void itemStateChanged (ItemEvent evt)
void keyPressed (KeyEvent evt)
void keyReleased (KeyEvent evt)
void keyTyped (KeyEvent evt)
void loadAnnotations ()
void loadTree (jalview.io.NewickFile tree, String treeFile)
void mouseClicked (MouseEvent evt)
void mouseEntered (MouseEvent evt)
void mouseExited (MouseEvent evt)
void mousePressed (MouseEvent evt)
void mouseReleased (MouseEvent evt)
void moveSelectedSequences (boolean up)
void neighbourTreeMenuItem_actionPerformed ()
void newStructureView (JalviewLite applet, PDBEntry pdb, SequenceI[] seqs, String[] chains, String protocol)
AlignFrame newView (String viewtitle)
String outputAnnotations (boolean displayTextbox)
String outputFeatures (boolean displayTextbox, String format)
void overviewMenuItem_actionPerformed ()
void pairwiseAlignmentMenuItem_actionPerformed ()
void parseFeaturesFile (String file, String type)
void PCAMenuItem_actionPerformed ()
void removeAllGapsMenuItem_actionPerformed ()
void removeGappedColumnMenuItem_actionPerformed ()
void removeRedundancyMenuItem_actionPerformed ()
void scrollTo (int row, int column)
void scrollToColumn (int column)
void scrollToRow (int row)
void select (SequenceGroup sel, ColumnSelection csel)
void selectAllSequenceMenuItem_actionPerformed ()
void seqLimits_itemStateChanged ()
void setFeatureGroupState (String[] groups, boolean state)
void showURL (String url, String target)
boolean sortBy (AlignmentOrder alorder, String undoname)
void sortByTree (TreePanel treePanel, String title)
void sortGroupMenuItem_actionPerformed ()
void sortIDMenuItem_actionPerformed ()
void sortLengthMenuItem_actionPerformed ()
void sortPairwiseMenuItem_actionPerformed ()

Public Attributes

AlignmentPanel alignPanel
Label statusBar = new Label()
AlignViewport viewport

Protected Member Functions

void about_actionPerformed ()
void addTreeMenuItem (final TreePanel treePanel, final String title)
void applyAutoAnnotationSettings_actionPerformed ()
void avTreeBlosumMenuItem_actionPerformed ()
void colourTextMenuItem_actionPerformed ()
void conservationMenuItem_actionPerformed ()
void copy_actionPerformed ()
void cut_actionPerformed ()
void delete_actionPerformed ()
void deleteGroups_actionPerformed ()
void displayNonconservedMenuItem_actionPerformed ()
void documentation_actionPerformed ()
boolean embedMenuIfNeeded (Panel tobeAdjusted)
Panel makeEmbeddedPopupMenu (MenuBar menuBar, String fn, int fstyle, int fsz, boolean overrideFonts, boolean append)
Panel makeEmbeddedPopupMenu (MenuBar menuBar, String fn, int fstyle, int fsz, boolean overrideFonts)
Panel makeEmbeddedPopupMenu (MenuBar menuBar, String fn, int fstyle, int fsz, boolean overrideFonts, Hashtable embeddedPopup, Panel embeddedMenu, MouseListener clickHandler)
void makeGrpsFromSelection_actionPerformed ()
void modifyConservation_actionPerformed ()
void modifyPID_actionPerformed ()
void njTreeBlosumMenuItem_actionPerformed ()
void outputText_actionPerformed (ActionEvent e)
void pasteNew_actionPerformed ()
void pasteThis_actionPerformed ()
void redoMenuItem_actionPerformed ()
void showConsensusHistogram_actionPerformed ()
void showGroupConsensus_actionPerformed ()
void showGroupConservation_actionPerformed ()
void showSequenceLogo_actionPerformed ()
void undoMenuItem_actionPerformed ()
void wrapMenuItem_actionPerformed ()

Protected Attributes

Panel embeddedMenu
Hashtable embeddedPopup

Package Functions

void addSequences (SequenceI[] seqs)
String appendProtocol (String url)
void changeColour (ColourSchemeI cs)
AlignViewport getOriginatingSource (CommandI command)
PopupMenu getPopupMenu (Label source)
void launchFullApplication ()
void loadTree_actionPerformed ()
void NewTreePanel (String type, String pwType, String title)
void paste (boolean newAlignment)
String removeWhiteSpace (String colour)
synchronized void slideSequences (boolean right, int size)
void trimAlignment (boolean trimLeft)
void updateEditMenuBar ()

Package Attributes

MenuItem about = new MenuItem()
CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem()
MenuBar alignFrameMenuBar = new MenuBar()
MenuItem alProperties = new MenuItem("Alignment Properties...")
MenuItem annotationColour = new MenuItem()
CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem()
CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem()
CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem()
Menu autoAnnMenu = new Menu()
CheckboxMenuItem autoCalculate
MenuItem avDistanceTreeBlosumMenuItem = new MenuItem()
MenuItem averageDistanceTreeMenuItem = new MenuItem()
MenuItem BLOSUM62Colour = new MenuItem()
BorderLayout borderLayout1 = new BorderLayout()
MenuItem buriedColour = new MenuItem()
Menu calculate = new Menu()
Menu calculateMenu = new Menu("Calculate")
CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem()
MenuItem closeMenuItem = new MenuItem("Close")
MenuItem clustalColour = new MenuItem()
Menu colourMenu = new Menu("Colour")
CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem()
CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem()
MenuItem copy = new MenuItem()
MenuItem cut = new MenuItem()
MenuItem delete = new MenuItem()
MenuItem deleteGroups = new MenuItem()
MenuItem deselectAllSequenceMenuItem = new MenuItem("Deselect All")
CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem()
MenuItem documentation = new MenuItem()
Menu editMenu = new Menu("Edit")
MenuItem featureSettings = new MenuItem()
Menu fileMenu = new Menu("File")
MenuItem findMenuItem = new MenuItem()
CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem()
MenuItem font = new MenuItem()
Menu formatMenu = new Menu()
MenuItem grpsFromSelection = new MenuItem()
MenuItem helixColour = new MenuItem()
Menu helpMenu = new Menu()
MenuItem hideAllButSelection = new MenuItem()
MenuItem hideAllSelection = new MenuItem()
MenuItem hideColumns = new MenuItem()
MenuItem hideSequences = new MenuItem()
MenuItem hydrophobicityColour = new MenuItem()
MenuItem inputText = new MenuItem()
MenuItem invertColSel = new MenuItem()
MenuItem invertSequenceMenuItem = new MenuItem("Invert Selection")
String jalviewServletURL
MenuItem loadAnnotations = new MenuItem("Load Features/Annotations ...")
MenuItem loadApplication = new MenuItem("View in Full Application")
MenuItem loadTree = new MenuItem("Load Associated Tree ...")
Menu menu1 = new Menu()
Menu menu2 = new Menu()
MenuItem modifyConservation = new MenuItem()
MenuItem modifyPID = new MenuItem()
MenuItem neighbourTreeMenuItem = new MenuItem()
MenuItem newView = new MenuItem()
MenuItem njTreeBlosumMenuItem = new MenuItem()
MenuItem noColourmenuItem = new MenuItem()
MenuItem nucleotideColour = new MenuItem()
MenuItem outputAnnotations = new MenuItem("Export Annotations ...")
MenuItem outputFeatures = new MenuItem("Export Features ...")
Menu outputTextboxMenu = new Menu()
MenuItem overviewMenuItem = new MenuItem()
MenuItem pairwiseAlignmentMenuItem = new MenuItem()
Menu pasteMenu = new Menu()
MenuItem pasteNew = new MenuItem()
MenuItem pasteThis = new MenuItem()
MenuItem PCAMenuItem = new MenuItem()
MenuItem PIDColour = new MenuItem()
MenuItem redoMenuItem = new MenuItem()
MenuItem remove2LeftMenuItem = new MenuItem()
MenuItem remove2RightMenuItem = new MenuItem()
MenuItem removeAllGapsMenuItem = new MenuItem()
MenuItem removeGappedColumnMenuItem = new MenuItem()
MenuItem removeRedundancyMenuItem = new MenuItem()
CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem()
CheckboxMenuItem scaleAbove = new CheckboxMenuItem()
CheckboxMenuItem scaleLeft = new CheckboxMenuItem()
CheckboxMenuItem scaleRight = new CheckboxMenuItem()
MenuItem selectAllSequenceMenuItem = new MenuItem("Select all")
Menu selectMenu = new Menu()
CheckboxMenuItem seqLimits = new CheckboxMenuItem()
CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem()
MenuItem showAllHidden = new MenuItem()
MenuItem showColumns = new MenuItem()
CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem()
CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem()
CheckboxMenuItem showGroupConservation = new CheckboxMenuItem()
MenuItem showSeqs = new MenuItem()
CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem()
Menu sort = new Menu()
CheckboxMenuItem sortByTree
Menu sortByTreeMenu = new Menu()
MenuItem sortGroupMenuItem = new MenuItem()
MenuItem sortIDMenuItem = new MenuItem()
MenuItem sortLengthMenuItem = new MenuItem()
MenuItem sortPairwiseMenuItem = new MenuItem()
MenuItem strandColour = new MenuItem()
MenuItem taylorColour = new MenuItem()
MenuItem turnColour = new MenuItem()
MenuItem undoMenuItem = new MenuItem()
MenuItem userDefinedColour = new MenuItem()
CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem()
Menu viewMenu = new Menu("View")
CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem()
CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem()
MenuItem zappoColour = new MenuItem()

Static Package Attributes

static Vector copiedHiddenColumns
static StringBuffer copiedSequences

Private Member Functions

void centreColumnLabelFlag_stateChanged ()
Object[] cleanSeqChainArrays (SequenceI[] seqs, String[] chains)
Hashtable getDisplayedFeatureCols ()
void jbInit () throws Exception
void mouseOverFlag_stateChanged ()
void toggleHiddenRegions (boolean toggleSeqs, boolean toggleCols)

Detailed Description

Definition at line 35 of file AlignFrame.java.

The documentation for this class was generated from the following file:

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