Logo Search packages:      
Sourcecode: jalview version File versions

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

jalview::gui::AlignFrame Class Reference

Inheritance diagram for jalview::gui::AlignFrame:
Inheritance graph
[legend]
Collaboration diagram for jalview::gui::AlignFrame:
Collaboration graph
[legend]

List of all members.

Public Member Functions

void abovePIDThreshold_actionPerformed (ActionEvent e)
void addAlignmentPanel (final AlignmentPanel ap, boolean newPanel)
void addFromFile_actionPerformed (ActionEvent e)
void addFromText_actionPerformed (ActionEvent e)
void addFromURL_actionPerformed (ActionEvent e)
void addHistoryItem (CommandI command)
void addSortByAnnotScoreMenuItem (JMenu sort, final String scoreLabel)
void addSortByOrderMenuItem (String title, final AlignmentOrder order)
 AlignFrame (AlignmentI al, int width, int height, String sequenceSetId)
 AlignFrame (AlignmentI al, ColumnSelection hiddenColumns, int width, int height)
 AlignFrame (AlignmentI al, ColumnSelection hiddenColumns, int width, int height, String sequenceSetId)
 AlignFrame (AlignmentI al, int width, int height)
 AlignFrame (AlignmentI al, ColumnSelection hiddenColumns, int width, int height, String sequenceSetId, String viewId)
 AlignFrame (AlignmentI al, int width, int height, String sequenceSetId, String viewId)
 AlignFrame (AlignmentPanel ap)
void alignmentProperties ()
void annotationColour_actionPerformed (ActionEvent e)
void annotationPanelMenuItem_actionPerformed (ActionEvent e)
void associatedData_actionPerformed (ActionEvent e)
void autoCalculate_actionPerformed (ActionEvent e)
void averageDistanceTreeMenuItem_actionPerformed (ActionEvent e)
void BLOSUM62Colour_actionPerformed (ActionEvent e)
void buildSortByAnnotationScoresMenu ()
void buildTreeMenu ()
void BuildWebServiceMenu ()
void buriedColour_actionPerformed (ActionEvent e)
boolean canShowProducts (SequenceI[] selection, boolean isRegionSelection, Alignment dataset)
boolean canShowTranslationProducts (SequenceI[] selection, AlignmentI alignment)
void centreColumnLabels_actionPerformed (ActionEvent e)
void changeColour (ColourSchemeI cs)
void closeMenuItem_actionPerformed (boolean closeAllTabs)
boolean closeView (AlignViewport av)
void closeView (AlignmentPanel alignPanel2)
void clustalColour_actionPerformed (ActionEvent e)
void createEPS (java.io.File f)
void createEPS (File f)
void createImageMap (File file, String image)
void createPNG (java.io.File f)
void createPNG (File f)
void deselectAllSequenceMenuItem_actionPerformed (ActionEvent e)
void dragEnter (DropTargetDragEvent evt)
void dragExit (DropTargetEvent evt)
void dragOver (DropTargetDragEvent evt)
void drop (DropTargetDropEvent evt)
void dropActionChanged (DropTargetDragEvent evt)
void enterPdbId_actionPerformed (ActionEvent e)
void expandViews_actionPerformed (ActionEvent e)
void exportAnnotations_actionPerformed (ActionEvent e)
void exportFeatures_actionPerformed (ActionEvent e)
void featureSettings_actionPerformed (ActionEvent e)
void fetchSequence_actionPerformed (ActionEvent e)
void findMenuItem_actionPerformed (ActionEvent e)
void findPdbId_actionPerformed (ActionEvent e)
void font_actionPerformed (ActionEvent e)
AlignmentView gatherSeqOrMsaForSecStrPrediction ()
jalview.datamodel.AlignmentView gatherSequencesForAlignment ()
void gatherViews_actionPerformed (ActionEvent e)
AlignViewport getCurrentView ()
FeatureRenderer getFeatureRenderer ()
String getVersion ()
AlignViewport getViewport ()
void helixColour_actionPerformed (ActionEvent e)
void hiddenMarkers_actionPerformed (ActionEvent e)
void hideAllButSelection_actionPerformed (ActionEvent e)
void hideAllSelection_actionPerformed (ActionEvent e)
void hideSelColumns_actionPerformed (ActionEvent e)
void hideSelSequences_actionPerformed (ActionEvent e)
void hydrophobicityColour_actionPerformed (ActionEvent e)
void idRightAlign_actionPerformed (ActionEvent e)
void invertColSel_actionPerformed (ActionEvent e)
void invertSequenceMenuItem_actionPerformed (ActionEvent e)
void loadJalviewDataFile (String file, String protocol, String format, SequenceI assocSeq)
void moveSelectedSequences (boolean up)
void neighbourTreeMenuItem_actionPerformed (ActionEvent e)
AlignmentPanel newView (boolean copyAnnotation)
AlignmentPanel newView (String viewTitle, boolean copyAnnotation)
AlignmentPanel newView (String viewTitle)
void newView_actionPerformed (ActionEvent e)
void nucleotideColour_actionPerformed (ActionEvent e)
boolean operationInProgress ()
void overviewMenuItem_actionPerformed (ActionEvent e)
void padGapsMenuitem_actionPerformed (ActionEvent e)
void pageSetup_actionPerformed (ActionEvent e)
void pairwiseAlignmentMenuItem_actionPerformed (ActionEvent e)
boolean parseFeaturesFile (String file, String type)
void PCAMenuItem_actionPerformed (ActionEvent e)
void pdbFile_actionPerformed (ActionEvent e)
void PIDColour_actionPerformed (ActionEvent e)
void printMenuItem_actionPerformed (ActionEvent e)
abstract void registerHandler (long id, IProgressIndicatorHandler handler)
void registerHandler (final long id, final IProgressIndicatorHandler handler)
void reload_actionPerformed (ActionEvent e)
void remove2LeftMenuItem_actionPerformed (ActionEvent e)
void remove2RightMenuItem_actionPerformed (ActionEvent e)
void removeAllGapsMenuItem_actionPerformed (ActionEvent e)
void removeGappedColumnMenuItem_actionPerformed (ActionEvent e)
void removeRedundancyMenuItem_actionPerformed (ActionEvent e)
void save_actionPerformed (ActionEvent e)
boolean saveAlignment (String file, String format)
void saveAs_actionPerformed (ActionEvent e)
void selectAllSequenceMenuItem_actionPerformed (ActionEvent e)
void seqDBRef_actionPerformed (ActionEvent e)
void setColourSelected (String defaultColour)
void setDisplayedView (AlignmentPanel alignmentPanel)
void setFileName (String file, String format)
void setGUINucleotide (boolean nucleotide)
void setInitialTabVisible ()
void setMenusForViewport ()
void setProgressBar (String message, long id)
void setShowSeqFeatures (boolean b)
void showAllColumns_actionPerformed (ActionEvent e)
void showAllhidden_actionPerformed (ActionEvent e)
void showAllSeqs_actionPerformed (ActionEvent e)
TreePanel ShowNewickTree (NewickFile nf, String title, int w, int h, int x, int y)
TreePanel ShowNewickTree (NewickFile nf, String title, AlignmentView input, int w, int h, int x, int y)
TreePanel ShowNewickTree (NewickFile nf, String title, AlignmentView input)
TreePanel ShowNewickTree (NewickFile nf, String title)
void showProducts_actionPerformed (ActionEvent e)
void showSeqFeatures_actionPerformed (ActionEvent evt)
void showSeqFeaturesHeight_actionPerformed (ActionEvent evt)
void showTranslation_actionPerformed (ActionEvent e)
void smoothFont_actionPerformed (ActionEvent e)
boolean sortBy (AlignmentOrder alorder, String undoname)
void sortByTreeOption_actionPerformed (ActionEvent e)
void sortGroupMenuItem_actionPerformed (ActionEvent e)
void sortIDMenuItem_actionPerformed (ActionEvent e)
void sortLengthMenuItem_actionPerformed (ActionEvent e)
void sortPairwiseMenuItem_actionPerformed (ActionEvent e)
void strandColour_actionPerformed (ActionEvent e)
void tabbedPane_focusGained (FocusEvent e)
void tabbedPane_mousePressed (MouseEvent e)
void tabSelectionChanged (int index)
void taylorColour_actionPerformed (ActionEvent e)
void textColour_actionPerformed (ActionEvent e)
void turnColour_actionPerformed (ActionEvent e)
void updateUserColourMenu ()
void userDefinedColour_actionPerformed (ActionEvent e)
void vamsasLoad_actionPerformed (ActionEvent e)
void vamsasStore_actionPerformed (ActionEvent e)
void viewBoxesMenuItem_actionPerformed (ActionEvent e)
void viewTextMenuItem_actionPerformed (ActionEvent e)
void wrapMenuItem_actionPerformed (ActionEvent e)
void zappoColour_actionPerformed (ActionEvent e)

Public Attributes

JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem()
AlignmentPanel alignPanel
JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem()
JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem()
JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem()
JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem()
FeatureSettings featureSettings
JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem()
JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem()
JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem()
JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem()
JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem()
JCheckBoxMenuItem showNonconservedMenuItem = new JCheckBoxMenuItem()
JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem()
JCheckBoxMenuItem showSeqFeaturesHeight = new JCheckBoxMenuItem()
JLabel statusBar = new JLabel()
JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem()
JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem()
JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem()

Static Public Attributes

static final int DEFAULT_HEIGHT = 500
static final int DEFAULT_WIDTH = 700

Protected Member Functions

void applyAutoAnnotationSettings_actionPerformed (ActionEvent e)
void applyToAllGroups_actionPerformed (ActionEvent e)
void avTreeBlosumMenuItem_actionPerformed (ActionEvent e)
void build_fetchdbmenu (JMenu webService)
void colourTextMenuItem_actionPerformed (ActionEvent e)
void conservationMenuItem_actionPerformed (ActionEvent e)
void copy_actionPerformed (ActionEvent e)
void cut_actionPerformed (ActionEvent e)
void delete_actionPerformed (ActionEvent evt)
void deleteGroups_actionPerformed (ActionEvent e)
void extractScores_actionPerformed (ActionEvent e)
void followHighlight_actionPerformed ()
void htmlMenuItem_actionPerformed (ActionEvent e)
void jpred_actionPerformed (ActionEvent e)
void justifyLeftMenuItem_actionPerformed (ActionEvent e)
void justifyRightMenuItem_actionPerformed (ActionEvent e)
void listenToViewSelections_actionPerformed (ActionEvent e)
void LoadtreeMenuItem_actionPerformed (ActionEvent e)
void makeGrpsFromSelection_actionPerformed (ActionEvent e)
void modifyConservation_actionPerformed (ActionEvent e)
void modifyPID_actionPerformed (ActionEvent e)
void njTreeBlosumMenuItem_actionPerformed (ActionEvent e)
void noColourmenuItem_actionPerformed (ActionEvent e)
void outputText_actionPerformed (ActionEvent e)
void pasteNew_actionPerformed (ActionEvent e)
void pasteThis_actionPerformed (ActionEvent e)
void redoMenuItem_actionPerformed (ActionEvent e)
void renderGapsMenuItem_actionPerformed (ActionEvent e)
void scaleAbove_actionPerformed (ActionEvent e)
void scaleLeft_actionPerformed (ActionEvent e)
void scaleRight_actionPerformed (ActionEvent e)
void seqLimit_actionPerformed (ActionEvent e)
void setShowProductsEnabled ()
void showConsensusHistogram_actionPerformed (ActionEvent e)
void showDbRefs_actionPerformed (ActionEvent e)
void showGroupConsensus_actionPerformed (ActionEvent e)
void showGroupConservation_actionPerformed (ActionEvent e)
void showNpFeats_actionPerformed (ActionEvent e)
void showProductsFor (SequenceI[] sel, Alignment ds, boolean isRegSel, boolean dna, String source)
void showSequenceLogo_actionPerformed (ActionEvent e)
void showUnconservedMenuItem_actionPerformed (ActionEvent e)
void undoMenuItem_actionPerformed (ActionEvent e)

Protected Attributes

int _annotationScoreVectorHash
JMenuBar alignFrameMenuBar = new JMenuBar()
JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem()
JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem()
JMenuItem averageDistanceTreeMenuItem = new JMenuItem()
JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem()
JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem()
JMenu calculateMenu = new JMenu()
JMenu calculateTree = new JMenu()
JCheckBoxMenuItem centreColumnLabelsMenuItem = new JCheckBoxMenuItem()
JMenuItem closeMenuItem = new JMenuItem()
JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem()
JMenu colourMenu = new JMenu()
ButtonGroup colours = new ButtonGroup()
JMenuItem deselectAllSequenceMenuItem = new JMenuItem()
JMenu editMenu = new JMenu()
JMenuItem expandViews = new JMenuItem()
JMenuItem extractScores = new JMenuItem()
JMenu fileMenu = new JMenu()
JCheckBoxMenuItem followHighlightMenuItem = new JCheckBoxMenuItem()
JMenuItem font = new JMenuItem()
JMenuItem gatherViews = new JMenuItem()
JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem()
JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem()
JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem()
JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem()
JMenuItem invertSequenceMenuItem = new JMenuItem()
JCheckBoxMenuItem listenToViewSelections = new JCheckBoxMenuItem()
JMenuItem modifyConservation = new JMenuItem()
JMenuItem modifyPID = new JMenuItem()
JMenuItem neighbourTreeMenuItem = new JMenuItem()
JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem()
JMenu outputTextboxMenu = new JMenu()
JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem()
JMenuItem pairwiseAlignmentMenuItem = new JMenuItem()
JMenuItem PCAMenuItem = new JMenuItem()
JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem()
JMenuItem redoMenuItem = new JMenuItem()
JMenuItem reload = new JMenuItem()
JMenuItem remove2LeftMenuItem = new JMenuItem()
JMenuItem remove2RightMenuItem = new JMenuItem()
JMenuItem removeAllGapsMenuItem = new JMenuItem()
JMenuItem removeGappedColumnMenuItem = new JMenuItem()
JMenuItem removeRedundancyMenuItem = new JMenuItem()
JMenuItem saveAs = new JMenuItem()
JMenuItem selectAllSequenceMenuItem = new JMenuItem()
JCheckBoxMenuItem showConsensusHistogram = new JCheckBoxMenuItem()
JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem()
JCheckBoxMenuItem showGroupConsensus = new JCheckBoxMenuItem()
JCheckBoxMenuItem showGroupConservation = new JCheckBoxMenuItem()
JCheckBoxMenuItem showNpFeatsMenuitem = new JCheckBoxMenuItem()
JMenu showProducts = new JMenu()
JCheckBoxMenuItem showSequenceLogo = new JCheckBoxMenuItem()
JMenuItem showTranslation = new JMenuItem()
JMenu sort = new JMenu()
JMenu sortByAnnotScore = new JMenu()
JCheckBoxMenuItem sortByTree = new JCheckBoxMenuItem()
JMenu sortByTreeMenu = new JMenu()
JMenuItem sortGroupMenuItem = new JMenuItem()
JMenuItem sortIDMenuItem = new JMenuItem()
JMenuItem sortLengthMenuItem = new JMenuItem()
JMenuItem sortPairwiseMenuItem = new JMenuItem()
JPanel statusPanel = new JPanel()
JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem()
JTabbedPane tabbedPane = new JTabbedPane()
JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem()
JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem()
JMenuItem undoMenuItem = new JMenuItem()
JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem()
JMenu viewMenu = new JMenu()
JMenu webService = new JMenu()
JMenuItem webServiceNoServices
JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem()

Package Functions

 [instance initializer]
void addKeyListener ()
AlignViewport getOriginatingSource (CommandI command)
AlignmentI[] getViewAlignments ()
void init ()
void NewTreePanel (String type, String pwType, String title)
void paste (boolean newAlignment)
void setMenusFromViewport (AlignViewport av)
synchronized void slideSequences (boolean right, int size)
void trimAlignment (boolean trimLeft)
void updateEditMenuBar ()

Package Attributes

JMenuItem addFromFile = new JMenuItem()
JMenuItem addFromText = new JMenuItem()
JMenuItem addFromURL = new JMenuItem()
JMenu addSequenceMenu = new JMenu()
JMenuItem alignmentProperties = new JMenuItem()
Vector alignPanels = new Vector()
JMenuItem annotationColour = new JMenuItem()
JMenuItem associatedData = new JMenuItem()
JMenu autoAnnMenu = new JMenu()
JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem()
BorderLayout borderLayout1 = new BorderLayout()
JMenuItem copy = new JMenuItem()
JMenuItem createPNG = new JMenuItem()
String currentFileFormat = null
JMenuItem cut = new JMenuItem()
JMenuItem delete = new JMenuItem()
JMenuItem deleteGroups = new JMenuItem()
JMenuItem epsFile = new JMenuItem()
JMenuItem exportAnnotations = new JMenuItem()
JMenuItem exportFeatures = new JMenuItem()
JMenuItem fetchSequence = new JMenuItem()
String fileName = null
JMenuItem findMenuItem = new JMenuItem()
JMenu formatMenu = new JMenu()
GridLayout gridLayout1 = new GridLayout()
JMenuItem hideAllButSelection = new JMenuItem()
JMenuItem hideAllSelection = new JMenuItem()
JMenu hideMenu = new JMenu()
JMenuItem hideSelColumns = new JMenuItem()
JMenuItem hideSelSequences = new JMenuItem()
JMenuItem htmlMenuItem = new JMenuItem()
JMenuItem invertColSel = new JMenuItem()
JMenu jMenu2 = new JMenu()
JMenu jMenu3 = new JMenu()
JMenuItem LoadtreeMenuItem = new JMenuItem()
JMenuItem newView = new JMenuItem()
JMenuItem njTreeBlosumMenuItem = new JMenuItem()
JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem()
JMenuItem overviewMenuItem = new JMenuItem()
JMenuItem pageSetup = new JMenuItem()
JMenu pasteMenu = new JMenu()
JMenuItem pasteNew = new JMenuItem()
JMenuItem pasteThis = new JMenuItem()
JMenuItem printMenuItem = new JMenuItem()
Hashtable progressBarHandlers
Hashtable progressBars
JMenuItem save = new JMenuItem()
JMenu selectMenu = new JMenu()
JMenuItem showAllColumns = new JMenuItem()
JMenuItem showAllhidden = new JMenuItem()
JMenuItem showAllSeqs = new JMenuItem()
JMenuItem textColour = new JMenuItem()
JMenu tooltipSettingsMenu = new JMenu()
JMenuItem vamsasStore = new JMenuItem()
AlignViewport viewport

Private Member Functions

void addServiceListeners ()
void build_urlServiceMenu (JMenu webService)
void toggleHiddenRegions (boolean toggleSeqs, boolean toggleCols)
void warningMessage (String warning, String title)

Private Attributes

boolean buildingMenu = false

Detailed Description

DOCUMENT ME!

Author:
$author$
Version:
$Revision$

Definition at line 129 of file AlignFrame.java.


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

Generated by  Doxygen 1.6.0   Back to index