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

jalview::jbgui::GAlignFrame Class Reference

Inheritance diagram for jalview::jbgui::GAlignFrame:
Inheritance graph
Collaboration diagram for jalview::jbgui::GAlignFrame:
Collaboration graph

List of all members.

Public Member Functions

void addFromFile_actionPerformed (ActionEvent e)
void addFromText_actionPerformed (ActionEvent e)
void addFromURL_actionPerformed (ActionEvent e)
void alignmentProperties ()
void annotationColour_actionPerformed (ActionEvent e)
void associatedData_actionPerformed (ActionEvent e)
void autoCalculate_actionPerformed (ActionEvent e)
void buildTreeMenu ()
void createEPS (java.io.File f)
void createPNG (java.io.File f)
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 findPdbId_actionPerformed (ActionEvent e)
void gatherViews_actionPerformed (ActionEvent e)
void hiddenMarkers_actionPerformed (ActionEvent e)
void hideSelColumns_actionPerformed (ActionEvent e)
void hideSelSequences_actionPerformed (ActionEvent e)
void idRightAlign_actionPerformed (ActionEvent e)
void invertColSel_actionPerformed (ActionEvent e)
void newView_actionPerformed (ActionEvent e)
void pageSetup_actionPerformed (ActionEvent e)
void pdbFile_actionPerformed (ActionEvent e)
void reload_actionPerformed (ActionEvent e)
void save_actionPerformed (ActionEvent e)
void seqDBRef_actionPerformed (ActionEvent e)
void setColourSelected (String defaultColour)
void showAllColumns_actionPerformed (ActionEvent e)
void showAllSeqs_actionPerformed (ActionEvent e)
void showSeqFeatures_actionPerformed (ActionEvent actionEvent)
void showTranslation_actionPerformed (ActionEvent e)
void smoothFont_actionPerformed (ActionEvent e)
void sortByTreeOption_actionPerformed (ActionEvent e)
void tabbedPane_focusGained (FocusEvent e)
void tabbedPane_mousePressed (MouseEvent e)
void tabSelectionChanged (int sel)
void textColour_actionPerformed (ActionEvent e)
void vamsasLoad_actionPerformed (ActionEvent e)
void vamsasStore_actionPerformed (ActionEvent e)

Public Attributes

JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem()
JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem()
JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem()
JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem()
JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem()
JMenuItem featureSettings = new JMenuItem()
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()

Protected Member Functions

void abovePIDThreshold_actionPerformed (ActionEvent e)
void annotationPanelMenuItem_actionPerformed (ActionEvent e)
void applyAutoAnnotationSettings_actionPerformed (ActionEvent e)
void applyToAllGroups_actionPerformed (ActionEvent e)
void averageDistanceTreeMenuItem_actionPerformed (ActionEvent e)
void avTreeBlosumMenuItem_actionPerformed (ActionEvent e)
void BLOSUM62Colour_actionPerformed (ActionEvent e)
void buildSortByAnnotationScoresMenu ()
void buriedColour_actionPerformed (ActionEvent e)
void centreColumnLabels_actionPerformed (ActionEvent e)
void closeMenuItem_actionPerformed (boolean b)
void clustalColour_actionPerformed (ActionEvent e)
void colourTextMenuItem_actionPerformed (ActionEvent e)
void conservationMenuItem_actionPerformed (ActionEvent e)
void copy_actionPerformed (ActionEvent e)
void cut_actionPerformed (ActionEvent e)
void delete_actionPerformed (ActionEvent e)
void deleteGroups_actionPerformed (ActionEvent e)
void deselectAllSequenceMenuItem_actionPerformed (ActionEvent e)
void extractScores_actionPerformed (ActionEvent e)
void findMenuItem_actionPerformed (ActionEvent e)
void followHighlight_actionPerformed ()
void font_actionPerformed (ActionEvent e)
void helixColour_actionPerformed (ActionEvent e)
void hideAllButSelection_actionPerformed (ActionEvent e)
void hideAllSelection_actionPerformed (ActionEvent e)
void htmlMenuItem_actionPerformed (ActionEvent e)
void hydrophobicityColour_actionPerformed (ActionEvent e)
void invertSequenceMenuItem_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 neighbourTreeMenuItem_actionPerformed (ActionEvent e)
void njTreeBlosumMenuItem_actionPerformed (ActionEvent e)
void noColourmenuItem_actionPerformed (ActionEvent e)
void nucleotideColour_actionPerformed (ActionEvent e)
void outputText_actionPerformed (ActionEvent e)
void overviewMenuItem_actionPerformed (ActionEvent e)
void padGapsMenuitem_actionPerformed (ActionEvent e)
void pairwiseAlignmentMenuItem_actionPerformed (ActionEvent e)
void pasteNew_actionPerformed (ActionEvent e)
void pasteThis_actionPerformed (ActionEvent e)
void PCAMenuItem_actionPerformed (ActionEvent e)
void PIDColour_actionPerformed (ActionEvent e)
void printMenuItem_actionPerformed (ActionEvent e)
void redoMenuItem_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 renderGapsMenuItem_actionPerformed (ActionEvent e)
void saveAs_actionPerformed (ActionEvent e)
void scaleAbove_actionPerformed (ActionEvent e)
void scaleLeft_actionPerformed (ActionEvent e)
void scaleRight_actionPerformed (ActionEvent e)
void selectAllSequenceMenuItem_actionPerformed (ActionEvent e)
void seqLimit_actionPerformed (ActionEvent e)
void showAllhidden_actionPerformed (ActionEvent e)
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 showProducts_actionPerformed (ActionEvent e)
void showSeqFeaturesHeight_actionPerformed (ActionEvent actionEvent)
void showSequenceLogo_actionPerformed (ActionEvent e)
void showUnconservedMenuItem_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 taylorColour_actionPerformed (ActionEvent e)
void turnColour_actionPerformed (ActionEvent e)
void undoMenuItem_actionPerformed (ActionEvent e)
void userDefinedColour_actionPerformed (ActionEvent e)
void viewBoxesMenuItem_actionPerformed (ActionEvent e)
void viewTextMenuItem_actionPerformed (ActionEvent e)
void wrapMenuItem_actionPerformed (ActionEvent e)
void zappoColour_actionPerformed (ActionEvent e)

Protected Attributes

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 Attributes

JMenuItem addFromFile = new JMenuItem()
JMenuItem addFromText = new JMenuItem()
JMenuItem addFromURL = new JMenuItem()
JMenu addSequenceMenu = new JMenu()
JMenuItem alignmentProperties = new JMenuItem()
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()
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()
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()
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()

Private Member Functions

void jbInit () throws Exception

Private Attributes

JMenuItem grpsFromSelection = new JMenuItem()
JMenuItem justifyLeftMenuItem = new JMenuItem()
JMenuItem justifyRightMenuItem = new JMenuItem()

Detailed Description

Definition at line 28 of file GAlignFrame.java.

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

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