");
+ if (!Platform.isJS())
+ {
+ calculateMenu.addSeparator();
+ calculateMenu.add(runGroovy);
+ }
+
+ webServiceNoServices = new JMenuItem(
+ MessageManager.getString("label.no_services"));
webService.add(webServiceNoServices);
- pasteMenu.add(pasteNew);
- pasteMenu.add(pasteThis);
- sort.add(sortIDMenuItem);
- sort.add(sortGroupMenuItem);
- sort.add(sortPairwiseMenuItem);
- sort.add(sortByTreeMenu);
- calculate.add(averageDistanceTreeMenuItem);
- calculate.add(neighbourTreeMenuItem);
- calculate.add(avDistanceTreeBlosumMenuItem);
- calculate.add(njTreeBlosumMenuItem);
- jMenu2.add(htmlMenuItem);
- jMenu2.add(epsFile);
- jMenu2.add(createPNG);
+ if (!Platform.isJS())
+ {
+ exportImageMenu.add(htmlMenuItem);
+ }
+ exportImageMenu.add(epsFile);
+ exportImageMenu.add(createPNG);
+ if (!Platform.isJS())
+ {
+ exportImageMenu.add(createBioJS);
+ exportImageMenu.add(createSVG);
+ }
addSequenceMenu.add(addFromFile);
addSequenceMenu.add(addFromText);
addSequenceMenu.add(addFromURL);
this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
statusPanel.add(statusBar, null);
this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
- jMenu3.add(showAllColumns);
- jMenu3.add(showAllSeqs);
- hideMenu.add(hideSelColumns);
- hideMenu.add(hideSelSequences);
+
formatMenu.add(font);
formatMenu.addSeparator();
formatMenu.add(wrapMenuItem);
@@ -1414,215 +1899,454 @@ public class GAlignFrame
formatMenu.add(viewTextMenuItem);
formatMenu.add(colourTextMenuItem);
formatMenu.add(renderGapsMenuItem);
+ formatMenu.add(centreColumnLabelsMenuItem);
+ formatMenu.add(showNonconservedMenuItem);
selectMenu.add(findMenuItem);
selectMenu.addSeparator();
selectMenu.add(selectAllSequenceMenuItem);
selectMenu.add(deselectAllSequenceMenuItem);
selectMenu.add(invertSequenceMenuItem);
selectMenu.add(invertColSel);
+ selectMenu.add(createGroup);
+ selectMenu.add(unGroup);
+ selectMenu.add(grpsFromSelection);
selectMenu.add(deleteGroups);
+ selectMenu.add(annotationColumn);
+ selectMenu.add(selectHighlighted);
+ // TODO - determine if the listenToViewSelections button is needed : see bug
+ // JAL-574
+ // selectMenu.addSeparator();
+ // selectMenu.add(listenToViewSelections);
+ }
+
+ protected void loadVcf_actionPerformed()
+ {
+ }
+
+ /**
+ * Constructs the entries on the Colour menu (but does not add them to the
+ * menu).
+ */
+ protected void initColourMenu()
+ {
+ applyToAllGroups = new JCheckBoxMenuItem(
+ MessageManager.getString("label.apply_colour_to_all_groups"));
+ applyToAllGroups.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ applyToAllGroups_actionPerformed(applyToAllGroups.isSelected());
+ }
+ });
+
+ textColour = new JMenuItem(
+ MessageManager.getString("label.text_colour"));
+ textColour.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ textColour_actionPerformed();
+ }
+ });
+
+ conservationMenuItem = new JCheckBoxMenuItem(
+ MessageManager.getString("action.by_conservation"));
+ conservationMenuItem.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ conservationMenuItem_actionPerformed(
+ conservationMenuItem.isSelected());
+ }
+ });
+
+ abovePIDThreshold = new JCheckBoxMenuItem(
+ MessageManager.getString("label.above_identity_threshold"));
+ abovePIDThreshold.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ abovePIDThreshold_actionPerformed(abovePIDThreshold.isSelected());
+ }
+ });
+ modifyPID = new JMenuItem(
+ MessageManager.getString("label.modify_identity_threshold"));
+ modifyPID.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ modifyPID_actionPerformed();
+ }
+ });
+ modifyConservation = new JMenuItem(MessageManager
+ .getString("label.modify_conservation_threshold"));
+ modifyConservation.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ modifyConservation_actionPerformed();
+ }
+ });
+
+ annotationColour = new JRadioButtonMenuItem(
+ MessageManager.getString("action.by_annotation"));
+ annotationColour.setName(ResidueColourScheme.ANNOTATION_COLOUR);
+ annotationColour.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ annotationColour_actionPerformed();
+ }
+ });
}
- protected void showProducts_actionPerformed(ActionEvent e)
+ protected void selectHighlightedColumns_actionPerformed(
+ ActionEvent actionEvent)
{
// TODO Auto-generated method stub
-
+
}
- protected void buildSortByAnnotationScoresMenu()
+ /**
+ * Generate the reverse sequence (or reverse complement if the flag is true)
+ * and add it to the alignment
+ *
+ * @param complement
+ */
+ protected void showReverse_actionPerformed(boolean complement)
{
}
- protected void extractScores_actionPerformed(ActionEvent e)
+ /**
+ * Try to run script in a Groovy console, having first ensured that this
+ * alignframe is set as currentAlignFrame in Desktop
+ */
+ protected void runGroovy_actionPerformed()
{
+
}
- protected void outputText_actionPerformed(ActionEvent e)
+ /**
+ * Adds the given action listener and key accelerator to the given menu item.
+ * Also saves in a lookup table to support lookup of action by key stroke.
+ *
+ * @param keyStroke
+ * @param menuItem
+ * @param actionListener
+ */
+ protected void addMenuActionAndAccelerator(KeyStroke keyStroke,
+ JMenuItem menuItem, ActionListener actionListener)
{
+ menuItem.setAccelerator(keyStroke);
+ accelerators.put(keyStroke, menuItem);
+ menuItem.addActionListener(actionListener);
}
- public void addFromFile_actionPerformed(ActionEvent e)
+ /**
+ * Action on clicking sort annotations by type.
+ *
+ * @param sortOrder
+ */
+ protected void sortAnnotations_actionPerformed()
{
+ }
+ /**
+ * Action on clicking Show all annotations.
+ *
+ * @param forSequences
+ * update sequence-related annotations
+ * @param forAlignment
+ * update non-sequence-related annotations
+ */
+ protected void showAllAnnotations_actionPerformed(boolean forSequences,
+ boolean forAlignment)
+ {
+ setAnnotationsVisibility(true, forSequences, forAlignment);
}
- public void addFromText_actionPerformed(ActionEvent e)
+ /**
+ * Action on clicking Hide all annotations.
+ *
+ * @param forSequences
+ * update sequence-related annotations
+ * @param forAlignment
+ * update non-sequence-related annotations
+ */
+ protected void hideAllAnnotations_actionPerformed(boolean forSequences,
+ boolean forAlignment)
+ {
+ setAnnotationsVisibility(false, forSequences, forAlignment);
+ }
+
+ /**
+ * Set the visibility of annotations to true or false. Can act on
+ * sequence-related annotations, or alignment-related, or both.
+ *
+ * @param visible
+ * @param forSequences
+ * update sequence-related annotations
+ * @param forAlignment
+ * update non-sequence-related annotations
+ */
+ protected void setAnnotationsVisibility(boolean visible,
+ boolean forSequences, boolean forAlignment)
{
}
- public void addFromURL_actionPerformed(ActionEvent e)
+ protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
{
+ // TODO Auto-generated method stub
}
- public void exportFeatures_actionPerformed(ActionEvent e)
+ protected void listenToViewSelections_actionPerformed(ActionEvent e)
{
+ // TODO Auto-generated method stub
}
- public void exportAnnotations_actionPerformed(ActionEvent e)
+ protected void showAllhidden_actionPerformed(ActionEvent e)
{
+ // TODO Auto-generated method stub
}
- protected void htmlMenuItem_actionPerformed(ActionEvent e)
+ protected void hideAllButSelection_actionPerformed(ActionEvent e)
{
+ // TODO Auto-generated method stub
+
}
- protected void closeMenuItem_actionPerformed(boolean b)
+ protected void hideAllSelection_actionPerformed(ActionEvent e)
{
+ // TODO Auto-generated method stub
+
}
- protected void redoMenuItem_actionPerformed(ActionEvent e)
+ protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
{
+ // TODO Auto-generated method stub
+
}
- protected void undoMenuItem_actionPerformed(ActionEvent e)
+ protected void showConsensusHistogram_actionPerformed(ActionEvent e)
{
+ // TODO Auto-generated method stub
+
}
- protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
+ protected void showSequenceLogo_actionPerformed(ActionEvent e)
{
+ // TODO Auto-generated method stub
+
}
- protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
+ protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
{
+ // TODO Auto-generated method stub
+
}
- protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
+ protected void showGroupConsensus_actionPerformed(ActionEvent e)
{
+ // TODO Auto-generated method stub
+
}
- protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
+ protected void showGroupConservation_actionPerformed(ActionEvent e)
{
+ // TODO Auto-generated method stub
+
}
- protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
+ protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
{
+ // TODO Auto-generated method stub
+
}
- protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
+ protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
{
+ // TODO Auto-generated method stub
+
}
- protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
+ protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
{
+ // TODO Auto-generated method stub
+
}
- protected void wrapMenuItem_actionPerformed(ActionEvent e)
+ protected void followHighlight_actionPerformed()
{
+ // TODO Auto-generated method stub
+
}
- protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
+ protected void showNpFeats_actionPerformed(ActionEvent e)
{
+ // TODO Auto-generated method stub
+
}
- protected void viewTextMenuItem_actionPerformed(ActionEvent e)
+ protected void showDbRefs_actionPerformed(ActionEvent e)
{
+ // TODO Auto-generated method stub
+
}
- protected void colourTextMenuItem_actionPerformed(ActionEvent e)
+ protected void centreColumnLabels_actionPerformed(ActionEvent e)
{
}
- protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
+ protected void buildSortByAnnotationScoresMenu()
{
}
- protected void overviewMenuItem_actionPerformed(ActionEvent e)
+ protected void extractScores_actionPerformed(ActionEvent e)
{
}
- protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
+ protected void outputText_actionPerformed(String formatName)
{
}
- protected void sortIDMenuItem_actionPerformed(ActionEvent e)
+ public void addFromFile_actionPerformed(ActionEvent e)
{
+
}
- protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
+ public void addFromText_actionPerformed(ActionEvent e)
{
+
}
- protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
+ public void addFromURL_actionPerformed(ActionEvent e)
{
+
}
- protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
+ public void exportFeatures_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ public void exportAnnotations_actionPerformed(ActionEvent e)
{
+
}
- protected void PCAMenuItem_actionPerformed(ActionEvent e)
+ protected void htmlMenuItem_actionPerformed(ActionEvent e)
{
}
- protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
+ protected void bioJSMenuItem_actionPerformed(ActionEvent e)
{
+
}
- protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
+ protected void closeMenuItem_actionPerformed(boolean b)
+ {
+ }
+
+ protected void redoMenuItem_actionPerformed(ActionEvent e)
+ {
+ }
+
+ protected void undoMenuItem_actionPerformed(ActionEvent e)
+ {
+ }
+
+ protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
+ {
+ }
+
+ protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
+ {
+ }
+
+ protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
+ {
+ }
+
+ protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
+ {
+ }
+
+ protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
+ {
+ }
+
+ protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
{
}
- protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
+ protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
{
}
- protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
+ protected void wrapMenuItem_actionPerformed(ActionEvent e)
{
}
- protected void clustalColour_actionPerformed(ActionEvent e)
+ protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
{
}
- protected void zappoColour_actionPerformed(ActionEvent e)
+ protected void viewTextMenuItem_actionPerformed(ActionEvent e)
{
}
- protected void taylorColour_actionPerformed(ActionEvent e)
+ protected void colourTextMenuItem_actionPerformed(ActionEvent e)
{
}
- protected void hydrophobicityColour_actionPerformed(ActionEvent e)
+ protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
{
}
- protected void helixColour_actionPerformed(ActionEvent e)
+ protected void overviewMenuItem_actionPerformed(ActionEvent e)
{
}
- protected void strandColour_actionPerformed(ActionEvent e)
+ protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
{
}
- protected void turnColour_actionPerformed(ActionEvent e)
+ protected void sortIDMenuItem_actionPerformed(ActionEvent e)
{
}
- protected void buriedColour_actionPerformed(ActionEvent e)
+ protected void sortLengthMenuItem_actionPerformed(ActionEvent e)
{
}
- protected void userDefinedColour_actionPerformed(ActionEvent e)
+ protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
{
}
- protected void PIDColour_actionPerformed(ActionEvent e)
+ protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
{
}
- protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
+ protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
{
}
- protected void noColourmenuItem_actionPerformed(ActionEvent e)
+ protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
{
}
- protected void conservationMenuItem_actionPerformed(ActionEvent e)
+ protected void conservationMenuItem_actionPerformed(boolean selected)
{
}
@@ -1638,7 +2362,7 @@ public class GAlignFrame
{
}
- protected void abovePIDThreshold_actionPerformed(ActionEvent e)
+ protected void abovePIDThreshold_actionPerformed(boolean selected)
{
}
@@ -1646,23 +2370,27 @@ public class GAlignFrame
{
}
- protected void nucleotideColour_actionPerformed(ActionEvent e)
+ protected void deleteGroups_actionPerformed(ActionEvent e)
{
}
- protected void deleteGroups_actionPerformed(ActionEvent e)
+ protected void createGroup_actionPerformed(ActionEvent e)
{
}
- protected void copy_actionPerformed(ActionEvent e)
+ protected void unGroup_actionPerformed(ActionEvent e)
{
}
- protected void cut_actionPerformed(ActionEvent e)
+ protected void copy_actionPerformed()
{
}
- protected void delete_actionPerformed(ActionEvent e)
+ protected void cut_actionPerformed()
+ {
+ }
+
+ protected void delete_actionPerformed()
{
}
@@ -1674,7 +2402,7 @@ public class GAlignFrame
{
}
- protected void applyToAllGroups_actionPerformed(ActionEvent e)
+ protected void applyToAllGroups_actionPerformed(boolean selected)
{
}
@@ -1699,8 +2427,27 @@ public class GAlignFrame
{
}
- protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
+ public void createSVG(java.io.File f)
+ {
+
+ }
+
+ protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ /**
+ * Template method to handle the 'load T-Coffee scores' menu event.
+ *
+ * Subclasses override this method to provide a custom action.
+ *
+ * @param event
+ * The raised event
+ */
+ protected void loadScores_actionPerformed(ActionEvent event)
{
+
}
protected void jpred_actionPerformed(ActionEvent e)
@@ -1719,15 +2466,15 @@ public class GAlignFrame
{
}
- protected void modifyPID_actionPerformed(ActionEvent e)
+ protected void modifyPID_actionPerformed()
{
}
- protected void modifyConservation_actionPerformed(ActionEvent e)
+ protected void modifyConservation_actionPerformed()
{
}
- protected void saveAs_actionPerformed(ActionEvent e)
+ protected void saveAs_actionPerformed()
{
}
@@ -1745,7 +2492,7 @@ public class GAlignFrame
}
- public void showTranslation_actionPerformed(ActionEvent e)
+ public void showTranslation_actionPerformed(GeneticCodeI codeTable)
{
}
@@ -1755,7 +2502,7 @@ public class GAlignFrame
}
- public void fetchSequence_actionPerformed(ActionEvent e)
+ public void fetchSequence_actionPerformed()
{
}
@@ -1765,9 +2512,12 @@ public class GAlignFrame
}
- public void annotationColour_actionPerformed(ActionEvent e)
+ public void annotationColour_actionPerformed()
{
+ }
+ public void annotationColumn_actionPerformed(ActionEvent e)
+ {
}
public void associatedData_actionPerformed(ActionEvent e)
@@ -1780,6 +2530,11 @@ public class GAlignFrame
}
+ public void sortByTreeOption_actionPerformed(ActionEvent e)
+ {
+
+ }
+
public void showAllSeqs_actionPerformed(ActionEvent e)
{
@@ -1855,7 +2610,7 @@ public class GAlignFrame
}
- public void textColour_actionPerformed(ActionEvent e)
+ public void textColour_actionPerformed()
{
}
@@ -1875,11 +2630,11 @@ public class GAlignFrame
}
- public void buildTreeMenu()
+ public void buildTreeSortMenu()
{
}
-
+
public void pageSetup_actionPerformed(ActionEvent e)
{
@@ -1889,4 +2644,77 @@ public class GAlignFrame
{
}
+
+ protected void expand_newalign(ActionEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ protected boolean isShowAutoCalculatedAbove()
+ {
+ return showAutoCalculatedAbove;
+ }
+
+ protected void setShowAutoCalculatedAbove(boolean showAutoCalculatedAbove)
+ {
+ this.showAutoCalculatedAbove = showAutoCalculatedAbove;
+ }
+
+ protected SequenceAnnotationOrder getAnnotationSortOrder()
+ {
+ return annotationSortOrder;
+ }
+
+ protected void setAnnotationSortOrder(
+ SequenceAnnotationOrder annotationSortOrder)
+ {
+ this.annotationSortOrder = annotationSortOrder;
+ }
+
+ public Map getAccelerators()
+ {
+ return this.accelerators;
+ }
+
+ /**
+ * Returns the selected index of the tabbed pane, or -1 if none selected
+ * (including the case where the tabbed pane has not been made visible).
+ *
+ * @return
+ */
+ public int getTabIndex()
+ {
+ return tabbedPane.getSelectedIndex();
+ }
+
+ public JPanel getStatusPanel()
+ {
+ return statusPanel;
+ }
+
+ /**
+ * Sets a reference to the containing split frame. Also makes the 'toggle
+ * split view' menu item visible and checked.
+ *
+ * @param sf
+ */
+ public void setSplitFrame(SplitContainerI sf)
+ {
+ this.splitFrame = sf;
+ if (sf != null)
+ {
+ this.showComplementMenuItem.setVisible(true);
+ this.showComplementMenuItem.setState(true);
+ }
+ }
+
+ public SplitContainerI getSplitViewContainer()
+ {
+ return this.splitFrame;
+ }
+
+ protected void showComplement_actionPerformed(boolean complement)
+ {
+ }
}