");
+ webServiceNoServices = new JMenuItem(
+ MessageManager.getString("label.no_services"));
webService.add(webServiceNoServices);
pasteMenu.add(pasteNew);
pasteMenu.add(pasteThis);
sort.add(sortIDMenuItem);
+ sort.add(sortLengthMenuItem);
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);
+ exportImageMenu.add(htmlMenuItem);
+ exportImageMenu.add(epsFile);
+ exportImageMenu.add(createPNG);
+ 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);
+ showMenu.add(showAllColumns);
+ showMenu.add(showAllSeqs);
+ showMenu.add(showAllhidden);
hideMenu.add(hideSelColumns);
hideMenu.add(hideSelSequences);
+ hideMenu.add(hideAllSelection);
+ hideMenu.add(hideAllButSelection);
+
formatMenu.add(font);
formatMenu.addSeparator();
formatMenu.add(wrapMenuItem);
@@ -1403,13 +2297,206 @@ 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);
+ calculateMenu.add(expandAlignment);
+ // TODO - determine if the listenToViewSelections button is needed : see bug
+ // JAL-574
+ // selectMenu.addSeparator();
+ // selectMenu.add(listenToViewSelections);
+ }
+
+ /**
+ * 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);
+ }
+
+ /**
+ * 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);
+ }
+
+ /**
+ * 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)
+ {
+
+ }
+
+ protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ protected void listenToViewSelections_actionPerformed(ActionEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ protected void showAllhidden_actionPerformed(ActionEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ protected void hideAllButSelection_actionPerformed(ActionEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ protected void hideAllSelection_actionPerformed(ActionEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ protected void showConsensusHistogram_actionPerformed(ActionEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ protected void showSequenceLogo_actionPerformed(ActionEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ protected void showGroupConsensus_actionPerformed(ActionEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ protected void showGroupConservation_actionPerformed(ActionEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ protected void showSeqFeaturesHeight_actionPerformed(
+ ActionEvent actionEvent)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ protected void followHighlight_actionPerformed()
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ protected void showNpFeats_actionPerformed(ActionEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ protected void showDbRefs_actionPerformed(ActionEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ protected void centreColumnLabels_actionPerformed(ActionEvent e)
+ {
}
protected void buildSortByAnnotationScoresMenu()
@@ -1453,6 +2540,11 @@ public class GAlignFrame
{
}
+ protected void bioJSMenuItem_actionPerformed(ActionEvent e)
+ {
+
+ }
+
protected void closeMenuItem_actionPerformed(boolean b)
{
}
@@ -1525,6 +2617,10 @@ public class GAlignFrame
{
}
+ protected void sortLengthMenuItem_actionPerformed(ActionEvent e)
+ {
+ }
+
protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
{
}
@@ -1601,6 +2697,18 @@ public class GAlignFrame
{
}
+ protected void purinePyrimidineColour_actionPerformed(ActionEvent e)
+ {
+ }
+
+ protected void RNAInteractionColour_actionPerformed(ActionEvent e)
+ {
+ }
+
+ /*
+ * protected void covariationColour_actionPerformed(ActionEvent e) { }
+ */
+
protected void noColourmenuItem_actionPerformed(ActionEvent e)
{
}
@@ -1637,6 +2745,14 @@ public class GAlignFrame
{
}
+ protected void createGroup_actionPerformed(ActionEvent e)
+ {
+ }
+
+ protected void unGroup_actionPerformed(ActionEvent e)
+ {
+ }
+
protected void copy_actionPerformed(ActionEvent e)
{
}
@@ -1682,8 +2798,40 @@ 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)
+ {
+
+ }
+
+ /**
+ * Template method to handle the 'Color T-Coffee scores' menu event.
+ *
+ * Subclasses override this method to provide a custom action.
+ *
+ * @param event
+ * The raised event
+ */
+ protected void tcoffeeColorScheme_actionPerformed(ActionEvent event)
{
+
}
protected void jpred_actionPerformed(ActionEvent e)
@@ -1753,6 +2901,16 @@ public class GAlignFrame
}
+ public void annotationColumn_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ public void rnahelicesColour_actionPerformed(ActionEvent e)
+ {
+
+ }
+
public void associatedData_actionPerformed(ActionEvent e)
{
@@ -1763,6 +2921,11 @@ public class GAlignFrame
}
+ public void sortByTreeOption_actionPerformed(ActionEvent e)
+ {
+
+ }
+
public void showAllSeqs_actionPerformed(ActionEvent e)
{
@@ -1862,7 +3025,7 @@ public class GAlignFrame
{
}
-
+
public void pageSetup_actionPerformed(ActionEvent e)
{
@@ -1872,4 +3035,77 @@ 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 state)
+ {
+ }
}