");
+ 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);
@@ -1547,8 +2263,12 @@ public class GAlignFrame extends JInternalFrame
this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
jMenu3.add(showAllColumns);
jMenu3.add(showAllSeqs);
+ jMenu3.add(showAllhidden);
hideMenu.add(hideSelColumns);
hideMenu.add(hideSelSequences);
+ hideMenu.add(hideAllSelection);
+ hideMenu.add(hideAllButSelection);
+
formatMenu.add(font);
formatMenu.addSeparator();
formatMenu.add(wrapMenuItem);
@@ -1563,13 +2283,171 @@ public class GAlignFrame extends JInternalFrame
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);
+ calculateMenu.add(expandAlignment);
+ // TODO - determine if the listenToViewSelections button is needed : see bug
+ // JAL-574
+ // selectMenu.addSeparator();
+ // selectMenu.add(listenToViewSelections);
+ }
+
+ /**
+ * Action on clicking sort annotations by type.
+ */
+ protected void sortAnnotationsByType_actionPerformed()
+ {
+ }
+
+ /**
+ * Action on clicking sort annotations by sequence
+ */
+ protected void sortAnnotationsBySequence_actionPerformed()
+ {
+ }
+
+ /**
+ * Action on clicking Show all annotations.
+ */
+ protected void showAllAnnotations_actionPerformed()
+ {
+ setAllAnnotationsVisibility(true);
+ }
+
+ /**
+ * Action on clicking Hide all annotations.
+ */
+ protected void hideAllAnnotations_actionPerformed()
+ {
+ setAllAnnotationsVisibility(false);
+ }
+
+ /**
+ * Set the visibility of all annotations to true or false.
+ *
+ * @param visible
+ */
+ protected void setAllAnnotationsVisibility(boolean visible)
+ {
+
+ }
+
+ 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)
@@ -1693,6 +2571,10 @@ public class GAlignFrame extends JInternalFrame
{
}
+ protected void sortLengthMenuItem_actionPerformed(ActionEvent e)
+ {
+ }
+
protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
{
}
@@ -1769,6 +2651,18 @@ public class GAlignFrame extends JInternalFrame
{
}
+ protected void purinePyrimidineColour_actionPerformed(ActionEvent e)
+ {
+ }
+
+ protected void RNAInteractionColour_actionPerformed(ActionEvent e)
+ {
+ }
+
+ /*
+ * protected void covariationColour_actionPerformed(ActionEvent e) { }
+ */
+
protected void noColourmenuItem_actionPerformed(ActionEvent e)
{
}
@@ -1805,6 +2699,14 @@ public class GAlignFrame extends JInternalFrame
{
}
+ protected void createGroup_actionPerformed(ActionEvent e)
+ {
+ }
+
+ protected void unGroup_actionPerformed(ActionEvent e)
+ {
+ }
+
protected void copy_actionPerformed(ActionEvent e)
{
}
@@ -1852,6 +2754,33 @@ public class GAlignFrame extends JInternalFrame
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)
@@ -1921,6 +2850,11 @@ public class GAlignFrame extends JInternalFrame
}
+ public void rnahelicesColour_actionPerformed(ActionEvent e)
+ {
+
+ }
+
public void associatedData_actionPerformed(ActionEvent e)
{
@@ -1931,6 +2865,11 @@ public class GAlignFrame extends JInternalFrame
}
+ public void sortByTreeOption_actionPerformed(ActionEvent e)
+ {
+
+ }
+
public void showAllSeqs_actionPerformed(ActionEvent e)
{
@@ -2040,4 +2979,10 @@ public class GAlignFrame extends JInternalFrame
{
}
+
+ protected void expand_newalign(ActionEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
}