");
- webService.add(webServiceNoServices);
- pasteMenu.add(pasteNew);
- pasteMenu.add(pasteThis);
- sort.add(sortIDMenuItem);
- sort.add(sortLengthMenuItem);
- sort.add(sortGroupMenuItem);
- sort.add(sortPairwiseMenuItem);
- sort.add(sortByTreeMenu);
- calculateTree.add(averageDistanceTreeMenuItem);
- calculateTree.add(neighbourTreeMenuItem);
- calculateTree.add(avDistanceTreeBlosumMenuItem);
- calculateTree.add(njTreeBlosumMenuItem);
- jMenu2.add(htmlMenuItem);
- jMenu2.add(epsFile);
- jMenu2.add(createPNG);
- 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);
- jMenu3.add(showAllhidden);
- hideMenu.add(hideSelColumns);
- hideMenu.add(hideSelSequences);
- hideMenu.add(hideAllSelection);
- hideMenu.add(hideAllButSelection);
+ tcoffeeColour = new JRadioButtonMenuItem(
+ MessageManager.getString("label.tcoffee_scores"));
+ tcoffeeColour.setEnabled(false);
+ tcoffeeColour.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ tcoffeeColorScheme_actionPerformed();
+ }
+ });
+
+ RNAInteractionColour = new JRadioButtonMenuItem("RNA Interaction type");
+ RNAInteractionColour.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ RNAInteractionColour_actionPerformed();
+ }
+ });
+ /*
+ * covariationColour = new JRadioButtonMenuItem("Covariation");
+ * covariationColour.addActionListener(new ActionListener() { public void
+ * actionPerformed(ActionEvent e) { covariationColour_actionPerformed(); }
+ * });
+ */
+
+ conservationMenuItem = new JCheckBoxMenuItem(
+ MessageManager.getString("action.by_conservation"));
+ conservationMenuItem.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ conservationMenuItem_actionPerformed();
+ }
+ });
+ noColourmenuItem = new JRadioButtonMenuItem(
+ MessageManager.getString("label.none"));
+ noColourmenuItem.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ noColourmenuItem_actionPerformed();
+ }
+ });
+
+ abovePIDThreshold = new JCheckBoxMenuItem(
+ MessageManager.getString("label.above_identity_threshold"));
+ abovePIDThreshold.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ abovePIDThreshold_actionPerformed();
+ }
+ });
+ 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 JMenuItem(
+ MessageManager.getString("action.by_annotation"));
+ annotationColour.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ annotationColour_actionPerformed();
+ }
+ });
+
+ rnahelicesColour = new JMenuItem(
+ MessageManager.getString("action.by_rna_helixes"));
+ rnahelicesColour.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ rnahelicesColour_actionPerformed();
+ }
+ });
+ }
+
+ protected void selectHighlightedColumns_actionPerformed(
+ ActionEvent actionEvent)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ /**
+ * 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)
+ {
+ }
+
+ /**
+ * Try to run script in a Groovy console, having first ensured that this
+ * alignframe is set as currentAlignFrame in Desktop
+ */
+ protected void runGroovy_actionPerformed()
+ {
+
+ }
+
+ /**
+ * 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)
+ {
- formatMenu.add(font);
- formatMenu.addSeparator();
- formatMenu.add(wrapMenuItem);
- formatMenu.add(scaleAbove);
- formatMenu.add(scaleLeft);
- formatMenu.add(scaleRight);
- formatMenu.add(seqLimits);
- formatMenu.add(idRightAlign);
- formatMenu.add(hiddenMarkers);
- formatMenu.add(viewBoxesMenuItem);
- 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(deleteGroups);
- selectMenu.add(grpsFromSelection);
- // TODO - determine if the listenToViewSelections button is needed : see bug JAL-574
- //selectMenu.addSeparator();
- //selectMenu.add(listenToViewSelections);
}
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)
@@ -1979,13 +2587,6 @@ public class GAlignFrame extends JInternalFrame
}
- protected void showSeqFeaturesHeight_actionPerformed(
- ActionEvent actionEvent)
- {
- // TODO Auto-generated method stub
-
- }
-
protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
{
// TODO Auto-generated method stub
@@ -2020,10 +2621,6 @@ public class GAlignFrame extends JInternalFrame
{
}
- protected void showProducts_actionPerformed(ActionEvent e)
- {
- }
-
protected void buildSortByAnnotationScoresMenu()
{
}
@@ -2065,6 +2662,11 @@ public class GAlignFrame extends JInternalFrame
{
}
+ protected void bioJSMenuItem_actionPerformed(ActionEvent e)
+ {
+
+ }
+
protected void closeMenuItem_actionPerformed(boolean b)
{
}
@@ -2173,35 +2775,35 @@ public class GAlignFrame extends JInternalFrame
{
}
- protected void clustalColour_actionPerformed(ActionEvent e)
+ protected void clustalColour_actionPerformed()
{
}
- protected void zappoColour_actionPerformed(ActionEvent e)
+ protected void zappoColour_actionPerformed()
{
}
- protected void taylorColour_actionPerformed(ActionEvent e)
+ protected void taylorColour_actionPerformed()
{
}
- protected void hydrophobicityColour_actionPerformed(ActionEvent e)
+ protected void hydrophobicityColour_actionPerformed()
{
}
- protected void helixColour_actionPerformed(ActionEvent e)
+ protected void helixColour_actionPerformed()
{
}
- protected void strandColour_actionPerformed(ActionEvent e)
+ protected void strandColour_actionPerformed()
{
}
- protected void turnColour_actionPerformed(ActionEvent e)
+ protected void turnColour_actionPerformed()
{
}
- protected void buriedColour_actionPerformed(ActionEvent e)
+ protected void buriedColour_actionPerformed()
{
}
@@ -2209,27 +2811,31 @@ public class GAlignFrame extends JInternalFrame
{
}
- protected void PIDColour_actionPerformed(ActionEvent e)
+ protected void PIDColour_actionPerformed()
+ {
+ }
+
+ protected void BLOSUM62Colour_actionPerformed()
{
}
- protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
+ protected void purinePyrimidineColour_actionPerformed()
{
}
- protected void purinePyrimidineColour_actionPerformed(ActionEvent e)
+ protected void RNAInteractionColour_actionPerformed()
{
}
/*
- * protected void covariationColour_actionPerformed(ActionEvent e) { }
+ * protected void covariationColour_actionPerformed() { }
*/
- protected void noColourmenuItem_actionPerformed(ActionEvent e)
+ protected void noColourmenuItem_actionPerformed()
{
}
- protected void conservationMenuItem_actionPerformed(ActionEvent e)
+ protected void conservationMenuItem_actionPerformed()
{
}
@@ -2245,7 +2851,7 @@ public class GAlignFrame extends JInternalFrame
{
}
- protected void abovePIDThreshold_actionPerformed(ActionEvent e)
+ protected void abovePIDThreshold_actionPerformed()
{
}
@@ -2253,7 +2859,7 @@ public class GAlignFrame extends JInternalFrame
{
}
- protected void nucleotideColour_actionPerformed(ActionEvent e)
+ protected void nucleotideColour_actionPerformed()
{
}
@@ -2261,6 +2867,14 @@ public class GAlignFrame extends JInternalFrame
{
}
+ protected void createGroup_actionPerformed(ActionEvent e)
+ {
+ }
+
+ protected void unGroup_actionPerformed(ActionEvent e)
+ {
+ }
+
protected void copy_actionPerformed(ActionEvent e)
{
}
@@ -2281,7 +2895,7 @@ public class GAlignFrame extends JInternalFrame
{
}
- protected void applyToAllGroups_actionPerformed(ActionEvent e)
+ protected void applyToAllGroups_actionPerformed()
{
}
@@ -2306,8 +2920,37 @@ public class GAlignFrame extends JInternalFrame
{
}
- 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.
+ */
+ protected void tcoffeeColorScheme_actionPerformed()
{
+
}
protected void jpred_actionPerformed(ActionEvent e)
@@ -2326,11 +2969,11 @@ public class GAlignFrame extends JInternalFrame
{
}
- protected void modifyPID_actionPerformed(ActionEvent e)
+ protected void modifyPID_actionPerformed()
{
}
- protected void modifyConservation_actionPerformed(ActionEvent e)
+ protected void modifyConservation_actionPerformed()
{
}
@@ -2372,12 +3015,15 @@ public class GAlignFrame extends JInternalFrame
}
- public void annotationColour_actionPerformed(ActionEvent e)
+ public void annotationColour_actionPerformed()
{
+ }
+ public void annotationColumn_actionPerformed(ActionEvent e)
+ {
}
- public void rnahelicesColour_actionPerformed(ActionEvent e)
+ public void rnahelicesColour_actionPerformed()
{
}
@@ -2472,7 +3118,7 @@ public class GAlignFrame extends JInternalFrame
}
- public void textColour_actionPerformed(ActionEvent e)
+ public void textColour_actionPerformed()
{
}
@@ -2506,4 +3152,77 @@ public class GAlignFrame extends JInternalFrame
{
}
+
+ 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)
+ {
+ }
}