+
+ /**
+ * Generate the reverse (optionally complemented) of the selected sequences,
+ * and add them to the alignment
+ */
+ @Override
+ protected void showReverse_actionPerformed(boolean complement)
+ {
+ AlignmentI al = null;
+ try
+ {
+ Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
+ al = dna.reverseCdna(complement);
+ viewport.addAlignment(al, "");
+ addHistoryItem(new EditCommand(
+ MessageManager.getString("label.add_sequences"), Action.PASTE,
+ al.getSequencesArray(), 0, al.getWidth(),
+ viewport.getAlignment()));
+ } catch (Exception ex)
+ {
+ System.err.println(ex.getMessage());
+ return;
+ }
+ }
+
+ /**
+ * Try to run a script in the Groovy console, having first ensured that this
+ * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
+ * be targeted at this alignment.
+ */
+ @Override
+ protected void runGroovy_actionPerformed()
+ {
+ Jalview.setCurrentAlignFrame(this);
+ groovy.ui.Console console = Desktop.getGroovyConsole();
+ if (console != null)
+ {
+ try
+ {
+ console.runScript();
+ } catch (Exception ex)
+ {
+ System.err.println((ex.toString()));
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ MessageManager.getString("label.couldnt_run_groovy_script"),
+ MessageManager.getString("label.groovy_support_failed"),
+ JvOptionPane.ERROR_MESSAGE);
+ }
+ }
+ else
+ {
+ System.err.println("Can't run Groovy script as console not found");
+ }
+ }
+
+ /**
+ * Hides columns containing (or not containing) a specified feature, provided
+ * that would not leave all columns hidden
+ *
+ * @param featureType
+ * @param columnsContaining
+ * @return
+ */
+ public boolean hideFeatureColumns(String featureType,
+ boolean columnsContaining)
+ {
+ boolean notForHiding = avc.markColumnsContainingFeatures(
+ columnsContaining, false, false, featureType);
+ if (notForHiding)
+ {
+ if (avc.markColumnsContainingFeatures(!columnsContaining, false,
+ false, featureType))
+ {
+ getViewport().hideSelectedColumns();
+ return true;
+ }
+ }
+ return false;
+ }
+
+ @Override
+ protected void selectHighlightedColumns_actionPerformed(
+ ActionEvent actionEvent)
+ {
+ // include key modifier check in case user selects from menu
+ avc.markHighlightedColumns(
+ (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0, true,
+ (actionEvent.getModifiers() & (ActionEvent.META_MASK
+ | ActionEvent.CTRL_MASK)) != 0);
+ }
+
+ /**
+ * Rebuilds the Colour menu, including any user-defined colours which have
+ * been loaded either on startup or during the session
+ */
+ public void buildColourMenu()
+ {
+ colourMenu.removeAll();
+
+ colourMenu.add(applyToAllGroups);
+ colourMenu.add(textColour);
+ colourMenu.addSeparator();
+
+ ColourMenuHelper.addMenuItems(colourMenu, this, viewport.getAlignment(),
+ false);
+
+ colourMenu.addSeparator();
+ colourMenu.add(conservationMenuItem);
+ colourMenu.add(modifyConservation);
+ colourMenu.add(abovePIDThreshold);
+ colourMenu.add(modifyPID);
+ colourMenu.add(annotationColour);
+
+ ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
+ ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
+ }
+
+ /**
+ * Open a dialog (if not already open) that allows the user to select and
+ * calculate PCA or Tree analysis
+ */
+ protected void openTreePcaDialog()
+ {
+ if (alignPanel.getCalculationDialog() == null)
+ {
+ new CalculationChooser(AlignFrame.this);
+ }
+ }
+
+ @Override
+ protected void loadVcf_actionPerformed()
+ {
+ JalviewFileChooser chooser = new JalviewFileChooser(
+ Cache.getProperty("LAST_DIRECTORY"));
+ chooser.setFileView(new JalviewFileView());
+ chooser.setDialogTitle(MessageManager.getString("label.load_vcf_file"));
+ chooser.setToolTipText(MessageManager.getString("label.load_vcf_file"));
+
+ int value = chooser.showOpenDialog(null);
+
+ if (value == JalviewFileChooser.APPROVE_OPTION)
+ {
+ String choice = chooser.getSelectedFile().getPath();
+ Cache.setProperty("LAST_DIRECTORY", choice);
+ new VCFLoader(viewport.getAlignment()).loadVCF(choice);
+ }
+
+ }