+ closeMenuItem_actionPerformed(false);
+ }
+ });
+ editMenu.setText(MessageManager.getString("action.edit"));
+ viewMenu.setText(MessageManager.getString("action.view"));
+ colourMenu.setText(MessageManager.getString("action.colour"));
+ calculateMenu.setText(MessageManager.getString("action.calculate"));
+ webService.setText(MessageManager.getString("action.web_service"));
+ selectAllSequenceMenuItem.setText(MessageManager.getString("action.select_all"));
+ selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
+ .getKeyStroke(java.awt.event.KeyEvent.VK_A, Toolkit
+ .getDefaultToolkit().getMenuShortcutKeyMask(), false));
+ selectAllSequenceMenuItem
+ .addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ selectAllSequenceMenuItem_actionPerformed(e);
+ }
+ });
+ deselectAllSequenceMenuItem.setText(MessageManager.getString("action.deselect_all"));
+ deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
+ .getKeyStroke(java.awt.event.KeyEvent.VK_ESCAPE, 0, false));
+ deselectAllSequenceMenuItem
+ .addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ deselectAllSequenceMenuItem_actionPerformed(e);
+ }
+ });
+ invertSequenceMenuItem.setText(MessageManager.getString("action.invert_sequence_selection"));
+ invertSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
+ .getKeyStroke(java.awt.event.KeyEvent.VK_I, Toolkit
+ .getDefaultToolkit().getMenuShortcutKeyMask(), false));
+ invertSequenceMenuItem
+ .addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ invertSequenceMenuItem_actionPerformed(e);
+ }
+ });
+ grpsFromSelection.setText(MessageManager.getString("action.make_groups_selection"));
+ grpsFromSelection.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ makeGrpsFromSelection_actionPerformed(e);
+ }
+ });
+ expandAlignment.setText(MessageManager.getString("action.view_flanking_regions"));
+ expandAlignment.addActionListener(new java.awt.event.ActionListener() {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ expand_newalign(e);
+ }
+ });
+ remove2LeftMenuItem.setText(MessageManager.getString("action.remove_left"));
+ remove2LeftMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+ java.awt.event.KeyEvent.VK_L, Toolkit.getDefaultToolkit()
+ .getMenuShortcutKeyMask(), false));
+ remove2LeftMenuItem
+ .addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ remove2LeftMenuItem_actionPerformed(e);
+ }
+ });
+ remove2RightMenuItem.setText(MessageManager.getString("action.remove_right"));
+ remove2RightMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+ java.awt.event.KeyEvent.VK_R, Toolkit.getDefaultToolkit()
+ .getMenuShortcutKeyMask(), false));
+ remove2RightMenuItem
+ .addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ remove2RightMenuItem_actionPerformed(e);
+ }
+ });
+ removeGappedColumnMenuItem.setText(MessageManager.getString("action.remove_empty_columns"));
+ removeGappedColumnMenuItem.setAccelerator(javax.swing.KeyStroke
+ .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
+ .getDefaultToolkit().getMenuShortcutKeyMask(), false));
+ removeGappedColumnMenuItem
+ .addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ removeGappedColumnMenuItem_actionPerformed(e);
+ }
+ });
+ removeAllGapsMenuItem.setText(MessageManager.getString("action.remove_all_gaps"));
+ removeAllGapsMenuItem.setAccelerator(javax.swing.KeyStroke
+ .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
+ .getDefaultToolkit().getMenuShortcutKeyMask()
+ | java.awt.event.KeyEvent.SHIFT_MASK, false));
+ removeAllGapsMenuItem
+ .addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ removeAllGapsMenuItem_actionPerformed(e);
+ }
+ });
+ justifyLeftMenuItem.setText(MessageManager.getString("action.left_justify_alignment"));
+ justifyLeftMenuItem
+ .addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ justifyLeftMenuItem_actionPerformed(e);
+ }
+ });
+ justifyRightMenuItem.setText(MessageManager.getString("action.right_justify_alignment"));
+ justifyRightMenuItem
+ .addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ justifyRightMenuItem_actionPerformed(e);
+ }
+ });
+ viewBoxesMenuItem.setText(MessageManager.getString("action.boxes"));
+ viewBoxesMenuItem.setState(true);
+ viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ viewBoxesMenuItem_actionPerformed(e);
+ }
+ });
+ viewTextMenuItem.setText(MessageManager.getString("action.text"));
+ viewTextMenuItem.setState(true);
+ viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ viewTextMenuItem_actionPerformed(e);
+ }
+ });
+ showNonconservedMenuItem.setText(MessageManager.getString("label.show_non_conversed"));
+ showNonconservedMenuItem.setState(false);
+ showNonconservedMenuItem
+ .addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ showUnconservedMenuItem_actionPerformed(e);
+ }
+ });
+ sortPairwiseMenuItem.setText(MessageManager.getString("action.by_pairwise_id"));
+ sortPairwiseMenuItem
+ .addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ sortPairwiseMenuItem_actionPerformed(e);
+ }
+ });
+ sortIDMenuItem.setText(MessageManager.getString("action.by_id"));
+ sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ sortIDMenuItem_actionPerformed(e);
+ }
+ });
+ sortLengthMenuItem.setText(MessageManager.getString("action.by_length"));
+ sortLengthMenuItem
+ .addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ sortLengthMenuItem_actionPerformed(e);
+ }
+ });
+ sortGroupMenuItem.setText(MessageManager.getString("action.by_group"));
+ sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ sortGroupMenuItem_actionPerformed(e);
+ }
+ });
+ removeRedundancyMenuItem.setText(MessageManager.getString("action.remove_redundancy"));
+ removeRedundancyMenuItem.setAccelerator(javax.swing.KeyStroke
+ .getKeyStroke(java.awt.event.KeyEvent.VK_D, Toolkit
+ .getDefaultToolkit().getMenuShortcutKeyMask(), false));
+ removeRedundancyMenuItem
+ .addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ removeRedundancyMenuItem_actionPerformed(e);
+ }
+ });
+ pairwiseAlignmentMenuItem.setText(MessageManager.getString("action.pairwise_alignment"));
+ pairwiseAlignmentMenuItem
+ .addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ pairwiseAlignmentMenuItem_actionPerformed(e);
+ }
+ });
+ PCAMenuItem.setText(MessageManager.getString("label.principal_component_analysis"));
+ PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ PCAMenuItem_actionPerformed(e);
+ }
+ });
+ averageDistanceTreeMenuItem
+ .setText(MessageManager.getString("label.average_distance_identity"));
+ averageDistanceTreeMenuItem
+ .addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ averageDistanceTreeMenuItem_actionPerformed(e);
+ }
+ });
+ neighbourTreeMenuItem.setText(MessageManager.getString("label.neighbour_joining_identity"));
+ neighbourTreeMenuItem
+ .addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ neighbourTreeMenuItem_actionPerformed(e);
+ }
+ });
+ this.getContentPane().setLayout(borderLayout1);
+ alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
+ statusBar.setBackground(Color.white);
+ statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
+ statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
+ statusBar.setText(MessageManager.getString("label.status_bar"));
+ outputTextboxMenu.setText(MessageManager.getString("label.out_to_textbox"));
+ clustalColour.setText(MessageManager.getString("label.clustalx"));
+
+ clustalColour.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ clustalColour_actionPerformed(e);
+ }
+ });
+ zappoColour.setText(MessageManager.getString("label.zappo"));
+ zappoColour.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ zappoColour_actionPerformed(e);
+ }
+ });
+ taylorColour.setText(MessageManager.getString("label.taylor"));
+ taylorColour.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ taylorColour_actionPerformed(e);
+ }
+ });
+ hydrophobicityColour.setText(MessageManager.getString("label.hydrophobicity"));
+ hydrophobicityColour
+ .addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ hydrophobicityColour_actionPerformed(e);
+ }
+ });
+ helixColour.setText(MessageManager.getString("label.helix_propensity"));
+ helixColour.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ helixColour_actionPerformed(e);
+ }
+ });
+ strandColour.setText(MessageManager.getString("label.strand_propensity"));
+ strandColour.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ strandColour_actionPerformed(e);
+ }
+ });
+ turnColour.setText(MessageManager.getString("Turn Propensity"));
+ turnColour.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ turnColour_actionPerformed(e);
+ }
+ });
+ buriedColour.setText(MessageManager.getString("Buried Index"));
+ buriedColour.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ buriedColour_actionPerformed(e);
+ }
+ });
+ userDefinedColour.setText(MessageManager.getString("action.user_defined"));
+ userDefinedColour.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ userDefinedColour_actionPerformed(e);
+ }
+ });
+ PIDColour.setText(MessageManager.getString("label.percentage_identity"));
+ PIDColour.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ PIDColour_actionPerformed(e);
+ }
+ });
+ BLOSUM62Colour.setText(MessageManager.getString("label.blosum62_score"));
+ BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ BLOSUM62Colour_actionPerformed(e);
+ }
+ });
+ nucleotideColour.setText(MessageManager.getString("label.nucleotide"));
+ nucleotideColour.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ nucleotideColour_actionPerformed(e);
+ }
+ });
+
+ purinePyrimidineColour.setText(MessageManager.getString("label.purine_pyrimidine"));
+ purinePyrimidineColour
+ .addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ purinePyrimidineColour_actionPerformed(e);
+ }
+ });
+ /*
+ * covariationColour.setText("Covariation");
+ * covariationColour.addActionListener(new java.awt.event.ActionListener() {
+ * public void actionPerformed(ActionEvent e) {
+ * covariationColour_actionPerformed(e); } });
+ */
+
+ avDistanceTreeBlosumMenuItem.setText(MessageManager.getString("label.average_distance_bloslum62"));
+ avDistanceTreeBlosumMenuItem
+ .addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ avTreeBlosumMenuItem_actionPerformed(e);
+ }
+ });
+ njTreeBlosumMenuItem.setText(MessageManager.getString("label.neighbour_blosum62"));
+ njTreeBlosumMenuItem
+ .addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ njTreeBlosumMenuItem_actionPerformed(e);
+ }
+ });
+ annotationPanelMenuItem.setActionCommand("");
+ annotationPanelMenuItem.setText(MessageManager.getString("label.show_annotations"));
+ annotationPanelMenuItem.setState(jalview.bin.Cache.getDefault(
+ "SHOW_ANNOTATIONS", true));
+ annotationPanelMenuItem
+ .addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ annotationPanelMenuItem_actionPerformed(e);
+ }
+ });
+ colourTextMenuItem.setText(MessageManager.getString("label.colour_text"));
+ colourTextMenuItem
+ .addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ colourTextMenuItem_actionPerformed(e);
+ }
+ });
+ htmlMenuItem.setText(MessageManager.getString("label.html"));
+ htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ htmlMenuItem_actionPerformed(e);
+ }
+ });
+ overviewMenuItem.setText(MessageManager.getString("label.overview_window"));
+ overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ overviewMenuItem_actionPerformed(e);
+ }
+ });
+ undoMenuItem.setEnabled(false);
+ undoMenuItem.setText(MessageManager.getString("action.undo"));
+ undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+ java.awt.event.KeyEvent.VK_Z, Toolkit.getDefaultToolkit()
+ .getMenuShortcutKeyMask(), false));
+ undoMenuItem.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ undoMenuItem_actionPerformed(e);
+ }
+ });
+ redoMenuItem.setEnabled(false);
+ redoMenuItem.setText(MessageManager.getString("action.redo"));
+ redoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+ java.awt.event.KeyEvent.VK_Y, Toolkit.getDefaultToolkit()
+ .getMenuShortcutKeyMask(), false));
+ redoMenuItem.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ redoMenuItem_actionPerformed(e);
+ }
+ });
+ conservationMenuItem.setText(MessageManager.getString("action.by_conservation"));
+ conservationMenuItem
+ .addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ conservationMenuItem_actionPerformed(e);
+ }
+ });
+ noColourmenuItem.setText(MessageManager.getString("label.none"));
+ noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ noColourmenuItem_actionPerformed(e);