/* * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * * Jalview is free software: you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation, either version 3 * of the License, or (at your option) any later version. * * Jalview is distributed in the hope that it will be useful, but * WITHOUT ANY WARRANTY; without even the implied warranty * of MERCHANTABILITY or FITNESS FOR A PARTICULAR * PURPOSE. See the GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with Jalview. If not, see . * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.jbgui; import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder; import jalview.api.SplitContainerI; import jalview.bin.Cache; import jalview.gui.JvSwingUtils; import jalview.gui.Preferences; import jalview.io.FileFormats; import jalview.util.MessageManager; import jalview.util.Platform; import java.awt.BorderLayout; import java.awt.Color; import java.awt.GridLayout; import java.awt.Toolkit; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.awt.event.FocusAdapter; import java.awt.event.FocusEvent; import java.awt.event.KeyEvent; import java.awt.event.MouseAdapter; import java.awt.event.MouseEvent; import java.util.HashMap; import java.util.Map; import javax.swing.BorderFactory; import javax.swing.ButtonGroup; import javax.swing.JCheckBoxMenuItem; import javax.swing.JInternalFrame; import javax.swing.JLabel; import javax.swing.JMenu; import javax.swing.JMenuBar; import javax.swing.JMenuItem; import javax.swing.JPanel; import javax.swing.JRadioButtonMenuItem; import javax.swing.JTabbedPane; import javax.swing.KeyStroke; import javax.swing.event.ChangeEvent; import javax.swing.event.MenuEvent; import javax.swing.event.MenuListener; public class GAlignFrame extends JInternalFrame { protected JMenuBar alignFrameMenuBar = new JMenuBar(); protected JMenuItem closeMenuItem = new JMenuItem(); protected JMenu webService = new JMenu(); protected JMenuItem webServiceNoServices; protected JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem(); protected JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem(); protected JMenu sortByAnnotScore = new JMenu(); public JLabel statusBar = new JLabel(); protected JMenu outputTextboxMenu = new JMenu(); protected JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem(); protected JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem(); protected JCheckBoxMenuItem showNonconservedMenuItem = new JCheckBoxMenuItem(); protected JMenuItem undoMenuItem = new JMenuItem(); protected JMenuItem redoMenuItem = new JMenuItem(); protected JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem(); protected JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem(); public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem(); JMenuItem copy = new JMenuItem(); JMenuItem cut = new JMenuItem(); JMenu pasteMenu = new JMenu(); protected JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem(); protected JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem(); protected JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem(); protected JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem(); protected JCheckBoxMenuItem applyToAllGroups; protected JMenu colourMenu = new JMenu(); protected JRadioButtonMenuItem textColour; protected JCheckBoxMenuItem conservationMenuItem; protected JMenuItem modifyConservation; protected JCheckBoxMenuItem abovePIDThreshold; protected JMenuItem modifyPID; protected JMenuItem annotationColour; protected JMenu sortByTreeMenu = new JMenu(); protected JMenu sort = new JMenu(); protected JMenuItem calculateTree = new JMenuItem(); protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem(); protected JCheckBoxMenuItem showNpFeatsMenuitem = new JCheckBoxMenuItem(); protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem(); protected JMenuItem showTranslation = new JMenuItem(); protected JMenuItem showReverse = new JMenuItem(); protected JMenuItem showReverseComplement = new JMenuItem(); protected JMenu showProducts = new JMenu(); protected JMenuItem runGroovy = new JMenuItem(); protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem(); protected JCheckBoxMenuItem sortByTree = new JCheckBoxMenuItem(); protected JCheckBoxMenuItem listenToViewSelections = new JCheckBoxMenuItem(); protected JPanel statusPanel = new JPanel(); protected JMenuItem showAllSeqAnnotations = new JMenuItem(); protected JMenuItem hideAllSeqAnnotations = new JMenuItem(); protected JMenuItem showAllAlAnnotations = new JMenuItem(); protected JMenuItem hideAllAlAnnotations = new JMenuItem(); protected JCheckBoxMenuItem showComplementMenuItem = new JCheckBoxMenuItem(); protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem(); protected JTabbedPane tabbedPane = new JTabbedPane(); protected JMenuItem reload = new JMenuItem(); protected JMenu formatMenu = new JMenu(); protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem(); protected JCheckBoxMenuItem centreColumnLabelsMenuItem = new JCheckBoxMenuItem(); protected JCheckBoxMenuItem followHighlightMenuItem = new JCheckBoxMenuItem(); protected JMenuItem gatherViews = new JMenuItem(); protected JMenuItem expandViews = new JMenuItem(); protected JCheckBoxMenuItem showGroupConsensus = new JCheckBoxMenuItem(); protected JCheckBoxMenuItem showGroupConservation = new JCheckBoxMenuItem(); protected JCheckBoxMenuItem showConsensusHistogram = new JCheckBoxMenuItem(); protected JCheckBoxMenuItem showSequenceLogo = new JCheckBoxMenuItem(); protected JCheckBoxMenuItem normaliseSequenceLogo = new JCheckBoxMenuItem(); protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem(); private SequenceAnnotationOrder annotationSortOrder; private boolean showAutoCalculatedAbove = false; private Map accelerators = new HashMap(); private SplitContainerI splitFrame; public GAlignFrame() { try { jbInit(); setJMenuBar(alignFrameMenuBar); // dynamically fill save as menu with available formats for (String ff : FileFormats.getInstance().getWritableFormats(true)) { JMenuItem item = new JMenuItem(ff); item.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { outputText_actionPerformed(e); } }); outputTextboxMenu.add(item); } } catch (Exception e) { System.err.println(e.toString()); } if (!Platform.isAMac()) { closeMenuItem.setMnemonic('C'); outputTextboxMenu.setMnemonic('T'); undoMenuItem.setMnemonic('Z'); redoMenuItem.setMnemonic('0'); copy.setMnemonic('C'); cut.setMnemonic('U'); pasteMenu.setMnemonic('P'); reload.setMnemonic('R'); } } private void jbInit() throws Exception { initColourMenu(); JMenuItem saveAs = new JMenuItem( MessageManager.getString("action.save_as")); ActionListener al = new ActionListener() { @Override public void actionPerformed(ActionEvent e) { saveAs_actionPerformed(e); } }; // FIXME getDefaultToolkit throws an exception in Headless mode KeyStroke keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S, Toolkit .getDefaultToolkit().getMenuShortcutKeyMask() | KeyEvent.SHIFT_MASK, false); addMenuActionAndAccelerator(keyStroke, saveAs, al); closeMenuItem.setText(MessageManager.getString("action.close")); keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_W, Toolkit .getDefaultToolkit().getMenuShortcutKeyMask(), false); al = new ActionListener() { @Override public void actionPerformed(ActionEvent e) { closeMenuItem_actionPerformed(false); } }; addMenuActionAndAccelerator(keyStroke, closeMenuItem, al); JMenu editMenu = new JMenu(MessageManager.getString("action.edit")); JMenu viewMenu = new JMenu(MessageManager.getString("action.view")); JMenu annotationsMenu = new JMenu( MessageManager.getString("action.annotations")); JMenu showMenu = new JMenu(MessageManager.getString("action.show")); colourMenu.setText(MessageManager.getString("action.colour")); JMenu calculateMenu = new JMenu( MessageManager.getString("action.calculate")); webService.setText(MessageManager.getString("action.web_service")); JMenuItem selectAllSequenceMenuItem = new JMenuItem( MessageManager.getString("action.select_all")); keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_A, Toolkit .getDefaultToolkit().getMenuShortcutKeyMask(), false); al = new ActionListener() { @Override public void actionPerformed(ActionEvent e) { selectAllSequenceMenuItem_actionPerformed(e); } }; addMenuActionAndAccelerator(keyStroke, selectAllSequenceMenuItem, al); JMenuItem deselectAllSequenceMenuItem = new JMenuItem( MessageManager.getString("action.deselect_all")); keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_ESCAPE, 0, false); al = new ActionListener() { @Override public void actionPerformed(ActionEvent e) { deselectAllSequenceMenuItem_actionPerformed(e); } }; addMenuActionAndAccelerator(keyStroke, deselectAllSequenceMenuItem, al); JMenuItem invertSequenceMenuItem = new JMenuItem( MessageManager.getString("action.invert_sequence_selection")); keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I, Toolkit .getDefaultToolkit().getMenuShortcutKeyMask(), false); al = new ActionListener() { @Override public void actionPerformed(ActionEvent e) { invertSequenceMenuItem_actionPerformed(e); } }; addMenuActionAndAccelerator(keyStroke, invertSequenceMenuItem, al); JMenuItem grpsFromSelection = new JMenuItem( MessageManager.getString("action.make_groups_selection")); grpsFromSelection.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { makeGrpsFromSelection_actionPerformed(e); } }); JMenuItem expandAlignment = new JMenuItem( MessageManager.getString("action.view_flanking_regions")); expandAlignment.setToolTipText(MessageManager .getString("label.view_flanking_regions")); expandAlignment.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { expand_newalign(e); } }); JMenuItem remove2LeftMenuItem = new JMenuItem( MessageManager.getString("action.remove_left")); keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_L, Toolkit .getDefaultToolkit().getMenuShortcutKeyMask(), false); al = new ActionListener() { @Override public void actionPerformed(ActionEvent e) { remove2LeftMenuItem_actionPerformed(e); } }; addMenuActionAndAccelerator(keyStroke, remove2LeftMenuItem, al); JMenuItem remove2RightMenuItem = new JMenuItem( MessageManager.getString("action.remove_right")); keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_R, Toolkit .getDefaultToolkit().getMenuShortcutKeyMask(), false); al = new ActionListener() { @Override public void actionPerformed(ActionEvent e) { remove2RightMenuItem_actionPerformed(e); } }; addMenuActionAndAccelerator(keyStroke, remove2RightMenuItem, al); JMenuItem removeGappedColumnMenuItem = new JMenuItem( MessageManager.getString("action.remove_empty_columns")); keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E, Toolkit .getDefaultToolkit().getMenuShortcutKeyMask(), false); al = new ActionListener() { @Override public void actionPerformed(ActionEvent e) { removeGappedColumnMenuItem_actionPerformed(e); } }; addMenuActionAndAccelerator(keyStroke, removeGappedColumnMenuItem, al); JMenuItem removeAllGapsMenuItem = new JMenuItem( MessageManager.getString("action.remove_all_gaps")); keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E, Toolkit .getDefaultToolkit().getMenuShortcutKeyMask() | KeyEvent.SHIFT_MASK, false); al = new ActionListener() { @Override public void actionPerformed(ActionEvent e) { removeAllGapsMenuItem_actionPerformed(e); } }; addMenuActionAndAccelerator(keyStroke, removeAllGapsMenuItem, al); JMenuItem justifyLeftMenuItem = new JMenuItem( MessageManager.getString("action.left_justify_alignment")); justifyLeftMenuItem.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { justifyLeftMenuItem_actionPerformed(e); } }); JMenuItem justifyRightMenuItem = new JMenuItem( MessageManager.getString("action.right_justify_alignment")); justifyRightMenuItem.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { justifyRightMenuItem_actionPerformed(e); } }); viewBoxesMenuItem.setText(MessageManager.getString("action.boxes")); viewBoxesMenuItem.setState(true); viewBoxesMenuItem.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { viewBoxesMenuItem_actionPerformed(e); } }); viewTextMenuItem.setText(MessageManager.getString("action.text")); viewTextMenuItem.setState(true); viewTextMenuItem.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { viewTextMenuItem_actionPerformed(e); } }); showNonconservedMenuItem.setText(MessageManager .getString("label.show_non_conserved")); showNonconservedMenuItem.setState(false); showNonconservedMenuItem.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { showUnconservedMenuItem_actionPerformed(e); } }); JMenuItem sortPairwiseMenuItem = new JMenuItem( MessageManager.getString("action.by_pairwise_id")); sortPairwiseMenuItem.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { sortPairwiseMenuItem_actionPerformed(e); } }); JMenuItem sortIDMenuItem = new JMenuItem( MessageManager.getString("action.by_id")); sortIDMenuItem.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { sortIDMenuItem_actionPerformed(e); } }); JMenuItem sortLengthMenuItem = new JMenuItem( MessageManager.getString("action.by_length")); sortLengthMenuItem.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { sortLengthMenuItem_actionPerformed(e); } }); JMenuItem sortGroupMenuItem = new JMenuItem( MessageManager.getString("action.by_group")); sortGroupMenuItem.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { sortGroupMenuItem_actionPerformed(e); } }); JMenuItem removeRedundancyMenuItem = new JMenuItem( MessageManager.getString("action.remove_redundancy")); keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_D, Toolkit .getDefaultToolkit().getMenuShortcutKeyMask(), false); al = new ActionListener() { @Override public void actionPerformed(ActionEvent e) { removeRedundancyMenuItem_actionPerformed(e); } }; addMenuActionAndAccelerator(keyStroke, removeRedundancyMenuItem, al); JMenuItem pairwiseAlignmentMenuItem = new JMenuItem( MessageManager.getString("action.pairwise_alignment")); pairwiseAlignmentMenuItem.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { pairwiseAlignmentMenuItem_actionPerformed(e); } }); JMenuItem PCAMenuItem = new JMenuItem( MessageManager.getString("label.principal_component_analysis")); PCAMenuItem.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { PCAMenuItem_actionPerformed(e); } }); this.getContentPane().setLayout(new BorderLayout()); 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")); annotationPanelMenuItem.setActionCommand(""); annotationPanelMenuItem.setText(MessageManager .getString("label.show_annotations")); annotationPanelMenuItem.setState(Cache.getDefault("SHOW_ANNOTATIONS", true)); annotationPanelMenuItem.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { annotationPanelMenuItem_actionPerformed(e); } }); showAllAlAnnotations.setText(MessageManager .getString("label.show_all_al_annotations")); final boolean isAnnotationPanelShown = annotationPanelMenuItem .getState(); showAllAlAnnotations.setEnabled(isAnnotationPanelShown); showAllAlAnnotations.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { showAllAnnotations_actionPerformed(false, true); } }); hideAllAlAnnotations.setText(MessageManager .getString("label.hide_all_al_annotations")); hideAllAlAnnotations.setEnabled(isAnnotationPanelShown); hideAllAlAnnotations.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { hideAllAnnotations_actionPerformed(false, true); } }); showAllSeqAnnotations.setText(MessageManager .getString("label.show_all_seq_annotations")); showAllSeqAnnotations.setEnabled(isAnnotationPanelShown); showAllSeqAnnotations.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { showAllAnnotations_actionPerformed(true, false); } }); hideAllSeqAnnotations.setText(MessageManager .getString("label.hide_all_seq_annotations")); hideAllSeqAnnotations.setEnabled(isAnnotationPanelShown); hideAllSeqAnnotations.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { hideAllAnnotations_actionPerformed(true, false); } }); SequenceAnnotationOrder sortAnnotationsBy = SequenceAnnotationOrder .valueOf(Cache.getDefault(Preferences.SORT_ANNOTATIONS, SequenceAnnotationOrder.NONE.name())); final JCheckBoxMenuItem sortAnnBySequence = new JCheckBoxMenuItem( MessageManager.getString("label.sort_annotations_by_sequence")); final JCheckBoxMenuItem sortAnnByLabel = new JCheckBoxMenuItem( MessageManager.getString("label.sort_annotations_by_label")); sortAnnBySequence .setSelected(sortAnnotationsBy == SequenceAnnotationOrder.SEQUENCE_AND_LABEL); sortAnnBySequence.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { boolean newState = sortAnnBySequence.getState(); sortAnnByLabel.setSelected(false); setAnnotationSortOrder(newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL : SequenceAnnotationOrder.NONE); sortAnnotations_actionPerformed(); } }); sortAnnByLabel .setSelected(sortAnnotationsBy == SequenceAnnotationOrder.LABEL_AND_SEQUENCE); sortAnnByLabel.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { boolean newState = sortAnnByLabel.getState(); sortAnnBySequence.setSelected(false); setAnnotationSortOrder(newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE : SequenceAnnotationOrder.NONE); sortAnnotations_actionPerformed(); } }); colourTextMenuItem = new JCheckBoxMenuItem( MessageManager .getString("label.colour_text")); colourTextMenuItem.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { colourTextMenuItem_actionPerformed(e); } }); JMenuItem htmlMenuItem = new JMenuItem( MessageManager.getString("label.html")); htmlMenuItem.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { htmlMenuItem_actionPerformed(e); } }); JMenuItem createBioJS = new JMenuItem( MessageManager.getString("label.biojs_html_export")); createBioJS.addActionListener(new java.awt.event.ActionListener() { @Override public void actionPerformed(ActionEvent e) { bioJSMenuItem_actionPerformed(e); } }); JMenuItem overviewMenuItem = new JMenuItem( MessageManager.getString("label.overview_window")); overviewMenuItem.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { overviewMenuItem_actionPerformed(e); } }); undoMenuItem.setEnabled(false); undoMenuItem.setText(MessageManager.getString("action.undo")); keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Z, Toolkit .getDefaultToolkit().getMenuShortcutKeyMask(), false); al = new ActionListener() { @Override public void actionPerformed(ActionEvent e) { undoMenuItem_actionPerformed(e); } }; addMenuActionAndAccelerator(keyStroke, undoMenuItem, al); redoMenuItem.setEnabled(false); redoMenuItem.setText(MessageManager.getString("action.redo")); keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Y, Toolkit .getDefaultToolkit().getMenuShortcutKeyMask(), false); al = new ActionListener() { @Override public void actionPerformed(ActionEvent e) { redoMenuItem_actionPerformed(e); } }; addMenuActionAndAccelerator(keyStroke, redoMenuItem, al); wrapMenuItem.setText(MessageManager.getString("label.wrap")); wrapMenuItem.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { wrapMenuItem_actionPerformed(e); } }); JMenuItem printMenuItem = new JMenuItem( MessageManager.getString("action.print")); keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_P, Toolkit .getDefaultToolkit().getMenuShortcutKeyMask(), false); al = new ActionListener() { @Override public void actionPerformed(ActionEvent e) { printMenuItem_actionPerformed(e); } }; addMenuActionAndAccelerator(keyStroke, printMenuItem, al); renderGapsMenuItem .setText(MessageManager.getString("action.show_gaps")); renderGapsMenuItem.setState(true); renderGapsMenuItem.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { renderGapsMenuItem_actionPerformed(e); } }); JMenuItem findMenuItem = new JMenuItem( MessageManager.getString("action.find")); keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_F, Toolkit .getDefaultToolkit().getMenuShortcutKeyMask(), false); findMenuItem.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.getString("label.find_tip"))); al = new ActionListener() { @Override public void actionPerformed(ActionEvent e) { findMenuItem_actionPerformed(e); } }; addMenuActionAndAccelerator(keyStroke, findMenuItem, al); showSeqFeatures.setText(MessageManager .getString("label.show_sequence_features")); showSeqFeatures.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent actionEvent) { showSeqFeatures_actionPerformed(actionEvent); } }); /* * showSeqFeaturesHeight.setText("Vary Sequence Feature Height"); * showSeqFeaturesHeight.addActionListener(new ActionListener() { public * void actionPerformed(ActionEvent actionEvent) { * showSeqFeaturesHeight_actionPerformed(actionEvent); } }); */ showDbRefsMenuitem.setText(MessageManager .getString("label.show_database_refs")); showDbRefsMenuitem.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { showDbRefs_actionPerformed(e); } }); showNpFeatsMenuitem.setText(MessageManager .getString("label.show_non_positional_features")); showNpFeatsMenuitem.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { showNpFeats_actionPerformed(e); } }); showGroupConservation.setText(MessageManager .getString("label.group_conservation")); showGroupConservation.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { showGroupConservation_actionPerformed(e); } }); showGroupConsensus.setText(MessageManager .getString("label.group_consensus")); showGroupConsensus.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { showGroupConsensus_actionPerformed(e); } }); showConsensusHistogram.setText(MessageManager .getString("label.show_consensus_histogram")); showConsensusHistogram.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { showConsensusHistogram_actionPerformed(e); } }); showSequenceLogo.setText(MessageManager .getString("label.show_consensus_logo")); showSequenceLogo.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { showSequenceLogo_actionPerformed(e); } }); normaliseSequenceLogo.setText(MessageManager .getString("label.norm_consensus_logo")); normaliseSequenceLogo.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { normaliseSequenceLogo_actionPerformed(e); } }); applyAutoAnnotationSettings.setText(MessageManager .getString("label.apply_all_groups")); applyAutoAnnotationSettings.setState(false); applyAutoAnnotationSettings.setVisible(true); applyAutoAnnotationSettings.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { applyAutoAnnotationSettings_actionPerformed(e); } }); ButtonGroup buttonGroup = new ButtonGroup(); final JRadioButtonMenuItem showAutoFirst = new JRadioButtonMenuItem( MessageManager.getString("label.show_first")); final JRadioButtonMenuItem showAutoLast = new JRadioButtonMenuItem( MessageManager.getString("label.show_last")); buttonGroup.add(showAutoFirst); buttonGroup.add(showAutoLast); final boolean autoFirst = Cache.getDefault( Preferences.SHOW_AUTOCALC_ABOVE, false); showAutoFirst.setSelected(autoFirst); setShowAutoCalculatedAbove(autoFirst); showAutoFirst.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { setShowAutoCalculatedAbove(showAutoFirst.isSelected()); sortAnnotations_actionPerformed(); } }); showAutoLast.setSelected(!showAutoFirst.isSelected()); showAutoLast.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { setShowAutoCalculatedAbove(!showAutoLast.isSelected()); sortAnnotations_actionPerformed(); } }); JMenuItem deleteGroups = new JMenuItem( MessageManager.getString("action.undefine_groups")); keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_U, Toolkit .getDefaultToolkit().getMenuShortcutKeyMask(), false); al = new ActionListener() { @Override public void actionPerformed(ActionEvent e) { deleteGroups_actionPerformed(e); } }; addMenuActionAndAccelerator(keyStroke, deleteGroups, al); JMenuItem annotationColumn = new JMenuItem( MessageManager.getString("action.select_by_annotation")); annotationColumn.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { annotationColumn_actionPerformed(e); } }); JMenuItem createGroup = new JMenuItem( MessageManager.getString("action.create_groups")); keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, Toolkit .getDefaultToolkit().getMenuShortcutKeyMask(), false); al = new ActionListener() { @Override public void actionPerformed(ActionEvent e) { createGroup_actionPerformed(e); } }; addMenuActionAndAccelerator(keyStroke, createGroup, al); JMenuItem unGroup = new JMenuItem( MessageManager.getString("action.remove_group")); keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, Toolkit .getDefaultToolkit().getMenuShortcutKeyMask() | KeyEvent.SHIFT_MASK, false); al = new ActionListener() { @Override public void actionPerformed(ActionEvent e) { unGroup_actionPerformed(e); } }; addMenuActionAndAccelerator(keyStroke, unGroup, al); copy.setText(MessageManager.getString("action.copy")); keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_C, Toolkit .getDefaultToolkit().getMenuShortcutKeyMask(), false); al = new ActionListener() { @Override public void actionPerformed(ActionEvent e) { copy_actionPerformed(e); } }; addMenuActionAndAccelerator(keyStroke, copy, al); cut.setText(MessageManager.getString("action.cut")); keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X, Toolkit .getDefaultToolkit().getMenuShortcutKeyMask(), false); al = new ActionListener() { @Override public void actionPerformed(ActionEvent e) { cut_actionPerformed(e); } }; addMenuActionAndAccelerator(keyStroke, cut, al); JMenuItem delete = new JMenuItem( MessageManager.getString("action.delete")); delete.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { delete_actionPerformed(e); } }); pasteMenu.setText(MessageManager.getString("action.paste")); JMenuItem pasteNew = new JMenuItem( MessageManager.getString("label.to_new_alignment")); keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V, Toolkit .getDefaultToolkit().getMenuShortcutKeyMask() | KeyEvent.SHIFT_MASK, false); al = new ActionListener() { @Override public void actionPerformed(ActionEvent e) { pasteNew_actionPerformed(e); } }; addMenuActionAndAccelerator(keyStroke, pasteNew, al); JMenuItem pasteThis = new JMenuItem( MessageManager.getString("label.to_this_alignment")); keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V, Toolkit .getDefaultToolkit().getMenuShortcutKeyMask(), false); al = new ActionListener() { @Override public void actionPerformed(ActionEvent e) { pasteThis_actionPerformed(e); } }; addMenuActionAndAccelerator(keyStroke, pasteThis, al); JMenuItem createPNG = new JMenuItem("PNG"); createPNG.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { createPNG(null); } }); createPNG.setActionCommand(MessageManager .getString("label.save_png_image")); JMenuItem font = new JMenuItem(MessageManager.getString("action.font")); font.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { font_actionPerformed(e); } }); seqLimits.setText(MessageManager .getString("label.show_sequence_limits")); seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true)); seqLimits.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { seqLimit_actionPerformed(e); } }); JMenuItem epsFile = new JMenuItem("EPS"); epsFile.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { createEPS(null); } }); JMenuItem createSVG = new JMenuItem("SVG"); createSVG.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { createSVG(null); } }); JMenuItem loadTreeMenuItem = new JMenuItem( MessageManager.getString("label.load_associated_tree")); loadTreeMenuItem.setActionCommand(MessageManager .getString("label.load_tree_for_sequence_set")); loadTreeMenuItem.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { loadTreeMenuItem_actionPerformed(e); } }); scaleAbove.setVisible(false); scaleAbove.setText(MessageManager.getString("action.scale_above")); scaleAbove.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { scaleAbove_actionPerformed(e); } }); scaleLeft.setVisible(false); scaleLeft.setSelected(true); scaleLeft.setText(MessageManager.getString("action.scale_left")); scaleLeft.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { scaleLeft_actionPerformed(e); } }); scaleRight.setVisible(false); scaleRight.setSelected(true); scaleRight.setText(MessageManager.getString("action.scale_right")); scaleRight.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { scaleRight_actionPerformed(e); } }); centreColumnLabelsMenuItem.setVisible(true); centreColumnLabelsMenuItem.setState(false); centreColumnLabelsMenuItem.setText(MessageManager .getString("label.centre_column_labels")); centreColumnLabelsMenuItem.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { centreColumnLabels_actionPerformed(e); } }); followHighlightMenuItem.setVisible(true); followHighlightMenuItem.setState(true); followHighlightMenuItem.setText(MessageManager .getString("label.automatic_scrolling")); followHighlightMenuItem.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { followHighlight_actionPerformed(); } }); sortByTreeMenu .setText(MessageManager.getString("action.by_tree_order")); sort.setText(MessageManager.getString("action.sort")); sort.addMenuListener(new MenuListener() { @Override public void menuSelected(MenuEvent e) { buildTreeSortMenu(); } @Override public void menuDeselected(MenuEvent e) { } @Override public void menuCanceled(MenuEvent e) { } }); sortByAnnotScore.setText(MessageManager .getString("label.sort_by_score")); sort.add(sortByAnnotScore); sort.addMenuListener(new javax.swing.event.MenuListener() { @Override public void menuCanceled(MenuEvent e) { } @Override public void menuDeselected(MenuEvent e) { } @Override public void menuSelected(MenuEvent e) { buildSortByAnnotationScoresMenu(); } }); sortByAnnotScore.setVisible(false); calculateTree .setText(MessageManager.getString("action.calculate_tree")); padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps")); padGapsMenuitem.setState(jalview.bin.Cache .getDefault("PAD_GAPS", false)); padGapsMenuitem.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { padGapsMenuitem_actionPerformed(e); } }); JMenuItem vamsasStore = new JMenuItem( MessageManager.getString("label.vamsas_store")); vamsasStore.setVisible(false); vamsasStore.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { vamsasStore_actionPerformed(e); } }); showTranslation.setText(MessageManager .getString("label.translate_cDNA")); showTranslation.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { showTranslation_actionPerformed(e); } }); showReverse.setText(MessageManager.getString("label.reverse")); showReverse.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { showReverse_actionPerformed(false); } }); showReverseComplement.setText(MessageManager .getString("label.reverse_complement")); showReverseComplement.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { showReverse_actionPerformed(true); } }); JMenuItem extractScores = new JMenuItem( MessageManager.getString("label.extract_scores")); extractScores.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { extractScores_actionPerformed(e); } }); extractScores.setVisible(true); // JBPNote: TODO: make gui for regex based score extraction // for show products actions see AlignFrame.canShowProducts showProducts.setText(MessageManager.getString("label.get_cross_refs")); runGroovy.setText(MessageManager.getString("label.run_groovy")); runGroovy.setToolTipText(MessageManager .getString("label.run_groovy_tip")); runGroovy.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { runGroovy_actionPerformed(); } }); JMenuItem openFeatureSettings = new JMenuItem( MessageManager.getString("action.feature_settings")); openFeatureSettings.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { featureSettings_actionPerformed(e); } }); JMenuItem fetchSequence = new JMenuItem( MessageManager.getString("label.fetch_sequences")); fetchSequence.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { fetchSequence_actionPerformed(e); } }); JMenuItem associatedData = new JMenuItem( MessageManager.getString("label.load_features_annotations")); associatedData.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { associatedData_actionPerformed(e); } }); autoCalculate.setText(MessageManager .getString("label.autocalculate_consensus")); autoCalculate.setState(jalview.bin.Cache.getDefault( "AUTO_CALC_CONSENSUS", true)); autoCalculate.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { autoCalculate_actionPerformed(e); } }); sortByTree.setText(MessageManager .getString("label.sort_alignment_new_tree")); sortByTree .setToolTipText("" + MessageManager .getString("label.enable_automatically_sort_alignment_when_open_new_tree")); sortByTree .setState(jalview.bin.Cache.getDefault("SORT_BY_TREE", false)); sortByTree.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { sortByTreeOption_actionPerformed(e); } }); listenToViewSelections.setText(MessageManager .getString("label.listen_for_selections")); listenToViewSelections .setToolTipText("" + MessageManager .getString("label.selections_mirror_selections_made_same_sequences_other_views")); listenToViewSelections.setState(false); listenToViewSelections.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { listenToViewSelections_actionPerformed(e); } }); JMenu addSequenceMenu = new JMenu( MessageManager.getString("label.add_sequences")); JMenuItem addFromFile = new JMenuItem( MessageManager.getString("label.from_file")); addFromFile.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { addFromFile_actionPerformed(e); } }); JMenuItem addFromText = new JMenuItem( MessageManager.getString("label.from_textbox")); addFromText.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { addFromText_actionPerformed(e); } }); JMenuItem addFromURL = new JMenuItem( MessageManager.getString("label.from_url")); addFromURL.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { addFromURL_actionPerformed(e); } }); JMenuItem exportFeatures = new JMenuItem( MessageManager.getString("label.export_features")); exportFeatures.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { exportFeatures_actionPerformed(e); } }); JMenuItem exportAnnotations = new JMenuItem( MessageManager.getString("label.export_annotations")); exportAnnotations.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { exportAnnotations_actionPerformed(e); } }); statusPanel.setLayout(new GridLayout()); JMenuItem showAllSeqs = new JMenuItem( MessageManager.getString("label.all_sequences")); showAllSeqs.setToolTipText(MessageManager .getString("label.toggle_sequence_visibility")); showAllSeqs.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { showAllSeqs_actionPerformed(e); } }); JMenuItem showAllColumns = new JMenuItem( MessageManager.getString("label.all_columns")); showAllColumns.setToolTipText(MessageManager .getString("label.toggle_columns_visibility")); showAllColumns.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { showAllColumns_actionPerformed(e); } }); JMenu hideMenu = new JMenu(MessageManager.getString("action.hide")); JMenuItem hideSelSequences = new JMenuItem( MessageManager.getString("label.selected_sequences")); hideSelSequences.setToolTipText(MessageManager .getString("label.toggle_sequence_visibility")); hideSelSequences.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { hideSelSequences_actionPerformed(e); } }); JMenuItem hideSelColumns = new JMenuItem( MessageManager.getString("label.selected_columns")); hideSelColumns.setToolTipText(MessageManager .getString("label.toggle_columns_visibility")); hideSelColumns.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { hideSelColumns_actionPerformed(e); } }); JMenuItem hideAllSelection = new JMenuItem( MessageManager.getString("label.selected_region")); hideAllSelection.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { hideAllSelection_actionPerformed(e); } }); // TODO: should be hidden if no selection exists. JMenuItem hideAllButSelection = new JMenuItem( MessageManager.getString("label.all_but_selected_region")); hideAllButSelection.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { hideAllButSelection_actionPerformed(e); } }); JMenuItem showAllhidden = new JMenuItem( MessageManager.getString("label.all_sequences_columns")); showAllhidden.setToolTipText(MessageManager .getString("label.toggles_visibility_hidden_selected_regions")); showAllhidden.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { showAllhidden_actionPerformed(e); } }); hiddenMarkers.setText(MessageManager .getString("action.show_hidden_markers")); hiddenMarkers.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { hiddenMarkers_actionPerformed(e); } }); JMenuItem invertColSel = new JMenuItem( MessageManager.getString("action.invert_column_selection")); keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I, Toolkit .getDefaultToolkit().getMenuShortcutKeyMask() | KeyEvent.ALT_MASK, false); al = new ActionListener() { @Override public void actionPerformed(ActionEvent e) { invertColSel_actionPerformed(e); } }; addMenuActionAndAccelerator(keyStroke, invertColSel, al); showComplementMenuItem.setVisible(false); showComplementMenuItem.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { showComplement_actionPerformed(showComplementMenuItem.getState()); } }); tabbedPane.addChangeListener(new javax.swing.event.ChangeListener() { @Override public void stateChanged(ChangeEvent evt) { JTabbedPane pane = (JTabbedPane) evt.getSource(); int sel = pane.getSelectedIndex(); tabSelectionChanged(sel); } }); tabbedPane.addMouseListener(new MouseAdapter() { @Override public void mousePressed(MouseEvent e) { if (e.isPopupTrigger()) // Mac { tabbedPane_mousePressed(e); } } @Override public void mouseReleased(MouseEvent e) { if (e.isPopupTrigger()) // Windows { tabbedPane_mousePressed(e); } } }); tabbedPane.addFocusListener(new FocusAdapter() { @Override public void focusGained(FocusEvent e) { tabbedPane_focusGained(e); } }); JMenuItem save = new JMenuItem(MessageManager.getString("action.save")); keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S, Toolkit .getDefaultToolkit().getMenuShortcutKeyMask(), false); al = new ActionListener() { @Override public void actionPerformed(ActionEvent e) { save_actionPerformed(e); } }; addMenuActionAndAccelerator(keyStroke, save, al); reload.setEnabled(false); reload.setText(MessageManager.getString("action.reload")); reload.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { reload_actionPerformed(e); } }); JMenuItem newView = new JMenuItem( MessageManager.getString("action.new_view")); keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_T, Toolkit .getDefaultToolkit().getMenuShortcutKeyMask(), false); al = new ActionListener() { @Override public void actionPerformed(ActionEvent e) { newView_actionPerformed(e); } }; addMenuActionAndAccelerator(keyStroke, newView, al); tabbedPane.setToolTipText("" + MessageManager.getString("label.rename_tab_eXpand_reGroup") + ""); formatMenu.setText(MessageManager.getString("action.format")); JMenu selectMenu = new JMenu(MessageManager.getString("action.select")); idRightAlign.setText(MessageManager .getString("label.right_align_sequence_id")); idRightAlign.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { idRightAlign_actionPerformed(e); } }); gatherViews.setEnabled(false); gatherViews.setText(MessageManager.getString("action.gather_views")); keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, 0, false); al = new ActionListener() { @Override public void actionPerformed(ActionEvent e) { gatherViews_actionPerformed(e); } }; addMenuActionAndAccelerator(keyStroke, gatherViews, al); expandViews.setEnabled(false); expandViews.setText(MessageManager.getString("action.expand_views")); keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X, 0, false); al = new ActionListener() { @Override public void actionPerformed(ActionEvent e) { expandViews_actionPerformed(e); } }; addMenuActionAndAccelerator(keyStroke, expandViews, al); JMenuItem pageSetup = new JMenuItem( MessageManager.getString("action.page_setup")); pageSetup.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { pageSetup_actionPerformed(e); } }); JMenuItem alignmentProperties = new JMenuItem( MessageManager.getString("label.alignment_props")); alignmentProperties.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent actionEvent) { alignmentProperties(); } }); JMenuItem selectHighlighted = new JMenuItem( MessageManager.getString("action.select_highlighted_columns")); selectHighlighted.setToolTipText(MessageManager .getString("tooltip.select_highlighted_columns")); al = new ActionListener() { @Override public void actionPerformed(ActionEvent actionEvent) { selectHighlightedColumns_actionPerformed(actionEvent); } }; selectHighlighted.addActionListener(al); JMenu tooltipSettingsMenu = new JMenu( MessageManager.getString("label.sequence_id_tooltip")); JMenu autoAnnMenu = new JMenu( MessageManager.getString("label.autocalculated_annotation")); JMenu exportImageMenu = new JMenu( MessageManager.getString("label.export_image")); JMenu fileMenu = new JMenu(MessageManager.getString("action.file")); alignFrameMenuBar.add(fileMenu); alignFrameMenuBar.add(editMenu); alignFrameMenuBar.add(selectMenu); alignFrameMenuBar.add(viewMenu); alignFrameMenuBar.add(annotationsMenu); alignFrameMenuBar.add(formatMenu); alignFrameMenuBar.add(colourMenu); alignFrameMenuBar.add(calculateMenu); alignFrameMenuBar.add(webService); fileMenu.add(fetchSequence); fileMenu.add(addSequenceMenu); fileMenu.add(reload); fileMenu.addSeparator(); fileMenu.add(vamsasStore); fileMenu.add(save); fileMenu.add(saveAs); fileMenu.add(outputTextboxMenu); fileMenu.add(pageSetup); fileMenu.add(printMenuItem); fileMenu.addSeparator(); fileMenu.add(exportImageMenu); fileMenu.add(exportFeatures); fileMenu.add(exportAnnotations); fileMenu.add(loadTreeMenuItem); fileMenu.add(associatedData); fileMenu.addSeparator(); fileMenu.add(closeMenuItem); pasteMenu.add(pasteNew); pasteMenu.add(pasteThis); editMenu.add(undoMenuItem); editMenu.add(redoMenuItem); editMenu.add(cut); editMenu.add(copy); editMenu.add(pasteMenu); editMenu.add(delete); editMenu.addSeparator(); editMenu.add(remove2LeftMenuItem); editMenu.add(remove2RightMenuItem); editMenu.add(removeGappedColumnMenuItem); editMenu.add(removeAllGapsMenuItem); editMenu.add(removeRedundancyMenuItem); editMenu.addSeparator(); // dont add these yet in the CVS build - they cannot be undone! // Excluded from Jalview 2.5 release - undo needs to be implemented. // editMenu.add(justifyLeftMenuItem); // editMenu.add(justifyRightMenuItem); // editMenu.addSeparator(); editMenu.add(padGapsMenuitem); showMenu.add(showAllColumns); showMenu.add(showAllSeqs); showMenu.add(showAllhidden); hideMenu.add(hideSelColumns); hideMenu.add(hideSelSequences); hideMenu.add(hideAllSelection); hideMenu.add(hideAllButSelection); viewMenu.add(newView); viewMenu.add(expandViews); viewMenu.add(gatherViews); viewMenu.addSeparator(); viewMenu.add(showMenu); viewMenu.add(hideMenu); viewMenu.add(showComplementMenuItem); viewMenu.addSeparator(); viewMenu.add(followHighlightMenuItem); viewMenu.addSeparator(); viewMenu.add(showSeqFeatures); // viewMenu.add(showSeqFeaturesHeight); viewMenu.add(openFeatureSettings); tooltipSettingsMenu.add(showDbRefsMenuitem); tooltipSettingsMenu.add(showNpFeatsMenuitem); viewMenu.add(tooltipSettingsMenu); viewMenu.addSeparator(); viewMenu.add(alignmentProperties); viewMenu.addSeparator(); viewMenu.add(overviewMenuItem); annotationsMenu.add(annotationPanelMenuItem); annotationsMenu.addSeparator(); annotationsMenu.add(showAllAlAnnotations); annotationsMenu.add(hideAllAlAnnotations); annotationsMenu.addSeparator(); annotationsMenu.add(showAllSeqAnnotations); annotationsMenu.add(hideAllSeqAnnotations); annotationsMenu.add(sortAnnBySequence); annotationsMenu.add(sortAnnByLabel); annotationsMenu.addSeparator(); autoAnnMenu.add(showAutoFirst); autoAnnMenu.add(showAutoLast); autoAnnMenu.addSeparator(); autoAnnMenu.add(applyAutoAnnotationSettings); autoAnnMenu.add(showConsensusHistogram); autoAnnMenu.add(showSequenceLogo); autoAnnMenu.add(normaliseSequenceLogo); autoAnnMenu.addSeparator(); autoAnnMenu.add(showGroupConservation); autoAnnMenu.add(showGroupConsensus); annotationsMenu.add(autoAnnMenu); sort.add(sortIDMenuItem); sort.add(sortLengthMenuItem); sort.add(sortGroupMenuItem); sort.add(sortPairwiseMenuItem); sort.add(sortByTreeMenu); calculateMenu.add(sort); calculateMenu.add(calculateTree); calculateMenu.addSeparator(); calculateMenu.add(pairwiseAlignmentMenuItem); calculateMenu.add(PCAMenuItem); calculateMenu.addSeparator(); calculateMenu.add(showTranslation); calculateMenu.add(showReverse); calculateMenu.add(showReverseComplement); calculateMenu.add(showProducts); calculateMenu.add(autoCalculate); calculateMenu.add(sortByTree); calculateMenu.addSeparator(); calculateMenu.add(expandAlignment); calculateMenu.add(extractScores); calculateMenu.addSeparator(); calculateMenu.add(runGroovy); webServiceNoServices = new JMenuItem( MessageManager.getString("label.no_services")); webService.add(webServiceNoServices); 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); 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(createGroup); selectMenu.add(unGroup); selectMenu.add(grpsFromSelection); selectMenu.add(deleteGroups); selectMenu.add(annotationColumn); selectMenu.add(selectHighlighted); // TODO - determine if the listenToViewSelections button is needed : see bug // JAL-574 // selectMenu.addSeparator(); // selectMenu.add(listenToViewSelections); } /** * Constructs the entries on the Colour menu (but does not add them to the * menu). */ protected void initColourMenu() { applyToAllGroups = new JCheckBoxMenuItem( MessageManager.getString("label.apply_colour_to_all_groups")); applyToAllGroups.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { applyToAllGroups_actionPerformed(applyToAllGroups.isSelected()); } }); textColour = new JRadioButtonMenuItem( MessageManager.getString("action.set_text_colour")); textColour.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { textColour_actionPerformed(); } }); conservationMenuItem = new JCheckBoxMenuItem( MessageManager.getString("action.by_conservation")); conservationMenuItem.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { conservationMenuItem_actionPerformed(conservationMenuItem .isSelected()); } }); abovePIDThreshold = new JCheckBoxMenuItem( MessageManager.getString("label.above_identity_threshold")); abovePIDThreshold.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { abovePIDThreshold_actionPerformed(abovePIDThreshold.isSelected()); } }); 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(); } }); } 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) { } 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 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() { } protected void extractScores_actionPerformed(ActionEvent e) { } protected void outputText_actionPerformed(ActionEvent e) { } public void addFromFile_actionPerformed(ActionEvent e) { } public void addFromText_actionPerformed(ActionEvent e) { } public void addFromURL_actionPerformed(ActionEvent e) { } public void exportFeatures_actionPerformed(ActionEvent e) { } public void exportAnnotations_actionPerformed(ActionEvent e) { } protected void htmlMenuItem_actionPerformed(ActionEvent e) { } protected void bioJSMenuItem_actionPerformed(ActionEvent e) { } protected void closeMenuItem_actionPerformed(boolean b) { } protected void redoMenuItem_actionPerformed(ActionEvent e) { } protected void undoMenuItem_actionPerformed(ActionEvent e) { } protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e) { } protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e) { } protected void invertSequenceMenuItem_actionPerformed(ActionEvent e) { } protected void remove2LeftMenuItem_actionPerformed(ActionEvent e) { } protected void remove2RightMenuItem_actionPerformed(ActionEvent e) { } protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e) { } protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e) { } protected void wrapMenuItem_actionPerformed(ActionEvent e) { } protected void viewBoxesMenuItem_actionPerformed(ActionEvent e) { } protected void viewTextMenuItem_actionPerformed(ActionEvent e) { } protected void colourTextMenuItem_actionPerformed(ActionEvent e) { } protected void annotationPanelMenuItem_actionPerformed(ActionEvent e) { } protected void overviewMenuItem_actionPerformed(ActionEvent e) { } protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e) { } protected void sortIDMenuItem_actionPerformed(ActionEvent e) { } protected void sortLengthMenuItem_actionPerformed(ActionEvent e) { } protected void sortGroupMenuItem_actionPerformed(ActionEvent e) { } protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e) { } protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e) { } protected void PCAMenuItem_actionPerformed(ActionEvent e) { } protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e) { } protected void conservationMenuItem_actionPerformed(boolean selected) { } protected void printMenuItem_actionPerformed(ActionEvent e) { } protected void renderGapsMenuItem_actionPerformed(ActionEvent e) { } protected void findMenuItem_actionPerformed(ActionEvent e) { } protected void abovePIDThreshold_actionPerformed(boolean selected) { } public void showSeqFeatures_actionPerformed(ActionEvent actionEvent) { } protected void deleteGroups_actionPerformed(ActionEvent e) { } protected void createGroup_actionPerformed(ActionEvent e) { } protected void unGroup_actionPerformed(ActionEvent e) { } protected void copy_actionPerformed(ActionEvent e) { } protected void cut_actionPerformed(ActionEvent e) { } protected void delete_actionPerformed(ActionEvent e) { } protected void pasteNew_actionPerformed(ActionEvent e) { } protected void pasteThis_actionPerformed(ActionEvent e) { } protected void applyToAllGroups_actionPerformed(boolean selected) { } public void createPNG(java.io.File f) { } protected void font_actionPerformed(ActionEvent e) { } protected void seqLimit_actionPerformed(ActionEvent e) { } public void seqDBRef_actionPerformed(ActionEvent e) { } public void createEPS(java.io.File f) { } 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) { } protected void jpred_actionPerformed(ActionEvent e) { } protected void scaleAbove_actionPerformed(ActionEvent e) { } protected void scaleLeft_actionPerformed(ActionEvent e) { } protected void scaleRight_actionPerformed(ActionEvent e) { } protected void modifyPID_actionPerformed() { } protected void modifyConservation_actionPerformed() { } protected void saveAs_actionPerformed(ActionEvent e) { } protected void padGapsMenuitem_actionPerformed(ActionEvent e) { } public void vamsasStore_actionPerformed(ActionEvent e) { } public void vamsasLoad_actionPerformed(ActionEvent e) { } public void showTranslation_actionPerformed(ActionEvent e) { } public void featureSettings_actionPerformed(ActionEvent e) { } public void fetchSequence_actionPerformed(ActionEvent e) { } public void smoothFont_actionPerformed(ActionEvent e) { } public void annotationColour_actionPerformed() { } public void annotationColumn_actionPerformed(ActionEvent e) { } public void associatedData_actionPerformed(ActionEvent e) { } public void autoCalculate_actionPerformed(ActionEvent e) { } public void sortByTreeOption_actionPerformed(ActionEvent e) { } public void showAllSeqs_actionPerformed(ActionEvent e) { } public void showAllColumns_actionPerformed(ActionEvent e) { } public void hideSelSequences_actionPerformed(ActionEvent e) { } public void hideSelColumns_actionPerformed(ActionEvent e) { } public void hiddenMarkers_actionPerformed(ActionEvent e) { } public void findPdbId_actionPerformed(ActionEvent e) { } public void enterPdbId_actionPerformed(ActionEvent e) { } public void pdbFile_actionPerformed(ActionEvent e) { } public void invertColSel_actionPerformed(ActionEvent e) { } public void tabSelectionChanged(int sel) { } public void tabbedPane_mousePressed(MouseEvent e) { } public void tabbedPane_focusGained(FocusEvent e) { requestFocus(); } public void save_actionPerformed(ActionEvent e) { } public void reload_actionPerformed(ActionEvent e) { } public void newView_actionPerformed(ActionEvent e) { } public void textColour_actionPerformed() { } public void idRightAlign_actionPerformed(ActionEvent e) { } public void expandViews_actionPerformed(ActionEvent e) { } public void gatherViews_actionPerformed(ActionEvent e) { } public void buildTreeSortMenu() { } public void pageSetup_actionPerformed(ActionEvent e) { } public void alignmentProperties() { } 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) { } }