X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGAlignFrame.java;h=cd8ad6f3cbb7e819ef6d24b1362ef73eebcf2511;hb=cb5d856b1304448cae13a333cbd9017f81520d90;hp=0e5d00e79000aebe44ae6a7ce8438ddaad672142;hpb=afbde8b4027ce614b43ab0949e74246364cd6013;p=jalview.git diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java index 0e5d00e..cd8ad6f 100755 --- a/src/jalview/jbgui/GAlignFrame.java +++ b/src/jalview/jbgui/GAlignFrame.java @@ -1,154 +1,354 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle - * - * This program 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 2 - * of the License, or (at your option) any later version. - * - * This program 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 this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1) + * Copyright (C) 2014 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 java.awt.*; -import java.awt.event.*; - -import javax.swing.*; -import javax.swing.event.*; - -import jalview.schemes.*; - -public class GAlignFrame - extends JInternalFrame +import jalview.schemes.ColourSchemeProperty; +import jalview.util.MessageManager; + +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.MouseAdapter; +import java.awt.event.MouseEvent; + +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.JOptionPane; +import javax.swing.JPanel; +import javax.swing.JRadioButtonMenuItem; +import javax.swing.JTabbedPane; +import javax.swing.SwingUtilities; +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 JMenu fileMenu = new JMenu(); + protected JMenuItem closeMenuItem = new JMenuItem(); + protected JMenu editMenu = new JMenu(); + protected JMenu viewMenu = new JMenu(); + protected JMenu colourMenu = new JMenu(); + protected JMenu calculateMenu = new JMenu(); + protected JMenu webService = new JMenu(); + protected JMenuItem webServiceNoServices; + protected JMenuItem selectAllSequenceMenuItem = new JMenuItem(); + protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem(); + protected JMenuItem invertSequenceMenuItem = new JMenuItem(); + protected JMenuItem remove2LeftMenuItem = new JMenuItem(); + protected JMenuItem remove2RightMenuItem = new JMenuItem(); + protected JMenuItem removeGappedColumnMenuItem = new JMenuItem(); + protected JMenuItem removeAllGapsMenuItem = new JMenuItem(); + public JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem(); + public JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem(); + protected JMenuItem sortPairwiseMenuItem = new JMenuItem(); + protected JMenuItem sortIDMenuItem = new JMenuItem(); + + protected JMenuItem sortLengthMenuItem = new JMenuItem(); + protected JMenuItem sortGroupMenuItem = new JMenuItem(); + protected JMenu sortByAnnotScore = new JMenu(); + protected JMenuItem removeRedundancyMenuItem = new JMenuItem(); + protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem(); + protected JMenuItem PCAMenuItem = new JMenuItem(); + protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem(); + protected JMenuItem neighbourTreeMenuItem = new JMenuItem(); + BorderLayout borderLayout1 = new BorderLayout(); + public JLabel statusBar = new JLabel(); + protected JMenuItem saveAs = new JMenuItem(); + protected JMenu outputTextboxMenu = new JMenu(); + protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem(); + protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem(); + protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem(); - protected JRadioButtonMenuItem hydrophobicityColour = new - JRadioButtonMenuItem(); + + protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem(); + protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem(); + protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem(); + protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem(); + protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem(); + protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem(); + protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem(); + protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem(); + + protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem(); + + protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem(); + + // protected JRadioButtonMenuItem covariationColour = new + // JRadioButtonMenuItem(); + + protected JRadioButtonMenuItem tcoffeeColour = new JRadioButtonMenuItem(); + JMenuItem njTreeBlosumMenuItem = new JMenuItem(); + JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem(); + public JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem(); + public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem(); + + public JCheckBoxMenuItem showNonconservedMenuItem = new JCheckBoxMenuItem(); + JMenuItem htmlMenuItem = new JMenuItem(); + JMenuItem overviewMenuItem = new JMenuItem(); + protected JMenuItem undoMenuItem = new JMenuItem(); + protected JMenuItem redoMenuItem = new JMenuItem(); + public JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem(); + JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem(); + public JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem(); + JMenuItem printMenuItem = new JMenuItem(); + public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem(); + JMenuItem findMenuItem = new JMenuItem(); + public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem(); + public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem(); - protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem(); + + public JCheckBoxMenuItem showSeqFeaturesHeight = new JCheckBoxMenuItem(); + JMenuItem deleteGroups = new JMenuItem(); + + JMenuItem createGroup = new JMenuItem(); + JMenuItem unGroup = new JMenuItem(); + JMenuItem delete = new JMenuItem(); + JMenuItem copy = new JMenuItem(); + JMenuItem cut = new JMenuItem(); + JMenu pasteMenu = new JMenu(); + JMenuItem pasteNew = new JMenuItem(); + JMenuItem pasteThis = new JMenuItem(); + public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem(); + JMenuItem createPNG = new JMenuItem(); + protected JMenuItem font = new JMenuItem(); + public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem(); + JMenuItem epsFile = new JMenuItem(); + JMenuItem LoadtreeMenuItem = new JMenuItem(); + public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem(); + public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem(); + public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem(); + protected JMenuItem modifyPID = new JMenuItem(); + protected JMenuItem modifyConservation = new JMenuItem(); + protected JMenu sortByTreeMenu = new JMenu(); + protected JMenu sort = new JMenu(); - JMenu calculate = new JMenu(); + + protected JMenu calculateTree = new JMenu(); + JMenu jMenu2 = new JMenu(); + protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem(); + + protected JCheckBoxMenuItem showNpFeatsMenuitem = new JCheckBoxMenuItem(); + + protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem(); + protected ButtonGroup colours = new ButtonGroup(); + JMenuItem vamsasStore = new JMenuItem(); + protected JMenuItem showTranslation = new JMenuItem(); + protected JMenuItem extractScores = new JMenuItem(); - public JMenuItem featureSettings = new JMenuItem(); + + protected JMenu showProducts = new JMenu(); + + public JMenuItem openFeatureSettings = new JMenuItem(); + JMenuItem fetchSequence = new JMenuItem(); + JMenuItem annotationColour = new JMenuItem(); + + protected JMenuItem rnahelicesColour = new JMenuItem(); + JMenuItem associatedData = new JMenuItem(); + protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem(); + + protected JCheckBoxMenuItem sortByTree = new JCheckBoxMenuItem(); + + protected JCheckBoxMenuItem listenToViewSelections = new JCheckBoxMenuItem(); + JMenu addSequenceMenu = new JMenu(); + JMenuItem addFromFile = new JMenuItem(); + JMenuItem addFromText = new JMenuItem(); + JMenuItem addFromURL = new JMenuItem(); + JMenuItem exportAnnotations = new JMenuItem(); + JMenuItem exportFeatures = new JMenuItem(); + protected JPanel statusPanel = new JPanel(); + GridLayout gridLayout1 = new GridLayout(); + JMenu jMenu3 = new JMenu(); + JMenuItem showAllSeqs = new JMenuItem(); + JMenuItem showAllColumns = new JMenuItem(); + JMenu hideMenu = new JMenu(); + JMenuItem hideSelSequences = new JMenuItem(); + JMenuItem hideSelColumns = new JMenuItem(); + + JMenuItem hideAllButSelection = new JMenuItem(); + + JMenuItem hideAllSelection = new JMenuItem(); + + JMenuItem showAllhidden = new JMenuItem(); + protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem(); + JMenuItem invertColSel = new JMenuItem(); + protected JTabbedPane tabbedPane = new JTabbedPane(); + JMenuItem save = new JMenuItem(); + protected JMenuItem reload = new JMenuItem(); + JMenuItem newView = new JMenuItem(); + JMenuItem textColour = new JMenuItem(); + JMenu formatMenu = new JMenu(); + JMenu selectMenu = 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(); + JMenuItem pageSetup = new JMenuItem(); + JMenuItem alignmentProperties = new JMenuItem(); + + JMenu tooltipSettingsMenu = new JMenu(); + + private JMenuItem justifyLeftMenuItem = new JMenuItem(); + + private JMenuItem justifyRightMenuItem = new JMenuItem(); + + JMenu autoAnnMenu = new JMenu(); + + 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 JMenuItem grpsFromSelection = new JMenuItem(); + public GAlignFrame() { try @@ -159,8 +359,8 @@ public class GAlignFrame // dynamically fill save as menu with available formats for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++) { - JMenuItem item = new JMenuItem(jalview.io.FormatAdapter. - WRITEABLE_FORMATS[i]); + JMenuItem item = new JMenuItem( + jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]); item.addActionListener(new java.awt.event.ActionListener() { @@ -172,12 +372,11 @@ public class GAlignFrame outputTextboxMenu.add(item); } - } - catch (Exception e) + } catch (Exception e) { } - if (!System.getProperty("os.name").startsWith("Mac")) + if (!new jalview.util.Platform().isAMac()) { closeMenuItem.setMnemonic('C'); outputTextboxMenu.setMnemonic('T'); @@ -191,32 +390,32 @@ public class GAlignFrame if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null) { - java.util.Enumeration userColours = jalview.gui.UserDefinedColours. - getUserColourSchemes().keys(); + java.util.Enumeration userColours = jalview.gui.UserDefinedColours + .getUserColourSchemes().keys(); while (userColours.hasMoreElements()) { final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem( - userColours. - nextElement().toString()); + userColours.nextElement().toString()); radioItem.setName("USER_DEFINED"); radioItem.addMouseListener(new MouseAdapter() { public void mousePressed(MouseEvent evt) { - if (evt.isControlDown() || SwingUtilities.isRightMouseButton(evt)) + if (evt.isControlDown() + || SwingUtilities.isRightMouseButton(evt)) { radioItem.removeActionListener(radioItem.getActionListeners()[0]); - int option = JOptionPane.showInternalConfirmDialog(jalview.gui. - Desktop.desktop, - "Remove from default list?", - "Remove user defined colour", - JOptionPane.YES_NO_OPTION); + int option = JOptionPane.showInternalConfirmDialog( + jalview.gui.Desktop.desktop, + MessageManager.getString("label.remove_from_default_list"), + MessageManager.getString("label.remove_user_defined_colour"), + JOptionPane.YES_NO_OPTION); if (option == JOptionPane.YES_OPTION) { - jalview.gui.UserDefinedColours.removeColourFromDefaults( - radioItem.getText()); + jalview.gui.UserDefinedColours + .removeColourFromDefaults(radioItem.getText()); colourMenu.remove(radioItem); } else @@ -256,8 +455,12 @@ public class GAlignFrame colours.add(PIDColour); colours.add(BLOSUM62Colour); colours.add(nucleotideColour); + colours.add(purinePyrimidineColour); + // colours.add(covariationColour); + colours.add(tcoffeeColour); - setColourSelected(jalview.bin.Cache.getDefault("DEFAULT_COLOUR", "None")); + setColourSelected(jalview.bin.Cache + .getDefault("DEFAULT_COLOUR", "None")); } @@ -266,85 +469,101 @@ public class GAlignFrame if (defaultColour != null) { - int index = ColourSchemeProperty.getColourIndexFromName(defaultColour); + int index = ColourSchemeProperty + .getColourIndexFromName(defaultColour); switch (index) { - case ColourSchemeProperty.NONE: - noColourmenuItem.setSelected(true); - break; - case ColourSchemeProperty.CLUSTAL: - clustalColour.setSelected(true); + case ColourSchemeProperty.CLUSTAL: + clustalColour.setSelected(true); + + break; + + case ColourSchemeProperty.BLOSUM: + BLOSUM62Colour.setSelected(true); - break; + break; - case ColourSchemeProperty.BLOSUM: - BLOSUM62Colour.setSelected(true); + case ColourSchemeProperty.PID: + PIDColour.setSelected(true); - break; + break; - case ColourSchemeProperty.PID: - PIDColour.setSelected(true); + case ColourSchemeProperty.ZAPPO: + zappoColour.setSelected(true); - break; + break; - case ColourSchemeProperty.ZAPPO: - zappoColour.setSelected(true); + case ColourSchemeProperty.TAYLOR: + taylorColour.setSelected(true); + break; - break; + case ColourSchemeProperty.HYDROPHOBIC: + hydrophobicityColour.setSelected(true); - case ColourSchemeProperty.TAYLOR: - taylorColour.setSelected(true); - break; + break; - case ColourSchemeProperty.HYDROPHOBIC: - hydrophobicityColour.setSelected(true); + case ColourSchemeProperty.HELIX: + helixColour.setSelected(true); - break; + break; - case ColourSchemeProperty.HELIX: - helixColour.setSelected(true); + case ColourSchemeProperty.STRAND: + strandColour.setSelected(true); - break; + break; - case ColourSchemeProperty.STRAND: - strandColour.setSelected(true); + case ColourSchemeProperty.TURN: + turnColour.setSelected(true); - break; + break; - case ColourSchemeProperty.TURN: - turnColour.setSelected(true); + case ColourSchemeProperty.BURIED: + buriedColour.setSelected(true); - break; + break; - case ColourSchemeProperty.BURIED: - buriedColour.setSelected(true); + case ColourSchemeProperty.NUCLEOTIDE: + nucleotideColour.setSelected(true); - break; + break; - case ColourSchemeProperty.NUCLEOTIDE: - nucleotideColour.setSelected(true); + case ColourSchemeProperty.TCOFFEE: + tcoffeeColour.setSelected(true); + break; - break; + case ColourSchemeProperty.PURINEPYRIMIDINE: + purinePyrimidineColour.setSelected(true); - case ColourSchemeProperty.USER_DEFINED: - userDefinedColour.setSelected(true); + break; + /* + * case ColourSchemeProperty.COVARIATION: + * covariationColour.setSelected(true); + * + * break; + */ + case ColourSchemeProperty.USER_DEFINED: + userDefinedColour.setSelected(true); + + break; + case ColourSchemeProperty.NONE: + default: + noColourmenuItem.setSelected(true); + break; - break; } } } - private void jbInit() - throws Exception + private void jbInit() throws Exception { - fileMenu.setText("File"); - saveAs.setText("Save As..."); - saveAs.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event. - KeyEvent.VK_S, - Toolkit.getDefaultToolkit().getMenuShortcutKeyMask() | - java.awt.event.KeyEvent.SHIFT_MASK, false)); + fileMenu.setText(MessageManager.getString("action.file")); + saveAs.setText(MessageManager.getString("action.save_as") + "..."); + saveAs.setAccelerator(javax.swing.KeyStroke.getKeyStroke( + java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit() + .getMenuShortcutKeyMask() + | java.awt.event.KeyEvent.SHIFT_MASK, false)); saveAs.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -352,9 +571,10 @@ public class GAlignFrame saveAs_actionPerformed(e); } }); - closeMenuItem.setText("Close"); - closeMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt. - event.KeyEvent.VK_W, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false)); + closeMenuItem.setText(MessageManager.getString("action.close")); + closeMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke( + java.awt.event.KeyEvent.VK_W, Toolkit.getDefaultToolkit() + .getMenuShortcutKeyMask(), false)); closeMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -362,93 +582,123 @@ public class GAlignFrame closeMenuItem_actionPerformed(false); } }); - editMenu.setText("Edit"); - viewMenu.setText("View"); - colourMenu.setText("Colour"); - calculateMenu.setText("Calculate"); - webService.setText("Web Service"); - selectAllSequenceMenuItem.setText("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("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("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); - } - }); - remove2LeftMenuItem.setText("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("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("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("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() + 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) { - removeAllGapsMenuItem_actionPerformed(e); + makeGrpsFromSelection_actionPerformed(e); } }); - viewBoxesMenuItem.setText("Boxes"); + + 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() { @@ -457,7 +707,7 @@ public class GAlignFrame viewBoxesMenuItem_actionPerformed(e); } }); - viewTextMenuItem.setText("Text"); + viewTextMenuItem.setText(MessageManager.getString("action.text")); viewTextMenuItem.setState(true); viewTextMenuItem.addActionListener(new java.awt.event.ActionListener() { @@ -466,15 +716,26 @@ public class GAlignFrame viewTextMenuItem_actionPerformed(e); } }); - sortPairwiseMenuItem.setText("by Pairwise Identity"); - sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - sortPairwiseMenuItem_actionPerformed(e); - } - }); - sortIDMenuItem.setText("by ID"); + 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) @@ -482,7 +743,16 @@ public class GAlignFrame sortIDMenuItem_actionPerformed(e); } }); - sortGroupMenuItem.setText("by Group"); + 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) @@ -490,28 +760,28 @@ public class GAlignFrame sortGroupMenuItem_actionPerformed(e); } }); - removeRedundancyMenuItem.setText("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("Pairwise Alignments..."); - pairwiseAlignmentMenuItem.addActionListener(new java.awt.event. - ActionListener() - { - public void actionPerformed(ActionEvent e) - { - pairwiseAlignmentMenuItem_actionPerformed(e); - } - }); - PCAMenuItem.setText("Principal Component Analysis"); + 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) @@ -519,32 +789,33 @@ public class GAlignFrame PCAMenuItem_actionPerformed(e); } }); - averageDistanceTreeMenuItem.setText( - "Average Distance Using % Identity"); - averageDistanceTreeMenuItem.addActionListener(new java.awt.event. - ActionListener() - { - public void actionPerformed(ActionEvent e) - { - averageDistanceTreeMenuItem_actionPerformed(e); - } - }); - neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity"); - neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - neighbourTreeMenuItem_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("Status bar"); - outputTextboxMenu.setText("Output to Textbox"); - clustalColour.setText("Clustalx"); + 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() { @@ -553,7 +824,7 @@ public class GAlignFrame clustalColour_actionPerformed(e); } }); - zappoColour.setText("Zappo"); + zappoColour.setText(MessageManager.getString("label.zappo")); zappoColour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -561,7 +832,7 @@ public class GAlignFrame zappoColour_actionPerformed(e); } }); - taylorColour.setText("Taylor"); + taylorColour.setText(MessageManager.getString("label.taylor")); taylorColour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -569,15 +840,16 @@ public class GAlignFrame taylorColour_actionPerformed(e); } }); - hydrophobicityColour.setText("Hydrophobicity"); - hydrophobicityColour.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - hydrophobicityColour_actionPerformed(e); - } - }); - helixColour.setText("Helix Propensity"); + 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) @@ -585,7 +857,7 @@ public class GAlignFrame helixColour_actionPerformed(e); } }); - strandColour.setText("Strand Propensity"); + strandColour.setText(MessageManager.getString("label.strand_propensity")); strandColour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -593,7 +865,7 @@ public class GAlignFrame strandColour_actionPerformed(e); } }); - turnColour.setText("Turn Propensity"); + turnColour.setText(MessageManager.getString("Turn Propensity")); turnColour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -601,7 +873,7 @@ public class GAlignFrame turnColour_actionPerformed(e); } }); - buriedColour.setText("Buried Index"); + buriedColour.setText(MessageManager.getString("Buried Index")); buriedColour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -609,7 +881,7 @@ public class GAlignFrame buriedColour_actionPerformed(e); } }); - userDefinedColour.setText("User Defined..."); + userDefinedColour.setText(MessageManager.getString("action.user_defined")); userDefinedColour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -617,7 +889,7 @@ public class GAlignFrame userDefinedColour_actionPerformed(e); } }); - PIDColour.setText("Percentage Identity"); + PIDColour.setText(MessageManager.getString("label.percentage_identity")); PIDColour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -625,182 +897,339 @@ public class GAlignFrame PIDColour_actionPerformed(e); } }); - BLOSUM62Colour.setText("BLOSUM62 Score"); + BLOSUM62Colour.setText(MessageManager.getString("label.blosum62_score")); BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { - BLOSUM62Colour_actionPerformed(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); } }); - avDistanceTreeBlosumMenuItem.setText( - "Average Distance Using BLOSUM62"); - avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event. - ActionListener() + wrapMenuItem.setText(MessageManager.getString("labe.wrap")); + wrapMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { - avTreeBlosumMenuItem_actionPerformed(e); + wrapMenuItem_actionPerformed(e); } }); - njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62"); - njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener() + printMenuItem.setText(MessageManager.getString("action.print") + "..."); + printMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke( + java.awt.event.KeyEvent.VK_P, Toolkit.getDefaultToolkit() + .getMenuShortcutKeyMask(), false)); + printMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { - njTreeBlosumMenuItem_actionPerformed(e); + printMenuItem_actionPerformed(e); } }); - annotationPanelMenuItem.setActionCommand(""); - annotationPanelMenuItem.setText("Show Annotations"); - annotationPanelMenuItem.setState(jalview.bin.Cache.getDefault( - "SHOW_ANNOTATIONS", true)); - annotationPanelMenuItem.addActionListener(new java.awt.event.ActionListener() + renderGapsMenuItem.setText(MessageManager.getString("action.show_gaps")); + renderGapsMenuItem.setState(true); + renderGapsMenuItem + .addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + renderGapsMenuItem_actionPerformed(e); + } + }); + findMenuItem.setText(MessageManager.getString("action.find")); + findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke( + java.awt.event.KeyEvent.VK_F, Toolkit.getDefaultToolkit() + .getMenuShortcutKeyMask(), false)); + findMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { - annotationPanelMenuItem_actionPerformed(e); + findMenuItem_actionPerformed(e); } }); - colourTextMenuItem.setText("Colour Text"); - colourTextMenuItem.addActionListener(new java.awt.event.ActionListener() + abovePIDThreshold.setText(MessageManager.getString("label.above_identity_threshold")); + abovePIDThreshold.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { - colourTextMenuItem_actionPerformed(e); + abovePIDThreshold_actionPerformed(e); } }); - htmlMenuItem.setText("HTML"); - htmlMenuItem.addActionListener(new java.awt.event.ActionListener() + showSeqFeatures.setText(MessageManager.getString("label.show_sequence_features")); + showSeqFeatures.addActionListener(new ActionListener() { - public void actionPerformed(ActionEvent e) + public void actionPerformed(ActionEvent actionEvent) { - htmlMenuItem_actionPerformed(e); + showSeqFeatures_actionPerformed(actionEvent); } }); - overviewMenuItem.setText("Overview Window"); - overviewMenuItem.addActionListener(new java.awt.event.ActionListener() + /* + * 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() { + public void actionPerformed(ActionEvent e) { - overviewMenuItem_actionPerformed(e); + showDbRefs_actionPerformed(e); } + }); - undoMenuItem.setEnabled(false); - undoMenuItem.setText("Undo"); - undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke( - java.awt.event.KeyEvent.VK_Z, - Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false)); - undoMenuItem.addActionListener(new java.awt.event.ActionListener() + showNpFeatsMenuitem.setText(MessageManager.getString("label.show_non_positional_features")); + showNpFeatsMenuitem.addActionListener(new ActionListener() { + public void actionPerformed(ActionEvent e) { - undoMenuItem_actionPerformed(e); + showNpFeats_actionPerformed(e); } + }); - redoMenuItem.setEnabled(false); - redoMenuItem.setText("Redo"); - redoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt. - event.KeyEvent.VK_Y, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false)); - redoMenuItem.addActionListener(new java.awt.event.ActionListener() + showGroupConservation.setText(MessageManager.getString("label.group_conservation")); + showGroupConservation.addActionListener(new ActionListener() { + public void actionPerformed(ActionEvent e) { - redoMenuItem_actionPerformed(e); + showGroupConservation_actionPerformed(e); } + }); - conservationMenuItem.setText("By Conservation"); - conservationMenuItem.addActionListener(new java.awt.event.ActionListener() + + showGroupConsensus.setText(MessageManager.getString("label.group_consensus")); + showGroupConsensus.addActionListener(new ActionListener() { + public void actionPerformed(ActionEvent e) { - conservationMenuItem_actionPerformed(e); + showGroupConsensus_actionPerformed(e); } + }); - noColourmenuItem.setText("None"); - noColourmenuItem.addActionListener(new java.awt.event.ActionListener() + showConsensusHistogram.setText(MessageManager.getString("label.show_consensus_histogram")); + showConsensusHistogram.addActionListener(new ActionListener() { + public void actionPerformed(ActionEvent e) { - noColourmenuItem_actionPerformed(e); + showConsensusHistogram_actionPerformed(e); } + }); - wrapMenuItem.setText("Wrap"); - wrapMenuItem.addActionListener(new java.awt.event.ActionListener() + showSequenceLogo.setText(MessageManager.getString("label.show_consensus_logo")); + showSequenceLogo.addActionListener(new ActionListener() { + public void actionPerformed(ActionEvent e) { - wrapMenuItem_actionPerformed(e); + showSequenceLogo_actionPerformed(e); } + }); - printMenuItem.setText("Print ..."); - printMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt. - event.KeyEvent.VK_P, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false)); - printMenuItem.addActionListener(new java.awt.event.ActionListener() + normaliseSequenceLogo.setText(MessageManager.getString("label.norm_consensus_logo")); + normaliseSequenceLogo.addActionListener(new ActionListener() { + public void actionPerformed(ActionEvent e) { - printMenuItem_actionPerformed(e); + normaliseSequenceLogo_actionPerformed(e); } + }); - renderGapsMenuItem.setText("Show Gaps"); - renderGapsMenuItem.setState(true); - renderGapsMenuItem.addActionListener(new java.awt.event.ActionListener() + applyAutoAnnotationSettings.setText(MessageManager.getString("label.apply_all_groups")); + applyAutoAnnotationSettings.setState(false); + applyAutoAnnotationSettings.setVisible(true); + applyAutoAnnotationSettings.addActionListener(new ActionListener() { + public void actionPerformed(ActionEvent e) { - renderGapsMenuItem_actionPerformed(e); + applyAutoAnnotationSettings_actionPerformed(e); } + }); - findMenuItem.setText("Find..."); - findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke( - java.awt.event.KeyEvent.VK_F, - Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false)); - findMenuItem.addActionListener(new java.awt.event.ActionListener() + + nucleotideColour.setText(MessageManager.getString("label.nucleotide")); + nucleotideColour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { - findMenuItem_actionPerformed(e); + nucleotideColour_actionPerformed(e); } }); - abovePIDThreshold.setText("Above Identity Threshold"); - abovePIDThreshold.addActionListener(new java.awt.event.ActionListener() + + tcoffeeColour.setText(MessageManager.getString("label.tcoffee_scores")); + tcoffeeColour.setEnabled(false); + tcoffeeColour.addActionListener(new ActionListener() { + + @Override public void actionPerformed(ActionEvent e) { - abovePIDThreshold_actionPerformed(e); + tcoffeeColorScheme_actionPerformed(e); } }); - showSeqFeatures.setText("Show Sequence Features"); - showSeqFeatures.addActionListener(new ActionListener() + + deleteGroups.setText(MessageManager.getString("action.undefine_groups")); + deleteGroups.setAccelerator(javax.swing.KeyStroke.getKeyStroke( + java.awt.event.KeyEvent.VK_U, Toolkit.getDefaultToolkit() + .getMenuShortcutKeyMask(), false)); + deleteGroups.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent actionEvent) + public void actionPerformed(ActionEvent e) { - showSeqFeatures_actionPerformed(actionEvent); + deleteGroups_actionPerformed(e); } }); - nucleotideColour.setText("Nucleotide"); - nucleotideColour.addActionListener(new java.awt.event.ActionListener() + createGroup.setText(MessageManager.getString("action.create_groups")); + createGroup.setAccelerator(javax.swing.KeyStroke.getKeyStroke( + java.awt.event.KeyEvent.VK_G, Toolkit.getDefaultToolkit() + .getMenuShortcutKeyMask(), false)); + createGroup.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { - nucleotideColour_actionPerformed(e); + createGroup_actionPerformed(e); } }); - deleteGroups.setText("Undefine groups"); - deleteGroups.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt. - event.KeyEvent.VK_U, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false)); - deleteGroups.addActionListener(new java.awt.event.ActionListener() + unGroup.setText(MessageManager.getString("action.remove_group")); + unGroup.setAccelerator(javax.swing.KeyStroke.getKeyStroke( + java.awt.event.KeyEvent.VK_G,Toolkit.getDefaultToolkit() + .getMenuShortcutKeyMask() | java.awt.event.KeyEvent.SHIFT_MASK, false)); + unGroup.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { - deleteGroups_actionPerformed(e); + unGroup_actionPerformed(e); } }); - copy.setText("Copy"); + copy.setText(MessageManager.getString("action.copy")); copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke( - java.awt.event.KeyEvent.VK_C, - Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false)); + java.awt.event.KeyEvent.VK_C, Toolkit.getDefaultToolkit() + .getMenuShortcutKeyMask(), false)); copy.addActionListener(new java.awt.event.ActionListener() { @@ -809,10 +1238,10 @@ public class GAlignFrame copy_actionPerformed(e); } }); - cut.setText("Cut"); + cut.setText(MessageManager.getString("action.cut")); cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke( - java.awt.event.KeyEvent.VK_X, - Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false)); + java.awt.event.KeyEvent.VK_X, Toolkit.getDefaultToolkit() + .getMenuShortcutKeyMask(), false)); cut.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -820,9 +1249,9 @@ public class GAlignFrame cut_actionPerformed(e); } }); - delete.setText("Delete"); - delete.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event. - KeyEvent.VK_BACK_SPACE, 0, false)); + delete.setText(MessageManager.getString("action.delete")); + delete.setAccelerator(javax.swing.KeyStroke.getKeyStroke( + java.awt.event.KeyEvent.VK_BACK_SPACE, 0, false)); delete.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -830,12 +1259,12 @@ public class GAlignFrame delete_actionPerformed(e); } }); - pasteMenu.setText("Paste"); - pasteNew.setText("To New Alignment"); + pasteMenu.setText(MessageManager.getString("action.paste")); + pasteNew.setText(MessageManager.getString("label.to_new_alignment")); pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke( - java.awt.event.KeyEvent.VK_V, - Toolkit.getDefaultToolkit().getMenuShortcutKeyMask() | - java.awt.event.KeyEvent.SHIFT_MASK, false)); + java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit() + .getMenuShortcutKeyMask() + | java.awt.event.KeyEvent.SHIFT_MASK, false)); pasteNew.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -843,10 +1272,10 @@ public class GAlignFrame pasteNew_actionPerformed(e); } }); - pasteThis.setText("Add To This Alignment"); + pasteThis.setText(MessageManager.getString("label.to_this_alignment")); pasteThis.setAccelerator(javax.swing.KeyStroke.getKeyStroke( - java.awt.event.KeyEvent.VK_V, - Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false)); + java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit() + .getMenuShortcutKeyMask(), false)); pasteThis.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -854,7 +1283,7 @@ public class GAlignFrame pasteThis_actionPerformed(e); } }); - applyToAllGroups.setText("Apply Colour To All Groups"); + applyToAllGroups.setText(MessageManager.getString("label.apply_colour_to_all_groups")); applyToAllGroups.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -869,9 +1298,9 @@ public class GAlignFrame createPNG(null); } }); - createPNG.setActionCommand("Save As PNG Image"); + createPNG.setActionCommand(MessageManager.getString("label.save_png_image")); createPNG.setText("PNG"); - font.setText("Font..."); + font.setText(MessageManager.getString("action.font")); font.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -880,7 +1309,7 @@ public class GAlignFrame } }); - seqLimits.setText("Show Sequence Limits"); + seqLimits.setText(MessageManager.getString("label.show_sequence_limits")); seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true)); seqLimits.addActionListener(new java.awt.event.ActionListener() { @@ -897,8 +1326,8 @@ public class GAlignFrame createEPS(null); } }); - LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set"); - LoadtreeMenuItem.setText("Load Associated Tree"); + LoadtreeMenuItem.setActionCommand(MessageManager.getString("label.load_tree_for_sequence_set")); + LoadtreeMenuItem.setText(MessageManager.getString("label.load_associated_tree")); LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -906,8 +1335,9 @@ public class GAlignFrame LoadtreeMenuItem_actionPerformed(e); } }); + scaleAbove.setVisible(false); - scaleAbove.setText("Scale Above"); + scaleAbove.setText(MessageManager.getString("action.scale_above")); scaleAbove.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -917,7 +1347,7 @@ public class GAlignFrame }); scaleLeft.setVisible(false); scaleLeft.setSelected(true); - scaleLeft.setText("Scale Left"); + scaleLeft.setText(MessageManager.getString("action.scale_left")); scaleLeft.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -927,7 +1357,7 @@ public class GAlignFrame }); scaleRight.setVisible(false); scaleRight.setSelected(true); - scaleRight.setText("Scale Right"); + scaleRight.setText(MessageManager.getString("action.scale_right")); scaleRight.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -935,24 +1365,49 @@ public class GAlignFrame scaleRight_actionPerformed(e); } }); - modifyPID.setText("Modify Identity Threshold..."); - modifyPID.addActionListener(new java.awt.event.ActionListener() + centreColumnLabelsMenuItem.setVisible(true); + centreColumnLabelsMenuItem.setState(false); + centreColumnLabelsMenuItem.setText(MessageManager.getString("label.centre_column_labels")); + centreColumnLabelsMenuItem + .addActionListener(new java.awt.event.ActionListener() + { + 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() { + public void actionPerformed(ActionEvent e) { - modifyPID_actionPerformed(e); + followHighlight_actionPerformed(); } + }); - modifyConservation.setText("Modify Conservation Threshold..."); - modifyConservation.addActionListener(new java.awt.event.ActionListener() + + modifyPID.setText(MessageManager.getString("label.modify_identity_thereshold")); + modifyPID.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { - modifyConservation_actionPerformed(e); + modifyPID_actionPerformed(e); } }); - sortByTreeMenu.setText("By Tree Order"); - sort.setText("Sort"); + modifyConservation.setText(MessageManager.getString("label.modify_conservation_thereshold")); + modifyConservation + .addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + modifyConservation_actionPerformed(e); + } + }); + sortByTreeMenu.setText(MessageManager.getString("action.by_tree_order")); + sort.setText(MessageManager.getString("action.sort")); sort.addMenuListener(new MenuListener() { public void menuSelected(MenuEvent e) @@ -968,32 +1423,32 @@ public class GAlignFrame { } }); - sortByAnnotScore.setText("by Score"); + sortByAnnotScore.setText(MessageManager.getString("label.sort_by_score")); sort.add(sortByAnnotScore); - sortByAnnotScore.addMenuListener( - new javax.swing.event.MenuListener() { - - public void menuCanceled(MenuEvent e) - { - } + sortByAnnotScore.addMenuListener(new javax.swing.event.MenuListener() + { - public void menuDeselected(MenuEvent e) - { - } + public void menuCanceled(MenuEvent e) + { + } - public void menuSelected(MenuEvent e) - { - buildSortByAnnotationScoresMenu(); - } - } - ); + public void menuDeselected(MenuEvent e) + { + } + + public void menuSelected(MenuEvent e) + { + buildSortByAnnotationScoresMenu(); + } + }); sortByAnnotScore.setVisible(false); - - calculate.setText("Calculate Tree"); - jMenu2.setText("Export Image"); - padGapsMenuitem.setText("Pad Gaps"); - padGapsMenuitem.setState(jalview.bin.Cache.getDefault("PAD_GAPS", false)); + calculateTree.setText(MessageManager.getString("action.calculate_tree")); + + jMenu2.setText(MessageManager.getString("label.export_image")); + padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps")); + padGapsMenuitem.setState(jalview.bin.Cache + .getDefault("PAD_GAPS", false)); padGapsMenuitem.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -1002,7 +1457,7 @@ public class GAlignFrame } }); vamsasStore.setVisible(false); - vamsasStore.setText("VAMSAS store"); + vamsasStore.setText(MessageManager.getString("label.vamsas_store")); vamsasStore.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -1010,7 +1465,7 @@ public class GAlignFrame vamsasStore_actionPerformed(e); } }); - showTranslation.setText("Translate cDNA"); + showTranslation.setText(MessageManager.getString("label.translate_cDNA")); showTranslation.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -1018,7 +1473,7 @@ public class GAlignFrame showTranslation_actionPerformed(e); } }); - extractScores.setText("Extract Scores..."); + extractScores.setText(MessageManager.getString("label.extract_scores") + "..."); extractScores.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -1026,16 +1481,24 @@ public class GAlignFrame extractScores_actionPerformed(e); } }); - extractScores.setVisible(false); // JBPNote: TODO: make gui for regex based score extraction - featureSettings.setText("Feature Settings..."); - featureSettings.addActionListener(new ActionListener() + extractScores.setVisible(true); // JBPNote: TODO: make gui for regex based + // score extraction + showProducts.setText(MessageManager.getString("label.get_cross_refs")); + /* + * showProducts.addActionListener(new ActionListener() { + * + * public void actionPerformed(ActionEvent e) { + * showProducts_actionPerformed(e); } }); + */ + openFeatureSettings.setText(MessageManager.getString("label.feature_settings")); + openFeatureSettings.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { featureSettings_actionPerformed(e); } }); - fetchSequence.setText("Fetch Sequence(s)..."); + fetchSequence.setText(MessageManager.getString("label.fetch_sequences")); fetchSequence.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -1044,7 +1507,7 @@ public class GAlignFrame } }); - annotationColour.setText("By Annotation..."); + annotationColour.setText(MessageManager.getString("action.by_annotation")); annotationColour.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -1052,7 +1515,17 @@ public class GAlignFrame annotationColour_actionPerformed(e); } }); - associatedData.setText("Load Features / Annotations"); + + rnahelicesColour.setText(MessageManager.getString("action.by_rna_helixes")); + rnahelicesColour.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + rnahelicesColour_actionPerformed(e); + } + }); + + associatedData.setText(MessageManager.getString("label.load_features_annotations")); associatedData.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -1060,8 +1533,9 @@ public class GAlignFrame associatedData_actionPerformed(e); } }); - autoCalculate.setText("Autocalculate Consensus"); - autoCalculate.setState(jalview.bin.Cache.getDefault("AUTO_CALC_CONSENSUS", true)); + autoCalculate.setText(MessageManager.getString("label.autocalculate_consensus")); + autoCalculate.setState(jalview.bin.Cache.getDefault( + "AUTO_CALC_CONSENSUS", true)); autoCalculate.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -1069,8 +1543,33 @@ public class GAlignFrame autoCalculate_actionPerformed(e); } }); - addSequenceMenu.setText("Add Sequences"); - addFromFile.setText("From File"); + 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() + { + 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() + { + public void actionPerformed(ActionEvent e) + { + listenToViewSelections_actionPerformed(e); + } + }); + + addSequenceMenu.setText(MessageManager.getString("label.add_sequences")); + addFromFile.setText(MessageManager.getString("label.from_file")); addFromFile.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -1078,7 +1577,7 @@ public class GAlignFrame addFromFile_actionPerformed(e); } }); - addFromText.setText("From Textbox"); + addFromText.setText(MessageManager.getString("label.from_textbox")); addFromText.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -1086,7 +1585,7 @@ public class GAlignFrame addFromText_actionPerformed(e); } }); - addFromURL.setText("From URL"); + addFromURL.setText(MessageManager.getString("label.from_url")); addFromURL.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -1094,7 +1593,7 @@ public class GAlignFrame addFromURL_actionPerformed(e); } }); - exportFeatures.setText("Export Features..."); + exportFeatures.setText(MessageManager.getString("label.export_features")); exportFeatures.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -1102,7 +1601,7 @@ public class GAlignFrame exportFeatures_actionPerformed(e); } }); - exportAnnotations.setText("Export Annotations..."); + exportAnnotations.setText(MessageManager.getString("label.export_annotations")); exportAnnotations.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -1111,8 +1610,9 @@ public class GAlignFrame } }); statusPanel.setLayout(gridLayout1); - jMenu3.setText("Show"); - showAllSeqs.setText("All Sequences"); + jMenu3.setText(MessageManager.getString("action.show")); + showAllSeqs.setText(MessageManager.getString("label.all_sequences")); + showAllSeqs.setToolTipText(MessageManager.getString("label.toggle_sequence_visibility")); showAllSeqs.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -1120,7 +1620,8 @@ public class GAlignFrame showAllSeqs_actionPerformed(e); } }); - showAllColumns.setText("All Columns"); + showAllColumns.setText(MessageManager.getString("label.all_columns")); + showAllColumns.setToolTipText(MessageManager.getString("label.toggle_columns_visibility")); showAllColumns.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -1128,8 +1629,9 @@ public class GAlignFrame showAllColumns_actionPerformed(e); } }); - hideMenu.setText("Hide"); - hideSelSequences.setText("Selected Sequences"); + hideMenu.setText(MessageManager.getString("action.hide")); + hideSelSequences.setText(MessageManager.getString("label.selected_sequences")); + hideSelSequences.setToolTipText(MessageManager.getString("label.toggle_sequence_visibility")); hideSelSequences.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -1137,7 +1639,8 @@ public class GAlignFrame hideSelSequences_actionPerformed(e); } }); - hideSelColumns.setText("Selected Columns"); + hideSelColumns.setText(MessageManager.getString("label.selected_columns")); + hideSelColumns.setToolTipText(MessageManager.getString("label.toggle_columns_visibility")); hideSelColumns.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -1145,7 +1648,35 @@ public class GAlignFrame hideSelColumns_actionPerformed(e); } }); - hiddenMarkers.setText("Show Hidden Markers"); + hideAllSelection.setText(MessageManager.getString("label.selected_region")); + hideAllSelection.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + hideAllSelection_actionPerformed(e); + } + }); + // TODO: should be hidden if no selection exists. + hideAllButSelection.setText(MessageManager.getString("label.all_but_selected_region")); + hideAllButSelection.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + hideAllButSelection_actionPerformed(e); + } + }); + showAllhidden.setText(MessageManager.getString("label.all_sequences_columns")); + showAllhidden + .setToolTipText(MessageManager.getString("label.toggles_visibility_hidden_selected_regions")); + showAllhidden.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + showAllhidden_actionPerformed(e); + } + }); + + hiddenMarkers.setText(MessageManager.getString("action.show_hidden_markers")); hiddenMarkers.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -1153,12 +1684,11 @@ public class GAlignFrame hiddenMarkers_actionPerformed(e); } }); - invertColSel.setText("Invert Column Selection"); - invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt. - event.KeyEvent.VK_I, - Toolkit.getDefaultToolkit().getMenuShortcutKeyMask() - | java.awt.event.KeyEvent.ALT_MASK, - false)); + invertColSel.setText(MessageManager.getString("action.invert_column_selection")); + invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke( + java.awt.event.KeyEvent.VK_I, Toolkit.getDefaultToolkit() + .getMenuShortcutKeyMask() + | java.awt.event.KeyEvent.ALT_MASK, false)); invertColSel.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -1189,9 +1719,10 @@ public class GAlignFrame tabbedPane_focusGained(e); } }); - save.setText("Save"); - save.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event. - KeyEvent.VK_S, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false)); + save.setText(MessageManager.getString("action.save")); + save.setAccelerator(javax.swing.KeyStroke.getKeyStroke( + java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit() + .getMenuShortcutKeyMask(), false)); save.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -1200,7 +1731,7 @@ public class GAlignFrame } }); reload.setEnabled(false); - reload.setText("Reload"); + reload.setText(MessageManager.getString("action.reload")); reload.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -1208,9 +1739,10 @@ public class GAlignFrame reload_actionPerformed(e); } }); - newView.setText("New View"); - newView.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event. - KeyEvent.VK_T, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false)); + newView.setText(MessageManager.getString("action.new_view")); + newView.setAccelerator(javax.swing.KeyStroke.getKeyStroke( + java.awt.event.KeyEvent.VK_T, Toolkit.getDefaultToolkit() + .getMenuShortcutKeyMask(), false)); newView.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -1218,10 +1750,8 @@ public class GAlignFrame newView_actionPerformed(e); } }); - tabbedPane.setToolTipText(" Right-click to rename tab" - + - "
Press X to eXpand tabs, G to reGroup."); - textColour.setText("Text Colour"); + tabbedPane.setToolTipText("" + MessageManager.getString("label.rename_tab_eXpand_reGroup") + ""); + textColour.setText(MessageManager.getString("label.colour_text") + "..."); textColour.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -1229,9 +1759,9 @@ public class GAlignFrame textColour_actionPerformed(e); } }); - formatMenu.setText("Format"); - selectMenu.setText("Select"); - idRightAlign.setText("Right Align Sequence Id"); + formatMenu.setText(MessageManager.getString("action.format")); + selectMenu.setText(MessageManager.getString("action.select")); + idRightAlign.setText(MessageManager.getString("label.right_align_sequence_id")); idRightAlign.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -1240,9 +1770,9 @@ public class GAlignFrame } }); gatherViews.setEnabled(false); - gatherViews.setText("Gather Views"); - gatherViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt. - event.KeyEvent.VK_G, 0, false)); + gatherViews.setText(MessageManager.getString("action.gather_views")); + gatherViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke( + java.awt.event.KeyEvent.VK_G, 0, false)); gatherViews.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -1251,9 +1781,9 @@ public class GAlignFrame } }); expandViews.setEnabled(false); - expandViews.setText("Expand Views"); - expandViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt. - event.KeyEvent.VK_X, 0, false)); + expandViews.setText(MessageManager.getString("action.expand_views")); + expandViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke( + java.awt.event.KeyEvent.VK_X, 0, false)); expandViews.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -1261,7 +1791,7 @@ public class GAlignFrame expandViews_actionPerformed(e); } }); - pageSetup.setText("Page Setup ..."); + pageSetup.setText(MessageManager.getString("action.page_setup") + "..."); pageSetup.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -1269,7 +1799,7 @@ public class GAlignFrame pageSetup_actionPerformed(e); } }); - alignmentProperties.setText("Alignment Properties..."); + alignmentProperties.setText(MessageManager.getString("label.alignment_props") + "..."); alignmentProperties.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent actionEvent) @@ -1277,7 +1807,8 @@ public class GAlignFrame alignmentProperties(); } }); - + tooltipSettingsMenu.setText(MessageManager.getString("label.sequence_id_tooltip")); + autoAnnMenu.setText(MessageManager.getString("label.autocalculated_annotation")); alignFrameMenuBar.add(fileMenu); alignFrameMenuBar.add(editMenu); alignFrameMenuBar.add(selectMenu); @@ -1317,6 +1848,11 @@ public class GAlignFrame 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); viewMenu.add(newView); viewMenu.add(expandViews); @@ -1325,10 +1861,24 @@ public class GAlignFrame viewMenu.add(jMenu3); viewMenu.add(hideMenu); viewMenu.addSeparator(); + viewMenu.add(followHighlightMenuItem); viewMenu.add(annotationPanelMenuItem); + autoAnnMenu.add(applyAutoAnnotationSettings); + autoAnnMenu.add(showConsensusHistogram); + autoAnnMenu.add(showSequenceLogo); + autoAnnMenu.add(normaliseSequenceLogo); + autoAnnMenu.addSeparator(); + autoAnnMenu.add(showGroupConservation); + autoAnnMenu.add(showGroupConsensus); + viewMenu.add(autoAnnMenu); viewMenu.addSeparator(); viewMenu.add(showSeqFeatures); - viewMenu.add(featureSettings); + // viewMenu.add(showSeqFeaturesHeight); + + viewMenu.add(openFeatureSettings); + tooltipSettingsMenu.add(showDbRefsMenuitem); + tooltipSettingsMenu.add(showNpFeatsMenuitem); + viewMenu.add(tooltipSettingsMenu); viewMenu.addSeparator(); viewMenu.add(alignmentProperties); viewMenu.addSeparator(); @@ -1348,6 +1898,9 @@ public class GAlignFrame colourMenu.add(turnColour); colourMenu.add(buriedColour); colourMenu.add(nucleotideColour); + colourMenu.add(purinePyrimidineColour); + // colourMenu.add(covariationColour); + colourMenu.add(tcoffeeColour); colourMenu.add(userDefinedColour); colourMenu.addSeparator(); colourMenu.add(conservationMenuItem); @@ -1355,28 +1908,32 @@ public class GAlignFrame colourMenu.add(abovePIDThreshold); colourMenu.add(modifyPID); colourMenu.add(annotationColour); + colourMenu.add(rnahelicesColour); calculateMenu.add(sort); - calculateMenu.add(calculate); + calculateMenu.add(calculateTree); calculateMenu.addSeparator(); calculateMenu.add(pairwiseAlignmentMenuItem); calculateMenu.add(PCAMenuItem); calculateMenu.addSeparator(); calculateMenu.add(showTranslation); + calculateMenu.add(showProducts); calculateMenu.add(autoCalculate); + calculateMenu.add(sortByTree); calculateMenu.addSeparator(); calculateMenu.add(extractScores); - webServiceNoServices = new JMenuItem(""); + webServiceNoServices = new JMenuItem(MessageManager.getString("label.no_services")); webService.add(webServiceNoServices); pasteMenu.add(pasteNew); pasteMenu.add(pasteThis); sort.add(sortIDMenuItem); + sort.add(sortLengthMenuItem); sort.add(sortGroupMenuItem); sort.add(sortPairwiseMenuItem); sort.add(sortByTreeMenu); - calculate.add(averageDistanceTreeMenuItem); - calculate.add(neighbourTreeMenuItem); - calculate.add(avDistanceTreeBlosumMenuItem); - calculate.add(njTreeBlosumMenuItem); + calculateTree.add(averageDistanceTreeMenuItem); + calculateTree.add(neighbourTreeMenuItem); + calculateTree.add(avDistanceTreeBlosumMenuItem); + calculateTree.add(njTreeBlosumMenuItem); jMenu2.add(htmlMenuItem); jMenu2.add(epsFile); jMenu2.add(createPNG); @@ -1388,8 +1945,12 @@ public class GAlignFrame this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER); jMenu3.add(showAllColumns); jMenu3.add(showAllSeqs); + jMenu3.add(showAllhidden); hideMenu.add(hideSelColumns); hideMenu.add(hideSelSequences); + hideMenu.add(hideAllSelection); + hideMenu.add(hideAllButSelection); + formatMenu.add(font); formatMenu.addSeparator(); formatMenu.add(wrapMenuItem); @@ -1403,13 +1964,139 @@ public class GAlignFrame 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); + // 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) + { + // TODO Auto-generated method stub + + } + + protected void hideAllButSelection_actionPerformed(ActionEvent e) + { + // TODO Auto-generated method stub + + } + + protected void hideAllSelection_actionPerformed(ActionEvent e) + { + // TODO Auto-generated method stub + + } + + protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e) + { + // TODO Auto-generated method stub + + } + + protected void showConsensusHistogram_actionPerformed(ActionEvent e) + { + // TODO Auto-generated method stub + + } + + protected void showSequenceLogo_actionPerformed(ActionEvent e) + { + // TODO Auto-generated method stub + + } + + protected void makeGrpsFromSelection_actionPerformed(ActionEvent e) + { + // TODO Auto-generated method stub + + } + + protected void showGroupConsensus_actionPerformed(ActionEvent e) + { + // TODO Auto-generated method stub + + } + + protected void showGroupConservation_actionPerformed(ActionEvent e) + { + // TODO Auto-generated method stub + + } + + protected void showUnconservedMenuItem_actionPerformed(ActionEvent e) + { + // TODO Auto-generated method stub + + } + + protected void showSeqFeaturesHeight_actionPerformed( + ActionEvent actionEvent) + { + // TODO Auto-generated method stub + + } + + protected void justifyRightMenuItem_actionPerformed(ActionEvent e) + { + // TODO Auto-generated method stub + + } + + protected void justifyLeftMenuItem_actionPerformed(ActionEvent e) + { + // TODO Auto-generated method stub + + } + + protected void followHighlight_actionPerformed() + { + // TODO Auto-generated method stub + + } + + protected void showNpFeats_actionPerformed(ActionEvent e) + { + // TODO Auto-generated method stub + + } + + protected void showDbRefs_actionPerformed(ActionEvent e) + { + // TODO Auto-generated method stub + + } + + protected void centreColumnLabels_actionPerformed(ActionEvent e) + { + } + + protected void showProducts_actionPerformed(ActionEvent e) + { } protected void buildSortByAnnotationScoresMenu() @@ -1525,6 +2212,10 @@ public class GAlignFrame { } + protected void sortLengthMenuItem_actionPerformed(ActionEvent e) + { + } + protected void sortGroupMenuItem_actionPerformed(ActionEvent e) { } @@ -1601,6 +2292,14 @@ public class GAlignFrame { } + protected void purinePyrimidineColour_actionPerformed(ActionEvent e) + { + } + + /* + * protected void covariationColour_actionPerformed(ActionEvent e) { } + */ + protected void noColourmenuItem_actionPerformed(ActionEvent e) { } @@ -1636,6 +2335,14 @@ public class GAlignFrame protected void deleteGroups_actionPerformed(ActionEvent e) { } + + protected void createGroup_actionPerformed(ActionEvent e) + { + } + + protected void unGroup_actionPerformed(ActionEvent e) + { + } protected void copy_actionPerformed(ActionEvent e) { @@ -1684,6 +2391,33 @@ public class GAlignFrame protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) { + + } + + /** + * Template method to handle the 'load T-Coffee scores' menu event. + *

+ * Subclasses override this method to provide a custom action. + * + * @param event + * The raised event + */ + protected void loadScores_actionPerformed(ActionEvent event) + { + + } + + /** + * Template method to handle the 'Color T-Coffee scores' menu event. + *

+ * Subclasses override this method to provide a custom action. + * + * @param event + * The raised event + */ + protected void tcoffeeColorScheme_actionPerformed(ActionEvent event) + { + } protected void jpred_actionPerformed(ActionEvent e) @@ -1753,6 +2487,11 @@ public class GAlignFrame } + public void rnahelicesColour_actionPerformed(ActionEvent e) + { + + } + public void associatedData_actionPerformed(ActionEvent e) { @@ -1763,6 +2502,11 @@ public class GAlignFrame } + public void sortByTreeOption_actionPerformed(ActionEvent e) + { + + } + public void showAllSeqs_actionPerformed(ActionEvent e) { @@ -1862,7 +2606,7 @@ public class GAlignFrame { } - + public void pageSetup_actionPerformed(ActionEvent e) {