X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGAlignFrame.java;h=d3154c7408f4ff0ebbf1844e9dd3ced60d788157;hb=7ab5d6b0ba5fec1ea4a4239e79c476d841622485;hp=020e617c42ecdc3af05b022342f0080528bacfd6;hpb=00fbef61d17235b3c266e20218e056e617267cc3;p=jalview.git diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java index 020e617..d3154c7 100755 --- a/src/jalview/jbgui/GAlignFrame.java +++ b/src/jalview/jbgui/GAlignFrame.java @@ -1,30 +1,55 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) - * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) + * Copyright (C) 2014 The Jalview Authors * - * 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 file is part of Jalview. * - * 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. + * 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 this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + * 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.*; +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 { @@ -114,6 +139,17 @@ public class GAlignFrame extends JInternalFrame protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem(); + protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem(); + + protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem(); + + protected JRadioButtonMenuItem RNAInteractionColour = new JRadioButtonMenuItem(); + + // protected JRadioButtonMenuItem covariationColour = new + // JRadioButtonMenuItem(); + + protected JRadioButtonMenuItem tcoffeeColour = new JRadioButtonMenuItem(); + JMenuItem njTreeBlosumMenuItem = new JMenuItem(); JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem(); @@ -122,7 +158,7 @@ public class GAlignFrame extends JInternalFrame public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem(); - public JCheckBoxMenuItem showUnconservedMenuItem = new JCheckBoxMenuItem(); + public JCheckBoxMenuItem showNonconservedMenuItem = new JCheckBoxMenuItem(); JMenuItem htmlMenuItem = new JMenuItem(); @@ -147,12 +183,15 @@ public class GAlignFrame extends JInternalFrame public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem(); public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem(); - public JCheckBoxMenuItem showSeqFeaturesHeight = 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(); @@ -196,7 +235,9 @@ public class GAlignFrame extends JInternalFrame JMenu jMenu2 = new JMenu(); protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem(); + protected JCheckBoxMenuItem showNpFeatsMenuitem = new JCheckBoxMenuItem(); + protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem(); protected ButtonGroup colours = new ButtonGroup(); @@ -207,18 +248,26 @@ public class GAlignFrame extends JInternalFrame protected JMenuItem extractScores = new JMenuItem(); + protected JMenuItem expandAlignment = new JMenuItem(); + protected JMenu showProducts = new JMenu(); - public JMenuItem featureSettings = new JMenuItem(); + 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(); @@ -236,7 +285,7 @@ public class GAlignFrame extends JInternalFrame GridLayout gridLayout1 = new GridLayout(); JMenu jMenu3 = new JMenu(); - + JMenuItem showAllSeqs = new JMenuItem(); JMenuItem showAllColumns = new JMenuItem(); @@ -247,6 +296,12 @@ public class GAlignFrame extends JInternalFrame 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(); @@ -270,7 +325,7 @@ public class GAlignFrame extends JInternalFrame protected JCheckBoxMenuItem centreColumnLabelsMenuItem = new JCheckBoxMenuItem(); protected JCheckBoxMenuItem followHighlightMenuItem = new JCheckBoxMenuItem(); - + protected JMenuItem gatherViews = new JMenuItem(); protected JMenuItem expandViews = new JMenuItem(); @@ -278,17 +333,29 @@ public class GAlignFrame extends JInternalFrame JMenuItem pageSetup = new JMenuItem(); JMenuItem alignmentProperties = new JMenuItem(); - + JMenu tooltipSettingsMenu = new JMenu(); - private JMenuItem justifyLeftMenuItem=new JMenuItem(); + private JMenuItem justifyLeftMenuItem = new JMenuItem(); + + private JMenuItem justifyRightMenuItem = new JMenuItem(); + + JMenu autoAnnMenu = new JMenu(); + + protected JCheckBoxMenuItem showGroupConsensus = new JCheckBoxMenuItem(); - private JMenuItem justifyRightMenuItem=new JMenuItem(); - - protected JCheckBoxMenuItem showGroupConsensus=new JCheckBoxMenuItem(); - protected JCheckBoxMenuItem showGroupConservation=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 @@ -345,13 +412,14 @@ public class GAlignFrame extends JInternalFrame if (evt.isControlDown() || SwingUtilities.isRightMouseButton(evt)) { - radioItem - .removeActionListener(radioItem.getActionListeners()[0]); + radioItem.removeActionListener(radioItem.getActionListeners()[0]); int option = JOptionPane.showInternalConfirmDialog( jalview.gui.Desktop.desktop, - "Remove from default list?", - "Remove user defined colour", + MessageManager + .getString("label.remove_from_default_list"), + MessageManager + .getString("label.remove_user_defined_colour"), JOptionPane.YES_NO_OPTION); if (option == JOptionPane.YES_OPTION) { @@ -396,7 +464,10 @@ public class GAlignFrame extends JInternalFrame colours.add(PIDColour); colours.add(BLOSUM62Colour); colours.add(nucleotideColour); - + colours.add(purinePyrimidineColour); + // colours.add(covariationColour); + colours.add(tcoffeeColour); + colours.add(RNAInteractionColour); setColourSelected(jalview.bin.Cache .getDefault("DEFAULT_COLOUR", "None")); @@ -412,9 +483,6 @@ public class GAlignFrame extends JInternalFrame switch (index) { - case ColourSchemeProperty.NONE: - noColourmenuItem.setSelected(true); - break; case ColourSchemeProperty.CLUSTAL: clustalColour.setSelected(true); @@ -469,10 +537,34 @@ public class GAlignFrame extends JInternalFrame break; + case ColourSchemeProperty.TCOFFEE: + tcoffeeColour.setSelected(true); + break; + + case ColourSchemeProperty.PURINEPYRIMIDINE: + purinePyrimidineColour.setSelected(true); + + break; + + case ColourSchemeProperty.RNAINTERACTION: + RNAInteractionColour.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; + } } @@ -480,8 +572,8 @@ public class GAlignFrame extends JInternalFrame private void jbInit() throws Exception { - fileMenu.setText("File"); - saveAs.setText("Save As..."); + 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() @@ -493,7 +585,7 @@ public class GAlignFrame extends JInternalFrame saveAs_actionPerformed(e); } }); - closeMenuItem.setText("Close"); + closeMenuItem.setText(MessageManager.getString("action.close")); closeMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke( java.awt.event.KeyEvent.VK_W, Toolkit.getDefaultToolkit() .getMenuShortcutKeyMask(), false)); @@ -504,12 +596,13 @@ public class GAlignFrame extends JInternalFrame closeMenuItem_actionPerformed(false); } }); - editMenu.setText("Edit"); - viewMenu.setText("View"); - colourMenu.setText("Colour"); - calculateMenu.setText("Calculate"); - webService.setText("Web Service"); - selectAllSequenceMenuItem.setText("Select All"); + 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)); @@ -521,7 +614,8 @@ public class GAlignFrame extends JInternalFrame selectAllSequenceMenuItem_actionPerformed(e); } }); - deselectAllSequenceMenuItem.setText("Deselect All"); + deselectAllSequenceMenuItem.setText(MessageManager + .getString("action.deselect_all")); deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke .getKeyStroke(java.awt.event.KeyEvent.VK_ESCAPE, 0, false)); deselectAllSequenceMenuItem @@ -532,7 +626,8 @@ public class GAlignFrame extends JInternalFrame deselectAllSequenceMenuItem_actionPerformed(e); } }); - invertSequenceMenuItem.setText("Invert Sequence Selection"); + invertSequenceMenuItem.setText(MessageManager + .getString("action.invert_sequence_selection")); invertSequenceMenuItem.setAccelerator(javax.swing.KeyStroke .getKeyStroke(java.awt.event.KeyEvent.VK_I, Toolkit .getDefaultToolkit().getMenuShortcutKeyMask(), false)); @@ -544,16 +639,29 @@ public class GAlignFrame extends JInternalFrame invertSequenceMenuItem_actionPerformed(e); } }); - grpsFromSelection.setText("Make Groups for selection"); + grpsFromSelection.setText(MessageManager + .getString("action.make_groups_selection")); grpsFromSelection.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { makeGrpsFromSelection_actionPerformed(e); - } + } }); - - remove2LeftMenuItem.setText("Remove Left"); + expandAlignment.setText(MessageManager + .getString("action.view_flanking_regions")); + expandAlignment.setToolTipText(MessageManager + .getString("label.view_flanking_regions")); + expandAlignment.addActionListener(new java.awt.event.ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + expand_newalign(e); + } + }); + remove2LeftMenuItem.setText(MessageManager + .getString("action.remove_left")); remove2LeftMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke( java.awt.event.KeyEvent.VK_L, Toolkit.getDefaultToolkit() .getMenuShortcutKeyMask(), false)); @@ -565,7 +673,8 @@ public class GAlignFrame extends JInternalFrame remove2LeftMenuItem_actionPerformed(e); } }); - remove2RightMenuItem.setText("Remove Right"); + remove2RightMenuItem.setText(MessageManager + .getString("action.remove_right")); remove2RightMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke( java.awt.event.KeyEvent.VK_R, Toolkit.getDefaultToolkit() .getMenuShortcutKeyMask(), false)); @@ -577,7 +686,8 @@ public class GAlignFrame extends JInternalFrame remove2RightMenuItem_actionPerformed(e); } }); - removeGappedColumnMenuItem.setText("Remove Empty Columns"); + removeGappedColumnMenuItem.setText(MessageManager + .getString("action.remove_empty_columns")); removeGappedColumnMenuItem.setAccelerator(javax.swing.KeyStroke .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit .getDefaultToolkit().getMenuShortcutKeyMask(), false)); @@ -589,7 +699,8 @@ public class GAlignFrame extends JInternalFrame removeGappedColumnMenuItem_actionPerformed(e); } }); - removeAllGapsMenuItem.setText("Remove All Gaps"); + removeAllGapsMenuItem.setText(MessageManager + .getString("action.remove_all_gaps")); removeAllGapsMenuItem.setAccelerator(javax.swing.KeyStroke .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit .getDefaultToolkit().getMenuShortcutKeyMask() @@ -602,23 +713,27 @@ public class GAlignFrame extends JInternalFrame removeAllGapsMenuItem_actionPerformed(e); } }); - justifyLeftMenuItem.setText("Left Justify Alignment"); - justifyLeftMenuItem.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - justifyLeftMenuItem_actionPerformed(e); - } - }); - justifyRightMenuItem.setText("Right Justify Alignment"); - justifyRightMenuItem.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - justifyRightMenuItem_actionPerformed(e); - } - }); - viewBoxesMenuItem.setText("Boxes"); + 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() { @@ -627,7 +742,7 @@ public class GAlignFrame extends JInternalFrame viewBoxesMenuItem_actionPerformed(e); } }); - viewTextMenuItem.setText("Text"); + viewTextMenuItem.setText(MessageManager.getString("action.text")); viewTextMenuItem.setState(true); viewTextMenuItem.addActionListener(new java.awt.event.ActionListener() { @@ -636,16 +751,19 @@ public class GAlignFrame extends JInternalFrame viewTextMenuItem_actionPerformed(e); } }); - showUnconservedMenuItem.setText("Show Unconserved"); - showUnconservedMenuItem.setState(false); - showUnconservedMenuItem.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - showUnconservedMenuItem_actionPerformed(e); - } - }); - sortPairwiseMenuItem.setText("by Pairwise Identity"); + 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() { @@ -654,7 +772,7 @@ public class GAlignFrame extends JInternalFrame sortPairwiseMenuItem_actionPerformed(e); } }); - sortIDMenuItem.setText("by ID"); + sortIDMenuItem.setText(MessageManager.getString("action.by_id")); sortIDMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -662,15 +780,17 @@ public class GAlignFrame extends JInternalFrame sortIDMenuItem_actionPerformed(e); } }); - sortLengthMenuItem.setText("By Length"); - sortLengthMenuItem.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - sortLengthMenuItem_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) @@ -678,7 +798,8 @@ public class GAlignFrame extends JInternalFrame sortGroupMenuItem_actionPerformed(e); } }); - removeRedundancyMenuItem.setText("Remove Redundancy..."); + removeRedundancyMenuItem.setText(MessageManager + .getString("action.remove_redundancy")); removeRedundancyMenuItem.setAccelerator(javax.swing.KeyStroke .getKeyStroke(java.awt.event.KeyEvent.VK_D, Toolkit .getDefaultToolkit().getMenuShortcutKeyMask(), false)); @@ -690,7 +811,8 @@ public class GAlignFrame extends JInternalFrame removeRedundancyMenuItem_actionPerformed(e); } }); - pairwiseAlignmentMenuItem.setText("Pairwise Alignments..."); + pairwiseAlignmentMenuItem.setText(MessageManager + .getString("action.pairwise_alignment")); pairwiseAlignmentMenuItem .addActionListener(new java.awt.event.ActionListener() { @@ -699,7 +821,8 @@ public class GAlignFrame extends JInternalFrame pairwiseAlignmentMenuItem_actionPerformed(e); } }); - PCAMenuItem.setText("Principal Component Analysis"); + PCAMenuItem.setText(MessageManager + .getString("label.principal_component_analysis")); PCAMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -707,8 +830,8 @@ public class GAlignFrame extends JInternalFrame PCAMenuItem_actionPerformed(e); } }); - averageDistanceTreeMenuItem - .setText("Average Distance Using % Identity"); + averageDistanceTreeMenuItem.setText(MessageManager + .getString("label.average_distance_identity")); averageDistanceTreeMenuItem .addActionListener(new java.awt.event.ActionListener() { @@ -717,7 +840,8 @@ public class GAlignFrame extends JInternalFrame averageDistanceTreeMenuItem_actionPerformed(e); } }); - neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity"); + neighbourTreeMenuItem.setText(MessageManager + .getString("label.neighbour_joining_identity")); neighbourTreeMenuItem .addActionListener(new java.awt.event.ActionListener() { @@ -731,9 +855,10 @@ public class GAlignFrame extends JInternalFrame 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() { @@ -742,7 +867,7 @@ public class GAlignFrame extends JInternalFrame clustalColour_actionPerformed(e); } }); - zappoColour.setText("Zappo"); + zappoColour.setText(MessageManager.getString("label.zappo")); zappoColour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -750,7 +875,7 @@ public class GAlignFrame extends JInternalFrame zappoColour_actionPerformed(e); } }); - taylorColour.setText("Taylor"); + taylorColour.setText(MessageManager.getString("label.taylor")); taylorColour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -758,7 +883,8 @@ public class GAlignFrame extends JInternalFrame taylorColour_actionPerformed(e); } }); - hydrophobicityColour.setText("Hydrophobicity"); + hydrophobicityColour.setText(MessageManager + .getString("label.hydrophobicity")); hydrophobicityColour .addActionListener(new java.awt.event.ActionListener() { @@ -767,7 +893,7 @@ public class GAlignFrame extends JInternalFrame hydrophobicityColour_actionPerformed(e); } }); - helixColour.setText("Helix Propensity"); + helixColour.setText(MessageManager.getString("label.helix_propensity")); helixColour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -775,7 +901,8 @@ public class GAlignFrame extends JInternalFrame 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) @@ -783,7 +910,7 @@ public class GAlignFrame extends JInternalFrame strandColour_actionPerformed(e); } }); - turnColour.setText("Turn Propensity"); + turnColour.setText(MessageManager.getString("label.turn_propensity")); turnColour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -791,7 +918,7 @@ public class GAlignFrame extends JInternalFrame turnColour_actionPerformed(e); } }); - buriedColour.setText("Buried Index"); + buriedColour.setText(MessageManager.getString("label.buried_index")); buriedColour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -799,7 +926,8 @@ public class GAlignFrame extends JInternalFrame 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) @@ -807,7 +935,8 @@ public class GAlignFrame extends JInternalFrame 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) @@ -815,7 +944,8 @@ public class GAlignFrame extends JInternalFrame 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) @@ -823,7 +953,44 @@ public class GAlignFrame extends JInternalFrame BLOSUM62Colour_actionPerformed(e); } }); - avDistanceTreeBlosumMenuItem.setText("Average Distance Using BLOSUM62"); + 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); + } + }); + + RNAInteractionColour.setText("RNA Interaction type"); + RNAInteractionColour + .addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + RNAInteractionColour_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() { @@ -832,7 +999,8 @@ public class GAlignFrame extends JInternalFrame avTreeBlosumMenuItem_actionPerformed(e); } }); - njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62"); + njTreeBlosumMenuItem.setText(MessageManager + .getString("label.neighbour_blosum62")); njTreeBlosumMenuItem .addActionListener(new java.awt.event.ActionListener() { @@ -842,7 +1010,8 @@ public class GAlignFrame extends JInternalFrame } }); annotationPanelMenuItem.setActionCommand(""); - annotationPanelMenuItem.setText("Show Annotations"); + annotationPanelMenuItem.setText(MessageManager + .getString("label.show_annotations")); annotationPanelMenuItem.setState(jalview.bin.Cache.getDefault( "SHOW_ANNOTATIONS", true)); annotationPanelMenuItem @@ -853,7 +1022,8 @@ public class GAlignFrame extends JInternalFrame annotationPanelMenuItem_actionPerformed(e); } }); - colourTextMenuItem.setText("Colour Text"); + colourTextMenuItem.setText(MessageManager + .getString("label.colour_text")); colourTextMenuItem .addActionListener(new java.awt.event.ActionListener() { @@ -862,7 +1032,7 @@ public class GAlignFrame extends JInternalFrame colourTextMenuItem_actionPerformed(e); } }); - htmlMenuItem.setText("HTML"); + htmlMenuItem.setText(MessageManager.getString("label.html")); htmlMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -870,7 +1040,8 @@ public class GAlignFrame extends JInternalFrame htmlMenuItem_actionPerformed(e); } }); - overviewMenuItem.setText("Overview Window"); + overviewMenuItem.setText(MessageManager + .getString("label.overview_window")); overviewMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -879,7 +1050,7 @@ public class GAlignFrame extends JInternalFrame } }); undoMenuItem.setEnabled(false); - undoMenuItem.setText("Undo"); + undoMenuItem.setText(MessageManager.getString("action.undo")); undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke( java.awt.event.KeyEvent.VK_Z, Toolkit.getDefaultToolkit() .getMenuShortcutKeyMask(), false)); @@ -891,7 +1062,7 @@ public class GAlignFrame extends JInternalFrame } }); redoMenuItem.setEnabled(false); - redoMenuItem.setText("Redo"); + redoMenuItem.setText(MessageManager.getString("action.redo")); redoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke( java.awt.event.KeyEvent.VK_Y, Toolkit.getDefaultToolkit() .getMenuShortcutKeyMask(), false)); @@ -902,7 +1073,8 @@ public class GAlignFrame extends JInternalFrame redoMenuItem_actionPerformed(e); } }); - conservationMenuItem.setText("By Conservation"); + conservationMenuItem.setText(MessageManager + .getString("action.by_conservation")); conservationMenuItem .addActionListener(new java.awt.event.ActionListener() { @@ -911,7 +1083,7 @@ public class GAlignFrame extends JInternalFrame conservationMenuItem_actionPerformed(e); } }); - noColourmenuItem.setText("None"); + noColourmenuItem.setText(MessageManager.getString("label.none")); noColourmenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -919,7 +1091,7 @@ public class GAlignFrame extends JInternalFrame noColourmenuItem_actionPerformed(e); } }); - wrapMenuItem.setText("Wrap"); + wrapMenuItem.setText(MessageManager.getString("label.wrap")); wrapMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -927,7 +1099,7 @@ public class GAlignFrame extends JInternalFrame wrapMenuItem_actionPerformed(e); } }); - printMenuItem.setText("Print ..."); + printMenuItem.setText(MessageManager.getString("action.print") + "..."); printMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke( java.awt.event.KeyEvent.VK_P, Toolkit.getDefaultToolkit() .getMenuShortcutKeyMask(), false)); @@ -938,7 +1110,8 @@ public class GAlignFrame extends JInternalFrame printMenuItem_actionPerformed(e); } }); - renderGapsMenuItem.setText("Show Gaps"); + renderGapsMenuItem + .setText(MessageManager.getString("action.show_gaps")); renderGapsMenuItem.setState(true); renderGapsMenuItem .addActionListener(new java.awt.event.ActionListener() @@ -948,7 +1121,7 @@ public class GAlignFrame extends JInternalFrame renderGapsMenuItem_actionPerformed(e); } }); - findMenuItem.setText("Find..."); + findMenuItem.setText(MessageManager.getString("action.find")); findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke( java.awt.event.KeyEvent.VK_F, Toolkit.getDefaultToolkit() .getMenuShortcutKeyMask(), false)); @@ -959,7 +1132,8 @@ public class GAlignFrame extends JInternalFrame findMenuItem_actionPerformed(e); } }); - abovePIDThreshold.setText("Above Identity Threshold"); + abovePIDThreshold.setText(MessageManager + .getString("label.above_identity_threshold")); abovePIDThreshold.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -967,7 +1141,8 @@ public class GAlignFrame extends JInternalFrame abovePIDThreshold_actionPerformed(e); } }); - showSeqFeatures.setText("Show Sequence Features"); + showSeqFeatures.setText(MessageManager + .getString("label.show_sequence_features")); showSeqFeatures.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent actionEvent) @@ -975,16 +1150,14 @@ public class GAlignFrame extends JInternalFrame showSeqFeatures_actionPerformed(actionEvent); } }); -/* - * showSeqFeaturesHeight.setText("Vary Sequence Feature Height"); - showSeqFeaturesHeight.addActionListener(new ActionListener() - { - public void actionPerformed(ActionEvent actionEvent) - { - showSeqFeaturesHeight_actionPerformed(actionEvent); - } - }); */ - showDbRefsMenuitem.setText("Show Database Refs"); + /* + * 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() { @@ -992,9 +1165,10 @@ public class GAlignFrame extends JInternalFrame { showDbRefs_actionPerformed(e); } - + }); - showNpFeatsMenuitem.setText("Show Non-Positional Features"); + showNpFeatsMenuitem.setText(MessageManager + .getString("label.show_non_positional_features")); showNpFeatsMenuitem.addActionListener(new ActionListener() { @@ -1002,9 +1176,10 @@ public class GAlignFrame extends JInternalFrame { showNpFeats_actionPerformed(e); } - + }); - showGroupConservation.setText("Group Conservation"); + showGroupConservation.setText(MessageManager + .getString("label.group_conservation")); showGroupConservation.addActionListener(new ActionListener() { @@ -1012,10 +1187,11 @@ public class GAlignFrame extends JInternalFrame { showGroupConservation_actionPerformed(e); } - + }); - showGroupConsensus.setText("Group Consensus"); + showGroupConsensus.setText(MessageManager + .getString("label.group_consensus")); showGroupConsensus.addActionListener(new ActionListener() { @@ -1023,10 +1199,56 @@ public class GAlignFrame extends JInternalFrame { showGroupConsensus_actionPerformed(e); } - + + }); + showConsensusHistogram.setText(MessageManager + .getString("label.show_consensus_histogram")); + showConsensusHistogram.addActionListener(new ActionListener() + { + + public void actionPerformed(ActionEvent e) + { + showConsensusHistogram_actionPerformed(e); + } + + }); + showSequenceLogo.setText(MessageManager + .getString("label.show_consensus_logo")); + showSequenceLogo.addActionListener(new ActionListener() + { + + public void actionPerformed(ActionEvent e) + { + showSequenceLogo_actionPerformed(e); + } + + }); + normaliseSequenceLogo.setText(MessageManager + .getString("label.norm_consensus_logo")); + normaliseSequenceLogo.addActionListener(new ActionListener() + { + + 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() + { + + public void actionPerformed(ActionEvent e) + { + applyAutoAnnotationSettings_actionPerformed(e); + } + }); - nucleotideColour.setText("Nucleotide"); + nucleotideColour.setText(MessageManager.getString("label.nucleotide")); nucleotideColour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -1034,7 +1256,21 @@ public class GAlignFrame extends JInternalFrame nucleotideColour_actionPerformed(e); } }); - deleteGroups.setText("Undefine groups"); + + tcoffeeColour.setText(MessageManager.getString("label.tcoffee_scores")); + tcoffeeColour.setEnabled(false); + tcoffeeColour.addActionListener(new ActionListener() + { + + @Override + public void actionPerformed(ActionEvent e) + { + tcoffeeColorScheme_actionPerformed(e); + } + }); + + deleteGroups + .setText(MessageManager.getString("action.undefine_groups")); deleteGroups.setAccelerator(javax.swing.KeyStroke.getKeyStroke( java.awt.event.KeyEvent.VK_U, Toolkit.getDefaultToolkit() .getMenuShortcutKeyMask(), false)); @@ -1045,7 +1281,30 @@ public class GAlignFrame extends JInternalFrame deleteGroups_actionPerformed(e); } }); - copy.setText("Copy"); + 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) + { + createGroup_actionPerformed(e); + } + }); + 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) + { + unGroup_actionPerformed(e); + } + }); + copy.setText(MessageManager.getString("action.copy")); copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke( java.awt.event.KeyEvent.VK_C, Toolkit.getDefaultToolkit() .getMenuShortcutKeyMask(), false)); @@ -1057,7 +1316,7 @@ public class GAlignFrame extends JInternalFrame 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)); @@ -1068,7 +1327,7 @@ public class GAlignFrame extends JInternalFrame cut_actionPerformed(e); } }); - delete.setText("Delete"); + 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() @@ -1078,8 +1337,8 @@ public class GAlignFrame extends JInternalFrame 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() @@ -1091,7 +1350,7 @@ public class GAlignFrame extends JInternalFrame 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)); @@ -1102,7 +1361,8 @@ public class GAlignFrame extends JInternalFrame 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) @@ -1117,9 +1377,10 @@ public class GAlignFrame extends JInternalFrame 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) @@ -1128,7 +1389,8 @@ public class GAlignFrame extends JInternalFrame } }); - 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() { @@ -1145,8 +1407,10 @@ public class GAlignFrame extends JInternalFrame 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) @@ -1154,8 +1418,9 @@ public class GAlignFrame extends JInternalFrame 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) @@ -1165,7 +1430,7 @@ public class GAlignFrame extends JInternalFrame }); 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) @@ -1175,7 +1440,7 @@ public class GAlignFrame extends JInternalFrame }); 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) @@ -1185,7 +1450,8 @@ public class GAlignFrame extends JInternalFrame }); centreColumnLabelsMenuItem.setVisible(true); centreColumnLabelsMenuItem.setState(false); - centreColumnLabelsMenuItem.setText("Centre Column Labels"); + centreColumnLabelsMenuItem.setText(MessageManager + .getString("label.centre_column_labels")); centreColumnLabelsMenuItem .addActionListener(new java.awt.event.ActionListener() { @@ -1196,7 +1462,8 @@ public class GAlignFrame extends JInternalFrame }); followHighlightMenuItem.setVisible(true); followHighlightMenuItem.setState(true); - followHighlightMenuItem.setText("Automatic Scrolling"); + followHighlightMenuItem.setText(MessageManager + .getString("label.automatic_scrolling")); followHighlightMenuItem.addActionListener(new ActionListener() { @@ -1204,10 +1471,11 @@ public class GAlignFrame extends JInternalFrame { followHighlight_actionPerformed(); } - + }); - - modifyPID.setText("Modify Identity Threshold..."); + + modifyPID.setText(MessageManager + .getString("label.modify_identity_thereshold")); modifyPID.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -1215,7 +1483,8 @@ public class GAlignFrame extends JInternalFrame modifyPID_actionPerformed(e); } }); - modifyConservation.setText("Modify Conservation Threshold..."); + modifyConservation.setText(MessageManager + .getString("label.modify_conservation_thereshold")); modifyConservation .addActionListener(new java.awt.event.ActionListener() { @@ -1224,8 +1493,9 @@ public class GAlignFrame extends JInternalFrame modifyConservation_actionPerformed(e); } }); - sortByTreeMenu.setText("By Tree Order"); - sort.setText("Sort"); + sortByTreeMenu + .setText(MessageManager.getString("action.by_tree_order")); + sort.setText(MessageManager.getString("action.sort")); sort.addMenuListener(new MenuListener() { public void menuSelected(MenuEvent e) @@ -1241,7 +1511,8 @@ public class GAlignFrame extends JInternalFrame { } }); - sortByAnnotScore.setText("by Score"); + sortByAnnotScore.setText(MessageManager + .getString("label.sort_by_score")); sort.add(sortByAnnotScore); sortByAnnotScore.addMenuListener(new javax.swing.event.MenuListener() { @@ -1261,10 +1532,11 @@ public class GAlignFrame extends JInternalFrame }); sortByAnnotScore.setVisible(false); - calculateTree.setText("Calculate Tree"); + calculateTree + .setText(MessageManager.getString("action.calculate_tree")); - jMenu2.setText("Export Image"); - padGapsMenuitem.setText("Pad Gaps"); + 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() @@ -1275,7 +1547,7 @@ public class GAlignFrame extends JInternalFrame } }); vamsasStore.setVisible(false); - vamsasStore.setText("VAMSAS store"); + vamsasStore.setText(MessageManager.getString("label.vamsas_store")); vamsasStore.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -1283,7 +1555,8 @@ public class GAlignFrame extends JInternalFrame vamsasStore_actionPerformed(e); } }); - showTranslation.setText("Translate cDNA"); + showTranslation.setText(MessageManager + .getString("label.translate_cDNA")); showTranslation.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -1291,7 +1564,8 @@ public class GAlignFrame extends JInternalFrame showTranslation_actionPerformed(e); } }); - extractScores.setText("Extract Scores..."); + extractScores.setText(MessageManager.getString("label.extract_scores") + + "..."); extractScores.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -1300,23 +1574,25 @@ public class GAlignFrame extends JInternalFrame } }); extractScores.setVisible(true); // JBPNote: TODO: make gui for regex based - // score extraction - showProducts.setText("Get Cross References"); + // score extraction + showProducts.setText(MessageManager.getString("label.get_cross_refs")); /* * showProducts.addActionListener(new ActionListener() { * * public void actionPerformed(ActionEvent e) { * showProducts_actionPerformed(e); } }); */ - featureSettings.setText("Feature Settings..."); - featureSettings.addActionListener(new ActionListener() + 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) @@ -1325,7 +1601,8 @@ public class GAlignFrame extends JInternalFrame } }); - annotationColour.setText("By Annotation..."); + annotationColour.setText(MessageManager + .getString("action.by_annotation")); annotationColour.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -1333,7 +1610,19 @@ public class GAlignFrame extends JInternalFrame 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) @@ -1341,7 +1630,8 @@ public class GAlignFrame extends JInternalFrame associatedData_actionPerformed(e); } }); - autoCalculate.setText("Autocalculate Consensus"); + autoCalculate.setText(MessageManager + .getString("label.autocalculate_consensus")); autoCalculate.setState(jalview.bin.Cache.getDefault( "AUTO_CALC_CONSENSUS", true)); autoCalculate.addActionListener(new ActionListener() @@ -1351,8 +1641,40 @@ public class GAlignFrame extends JInternalFrame 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) @@ -1360,7 +1682,7 @@ public class GAlignFrame extends JInternalFrame addFromFile_actionPerformed(e); } }); - addFromText.setText("From Textbox"); + addFromText.setText(MessageManager.getString("label.from_textbox")); addFromText.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -1368,7 +1690,7 @@ public class GAlignFrame extends JInternalFrame addFromText_actionPerformed(e); } }); - addFromURL.setText("From URL"); + addFromURL.setText(MessageManager.getString("label.from_url")); addFromURL.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -1376,7 +1698,8 @@ public class GAlignFrame extends JInternalFrame addFromURL_actionPerformed(e); } }); - exportFeatures.setText("Export Features..."); + exportFeatures.setText(MessageManager + .getString("label.export_features")); exportFeatures.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -1384,7 +1707,8 @@ public class GAlignFrame extends JInternalFrame exportFeatures_actionPerformed(e); } }); - exportAnnotations.setText("Export Annotations..."); + exportAnnotations.setText(MessageManager + .getString("label.export_annotations")); exportAnnotations.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -1393,8 +1717,10 @@ public class GAlignFrame extends JInternalFrame } }); 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) @@ -1402,7 +1728,9 @@ public class GAlignFrame extends JInternalFrame 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) @@ -1410,8 +1738,11 @@ public class GAlignFrame extends JInternalFrame 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) @@ -1419,7 +1750,10 @@ public class GAlignFrame extends JInternalFrame 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) @@ -1427,7 +1761,39 @@ public class GAlignFrame extends JInternalFrame 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) @@ -1435,7 +1801,8 @@ public class GAlignFrame extends JInternalFrame hiddenMarkers_actionPerformed(e); } }); - invertColSel.setText("Invert Column Selection"); + invertColSel.setText(MessageManager + .getString("action.invert_column_selection")); invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke( java.awt.event.KeyEvent.VK_I, Toolkit.getDefaultToolkit() .getMenuShortcutKeyMask() @@ -1470,7 +1837,7 @@ public class GAlignFrame extends JInternalFrame tabbedPane_focusGained(e); } }); - save.setText("Save"); + save.setText(MessageManager.getString("action.save")); save.setAccelerator(javax.swing.KeyStroke.getKeyStroke( java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit() .getMenuShortcutKeyMask(), false)); @@ -1482,7 +1849,7 @@ public class GAlignFrame extends JInternalFrame } }); reload.setEnabled(false); - reload.setText("Reload"); + reload.setText(MessageManager.getString("action.reload")); reload.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -1490,7 +1857,7 @@ public class GAlignFrame extends JInternalFrame reload_actionPerformed(e); } }); - newView.setText("New View"); + newView.setText(MessageManager.getString("action.new_view")); newView.setAccelerator(javax.swing.KeyStroke.getKeyStroke( java.awt.event.KeyEvent.VK_T, Toolkit.getDefaultToolkit() .getMenuShortcutKeyMask(), false)); @@ -1501,9 +1868,11 @@ public class GAlignFrame extends JInternalFrame newView_actionPerformed(e); } }); - tabbedPane.setToolTipText(" Right-click to rename tab" - + "
Press X to eXpand tabs, G to reGroup."); - textColour.setText("Colour Text ..."); + 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) @@ -1511,9 +1880,10 @@ public class GAlignFrame extends JInternalFrame 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) @@ -1522,7 +1892,7 @@ public class GAlignFrame extends JInternalFrame } }); gatherViews.setEnabled(false); - gatherViews.setText("Gather Views"); + 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() @@ -1533,7 +1903,7 @@ public class GAlignFrame extends JInternalFrame } }); expandViews.setEnabled(false); - expandViews.setText("Expand Views"); + 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() @@ -1543,7 +1913,8 @@ public class GAlignFrame extends JInternalFrame expandViews_actionPerformed(e); } }); - pageSetup.setText("Page Setup ..."); + pageSetup + .setText(MessageManager.getString("action.page_setup") + "..."); pageSetup.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -1551,7 +1922,8 @@ public class GAlignFrame extends JInternalFrame pageSetup_actionPerformed(e); } }); - alignmentProperties.setText("Alignment Properties..."); + alignmentProperties.setText(MessageManager + .getString("label.alignment_props") + "..."); alignmentProperties.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent actionEvent) @@ -1559,7 +1931,10 @@ public class GAlignFrame extends JInternalFrame alignmentProperties(); } }); - tooltipSettingsMenu.setText("Sequence ID Tooltip"); + tooltipSettingsMenu.setText(MessageManager + .getString("label.sequence_id_tooltip")); + autoAnnMenu.setText(MessageManager + .getString("label.autocalculated_annotation")); alignFrameMenuBar.add(fileMenu); alignFrameMenuBar.add(editMenu); alignFrameMenuBar.add(selectMenu); @@ -1600,9 +1975,10 @@ public class GAlignFrame extends JInternalFrame editMenu.add(removeRedundancyMenuItem); editMenu.addSeparator(); // dont add these yet in the CVS build - they cannot be undone! - editMenu.add(justifyLeftMenuItem); - editMenu.add(justifyRightMenuItem); - editMenu.addSeparator(); + // 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); @@ -1613,13 +1989,19 @@ public class GAlignFrame extends JInternalFrame viewMenu.addSeparator(); viewMenu.add(followHighlightMenuItem); viewMenu.add(annotationPanelMenuItem); - viewMenu.add(showGroupConservation); - viewMenu.add(showGroupConsensus); + 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(showSeqFeaturesHeight); - - viewMenu.add(featureSettings); + // viewMenu.add(showSeqFeaturesHeight); + + viewMenu.add(openFeatureSettings); tooltipSettingsMenu.add(showDbRefsMenuitem); tooltipSettingsMenu.add(showNpFeatsMenuitem); viewMenu.add(tooltipSettingsMenu); @@ -1642,6 +2024,10 @@ public class GAlignFrame extends JInternalFrame colourMenu.add(turnColour); colourMenu.add(buriedColour); colourMenu.add(nucleotideColour); + colourMenu.add(purinePyrimidineColour); + colourMenu.add(RNAInteractionColour); + // colourMenu.add(covariationColour); + colourMenu.add(tcoffeeColour); colourMenu.add(userDefinedColour); colourMenu.addSeparator(); colourMenu.add(conservationMenuItem); @@ -1649,6 +2035,7 @@ public class GAlignFrame extends JInternalFrame colourMenu.add(abovePIDThreshold); colourMenu.add(modifyPID); colourMenu.add(annotationColour); + colourMenu.add(rnahelicesColour); calculateMenu.add(sort); calculateMenu.add(calculateTree); calculateMenu.addSeparator(); @@ -1658,9 +2045,11 @@ public class GAlignFrame extends JInternalFrame 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); @@ -1669,10 +2058,6 @@ public class GAlignFrame extends JInternalFrame sort.add(sortGroupMenuItem); sort.add(sortPairwiseMenuItem); sort.add(sortByTreeMenu); - calculateTree.add(averageDistanceTreeMenuItem); - calculateTree.add(neighbourTreeMenuItem); - calculateTree.add(avDistanceTreeBlosumMenuItem); - calculateTree.add(njTreeBlosumMenuItem); jMenu2.add(htmlMenuItem); jMenu2.add(epsFile); jMenu2.add(createPNG); @@ -1684,8 +2069,12 @@ public class GAlignFrame extends JInternalFrame 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); @@ -1700,76 +2089,131 @@ public class GAlignFrame extends JInternalFrame formatMenu.add(colourTextMenuItem); formatMenu.add(renderGapsMenuItem); formatMenu.add(centreColumnLabelsMenuItem); - formatMenu.add(showUnconservedMenuItem); + formatMenu.add(showNonconservedMenuItem); selectMenu.add(findMenuItem); selectMenu.addSeparator(); selectMenu.add(selectAllSequenceMenuItem); selectMenu.add(deselectAllSequenceMenuItem); selectMenu.add(invertSequenceMenuItem); selectMenu.add(invertColSel); - selectMenu.add(deleteGroups); + selectMenu.add(createGroup); + selectMenu.add(unGroup); selectMenu.add(grpsFromSelection); + selectMenu.add(deleteGroups); + calculateMenu.add(expandAlignment); + // 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) @@ -1973,6 +2417,18 @@ public class GAlignFrame extends JInternalFrame { } + protected void purinePyrimidineColour_actionPerformed(ActionEvent e) + { + } + + protected void RNAInteractionColour_actionPerformed(ActionEvent e) + { + } + + /* + * protected void covariationColour_actionPerformed(ActionEvent e) { } + */ + protected void noColourmenuItem_actionPerformed(ActionEvent e) { } @@ -2009,6 +2465,14 @@ public class GAlignFrame extends JInternalFrame { } + protected void createGroup_actionPerformed(ActionEvent e) + { + } + + protected void unGroup_actionPerformed(ActionEvent e) + { + } + protected void copy_actionPerformed(ActionEvent e) { } @@ -2056,6 +2520,33 @@ public class GAlignFrame extends JInternalFrame 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) @@ -2125,6 +2616,11 @@ public class GAlignFrame extends JInternalFrame } + public void rnahelicesColour_actionPerformed(ActionEvent e) + { + + } + public void associatedData_actionPerformed(ActionEvent e) { @@ -2135,6 +2631,11 @@ public class GAlignFrame extends JInternalFrame } + public void sortByTreeOption_actionPerformed(ActionEvent e) + { + + } + public void showAllSeqs_actionPerformed(ActionEvent e) { @@ -2244,4 +2745,10 @@ public class GAlignFrame extends JInternalFrame { } + + protected void expand_newalign(ActionEvent e) + { + // TODO Auto-generated method stub + + } }