X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGAlignFrame.java;h=d3154c7408f4ff0ebbf1844e9dd3ced60d788157;hb=ad5029edaf36ceaafb4e269f2e00b0e1e0d7ffc4;hp=6e8b420d39d4a4dd831ceeb60d3c5a087877bd09;hpb=a79f9e113c51c032070c670e45ce3eb464691166;p=jalview.git diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java index 6e8b420..d3154c7 100755 --- a/src/jalview/jbgui/GAlignFrame.java +++ b/src/jalview/jbgui/GAlignFrame.java @@ -1,23 +1,27 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) - * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) + * 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. - * + * 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 . + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.jbgui; import jalview.schemes.ColourSchemeProperty; +import jalview.util.MessageManager; import java.awt.BorderLayout; import java.awt.Color; @@ -139,12 +143,13 @@ public class GAlignFrame extends JInternalFrame 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(); @@ -183,6 +188,10 @@ public class GAlignFrame extends JInternalFrame JMenuItem deleteGroups = new JMenuItem(); + JMenuItem createGroup = new JMenuItem(); + + JMenuItem unGroup = new JMenuItem(); + JMenuItem delete = new JMenuItem(); JMenuItem copy = new JMenuItem(); @@ -206,8 +215,6 @@ public class GAlignFrame extends JInternalFrame JMenuItem epsFile = new JMenuItem(); JMenuItem LoadtreeMenuItem = new JMenuItem(); - - JMenuItem loadScoresMenuItem = new JMenuItem(); public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem(); @@ -241,6 +248,8 @@ public class GAlignFrame extends JInternalFrame protected JMenuItem extractScores = new JMenuItem(); + protected JMenuItem expandAlignment = new JMenuItem(); + protected JMenu showProducts = new JMenu(); public JMenuItem openFeatureSettings = new JMenuItem(); @@ -407,8 +416,10 @@ public class GAlignFrame extends JInternalFrame 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) { @@ -456,7 +467,7 @@ public class GAlignFrame extends JInternalFrame colours.add(purinePyrimidineColour); // colours.add(covariationColour); colours.add(tcoffeeColour); - + colours.add(RNAInteractionColour); setColourSelected(jalview.bin.Cache .getDefault("DEFAULT_COLOUR", "None")); @@ -525,15 +536,20 @@ public class GAlignFrame extends JInternalFrame nucleotideColour.setSelected(true); break; - + case ColourSchemeProperty.TCOFFEE: - tcoffeeColour.setSelected(true); - break; + tcoffeeColour.setSelected(true); + break; case ColourSchemeProperty.PURINEPYRIMIDINE: purinePyrimidineColour.setSelected(true); break; + + case ColourSchemeProperty.RNAINTERACTION: + RNAInteractionColour.setSelected(true); + + break; /* * case ColourSchemeProperty.COVARIATION: * covariationColour.setSelected(true); @@ -556,8 +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() @@ -569,7 +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)); @@ -580,12 +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)); @@ -597,7 +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 @@ -608,7 +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)); @@ -620,7 +639,8 @@ 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) @@ -628,8 +648,20 @@ public class GAlignFrame extends JInternalFrame 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)); @@ -641,7 +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)); @@ -653,7 +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)); @@ -665,7 +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() @@ -678,7 +713,8 @@ public class GAlignFrame extends JInternalFrame removeAllGapsMenuItem_actionPerformed(e); } }); - justifyLeftMenuItem.setText("Left Justify Alignment"); + justifyLeftMenuItem.setText(MessageManager + .getString("action.left_justify_alignment")); justifyLeftMenuItem .addActionListener(new java.awt.event.ActionListener() { @@ -687,7 +723,8 @@ public class GAlignFrame extends JInternalFrame justifyLeftMenuItem_actionPerformed(e); } }); - justifyRightMenuItem.setText("Right Justify Alignment"); + justifyRightMenuItem.setText(MessageManager + .getString("action.right_justify_alignment")); justifyRightMenuItem .addActionListener(new java.awt.event.ActionListener() { @@ -696,7 +733,7 @@ public class GAlignFrame extends JInternalFrame justifyRightMenuItem_actionPerformed(e); } }); - viewBoxesMenuItem.setText("Boxes"); + viewBoxesMenuItem.setText(MessageManager.getString("action.boxes")); viewBoxesMenuItem.setState(true); viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener() { @@ -705,7 +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() { @@ -714,7 +751,8 @@ public class GAlignFrame extends JInternalFrame viewTextMenuItem_actionPerformed(e); } }); - showNonconservedMenuItem.setText("Show nonconserved"); + showNonconservedMenuItem.setText(MessageManager + .getString("label.show_non_conversed")); showNonconservedMenuItem.setState(false); showNonconservedMenuItem .addActionListener(new java.awt.event.ActionListener() @@ -724,7 +762,8 @@ public class GAlignFrame extends JInternalFrame showUnconservedMenuItem_actionPerformed(e); } }); - sortPairwiseMenuItem.setText("by Pairwise Identity"); + sortPairwiseMenuItem.setText(MessageManager + .getString("action.by_pairwise_id")); sortPairwiseMenuItem .addActionListener(new java.awt.event.ActionListener() { @@ -733,7 +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) @@ -741,7 +780,8 @@ public class GAlignFrame extends JInternalFrame sortIDMenuItem_actionPerformed(e); } }); - sortLengthMenuItem.setText("By Length"); + sortLengthMenuItem + .setText(MessageManager.getString("action.by_length")); sortLengthMenuItem .addActionListener(new java.awt.event.ActionListener() { @@ -750,7 +790,7 @@ public class GAlignFrame extends JInternalFrame sortLengthMenuItem_actionPerformed(e); } }); - sortGroupMenuItem.setText("by Group"); + sortGroupMenuItem.setText(MessageManager.getString("action.by_group")); sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -758,7 +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)); @@ -770,7 +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() { @@ -779,7 +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) @@ -787,8 +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() { @@ -797,7 +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() { @@ -811,9 +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() { @@ -822,7 +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) @@ -830,7 +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) @@ -838,7 +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() { @@ -847,7 +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) @@ -855,7 +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) @@ -863,7 +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) @@ -871,7 +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) @@ -879,7 +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) @@ -887,7 +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) @@ -895,7 +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) @@ -903,7 +953,7 @@ public class GAlignFrame extends JInternalFrame BLOSUM62Colour_actionPerformed(e); } }); - nucleotideColour.setText("Nucleotide"); + nucleotideColour.setText(MessageManager.getString("label.nucleotide")); nucleotideColour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -912,7 +962,8 @@ public class GAlignFrame extends JInternalFrame } }); - purinePyrimidineColour.setText("Purine/Pyrimidine"); + purinePyrimidineColour.setText(MessageManager + .getString("label.purine_pyrimidine")); purinePyrimidineColour .addActionListener(new java.awt.event.ActionListener() { @@ -921,6 +972,16 @@ public class GAlignFrame extends JInternalFrame 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() { @@ -928,7 +989,8 @@ public class GAlignFrame extends JInternalFrame * covariationColour_actionPerformed(e); } }); */ - avDistanceTreeBlosumMenuItem.setText("Average Distance Using BLOSUM62"); + avDistanceTreeBlosumMenuItem.setText(MessageManager + .getString("label.average_distance_bloslum62")); avDistanceTreeBlosumMenuItem .addActionListener(new java.awt.event.ActionListener() { @@ -937,7 +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() { @@ -947,7 +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 @@ -958,7 +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() { @@ -967,7 +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) @@ -975,7 +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) @@ -984,7 +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)); @@ -996,7 +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)); @@ -1007,7 +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() { @@ -1016,7 +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) @@ -1024,7 +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) @@ -1032,7 +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)); @@ -1043,7 +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() @@ -1053,7 +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)); @@ -1064,7 +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) @@ -1072,7 +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) @@ -1086,7 +1156,8 @@ public class GAlignFrame extends JInternalFrame * void actionPerformed(ActionEvent actionEvent) { * showSeqFeaturesHeight_actionPerformed(actionEvent); } }); */ - showDbRefsMenuitem.setText("Show Database Refs"); + showDbRefsMenuitem.setText(MessageManager + .getString("label.show_database_refs")); showDbRefsMenuitem.addActionListener(new ActionListener() { @@ -1096,7 +1167,8 @@ public class GAlignFrame extends JInternalFrame } }); - showNpFeatsMenuitem.setText("Show Non-Positional Features"); + showNpFeatsMenuitem.setText(MessageManager + .getString("label.show_non_positional_features")); showNpFeatsMenuitem.addActionListener(new ActionListener() { @@ -1106,7 +1178,8 @@ public class GAlignFrame extends JInternalFrame } }); - showGroupConservation.setText("Group Conservation"); + showGroupConservation.setText(MessageManager + .getString("label.group_conservation")); showGroupConservation.addActionListener(new ActionListener() { @@ -1117,7 +1190,8 @@ public class GAlignFrame extends JInternalFrame }); - showGroupConsensus.setText("Group Consensus"); + showGroupConsensus.setText(MessageManager + .getString("label.group_consensus")); showGroupConsensus.addActionListener(new ActionListener() { @@ -1127,7 +1201,8 @@ public class GAlignFrame extends JInternalFrame } }); - showConsensusHistogram.setText("Show Consensus Histogram"); + showConsensusHistogram.setText(MessageManager + .getString("label.show_consensus_histogram")); showConsensusHistogram.addActionListener(new ActionListener() { @@ -1137,7 +1212,8 @@ public class GAlignFrame extends JInternalFrame } }); - showSequenceLogo.setText("Show Consensus Logo"); + showSequenceLogo.setText(MessageManager + .getString("label.show_consensus_logo")); showSequenceLogo.addActionListener(new ActionListener() { @@ -1147,7 +1223,8 @@ public class GAlignFrame extends JInternalFrame } }); - normaliseSequenceLogo.setText("Normalise Consensus Logo"); + normaliseSequenceLogo.setText(MessageManager + .getString("label.norm_consensus_logo")); normaliseSequenceLogo.addActionListener(new ActionListener() { @@ -1157,7 +1234,8 @@ public class GAlignFrame extends JInternalFrame } }); - applyAutoAnnotationSettings.setText("Apply to all groups"); + applyAutoAnnotationSettings.setText(MessageManager + .getString("label.apply_all_groups")); applyAutoAnnotationSettings.setState(false); applyAutoAnnotationSettings.setVisible(true); applyAutoAnnotationSettings.addActionListener(new ActionListener() @@ -1170,7 +1248,7 @@ public class GAlignFrame extends JInternalFrame }); - nucleotideColour.setText("Nucleotide"); + nucleotideColour.setText(MessageManager.getString("label.nucleotide")); nucleotideColour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -1178,19 +1256,21 @@ public class GAlignFrame extends JInternalFrame nucleotideColour_actionPerformed(e); } }); - - tcoffeeColour.setText("T-Coffee scores"); + + 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("Undefine groups"); + 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)); @@ -1201,7 +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)); @@ -1213,7 +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)); @@ -1224,7 +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() @@ -1234,8 +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() @@ -1247,7 +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)); @@ -1258,7 +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) @@ -1273,9 +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) @@ -1284,7 +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() { @@ -1301,8 +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) @@ -1310,19 +1418,9 @@ public class GAlignFrame extends JInternalFrame LoadtreeMenuItem_actionPerformed(e); } }); - - loadScoresMenuItem.setActionCommand("Load T-Coffee scores"); - loadScoresMenuItem.setText("Load T-Coffee scores"); - loadScoresMenuItem.addActionListener(new ActionListener() { - - @Override - public void actionPerformed(ActionEvent e) { - loadScores_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) @@ -1332,7 +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) @@ -1342,7 +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) @@ -1352,7 +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() { @@ -1363,7 +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() { @@ -1374,7 +1474,8 @@ public class GAlignFrame extends JInternalFrame }); - 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) @@ -1382,7 +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() { @@ -1391,8 +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) @@ -1408,7 +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() { @@ -1428,10 +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() @@ -1442,7 +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) @@ -1450,7 +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) @@ -1458,7 +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) @@ -1468,14 +1575,15 @@ public class GAlignFrame extends JInternalFrame }); extractScores.setVisible(true); // JBPNote: TODO: make gui for regex based // score extraction - showProducts.setText("Get Cross References"); + showProducts.setText(MessageManager.getString("label.get_cross_refs")); /* * showProducts.addActionListener(new ActionListener() { * * public void actionPerformed(ActionEvent e) { * showProducts_actionPerformed(e); } }); */ - openFeatureSettings.setText("Feature Settings..."); + openFeatureSettings.setText(MessageManager + .getString("label.feature_settings")); openFeatureSettings.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -1483,7 +1591,8 @@ public class GAlignFrame extends JInternalFrame featureSettings_actionPerformed(e); } }); - fetchSequence.setText("Fetch Sequence(s)..."); + fetchSequence + .setText(MessageManager.getString("label.fetch_sequences")); fetchSequence.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -1492,7 +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) @@ -1501,7 +1611,8 @@ public class GAlignFrame extends JInternalFrame } }); - rnahelicesColour.setText("By RNA helices"); + rnahelicesColour.setText(MessageManager + .getString("action.by_rna_helixes")); rnahelicesColour.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -1510,7 +1621,8 @@ public class GAlignFrame extends JInternalFrame } }); - associatedData.setText("Load Features / Annotations"); + associatedData.setText(MessageManager + .getString("label.load_features_annotations")); associatedData.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -1518,7 +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() @@ -1528,10 +1641,14 @@ public class GAlignFrame extends JInternalFrame autoCalculate_actionPerformed(e); } }); - sortByTree.setText("Sort Alignment With New Tree"); - sortByTree.setToolTipText("Enable this to automatically sort
the alignment when you open
a new tree."); - sortByTree.setState(jalview.bin.Cache.getDefault( - "SORT_BY_TREE", false)); + 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) @@ -1540,9 +1657,13 @@ public class GAlignFrame extends JInternalFrame } }); - listenToViewSelections.setText("Listen for selections"); - listenToViewSelections.setToolTipText("When selected, selections in this view will mirror
selections made on the same sequences in other views."); - listenToViewSelections.setState(false); + 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) @@ -1551,8 +1672,9 @@ public class GAlignFrame extends JInternalFrame } }); - addSequenceMenu.setText("Add Sequences"); - addFromFile.setText("From File"); + addSequenceMenu + .setText(MessageManager.getString("label.add_sequences")); + addFromFile.setText(MessageManager.getString("label.from_file")); addFromFile.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -1560,7 +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) @@ -1568,7 +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) @@ -1576,7 +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) @@ -1584,7 +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) @@ -1593,9 +1717,10 @@ public class GAlignFrame extends JInternalFrame } }); statusPanel.setLayout(gridLayout1); - jMenu3.setText("Show"); - showAllSeqs.setText("All Sequences"); - showAllSeqs.setToolTipText("Shift+H toggles sequence visiblity."); + 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) @@ -1603,8 +1728,9 @@ public class GAlignFrame extends JInternalFrame showAllSeqs_actionPerformed(e); } }); - showAllColumns.setText("All Columns"); - showAllColumns.setToolTipText("Ctrl+H toggles column visiblity."); + showAllColumns.setText(MessageManager.getString("label.all_columns")); + showAllColumns.setToolTipText(MessageManager + .getString("label.toggle_columns_visibility")); showAllColumns.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -1612,9 +1738,11 @@ public class GAlignFrame extends JInternalFrame showAllColumns_actionPerformed(e); } }); - hideMenu.setText("Hide"); - hideSelSequences.setText("Selected Sequences"); - hideSelSequences.setToolTipText("Shift+H toggles sequence visiblity."); + 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) @@ -1622,8 +1750,10 @@ public class GAlignFrame extends JInternalFrame hideSelSequences_actionPerformed(e); } }); - hideSelColumns.setText("Selected Columns"); - hideSelColumns.setToolTipText("Ctrl+H toggles column visiblity."); + hideSelColumns.setText(MessageManager + .getString("label.selected_columns")); + hideSelColumns.setToolTipText(MessageManager + .getString("label.toggle_columns_visibility")); hideSelColumns.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -1631,7 +1761,8 @@ public class GAlignFrame extends JInternalFrame hideSelColumns_actionPerformed(e); } }); - hideAllSelection.setText("Selected Region"); + hideAllSelection.setText(MessageManager + .getString("label.selected_region")); hideAllSelection.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -1640,7 +1771,8 @@ public class GAlignFrame extends JInternalFrame } }); // TODO: should be hidden if no selection exists. - hideAllButSelection.setText("All but Selected Region (Shift+Ctrl+H)"); + hideAllButSelection.setText(MessageManager + .getString("label.all_but_selected_region")); hideAllButSelection.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -1648,9 +1780,10 @@ public class GAlignFrame extends JInternalFrame hideAllButSelection_actionPerformed(e); } }); - showAllhidden.setText("All Sequences and Columns"); - showAllhidden - .setToolTipText("H toggles visibility of hidden or selected regions."); + 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) @@ -1659,7 +1792,8 @@ public class GAlignFrame extends JInternalFrame } }); - hiddenMarkers.setText("Show Hidden Markers"); + hiddenMarkers.setText(MessageManager + .getString("action.show_hidden_markers")); hiddenMarkers.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -1667,7 +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() @@ -1702,7 +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)); @@ -1714,7 +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) @@ -1722,7 +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)); @@ -1733,9 +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) @@ -1743,9 +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) @@ -1754,7 +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() @@ -1765,7 +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() @@ -1775,7 +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) @@ -1783,7 +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) @@ -1791,8 +1931,10 @@ public class GAlignFrame extends JInternalFrame alignmentProperties(); } }); - tooltipSettingsMenu.setText("Sequence ID Tooltip"); - autoAnnMenu.setText("Autocalculated Annotation"); + tooltipSettingsMenu.setText(MessageManager + .getString("label.sequence_id_tooltip")); + autoAnnMenu.setText(MessageManager + .getString("label.autocalculated_annotation")); alignFrameMenuBar.add(fileMenu); alignFrameMenuBar.add(editMenu); alignFrameMenuBar.add(selectMenu); @@ -1817,7 +1959,6 @@ public class GAlignFrame extends JInternalFrame fileMenu.add(exportAnnotations); fileMenu.add(LoadtreeMenuItem); fileMenu.add(associatedData); - fileMenu.add(loadScoresMenuItem); fileMenu.addSeparator(); fileMenu.add(closeMenuItem); editMenu.add(undoMenuItem); @@ -1884,6 +2025,7 @@ public class GAlignFrame extends JInternalFrame colourMenu.add(buriedColour); colourMenu.add(nucleotideColour); colourMenu.add(purinePyrimidineColour); + colourMenu.add(RNAInteractionColour); // colourMenu.add(covariationColour); colourMenu.add(tcoffeeColour); colourMenu.add(userDefinedColour); @@ -1906,7 +2048,8 @@ public class GAlignFrame extends JInternalFrame 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); @@ -1915,10 +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); @@ -1957,23 +2096,27 @@ public class GAlignFrame extends JInternalFrame selectMenu.add(deselectAllSequenceMenuItem); selectMenu.add(invertSequenceMenuItem); selectMenu.add(invertColSel); - selectMenu.add(deleteGroups); + selectMenu.add(createGroup); + selectMenu.add(unGroup); selectMenu.add(grpsFromSelection); - // TODO - determine if the listenToViewSelections button is needed : see bug JAL-574 - //selectMenu.addSeparator(); - //selectMenu.add(listenToViewSelections); + 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) @@ -2278,6 +2421,10 @@ public class GAlignFrame extends JInternalFrame { } + protected void RNAInteractionColour_actionPerformed(ActionEvent e) + { + } + /* * protected void covariationColour_actionPerformed(ActionEvent e) { } */ @@ -2318,6 +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) { } @@ -2367,30 +2522,32 @@ public class GAlignFrame extends JInternalFrame { } - + /** - * Template method to handle the 'load T-Coffee scores' menu event. + * 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 + * + * @param event + * The raised event */ - protected void loadScores_actionPerformed(ActionEvent event) { - + protected void loadScores_actionPerformed(ActionEvent event) + { + } - /** - * Template method to handle the 'Color T-Coffee scores' menu 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 + * + * @param event + * The raised event */ - protected void tcoffeeColorScheme_actionPerformed(ActionEvent event) { - + protected void tcoffeeColorScheme_actionPerformed(ActionEvent event) + { + } - protected void jpred_actionPerformed(ActionEvent e) { @@ -2588,4 +2745,10 @@ public class GAlignFrame extends JInternalFrame { } + + protected void expand_newalign(ActionEvent e) + { + // TODO Auto-generated method stub + + } }