X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGAlignFrame.java;h=16e78f546ed8babed9b14fa2452476c9b44215c8;hb=47168f025aefdaa044802bd5f8f510ffe43a4808;hp=de1487a6785251663546b136aee0ec0866a03565;hpb=21c29b20790ac555b2e2a124a034f6c6b4486270;p=jalview.git
diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index de1487a..16e78f5 100755
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -1,19 +1,22 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, 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;
@@ -139,6 +142,8 @@ public class GAlignFrame extends JInternalFrame
protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
+
+ protected JRadioButtonMenuItem RNAInteractionColour = new JRadioButtonMenuItem();
// protected JRadioButtonMenuItem covariationColour = new
// JRadioButtonMenuItem();
@@ -182,6 +187,9 @@ public class GAlignFrame extends JInternalFrame
public JCheckBoxMenuItem showSeqFeaturesHeight = new JCheckBoxMenuItem();
JMenuItem deleteGroups = new JMenuItem();
+
+ JMenuItem createGroup = new JMenuItem();
+ JMenuItem unGroup = new JMenuItem();
JMenuItem delete = new JMenuItem();
@@ -238,6 +246,8 @@ public class GAlignFrame extends JInternalFrame
protected JMenuItem showTranslation = new JMenuItem();
protected JMenuItem extractScores = new JMenuItem();
+
+ protected JMenuItem expandAlignment = new JMenuItem();
protected JMenu showProducts = new JMenu();
@@ -454,7 +464,7 @@ 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"));
@@ -532,6 +542,11 @@ public class GAlignFrame extends JInternalFrame
purinePyrimidineColour.setSelected(true);
break;
+
+ case ColourSchemeProperty.RNAINTERACTION:
+ RNAInteractionColour.setSelected(true);
+
+ break;
/*
* case ColourSchemeProperty.COVARIATION:
* covariationColour.setSelected(true);
@@ -554,8 +569,8 @@ 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()
@@ -567,7 +582,7 @@ 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));
@@ -578,12 +593,12 @@ 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));
@@ -595,7 +610,7 @@ 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
@@ -606,7 +621,7 @@ 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));
@@ -618,7 +633,7 @@ 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)
@@ -626,8 +641,16 @@ 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));
@@ -639,7 +662,7 @@ 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));
@@ -651,7 +674,7 @@ 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));
@@ -663,7 +686,7 @@ 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()
@@ -676,7 +699,7 @@ 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()
{
@@ -685,7 +708,7 @@ 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()
{
@@ -694,7 +717,7 @@ 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()
{
@@ -703,7 +726,7 @@ 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()
{
@@ -712,7 +735,7 @@ 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()
@@ -722,7 +745,7 @@ 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()
{
@@ -731,7 +754,7 @@ 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)
@@ -739,7 +762,7 @@ 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()
{
@@ -748,7 +771,7 @@ 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)
@@ -756,7 +779,7 @@ 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));
@@ -768,7 +791,7 @@ 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()
{
@@ -777,7 +800,7 @@ 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)
@@ -786,7 +809,7 @@ public class GAlignFrame extends JInternalFrame
}
});
averageDistanceTreeMenuItem
- .setText("Average Distance Using % Identity");
+ .setText(MessageManager.getString("label.average_distance_identity"));
averageDistanceTreeMenuItem
.addActionListener(new java.awt.event.ActionListener()
{
@@ -795,7 +818,7 @@ 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()
{
@@ -809,9 +832,9 @@ 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()
{
@@ -820,7 +843,7 @@ 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)
@@ -828,7 +851,7 @@ 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)
@@ -836,7 +859,7 @@ public class GAlignFrame extends JInternalFrame
taylorColour_actionPerformed(e);
}
});
- hydrophobicityColour.setText("Hydrophobicity");
+ hydrophobicityColour.setText(MessageManager.getString("label.hydrophobicity"));
hydrophobicityColour
.addActionListener(new java.awt.event.ActionListener()
{
@@ -845,7 +868,7 @@ 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)
@@ -853,7 +876,7 @@ 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)
@@ -861,7 +884,7 @@ 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)
@@ -869,7 +892,7 @@ 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)
@@ -877,7 +900,7 @@ 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)
@@ -885,7 +908,7 @@ 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)
@@ -893,7 +916,7 @@ 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)
@@ -901,7 +924,7 @@ 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)
@@ -910,7 +933,7 @@ public class GAlignFrame extends JInternalFrame
}
});
- purinePyrimidineColour.setText("Purine/Pyrimidine");
+ purinePyrimidineColour.setText(MessageManager.getString("label.purine_pyrimidine"));
purinePyrimidineColour
.addActionListener(new java.awt.event.ActionListener()
{
@@ -919,6 +942,15 @@ 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() {
@@ -926,7 +958,7 @@ 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()
{
@@ -935,7 +967,7 @@ 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()
{
@@ -945,7 +977,7 @@ 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
@@ -956,7 +988,7 @@ 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()
{
@@ -965,7 +997,7 @@ 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)
@@ -973,7 +1005,7 @@ 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)
@@ -982,7 +1014,7 @@ 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));
@@ -994,7 +1026,7 @@ 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));
@@ -1005,7 +1037,7 @@ 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()
{
@@ -1014,7 +1046,7 @@ 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)
@@ -1022,7 +1054,7 @@ 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)
@@ -1030,7 +1062,7 @@ 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));
@@ -1041,7 +1073,7 @@ 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()
@@ -1051,7 +1083,7 @@ 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));
@@ -1062,7 +1094,7 @@ 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)
@@ -1070,7 +1102,7 @@ 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)
@@ -1084,7 +1116,7 @@ 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()
{
@@ -1094,7 +1126,7 @@ public class GAlignFrame extends JInternalFrame
}
});
- showNpFeatsMenuitem.setText("Show Non-Positional Features");
+ showNpFeatsMenuitem.setText(MessageManager.getString("label.show_non_positional_features"));
showNpFeatsMenuitem.addActionListener(new ActionListener()
{
@@ -1104,7 +1136,7 @@ public class GAlignFrame extends JInternalFrame
}
});
- showGroupConservation.setText("Group Conservation");
+ showGroupConservation.setText(MessageManager.getString("label.group_conservation"));
showGroupConservation.addActionListener(new ActionListener()
{
@@ -1115,7 +1147,7 @@ public class GAlignFrame extends JInternalFrame
});
- showGroupConsensus.setText("Group Consensus");
+ showGroupConsensus.setText(MessageManager.getString("label.group_consensus"));
showGroupConsensus.addActionListener(new ActionListener()
{
@@ -1125,7 +1157,7 @@ public class GAlignFrame extends JInternalFrame
}
});
- showConsensusHistogram.setText("Show Consensus Histogram");
+ showConsensusHistogram.setText(MessageManager.getString("label.show_consensus_histogram"));
showConsensusHistogram.addActionListener(new ActionListener()
{
@@ -1135,7 +1167,7 @@ public class GAlignFrame extends JInternalFrame
}
});
- showSequenceLogo.setText("Show Consensus Logo");
+ showSequenceLogo.setText(MessageManager.getString("label.show_consensus_logo"));
showSequenceLogo.addActionListener(new ActionListener()
{
@@ -1145,7 +1177,7 @@ public class GAlignFrame extends JInternalFrame
}
});
- normaliseSequenceLogo.setText("Normalise Consensus Logo");
+ normaliseSequenceLogo.setText(MessageManager.getString("label.norm_consensus_logo"));
normaliseSequenceLogo.addActionListener(new ActionListener()
{
@@ -1155,7 +1187,7 @@ 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()
@@ -1168,7 +1200,7 @@ 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)
@@ -1177,7 +1209,7 @@ public class GAlignFrame extends JInternalFrame
}
});
- tcoffeeColour.setText("T-Coffee scores");
+ tcoffeeColour.setText(MessageManager.getString("label.tcoffee_scores"));
tcoffeeColour.setEnabled(false);
tcoffeeColour.addActionListener(new ActionListener()
{
@@ -1189,7 +1221,7 @@ public class GAlignFrame extends JInternalFrame
}
});
- deleteGroups.setText("Undefine groups");
+ deleteGroups.setText(MessageManager.getString("action.undefine_groups"));
deleteGroups.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
java.awt.event.KeyEvent.VK_U, Toolkit.getDefaultToolkit()
.getMenuShortcutKeyMask(), false));
@@ -1200,7 +1232,29 @@ 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));
@@ -1212,7 +1266,7 @@ 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));
@@ -1223,7 +1277,7 @@ 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()
@@ -1233,8 +1287,8 @@ 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()
@@ -1246,7 +1300,7 @@ 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));
@@ -1257,7 +1311,7 @@ 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)
@@ -1272,9 +1326,9 @@ 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)
@@ -1283,7 +1337,7 @@ 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()
{
@@ -1300,8 +1354,8 @@ 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)
@@ -1311,7 +1365,7 @@ public class GAlignFrame extends JInternalFrame
});
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)
@@ -1321,7 +1375,7 @@ 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)
@@ -1331,7 +1385,7 @@ 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)
@@ -1341,7 +1395,7 @@ 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()
{
@@ -1352,7 +1406,7 @@ 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()
{
@@ -1363,7 +1417,7 @@ 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)
@@ -1371,7 +1425,7 @@ 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()
{
@@ -1380,8 +1434,8 @@ 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)
@@ -1397,7 +1451,7 @@ 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()
{
@@ -1417,10 +1471,10 @@ 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()
@@ -1431,7 +1485,7 @@ 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)
@@ -1439,7 +1493,7 @@ 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)
@@ -1447,7 +1501,7 @@ 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)
@@ -1457,14 +1511,14 @@ 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)
@@ -1472,7 +1526,7 @@ 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)
@@ -1481,7 +1535,7 @@ 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)
@@ -1490,7 +1544,7 @@ 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)
@@ -1499,7 +1553,7 @@ 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)
@@ -1507,7 +1561,7 @@ 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()
@@ -1517,9 +1571,9 @@ public class GAlignFrame extends JInternalFrame
autoCalculate_actionPerformed(e);
}
});
- sortByTree.setText("Sort Alignment With New Tree");
+ sortByTree.setText(MessageManager.getString("label.sort_alignment_new_tree"));
sortByTree
- .setToolTipText("Enable this to automatically sort
the alignment when you open
a new tree.");
+ .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()
@@ -1530,9 +1584,9 @@ public class GAlignFrame extends JInternalFrame
}
});
- listenToViewSelections.setText("Listen for selections");
+ listenToViewSelections.setText(MessageManager.getString("label.listen_for_selections"));
listenToViewSelections
- .setToolTipText("When selected, selections in this view will mirror
selections made on the same sequences in other views.");
+ .setToolTipText("" + MessageManager.getString("label.selections_mirror_selections_made_same_sequences_other_views"));
listenToViewSelections.setState(false);
listenToViewSelections.addActionListener(new ActionListener()
{
@@ -1542,8 +1596,8 @@ 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)
@@ -1551,7 +1605,7 @@ 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)
@@ -1559,7 +1613,7 @@ 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)
@@ -1567,7 +1621,7 @@ 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)
@@ -1575,7 +1629,7 @@ 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)
@@ -1584,9 +1638,9 @@ 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)
@@ -1594,8 +1648,8 @@ 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)
@@ -1603,9 +1657,9 @@ 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)
@@ -1613,8 +1667,8 @@ 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)
@@ -1622,7 +1676,7 @@ 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)
@@ -1631,7 +1685,7 @@ 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)
@@ -1639,9 +1693,9 @@ public class GAlignFrame extends JInternalFrame
hideAllButSelection_actionPerformed(e);
}
});
- showAllhidden.setText("All Sequences and Columns");
+ showAllhidden.setText(MessageManager.getString("label.all_sequences_columns"));
showAllhidden
- .setToolTipText("H toggles visibility of hidden or selected regions.");
+ .setToolTipText(MessageManager.getString("label.toggles_visibility_hidden_selected_regions"));
showAllhidden.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -1650,7 +1704,7 @@ 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)
@@ -1658,7 +1712,7 @@ 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()
@@ -1693,7 +1747,7 @@ 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));
@@ -1705,7 +1759,7 @@ 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)
@@ -1713,7 +1767,7 @@ 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));
@@ -1724,9 +1778,8 @@ 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)
@@ -1734,9 +1787,9 @@ 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)
@@ -1745,7 +1798,7 @@ 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()
@@ -1756,7 +1809,7 @@ 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()
@@ -1766,7 +1819,7 @@ 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)
@@ -1774,7 +1827,7 @@ 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)
@@ -1782,8 +1835,8 @@ 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);
@@ -1874,6 +1927,7 @@ 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);
@@ -1883,7 +1937,7 @@ public class GAlignFrame extends JInternalFrame
colourMenu.add(abovePIDThreshold);
colourMenu.add(modifyPID);
colourMenu.add(annotationColour);
- colourMenu.add(rnahelicesColour);
+ colourMenu.add(rnahelicesColour);
calculateMenu.add(sort);
calculateMenu.add(calculateTree);
calculateMenu.addSeparator();
@@ -1896,7 +1950,7 @@ 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);
@@ -1905,10 +1959,6 @@ 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);
@@ -1947,8 +1997,11 @@ 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);
+ selectMenu.add(deleteGroups);
+ calculateMenu.add(expandAlignment);
// TODO - determine if the listenToViewSelections button is needed : see bug
// JAL-574
// selectMenu.addSeparator();
@@ -2268,6 +2321,11 @@ public class GAlignFrame extends JInternalFrame
protected void purinePyrimidineColour_actionPerformed(ActionEvent e)
{
}
+
+ protected void RNAInteractionColour_actionPerformed(ActionEvent e)
+ {
+ }
+
/*
* protected void covariationColour_actionPerformed(ActionEvent e) { }
@@ -2308,6 +2366,14 @@ public class GAlignFrame extends JInternalFrame
protected void deleteGroups_actionPerformed(ActionEvent e)
{
}
+
+ protected void createGroup_actionPerformed(ActionEvent e)
+ {
+ }
+
+ protected void unGroup_actionPerformed(ActionEvent e)
+ {
+ }
protected void copy_actionPerformed(ActionEvent e)
{
@@ -2581,4 +2647,10 @@ public class GAlignFrame extends JInternalFrame
{
}
+
+ protected void expand_newalign(ActionEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
}