From: Jim Procter <jprocter@compbio.dundee.ac.uk>
Date: Tue, 18 Feb 2014 17:12:38 +0000 (+0000)
Subject: Merge branch 'JAL-1445' into develop
X-Git-Tag: Jalview_2_9~207
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=8d2724b83aca38ef75d68787cc5939d950467e63;p=jalview.git

Merge branch 'JAL-1445' into develop
Carried over source formatting from 2.8.0b1 release

Conflicts:
	src/jalview/analysis/StructureFrequency.java
	src/jalview/ext/varna/VarnaCommands.java
	src/jalview/gui/AppVarna.java
	src/jalview/gui/PopupMenu.java
	src/jalview/io/AppletFormatAdapter.java
	src/jalview/io/StockholmFile.java
	src/jalview/jbgui/GAlignFrame.java
	src/jalview/jbgui/GDesktop.java
---

8d2724b83aca38ef75d68787cc5939d950467e63
diff --cc build.xml
index dc93408,82cbabb..31419c8
--- a/build.xml
+++ b/build.xml
@@@ -93,13 -94,14 +94,15 @@@
  		<!-- Webstart Image - looked for in resources/images -->
  		<property name="WebStartImage" value="JalviewLogo_big.png"/>
  		<!-- J2SE version needed for webstart launch -->
 -		<property name="j2sev" value="1.6+"/>
 +<!-- Anne's version needs 1.7 - should rebuild VARNA to java 1.6 for release -->
 +		<property name="j2sev" value="1.7+"/>
  
-     <!-- Permissions for running Java applets and applications. Defaults are those suitable for deploying jalview webstart/jalviewLite at www.jalview.org -->
-     <property name="application.codebase" value="*.jalview.org"/>
-     <property name="applet.codebase" value="*.jalview.org"/>
-     <property name="applet.caller-codebase" value="${applet.codebase}"/>
+     <!-- Permissions for running Java applets and applications. -->
+     <!-- Defaults are those suitable for deploying jalview webstart www.jalview.org -->
+     <property name="application.codebase" value="*.jalview.org" />
+     <!-- and allowing the applet to be deployed from any URL -->
+     <property name="applet.codebase" value="*" />
+     <property name="applet.caller-codebase" value="${applet.codebase}" />
  
  		<!-- build directory configuration -->
  		<property name="libDir" value="lib" />
diff --cc src/jalview/analysis/AlignSeq.java
index 6d8c0cd,573c545..9b09456
--- a/src/jalview/analysis/AlignSeq.java
+++ b/src/jalview/analysis/AlignSeq.java
@@@ -14,8 -14,10 +14,9 @@@
   * 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 <http://www.gnu.org/licenses/>.
+  * The Jalview Authors are detailed in the 'AUTHORS' file.
   */
  package jalview.analysis;
 -
  import java.util.*;
  
  import java.awt.*;
diff --cc src/jalview/analysis/StructureFrequency.java
index 9ebbe51,6409413..6816547
--- a/src/jalview/analysis/StructureFrequency.java
+++ b/src/jalview/analysis/StructureFrequency.java
@@@ -14,8 -14,8 +14,9 @@@
   * 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 <http://www.gnu.org/licenses/>.
+  * The Jalview Authors are detailed in the 'AUTHORS' file.
   */
 +
  package jalview.analysis;
  
  import java.util.*;
diff --cc src/jalview/ext/varna/VarnaCommands.java
index 21f626f,8ed7462..b5f0dc9
--- a/src/jalview/ext/varna/VarnaCommands.java
+++ b/src/jalview/ext/varna/VarnaCommands.java
@@@ -1,157 -1,168 +1,170 @@@
 -/*
 +/*
-  * 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 2.8.0b1)
+  * Copyright (C) 2014 The Jalview Authors
 - * 
 - * This file is part of Jalview.
 - * 
 - * Jalview is free software: you can redistribute it and/or
 - * modify it under the terms of the GNU General Public License 
 - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
 - *  
 - * Jalview is distributed in the hope that it will be useful, but 
 - * WITHOUT ANY WARRANTY; without even the implied warranty 
 - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
 - * PURPOSE.  See the GNU General Public License for more details.
 - * 
 - * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
 + * 
 + * This file is part of Jalview.
 + * 
 + * Jalview is free software: you can redistribute it and/or
 + * modify it under the terms of the GNU General Public License 
 + * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
 + *  
 + * Jalview is distributed in the hope that it will be useful, but 
 + * WITHOUT ANY WARRANTY; without even the implied warranty 
 + * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
 + * PURPOSE.  See the GNU General Public License for more details.
 + * 
 + * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+  * The Jalview Authors are detailed in the 'AUTHORS' file.
 - */
 -package jalview.ext.varna;
 -
 -import jalview.api.FeatureRenderer;
 -import jalview.api.SequenceRenderer;
 -import jalview.datamodel.AlignmentI;
 -import jalview.datamodel.SequenceI;
 -import jalview.structure.StructureMapping;
 -import jalview.structure.StructureSelectionManager;
 -
 -import java.awt.Color;
 -import java.util.ArrayList;
 -
 -/**
 + */
 +package jalview.ext.varna;
 +
 +import jalview.api.FeatureRenderer;
 +import jalview.api.SequenceRenderer;
 +import jalview.datamodel.AlignmentI;
 +import jalview.datamodel.SequenceI;
 +import jalview.structure.StructureMapping;
 +import jalview.structure.StructureSelectionManager;
 +import jalview.util.Comparison;
 +
 +import java.awt.Color;
 +import java.util.ArrayList;
 +
 +/**
-  * Routines for generating Jmol commands for Jalview/Jmol binding
-  * another cruisecontrol test.
+  * Routines for generating Jmol commands for Jalview/Jmol binding another
+  * cruisecontrol test.
 - * 
 - * @author JimP
 - * 
 - */
 -public class VarnaCommands
 -{
 -
 -  /**
 + * 
 + * @author JimP
 + *
 + */
 +public class VarnaCommands
 +{
 +
 +  /**
-    * Jmol utility which constructs the commands to colour chains by the given alignment
+    * Jmol utility which constructs the commands to colour chains by the given
+    * alignment
 -   * 
 -   */
 +   * 
 +   */
-   public static String[] getColourBySequenceCommand(StructureSelectionManager ssm, String[] files, SequenceI[][] sequence, SequenceRenderer sr, FeatureRenderer fr, AlignmentI alignment)
+   public static String[] getColourBySequenceCommand(
+           StructureSelectionManager ssm, String[] files,
+           SequenceI[][] sequence, SequenceRenderer sr, FeatureRenderer fr,
+           AlignmentI alignment)
 -  {
 -    ArrayList<String> str = new ArrayList<String>();
 -    StringBuffer command = new StringBuffer();
 -
 -    for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
 -    {
 -      StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
 -
 -      if (mapping == null || mapping.length < 1)
 -        continue;
 -
 -      int lastPos = -1;
 -      for (int s = 0; s < sequence[pdbfnum].length; s++)
 -      {
 -        for (int sp, m = 0; m < mapping.length; m++)
 -        {
 -          if (mapping[m].getSequence() == sequence[pdbfnum][s]
 -                  && (sp = alignment.findIndex(sequence[pdbfnum][s])) > -1)
 -          {
 -            SequenceI asp = alignment.getSequenceAt(sp);
 -            for (int r = 0; r < asp.getLength(); r++)
 -            {
 -              // no mapping to gaps in sequence
 -              if (jalview.util.Comparison.isGap(asp.getCharAt(r)))
 -              {
 -                continue;
 -              }
 -              int pos = mapping[m].getPDBResNum(asp.findPosition(r));
 -
 -              if (pos < 1 || pos == lastPos)
 -                continue;
 -
 -              lastPos = pos;
 -
 -              Color col = sr.getResidueBoxColour(sequence[pdbfnum][s], r);
 -
 -              if (fr != null)
 -                col = fr.findFeatureColour(col, sequence[pdbfnum][s], r);
 -              String newSelcom = (mapping[m].getChain() != " " ? ":"
 -                      + mapping[m].getChain() : "")
 -                      + "/"
 -                      + (pdbfnum + 1)
 -                      + ".1"
 -                      + ";color["
 -                      + col.getRed()
 -                      + ","
 -                      + col.getGreen()
 -                      + ","
 -                      + col.getBlue() + "]";
 +  {
 +	
 +    ArrayList<String> str = new ArrayList<String>();
 +    StringBuffer command = new StringBuffer();
 +  
 +    for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
 +    {
 +      StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
 +  
 +      if (mapping == null || mapping.length < 1)
 +        continue;
 +  
 +      int lastPos = -1;
 +      for (int s = 0; s < sequence[pdbfnum].length; s++)
 +      {
 +        for (int sp, m = 0; m < mapping.length; m++)
 +        {
 +          if (mapping[m].getSequence() == sequence[pdbfnum][s]
 +                  && (sp = alignment.findIndex(sequence[pdbfnum][s])) > -1)
 +          {
 +            SequenceI asp = alignment.getSequenceAt(sp);
 +            for (int r = 0; r < asp.getLength(); r++)
 +            {
 +              // no mapping to gaps in sequence
 +              if (jalview.util.Comparison.isGap(asp.getCharAt(r)))
 +              {
 +                continue;
 +              }
 +              int pos = mapping[m].getPDBResNum(asp.findPosition(r));
 +  
 +              if (pos < 1 || pos == lastPos)
 +                continue;
 +  
 +              lastPos = pos;
 +  
 +              Color col = sr.getResidueBoxColour(sequence[pdbfnum][s], r);
 +  
 +              if (fr != null)
 +                col = fr.findFeatureColour(col, sequence[pdbfnum][s], r);
 +              String newSelcom = (mapping[m].getChain() != " " ? ":"
 +                      + mapping[m].getChain() : "")
 +                      + "/"
 +                      + (pdbfnum + 1)
 +                      + ".1"
 +                      + ";color["
 +                      + col.getRed()
 +                      + ","
 +                      + col.getGreen()
 +                      + ","
 +                      + col.getBlue() + "]";
-               if (command.length()>newSelcom.length() && command.substring(command.length()-newSelcom.length()).equals(newSelcom))
+               if (command.length() > newSelcom.length()
+                       && command.substring(
+                               command.length() - newSelcom.length())
+                               .equals(newSelcom))
 -              {
 -                command = VarnaCommands.condenseCommand(command, pos);
 -                continue;
 -              }
 -              // TODO: deal with case when buffer is too large for Jmol to parse
 -              // - execute command and flush
 -
 -              command.append(";");
 -              if (command.length() > 51200)
 -              {
 -                // add another chunk
 -                str.add(command.toString());
 -                command.setLength(0);
 -              }
 -              command.append("select " + pos);
 -              command.append(newSelcom);
 -            }
 -            break;
 -          }
 -        }
 -      }
 -    }
 -    {
 -      // add final chunk
 -      str.add(command.toString());
 -      command.setLength(0);
 -    }
 -    return str.toArray(new String[str.size()]);
 -  }
 -
 -  public static StringBuffer condenseCommand(StringBuffer command, int pos)
 -  {
 -
 -    // work back to last 'select'
 -    int p = command.length(), q = p;
 +              {
 +                command = VarnaCommands.condenseCommand(command, pos);
 +                continue;
 +              }
 +              // TODO: deal with case when buffer is too large for Jmol to parse
 +              // - execute command and flush
 +  
 +              command.append(";");
 +              if (command.length()>51200)
 +              {
 +                // add another chunk
 +                str.add(command.toString());
 +                command.setLength(0);
 +              }
 +              command.append("select " + pos);
 +              command.append(newSelcom);
 +            }
 +            break;
 +          }
 +        }
 +      }
 +    }
 +    {
 +      // add final chunk
 +      str.add(command.toString());
 +      command.setLength(0);
 +    }
 +    return str.toArray(new String[str.size()]);
 +  }
 +
 +  public static StringBuffer condenseCommand(StringBuffer command, int pos)
 +  {
 +  
 +    // work back to last 'select'
 +    int p=command.length(),q=p;
-     do {
+     do
+     {
 -      p -= 6;
 +      p-=6;
-       if (p<1) { p=0; };
+       if (p < 1)
+       {
+         p = 0;
+       }
+       ;
 -    } while ((q = command.indexOf("select", p)) == -1 && p > 0);
 -
 -    StringBuffer sb = new StringBuffer(command.substring(0, q + 7));
 -
 -    command = command.delete(0, q + 7);
 -
 -    String start;
 -
 -    if (command.indexOf("-") > -1)
 -    {
 -      start = command.substring(0, command.indexOf("-"));
 -    }
 -    else
 -    {
 -      start = command.substring(0, command.indexOf(":"));
 -    }
 -
 -    sb.append(start + "-" + pos + command.substring(command.indexOf(":")));
 -
 -    return sb;
 -  }
 -
 -}
 +    } while ((q=command.indexOf("select",p))==-1 && p>0);
 +    
 +    StringBuffer sb = new StringBuffer(command.substring(0,q+7));
 +  
 +    command =  command.delete(0,q+7);
 +  
 +    String start;
 +  
 +    if (command.indexOf("-") > -1)
 +    {
 +      start = command.substring(0, command.indexOf("-"));
 +    }
 +    else
 +    {
 +      start = command.substring(0, command.indexOf(":"));
 +    }
 +  
 +    sb.append(start + "-" + pos + command.substring(command.indexOf(":")));
 +  
 +    return sb;
 +  }
 +
 +}
diff --cc src/jalview/gui/AppVarna.java
index 4bff08c,1de0cf2..a1f9a3d
--- a/src/jalview/gui/AppVarna.java
+++ b/src/jalview/gui/AppVarna.java
@@@ -17,28 -18,18 +18,32 @@@
   */
  package jalview.gui;
  
 -import java.util.*;
 +import jalview.bin.Cache;
 +import jalview.datamodel.ColumnSelection;
 +import jalview.datamodel.SequenceGroup;
 +import jalview.datamodel.SequenceI;
 +import jalview.structure.SecondaryStructureListener;
 +import jalview.structure.SelectionListener;
 +import jalview.structure.SelectionSource;
 +import jalview.structure.StructureSelectionManager;
 +import jalview.structure.VamsasSource;
 +import jalview.util.ShiftList;
 +
 +import java.awt.BorderLayout;
 +import java.awt.Color;
 +import java.util.ArrayList;
 +import java.util.Hashtable;
 +import java.util.Map;
  import java.util.regex.Matcher;
  import java.util.regex.Pattern;
 -import java.awt.*;
  
 -import javax.swing.*;
 +import javax.swing.JInternalFrame;
 +import javax.swing.JSplitPane;
  
+ import jalview.bin.Cache;
 -import jalview.datamodel.*;
 -import jalview.structure.*;
+ import jalview.util.MessageManager;
+ import jalview.util.ShiftList;
++
  import fr.orsay.lri.varna.VARNAPanel;
  import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
  import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
diff --cc src/jalview/gui/PopupMenu.java
index 037f007,0e39f34..fb4e237
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@@ -284,9 -280,8 +286,9 @@@ public class PopupMenu extends JPopupMe
              final String rnastruc = aa[i].getRNAStruc();
              final String structureLine = aa[i].label;
              menuItem = new JMenuItem();
-             menuItem.setText("2D RNA " + structureLine);
+             menuItem.setText(MessageManager.formatMessage("label.2d_rna_structure_line", new String[]{structureLine}));
              menuItem.addActionListener(new java.awt.event.ActionListener()
 +            
              {
                public void actionPerformed(ActionEvent e)
                {
@@@ -1074,33 -1045,7 +1066,33 @@@
          pdbFromFile_actionPerformed();
        }
      });
 +//    RNAFold.setText("From RNA Fold with predict2D");
 +//    RNAFold.addActionListener(new ActionListener()
 +//    {
 +//      public void actionPerformed(ActionEvent e)
 +//      {
 +//    	  try {
 +//			RNAFold_actionPerformed();
 +//		} catch (Exception e1) {
 +//			// TODO Auto-generated catch block
 +//			e1.printStackTrace();
 +//		}
 +//      }   
 +//    });
 +//    ContraFold.setText("From Contra Fold with predict2D");
 +//    ContraFold.addActionListener(new ActionListener()
 +//    {
 +//      public void actionPerformed(ActionEvent e)
 +//      {
 +//    	  try {
 +//			ContraFold_actionPerformed();
 +//		} catch (Exception e1) {
 +//			// TODO Auto-generated catch block
 +//			e1.printStackTrace();
 +//		}
 +//      }   
 +//    });
-     enterPDB.setText("Enter PDB Id");
+     enterPDB.setText(MessageManager.getString("label.enter_pdb_id"));
      enterPDB.addActionListener(new ActionListener()
      {
        public void actionPerformed(ActionEvent e)
diff --cc src/jalview/io/AppletFormatAdapter.java
index eac7cf2,6679a03..ae742c8
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@@ -68,10 -70,10 +69,8 @@@ public class AppletFormatAdapte
     * corresponding to READABLE_FNAMES
     */
    public static final String[] READABLE_EXTENSIONS = new String[]
-   { "fa,faa,fasta,fastq", "aln", "pfam", "msf", "pir", "blc", "amsa", "jar",
-       "sto,stk","xml,rnaml" }; // ,
- 
-   // ".blast"
+   { "fa, fasta, mfa, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa", "jar",
 -      "sto,stk" }; // ,
 -
 -  // ".blast"
++      "sto,stk","xml,rnaml" }; // ".blast"
    // };
  
    /**
diff --cc src/jalview/io/StockholmFile.java
index 4d8f136,4566bac..9064ad8
--- a/src/jalview/io/StockholmFile.java
+++ b/src/jalview/io/StockholmFile.java
@@@ -1,73 -1,50 +1,74 @@@
 -/*
 +/*
-  * 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 2.8.0b1)
+  * Copyright (C) 2014 The Jalview Authors
 - * 
 - * This file is part of Jalview.
 - * 
 - * Jalview is free software: you can redistribute it and/or
 - * modify it under the terms of the GNU General Public License 
 - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
 - *  
 - * Jalview is distributed in the hope that it will be useful, but 
 - * WITHOUT ANY WARRANTY; without even the implied warranty 
 - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
 - * PURPOSE.  See the GNU General Public License for more details.
 - * 
 - * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
 + * 
 + * This file is part of Jalview.
 + * 
 + * Jalview is free software: you can redistribute it and/or
 + * modify it under the terms of the GNU General Public License 
 + * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
 + *  
 + * Jalview is distributed in the hope that it will be useful, but 
 + * WITHOUT ANY WARRANTY; without even the implied warranty 
 + * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
 + * PURPOSE.  See the GNU General Public License for more details.
 + * 
 + * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+  * The Jalview Authors are detailed in the 'AUTHORS' file.
 - */
 -/*
 - * This extension was written by Benjamin Schuster-Boeckler at sanger.ac.uk
 - */
 -package jalview.io;
 -
 -import java.io.*;
 -import java.util.*;
 -
 -import com.stevesoft.pat.*;
 -import jalview.datamodel.*;
 -import jalview.util.Format;
 -
 -// import org.apache.log4j.*;
 -
 -/**
 - * This class is supposed to parse a Stockholm format file into Jalview There
 - * are TODOs in this class: we do not know what the database source and version
 - * is for the file when parsing the #GS= AC tag which associates accessions with
 - * sequences. Database references are also not parsed correctly: a separate
 - * reference string parser must be added to parse the database reference form
 - * into Jalview's local representation.
 - * 
 - * @author bsb at sanger.ac.uk
 - * @version 0.3 + jalview mods
 - * 
 - */
 -public class StockholmFile extends AlignFile
 -{
 -  // static Logger logger = Logger.getLogger("jalview.io.StockholmFile");
 + */
 +/*
 + * This extension was written by Benjamin Schuster-Boeckler at sanger.ac.uk
 + */
 +package jalview.io;
 +
 +import jalview.datamodel.AlignmentI;
 +import jalview.datamodel.AlignmentAnnotation;
 +import jalview.datamodel.AlignmentI;
 +import jalview.datamodel.Annotation;
 +import jalview.datamodel.DBRefEntry;
 +import jalview.datamodel.Mapping;
 +import jalview.datamodel.Sequence;
 +import jalview.datamodel.SequenceFeature;
 +import jalview.datamodel.SequenceI;
 +import jalview.util.Format;
 +
 +import java.io.BufferedReader;
 +import java.io.FileReader;
 +import java.io.IOException;
 +import java.util.ArrayList;
 +import java.util.Enumeration;
 +import java.util.Hashtable;
 +import java.util.List;
 +import java.util.StringTokenizer;
 +import java.util.Vector;
 +
 +import com.stevesoft.pat.Regex;
 +
 +import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
 +import fr.orsay.lri.varna.factories.RNAFactory;
 +import fr.orsay.lri.varna.models.rna.RNA;
 +
 +// import org.apache.log4j.*;
 +
 +/**
 + * This class is supposed to parse a Stockholm format file into Jalview There
 + * are TODOs in this class: we do not know what the database source and version
 + * is for the file when parsing the #GS= AC tag which associates accessions with
 + * sequences. Database references are also not parsed correctly: a separate
 + * reference string parser must be added to parse the database reference form
 + * into Jalview's local representation.
 + * 
 + * @author bsb at sanger.ac.uk
 + * @author Natasha Shersnev (Dundee, UK) (Stockholm file writer)
 + * @author Lauren Lui (UCSC, USA) (RNA secondary structure annotation import as stockholm)
 + * @author Anne Menard (Paris, FR) (VARNA parsing of Stockholm file data)
 + * @version 0.3 + jalview mods
 + * 
 + */
 +public class StockholmFile extends AlignFile
 +{
 +  // static Logger logger = Logger.getLogger("jalview.io.StockholmFile");
 +  protected ArrayList<RNA> result;
    StringBuffer out; // output buffer
  
    AlignmentI al;
diff --cc src/jalview/jbgui/GDesktop.java
index 5742337,4ef6fdd..f109058
--- a/src/jalview/jbgui/GDesktop.java
+++ b/src/jalview/jbgui/GDesktop.java
@@@ -126,14 -129,13 +129,14 @@@ public class GDesktop extends JFram
     */
    private void jbInit() throws Exception
    {
 +	 
-     FileMenu.setText("File");
-     HelpMenu.setText("Help");
+     FileMenu.setText(MessageManager.getString("action.file"));
+     HelpMenu.setText(MessageManager.getString("action.help"));
      VamsasMenu.setText("Vamsas");
-     VamsasMenu.setToolTipText("Share data with other vamsas applications.");
-     VamsasStMenu.setText("Connect to");
-     VamsasStMenu.setToolTipText("Join an existing vamsas session");
-     inputLocalFileMenuItem.setText("from File");
+     VamsasMenu.setToolTipText(MessageManager.getString("label.share_data_vamsas_applications"));
+     VamsasStMenu.setText(MessageManager.getString("label.connect_to"));
+     VamsasStMenu.setToolTipText(MessageManager.getString("label.join_existing_vamsas_session"));
+     inputLocalFileMenuItem.setText(MessageManager.getString("label.load_tree_from_file"));
      inputLocalFileMenuItem.setAccelerator(javax.swing.KeyStroke
              .getKeyStroke(java.awt.event.KeyEvent.VK_O, Toolkit
                      .getDefaultToolkit().getMenuShortcutKeyMask(), false));