Merge branch 'jims_marckhacks' into Release_2_8_1_Branch

diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties
index 56d6ca7..775df57 100644 (file)
--- a/resources/lang/Messages.properties
+++ b/resources/lang/Messages.properties
@@ -133,6 +133,8 @@ action.show_chain = Show Chain
 action.show_group = Show Group\r
 action.fetch_db_references = Fetch DB References\r
 action.edit = Edit\r
+action.view_flanking_regions = Show flanking regions\r
+label.view_flanking_regions = Show sequence data either side of the subsequences involved in this alignment\r
 label.str = Str:\r
 label.seq = Seq:\r
 label.structures_manager = Structures Manager\r
@@ -163,6 +165,15 @@ label.redo_command = Redo {0}
 label.principal_component_analysis = Principal Component Analysis\r
 label.average_distance_identity = Average Distance Using % Identity\r
 label.neighbour_joining_identity = Neighbour Joining Using % Identity\r
+label.treecalc_title = {0} Using {1}\r
+label.tree_calc_av = Average Distance\r
+label.tree_calc_nj = Neighbour Joining\r
+label.select_score_model = Select score model\r
+label.score_model_pid = % Identity\r
+label.score_model_blosum62 = BLOSUM62\r
+label.score_model_pam250 = PAM 250\r
+label.score_model_conservation = Physicochemical property conservation\r
+label.score_model_enhconservation = Physicochemical property conservation\r
 label.status_bar = Status bar\r
 label.out_to_textbox = Output to Textbox\r
 label.clustalx = Clustalx\r

diff --git a/src/jalview/analysis/AlignmentUtils.java b/src/jalview/analysis/AlignmentUtils.java
index 5bbdc4a..85699a4 100644 (file)
--- a/src/jalview/analysis/AlignmentUtils.java
+++ b/src/jalview/analysis/AlignmentUtils.java
@@ -28,7 +28,7 @@ public class AlignmentUtils
     for (SequenceI s:core.getSequences())
     {
       SequenceI newSeq = s.deriveSequence();
-      if (newSeq.getStart()>maxoffset)
+      if (newSeq.getStart()>maxoffset && newSeq.getDatasetSequence().getStart()<s.getStart())
       {
         maxoffset = newSeq.getStart();
       }

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 3f9ebaf..da34013 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -3945,23 +3945,30 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   {
     calculateTree.removeAll();
     // build the calculate menu
+    
     for (final String type:new String[] {"NJ", "AV"})
     {
+      String treecalcnm = MessageManager.getString("label.tree_calc_"+type.toLowerCase());
       for (final Object pwtype: ResidueProperties.scoreMatrices.keySet())
       {
         JMenuItem tm = new JMenuItem();
         ScoreModelI sm = ResidueProperties.scoreMatrices.get(pwtype);
-        final String title="Calculate "+type+" using "+sm.getName();
-        tm.setText(title);// MessageManager.getString("label.neighbour_blosum62"));
-        tm
-                .addActionListener(new java.awt.event.ActionListener()
-                {
-                  public void actionPerformed(ActionEvent e)
-                  {
-                    NewTreePanel(type, (String) pwtype, title);
-                  }
-                });
-        calculateTree.add(tm);
+        if (sm.isProtein()==!viewport.getAlignment().isNucleotide())
+        {
+          String smn = MessageManager.getStringOrReturn(
+                  "label.score_model_", sm.getName());
+          final String title = MessageManager.formatMessage(
+                  "label.treecalc_title", treecalcnm, smn);
+          tm.setText(title);//
+          tm.addActionListener(new java.awt.event.ActionListener()
+          {
+            public void actionPerformed(ActionEvent e)
+            {
+              NewTreePanel(type, (String) pwtype, title);
+            }
+          });
+          calculateTree.add(tm);
+        }
 
       }
     }

diff --git a/src/jalview/gui/PCAPanel.java b/src/jalview/gui/PCAPanel.java
index fc32e54..ccc4697 100644 (file)
--- a/src/jalview/gui/PCAPanel.java
+++ b/src/jalview/gui/PCAPanel.java
@@ -28,7 +28,6 @@ import javax.swing.*;
 import jalview.datamodel.*;
 import jalview.jbgui.*;
 import jalview.schemes.ResidueProperties;
-import jalview.schemes.ScoreMatrix;
 import jalview.util.MessageManager;
 import jalview.viewmodel.PCAModel;
 
@@ -115,26 +114,29 @@ public class PCAPanel extends GPCAPanel implements Runnable,
   protected void scoreMatrix_menuSelected()
   {
     scoreMatrixMenu.removeAll();
-    for (final Object sm:ResidueProperties.scoreMatrices.keySet())
+    for (final String sm:ResidueProperties.scoreMatrices.keySet())
     {
-      JMenuItem jm=new JMenuItem();
-      jm.setText((String)sm);
-      jm.setSelected(pcaModel.getScore_matrix().equals((String)sm));
-      final PCAPanel us = this;
-      jm.addActionListener(new ActionListener()
+      JCheckBoxMenuItem jm=new JCheckBoxMenuItem();
+      jm.setText(MessageManager.getStringOrReturn("label.score_model", sm));
+      jm.setSelected(pcaModel.getScore_matrix().equals(sm));
+      if (pcaModel.isNucleotide()==ResidueProperties.scoreMatrices.get(sm).isDNA())
       {
-        @Override
-        public void actionPerformed(ActionEvent e)
+        final PCAPanel us = this;
+        jm.addActionListener(new ActionListener()
         {
-          if (!pcaModel.getScore_matrix().equals((String)sm))
+          @Override
+          public void actionPerformed(ActionEvent e)
           {
-            pcaModel.setScore_matrix((String) sm);
-            Thread worker = new Thread(us);
-            worker.start();
+            if (!pcaModel.getScore_matrix().equals((String) sm))
+            {
+              pcaModel.setScore_matrix((String) sm);
+              Thread worker = new Thread(us);
+              worker.start();
+            }
           }
-        }
-      });
-      scoreMatrixMenu.add(jm);   
+        });
+        scoreMatrixMenu.add(jm);
+      }
     }
   }
   public void bgcolour_actionPerformed(ActionEvent e)
@@ -203,6 +205,7 @@ public class PCAPanel extends GPCAPanel implements Runnable,
     if (!pcaModel.isNucleotide())
     {
       pcaModel.setNucleotide(true);
+      pcaModel.setScore_matrix("DNA");
       Thread worker = new Thread(this);
       worker.start();
     }
@@ -216,6 +219,7 @@ public class PCAPanel extends GPCAPanel implements Runnable,
     if (pcaModel.isNucleotide())
     {
       pcaModel.setNucleotide(false);
+      pcaModel.setScore_matrix("BLOSUM62");
       Thread worker = new Thread(this);
       worker.start();
     }

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index 6feca56..698d4af 100755 (executable)
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -633,6 +633,7 @@ public class GAlignFrame extends JInternalFrame
       }
     });
     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)

diff --git a/src/jalview/jbgui/GPCAPanel.java b/src/jalview/jbgui/GPCAPanel.java
index 1eb73bd..266bfc6 100755 (executable)
--- a/src/jalview/jbgui/GPCAPanel.java
+++ b/src/jalview/jbgui/GPCAPanel.java
@@ -223,7 +223,7 @@ public class GPCAPanel extends JInternalFrame
       {
       }
     });
-    scoreMatrixMenu.setText(MessageManager.getString("label.score_matrices"));
+    scoreMatrixMenu.setText(MessageManager.getString("label.select_score_model"));
     scoreMatrixMenu.addMenuListener(new MenuListener()
     {
       public void menuSelected(MenuEvent e)

diff --git a/src/jalview/util/MessageManager.java b/src/jalview/util/MessageManager.java
index 5f7f0e2..0ba7566 100644 (file)
--- a/src/jalview/util/MessageManager.java
+++ b/src/jalview/util/MessageManager.java
@@ -64,4 +64,25 @@ public class MessageManager {
        public static String formatMessage(String key, Object... params){
                return MessageFormat.format(rb.getString(key), (Object[]) params);
        }
+
+  /**
+   * lookup and return a key given a root and a human-readable(ish) name that when combined might resolve to an i18n string.
+   * If the key doesn't resolve, then name is returned.if the key doesn't exist.
+   * Use this for programatically constructed keys that have have a human readable alternative used in the program (e.g. BLOSUM62 and label.score_blosum62) 
+   * @param keyroot
+   * @param name
+   * @return
+   */
+  public static String getStringOrReturn(String keyroot, String name)
+  {
+    String smkey = keyroot
+            + name.toLowerCase().replaceAll(" ", "");
+    try {
+      name = rb.getString(smkey); 
+    }
+    catch (Exception x) {
+      log.finest("I18N missing key with root "+keyroot+": "+loc+"\t"+smkey);
+    }
+    return name;
+  }
 }

diff --git a/src/jalview/ws/DBRefFetcher.java b/src/jalview/ws/DBRefFetcher.java
index d742eaa..84eba02 100644 (file)
--- a/src/jalview/ws/DBRefFetcher.java
+++ b/src/jalview/ws/DBRefFetcher.java
@@ -658,6 +658,11 @@ public class DBRefFetcher implements Runnable
         // unknownSequences.remove(sequence);
         int absEnd = absStart + nonGapped.length();
         absStart += 1;
+        if (!trimDatasetSeqs) {
+          // insert full length sequence from record
+          sequence.setSequence(entry.getSequenceAsString());
+          sequence.setStart(entry.getStart());
+        }
         if (updateRefFrame)
         {
           // finally, update local sequence reference frame if we're allowed
@@ -665,9 +670,6 @@ public class DBRefFetcher implements Runnable
             // just fix start/end
             sequence.setStart(absStart);
             sequence.setEnd(absEnd);
-          } else {
-            // insert full length sequence from record
-            sequence.setSequence(entry.getSequenceAsString());
           }
           // search for alignment sequences to update coordinate frame for
           for (int alsq = 0; alsq < alseqs.length; alsq++)