Merge commit 'ab43013b7e357b84b4abade0dba949668dfb2a0e' into develop

[jalview.git] / src / jalview / gui / PopupMenu.java

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 957ca46..07b8d16 100644 (file)
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -29,6 +29,7 @@ import jalview.commands.EditCommand.Action;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Annotation;
+import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.Sequence;
@@ -140,6 +141,8 @@ public class PopupMenu extends JPopupMenu
   JMenuItem sequenceDetails = new JMenuItem();
 
   JMenuItem sequenceSelDetails = new JMenuItem();
+  
+  JMenuItem makeReferenceSeq = new JMenuItem();
 
   JMenuItem chooseAnnotations = new JMenuItem();
 
@@ -220,6 +223,8 @@ public class PopupMenu extends JPopupMenu
 
   JMenu groupLinksMenu;
 
+  JMenuItem hideInsertions = new JMenuItem();
+
   /**
    * Creates a new PopupMenu object.
    * 
@@ -322,6 +327,12 @@ public class PopupMenu extends JPopupMenu
     if (seq != null)
     {
       sequenceMenu.setText(sequence.getName());
+      if (seq == ap.av.getAlignment().getSeqrep())
+      {
+        makeReferenceSeq.setText("Unmark representative");
+      } else {
+        makeReferenceSeq.setText("Mark as representative");
+      }
 
       if (seq.getDatasetSequence().getPDBId() != null
               && seq.getDatasetSequence().getPDBId().size() > 0)
@@ -369,7 +380,6 @@ public class PopupMenu extends JPopupMenu
         }
         // structureMenu.remove(colStructureMenu);
       }
-
       if (ap.av.getAlignment().isNucleotide() == true)
       {
         AlignmentAnnotation[] aa = ap.av.getAlignment()
@@ -441,7 +451,6 @@ public class PopupMenu extends JPopupMenu
             }
           }
         }
-
       }
 
       menuItem = new JMenuItem(
@@ -1507,7 +1516,28 @@ public class PopupMenu extends JPopupMenu
         editSequence_actionPerformed(actionEvent);
       }
     });
+    makeReferenceSeq.setText(MessageManager
+            .getString("label.mark_as_representative"));
+    makeReferenceSeq.addActionListener(new ActionListener()
+    {
+      
+      @Override
+      public void actionPerformed(ActionEvent actionEvent)
+      {
+        makeReferenceSeq_actionPerformed(actionEvent);
+        
+      }
+    });
+    hideInsertions.setText(MessageManager.getString("label.hide_insertions"));
+    hideInsertions.addActionListener(new ActionListener()
+    {
 
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        hideInsertions_actionPerformed(e);
+      }
+    });
     /*
      * annotationMenuItem.setText("By Annotation");
      * annotationMenuItem.addActionListener(new ActionListener() { public void
@@ -1517,7 +1547,11 @@ public class PopupMenu extends JPopupMenu
     groupMenu.add(sequenceSelDetails);
     add(groupMenu);
     add(sequenceMenu);
-    this.add(structureMenu);
+    add(structureMenu);
+    if (sequence!=null)
+    {
+      add(hideInsertions);
+    }
     // annotations configuration panel suppressed for now
     // groupMenu.add(chooseAnnotations);
 
@@ -1539,6 +1573,7 @@ public class PopupMenu extends JPopupMenu
     groupMenu.add(jMenu1);
     sequenceMenu.add(sequenceName);
     sequenceMenu.add(sequenceDetails);
+    sequenceMenu.add(makeReferenceSeq);
     colourMenu.add(textColour);
     colourMenu.add(noColourmenuItem);
     colourMenu.add(clustalColour);
@@ -1913,6 +1948,43 @@ public class PopupMenu extends JPopupMenu
     refresh();
   }
 
+  protected void makeReferenceSeq_actionPerformed(ActionEvent actionEvent)
+  {
+    if (!ap.av.getAlignment().hasSeqrep())
+    {
+      // initialise the display flags so the user sees something happen
+      ap.av.setDisplayReferenceSeq(true);
+      ap.av.setColourByReferenceSeq(true);
+      ap.av.getAlignment().setSeqrep(sequence);
+    }
+    else
+    {
+      if (ap.av.getAlignment().getSeqrep() == sequence)
+      {
+        ap.av.getAlignment().setSeqrep(null);
+      }
+      else
+      {
+        ap.av.getAlignment().setSeqrep(sequence);
+      }
+    }
+    refresh();
+  }
+
+  protected void hideInsertions_actionPerformed(ActionEvent actionEvent)
+  {
+    if (sequence != null)
+    {
+      ColumnSelection cs = ap.av.getColumnSelection();
+      if (cs == null)
+      {
+        cs = new ColumnSelection();
+      }
+      cs.hideInsertionsFor(sequence);
+      ap.av.setColumnSelection(cs);
+    }
+    refresh();
+  }
   protected void sequenceSelectionDetails_actionPerformed()
   {
     createSequenceDetailsReport(ap.av.getSequenceSelection());
@@ -1943,7 +2015,9 @@ public class PopupMenu extends JPopupMenu
                       true,
                       true,
                       false,
-                      (ap.seqPanel.seqCanvas.fr != null) ? ap.seqPanel.seqCanvas.fr.minmax
+                      (ap.getSeqPanel().seqCanvas.fr != null) ? ap
+                              .getSeqPanel().seqCanvas.fr
+                              .getMinMax()
                               : null);
       contents.append("</p>");
     }
@@ -2660,7 +2734,7 @@ public class PopupMenu extends JPopupMenu
     System.arraycopy(features, 0, tfeatures, 0, rsize);
     features = tfeatures;
     seqs = rseqs;
-    if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs,
+    if (ap.getSeqPanel().seqCanvas.getFeatureRenderer().amendFeatures(seqs,
             features, true, ap))
     {
       ap.alignFrame.setShowSeqFeatures(true);