X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=e11830ccb0c15d1c290c006cc6d6ac4961294584;hb=012fc200ee0d124003524855ac7cd50be4b7456c;hp=88ea11b281b18cdc804352cae7d69eee02e4909b;hpb=8797ce6a98df4aa29eefecb25b10fed4f2ab9e86;p=jalview.git

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 88ea11b..e11830c 100755
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -82,6 +82,7 @@ public class PopupMenu extends JPopupMenu
   JMenuItem enterPDB = new JMenuItem();
   JMenuItem discoverPDB = new JMenuItem();
   JMenu outputMenu = new JMenu();
+  JMenuItem sequenceFeature = new JMenuItem();
 
   /**
      * Creates a new PopupMenu object.
@@ -504,12 +505,22 @@ public class PopupMenu extends JPopupMenu
       }
     });
     outputMenu.setText("Output to Textbox...");
+    sequenceFeature.setText("Create Sequence Feature");
+    sequenceFeature.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        sequenceFeature_actionPerformed(e);
+      }
+    });
     add(groupMenu);
 
     add(sequenceMenu);
     groupMenu.add(editMenu);
     groupMenu.add(outputMenu);
     groupMenu.addSeparator();
+    groupMenu.add(sequenceFeature);
+    groupMenu.addSeparator();
     groupMenu.add(groupName);
     groupMenu.add(unGroupMenuItem);
         groupMenu.add(colourMenu);
@@ -842,6 +853,7 @@ public class PopupMenu extends JPopupMenu
 
          sg.cs = udc;
        }
+       refresh();
      }
     /**
      * DOCUMENT ME!
@@ -1309,4 +1321,31 @@ public class PopupMenu extends JPopupMenu
     new jalview.io.DBRefFetcher(
              ap.av.getAlignment(), ap.alignFrame).fetchDBRefs(false);
   }
+
+  public void sequenceFeature_actionPerformed(ActionEvent e)
+  {
+    SequenceGroup sg = ap.av.getSelectionGroup();
+    if(sg==null)
+      return;
+
+    int gSize= sg.getSize(false);
+    SequenceI [] seqs = new SequenceI[gSize];
+    SequenceFeature [] features = new SequenceFeature[gSize];
+
+    for (int i = 0; i < gSize; i++)
+    {
+      seqs[i] = sg.getSequenceAt(i).getDatasetSequence();
+      int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
+      int end = sg.findEndRes(sg.getSequenceAt(i));
+      features[i] = new SequenceFeature(null,null, null,start,end,"Jalview");
+    }
+
+    if (ap.seqPanel.seqCanvas.getFeatureRenderer()
+        .createNewFeatures(seqs, features))
+    {
+      ap.alignFrame.showSeqFeatures.setSelected(true);
+      ap.av.setShowSequenceFeatures(true);
+      ap.highlightSearchResults(null);
+    }
+  }
 }