X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAPopupMenu.java;h=ede493e88f44ee51e47c3392d95f02879218457c;hb=4f1f764c09427cd63c3e355fa729da86735a8194;hp=fde6bb8c91be72c8caacf5a4fdedefd7d05728ef;hpb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;p=jalview.git

diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index fde6bb8..ede493e 100755
--- a/src/jalview/appletgui/APopupMenu.java
+++ b/src/jalview/appletgui/APopupMenu.java
@@ -68,6 +68,7 @@ public class APopupMenu
   MenuItem hideSeqs = new MenuItem();
   MenuItem repGroup = new MenuItem();
   MenuItem sequenceName = new MenuItem("Edit Name/Description");
+  MenuItem sequenceFeature = new MenuItem("Create Sequence Feature");
 
   Sequence seq;
   MenuItem revealAll = new MenuItem();
@@ -302,8 +303,9 @@ public class APopupMenu
           getGroup().getDescription(),
           "       Group Name",
           "Group Description",
-          ap,
-          "Edit Group Name / Description");
+          ap.alignFrame,
+          "Edit Group Name / Description",
+          500,100);
 
       if (dialog.accept)
       {
@@ -398,6 +400,35 @@ public class APopupMenu
 
       }
     }
+    else if(source == sequenceFeature)
+    {
+      SequenceGroup sg = ap.av.getSelectionGroup();
+      if (sg == null)
+      {
+        return;
+      }
+
+      int gSize = sg.getSize();
+      SequenceI[] seqs = new SequenceI[gSize];
+      SequenceFeature[] features = new SequenceFeature[gSize];
+
+      for (int i = 0; i < gSize; i++)
+      {
+        seqs[i] = sg.getSequenceAt(i);
+        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))
+      {
+        ap.alignFrame.sequenceFeatures.setState(true);
+        ap.av.showSequenceFeatures(true);
+        ap.highlightSearchResults(null);
+      }
+    }
     else
     {
       outputText(evt);
@@ -429,14 +460,15 @@ public class APopupMenu
         seq.getDescription(),
         "       Sequence Name",
         "Sequence Description",
-        ap,
-        "Edit Sequence Name / Description");
+        ap.alignFrame,
+        "Edit Sequence Name / Description",
+        500,100);
 
     if (dialog.accept)
     {
       seq.setName(dialog.getName());
       seq.setDescription(dialog.getDescription());
-      ap.repaint();
+      ap.paintAlignment(false);
     }
   }
 
@@ -455,6 +487,7 @@ public class APopupMenu
   {
     groupMenu.setLabel("Group");
     groupMenu.setLabel("Selection");
+    sequenceFeature.addActionListener(this);
 
     editGroupName.addActionListener(this);
     unGroupMenuItem.setLabel("Remove Group");
@@ -488,7 +521,9 @@ public class APopupMenu
     groupMenu.add(editGroupName);
     groupMenu.add(editMenu);
     groupMenu.add(outputmenu);
+    groupMenu.add(sequenceFeature);
     groupMenu.add(menu1);
+
     colourMenu.add(noColourmenuItem);
     colourMenu.add(clustalColour);
     colourMenu.add(BLOSUM62Colour);
@@ -561,11 +596,7 @@ public class APopupMenu
 
   void refresh()
   {
-    ap.seqPanel.seqCanvas.repaint();
-    if (ap.overviewPanel != null)
-    {
-      ap.overviewPanel.updateOverviewImage();
-    }
+    ap.paintAlignment(true);
   }
 
   protected void clustalColour_actionPerformed()
@@ -739,7 +770,7 @@ public class APopupMenu
     SequenceGroup sg = ap.av.getSelectionGroup();
     ap.av.alignment.deleteGroup(sg);
     ap.av.setSelectionGroup(null);
-    ap.repaint();
+    ap.paintAlignment(true);
   }
 
   public void showColourText_itemStateChanged()