X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqPanel.java;h=aaad2aed632c844ebad2b1c199613378fa44daa4;hb=6de402db90987d3645f3429d9073c13678d8e980;hp=0b9af01ca9a08ee2b0b749eb09f40fe9cec2d190;hpb=890bd0eac47a4b0f55bd062a359c16a43c3780a0;p=jalview.git

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 0b9af01..aaad2ae 100755
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -86,20 +86,20 @@ public class SeqPanel
    * @param avp DOCUMENT ME!
    * @param p DOCUMENT ME!
    */
-  public SeqPanel(AlignViewport avp, AlignmentPanel p)
+  public SeqPanel(AlignViewport av, AlignmentPanel ap)
   {
     linkImageURL = getClass().getResource("/images/link.gif");
     ToolTipManager.sharedInstance().registerComponent(this);
     ToolTipManager.sharedInstance().setInitialDelay(0);
     ToolTipManager.sharedInstance().setDismissDelay(10000);
-    this.av = avp;
+    this.av = av;
     setBackground(Color.white);
 
-    seqCanvas = new SeqCanvas(avp);
+    seqCanvas = new SeqCanvas(ap);
     setLayout(new BorderLayout());
     add(seqCanvas, BorderLayout.CENTER);
 
-    ap = p;
+    this.ap = ap;
 
     if (!av.isDataset())
     {
@@ -204,6 +204,13 @@ public class SeqPanel
           continue;
         }
 
+        if (features[i].featureGroup != null
+           && seqCanvas.fr.featureGroups!=null
+            && seqCanvas.fr.featureGroups.containsKey(features[i].featureGroup)
+            && !((Boolean)seqCanvas.fr.featureGroups.get(features[i].featureGroup)).booleanValue())
+          continue;
+
+
         if ( (features[i].getBegin() <= res) &&
             (features[i].getEnd() >= res))
         {
@@ -213,36 +220,11 @@ public class SeqPanel
     }
 
     features = new SequenceFeature[tmp.size()];
-    for (int i = 0; i < tmp.size(); i++)
-    {
-      features[i] = (SequenceFeature) tmp.elementAt(i);
-    }
+    tmp.copyInto(features);
 
     return features;
   }
 
-  Vector getAllFeaturesAtRes(SequenceI seq, int res)
-  {
-    Vector allFeatures = new Vector();
-    int index = 0;
-    if (seq.getSequenceFeatures() != null && av.featuresDisplayed != null)
-    {
-      while (index < seq.getSequenceFeatures().length)
-      {
-        SequenceFeature sf = seq.getSequenceFeatures()[index];
-        if (sf.getBegin() <= res &&
-            sf.getEnd() >= res)
-        {
-          if (av.featuresDisplayed.containsKey(sf.getType()))
-          {
-            allFeatures.addElement(sf);
-          }
-        }
-        index++;
-      }
-    }
-    return allFeatures;
-  }
 
   void endEditing()
   {
@@ -534,8 +516,6 @@ public class SeqPanel
     }
 
     endEditing();
-
-    ap.paintAlignment(true);
   }
 
   /**
@@ -1486,17 +1466,16 @@ public class SeqPanel
 
     if (javax.swing.SwingUtilities.isRightMouseButton(evt))
     {
-      Vector allFeatures = getAllFeaturesAtRes(sequence.getDatasetSequence(),
+      SequenceFeature [] allFeatures = findFeaturesAtRes(sequence.getDatasetSequence(),
                                                sequence.findPosition(res));
       Vector links = new Vector();
-      for (int i = 0; i < allFeatures.size(); i++)
+      for (int i = 0; i < allFeatures.length; i++)
       {
-        SequenceFeature sf = (SequenceFeature) allFeatures.elementAt(i);
-        if (sf.links != null)
+        if (allFeatures[i].links != null)
         {
-          for (int j = 0; j < sf.links.size(); j++)
+          for (int j = 0; j < allFeatures[i].links.size(); j++)
           {
-            links.addElement(sf.links.elementAt(j));
+            links.addElement(allFeatures[i].links.elementAt(j));
           }
         }
       }
@@ -1594,13 +1573,14 @@ public class SeqPanel
         SliderPanel.setPIDSliderSource(ap, stretchGroup.cs,
                                        stretchGroup.getName());
       }
+      PaintRefresher.Refresh(this, av.getSequenceSetId());
+      ap.paintAlignment(true);
     }
+
     changeEndRes = false;
     changeStartRes = false;
     stretchGroup = null;
 
-    PaintRefresher.Refresh(this, av.getSequenceSetId());
-    ap.paintAlignment(true);
   }
 
   /**