X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FFeatureRenderer.java;h=c71a3ccc2088be6fbffcf52fc14d6fe15a8885e2;hb=9175e97621ea51c3e98145545b3957842126c09e;hp=21c401a447ee1d0cbf52a97dd56deedb57b65cc8;hpb=011c92dbea927aa8ae693ae75bf1b42a1c564aef;p=jalview.git

diff --git a/src/jalview/appletgui/FeatureRenderer.java b/src/jalview/appletgui/FeatureRenderer.java
index 21c401a..c71a3cc 100755
--- a/src/jalview/appletgui/FeatureRenderer.java
+++ b/src/jalview/appletgui/FeatureRenderer.java
@@ -45,7 +45,6 @@ public class FeatureRenderer
 
     String [] renderOrder;
 
-    boolean drawText = true;
     FontMetrics fm;
     int charOffset;
 
@@ -85,11 +84,11 @@ public class FeatureRenderer
 
       return new Color( ((Integer)currentColour).intValue() );
     }
+
     /**
      * This is used by the Molecule Viewer to get the accurate colour
      * of the rendered sequence
      */
-
     boolean overview = false;
 
     int white = Color.white.getRGB();
@@ -152,12 +151,12 @@ public class FeatureRenderer
         return;
 
 
-      if(g!=null)
-        fm = g.getFontMetrics();
-
       if (av.featuresDisplayed == null || renderOrder==null)
        {
          findAllFeatures();
+         if(av.featuresDisplayed.size()<1)
+           return;
+
          sequenceFeatures = seq.getSequenceFeatures();
          sfSize = sequenceFeatures.length;
        }
@@ -171,11 +170,15 @@ public class FeatureRenderer
       {
         spos = lastSequence.findPosition(start);
         epos = lastSequence.findPosition(end);
+        if(g!=null)
+          fm = g.getFontMetrics();
       }
       String type;
       for(int renderIndex=0; renderIndex<renderOrder.length; renderIndex++)
        {
         type =  renderOrder[renderIndex];
+        if(!av.featuresDisplayed.containsKey(type))
+          continue;
 
         // loop through all features in sequence to find
         // current feature to render
@@ -201,9 +204,8 @@ public class FeatureRenderer
 
           if (overview)
           {
-
-            if (sequenceFeatures[sfindex].begin - 1 <= start &&
-                sequenceFeatures[sfindex].end + 1 >= start)
+            if (sequenceFeatures[sfindex].begin <= start &&
+                sequenceFeatures[sfindex].end >= start)
             {
               currentColour = av.featuresDisplayed.get(sequenceFeatures[sfindex].
                   type);
@@ -234,9 +236,7 @@ public class FeatureRenderer
                           getColour(sequenceFeatures[sfindex].type),
                           start, end, y1, width, height);
 
-
         }
-
       }
     }
 
@@ -285,6 +285,7 @@ public class FeatureRenderer
     void findAllFeatures()
     {
       av.featuresDisplayed = new Hashtable();
+      Vector allfeatures = new Vector();
       for (int i = 0; i < av.alignment.getHeight(); i++)
       {
         SequenceFeature [] features = av.alignment.getSequenceAt(i).getSequenceFeatures();
@@ -299,18 +300,19 @@ public class FeatureRenderer
           {
             av.featuresDisplayed.put(features[index].getType(),
                                   new Integer( getColour(features[index].getType()).getRGB()) );
+            allfeatures.addElement(features[index].getType());
           }
           index++;
         }
       }
 
-      renderOrder = new String[av.featuresDisplayed.size()];
-      Enumeration en = av.featuresDisplayed.keys();
-      int i = 0;
+      renderOrder = new String[allfeatures.size()];
+      Enumeration en = allfeatures.elements();
+      int i = allfeatures.size()-1;
       while(en.hasMoreElements())
       {
         renderOrder[i] = en.nextElement().toString();
-        i++;
+        i--;
       }
     }
 
@@ -337,26 +339,26 @@ public class FeatureRenderer
 
     public void setFeaturePriority(Object [][] data)
     {
-      // The feature table will display high priority
-      // features at the top, but theses are the ones
-      // we need to render last, so invert the data
-      av.featuresDisplayed.clear();
+        // The feature table will display high priority
+        // features at the top, but theses are the ones
+        // we need to render last, so invert the data
+        if(av.featuresDisplayed!=null)
+          av.featuresDisplayed.clear();
 
-      renderOrder = new String[data.length];
+        renderOrder = new String[data.length];
 
-      if(data.length>0)
-      for(int i=0; i<data.length; i++)
-      {
-       String type = data[i][0].toString();
-       setColour(type, (Color)data[i][1]);
-       if( ((Boolean)data[i][2]).booleanValue() )
-       {
-         av.featuresDisplayed.put(type, new Integer(getColour(type).getRGB()));
-       }
-
-       renderOrder[i] = type;
-      }
+        if (data.length > 0)
+          for (int i = 0; i < data.length; i++)
+          {
+            String type = data[i][0].toString();
+            setColour(type, (Color) data[i][1]);
+            if ( ( (Boolean) data[i][2]).booleanValue())
+            {
+              av.featuresDisplayed.put(type, new Integer(getColour(type).getRGB()));
+            }
 
+            renderOrder[data.length - i - 1] = type;
+          }
     }
 
     Hashtable featureColours = new Hashtable();