X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FFeatureRenderer.java;h=900de839e519dfba43a70d156243e9ba9e368bf9;hb=92c28d1a4ec6178c3e8f1bd304a1c94ad9e16bf1;hp=0b504be57b500af56ebac59cb8f562b70a763d2a;hpb=be9cbda993c0cb66255c0eb8274ee2bfa9199220;p=jalview.git

diff --git a/src/jalview/appletgui/FeatureRenderer.java b/src/jalview/appletgui/FeatureRenderer.java
index 0b504be..900de83 100755
--- a/src/jalview/appletgui/FeatureRenderer.java
+++ b/src/jalview/appletgui/FeatureRenderer.java
@@ -1,3 +1,4 @@
+
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
  * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
@@ -60,8 +61,17 @@ public class FeatureRenderer
     }
 
 
+    public void transferSettings(FeatureRenderer fr)
+    {
+      renderOrder = fr.renderOrder;
+      featureGroups = fr.featureGroups;
+      featureColours = fr.featureColours;
+    }
+
+
     public Color findFeatureColour(Color initialCol, SequenceI seq, int i)
     {
+      overview = true;
       if(!av.showSequenceFeatures)
         return initialCol;
 
@@ -187,10 +197,7 @@ public class FeatureRenderer
           if (!sequenceFeatures[sfindex].type.equals(type))
             continue;
 
-          if(sequenceFeatures[sfindex]==null)
-          {
-          }
-          else  if (featureGroups != null
+          if (featureGroups != null
               && sequenceFeatures[sfindex].featureGroup != null
               &&
               featureGroups.containsKey(sequenceFeatures[sfindex].featureGroup)
@@ -207,9 +214,8 @@ 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);
@@ -240,9 +246,7 @@ public class FeatureRenderer
                           getColour(sequenceFeatures[sfindex].type),
                           start, end, y1, width, height);
 
-
         }
-
       }
     }
 
@@ -278,6 +282,9 @@ public class FeatureRenderer
 
             g.fillRect( (i - start) * width, y1, width, height);
 
+            if(!av.validCharWidth)
+              continue;
+
             g.setColor(Color.white);
             charOffset = (width - fm.charWidth(s)) / 2;
             g.drawString(String.valueOf(s),