X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FFeatureRenderer.java;h=44bd15132dae0eedaf9878d46af4eb7de0e27559;hb=c42fcf7bf5cfcf51e67dd0f683edb9ab6683d157;hp=628de4ee9c0f80e1b26ca5ca61f32ad2a3123188;hpb=2eaaec9b53681e44e6c109e71aecdd3cadd7f727;p=jalview.git

diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java
index 628de4e..44bd151 100755
--- a/src/jalview/gui/FeatureRenderer.java
+++ b/src/jalview/gui/FeatureRenderer.java
@@ -54,6 +54,8 @@ public class FeatureRenderer
 
     String [] renderOrder;
 
+    boolean newFeatureAdded = false;
+
 
     /**
      * Creates a new FeatureRenderer object.
@@ -77,33 +79,30 @@ public class FeatureRenderer
     boolean offscreenRender = false;
     public Color findFeatureColour(Color initialCol, SequenceI seq, int res)
     {
-      int seqindex = av.alignment.findIndex(seq);
-
       return new Color( findFeatureColour (initialCol.getRGB(),
-                        seqindex, res ));
+                        seq, res ));
     }
 
     /**
-     * This is used by the Molecule Viewer to get the accurate colour
-     * of the rendered sequence
+     * This is used by the Molecule Viewer and Overview to
+     * get the accurate colourof the rendered sequence
      */
-    public int findFeatureColour(int initialCol, int seqIndex, int column)
+    public int findFeatureColour(int initialCol, SequenceI seq, int column)
     {
       if(!av.showSequenceFeatures)
         return initialCol;
 
-      if(seqIndex!=lastSequenceIndex)
+      if(seq!=lastSeq)
       {
-        lastSequence = av.alignment.getSequenceAt(seqIndex);
-        lastSequenceIndex = seqIndex;
-        sequenceFeatures = lastSequence.getDatasetSequence().getSequenceFeatures();
+        lastSeq = seq;
+        sequenceFeatures = lastSeq.getDatasetSequence().getSequenceFeatures();
         if(sequenceFeatures==null)
           return initialCol;
 
         sfSize = sequenceFeatures.length;
       }
 
-      if(jalview.util.Comparison.isGap(lastSequence.getCharAt(column)))
+      if(jalview.util.Comparison.isGap(lastSeq.getCharAt(column)))
         return Color.white.getRGB();
 
 
@@ -121,7 +120,7 @@ public class FeatureRenderer
       {
         offscreenImage.setRGB(0,0,initialCol);
         drawSequence(offscreenImage.getGraphics(),
-                     lastSequence,
+                     lastSeq,
                      column,column,0);
 
         return offscreenImage.getRGB(0,0);
@@ -129,8 +128,8 @@ public class FeatureRenderer
       else
       {
         drawSequence(null,
-                    lastSequence,
-                    lastSequence.findPosition(column),
+                    lastSeq,
+                    lastSeq.findPosition(column),
                     -1, -1);
 
         if (currentColour == null)
@@ -158,8 +157,7 @@ public class FeatureRenderer
      */
    // String type;
    // SequenceFeature sf;
-    int lastSequenceIndex=-1;
-    SequenceI lastSequence;
+    SequenceI lastSeq;
     SequenceFeature [] sequenceFeatures;
     int sfSize, sfindex, spos, epos;
 
@@ -170,12 +168,13 @@ public class FeatureRenderer
           || seq.getDatasetSequence().getSequenceFeatures().length==0)
         return;
 
-
       if(g!=null)
         fm = g.getFontMetrics();
 
 
-      if (av.featuresDisplayed == null || renderOrder==null)
+      if (av.featuresDisplayed == null
+          || renderOrder==null
+          || newFeatureAdded)
        {
          findAllFeatures();
          if(av.featuresDisplayed.size()<1)
@@ -185,9 +184,9 @@ public class FeatureRenderer
          sfSize = sequenceFeatures.length;
        }
 
-       if(lastSequence==null || seq!=lastSequence)
+       if(lastSeq==null || seq!=lastSeq)
       {
-        lastSequence = seq;
+        lastSeq = seq;
         sequenceFeatures = seq.getDatasetSequence().getSequenceFeatures();
         sfSize = sequenceFeatures.length;
       }
@@ -203,8 +202,8 @@ public class FeatureRenderer
 
       if(!offscreenRender)
       {
-        spos = lastSequence.findPosition(start);
-        epos = lastSequence.findPosition(end);
+        spos = lastSeq.findPosition(start);
+        epos = lastSeq.findPosition(end);
       }
 
 
@@ -212,6 +211,7 @@ public class FeatureRenderer
       for(int renderIndex=0; renderIndex<renderOrder.length; renderIndex++)
        {
         type =  renderOrder[renderIndex];
+
         if(!av.featuresDisplayed.containsKey(type))
           continue;
 
@@ -333,12 +333,23 @@ public class FeatureRenderer
       }
     }
 
-    synchronized void findAllFeatures()
+    synchronized public void featuresAdded()
     {
+      newFeatureAdded = true;
+      findAllFeatures();
+      newFeatureAdded = false;
+    }
+
+   synchronized void findAllFeatures()
+   {
       jalview.schemes.UserColourScheme ucs = new
           jalview.schemes.UserColourScheme();
 
-          av.featuresDisplayed = new Hashtable();
+      if(av.featuresDisplayed==null)
+        av.featuresDisplayed = new Hashtable();
+
+      av.featuresDisplayed.clear();
+
       Vector allfeatures = new Vector();
       for (int i = 0; i < av.alignment.getHeight(); i++)
       {