X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fappletgui%2FFeatureRenderer.java;h=6e9da1af560173be329e1c1ca0e929062859546d;hb=8a6fa9ea9900d0f106529c3f6283e7f9d76dd2cb;hp=50bb6653530f3b9386109de967d60c4b70787d32;hpb=d423f22792e47dbc800ae220a58677f988971d06;p=jalview.git

diff --git a/src/jalview/appletgui/FeatureRenderer.java b/src/jalview/appletgui/FeatureRenderer.java
index 50bb665..6e9da1a 100755
--- a/src/jalview/appletgui/FeatureRenderer.java
+++ b/src/jalview/appletgui/FeatureRenderer.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
  * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
@@ -34,7 +34,7 @@ import jalview.schemes.GraduatedColor;
  * @author $author$
  * @version $Revision$
  */
-public class FeatureRenderer
+public class FeatureRenderer implements jalview.api.FeatureRenderer
 {
   AlignViewport av;
 
@@ -661,16 +661,16 @@ public class FeatureRenderer
         else if (sequenceFeatures[sfindex].type.equals("disulfide bond"))
         {
 
-          renderFeature(g, seq, seq
-                  .findIndex(sequenceFeatures[sfindex].begin) - 1, seq
-                  .findIndex(sequenceFeatures[sfindex].begin) - 1,
+          renderFeature(g, seq,
+                  seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
+                  seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
                   getColour(sequenceFeatures[sfindex])
                   // new Color(((Integer) av.featuresDisplayed
                   // .get(sequenceFeatures[sfindex].type)).intValue())
                   , start, end, y1);
-          renderFeature(g, seq, seq
-                  .findIndex(sequenceFeatures[sfindex].end) - 1, seq
-                  .findIndex(sequenceFeatures[sfindex].end) - 1,
+          renderFeature(g, seq,
+                  seq.findIndex(sequenceFeatures[sfindex].end) - 1,
+                  seq.findIndex(sequenceFeatures[sfindex].end) - 1,
                   getColour(sequenceFeatures[sfindex])
                   // new Color(((Integer) av.featuresDisplayed
                   // .get(sequenceFeatures[sfindex].type)).intValue())
@@ -681,9 +681,9 @@ public class FeatureRenderer
         {
           if (showFeature(sequenceFeatures[sfindex]))
           {
-            renderFeature(g, seq, seq
-                    .findIndex(sequenceFeatures[sfindex].begin) - 1, seq
-                    .findIndex(sequenceFeatures[sfindex].end) - 1,
+            renderFeature(g, seq,
+                    seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
+                    seq.findIndex(sequenceFeatures[sfindex].end) - 1,
                     getColour(sequenceFeatures[sfindex]), start, end, y1);
           }
         }
@@ -748,6 +748,20 @@ public class FeatureRenderer
 
   Hashtable minmax = null;
 
+  /**
+   * Called when alignment in associated view has new/modified features to
+   * discover and display.
+   * 
+   */
+  public void featuresAdded()
+  {
+    lastSeq = null;
+    findAllFeatures();
+  }
+
+  /**
+   * find all features on the alignment
+   */
   void findAllFeatures()
   {
     jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme();
@@ -778,8 +792,8 @@ public class FeatureRenderer
         {
           if (getColour(features[index].getType()) == null)
           {
-            featureColours.put(features[index].getType(), ucs
-                    .createColourFromName(features[index].getType()));
+            featureColours.put(features[index].getType(),
+                    ucs.createColourFromName(features[index].getType()));
           }
 
           av.featuresDisplayed.put(features[index].getType(), new Integer(