X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFeatureRenderer.java;h=d613a30fd4ec831b58fc083c32cc9339e98bc796;hb=7dd9c4874042f584dc1feb6a345fe929a8509e2b;hp=e4c6c5c473298006b3a2e09b3674348e040e38e6;hpb=18d7bc952d686c806d883a6e7cc80bc2954c1289;p=jalview.git

diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java
index e4c6c5c..d613a30 100755
--- a/src/jalview/gui/FeatureRenderer.java
+++ b/src/jalview/gui/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.
@@ -36,7 +36,7 @@ import jalview.schemes.GraduatedColor;
  * @author $author$
  * @version $Revision$
  */
-public class FeatureRenderer
+public class FeatureRenderer implements jalview.api.FeatureRenderer
 {
   AlignmentPanel ap;
 
@@ -165,11 +165,37 @@ public class FeatureRenderer
 
   public void transferSettings(FeatureRenderer fr)
   {
-    this.renderOrder = fr.renderOrder;
-    this.featureGroups = fr.featureGroups;
-    this.featureColours = fr.featureColours;
-    this.transparency = fr.transparency;
-    this.featureOrder = fr.featureOrder;
+    FeatureRendererSettings frs = new FeatureRendererSettings(fr);
+    this.renderOrder = frs.renderOrder;
+    this.featureGroups = frs.featureGroups;
+    this.featureColours = frs.featureColours;
+    this.transparency = frs.transparency;
+    this.featureOrder = frs.featureOrder;
+    if (av != null && av!=fr.av)
+    {
+      // copy over the displayed feature settings
+      if (fr.av != null)
+      {
+        if (fr.av.featuresDisplayed != null)
+        {
+          // update display settings
+          if (av.featuresDisplayed == null)
+          {
+            av.featuresDisplayed = new Hashtable(fr.av.featuresDisplayed);
+          }
+          else
+          {
+            av.featuresDisplayed.clear();
+            Enumeration en = fr.av.featuresDisplayed.keys();
+            while (en.hasMoreElements())
+            {
+              av.featuresDisplayed.put(en.nextElement(), Boolean.TRUE);
+            }
+
+          }
+        }
+      }
+  }
   }
 
   BufferedImage offscreenImage;
@@ -185,7 +211,7 @@ public class FeatureRenderer
    * This is used by the Molecule Viewer and Overview to get the accurate
    * colourof the rendered sequence
    */
-  public int findFeatureColour(int initialCol, SequenceI seq, int column)
+  public synchronized int findFeatureColour(int initialCol, SequenceI seq, int column)
   {
     if (!av.showSequenceFeatures)
     {
@@ -229,7 +255,7 @@ public class FeatureRenderer
     }
 
     currentColour = null;
-
+    // TODO: non-threadsafe - each rendering thread needs its own instance of the feature renderer - or this should be synchronized.
     offscreenRender = true;
 
     if (offscreenImage != null)
@@ -396,16 +422,16 @@ 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())
@@ -417,17 +443,17 @@ public class FeatureRenderer
           if (av.showSeqFeaturesHeight
                   && sequenceFeatures[sfindex].score != Float.NaN)
           {
-            renderScoreFeature(g, seq, seq
-                    .findIndex(sequenceFeatures[sfindex].begin) - 1, seq
-                    .findIndex(sequenceFeatures[sfindex].end) - 1,
+            renderScoreFeature(g, seq,
+                    seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
+                    seq.findIndex(sequenceFeatures[sfindex].end) - 1,
                     getColour(sequenceFeatures[sfindex]), start, end, y1,
                     normaliseScore(sequenceFeatures[sfindex]));
           }
           else
           {
-            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);
           }
         }