JAL-1378 JWS-71 update to from-source build of JABA v2.1 client for use with JABA...

[jalview.git] / src / jalview / gui / FeatureRenderer.java

diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java
index 0aee327..cc2c048 100755 (executable)
--- a/src/jalview/gui/FeatureRenderer.java
+++ b/src/jalview/gui/FeatureRenderer.java
@@ -1,13 +1,13 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- * 
+ *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
@@ -53,7 +53,7 @@ public class FeatureRenderer implements jalview.api.FeatureRenderer
   FontMetrics fm;
 
   int charOffset;
- 
+
   Map featureColours = new ConcurrentHashMap();
 
   // A higher level for grouping features of a
@@ -80,6 +80,11 @@ public class FeatureRenderer implements jalview.api.FeatureRenderer
   {
     this.ap = ap;
     this.av = ap.av;
+    if (ap != null && ap.seqPanel != null && ap.seqPanel.seqCanvas != null
+            && ap.seqPanel.seqCanvas.fr != null)
+    {
+      transferSettings(ap.seqPanel.seqCanvas.fr);
+    }
   }
 
   public class FeatureRendererSettings implements Cloneable
@@ -121,7 +126,7 @@ public class FeatureRenderer implements jalview.api.FeatureRenderer
       {
         this.renderOrder = new String[fr.renderOrder.length];
         System.arraycopy(fr.renderOrder, 0, renderOrder, 0,
-                renderOrder.length);
+                fr.renderOrder.length);
       }
       if (fr.featureGroups != null)
       {
@@ -163,7 +168,10 @@ public class FeatureRenderer implements jalview.api.FeatureRenderer
     this.transparency = fr.transparency;
     this.featureOrder = fr.featureOrder;
   }
-
+  /**
+   * update from another feature renderer
+   * @param fr settings to copy
+   */
   public void transferSettings(FeatureRenderer fr)
   {
     FeatureRendererSettings frs = new FeatureRendererSettings(fr);
@@ -172,7 +180,7 @@ public class FeatureRenderer implements jalview.api.FeatureRenderer
     this.featureColours = frs.featureColours;
     this.transparency = frs.transparency;
     this.featureOrder = frs.featureOrder;
-    if (av != null && av!=fr.av)
+    if (av != null && av != fr.av)
     {
       // copy over the displayed feature settings
       if (fr.av != null)
@@ -196,7 +204,7 @@ public class FeatureRenderer implements jalview.api.FeatureRenderer
           }
         }
       }
-  }
+    }
   }
 
   BufferedImage offscreenImage;
@@ -212,7 +220,8 @@ public class FeatureRenderer implements jalview.api.FeatureRenderer
    * This is used by the Molecule Viewer and Overview to get the accurate
    * colourof the rendered sequence
    */
-  public synchronized int findFeatureColour(int initialCol, SequenceI seq, int column)
+  public synchronized int findFeatureColour(int initialCol, SequenceI seq,
+          int column)
   {
     if (!av.showSequenceFeatures)
     {
@@ -256,7 +265,8 @@ public class FeatureRenderer implements jalview.api.FeatureRenderer
     }
 
     currentColour = null;
-    // TODO: non-threadsafe - each rendering thread needs its own instance of the feature renderer - or this should be synchronized.
+    // TODO: non-threadsafe - each rendering thread needs its own instance of
+    // the feature renderer - or this should be synchronized.
     offscreenRender = true;
 
     if (offscreenImage != null)
@@ -686,7 +696,7 @@ public class FeatureRenderer implements jalview.api.FeatureRenderer
     {
       minmax = new Hashtable();
     }
-    AlignmentI alignment=av.getAlignment();
+    AlignmentI alignment = av.getAlignment();
     for (int i = 0; i < alignment.getHeight(); i++)
     {
       SequenceFeature[] features = alignment.getSequenceAt(i)