X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFeatureRenderer.java;h=cc2c04870fa801287daaf6f0cf32e33ed912a7d8;hb=fe76692596c7d98452e2c93bcd934cb8c0dbf5b5;hp=8d194f39af0d2719bb47277c3436c2e7747d3ee9;hpb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;p=jalview.git

diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java
index 8d194f3..cc2c048 100755
--- 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 
@@ -18,6 +18,7 @@
 package jalview.gui;
 
 import java.util.*;
+import java.util.concurrent.ConcurrentHashMap;
 
 import java.awt.*;
 import java.awt.event.*;
@@ -53,11 +54,11 @@ public class FeatureRenderer implements jalview.api.FeatureRenderer
 
   int charOffset;
 
-  Hashtable featureColours = new Hashtable();
+  Map featureColours = new ConcurrentHashMap();
 
   // A higher level for grouping features of a
   // particular type
-  Hashtable featureGroups = new Hashtable();
+  Map featureGroups = new ConcurrentHashMap();
 
   // This is actually an Integer held in the hashtable,
   // Retrieved using the key feature type
@@ -79,19 +80,24 @@ 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
   {
     String[] renderOrder;
 
-    Hashtable featureGroups;
+    Map featureGroups;
 
-    Hashtable featureColours;
+    Map featureColours;
 
     float transparency;
 
-    Hashtable featureOrder;
+    Map featureOrder;
 
     public FeatureRendererSettings(String[] renderOrder,
             Hashtable featureGroups, Hashtable featureColours,
@@ -113,27 +119,27 @@ public class FeatureRenderer implements jalview.api.FeatureRenderer
     public FeatureRendererSettings(FeatureRenderer fr)
     {
       renderOrder = null;
-      featureGroups = new Hashtable();
-      featureColours = new Hashtable();
-      featureOrder = new Hashtable();
+      featureGroups = new ConcurrentHashMap();
+      featureColours = new ConcurrentHashMap();
+      featureOrder = new ConcurrentHashMap();
       if (fr.renderOrder != null)
       {
         this.renderOrder = new String[fr.renderOrder.length];
         System.arraycopy(fr.renderOrder, 0, renderOrder, 0,
-                renderOrder.length);
+                fr.renderOrder.length);
       }
       if (fr.featureGroups != null)
       {
-        this.featureGroups = new Hashtable(fr.featureGroups);
+        this.featureGroups = new ConcurrentHashMap(fr.featureGroups);
       }
       if (fr.featureColours != null)
       {
-        this.featureColours = new Hashtable(fr.featureColours);
+        this.featureColours = new ConcurrentHashMap(fr.featureColours);
       }
-      Enumeration en = fr.featureColours.keys();
-      while (en.hasMoreElements())
+      Iterator en = fr.featureColours.keySet().iterator();
+      while (en.hasNext())
       {
-        Object next = en.nextElement();
+        Object next = en.next();
         Object val = featureColours.get(next);
         if (val instanceof GraduatedColor)
         {
@@ -144,7 +150,7 @@ public class FeatureRenderer implements jalview.api.FeatureRenderer
       this.transparency = fr.transparency;
       if (fr.featureOrder != null)
       {
-        this.featureOrder = new Hashtable(fr.featureOrder);
+        this.featureOrder = new ConcurrentHashMap(fr.featureOrder);
       }
     }
   }
@@ -162,7 +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);
@@ -171,7 +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)
@@ -195,7 +204,7 @@ public class FeatureRenderer implements jalview.api.FeatureRenderer
           }
         }
       }
-  }
+    }
   }
 
   BufferedImage offscreenImage;
@@ -211,7 +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)
     {
@@ -255,7 +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)
@@ -685,9 +696,10 @@ public class FeatureRenderer implements jalview.api.FeatureRenderer
     {
       minmax = new Hashtable();
     }
-    for (int i = 0; i < av.alignment.getHeight(); i++)
+    AlignmentI alignment = av.getAlignment();
+    for (int i = 0; i < alignment.getHeight(); i++)
     {
-      SequenceFeature[] features = av.alignment.getSequenceAt(i)
+      SequenceFeature[] features = alignment.getSequenceAt(i)
               .getDatasetSequence().getSequenceFeatures();
 
       if (features == null)
@@ -1402,7 +1414,7 @@ public class FeatureRenderer implements jalview.api.FeatureRenderer
 
   }
 
-  Hashtable featureOrder = null;
+  Map featureOrder = null;
 
   /**
    * analogous to colour - store a normalized ordering for all feature types in