X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFeatureRenderer.java;h=8d194f39af0d2719bb47277c3436c2e7747d3ee9;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=09dccfec441f4478df02a8c32f56a41a4265d4c9;hpb=d423f22792e47dbc800ae220a58677f988971d06;p=jalview.git

diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java
index 09dccfe..8d194f3 100755
--- a/src/jalview/gui/FeatureRenderer.java
+++ b/src/jalview/gui/FeatureRenderer.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * 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
  * 
  * 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;
 
@@ -105,13 +105,47 @@ public class FeatureRenderer
       this.featureOrder = featureOrder;
     }
 
+    /**
+     * create an independent instance of the feature renderer settings
+     * 
+     * @param fr
+     */
     public FeatureRendererSettings(FeatureRenderer fr)
     {
-      this.renderOrder = fr.renderOrder;
-      this.featureGroups = fr.featureGroups;
-      this.featureColours = fr.featureColours;
+      renderOrder = null;
+      featureGroups = new Hashtable();
+      featureColours = new Hashtable();
+      featureOrder = new Hashtable();
+      if (fr.renderOrder != null)
+      {
+        this.renderOrder = new String[fr.renderOrder.length];
+        System.arraycopy(fr.renderOrder, 0, renderOrder, 0,
+                renderOrder.length);
+      }
+      if (fr.featureGroups != null)
+      {
+        this.featureGroups = new Hashtable(fr.featureGroups);
+      }
+      if (fr.featureColours != null)
+      {
+        this.featureColours = new Hashtable(fr.featureColours);
+      }
+      Enumeration en = fr.featureColours.keys();
+      while (en.hasMoreElements())
+      {
+        Object next = en.nextElement();
+        Object val = featureColours.get(next);
+        if (val instanceof GraduatedColor)
+        {
+          featureColours
+                  .put(next, new GraduatedColor((GraduatedColor) val));
+        }
+      }
       this.transparency = fr.transparency;
-      this.featureOrder = fr.featureOrder;
+      if (fr.featureOrder != null)
+      {
+        this.featureOrder = new Hashtable(fr.featureOrder);
+      }
     }
   }
 
@@ -131,11 +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;
@@ -151,7 +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)
     {
@@ -195,7 +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)
@@ -362,16 +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())
@@ -383,17 +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);
           }
         }
@@ -1062,7 +1122,7 @@ public class FeatureRenderer
 
     panel = new JPanel();
     panel.add(new JLabel("Description: ", JLabel.RIGHT));
-    description.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+    description.setFont(JvSwingUtils.getTextAreaFont());
     description.setLineWrap(true);
     panel.add(new JScrollPane(description));
 
@@ -1329,7 +1389,7 @@ public class FeatureRenderer
       {
         String type = data[i][0].toString();
         setColour(type, data[i][1]); // todo : typesafety - feature color
-                                     // interface object
+        // interface object
         if (((Boolean) data[i][2]).booleanValue())
         {
           av.featuresDisplayed.put(type, new Integer(getColour(type)