X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Frenderer%2Fseqfeatures%2FFeatureRenderer.java;h=0d14cd91305a3b4cb2178aac098ddb6e705247c8;hb=a9474b488d0756b465ee507dbba639f62d0dcb85;hp=7eda2f7ebb279b505c7ccbfb466412c2b6169305;hpb=c77a1af8ef91918f935bbf493d348eb022fa73f7;p=jalview.git

diff --git a/src/jalview/renderer/seqfeatures/FeatureRenderer.java b/src/jalview/renderer/seqfeatures/FeatureRenderer.java
index 7eda2f7..0d14cd9 100644
--- a/src/jalview/renderer/seqfeatures/FeatureRenderer.java
+++ b/src/jalview/renderer/seqfeatures/FeatureRenderer.java
@@ -1,7 +1,28 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * 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 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.renderer.seqfeatures;
 
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
+import jalview.viewmodel.seqfeatures.FeatureRendererModel;
 
 import java.awt.AlphaComposite;
 import java.awt.Color;
@@ -10,8 +31,7 @@ import java.awt.Graphics;
 import java.awt.Graphics2D;
 import java.awt.image.BufferedImage;
 
-public class FeatureRenderer extends
-        jalview.viewmodel.seqfeatures.FeatureRendererModel
+public class FeatureRenderer extends FeatureRendererModel
 {
 
   FontMetrics fm;
@@ -148,6 +168,7 @@ public class FeatureRenderer extends
 
   BufferedImage offscreenImage;
 
+  @Override
   public Color findFeatureColour(Color initialCol, SequenceI seq, int res)
   {
     return new Color(findFeatureColour(initialCol.getRGB(), seq, res));
@@ -157,8 +178,8 @@ public class FeatureRenderer extends
    * This is used by the Molecule Viewer and Overview to get the accurate
    * colourof the rendered sequence
    */
-  public synchronized int findFeatureColour(int initialCol, final SequenceI seq,
-          int column)
+  public synchronized int findFeatureColour(int initialCol,
+          final SequenceI seq, int column)
   {
     if (!av.isShowSequenceFeatures())
     {
@@ -316,7 +337,7 @@ public class FeatureRenderer extends
         }
 
         if (offscreenRender && offscreenImage == null)
-        {      
+        {
           if (sequenceFeature.begin <= start
                   && sequenceFeature.end >= start)
           {
@@ -349,7 +370,7 @@ public class FeatureRenderer extends
         else if (showFeature(sequenceFeature))
         {
           if (av_isShowSeqFeatureHeight
-                  && sequenceFeature.score != Float.NaN)
+                  && !Float.isNaN(sequenceFeature.score))
           {
             renderScoreFeature(g, seq,
                     seq.findIndex(sequenceFeature.begin) - 1,
@@ -369,7 +390,7 @@ public class FeatureRenderer extends
 
     }
 
-    if (transparency != 1.0f && g != null && transparencyAvailable)
+    if (transparency != 1.0f && g != null)
     {
       Graphics2D g2 = (Graphics2D) g;
       g2.setComposite(AlphaComposite.getInstance(AlphaComposite.SRC_OVER,
@@ -377,24 +398,12 @@ public class FeatureRenderer extends
     }
   }
 
-  boolean transparencyAvailable = true;
-
-  protected void setTransparencyAvailable(boolean isTransparencyAvailable)
-  {
-    transparencyAvailable = isTransparencyAvailable;
-  }
-
-  @Override
-  public boolean isTransparencyAvailable()
-  {
-    return transparencyAvailable;
-  }
-
   /**
    * Called when alignment in associated view has new/modified features to
    * discover and display.
    * 
    */
+  @Override
   public void featuresAdded()
   {
     lastSeq = null;