JAL-2089 Merge branch releases/Release_2_10_Branch to master

[jalview.git] / src / jalview / renderer / seqfeatures / FeatureRenderer.java

diff --git a/src/jalview/renderer/seqfeatures/FeatureRenderer.java b/src/jalview/renderer/seqfeatures/FeatureRenderer.java
index 4d00014..f8e2cef 100644 (file)
--- a/src/jalview/renderer/seqfeatures/FeatureRenderer.java
+++ b/src/jalview/renderer/seqfeatures/FeatureRenderer.java
@@ -20,8 +20,10 @@
  */
 package jalview.renderer.seqfeatures;
 
+import jalview.api.AlignViewportI;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
+import jalview.viewmodel.seqfeatures.FeatureRendererModel;
 
 import java.awt.AlphaComposite;
 import java.awt.Color;
@@ -30,8 +32,7 @@ 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;
@@ -50,6 +51,18 @@ public class FeatureRenderer extends
 
   boolean av_validCharWidth, av_isShowSeqFeatureHeight;
 
+  private Integer currentColour;
+
+  /**
+   * Constructor given a viewport
+   * 
+   * @param viewport
+   */
+  public FeatureRenderer(AlignViewportI viewport)
+  {
+    this.av = viewport;
+  }
+
   protected void updateAvConfig()
   {
     av_charHeight = av.getCharHeight();
@@ -168,14 +181,15 @@ public class FeatureRenderer extends
 
   BufferedImage offscreenImage;
 
+  @Override
   public Color findFeatureColour(Color initialCol, SequenceI seq, int res)
   {
     return new Color(findFeatureColour(initialCol.getRGB(), seq, res));
   }
 
   /**
-   * This is used by the Molecule Viewer and Overview to get the accurate
-   * colourof the rendered sequence
+   * This is used by the Molecule Viewer and Overview to get the accurate colour
+   * of the rendered sequence
    */
   public synchronized int findFeatureColour(int initialCol,
           final SequenceI seq, int column)
@@ -245,7 +259,7 @@ public class FeatureRenderer extends
       }
       else
       {
-        return ((Integer) currentColour).intValue();
+        return currentColour.intValue();
       }
     }
 
@@ -389,7 +403,7 @@ 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,
@@ -397,24 +411,12 @@ 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;