Merge branch 'features/JAL-2068groovyAnnotationWorker' into develop

[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 648f776..b007365 100644 (file)
--- a/src/jalview/renderer/seqfeatures/FeatureRenderer.java
+++ b/src/jalview/renderer/seqfeatures/FeatureRenderer.java
@@ -1,7 +1,29 @@
+/*
+ * 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.api.AlignViewportI;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
+import jalview.viewmodel.seqfeatures.FeatureRendererModel;
 
 import java.awt.AlphaComposite;
 import java.awt.Color;
@@ -10,8 +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;
@@ -30,6 +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();
@@ -77,6 +110,7 @@ public class FeatureRenderer extends
         charOffset = (av_charWidth - fm.charWidth(s)) / 2;
         g.drawString(String.valueOf(s), charOffset
                 + (av_charWidth * (i - start)), pady);
+
       }
     }
   }
@@ -147,17 +181,18 @@ 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)
+  public synchronized int findFeatureColour(int initialCol,
+          final SequenceI seq, int column)
   {
     if (!av.isShowSequenceFeatures())
     {
@@ -224,7 +259,7 @@ public class FeatureRenderer extends
       }
       else
       {
-        return ((Integer) currentColour).intValue();
+        return currentColour.intValue();
       }
     }
 
@@ -348,7 +383,7 @@ 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,
@@ -368,7 +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,
@@ -376,24 +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;