Merge branch 'develop' into features/JAL-2446NCList

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

diff --git a/src/jalview/renderer/seqfeatures/FeatureColourFinder.java b/src/jalview/renderer/seqfeatures/FeatureColourFinder.java
index 9a1ecf9..cfe2735 100644 (file)
--- a/src/jalview/renderer/seqfeatures/FeatureColourFinder.java
+++ b/src/jalview/renderer/seqfeatures/FeatureColourFinder.java
@@ -1,5 +1,26 @@
+/*
+ * 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.FeatureRenderer;
 import jalview.api.FeaturesDisplayedI;
 import jalview.datamodel.SequenceI;
 import jalview.viewmodel.seqfeatures.FeatureRendererModel;
@@ -19,7 +40,7 @@ public class FeatureColourFinder
   /*
    * the class we delegate feature finding to
    */
-  private jalview.api.FeatureRenderer featureRenderer;
+  private FeatureRenderer featureRenderer;
 
   /*
    * a 1-pixel image on which features can be drawn, for the case where
@@ -32,7 +53,7 @@ public class FeatureColourFinder
    * 
    * @param fr
    */
-  public FeatureColourFinder(jalview.api.FeatureRenderer fr)
+  public FeatureColourFinder(FeatureRenderer fr)
   {
     featureRenderer = fr;
     offscreenImage = new BufferedImage(1, 1, BufferedImage.TYPE_INT_ARGB);
@@ -46,45 +67,78 @@ public class FeatureColourFinder
    * transparency, this class provides a dummy 'offscreen' graphics context
    * where multiple feature colours can be overlaid and the combined colour read
    * back.
+   * <p>
+   * This method is not thread-safe when transparency is applied, since a shared
+   * BufferedImage would be used by all threads to hold the composite colour at
+   * a position. Each thread should use a separate instance of this class.
    * 
    * @param defaultColour
    * @param seq
    * @param column
-   *          alignment column position (base zero)
+   *          alignment column position (0..)
    * @return
    */
   public Color findFeatureColour(Color defaultColour, SequenceI seq,
           int column)
   {
-    if (!((FeatureRendererModel) featureRenderer).hasRenderOrder())
+    if (noFeaturesDisplayed())
     {
       return defaultColour;
     }
 
-    FeaturesDisplayedI displayed = featureRenderer.getFeaturesDisplayed();
-    if (displayed == null || displayed.getVisibleFeatureCount() == 0)
-    {
-      return defaultColour; // nothing to see here folks
-    }
-
     Graphics g = null;
 
     /*
-     * if transparency applies, get colours drawn to a 1x1 pixel
-     * graphics context that has been primed with the default colour
+     * if transparency applies, provide a notional 1x1 graphics context 
+     * that has been primed with the default colour
      */
     if (featureRenderer.getTransparency() != 1f)
     {
       g = offscreenImage.getGraphics();
-      offscreenImage.setRGB(0, 0, defaultColour.getRGB());
+      if (defaultColour != null)
+      {
+        offscreenImage.setRGB(0, 0, defaultColour.getRGB());
+      }
     }
 
-    Color c = featureRenderer.findFeatureColour(seq, column, g);
+    Color c = featureRenderer.findFeatureColour(seq, column + 1, g);
+    if (c == null)
+    {
+      return defaultColour;
+    }
 
-    if (c != null && g != null)
+    if (g != null)
     {
       c = new Color(offscreenImage.getRGB(0, 0));
     }
-    return c == null ? defaultColour : c;
+    return c;
+  }
+
+  /**
+   * Answers true if feature display is turned off, or there are no features
+   * configured to be visible
+   * 
+   * @return
+   */
+  boolean noFeaturesDisplayed()
+  {
+    if (featureRenderer == null
+            || !featureRenderer.getViewport().isShowSequenceFeatures())
+    {
+      return true;
+    }
+
+    if (!((FeatureRendererModel) featureRenderer).hasRenderOrder())
+    {
+      return true;
+    }
+
+    FeaturesDisplayedI displayed = featureRenderer.getFeaturesDisplayed();
+    if (displayed == null || displayed.getVisibleFeatureCount() == 0)
+    {
+      return true;
+    }
+
+    return false;
   }
 }