JAL-3187 (hacked up) show complement features on structure/Overview

[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 d4a545b..52090e1 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.AlignViewportI;
 import jalview.api.FeatureRenderer;
 import jalview.api.FeaturesDisplayedI;
 import jalview.datamodel.SequenceI;
@@ -55,7 +76,7 @@ public class FeatureColourFinder
    * @param defaultColour
    * @param seq
    * @param column
-   *          alignment column position (base zero)
+   *          alignment column position (0..)
    * @return
    */
   public Color findFeatureColour(Color defaultColour, SequenceI seq,
@@ -81,7 +102,7 @@ public class FeatureColourFinder
       }
     }
 
-    Color c = featureRenderer.findFeatureColour(seq, column, g);
+    Color c = featureRenderer.findFeatureColour(seq, column + 1, g);
     if (c == null)
     {
       return defaultColour;
@@ -102,7 +123,12 @@ public class FeatureColourFinder
    */
   boolean noFeaturesDisplayed()
   {
-    if (!featureRenderer.getViewport().isShowSequenceFeatures())
+    AlignViewportI av = featureRenderer.getViewport();
+    if (av.isShowComplementFeatures())
+    {
+      return false;
+    }
+    if (featureRenderer == null || !av.isShowSequenceFeatures())
     {
       return true;
     }