X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Frenderer%2FOverviewResColourFinder.java;fp=src%2Fjalview%2Frenderer%2FOverviewResColourFinder.java;h=793d349dbc1771dbf7910cc0a185161a68e3f776;hb=fb548a8458941602b0b8b45da5aaf60206e10ec2;hp=0000000000000000000000000000000000000000;hpb=060557f7086fd2aab4fea43ecbf21e2ef4191dd1;p=jalview.git

diff --git a/src/jalview/renderer/OverviewResColourFinder.java b/src/jalview/renderer/OverviewResColourFinder.java
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+++ b/src/jalview/renderer/OverviewResColourFinder.java
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+/*
+ * 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;
+
+import jalview.datamodel.SequenceI;
+import jalview.util.Comparison;
+
+import java.awt.Color;
+
+public class OverviewResColourFinder extends ResidueColourFinder
+{
+  @Override
+  public Color getBoxColour(ResidueShaderI shader, SequenceI seq, int i)
+  {
+    Color resBoxColour = Color.white;
+    char currentChar = seq.getCharAt(i);
+
+    if (shader.getColourScheme() != null)
+    {
+      if (Comparison.isGap(currentChar)
+              && !shader.getColourScheme().hasGapColour())
+      {
+        resBoxColour = Color.lightGray;
+      }
+      else
+      {
+        resBoxColour = shader.findColour(currentChar, i, seq);
+      }
+    }
+    else if (Comparison.isGap(currentChar))
+    {
+      resBoxColour = Color.lightGray;
+    }
+
+    return resBoxColour;
+  }
+}