JAL-4036 use the legacy endpoint (and report the FTS query when debug/trace enabled)

[jalview.git] / src / jalview / renderer / ResidueShader.java

diff --git a/src/jalview/renderer/ResidueShader.java b/src/jalview/renderer/ResidueShader.java
index b381f32..c031170 100644 (file)
--- a/src/jalview/renderer/ResidueShader.java
+++ b/src/jalview/renderer/ResidueShader.java
@@ -1,3 +1,23 @@
+/*
+ * 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.analysis.Conservation;
@@ -215,6 +235,11 @@ public class ResidueShader implements ResidueShaderI
   @Override
   public Color findColour(char symbol, int position, SequenceI seq)
   {
+    if (colourScheme == null)
+    {
+      return Color.white; // Colour is 'None'
+    }
+
     /*
      * get 'base' colour
      */
@@ -223,14 +248,16 @@ public class ResidueShader implements ResidueShaderI
             : profile.getModalResidue();
     float pid = profile == null ? 0f
             : profile.getPercentageIdentity(ignoreGaps);
-    Color colour = colourScheme == null ? Color.white
-            : colourScheme.findColour(symbol, position, seq, modalResidue,
-                    pid);
+    Color colour = colourScheme.findColour(symbol, position, seq,
+            modalResidue, pid);
 
     /*
      * apply PID threshold and consensus fading if in force
      */
-    colour = adjustColour(symbol, position, colour);
+    if (!Comparison.isGap(symbol))
+    {
+      colour = adjustColour(symbol, position, colour);
+    }
 
     return colour;
   }