Merge branch 'documentation/JAL-2675_release2102b1' into feature/JAL-2611

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

diff --git a/src/jalview/renderer/ResidueShader.java b/src/jalview/renderer/ResidueShader.java
index 8ecb2ad..7e4f211 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;
@@ -19,7 +39,8 @@ import java.util.Map;
  * the factors that may influence residue colouring are
  * <ul>
  * <li>the colour scheme that provides a colour for each aligned residue</li>
- * <li>any threshold for colour, based on percentage identity with consensus</li>
+ * <li>any threshold for colour, based on percentage identity with
+ * consensus</li>
  * <li>any graduation based on conservation of physico-chemical properties</li>
  * </ul>
  * 
@@ -153,7 +174,7 @@ public class ResidueShader implements ResidueShaderI
       conservation = cons.getConsSequence().getSequenceAsString()
               .toCharArray();
     }
-  
+
   }
 
   /**
@@ -218,12 +239,13 @@ public class ResidueShader implements ResidueShaderI
      * get 'base' colour
      */
     ProfileI profile = consensus == null ? null : consensus.get(position);
-    String modalResidue = profile == null ? null : profile
-            .getModalResidue();
-    float pid = profile == null ? 0f : profile
-            .getPercentageIdentity(ignoreGaps);
-    Color colour = colourScheme == null ? Color.white : colourScheme
-            .findColour(symbol, position, seq, modalResidue, pid);
+    String modalResidue = profile == null ? null
+            : profile.getModalResidue();
+    float pid = profile == null ? 0f
+            : profile.getPercentageIdentity(ignoreGaps);
+    Color colour = colourScheme == null ? Color.white
+            : colourScheme.findColour(symbol, position, seq, modalResidue,
+                    pid);
 
     /*
      * apply PID threshold and consensus fading if in force
@@ -256,7 +278,7 @@ public class ResidueShader implements ResidueShaderI
     {
       colour = Color.white;
     }
-  
+
     if (conservationColouring)
     {
       colour = applyConservation(colour, column);
@@ -290,14 +312,14 @@ public class ResidueShader implements ResidueShaderI
       // Faster than toUpperCase
       residue -= ('a' - 'A');
     }
-  
+
     if (consensus == null)
     {
       return false;
     }
-  
+
     ProfileI profile = consensus.get(column);
-  
+
     /*
      * test whether this is the consensus (or joint consensus) residue
      */
@@ -309,7 +331,7 @@ public class ResidueShader implements ResidueShaderI
         return true;
       }
     }
-  
+
     return false;
   }
 
@@ -337,7 +359,7 @@ public class ResidueShader implements ResidueShaderI
       return currentColour;
     }
     char conservationScore = conservation[column];
-  
+
     /*
      * if residues are fully conserved (* or 11), or all properties
      * are conserved (+ or 10), leave colour unchanged
@@ -348,24 +370,24 @@ public class ResidueShader implements ResidueShaderI
     {
       return currentColour;
     }
-  
+
     if (Comparison.isGap(conservationScore))
     {
       return Color.white;
     }
-  
+
     /*
      * convert score 0-9 to a bleaching factor 1.1 - 0.2
      */
     float bleachFactor = (11 - (conservationScore - '0')) / 10f;
-  
+
     /*
      * scale this up by 0-5 (percentage slider / 20)
      * as a result, scores of:         0  1  2  3  4  5  6  7  8  9
      * fade to white at slider value: 18 20 22 25 29 33 40 50 67 100%
      */
     bleachFactor *= (conservationIncrement / 20f);
-  
+
     return ColorUtils.bleachColour(currentColour, bleachFactor);
   }