X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Frenderer%2FResidueShader.java;h=73a5efdc71835e7e983a41b9674dbdb7efba2d8b;hb=3d4ead4880755ec949de0300c232544ba965e60d;hp=aa84816a83108d0c89aa859acd7ae8e3a214c944;hpb=991d2210e8e086bde29a90bdf21979261442d889;p=jalview.git

diff --git a/src/jalview/renderer/ResidueShader.java b/src/jalview/renderer/ResidueShader.java
index aa84816..73a5efd 100644
--- a/src/jalview/renderer/ResidueShader.java
+++ b/src/jalview/renderer/ResidueShader.java
@@ -235,6 +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
      */
@@ -243,9 +248,8 @@ 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
@@ -258,6 +262,36 @@ public class ResidueShader implements ResidueShaderI
     return colour;
   }
 
+  @Override
+  public int findColourInt(char symbol, int position, SequenceI seq)
+  {
+    if (colourScheme == null)
+    {
+      return -1;// Color.white; // Colour is 'None'
+    }
+
+    /*
+     * 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);
+    int colour = colourScheme
+            .findColour(symbol, position, seq, modalResidue, pid).getRGB();
+
+    /*
+     * apply PID threshold and consensus fading if in force
+     */
+    if (!Comparison.isGap(symbol))
+    {
+      colour = adjustColourInt(symbol, position, colour);
+    }
+
+    return colour;
+  }
+
   /**
    * Adjusts colour by applying thresholding or conservation shading, if in
    * force. That is
@@ -289,6 +323,20 @@ public class ResidueShader implements ResidueShaderI
     return colour;
   }
 
+  protected int adjustColourInt(char symbol, int column, int colour)
+  {
+    if (!aboveThreshold(symbol, column))
+    {
+      colour = -1;// Color.white;
+    }
+
+    if (conservationColouring)
+    {
+      colour = applyConservationInt(colour, column);
+    }
+    return colour;
+  }
+
   /**
    * Answers true if there is a consensus profile for the specified column, and
    * the given residue matches the consensus (or joint consensus) residue for
@@ -394,6 +442,45 @@ public class ResidueShader implements ResidueShaderI
     return ColorUtils.bleachColour(currentColour, bleachFactor);
   }
 
+  protected int applyConservationInt(int currentColour, int column)
+  {
+    if (conservation == null || conservation.length <= column)
+    {
+      return currentColour;
+    }
+    char conservationScore = conservation[column];
+
+    /*
+     * if residues are fully conserved (* or 11), or all properties
+     * are conserved (+ or 10), leave colour unchanged
+     */
+    if (conservationScore == '*' || conservationScore == '+'
+            || conservationScore == (char) 10
+            || conservationScore == (char) 11)
+    {
+      return currentColour;
+    }
+
+    if (Comparison.isGap(conservationScore))
+    {
+      return -1;// 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.bleachColourInt(currentColour, bleachFactor);
+  }
+
   /**
    * @see jalview.renderer.ResidueShaderI#getColourScheme()
    */