X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Frenderer%2FResidueShader.java;h=c0311700f1e61e5afc93c16984a6d8b98f14d5c5;hb=732b23aab5c88efbd8ca24db9e432345492ed9b1;hp=73a5efdc71835e7e983a41b9674dbdb7efba2d8b;hpb=f5974107dd25f8122ebb924e400335e62b1e5daf;p=jalview.git

diff --git a/src/jalview/renderer/ResidueShader.java b/src/jalview/renderer/ResidueShader.java
index 73a5efd..c031170 100644
--- a/src/jalview/renderer/ResidueShader.java
+++ b/src/jalview/renderer/ResidueShader.java
@@ -262,36 +262,6 @@ 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
@@ -323,20 +293,6 @@ 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
@@ -442,45 +398,6 @@ 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()
    */