X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FResidueColourScheme.java;h=f6b7c5e16e31cd3da8f34f14597aa751cb071c90;hb=8b1e1c7cf7bcf6499dad546699c85d8d52e6d86c;hp=e6b28db3ee5f829c04a4dd4e9c9fadfb20fa9220;hpb=1c757dc1e6ee864277825c1ebd9c6a9fbe0da7b2;p=jalview.git

diff --git a/src/jalview/schemes/ResidueColourScheme.java b/src/jalview/schemes/ResidueColourScheme.java
index e6b28db..f6b7c5e 100755
--- a/src/jalview/schemes/ResidueColourScheme.java
+++ b/src/jalview/schemes/ResidueColourScheme.java
@@ -21,10 +21,13 @@
 package jalview.schemes;
 
 import jalview.analysis.Conservation;
-import jalview.analysis.Profile;
 import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.ProfileI;
+import jalview.datamodel.ProfilesI;
 import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceI;
+import jalview.util.ColorUtils;
+import jalview.util.Comparison;
 import jalview.util.MessageManager;
 
 import java.awt.Color;
@@ -49,15 +52,19 @@ public class ResidueColourScheme implements ColourSchemeI
   /* Set when threshold colouring to either pid_gaps or pid_nogaps */
   protected boolean ignoreGaps = false;
 
-  /** Consenus as a hashtable array */
-  Profile[] consensus;
+  /*
+   * Consensus data indexed by column
+   */
+  ProfilesI consensus;
 
-  /** Conservation string as a char array */
+  /*
+   * Conservation string as a char array 
+   */
   char[] conservation;
 
-  int conservationLength = 0;
-
-  /** DOCUMENT ME!! */
+  /*
+   * The conservation slider percentage setting 
+   */
   int inc = 30;
 
   /**
@@ -140,45 +147,56 @@ public class ResidueColourScheme implements ColourSchemeI
   }
 
   /**
-   * DOCUMENT ME!
+   * Sets the percentage consensus threshold value, and whether gaps are ignored
+   * in percentage identity calculation
    * 
-   * @param ct
-   *          DOCUMENT ME!
+   * @param consensusThreshold
+   * @param ignoreGaps
    */
   @Override
-  public void setThreshold(int ct, boolean ignoreGaps)
+  public void setThreshold(int consensusThreshold, boolean ignoreGaps)
   {
-    threshold = ct;
+    threshold = consensusThreshold;
     this.ignoreGaps = ignoreGaps;
   }
 
   /**
-   * DOCUMENT ME!
+   * Answers true if there is a consensus profile for the specified column, and
+   * the given residue matches the consensus (or joint consensus) residue for
+   * the column, and the percentage identity for the profile is equal to or
+   * greater than the current threshold; else answers false. The percentage
+   * calculation depends on whether or not we are ignoring gapped sequences.
    * 
-   * @param s
-   *          DOCUMENT ME!
-   * @param j
-   *          DOCUMENT ME!
+   * @param residue
+   * @param column
+   *          (index into consensus profiles)
    * 
-   * @return DOCUMENT ME!
+   * @return
+   * @see #setThreshold(int, boolean)
    */
-  public boolean aboveThreshold(char c, int j)
+  public boolean aboveThreshold(char residue, int column)
   {
-    if ('a' <= c && c <= 'z')
+    if ('a' <= residue && residue <= 'z')
     {
       // TO UPPERCASE !!!
       // Faster than toUpperCase
-      c -= ('a' - 'A');
+      residue -= ('a' - 'A');
     }
 
-    if (consensus == null || consensus.length < j || consensus[j] == null)
+    if (consensus == null)
     {
       return false;
     }
 
-    if (consensus[j].getMaxCount() > 0) // != -1))
+    ProfileI profile = consensus.get(column);
+
+    /*
+     * test whether this is the consensus (or joint consensus) residue
+     */
+    if (profile != null
+            && profile.getModalResidue().contains(String.valueOf(residue)))
     {
-      if (consensus[j].getPercentageIdentity(ignoreGaps) >= threshold)
+      if (profile.getPercentageIdentity(ignoreGaps) >= threshold)
       {
         return true;
       }
@@ -218,7 +236,7 @@ public class ResidueColourScheme implements ColourSchemeI
    *          DOCUMENT ME!
    */
   @Override
-  public void setConsensus(Profile[] consensus)
+  public void setConsensus(ProfilesI consensus)
   {
     if (consensus == null)
     {
@@ -239,73 +257,70 @@ public class ResidueColourScheme implements ColourSchemeI
     else
     {
       conservationColouring = true;
-      int i, iSize = cons.getConsSequence().getLength();
+      int iSize = cons.getConsSequence().getLength();
       conservation = new char[iSize];
-      for (i = 0; i < iSize; i++)
+      for (int i = 0; i < iSize; i++)
       {
         conservation[i] = cons.getConsSequence().getCharAt(i);
       }
-      conservationLength = conservation.length;
     }
 
   }
 
   /**
-   * DOCUMENT ME!
+   * Applies a combination of column conservation score, and conservation
+   * percentage slider, to 'bleach' out the residue colours towards white.
+   * <p>
+   * If a column is fully conserved (identical residues, conservation score 11,
+   * shown as *), or all 10 physico-chemical properties are conserved
+   * (conservation score 10, shown as +), then the colour is left unchanged.
+   * <p>
+   * Otherwise a 'bleaching' factor is computed and applied to the colour. This
+   * is designed to fade colours for scores of 0-9 completely to white at slider
+   * positions ranging from 18% - 100% respectively.
    * 
-   * @param s
-   *          DOCUMENT ME!
-   * @param i
-   *          DOCUMENT ME!
+   * @param currentColour
+   * @param column
    * 
-   * @return DOCUMENT ME!
+   * @return bleached (or unmodified) colour
    */
-
-  Color applyConservation(Color currentColour, int i)
+  Color applyConservation(Color 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 ((conservationLength > i) && (conservation[i] != '*')
-            && (conservation[i] != '+'))
+    if (Comparison.isGap(conservationScore))
     {
-      if (jalview.util.Comparison.isGap(conservation[i]))
-      {
-        currentColour = Color.white;
-      }
-      else
-      {
-        float t = 11 - (conservation[i] - '0');
-        if (t == 0)
-        {
-          return Color.white;
-        }
-
-        int red = currentColour.getRed();
-        int green = currentColour.getGreen();
-        int blue = currentColour.getBlue();
-
-        int dr = 255 - red;
-        int dg = 255 - green;
-        int db = 255 - blue;
-
-        dr *= t / 10f;
-        dg *= t / 10f;
-        db *= t / 10f;
-
-        red += (inc / 20f) * dr;
-        green += (inc / 20f) * dg;
-        blue += (inc / 20f) * db;
-
-        if (red > 255 || green > 255 || blue > 255)
-        {
-          currentColour = Color.white;
-        }
-        else
-        {
-          currentColour = new Color(red, green, blue);
-        }
-      }
+      return Color.white;
     }
-    return currentColour;
+
+    /*
+     * 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 *= (inc / 20f);
+
+    return ColorUtils.bleachColour(currentColour, bleachFactor);
   }
 
   @Override