X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FClustalxColourScheme.java;h=ec1334390adf639547b1816a6cdacaee368eb3cd;hb=a5f48be3f383f9d2a0de386c95647c593f7db1e3;hp=7ff1c65a3de6c1281c8fe4dd23fbc83aa8718ee8;hpb=b0cee3aaf7d8873910939f97b6acb217d518968d;p=jalview.git

diff --git a/src/jalview/schemes/ClustalxColourScheme.java b/src/jalview/schemes/ClustalxColourScheme.java
index 7ff1c65..ec13343 100755
--- a/src/jalview/schemes/ClustalxColourScheme.java
+++ b/src/jalview/schemes/ClustalxColourScheme.java
@@ -23,6 +23,7 @@ package jalview.schemes;
 import jalview.datamodel.AnnotatedCollectionI;
 import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceI;
+import jalview.util.Comparison;
 
 import java.awt.Color;
 import java.util.List;
@@ -42,8 +43,8 @@ public class ClustalxColourScheme extends ResidueColourScheme
   {
     RED(0.9f, 0.2f, 0.1f), BLUE(0.5f, 0.7f, 0.9f), GREEN(0.1f, 0.8f, 0.1f),
     ORANGE(0.9f, 0.6f, 0.3f), CYAN(0.1f, 0.7f, 0.7f),
-    PINK(0.9f, 0.5f, 0.5f), MAGENTA(0.8f, 0.3f, 0.8f), YELLOW(0.8f, 0.8f,
-            0.0f);
+    PINK(0.9f, 0.5f, 0.5f), MAGENTA(0.8f, 0.3f, 0.8f),
+    YELLOW(0.8f, 0.8f, 0.0f);
 
     final Color colour;
 
@@ -52,6 +53,7 @@ public class ClustalxColourScheme extends ResidueColourScheme
       colour = new Color(r, g, b);
     }
   }
+
   private class ConsensusColour
   {
     Consensus[] cons;
@@ -77,6 +79,14 @@ public class ClustalxColourScheme extends ResidueColourScheme
 
   private boolean includeGaps = true;
 
+  /**
+   * Default constructor (required for Class.newInstance())
+   */
+  public ClustalxColourScheme()
+  {
+
+  }
+
   public ClustalxColourScheme(AnnotatedCollectionI alignment,
           Map<SequenceI, SequenceCollectionI> hiddenReps)
   {
@@ -97,19 +107,18 @@ public class ClustalxColourScheme extends ResidueColourScheme
 
     for (SequenceI sq : seqs)
     {
-      char[] seq = sq.getSequence();
-
-      int end_j = seq.length - 1;
+      int end_j = sq.getLength() - 1;
+      int length = sq.getLength();
 
       for (int i = 0; i <= end_j; i++)
       {
-        if ((seq.length - 1) < i)
+        if (length - 1 < i)
         {
           res = 23;
         }
         else
         {
-          res = ResidueProperties.aaIndex[seq[i]];
+          res = ResidueProperties.aaIndex[sq.getCharAt(i)];
         }
         cons2[i][res]++;
       }
@@ -268,48 +277,44 @@ public class ClustalxColourScheme extends ResidueColourScheme
   }
 
   @Override
-  public Color findColour(char c, int j, SequenceI seq)
+  protected Color findColour(char c, int j, SequenceI seq)
   {
-    Color currentColour;
-
-    if (cons2.length <= j
-            || (includeGaps && threshold != 0 && !aboveThreshold(c, j)))
+    // TODO why the test for includeGaps here?
+    if (cons2.length <= j || Comparison.isGap(c)
+    /*|| (includeGaps && threshold != 0 && !aboveThreshold(c, j))*/)
     {
       return Color.white;
     }
 
     int i = ResidueProperties.aaIndex[c];
 
-    currentColour = Color.white;
+    Color colour = Color.white;
 
     if (i > 19)
     {
-      return currentColour;
+      return colour;
     }
 
     for (int k = 0; k < residueColour[i].cons.length; k++)
     {
-      if (residueColour[i].cons[k].isConserved(cons2, j, size,
-              includeGaps))
+      if (residueColour[i].cons[k].isConserved(cons2, j, size, includeGaps))
       {
-        currentColour = residueColour[i].c;
+        colour = residueColour[i].c;
       }
     }
 
     if (i == 4)
     {
+      /*
+       * override to colour C pink if >85% conserved
+       */
       if (conses[27].isConserved(cons2, j, size, includeGaps))
       {
-        currentColour = ClustalColour.PINK.colour;
+        colour = ClustalColour.PINK.colour;
       }
     }
 
-    if (conservationColouring)
-    {
-      currentColour = applyConservation(currentColour, j);
-    }
-
-    return currentColour;
+    return colour;
   }
 
   /**
@@ -330,7 +335,7 @@ public class ClustalxColourScheme extends ResidueColourScheme
   }
 
   @Override
-  public ColourSchemeI applyTo(AnnotatedCollectionI sg,
+  public ColourSchemeI getInstance(AnnotatedCollectionI sg,
           Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
   {
     ClustalxColourScheme css = new ClustalxColourScheme(sg,
@@ -350,4 +355,10 @@ public class ClustalxColourScheme extends ResidueColourScheme
   {
     return JalviewColourScheme.Clustal.toString();
   }
+
+  @Override
+  public boolean isSimple()
+  {
+    return false;
+  }
 }