X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FResidueColourScheme.java;h=df905006fe4f1fe03ac5112a1b15e13799258a84;hb=2e699d341f8e64868e3c279f9c02af617c4e9b44;hp=78ebab04388ae4b825c59f49226c7ba56a1d1275;hpb=95ebd2cf76003f52476a7802c99831dfa98945f7;p=jalview.git

diff --git a/src/jalview/schemes/ResidueColourScheme.java b/src/jalview/schemes/ResidueColourScheme.java
index 78ebab0..df90500 100755
--- a/src/jalview/schemes/ResidueColourScheme.java
+++ b/src/jalview/schemes/ResidueColourScheme.java
@@ -1,6 +1,6 @@
 /*
 * Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
 *
 * This program is free software; you can redistribute it and/or
 * modify it under the terms of the GNU General Public License
@@ -41,7 +41,7 @@ public class ResidueColourScheme implements ColourSchemeI
     int threshold = 0;
 
     /* Set when threshold colouring to either pid_gaps or pid_nogaps*/
-    protected String ignoreGaps = "pid_gaps";
+    protected String ignoreGaps = AAFrequency.PID_GAPS;
 
     /** Consenus as a hashtable array */
     Hashtable [] consensus;
@@ -52,12 +52,6 @@ public class ResidueColourScheme implements ColourSchemeI
    /** DOCUMENT ME!! */
    int inc = 30;
 
-   /**
-    * The colour to be calculated, manipulated and returned
-    */
-   Color currentColour = null;
-
-
 
     /**
      * Creates a new ResidueColourScheme object.
@@ -81,21 +75,20 @@ public class ResidueColourScheme implements ColourSchemeI
     /**
     * Find a colour without an index in a sequence
     */
-   public Color findColour(String aa)
+   public Color findColour(char c)
    {
-       return colors[((Integer) (ResidueProperties.aaHash.get(aa))).intValue()];
+       return colors[ResidueProperties.aaIndex[c]];
    }
 
 
 
-   public Color findColour(String s, int j)
+   public Color findColour(char c, int j)
    {
+       Color currentColour;
 
-       int index = ((Integer) (ResidueProperties.aaHash.get(s))).intValue();
-
-       if ((threshold == 0) || aboveThreshold(ResidueProperties.aa[index], j))
+       if ((threshold == 0) || aboveThreshold(c, j))
        {
-           currentColour = colors[index];
+           currentColour = colors[ResidueProperties.aaIndex[c]];
        }
        else
        {
@@ -103,7 +96,7 @@ public class ResidueColourScheme implements ColourSchemeI
        }
 
        if(conservationColouring)
-         applyConservation(j);
+         currentColour = applyConservation(currentColour, j);
 
 
        return currentColour;
@@ -129,9 +122,9 @@ public class ResidueColourScheme implements ColourSchemeI
     {
         threshold = ct;
         if(ignoreGaps)
-          this.ignoreGaps = "pid_nogaps";
+          this.ignoreGaps = AAFrequency.PID_NOGAPS;
         else
-          this.ignoreGaps = "pid_gaps";
+          this.ignoreGaps = AAFrequency.PID_GAPS;
     }
 
     /**
@@ -142,15 +135,25 @@ public class ResidueColourScheme implements ColourSchemeI
      *
      * @return DOCUMENT ME!
      */
-    public boolean aboveThreshold(String s, int j)
+    public boolean aboveThreshold(char c, int j)
     {
-        if ((((Integer) consensus[j].get("maxCount")).intValue() != -1) &&
-                consensus[j].contains(s))
+      if ('a' <= c && c <= 'z')
+        {
+          // TO UPPERCASE !!!
+          //Faster than toUpperCase
+          c -= ('a' - 'A');
+        }
+
+        if (consensus == null || consensus[j] == null)
+          return false;
+
+        if ( ( ( (Integer) consensus[j].get(AAFrequency.MAXCOUNT)).intValue() != -1) &&
+            consensus[j].contains(String.valueOf(c)))
         {
-            if (((Float)consensus[j].get(ignoreGaps)).floatValue() >= threshold)
-            {
-                return true;
-            }
+          if ( ( (Float) consensus[j].get(ignoreGaps)).floatValue() >= threshold)
+          {
+            return true;
+          }
         }
 
         return false;
@@ -177,18 +180,16 @@ public class ResidueColourScheme implements ColourSchemeI
      *
      * @param consensus DOCUMENT ME!
      */
-    public void setConsensus(Vector vconsensus)
+    public void setConsensus(Hashtable [] consensus)
     {
-      if(vconsensus==null)
+      if(consensus==null)
         return;
 
-       int i, iSize=vconsensus.size();
-       consensus = new Hashtable[iSize];
-       for(i=0; i<iSize; i++)
-        consensus[i] = (Hashtable)vconsensus.elementAt(i);
+      this.consensus = consensus;
     }
 
 
+
     public void setConservation(Conservation cons)
     {
       if(cons==null)
@@ -217,7 +218,7 @@ public class ResidueColourScheme implements ColourSchemeI
     * @return DOCUMENT ME!
     */
 
-   void applyConservation(int i)
+   Color applyConservation(Color currentColour, int i)
    {
 
      if ((conservation[i] != '*') && (conservation[i] != '+'))
@@ -229,6 +230,10 @@ public class ResidueColourScheme implements ColourSchemeI
        else
        {
          float t = 11 - (conservation[i] - '0');
+         if(t==0)
+         {
+           return Color.white;
+         }
 
          int red = currentColour.getRed();
          int green = currentColour.getGreen();
@@ -252,6 +257,7 @@ public class ResidueColourScheme implements ColourSchemeI
            currentColour = new Color(red, green, blue);
        }
        }
+       return currentColour;
    }