X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FResidueColourScheme.java;h=64fd62e1cb2c921ddaaf9de7519c94fd0ec31d01;hb=7f7fc2e5533f7b00c86465f964e37c55bcf12fd7;hp=71f12c13ab9170442021fdeefc2bfc5a3cf6278b;hpb=89805aa27a9d87b25010f9fbc0e0e4c853c3a1e1;p=jalview.git

diff --git a/src/jalview/schemes/ResidueColourScheme.java b/src/jalview/schemes/ResidueColourScheme.java
index 71f12c1..64fd62e 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
@@ -18,6 +18,8 @@
 */
 package jalview.schemes;
 
+import jalview.analysis.*;
+
 import java.awt.*;
 
 import java.util.*;
@@ -31,14 +33,31 @@ import java.util.*;
  */
 public class ResidueColourScheme implements ColourSchemeI
 {
+
+    boolean conservationColouring = false;
+    boolean consensusColouring = false;
+
     Color[] colors;
     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;
+
+    /** Conservation string as a char array */
+   char [] conservation;
+
+   /** DOCUMENT ME!! */
+   int inc = 30;
+
+   /**
+    * The colour to be calculated, manipulated and returned
+    */
+   Color currentColour = null;
+
 
-    /** DOCUMENT ME!! */
-    public Hashtable [] consensus;
 
     /**
      * Creates a new ResidueColourScheme object.
@@ -46,9 +65,9 @@ public class ResidueColourScheme implements ColourSchemeI
      * @param colors DOCUMENT ME!
      * @param threshold DOCUMENT ME!
      */
-    public ResidueColourScheme(Color[] colors, int threshold)
+    public ResidueColourScheme(Color[] colours, int threshold)
     {
-        this.colors = colors;
+        this.colors = colours;
         this.threshold = threshold;
     }
 
@@ -60,28 +79,59 @@ public class ResidueColourScheme implements ColourSchemeI
     }
 
     /**
-     * DOCUMENT ME!
+    * Find a colour without an index in a sequence
+    */
+   public Color findColour(String aa)
+   {
+       return colors[ResidueProperties.aaIndex[aa.charAt(0)]];
+   }
+
+
+
+   public Color findColour(String s, int j)
+   {
+
+       int index = ResidueProperties.aaIndex[s.charAt(0)];
+
+       if ((threshold == 0) || aboveThreshold(ResidueProperties.aa[index], j))
+       {
+           currentColour = colors[index];
+       }
+       else
+       {
+           currentColour = Color.white;
+       }
+
+       if(conservationColouring)
+         applyConservation(j);
+
+
+       return currentColour;
+   }
+
+
+    /**
+     * Get the percentage threshold for this colour scheme
      *
-     * @param consensus DOCUMENT ME!
+     * @return Returns the percentage threshold
      */
-    public void setConsensus(Vector vconsensus)
+    public int getThreshold()
     {
-       int i, iSize=vconsensus.size();
-       consensus = new Hashtable[iSize];
-       for(i=0; i<iSize; i++)
-        consensus[i] = (Hashtable)vconsensus.elementAt(i);
+        return threshold;
     }
 
     /**
      * DOCUMENT ME!
      *
-     * @param aa DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
+     * @param ct DOCUMENT ME!
      */
-    public Color findColour(String aa)
+    public void setThreshold(int ct, boolean ignoreGaps)
     {
-        return colors[((Integer) (ResidueProperties.aaHash.get(aa))).intValue()];
+        threshold = ct;
+        if(ignoreGaps)
+          this.ignoreGaps = AAFrequency.PID_NOGAPS;
+        else
+          this.ignoreGaps = AAFrequency.PID_GAPS;
     }
 
     /**
@@ -92,63 +142,132 @@ public class ResidueColourScheme implements ColourSchemeI
      *
      * @return DOCUMENT ME!
      */
-    public Color findColour(String s, int j)
+    public boolean aboveThreshold(String s, int j)
     {
-        if ((threshold == 0) || aboveThreshold(s, j))
+      char c = s.charAt(0);
+      if ('a' <= c && c <= 'z')
         {
-            return colors[((Integer) (ResidueProperties.aaHash.get(s))).intValue()];
+          // TO UPPERCASE !!!
+          //Faster than toUpperCase
+          c -= ('a' - 'A');
+          s = String.valueOf(c);
         }
-        else
+
+        if (consensus == null || consensus[j] == null)
+          return false;
+
+        if ( ( ( (Integer) consensus[j].get(AAFrequency.MAXCOUNT)).intValue() != -1) &&
+            consensus[j].contains(s))
         {
-            return Color.white;
+          if ( ( (Float) consensus[j].get(ignoreGaps)).floatValue() >= threshold)
+          {
+            return true;
+          }
         }
+
+        return false;
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int getThreshold()
+
+    public boolean conservationApplied()
     {
-        return threshold;
+      return conservationColouring;
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param ct DOCUMENT ME!
-     */
-    public void setThreshold(int ct, boolean ignoreGaps)
+    public void setConservationInc(int i)
     {
-        threshold = ct;
-        if(ignoreGaps)
-          this.ignoreGaps = "pid_nogaps";
-        else
-          this.ignoreGaps = "pid_gaps";
+      inc = i;
+    }
+
+    public int getConservationInc()
+    {
+      return inc;
     }
 
     /**
      * DOCUMENT ME!
      *
-     * @param s DOCUMENT ME!
-     * @param j DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
+     * @param consensus DOCUMENT ME!
      */
-    public boolean aboveThreshold(String s, int j)
+    public void setConsensus(Hashtable [] consensus)
     {
-        if ((((Integer) consensus[j].get("maxCount")).intValue() != -1) &&
-                consensus[j].contains(s))
-        {
-            float ratio =  ((Float)consensus[j].get(ignoreGaps)).floatValue();
+      if(consensus==null)
+        return;
 
-            if (ratio >= threshold)
-            {
-                return true;
-            }
-        }
+      this.consensus = consensus;
+    }
+
+
+
+    public void setConservation(Conservation cons)
+    {
+      if(cons==null)
+      {
+        conservationColouring = false;
+        conservation = null;
+      }
+      else
+      {
+        conservationColouring = true;
+        int i, iSize = cons.getConsSequence().getLength();
+        conservation = new char[iSize];
+        for (i = 0; i < iSize; i++)
+          conservation[i] = cons.getConsSequence().getCharAt(i);
+      }
 
-        return false;
     }
+
+
+    /**
+    * DOCUMENT ME!
+    *
+    * @param s DOCUMENT ME!
+    * @param i DOCUMENT ME!
+    *
+    * @return DOCUMENT ME!
+    */
+
+   void applyConservation(int i)
+   {
+
+     if ((conservation[i] != '*') && (conservation[i] != '+'))
+     {
+       if(jalview.util.Comparison.isGap(conservation[i]))
+       {
+         currentColour = Color.white;
+       }
+       else
+       {
+         float t = 11 - (conservation[i] - '0');
+         if(t==0)
+         {
+           currentColour = Color.white;
+           return;
+         }
+
+         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);
+       }
+       }
+   }
+
+
 }