X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FResidueColourScheme.java;h=b905c452ba87dcce2683ded2f74c2ec0fdc5cd36;hb=d640a8ce605b836b2e6eb1771994d3baef5c31a0;hp=3bd9bca184b107beb4e8191320f0f7eec23daa4e;hpb=66b1bf1a6480b320ddaa00d4f5e70b2051041c11;p=jalview.git

diff --git a/src/jalview/schemes/ResidueColourScheme.java b/src/jalview/schemes/ResidueColourScheme.java
index 3bd9bca..b905c45 100755
--- a/src/jalview/schemes/ResidueColourScheme.java
+++ b/src/jalview/schemes/ResidueColourScheme.java
@@ -1,62 +1,267 @@
+/*
+* Jalview - A Sequence Alignment Editor and Viewer
+* 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
+* as published by the Free Software Foundation; either version 2
+* of the License, or (at your option) any later version.
+*
+* This program is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+* GNU General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with this program; if not, write to the Free Software
+* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+*/
 package jalview.schemes;
 
-import java.util.*;
+import jalview.analysis.*;
+
 import java.awt.*;
 
-public class ResidueColourScheme implements ColourSchemeI{
-    Color    [] colors;
-    int       threshold = 0;
-    public Vector   consensus;
+import java.util.*;
 
-    public ResidueColourScheme(Color[] colors, int threshold) {
-        this.colors    = colors;
-	this.threshold = threshold;
-    }
 
-    public ResidueColourScheme()
-    {   }
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+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 = AAFrequency.PID_GAPS;
 
-    public void setConsensus(Vector consensus)
+    /** Consenus as a hashtable array */
+    Hashtable [] consensus;
+
+    /** Conservation string as a char array */
+   char [] conservation;
+
+   /** DOCUMENT ME!! */
+   int inc = 30;
+
+
+    /**
+     * Creates a new ResidueColourScheme object.
+     *
+     * @param colors DOCUMENT ME!
+     * @param threshold DOCUMENT ME!
+     */
+    public ResidueColourScheme(Color[] colours, int threshold)
     {
-      this.consensus = consensus;
+        this.colors = colours;
+        this.threshold = threshold;
     }
 
-    public Color findColour(String aa)
+    /**
+     * Creates a new ResidueColourScheme object.
+     */
+    public ResidueColourScheme()
     {
-      return colors[((Integer)(ResidueProperties.aaHash.get(aa))).intValue()];
     }
 
-    public Color findColour(String s, int j) {
+    /**
+    * Find a colour without an index in a sequence
+    */
+   public Color findColour(String aa)
+   {
+       return colors[ResidueProperties.aaIndex[aa.charAt(0)]];
+   }
+
+
 
-       if( threshold==0 || aboveThreshold(s,j))
-          return colors[((Integer)(ResidueProperties.aaHash.get(s))).intValue()];
+   public Color findColour(String s, int j)
+   {
+       Color currentColour;
+       int index = ResidueProperties.aaIndex[s.charAt(0)];
+
+       if ((threshold == 0) || aboveThreshold(ResidueProperties.aa[index], j))
+       {
+           currentColour = colors[index];
+       }
        else
-          return Color.white;
+       {
+           currentColour = Color.white;
+       }
 
-    }
+       if(conservationColouring)
+         currentColour = applyConservation(currentColour, j);
+
+
+       return currentColour;
+   }
 
-    public int getThreshold() {
-	return threshold;
+
+    /**
+     * Get the percentage threshold for this colour scheme
+     *
+     * @return Returns the percentage threshold
+     */
+    public int getThreshold()
+    {
+        return threshold;
     }
 
-    public void setThreshold(int ct) {
-	threshold = ct;
+    /**
+     * DOCUMENT ME!
+     *
+     * @param ct DOCUMENT ME!
+     */
+    public void setThreshold(int ct, boolean ignoreGaps)
+    {
+        threshold = ct;
+        if(ignoreGaps)
+          this.ignoreGaps = AAFrequency.PID_NOGAPS;
+        else
+          this.ignoreGaps = AAFrequency.PID_GAPS;
     }
 
+    /**
+     * DOCUMENT ME!
+     *
+     * @param s DOCUMENT ME!
+     * @param j DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
     public boolean aboveThreshold(String s, int j)
     {
-	Hashtable hash = (Hashtable)consensus.elementAt(j);
-
-        if ( ( (Integer) hash.get("maxCount")).intValue() != -1 && hash.contains(s))
+      char c = s.charAt(0);
+      if ('a' <= c && c <= 'z')
         {
-               ////  resCount////////////////////                  ///////////////seq count////////////
-          double sc = ( (Integer) hash.get(s)).intValue()  * 100.0 / ( (Integer) hash.get("size")).intValue();
+          // TO UPPERCASE !!!
+          //Faster than toUpperCase
+          c -= ('a' - 'A');
+          s = String.valueOf(c);
+        }
 
-          if (sc >= threshold)
-            return true;
+        if (consensus == null || consensus[j] == null)
+          return false;
 
+        if ( ( ( (Integer) consensus[j].get(AAFrequency.MAXCOUNT)).intValue() != -1) &&
+            consensus[j].contains(s))
+        {
+          if ( ( (Float) consensus[j].get(ignoreGaps)).floatValue() >= threshold)
+          {
+            return true;
+          }
         }
 
-	return false;
+        return false;
     }
+
+
+    public boolean conservationApplied()
+    {
+      return conservationColouring;
+    }
+
+    public void setConservationInc(int i)
+    {
+      inc = i;
+    }
+
+    public int getConservationInc()
+    {
+      return inc;
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param consensus DOCUMENT ME!
+     */
+    public void setConsensus(Hashtable [] consensus)
+    {
+      if(consensus==null)
+        return;
+
+      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);
+      }
+
+    }
+
+
+    /**
+    * DOCUMENT ME!
+    *
+    * @param s DOCUMENT ME!
+    * @param i DOCUMENT ME!
+    *
+    * @return DOCUMENT ME!
+    */
+
+   Color applyConservation(Color currentColour, 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)
+         {
+           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 currentColour;
+   }
+
+
 }