X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FResidueColourScheme.java;h=b83244d61ea9d2a8857ff451c5e46076a4db6e81;hb=20bddfcf8ef1a53bce455b7599f8066b8ccba0d4;hp=e90e6cc27e9264e7fd3cf7edb3ed6f4dd85b2d76;hpb=99c58ee0ae2a848f982552e53feaf6d5cb9925e5;p=jalview.git

diff --git a/src/jalview/schemes/ResidueColourScheme.java b/src/jalview/schemes/ResidueColourScheme.java
index e90e6cc..b83244d 100755
--- a/src/jalview/schemes/ResidueColourScheme.java
+++ b/src/jalview/schemes/ResidueColourScheme.java
@@ -16,66 +16,248 @@
 * 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.*;
+
+
+/**
+ * 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 = "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;
+
 
-    public ResidueColourScheme(Color[] colors, int threshold) {
-        this.colors    = colors;
-	this.threshold = threshold;
+
+    /**
+     * Creates a new ResidueColourScheme object.
+     *
+     * @param colors DOCUMENT ME!
+     * @param threshold DOCUMENT ME!
+     */
+    public ResidueColourScheme(Color[] colours, int threshold)
+    {
+        this.colors = colours;
+        this.threshold = threshold;
     }
 
+    /**
+     * Creates a new ResidueColourScheme object.
+     */
     public ResidueColourScheme()
-    {   }
+    {
+    }
+
+    /**
+    * Find a colour without an index in a sequence
+    */
+   public Color findColour(String aa)
+   {
+       return colors[((Integer) (ResidueProperties.aaHash.get(aa))).intValue()];
+   }
+
+
+
+   public Color findColour(String s, int j)
+   {
+
+       int index = ((Integer) (ResidueProperties.aaHash.get(s))).intValue();
+
+       if ((threshold == 0) || aboveThreshold(ResidueProperties.aa[index], j))
+       {
+           currentColour = colors[index];
+       }
+       else
+       {
+           currentColour = Color.white;
+       }
+
+       if(conservationColouring)
+         applyConservation(j);
+
+
+       return currentColour;
+   }
 
-    public void setConsensus(Vector consensus)
+
+    /**
+     * Get the percentage threshold for this colour scheme
+     *
+     * @return Returns the percentage threshold
+     */
+    public int getThreshold()
     {
-      this.consensus = consensus;
+        return threshold;
     }
 
-    public Color findColour(String aa)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param ct DOCUMENT ME!
+     */
+    public void setThreshold(int ct, boolean ignoreGaps)
     {
-      return colors[((Integer)(ResidueProperties.aaHash.get(aa))).intValue()];
+        threshold = ct;
+        if(ignoreGaps)
+          this.ignoreGaps = "pid_nogaps";
+        else
+          this.ignoreGaps = "pid_gaps";
     }
 
-    public Color findColour(String s, int j) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param s DOCUMENT ME!
+     * @param j DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public boolean aboveThreshold(String s, int j)
+    {
+        if ((((Integer) consensus[j].get("maxCount")).intValue() != -1) &&
+                consensus[j].contains(s))
+        {
+            if (((Float)consensus[j].get(ignoreGaps)).floatValue() >= threshold)
+            {
+                return true;
+            }
+        }
 
-       if( threshold==0 || aboveThreshold(s,j))
-          return colors[((Integer)(ResidueProperties.aaHash.get(s))).intValue()];
-       else
-          return Color.white;
+        return false;
+    }
 
+
+    public boolean conservationApplied()
+    {
+      return conservationColouring;
     }
 
-    public int getThreshold() {
-	return threshold;
+    public void setConservationInc(int i)
+    {
+      inc = i;
     }
 
-    public void setThreshold(int ct) {
-	threshold = ct;
+    public int getConservationInc()
+    {
+      return inc;
     }
 
-    public boolean aboveThreshold(String s, int j)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param consensus DOCUMENT ME!
+     */
+    public void setConsensus(Vector vconsensus)
     {
-	Hashtable hash = (Hashtable)consensus.elementAt(j);
+      if(vconsensus==null)
+        return;
 
-        if ( ( (Integer) hash.get("maxCount")).intValue() != -1 && hash.contains(s))
-        {
-               ////  resCount////////////////////                  ///////////////seq count////////////
-          double sc = ( (Integer) hash.get(s)).intValue()  * 100.0 / ( (Integer) hash.get("size")).intValue();
+       int i, iSize=vconsensus.size();
+       consensus = new Hashtable[iSize];
+       for(i=0; i<iSize; i++)
+        consensus[i] = (Hashtable)vconsensus.elementAt(i);
+    }
 
-          if (sc >= threshold)
-            return true;
 
-        }
+    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);
+       }
+       }
+   }
+
+
 }