X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fschemes%2FResidueColourScheme.java;h=c435f7dc264687811c7001b68c8d62b6800d1c23;hb=95a46891288f4fc63d690cab4f56879678f54fb6;hp=9c10e7d8e1101c95b193233ff6c60c781de3b020;hpb=efc31b4a8d5cee63555586804a2b79c06bdb5a14;p=jalview.git

diff --git a/src/jalview/schemes/ResidueColourScheme.java b/src/jalview/schemes/ResidueColourScheme.java
index 9c10e7d..c435f7d 100755
--- a/src/jalview/schemes/ResidueColourScheme.java
+++ b/src/jalview/schemes/ResidueColourScheme.java
@@ -18,6 +18,8 @@
 */
 package jalview.schemes;
 
+import jalview.analysis.*;
+
 import java.awt.*;
 
 import java.util.*;
@@ -31,11 +33,31 @@ import java.util.*;
  */
 public class ResidueColourScheme implements ColourSchemeI
 {
+
+    boolean conservationColouring = false;
+    boolean consensusColouring = false;
+
     Color[] colors;
     int threshold = 0;
 
-    /** DOCUMENT ME!! */
-    public Vector consensus;
+    /* 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;
+
+
 
     /**
      * Creates a new ResidueColourScheme object.
@@ -43,9 +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;
     }
 
@@ -57,25 +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[((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;
+   }
+
+
+    /**
+     * Get the percentage threshold for this colour scheme
      *
-     * @param consensus DOCUMENT ME!
+     * @return Returns the percentage threshold
      */
-    public void setConsensus(Vector consensus)
+    public int getThreshold()
     {
-        this.consensus = consensus;
+        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 = "pid_nogaps";
+        else
+          this.ignoreGaps = "pid_gaps";
     }
 
     /**
@@ -86,63 +142,141 @@ 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))
+        if ((((Integer) consensus[j].get("maxCount")).intValue() != -1) &&
+                consensus[j].contains(s))
         {
-            return colors[((Integer) (ResidueProperties.aaHash.get(s))).intValue()];
-        }
-        else
-        {
-            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)
+    public void setConservationInc(int i)
     {
-        threshold = ct;
+      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(Vector vconsensus)
     {
-        Hashtable hash = (Hashtable) consensus.elementAt(j);
+       int i, iSize=vconsensus.size();
+       consensus = new Hashtable[iSize];
+       for(i=0; i<iSize; i++)
+        consensus[i] = (Hashtable)vconsensus.elementAt(i);
+    }
 
-        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();
 
-            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] != '+'))
+       {
+           int tmp = 10;
+           int t = 0;
+
+           if (!jalview.util.Comparison.isGap(conservation[i]))
+           {
+               t = conservation[i]-'0';
+           }
+
+           while (tmp >= t)
+           {
+               lighter(inc);
+               tmp--;
+           }
+       }
+
+   }
+
+    /**
+    * DOCUMENT ME!
+    *
+    * @param c DOCUMENT ME!
+    * @param inc DOCUMENT ME!
+    *
+    * @return DOCUMENT ME!
+    */
+   void lighter(int inc)
+   {
+       int red = currentColour.getRed();
+       int blue = currentColour.getBlue();
+       int green = currentColour.getGreen();
+
+       if (red < (255 - inc))
+       {
+           red = red + inc;
+       }
+       else
+       {
+           red = 255;
+       }
+
+       if (blue < (255 - inc))
+       {
+           blue = blue + inc;
+       }
+       else
+       {
+           blue = 255;
+       }
+
+       if (green < (255 - inc))
+       {
+           green = green + inc;
+       }
+       else
+       {
+           green = 255;
+       }
+
+       currentColour = new Color(red, green, blue);
+   }
+
+
 }