X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FResidueColourScheme.java;h=c435f7dc264687811c7001b68c8d62b6800d1c23;hb=95a46891288f4fc63d690cab4f56879678f54fb6;hp=95946f92c26d8f15522d232ce4728256f96ba226;hpb=bcfc2937c9284fb9611008dbcfa712f14447dd1f;p=jalview.git

diff --git a/src/jalview/schemes/ResidueColourScheme.java b/src/jalview/schemes/ResidueColourScheme.java
index 95946f9..c435f7d 100755
--- a/src/jalview/schemes/ResidueColourScheme.java
+++ b/src/jalview/schemes/ResidueColourScheme.java
@@ -1,111 +1,282 @@
+/*
+* Jalview - A Sequence Alignment Editor and Viewer
+* Copyright (C) 2005 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 jalview.datamodel.*;
-import java.util.*;
+import jalview.analysis.*;
+
 import java.awt.*;
 
-public class ResidueColourScheme implements ColourSchemeI {
-    Color    [] colors;
-    int         threshold = 90;
+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;
     }
 
-    public ResidueColourScheme() {
+    /**
+     * Creates a new ResidueColourScheme object.
+     */
+    public ResidueColourScheme()
+    {
     }
 
-    public Color findColour(String aa)
+    /**
+    * 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
+     *
+     * @return Returns the percentage threshold
+     */
+    public int getThreshold()
     {
-      return colors[((Integer)(ResidueProperties.aaHash.get(aa))).intValue()];
+        return threshold;
     }
 
-    public Color findColour(SequenceI seq,String s, int j, Vector aa) {
-  try {
-	    return colors[((Integer)(ResidueProperties.aaHash.get(s))).intValue()];
-	} catch (Exception e) {
-	    return Color.white;
-	}
+    /**
+     * DOCUMENT ME!
+     *
+     * @param ct DOCUMENT ME!
+     */
+    public void setThreshold(int ct, boolean ignoreGaps)
+    {
+        threshold = ct;
+        if(ignoreGaps)
+          this.ignoreGaps = "pid_nogaps";
+        else
+          this.ignoreGaps = "pid_gaps";
     }
 
-    // aa should maybe be a class
-    public Color getColour(SequenceI seq, int j,Vector aa) {
+    /**
+     * 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;
+            }
+        }
 
-	Color  c       = Color.white;
-	String s       = seq.getSequence(j,j+1);
+        return false;
+    }
 
-	if (threshold > 0 && aa != null)
-        {
-	    if (aboveThreshold(aa,seq,j,threshold))
-		c = findColour(seq,s,j,aa);
-	}
-        else
-	    c = findColour(seq,s,j,aa);
 
+    public boolean conservationApplied()
+    {
+      return conservationColouring;
+    }
 
-      return c;
+    public void setConservationInc(int i)
+    {
+      inc = i;
     }
-    public int getThreshold() {
-	return threshold;
+
+    public int getConservationInc()
+    {
+      return inc;
     }
 
-    public void setThreshold(int ct) {
-	threshold = ct;
+    /**
+     * DOCUMENT ME!
+     *
+     * @param consensus DOCUMENT ME!
+     */
+    public void setConsensus(Vector vconsensus)
+    {
+       int i, iSize=vconsensus.size();
+       consensus = new Hashtable[iSize];
+       for(i=0; i<iSize; i++)
+        consensus[i] = (Hashtable)vconsensus.elementAt(i);
     }
 
-    public Vector  getColours(SequenceI s, Vector aa) {
-	Vector colours = new Vector();
 
-	for (int j = 0; j < s.getLength(); j++)
-	    colours.addElement(getColour(s,j,aa));
+    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 colours;
     }
 
-    public Vector getColours(SequenceGroup sg, Vector aa) {
-	Vector colours = new Vector();
 
-	for (int j = 0; j < sg.getSize(); j++) {
-	    SequenceI s = sg.getSequenceAt(j);
+    /**
+    * 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;
 
-	    for (int i = 0; i < s.getLength();i++) {
-		colours.addElement(getColour(s,i,aa));
-	    }
-	}
-	return colours;
-    }
+           if (!jalview.util.Comparison.isGap(conservation[i]))
+           {
+               t = conservation[i]-'0';
+           }
 
-    public boolean aboveThreshold(Vector aa,SequenceI seq, int j, int threshold) {
-	String    s    = seq.getSequence(j,j+1);
-	Hashtable hash = (Hashtable)aa.elementAt(j);
+           while (tmp >= t)
+           {
+               lighter(inc);
+               tmp--;
+           }
+       }
 
-	if (j < aa.size()) {
-	    String maxRes = (String)hash.get("maxResidue");
+   }
 
-	    double sc = 0;
+    /**
+    * 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 (((Integer)hash.get("maxCount")).intValue() != -1  && hash.contains(s)) {
-		int maxCount = ((Integer)hash.get("maxCount")).intValue();
-		int resCount = ((Integer)hash.get(s)).intValue();
+       if (red < (255 - inc))
+       {
+           red = red + inc;
+       }
+       else
+       {
+           red = 255;
+       }
 
-		sc = resCount * 100.0 / resCount;
+       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);
+   }
 
-		// This should be isGap somewhere
-		if  ( !s.equals("-")  && !s.equals(".") && !s.equals(" ")) {
-		    if (sc >= (double)threshold) {
-			return true;
-		    }
-		}
-	    }
-	}
-	return false;
-    }
 
-    public boolean canThreshold() {
-	return true;
-    }
-    public boolean isUserDefinable() {
-	return false;
-    }
 }