X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FResidueColourScheme.java;h=f43aa020f193df136b1492ce5918b48d149bf873;hb=349ef01fe53c28dc78bec2d321f9c833a4b6e023;hp=f90f47589dbfa715e43d21a257478fc0dc1c32e6;hpb=1ecf6419aba86993b3c223bf5ec0fa79427baf85;p=jalview.git

diff --git a/src/jalview/schemes/ResidueColourScheme.java b/src/jalview/schemes/ResidueColourScheme.java
index f90f475..f43aa02 100755
--- a/src/jalview/schemes/ResidueColourScheme.java
+++ b/src/jalview/schemes/ResidueColourScheme.java
@@ -1,113 +1,271 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2007 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 jalview.jbgui.*;
-
 import java.util.*;
+
 import java.awt.*;
 
-public class ResidueColourScheme implements ColourSchemeI {
-    Color    [] colors;
-    int         threshold = 90;
+import jalview.analysis.*;
 
-    public ResidueColourScheme(Color[] colors, int threshold) {
-	this.colors    = colors;
-	this.threshold = threshold;
-    }
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class ResidueColourScheme
+    implements ColourSchemeI
+{
 
-    public ResidueColourScheme() {
-    }
+  boolean conservationColouring = false;
 
-    public Color findColour(String aa)
-    {
-      return colors[((Integer)(ResidueProperties.aaHash.get(aa))).intValue()];
-    }
+  Color[] colors;
+  int threshold = 0;
 
-    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;
-	}
-    }
+  /* Set when threshold colouring to either pid_gaps or pid_nogaps*/
+  protected String ignoreGaps = AAFrequency.PID_GAPS;
 
-    // aa should maybe be a class
-    public Color getColour(SequenceI seq, int j,Vector aa) {
+  /** Consenus as a hashtable array */
+  Hashtable[] consensus;
 
-	Color  c       = Color.white;
-	String s       = seq.getSequence(j,j+1);
+  /** Conservation string as a char array */
+  char[] conservation;
+  int conservationLength=0;
 
-	if (threshold > 0 && aa != null)
-        {
-	    if (aboveThreshold(aa,seq,j,threshold))
-		c = findColour(seq,s,j,aa);
-	}
-        else
-	    c = findColour(seq,s,j,aa);
+  /** 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.colors = colours;
+    this.threshold = threshold;
+  }
+
+  /**
+   * Creates a new ResidueColourScheme object.
+   */
+  public ResidueColourScheme()
+  {
+  }
 
+  /**
+   * Find a colour without an index in a sequence
+   */
+  public Color findColour(char c)
+  {
+    return colors[ResidueProperties.aaIndex[c]];
+  }
 
-      return c;
+  public Color findColour(char c, int j)
+  {
+    Color currentColour;
+
+    if ( (threshold == 0) || aboveThreshold(c, j))
+    {
+      currentColour = colors[ResidueProperties.aaIndex[c]];
     }
-    public int getThreshold() {
-	return threshold;
+    else
+    {
+      currentColour = Color.white;
     }
 
-    public void setThreshold(int ct) {
-	threshold = ct;
+    if (conservationColouring)
+    {
+      currentColour = applyConservation(currentColour, j);
     }
 
-    public Vector  getColours(SequenceI s, Vector aa) {
-	Vector colours = new Vector();
+    return currentColour;
+  }
 
-	for (int j = 0; j < s.getLength(); j++)
-	    colours.addElement(getColour(s,j,aa));
+  /**
+   * Get the percentage threshold for this colour scheme
+   *
+   * @return Returns the percentage threshold
+   */
+  public int getThreshold()
+  {
+    return threshold;
+  }
 
-	return colours;
+  /**
+   * 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;
+    }
+  }
 
-    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 j DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public boolean aboveThreshold(char c, int j)
+  {
+    if ('a' <= c && c <= 'z')
+    {
+      // TO UPPERCASE !!!
+      //Faster than toUpperCase
+      c -= ('a' - 'A');
+    }
 
-	    for (int i = 0; i < s.getLength();i++) {
-		colours.addElement(getColour(s,i,aa));
-	    }
-	}
-	return colours;
+    if (consensus == null || consensus.length<j || consensus[j] == null)
+    {
+      return false;
     }
 
-    public boolean aboveThreshold(Vector aa,SequenceI seq, int j, int threshold) {
-	String    s    = seq.getSequence(j,j+1);
-	Hashtable hash = (Hashtable)aa.elementAt(j);
+    if ( ( ( (Integer) consensus[j].get(AAFrequency.MAXCOUNT)).intValue() != -1) &&
+        consensus[j].contains(String.valueOf(c)))
+    {
+      if ( ( (Float) consensus[j].get(ignoreGaps)).floatValue() >= threshold)
+      {
+        return true;
+      }
+    }
 
-	if (j < aa.size()) {
-	    String maxRes = (String)hash.get("maxResidue");
+    return false;
+  }
 
-	    double sc = 0;
+  public boolean conservationApplied()
+  {
+    return conservationColouring;
+  }
 
-	    if (((Integer)hash.get("maxCount")).intValue() != -1  && hash.contains(s)) {
-		int maxCount = ((Integer)hash.get("maxCount")).intValue();
-		int resCount = ((Integer)hash.get(s)).intValue();
+  public void setConservationInc(int i)
+  {
+    inc = i;
+  }
 
-		sc = resCount * 100.0 / resCount;
+  public int getConservationInc()
+  {
+    return inc;
+  }
 
-		// This should be isGap somewhere
-		if  ( !s.equals("-")  && !s.equals(".") && !s.equals(" ")) {
-		    if (sc >= (double)threshold) {
-			return true;
-		    }
-		}
-	    }
-	}
-	return false;
+  /**
+   * DOCUMENT ME!
+   *
+   * @param consensus DOCUMENT ME!
+   */
+  public void setConsensus(Hashtable[] consensus)
+  {
+    if (consensus == null)
+    {
+      return;
     }
 
-    public boolean canThreshold() {
-	return true;
+    this.consensus = consensus;
+  }
+
+  public void setConservation(Conservation cons)
+  {
+    if (cons == null)
+    {
+      conservationColouring = false;
+      conservation = null;
     }
-    public boolean isUserDefinable() {
-	return false;
+    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);
+      }
+      conservationLength = conservation.length;
+    }
+
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param s DOCUMENT ME!
+   * @param i DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+
+  Color applyConservation(Color currentColour, int i)
+  {
+
+    if ((conservationLength>i) && (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;
+  }
+
 }