X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FResidueColourScheme.java;h=bc1e92bc454d52cfc0eddd70184034bfdb1f6796;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=b0a5caa81f8f172cb75d9d326521c5cd65fb63a0;hpb=d4505fe7ead8da6d4fdf7e0b4680f66b3a408e87;p=jalview.git

diff --git a/src/jalview/schemes/ResidueColourScheme.java b/src/jalview/schemes/ResidueColourScheme.java
index b0a5caa..bc1e92b 100755
--- a/src/jalview/schemes/ResidueColourScheme.java
+++ b/src/jalview/schemes/ResidueColourScheme.java
@@ -1,65 +1,281 @@
-package jalview.schemes;
-
-import jalview.datamodel.*;
-import java.util.*;
-import java.awt.*;
-
-public class ResidueColourScheme implements ColourSchemeI{
-    Color    [] colors;
-    int       threshold = 0;
-
-    public ResidueColourScheme(Color[] colors, int threshold) {
-	this.colors    = colors;
-	this.threshold = threshold;
-    }
-
-    public ResidueColourScheme() {
-    }
-
-    public Color findColour(String aa)
-    {
-      return colors[((Integer)(ResidueProperties.aaHash.get(aa))).intValue()];
-    }
-
-    public Color findColour(String s, int j, Vector aa) {
-
-       if( threshold==0 || aboveThreshold(aa,s,j))
-          return colors[((Integer)(ResidueProperties.aaHash.get(s))).intValue()];
-       else
-          return Color.white;
-
-    }
-
-    public int getThreshold() {
-	return threshold;
-    }
-
-    public void setThreshold(int ct) {
-	threshold = ct;
-    }
-
-    public boolean aboveThreshold(Vector aa,String s, int j)
-    {
-
-	Hashtable hash = (Hashtable)aa.elementAt(j);
-
-        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;
-
-        }
-
-	return false;
-    }
-
-    public boolean canThreshold() {
-	return true;
-    }
-    public boolean isUserDefinable() {
-	return false;
-    }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview 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 3 of the License, or (at your option) any later version.
+ * 
+ * Jalview 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 Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ */
+package jalview.schemes;
+
+import java.util.*;
+
+import java.awt.*;
+
+import jalview.analysis.*;
+
+/**
+ * DOCUMENT ME!
+ * 
+ * @author $author$
+ * @version $Revision$
+ */
+public class ResidueColourScheme implements ColourSchemeI
+{
+
+  boolean conservationColouring = false;
+
+  Color[] colors = null;
+
+  int threshold = 0;
+
+  /* Set when threshold colouring to either pid_gaps or pid_nogaps */
+  protected String ignoreGaps = AAFrequency.PID_GAPS;
+
+  /** Consenus as a hashtable array */
+  Hashtable[] consensus;
+
+  /** Conservation string as a char array */
+  char[] conservation;
+
+  int conservationLength = 0;
+
+  /** 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 == null ? Color.white
+            : colors[ResidueProperties.aaIndex[c]];
+  }
+
+  public Color findColour(char c, int j)
+  {
+    Color currentColour;
+
+    if ((threshold == 0) || aboveThreshold(c, j))
+    {
+      currentColour = colors[ResidueProperties.aaIndex[c]];
+    }
+    else
+    {
+      currentColour = Color.white;
+    }
+
+    if (conservationColouring)
+    {
+      currentColour = applyConservation(currentColour, j);
+    }
+
+    return currentColour;
+  }
+
+  /**
+   * Get the percentage threshold for this colour scheme
+   * 
+   * @return Returns the percentage threshold
+   */
+  public int getThreshold()
+  {
+    return threshold;
+  }
+
+  /**
+   * 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(char c, int j)
+  {
+    if ('a' <= c && c <= 'z')
+    {
+      // TO UPPERCASE !!!
+      // Faster than toUpperCase
+      c -= ('a' - 'A');
+    }
+
+    if (consensus == null || consensus.length < j || consensus[j] == null)
+    {
+      return false;
+    }
+
+    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;
+      }
+    }
+
+    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);
+      }
+      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;
+  }
+
+}