JAL-1503 update version in GPL header

[jalview.git] / src / jalview / schemes / ResidueProperties.java

diff --git a/src/jalview/schemes/ResidueProperties.java b/src/jalview/schemes/ResidueProperties.java
index bfff972..2050147 100755 (executable)
--- a/src/jalview/schemes/ResidueProperties.java
+++ b/src/jalview/schemes/ResidueProperties.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
+ * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -14,17 +14,20 @@
  * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.schemes;
 
+import jalview.analysis.scoremodels.PIDScoreModel;
+import jalview.api.analysis.ScoreModelI;
+
 import java.util.*;
 import java.util.List;
-
 import java.awt.*;
 
 public class ResidueProperties
 {
-  public static Hashtable scoreMatrices = new Hashtable();
+  public static Hashtable<String,ScoreModelI> scoreMatrices = new Hashtable();
 
   // Stores residue codes/names and colours and other things
   public static final int[] aaIndex; // aaHash version 2.1.1 and below
@@ -1415,6 +1418,45 @@ public class ResidueProperties
     propHash.put("proline", proline);
     propHash.put("polar", polar);
   }
+  static
+  {
+    int[][][] propMatrix = new int[3][maxProteinIndex][maxProteinIndex];
+    for (int i=0;i<maxProteinIndex;i++)
+    {
+      String ic="";
+      if (aa.length<i) {
+        ic+=aa[i];
+      }
+      else {ic = "-";}
+      propMatrix[0][i][i]=propHash.size();
+      propMatrix[1][i][i]=propHash.size();
+      propMatrix[2][i][i]=propHash.size();
+      for (int j=i+1;j<maxProteinIndex; j++)
+      {
+        String jc="";
+        if (aa.length<j) {
+          jc+=aa[j];
+        }
+        else {jc = "-";}
+        propMatrix[0][i][j]=0;
+        propMatrix[1][i][j]=0;
+        propMatrix[2][i][j]=0;
+        for (Enumeration<String> en= (Enumeration<String>)propHash.keys(); en.hasMoreElements(); )
+        {
+          String ph = en.nextElement();
+          Map<String,Integer> pph=(Map<String,Integer>)propHash.get(ph);
+          propMatrix[0][i][j]+= pph.get(ic).equals(pph.get(jc)) ? pph.get(ic) : -1;
+          propMatrix[1][i][j]+= pph.get(ic).equals(pph.get(jc)) ? 1 : -1;
+          propMatrix[2][i][j]+= pph.get(ic).equals(pph.get(jc)) ? pph.get(ic)*2 : 0;
+        }
+      }
+    }
+    
+    scoreMatrices.put("Conservation Pos", new ScoreMatrix("Conservation Pos",propMatrix[0],0));
+    scoreMatrices.put("Conservation Both", new ScoreMatrix("Conservation Both",propMatrix[1],0));
+    scoreMatrices.put("Conservation EnhPos", new ScoreMatrix("Conservation EnhPos",propMatrix[2],0));
+    scoreMatrices.put("PID", new PIDScoreModel());
+  }
 
   private ResidueProperties()
   {
@@ -1539,12 +1581,22 @@ public class ResidueProperties
   public static ScoreMatrix getScoreMatrix(String pwtype)
   {
     Object val = scoreMatrices.get(pwtype);
-    if (val != null)
+    if (val != null && val instanceof ScoreMatrix)
     {
       return (ScoreMatrix) val;
     }
     return null;
   }
+  /**
+   * get a ScoreModel based on its string name
+   * 
+   * @param pwtype
+   * @return scoremodel of type pwtype or null
+   */
+  public static ScoreModelI getScoreModel(String pwtype)
+  {
+    return scoreMatrices.get(pwtype);
+  }
 
   public static int getPAM250(char c, char d)
   {