JAL-1517 update copyright to version 2.8.2

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

diff --git a/src/jalview/schemes/ResidueProperties.java b/src/jalview/schemes/ResidueProperties.java
index d360995..301a410 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 2.8.2)
+ * 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 +1418,66 @@ public class ResidueProperties
     propHash.put("proline", proline);
     propHash.put("polar", polar);
   }
+  static
+  {
+    int[][] propMatrixF = new int[maxProteinIndex][maxProteinIndex],
+            propMatrixPos = new int[maxProteinIndex][maxProteinIndex],
+            propMatrixEpos = new int[maxProteinIndex][maxProteinIndex];
+    for (int i=0;i<maxProteinIndex;i++)
+    {
+      int maxF=0,maxP=0,maxEP=0;
+      String ic="";
+      if (aa.length>i) {
+        ic+=aa[i];
+      }
+      else {ic = "-";}
+      for (int j=i+1;j<maxProteinIndex; j++)
+      {
+        String jc="";
+        if (aa.length>j) {
+          jc+=aa[j];
+        }
+        else {jc = "-";}
+        propMatrixF[i][j]=0;
+        propMatrixPos[i][j]=0;
+        propMatrixEpos[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);
+          if (pph.get(ic)!=null && pph.get(jc)!=null) {
+            int icp=pph.get(ic).intValue(),jcp=pph.get(jc).intValue();
+            // Still working on these definitions.
+            propMatrixPos[i][j] += icp == jcp && icp>0 ? 2 : 0;
+            propMatrixPos[j][i] += icp == jcp && icp>0 ? 2 : 0;
+            propMatrixF[i][j] += icp == jcp ? 2 : 0;
+            propMatrixF[j][i] += icp == jcp ? 2 : 0;
+            propMatrixEpos[i][j] += icp == jcp ? (1+icp * 2) : 0;
+            propMatrixEpos[j][i] += icp == jcp ? (1+icp * 2) : 0;
+        }}
+        if (maxF<propMatrixF[i][j])
+        {
+          maxF=propMatrixF[i][j];
+        }
+        if (maxP<propMatrixPos[i][j])
+        {
+          maxP=propMatrixPos[i][j];
+        }
+        if (maxEP<propMatrixEpos[i][j])
+        {
+          maxEP=propMatrixEpos[i][j];
+        }
+      }
+      propMatrixF[i][i]=maxF;
+      propMatrixPos[i][i]=maxP;
+      propMatrixEpos[i][i]=maxEP;
+    }
+    // JAL-1512 comment out physicochemical score matrices for 2.8.1 release
+    //scoreMatrices.put("Conservation Pos", new ScoreMatrix("Conservation Pos",propMatrixPos,0));
+    //scoreMatrices.put("Conservation Both", new ScoreMatrix("Conservation Both",propMatrixF,0));
+    //scoreMatrices.put("Conservation EnhPos", new ScoreMatrix("Conservation EnhPos",propMatrixEpos,0));
+    scoreMatrices.put("PID", new PIDScoreModel());
+  }
 
   private ResidueProperties()
   {
@@ -1539,12 +1602,22 @@ 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)
   {
@@ -1606,7 +1679,7 @@ public class ResidueProperties
   public static Hashtable toRNAssState;
   static
   {
-    toRNAssState = new Hashtable();
+       toRNAssState = new Hashtable<String,String>();
     toRNAssState.put(")", "(");
     toRNAssState.put("(", "(");
     toRNAssState.put("]", "[");
@@ -1623,14 +1696,14 @@ public class ResidueProperties
     toRNAssState.put("c", "C");
     toRNAssState.put("D", "D");
     toRNAssState.put("d", "D");
-    toRNAssState.put("1", "1");
-    toRNAssState.put("e", "1");
+    toRNAssState.put("E", "E");
+    toRNAssState.put("e", "E");
     toRNAssState.put("F", "F");
     toRNAssState.put("f", "F");
     toRNAssState.put("G", "G");
     toRNAssState.put("g", "G");
-    toRNAssState.put("2", "2");
-    toRNAssState.put("h", "2");
+    toRNAssState.put("H", "H");
+    toRNAssState.put("h", "H");
     toRNAssState.put("I", "I");
     toRNAssState.put("i", "I");
     toRNAssState.put("J", "J");