JAL-1512 comment out for 2.8.1 release

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

diff --git a/src/jalview/schemes/ResidueProperties.java b/src/jalview/schemes/ResidueProperties.java
index 98be0c8..0cd4cba 100755 (executable)
--- a/src/jalview/schemes/ResidueProperties.java
+++ b/src/jalview/schemes/ResidueProperties.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
@@ -1420,6 +1420,62 @@ public class ResidueProperties
   }
   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());
   }