X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FResidueProperties.java;h=0cd4cba405992077f5d8c566b0d31b4355fcf316;hb=ac3d9833fe58e6d40db34203eea222ea3c10c3f0;hp=7dd6520547a073604a78c81dcc67fb5e39130968;hpb=7b4ec47748c8785073981750de8a4f9d716395bb;p=jalview.git

diff --git a/src/jalview/schemes/ResidueProperties.java b/src/jalview/schemes/ResidueProperties.java
index 7dd6520..0cd4cba 100755
--- a/src/jalview/schemes/ResidueProperties.java
+++ b/src/jalview/schemes/ResidueProperties.java
@@ -1425,14 +1425,12 @@ public class ResidueProperties
             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 = "-";}
-      propMatrixF[i][i]=propHash.size();
-      propMatrixPos[i][i]=propHash.size();
-      propMatrixEpos[i][i]=propHash.size();
       for (int j=i+1;j<maxProteinIndex; j++)
       {
         String jc="";
@@ -1449,20 +1447,35 @@ public class ResidueProperties
           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();
-
-            propMatrixPos[i][j] += icp == jcp ? icp : -1;
-            propMatrixPos[j][i] += icp == jcp ? icp : -1;
-            propMatrixF[i][j] += icp == jcp ? 2 : -1;
-            propMatrixF[j][i] += icp == jcp ? 2 : -1;
-            propMatrixEpos[i][j] += icp == jcp ? (1+icp * 2) : -1;
-            propMatrixEpos[j][i] += icp == jcp ? (1+icp * 2) : -1;
+            // 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;
     }
-    
-    scoreMatrices.put("Conservation Pos", new ScoreMatrix("Conservation Pos",propMatrixF,0));
-    scoreMatrices.put("Conservation Both", new ScoreMatrix("Conservation Both",propMatrixPos,0));
-    scoreMatrices.put("Conservation EnhPos", new ScoreMatrix("Conservation EnhPos",propMatrixEpos,0));
+    // 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());
   }