JAL-1512 rejig buggy conservation-basesd score matrix calculation

diff --git a/src/jalview/schemes/ResidueProperties.java b/src/jalview/schemes/ResidueProperties.java
index 2050147..7dd6520 100755 (executable)
--- a/src/jalview/schemes/ResidueProperties.java
+++ b/src/jalview/schemes/ResidueProperties.java
@@ -1420,41 +1420,49 @@ public class ResidueProperties
   }
   static
   {
-    int[][][] propMatrix = new int[3][maxProteinIndex][maxProteinIndex];
+    int[][] propMatrixF = new int[maxProteinIndex][maxProteinIndex],
+            propMatrixPos = new int[maxProteinIndex][maxProteinIndex],
+            propMatrixEpos = new int[maxProteinIndex][maxProteinIndex];
     for (int i=0;i<maxProteinIndex;i++)
     {
       String ic="";
-      if (aa.length<i) {
+      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();
+      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="";
-        if (aa.length<j) {
+        if (aa.length>j) {
           jc+=aa[j];
         }
         else {jc = "-";}
-        propMatrix[0][i][j]=0;
-        propMatrix[1][i][j]=0;
-        propMatrix[2][i][j]=0;
+        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);
-          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;
-        }
+          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;
+        }}
       }
     }
     
-    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("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));
     scoreMatrices.put("PID", new PIDScoreModel());
   }