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="";
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());
}