/*
- * 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.
}
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++)
{
+ int maxF=0,maxP=0,maxEP=0;
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();
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();
+ // 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",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));
+ // 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());
}