public void calculatePssm() {
pssm = new double[fragments.get(0).fragLength][25];
char c = 'a';
for (ProteinFragment f : fragments) {
for (int i = 0; i < f.getSequence().length(); i++) {
c = f.getSequence().charAt(i);
pssm[i][c - 65] += (1.0 / fragments.size());
}
}
}
/**
* returns a string representation of the fragment cluster in pdb format. Each fragment in the
* cluster is wrapped as a pdb model.
*/
@Override
public String toString() {
int i = 0;
StringBuilder result = new StringBuilder();
try {
for (ProteinFragment f : fragments) {
result.append("REMARK 500 " + f.getSequence() + "\n");
result.append("MODEL " + ++i + "\n");
result.append(f.toString());
result.append("ENDMDL" + "\n");
}
return result.toString();
} catch (Exception e) {
e.printStackTrace();
}
return "problem printing";
// the try-catch block owes its existence to InvocationException calls
// from phantom functions. We still don't know what was wrong there, but
// apparently we fixed it.
}
