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());
}
}
}
/**
* Compares another cluster to this one by comparing their centroid coordinates. NOT an override
* of the equals(Object o) function.
*
* @param f the fragment cluster to compare with
* @return true if the coordinates are within an epsilon of each other; false if not
*/
public boolean equals(FragmentCluster f) {
if (f.getCentroid().getFragmentLength() != centroid.getFragmentLength()) return false;
for (int i = 0; i < centroid.getFragmentLength(); i++) {
for (int j = 0; j < 3; j++) {
if (!isInEpsilon(f.getCentroid().getAllResidues()[i][j], centroid.getAllResidues()[i][j]))
return false;
}
}
return true;
}
/**
* 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.
}
/** this function calculates the centroid of a cluster. */
public void calculateCentroid() {
int clusterSize = fragments.size();
int fragLength = fragments.getFirst().fragLength;
double[][] newCentroid = new double[fragLength][3];
ProteinFragment curFragment;
double[] curResidue = new double[3];
for (int j = 0; j < clusterSize; j++) {
curFragment = fragments.get(j);
for (int i = 0; i < fragLength; i++) {
curResidue = curFragment.getResidue(i);
newCentroid[i][0] += curResidue[0];
newCentroid[i][1] += curResidue[1];
newCentroid[i][2] += curResidue[2];
}
}
for (int i = 0; i < newCentroid.length; i++) {
newCentroid[i][0] /= clusterSize * 1.;
newCentroid[i][1] /= clusterSize * 1.;
newCentroid[i][2] /= clusterSize * 1.;
}
if (centroid != null) centroid.setCoordinates(newCentroid);
else centroid = new ProteinFragment(name, newCentroid, fragLength);
}
