public synchronized void addProfile(Profile p) {
if (p.isStranded()) {
stranded = true;
}
if (p.length() != params.getNumBins()) {
throw new IllegalArgumentException(
String.format(
"Profile length %d doesn't" + " match bin-length %d",
p.length(), params.getNumBins()));
}
if (isNormalized()) {
throw new IllegalArgumentException("Can't add profile to a normalized MetaProfile");
}
if (profiles.contains(p)) {
/*throw new IllegalArgumentException(String.format(
"Can't add same profile %s to MetaProfile",
p.getName()));*/
} else {
profiles.add(p);
p.addProfileListener(this);
for (int i = 0; i < values.length; i++) {
values[i] += p.value(i);
max = Math.max(max, values[i]);
min = Math.min(min, values[i]);
}
dispatchChange(new ProfileEvent(this, p));
}
}
public MetaProfile(String n, BinningParameters bps) {
name = n;
params = bps;
values = new double[params.getNumBins()];
max = min = 0.0;
profiles = new Vector<Profile>();
normalization = null;
}
public void saveToFile(String fileName) {
if (profiles.size() > 0) {
try {
FileWriter fout = new FileWriter(fileName);
int start = (-1 * (params.getWindowSize() / 2)) + params.getBinSize() / 2;
int step = params.getWindowSize() / params.getNumBins();
fout.write(name + "\n");
int k = start;
for (int i = 0; i < values.length; i++) {
fout.write(k + "\t" + values[i] + "\n");
k += step;
}
fout.close();
} catch (IOException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
} else {
System.err.println("Empty MetaProfile: nothing to write to file");
}
}