public class Nuccore {
private static int nb_proc = Runtime.getRuntime().availableProcessors();
private List<Erreur> listErr;
private static MainWindow w = MainWindow.getInstance();
public Nuccore(GenomeData gen) throws Exception {
if (nb_proc > 4) {
nb_proc = 4;
}
int used_core = 0;
NuccoreProcessThread[] npts = new NuccoreProcessThread[nb_proc];
listErr = new ArrayList<Erreur>();
if (gen.chromosomes.size() > 0) {
w.add_to_log("Analysis of chromosomes...");
npts[used_core] =
new NuccoreProcessThread(gen.chromosomes, gen.name, gen.path, "chromosomes", listErr);
npts[used_core].start();
used_core++;
}
if (used_core >= nb_proc) {
for (int i = 0; i < used_core; i++) {
try {
npts[i].join();
} catch (InterruptedException ie) {
}
}
used_core = 0;
}
if (gen.mitochondrions.size() > 0) {
w.add_to_log("Analysis of mitochondrions...");
npts[used_core] =
new NuccoreProcessThread(
gen.mitochondrions, gen.name, gen.path, "mitochondrions", listErr);
npts[used_core].start();
used_core++;
}
if (used_core >= nb_proc) {
for (int i = 0; i < used_core; i++) {
try {
npts[i].join();
} catch (InterruptedException ie) {
}
}
used_core = 0;
}
if (gen.plasmids.size() > 0) {
w.add_to_log("Analysis of plasmids...");
npts[used_core] =
new NuccoreProcessThread(gen.plasmids, gen.name, gen.path, "plasmids", listErr);
npts[used_core].start();
used_core++;
}
if (used_core >= nb_proc) {
for (int i = 0; i < used_core; i++) {
try {
npts[i].join();
} catch (InterruptedException ie) {
}
}
used_core = 0;
}
if (gen.chloroplasts.size() > 0) {
w.add_to_log("Analysis of chloroplasts...");
npts[used_core] =
new NuccoreProcessThread(gen.chloroplasts, gen.name, gen.path, "chloroplasts", listErr);
npts[used_core].start();
used_core++;
}
for (int i = 0; i < used_core; i++) {
try {
npts[i].join();
} catch (InterruptedException ie) {
}
}
} // Nuccore
public List<Erreur> getErreurs() {
return listErr;
}
} // class Nuccore
private void notifyViews(Update upd) {
idleThread.resetTimer();
textView.textFromXMLView(getContent());
mw.setFileStatus(true);
mw.setGotInput(true);
}
public Nuccore(GenomeData gen) throws Exception {
if (nb_proc > 4) {
nb_proc = 4;
}
int used_core = 0;
NuccoreProcessThread[] npts = new NuccoreProcessThread[nb_proc];
listErr = new ArrayList<Erreur>();
if (gen.chromosomes.size() > 0) {
w.add_to_log("Analysis of chromosomes...");
npts[used_core] =
new NuccoreProcessThread(gen.chromosomes, gen.name, gen.path, "chromosomes", listErr);
npts[used_core].start();
used_core++;
}
if (used_core >= nb_proc) {
for (int i = 0; i < used_core; i++) {
try {
npts[i].join();
} catch (InterruptedException ie) {
}
}
used_core = 0;
}
if (gen.mitochondrions.size() > 0) {
w.add_to_log("Analysis of mitochondrions...");
npts[used_core] =
new NuccoreProcessThread(
gen.mitochondrions, gen.name, gen.path, "mitochondrions", listErr);
npts[used_core].start();
used_core++;
}
if (used_core >= nb_proc) {
for (int i = 0; i < used_core; i++) {
try {
npts[i].join();
} catch (InterruptedException ie) {
}
}
used_core = 0;
}
if (gen.plasmids.size() > 0) {
w.add_to_log("Analysis of plasmids...");
npts[used_core] =
new NuccoreProcessThread(gen.plasmids, gen.name, gen.path, "plasmids", listErr);
npts[used_core].start();
used_core++;
}
if (used_core >= nb_proc) {
for (int i = 0; i < used_core; i++) {
try {
npts[i].join();
} catch (InterruptedException ie) {
}
}
used_core = 0;
}
if (gen.chloroplasts.size() > 0) {
w.add_to_log("Analysis of chloroplasts...");
npts[used_core] =
new NuccoreProcessThread(gen.chloroplasts, gen.name, gen.path, "chloroplasts", listErr);
npts[used_core].start();
used_core++;
}
for (int i = 0; i < used_core; i++) {
try {
npts[i].join();
} catch (InterruptedException ie) {
}
}
} // Nuccore