public static ChromosomeArray regenNBlocks(
ChromosomeArray cha, int blocksize, int trigger, int endsize) {
ChromosomeArray chb =
new ChromosomeArray(cha.chromosome, cha.strand, cha.minIndex, cha.maxIndex);
chb.maxIndex = -1;
int aloc = 0;
int bloc = 0;
int ns = 0;
// Process start
while (cha.get(aloc) == 'N') {
chb.set(bloc, 'N');
ns++;
aloc++;
bloc++;
}
while (ns < endsize) {
chb.set(bloc, 'N');
ns++;
bloc++;
}
ns = 0;
// Process middle
while (aloc <= cha.maxIndex) {
byte b = cha.get(aloc);
if (b == 'N') {
ns++;
} else {
if (ns >= trigger) {
while (ns < blocksize) {
chb.set(bloc, 'N');
bloc++;
ns++;
}
}
ns = 0;
}
chb.set(bloc, b);
aloc++;
bloc++;
}
// Process end
ns = 0;
for (int i = chb.maxIndex; i >= 0; i--) {
if (chb.get(i) != 'N') {
break;
}
}
while (ns < endsize) {
chb.set(chb.maxIndex + 1, 'N');
ns++;
}
return chb;
}
