VectorSiteContainer::VectorSiteContainer(const SequenceContainer& sc) :
AbstractSequenceContainer(sc),
sites_(0),
names_(0),
comments_(0),
sequences_(0)
{
vector<string> names = sc.getSequencesNames();
for (size_t i = 0; i < names.size(); i++)
{
addSequence(sc.getSequence(names[i]), false);
}
reindexSites();
}
void Mase::write(ostream & output, const SequenceContainer & sc) const throw (Exception)
{
// Checking the existence of specified file, and possibility to open it in write mode
if (!output) { throw IOException ("Mase::write : failed to open file"); }
Comments comments = sc.getGeneralComments();
// Writing all general commentaries in file
for (unsigned int i = 0 ; i < comments.size() ; i++) {
output << ";;" << comments[i] << endl;
}
string seq, temp = ""; // Initialization
// Main loop : for all sequences
vector<string> names = sc.getSequencesNames();
for (unsigned int i = 0 ; i < names.size() ; i ++) {
comments = sc.getComments(names[i]);
// Writing all sequence comments in file
// If no comments are associated with current sequence, an empy commentary line will be writed
if (comments.size() == 0) {
output << ";" << endl;
} else {
for (unsigned int j = 0 ; j < comments.size() ; j++) {
output << ";" << comments[j] << endl;
}
}
// Sequence name writing
output << names[i] << endl;
// Sequence cutting to specified characters number per line
seq = sc.toString(names[i]);
while (seq != "") {
if (seq.size() > _charsByLine) {
temp = seq;
temp.erase(temp.begin() + _charsByLine , temp.end());
output << temp << endl;
seq.erase(seq.begin(), seq.begin() + _charsByLine);
}
else {
output << seq << endl;
seq = "";
}
}
}
}