void Mase::writeSequences(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 comments in file
if (comments.size() == 0) {
output << ";;" << endl;
}
for (size_t 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 (size_t 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 (size_t 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() + static_cast<ptrdiff_t>(charsByLine_), temp.end());
output << temp << endl;
seq.erase(seq.begin(), seq.begin() + static_cast<ptrdiff_t>(charsByLine_));
}
else
{
output << seq << endl;
seq = "";
}
}
}
}
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::appendSequencesFromStream(std::istream& input, SequenceContainer& vsc) const throw (Exception)
{
if (!input) { throw IOException ("Mase::read : fail to open file"); }
// Initialization
Comments seqComments, fileComments;
string temp, name, sequence = "";
bool comments = false;
// Get current general comments is VectorSequenceContainer
fileComments = vsc.getGeneralComments();
// Main loop : for all file lines
while (!input.eof())
{
getline(input, temp, '\n'); // Copy current line in temporary string
// If first character is ;
if (temp[0] == ';')
{
// If second character is also ;
if (temp[1] == ';')
{
// File comments isolation
temp.erase(0,2); // Characters ;; deletion
if(temp != "") fileComments.push_back(temp);
}
else
{
// If a name and a sequence were founded
if ((name != "") && (sequence != ""))
{
// New sequence creation, and addition in existing VectorSequenceContainer
vsc.addSequence(BasicSequence(name, sequence, seqComments, vsc.getAlphabet()), checkNames_);
name = "";
sequence = "";
seqComments.clear();
}
// Sequence commentaries isolation
temp.erase(temp.begin()); // Character ; deletion
if (temp != "") seqComments.push_back(temp);
comments = true;
}
}
else
{
// If sequence commentaries were just isolated
if (comments)
{
// Sequence name isolation
name = temp;
comments = false;
}
else sequence += temp; // Sequence isolation
}
}
// Addition of the last sequence in file
if ((name != "") && (sequence != ""))
{
vsc.addSequence(BasicSequence(name, sequence, seqComments, vsc.getAlphabet()), checkNames_);
}
// Set new general comments in VectorSequenceContainer (old + new comments)
vsc.setGeneralComments(fileComments);
}
