void Mase::writeHeader_(std::ostream& output, const MaseHeader& header) const
{
//Write trees:
vector<string> treeNames = header.getTreeNames();
for (size_t i = 0; i < treeNames.size(); ++i) {
output << ";;$ " + treeNames[i] << endl;
output << ";;" + header.getTree(treeNames[i]);
output << endl;
}
//Write site selections:
vector<string> siteSelectionNames = header.getSiteSelectionNames();
for (size_t i = 0; i < siteSelectionNames.size(); ++i) {
MultiRange<size_t> ranges = header.getSiteSelection(siteSelectionNames[i]);
output << ";;Site selection " << siteSelectionNames[i] << " (" << ranges.totalLength() << " sites)" << endl;
output << ";;# of segments=" << ranges.size() << " " << siteSelectionNames[i] << endl;
output << ";;";
for (size_t j = 0; j < ranges.size(); ++j) {
output << " " << (ranges.getRange(j).begin() + 1) << "," << ranges.getRange(j).end();
if ((j + 1) % 10 == 0)
output << endl << ";;";
}
output << endl;
}
//Write sequence selections:
vector<string> sequenceSelectionNames = header.getSequenceSelectionNames();
for (size_t i = 0; i < sequenceSelectionNames.size(); ++i) {
vector<size_t> set = header.getSequenceSelection(sequenceSelectionNames[i]);
output << ";;@ of species=" << set.size() << " " << sequenceSelectionNames[i] << endl;
output << ";;";
for (unsigned int j = 0; j < set.size(); ++j) {
output << " " << set[j];
if ((j + 1) % 10 == 0)
output << endl << ";;";
}
output << endl;
}
}
void Mase::readHeader_(std::istream& input, MaseHeader& header) const throw (Exception)
{
do {
//Check if the line is a header line:
if (input.peek() == ';') {
char c;
input.get(c);
if (input.peek() == ';') {
input.get(c);
string line = FileTools::getNextLine(input);
//Check the type of line...
//Site selection:
string::size_type index = line.find("# of");
if (index < line.npos) {
StringTokenizer st(string(line.begin() + static_cast<ptrdiff_t>(index + 4), line.end()), " \t=;");
st.nextToken(); //skip next word: may be 'regions' or 'segments' or else ;-)
unsigned int numberOfSegments = TextTools::to<unsigned int>(st.nextToken());
string name = st.unparseRemainingTokens();
//Then look for the set definition:
MultiRange<size_t> siteSelection;
while (siteSelection.size() < numberOfSegments) {
line = FileTools::getNextLine(input);
if (line[0] != ';' || line[1] != ';')
throw Exception("Mase::readHeader_(): corrupted file, site selection " + name + " is incomplete. Aborting.");
line = line.substr(2);
StringTokenizer st2(line);
while (st2.hasMoreToken()) {
StringTokenizer st3(st2.nextToken(), ",");
unsigned int begin = TextTools::to<unsigned int>(st3.nextToken());
unsigned int end = TextTools::to<unsigned int>(st3.nextToken());
//WARNING!!! In the mase+ format, sites numerotation is 1-based, including, while ranges are 0-based, [a, b[:
siteSelection.addRange(Range<size_t>(begin - 1, end));
}
if (siteSelection.size() > numberOfSegments)
throw Exception("Mase::readHeader_(): incorrected file, found " + TextTools::toString(siteSelection.size()) + "segments while expected " + TextTools::toString(numberOfSegments));
}
header.setSiteSelection(name, siteSelection);
} else {
//Sequence selection:
index = line.find("@ of");
if (index < line.npos) {
StringTokenizer st(line.substr(index + 4), " \t=;");
st.nextToken(); //skip next word: may be 'sequences' or else ;-)
unsigned int numberOfSequences = TextTools::to<unsigned int>(st.nextToken());
string name = st.unparseRemainingTokens();
//The look for the set definition:
vector<size_t> sequenceSelection;
while (sequenceSelection.size() < numberOfSequences) {
line = FileTools::getNextLine(input);
if (line[0] != ';' || line[1] != ';')
throw Exception("Mase::readHeader_(): corrupted file, sequence selection " + name + " is incomplete. Aborting.");
line = line.substr(2);
StringTokenizer st2(line, ", ");
while (st2.hasMoreToken()) {
unsigned int pos = TextTools::to<unsigned int>(st2.nextToken());
//WARNING!!! In the mase+ format, sequence numerotation is 1-based
sequenceSelection.push_back(pos);
}
if (sequenceSelection.size() > numberOfSequences)
throw Exception("Mase::readHeader_(): incorrected file, found " + TextTools::toString(sequenceSelection.size()) + "sequences while expected " + TextTools::toString(numberOfSequences));
}
header.setSequenceSelection(name, sequenceSelection);
} else {
//Tree:
index = line.find("$");
if (index < line.npos) {
string name = TextTools::removeSurroundingWhiteSpaces(line.substr(index + 1));
//Here we stop if the line ends with a ";"
string tree = "";
do {
line = FileTools::getNextLine(input);
if (line[0] != ';' || line[1] != ';')
throw Exception("Mase::readHeader_(): corrupted file, tree " + name + " is incomplete. Aborting.");
line = TextTools::removeSurroundingWhiteSpaces(line.substr(2));
tree += line;
} while (! TextTools::endsWith(line, ";"));
header.setTree(name, tree);
}
}
}
} else {
input.putback(c);
break;
}
}
} while (true);
}
