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#include "fasta.h"
Fasta::Fasta() : id_(""), seq_("") {}
Fasta::Fasta(string id, string seq) : id_(id), seq_(seq) {}
void Fasta::toString(ostream& outStream, unsigned int lineWidth) const
{
outStream << ">" << id_ << '\n';
if (lineWidth)
{
for (unsigned long i = 0; i < length(); i += lineWidth)
{
outStream << seq_.substr(i, lineWidth) << '\n';
}
}
else
{
outStream << seq_ << '\n';
}
}
string Fasta::name() const
{
return id_;
}
string Fasta::qual() const
{
return "";
}
void Fasta::seq(string s)
{
seq_ = s;
}
void Fasta::setQual(string s)
{
}
string Fasta::seq() const
{
return seq_;
}
void Fasta::name(string s)
{
id_ = s;
}
unsigned long Fasta::length() const
{
return seq_.length();
}
unsigned long Fasta::nCount() const
{
return count(seq_.begin(), seq_.end(), 'n') + count(seq_.begin(), seq_.end(), 'N');
}
vector< pair<unsigned long, unsigned long> > Fasta::gaps() const
{
vector< pair<unsigned long, unsigned long> > gaps;
string seq = seq_;
transform(seq.begin(), seq.end(), seq.begin(), ::toupper);
unsigned long pos = seq.find('N');
while (pos != string::npos)
{
unsigned long start = pos;
pos = seq.find_first_not_of('N', pos);
if (pos == string::npos)
{
gaps.push_back(make_pair(start, seq_.length() - 1));
}
else
{
gaps.push_back(make_pair(start, pos - 1));
pos = seq.find('N', pos);
}
}
return gaps;
}
bool Fasta::fillFromFile(istream& inStream)
{
string line;
seq_ = "";
id_ = "";
getline(inStream, line);
if (inStream.eof())
{
return false;
}
// Expecting a header line. If not, abort
else if (line[0] == '>')
{
id_ = line.substr(1);
}
else
{
cerr << "Error reading fasta file!" << endl
<< "Expected line starting with '>', but got this:" << endl
<< line << endl;
exit(1);
}
// Next lines should be sequence, up to next header, or end of file
while ((inStream.peek() != '>') && (!inStream.eof()))
{
getline(inStream, line);
seq_ += line;
}
return true;
}
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