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// Copyright 2010, 2011 Martin C. Frith
#include "mcf_fasta_sequence.hh"
#include <cctype> // isspace
//#include <iostream> // for debugging
#include <istream>
#include <iterator> // istreambuf_iterator, ostreambuf_iterator
#include <ostream>
namespace mcf {
static void readSequence(std::istream &s, std::vector<uchar> &sequence,
char delimiter) {
if (!s) return;
std::istreambuf_iterator<char> inpos(s);
std::istreambuf_iterator<char> endpos;
while (inpos != endpos) {
char c = *inpos;
if (c == delimiter) break;
uchar u = static_cast<uchar>(c);
if (!std::isspace(u)) sequence.push_back(u);
++inpos;
}
}
static void readQualityCodes(std::istream &s, std::vector<uchar> &qualityCodes,
std::vector<uchar>::size_type howMany) {
if (!s) return;
std::istreambuf_iterator<char> inpos(s);
std::istreambuf_iterator<char> endpos;
while (inpos != endpos) {
if (qualityCodes.size() == howMany) break;
char c = *inpos;
uchar u = static_cast<uchar>(c);
if (!std::isspace(u)) qualityCodes.push_back(u);
++inpos;
}
}
std::istream &operator>>(std::istream &s, FastaSequence &f) {
std::string title;
std::vector<uchar> sequence;
std::string secondTitle;
std::vector<uchar> qualityCodes;
char firstChar = '>';
s >> firstChar;
if (firstChar != '>' && firstChar != '@') s.setstate(std::ios::failbit);
getline(s, title);
if (firstChar == '>') {
readSequence(s, sequence, '>');
} else {
readSequence(s, sequence, '+');
char secondChar;
s >> secondChar;
getline(s, secondTitle);
readQualityCodes(s, qualityCodes, sequence.size());
// perhaps check whether we read enough quality codes
}
if (!s) return s;
f.title.swap(title);
f.sequence.swap(sequence);
f.secondTitle.swap(secondTitle);
f.qualityCodes.swap(qualityCodes);
return s;
}
static void writeOneLine(std::ostream &s, const std::vector<uchar> &v) {
std::ostreambuf_iterator<char> o(s);
std::vector<uchar>::const_iterator b = v.begin();
std::vector<uchar>::const_iterator e = v.end();
while (b != e) {
o = static_cast<char>(*b);
++b;
}
o = '\n';
}
static void writeMultiLines(std::ostream &s, const std::vector<uchar> &v) {
const int lettersPerLine = 50; // ?
std::ostreambuf_iterator<char> o(s);
std::vector<uchar>::const_iterator b = v.begin();
std::vector<uchar>::const_iterator e = v.end();
std::vector<uchar>::const_iterator i = b;
while (i != e) {
o = static_cast<char>(*i);
++i;
if (i - b == lettersPerLine || i == e) {
o = '\n';
b = i;
}
}
}
std::ostream &operator<<(std::ostream &s, const FastaSequence &f) {
if (f.qualityCodes.empty()) {
s << '>' << f.title << '\n';
writeMultiLines(s, f.sequence);
} else {
s << '@' << f.title << '\n';
writeOneLine(s, f.sequence);
s << '+' << f.secondTitle << '\n';
writeOneLine(s, f.qualityCodes);
}
return s;
}
}
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