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#ifndef FASTACONCAT_H
#define FASTACONCAT_H 1
#include "FastaReader.h"
#include <cassert>
#include <vector>
#include <iostream>
class FastaConcat
{
public:
FastaConcat(char** first, char** last, int flags)
: m_fail(false), m_flags(flags), m_fileIndex(0),
m_reader(NULL)
{
assert(first != last);
for (char** p = first; p != last; p++)
m_filenames.push_back(*p);
m_reader = new FastaReader(
m_filenames.at(m_fileIndex).c_str(), flags);
}
~FastaConcat()
{
if(m_reader != NULL)
delete m_reader;
}
bool eof() const
{
return m_fileIndex == m_filenames.size();
}
/** Return true if all of the streams are still good. */
operator void*() const
{
return m_fail ? NULL : const_cast<FastaConcat*>(this);
}
template <typename Record>
friend FastaConcat& operator>>(
FastaConcat& in, Record& o)
{
in.m_fail = false;
for (; in.m_fileIndex < in.m_filenames.size(); in.m_fileIndex++) {
assert(in.m_reader != NULL);
*in.m_reader >> o;
if (!in.m_reader->fail()) {
return in;
} else if (in.m_reader->fail() && !in.m_reader->eof()) {
in.m_fail = true;
return in;
} else {
delete in.m_reader;
in.m_reader = NULL;
if (in.m_fileIndex < in.m_filenames.size() - 1) {
in.m_reader = new FastaReader(
in.m_filenames.at(in.m_fileIndex + 1).c_str(),
in.m_flags);
}
}
}
// set fail when attempting to read at eof
// (like normal iostreams)
in.m_fail = true;
return in;
}
private:
/** Emulates failbit of iostream */
bool m_fail;
/** FastaReader flags */
int m_flags;
/** Index of current file */
unsigned m_fileIndex;
/** FastaReader for current file */
FastaReader* m_reader;
/** List of filenames to read */
std::vector<std::string> m_filenames;
};
#endif
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