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/////////////////////////////////////////////////////////////////
// ProjectPairwise
//
// Program for projecting multiple alignments to all pairwise
// alignments.
/////////////////////////////////////////////////////////////////
#include "SafeVector.h"
#include "MultiSequence.h"
#include <string>
#include <sstream>
#include <iomanip>
#include <iostream>
#include <list>
#include <set>
#include <limits>
#include <cstdio>
#include <cstdlib>
#include <cstring>
#include <cerrno>
#include <iomanip>
bool compressGaps = true;
/////////////////////////////////////////////////////////////////
// main()
//
// Main program.
/////////////////////////////////////////////////////////////////
int main (int argc, char **argv){
// check arguments
if (argc < 2){
cerr << "Usage: project ALIGNMENT [-nocompressgaps]" << endl;
exit (1);
}
for (int i = 2; i < argc; i++){
if (strcmp (argv[i], "-nocompressgaps") == 0)
compressGaps = false;
else {
cerr << "Unrecognized option: " << argv[i] << endl;
exit (1);
}
}
MultiSequence *align = new MultiSequence (string (argv[1])); assert (align);
int N = align->GetNumSequences();
for (int i = 0; i < N; i++){
for (int j = i+1; j < N; j++){
string name = align->GetSequence(i)->GetHeader() + "-" + align->GetSequence(j)->GetHeader() + ".fasta";
ofstream outfile (name.c_str());
if (compressGaps){
set<int> s;
s.insert (i); s.insert (j);
MultiSequence *proj = align->Project (s);
proj->WriteMFA (outfile);
delete proj;
}
else {
align->GetSequence(i)->WriteMFA (outfile, 60);
align->GetSequence(j)->WriteMFA (outfile, 60);
}
outfile.close();
}
}
delete align;
}
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