void SequenceConcatenater::write_partition_information (vector <string> const& inputFiles,
string & partfile) {
ofstream outfile(partfile.c_str());
int charIndex = 1;
int stopIndex = 1;
// need to check seq type when writing this
// use infer_alpha / get_alpha_name
// but: are mixed seq types allowed? prolly...
// - so: need to check each one
for (unsigned int i = 0; i < partition_sizes_.size(); i++) {
stopIndex = charIndex + partition_sizes_[i] - 1;
bool going = true;
string alpha = "";
int j = 0;
while (going) {
Sequence terp = seqs_[j];
string subseq = terp.get_sequence().substr((charIndex - 1), partition_sizes_[i]);
// check if all are the same character (presumably all N, but useful either way)
if (subseq.find_first_not_of(subseq.front()) != std::string::npos) {
terp.set_sequence(subseq);
alpha = terp.get_alpha_name();
going = false;
}
j++;
}
outfile << alpha << ", " << inputFiles[i] << " = " << charIndex << "-" << stopIndex << endl;
charIndex = stopIndex + 1;
}
outfile.close();
}
void SequenceCleaner::read_sequences (istream* pios) {
Sequence seq;
string retstring;
int ft = test_seq_filetype_stream(*pios, retstring);
int num_current_char = 0;
bool first = true;
while (read_next_seq_from_stream(*pios, ft, retstring, seq)) {
sequences_[seq.get_id()] = seq.get_sequence();
num_current_char = seq.get_sequence().size();
if (first) {
num_char_ = num_current_char; // just getting this from an arbitrary (first) sequence for now
if (is_dna_) {
string alpha_name = seq.get_alpha_name();
if (alpha_name == "AA") {
is_dna_ = false;
//cout << "I believe this is a protein!" << endl;
}
}
first = false;
continue;
} else {
if (num_current_char != num_char_) {
cout << "Error: sequences are not all of the same length. Exiting."
<< endl;
exit(0);
}
}
}
if (ft == 2) {
sequences_[seq.get_id()] = seq.get_sequence();
num_current_char = seq.get_sequence().size();
if (num_current_char != num_char_) {
cout << "Error: sequences are not all of the same length. Exiting."
<< endl;
exit(0);
}
}
num_taxa_ = sequences_.size();
}
