void operator()(std::string::const_iterator,
std::string::const_iterator) const
{
+ std::string::iterator seq_i = seq.begin();
+ std::string::iterator seq_end = seq.end();
+
+ // this if block is a hack, for some reason spirit was
+ // duplicating the last character if the file didn't end
+ // with a new line.
+ // this checks for the trailing newline, and if it is missing
+ // removes the last character ( which should be the duplicated character.
+ // check test_sequence.cpp:sequence_no_trailing_newline for test case
+ // also see ticket:265 for more information
+ if (seq.size() > 0) {
+ std::string::value_type c = seq[seq.size()-1];
+ if (not (c == '\015' or c == '\012')) {
+ // doesn't end with a new line character
+ seq_end--;
+ }
+ }
+ // end hack
+
// filter out newlines from our sequence
std::string new_seq;
- for(std::string::const_iterator seq_i = seq.begin();
- seq_i != seq.end();
- ++seq_i)
+ for(; seq_i != seq_end; ++seq_i)
{
if (*seq_i != '\015' && *seq_i != '\012') new_seq += *seq_i;
}
//std::cout << "adding seq: " << name << " " << new_seq << std::endl;
-
Sequence s(new_seq);
s.set_fasta_header(name);
seq_list.push_back(s);
SeqSpanRefList::iterator annots_i;
AnnotationsRef metadata;
- // not sure why, or if i'm doing something wrong, but can't seem to pass
- // file pointers down to this method from the mussa control class
- // so each call to save a sequence appends to the file started by mussa_class
- //save_file.open(save_file_path.c_str(), std::ios::app);
-
save_file << "<Sequence>" << std::endl;
save_file << *this << std::endl;
save_file << "</Sequence>" << std::endl;
}
}
-BOOST_AUTO_TEST_CASE( sequence_annoted_with_reversed_sequence )
+BOOST_AUTO_TEST_CASE( sequence_no_trailing_newline )
{
// sorry about the long string...
- string s = "CTGGGTCGGGGGCGCTGGGGGCTGCTGGTAnnnnnnnnnnnnnnnnnnnnnnnnnTCTGCGCCGCCCGAGCCGCTGTGCTGCGCGTACTCCTCGAAGGGAGGGAACTTGGGCTCGATGTAGTTGGAGTTTATCAAAAACGAGCTCATGGTCATTAATTTGTGAAGTGCAAAAATACTAATTTTTCTCGCGTTGTCGTTTTTTCTGGGCTTGCCGAGGnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnGCAGACGCCGCCACCAAAGTTCGAGCCGCTCCTCCCCAGCCCAGCGCGCGCCCCGCCCCGTGCCCCACGTGCAGCGCCCCCACCAATGGGCGCACCGCGCGCGCGGACCCGGATCAGGAAACGCGCGGGTGCGTGATGGATGCTGCTGTCCGGCCCCTGGGCTGGGGGAGGGAGCAGGAGCTTTGGACCCCAGCCCCCCAGCTTTGGTTCCCGCTGGGAATTCAGGCCCTGTCAGGCTGTAGGTCCTCTCGGGAGCCCTCTGCCTGCCCTACTGCTGGCCTAGGCCTCGGGCTGTCTGGCGGCCGCGACTCAGCGCTGACCTCGGGCGCAACCCAGTCAGGCTTCGTGTCCTTCAGGGGTTCTAGGCTAACAGGCGAAAGGAAGGGCGTTGGGACCGAGGGGCATCCTGGTTTTTATGTACGCCACTGAGAGGCCACCAGACACATTTTCTCAACCGCAGATCCCCCTTCCCCACACCCTGCTCCTTGCGTGTCAGCCTGAGAGCCCTTGCTTTGAGAAGCTTGGCAGAAGCTGCAAAGGGTGGGCGGGCAGCTAAGAGAAATCGACCCAAGGATGTAAATCGAGGCCATTCCATTATAACTGGATGGACACTTTTCATTTTTTCCTTCTTTCAGAGACAATCTGTTTCGTGTTTTCCTAAGAAAAATTGGAACCTTCGTAATAGCATCTAATTTGACGGGGGTTGTCGATGTGAGAGCTAAATATGCCCGCATTTACTAGGTGCGATTGTGAGAGAGAAGGTGGCCCAAGGATGGGAATGGATAGAAGCAACACCTCCACAGAACCGAGCTTTGAAAACAATAACTTCCTATTTCAGAACTATCCCCAAACAAAAACAAGCTAAGGGTAGAATAAACACCTTGCCGGGTCTGATCGCTGATGGGTCTTTTCCAGCTAAGAATTTCATGTTTTCTCTTTTAGATCCTGCTTTCTCAGGCAGTATCTGAGGCTAGAGTTATATTTGCAGGACAGTCTATAATTTCTGAATTGCTGAAAATTAGCGTATTAACGATATCAGAAGCTCCGGAAAGGAGGGAGAGGAGACTGTTGCCTGCTATTTGGTAATTGAAATTTGATGGGTACACTAATTACGCCATTATTAACAAATAAATTACTTATTAATTCCACCTAATGTTGATCTTTGAAGTAAATACTGATGCCTTATTTGTGCTGTGTGCTTTCTCCCTTTCTTTTCTGAGTAGTAGACATATCTAGATCCTCTACTTTTCAGCCTAAATTAAAGCAGTGTAAACTAGCATAGTCACCATTCTAAAAATATTTTCATATTGGCATGCAAAAGCAAGGATTTTTCAGCTGGTGCACCTTAGTTGATTTTTCAAAGAGCAGTATAAACAGCCTTCTCACAACTGAGTCTGGAACGCAGACAAGGAAAATTATTTCCTAAGCCTGGAGACACTTGAAAAGGAATGTCAATTCTATCTTCATTCATACTGGTTACTCATATGAGTTACTAAATGCTGGAATATATCCATTTGATGGATAGTCACTTAATGCTTAGCCACATAAAGCCTATTATATGGGACTAATCTTTAAACTAATTTAGGAAAAGAGGTTAAAAAGGGGATCATATTAGCTTTCTAACTGGAATCACCCTGAAGAGGTACAAAGAGATTTTCCACGTTAGGTGTATATGAGTGTGAAGAGTGCTGTCCATTCACATGAGGCACCCTGAAAATTTGTTTTTAAAGAAATTTGAGCCACAGACAGAAATCAACACTGAGTGTAATCTTTAGCCATCCTCTCTAGACTGGAGGAAAAATTTAGAATGTGATACATCTACCTGAACCAATATCTCTCCCTAGCAAGAAAAAATAATATACACATAGGnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnGACATACGTATTACAAATCTGAACCCTATAAGTTTCAGGGGGACAAAAAGCATGACAAGGAAATCTTCCCTCCTTCTCATGTCATCAGCCTTGAGTACTAGGGTCTTAACCATATCTGTTTAATATTTACAGACACTAAAACACAAAATTCTGTTGTTTAGCCTCAGAACCTTGTACCAAGTTTCTATTTTTAAGTATTAACGAGACATAAACACTGTTTTGTATACGGTTAACCCAAACGAGTTAGCTGTGCCTGTGTTTTGTGTGATTCTATTACTTTAGGAAGATGGCCTTACACAGAATCCCCCAAGGCCTGTAACTTGTCTTTGTGGTTCGTATCATAAACACAAACGGAGCCAGGACCACCAAGTGTTATCTCAACACCGACATTTTGACATTTTACTGCAAGATTTATGGCTGTAATAAACAATCTCAGTACCTTTTCTGAACCTTCCTCAATCTCCCTTTGCAAACCATAGCATCATTCCATTGAATCAAATAATCTTTTGAAAAACATTTAAAAAAAATACCTCTTGCCTTTACACAATATCCAAGACACCAAAGTAAAGCCAGGAAGAAACTAACTCAATTAATAAACAAACTGAAGTTTACCAGCAGCATCTCGCCTGAGAAAAGATGGGATGCCCTGAAATGTAGCAGAGAGGGAGCATGCTAATCCTCACACACCAACTGGCTCCAGTCCCAAGCGGGGTGAAAGCGTTATCCTTTCCTTAGGAAACTGGTGAGCACGTTTGCTCATTTCCACGTGCAGGGATAACATATATTCCCAACAAAAGCTTTCTTAAAATCCCATTAGGTGAAATAACTTTTCATCATGTCCTCGAATCCCAGATGGAGAAGAGTGAAGGGAGTCGGAGGGAGAGGGAGGGTGCAAGGGAGGCAATGTTTTGCAGCTTGGTTTGAATCTGATTTGAATCATTTTGAATATATTTGTAACAGCATTCCCTCTTGAATGCAACCCTGTCCCAAGTTTCAAAGTGACCGAACAGTGACACCGTGTGCATTTTGTTTCTTATTAATCTTACACATTGACAGTCTTTGTTAAATCACAAGGCGCGCCCTTCACTAGCCGACATTTTCATATTTGTTAGACGCACTGACCTGAAGTTCACCTCGGCCTTGGACTTTGCGCTTCTAAAAGGTCTATACAGTGTCTTTTAGAGAGCAGGGTGCTTTGCCCAGGTCACTCCTTCTCAGGAAAAACCAAGGGGAAAAGCCAAAGGAAATGTAAACGTTATGGAATGTATTGACTGTATTTGTCCTTTGTTCTTTAGAGCGAGAGTCCCCCAGACTGTTCTCTATCTGATGCATGTCTCTAGAGCTGAACAGTGGAATGGCAGAATTTCAAAACGCCTGATGGTGGCATTTGAAGGCTTCCCCACCACCTACACTAGACACAAGATTTGAGAGGAACAACACTTTACCAGCCATTTGACCAATTAATTCTTTGGGGATAATTTTCTTGTAGTAGTTTAAAATAATGCACACAACGCAGGGATGAGGACTGATATTCATATTGGGATTACACATGAATTTTAACTGGGATTGTTTGAGAGGCCTGAGGTTCAAAATCCTCCAGATAAAGCAAGCACACTAAAAGCAATAAATTCTGCAAGTACTCTTTTCTTTTACTTTGAAGACTAGCTAAGAGGTATCTATGGTTTTTGAAGCTGACATGTCTATAAGGTGTGTCACATGTTTTTAACCAAAAAGCACAATAAAAAGGTTTTTCCCAAAGAGACACGTAATTGTCTTGTTGACTCATCGAGGGGTTTCAGTTTTCCTCATTTCACTAGCCCAAATGTGGTGAAATGTTCACTGCTGCAACAGCAATCACCACAGTTGTTTCCTTTCTTCTGTTTCATCTGGCAAACCCCCATTTGGCTTCAAGCTCTTGGCCAGAGTGAAAACTTTACACATTGCACAGAAGCACCCTGATTACTTCCATGAAGGCAGTGTTTGGAAAATATTTACTTTACCACTGAACATACCTGGCACCATTAAATCCAATCAACCAAAATATTGGGATGATCTTAAACATTCCTGCAAGAGTCCACATTCTGAGTAGATGAATTATTTCCAAAGTTAAAAAAGAAAAACCTAGGGAAAATATTTCACTTTTCTCTTCTCTGTTTTCCTATACTGATCCCTTGAAGGTCAATTCATAGAAAAGGGAAATATGTCCTCTGGAAAATAGATTCTTACAGCACCAACACTTAAAGCCATTCTAGATGCATGAAAAATAAAATATTGTTTAGCTCTTCAGTTGCAACTCACACATGAGGCATGGTTCTAGTCGGCTTCCTTAATACACTATTCTCTTTCTTTTCTGCTCTCCCACCCTTCTTCTTAGGTTGCTTTATCTTCTCCTTGGCTTTTTTTTTTAATTCCACGTGTATCATTAAAAAGTACATTCTGAAGAATAGAAAATATTCTATTCTGTCCTGGTGGTCTTACAGAGTAGCCTGTTATTTGTGGATTTCACCTTTCTGCATTCCCTACAGTCTAGTTATTCACTTATAGCTTGTAGCATTTCTCTTACATTCAATTGTGGTTTAATAATAAACATTAAAAAAATTTCCAAACAGGAACATTTTCATGGCACCAGTAAGCATTTTGTCACTGGCAGTGGTGGTGGAAGGGGTGAAGGGAGAATTCTGTGTCTTTCAGGAGGGTTTCCACTTCCTTCCTTCCCCTTCTCAGATCTCAGAACGCTTTGCATTCAGCGGACTGTAGTTTCAGAAAAAGCATATTCTGTGTTTGAAAACTGCAAAGATTATATTTTGCAAGAAGTGTCTGTGTTTGCATTTATTCTTACACACTTTAGGGGTCATCATGTGTACTAAAAAGACAAAAAACCGGCCAATCAGAATCCCTCTTTTCAAATAAAGGAGGTTTCCTGCACCATTCTGTTGCCTTTGAAGGCATAATGAAATATTGGAAACTTGTGACATTAGTTTTTAAAGCTCCACAGATGAGTTTTTAGCATTTTTATTTTGTGACAAACCCACAGACTCCTGGTTCTCCAACACCTAAGGTGTTGATGTTTCAGTAATCTATGCCTATTTACCTGCTGCTATTCCCTCAGAATGGGAGCGATAATTCAAGATGAGATACAGCATGTATTACTCTTGAAAAGAGGAATTTTCTATCCTTTCCTCCGTAATTGAGGTCATTCAACCACTAGGGTTCACCTGGAGTCCATACCGTGATACACGCGTCACTCTGAGCCATTTTATCTTTTGTGCTGATAGTCAAGATCACAGCTCTAACATTGACATCAAACTCTGTCTGGGCAGATGACTAAGAGCACTGCACAATGTAAACTTTTGACCCTCAACTTTTTGACCTGCAGTTGTAACGCACTAACCGCAAAGATACACAAAGCCGAGCCTCTTCTTTCAGGGGGAAGGGGCCCCCCAGCATCTCAGGATGCCCTGCTTCTGCCACTGCCATTTGAAATTAGAGGGTGAAATGGATATTTTTGTGTGTTTGTGACTGTACTTTTTGTTAAATCAGCCTATGACCTCTTCGTTAGCACCTAGGAACTAGATTAACTTGAAATCACTCGTGATTCTATTTTACAAGGAAAATTTGGAGCAGAATGGGAGAACCTTGCAAAAAGTGAAAGAAAAGAGAAGATGGGGGAAAGCAGGCAATGGGAGGTGGAGACACTTTTTCCCTTTATTTAAAACTAAAGACGCAGCCCTAATTGTTGGGAGAGCTGGCCCAAGCGGGTGAATTGACTGTGAACTTGTACTAAAGCGTGCTCTGCTGGCGATTCCTAGGGTGTGCAGATTTATCTTCTCTGCATTTACTTAACCCGGCAGTGAACTGCGCGGGCGTCATTTGTTAGGCGATGACAGACTTCACCTCCAGCAAGGGCTGCTTCACAAAATCGCAATAATTATCTAATAACCTTCATAACAAATATTATTATTGAAAAGACTGGTTTGTGGGGAGGGGACCTGGTGGGAGAACAAATTTATTTGTGAACAACAACAAACAAAACAAACCTGGGCAGACCTTCAAGTTCTGGGGCTTAGAATGGCTGGGGCTGTGGATCCCCTCCCCTACTTGGGTGGGAGCTTAGGCTGACCCCCTCAGCCCTGCCTGGGAGCCCCGTTTATAGTTTTGCCATTGACTAGAAGGAAACTCCTCCTCAGAAACCAAAGGGAGGGAGCCCACAATGCTCTGCACTCTCCATGGTGGGCAAGCCATGGACAGACCCCCAGCCAAGGCAGGGGGGAGGCTGAGAAGGGCATCTTTTAAGCTAAAAGGATTGTTTTCCTCTTTAATTGCCTATCTTTTAAGATGTGATTTGCTTTCCACTCACTAATTATTTCGATATAATACTCTCAGAATCTCAACAAATGAACAGGACTCTGTTTTTTGGTGGGAAATTCTGTCTTGCTCTCTCAGAGCCGCCAACAATGAAGCAGGGGAAAGAGCAGGAGAAAGGGAATCTTGGCATAATGTTGTGAAATTAGACCATGGAAACCCTAACAAACCACTAAGTAAGTGTGACCAGAAGCTTCCTGTTGTATTTATAGTTCAGAAATATTGTCTCTTCAGCTTGTGGGAACAAACGAGCCCCCGCACATTGCCGCTGAGGAGGAGCACAGACACGCACTTCTGCCACCGGCTGAGGCTGGATGTCTTCATAAAGCCCTCAGTGACAGACATATTTTTTCTTAGTAAGTTCCTCTGCAAGAACAACCCAAAAGAATCCACAAAAGAAATAACTTATCTACAGAATGAGCAGAAAACCAGCCATCCTCTTTATTATGCTTCCTATGAAAATAGGAAGAAAGAAAAAAATCTTCCAGTAACACATAGGTCTGACTGCATGATGTATTTTTAAAGTCATTTTAATTCCATGTGGCCATGTGGGTTTGCCTGCTCTCTTAAATTCTACTTAAGTTTTGTGAAGATTAAAACAGACAGAAATAAGCAAGCTGACAATATTTACAGCCTGTAATTTTTCTCATTCCTTGGAAAGATTCTCTATGTTCTGTGGTACTGGATATGACTTCAACAGGCTTTCTGCTCATTCCCACACCCCAGGGTGGAATATGGCCATGAAGTAGTGTGGATATTTTCTGTGTAAGTAACTCAAATTAAACTGGCAGAATCCCCGTCACTCTTTTTTTTTTCTAATTTCAATCACCAAGAAATCACTCAAGCAAGATCACCAAATCAGTAACTAAAATGGAACCATAACGCAATATTTTCCAATAAGGAGCCCAAAATTCAGAGCAGCAAAACAAGGAATCCAGTATTCTCACAGACACATAACATTATAAAAGAGAACCCATACCCATGTAGAGTTTATATCCTTGTTCCCACTAAGATGTGGACACATCTTCTTGAATGCTGAAATACCAATGTTTACTTTAATAGGTTACACACAATGACTTCAGGATTCTTCACCTTGCCACTATTCATGAGAAGTAGCACTTGTGGGAGGGTTTTGATTTTTCAAAAAAACTTTCTAGGTTTTGCTTTCTGGACCTCTGACTTTAGGGACATCTGTTGGACTTATGTTGAGTGTAGGTGGCCTCTGCACAATAAGTTTATTGAAATTCCAAATCTATACTTTCAATTTTTTCACTTTAAGCACTTAATAGGTATCTTTACCAATTAATACTTGCTGAAAACTGCCCAGCTCCTAAGGAGAAAAGCAGATCCTATTTTTTGTTTCATTTCTGAATGCAGTAGGAGAATTTGGCTTAATTCCTAAAATAGGATTGGAGGAAATCTACTGGGTCCCTTGTGGGTACCCATCCAGAAAAAGATCCCAGGACAGGCCACAGTCCCCAGTCACTGGGCTTGGGTTTTGCCATTGAAGAATATGGGGGGTTGGGGCCAGAAGGGGTGACTGGGGCCAATATGGAATTGTGCCCAGGATAAACTTATTTCACCTTACTTCACCCATTGGTGCAATTTTGGAGACTGTTCTGGAAATCATAGATTATGTAAATTTCCTGGGATCAAACAGAAAGAGCAACTAACAAAAGAAAGGCGGAAATCTCCTACTGACAAAGGACCAATTTCTTCCCTAAACTACCGTTTATGATGTGTCAGGAAAAACAACCTAATGGCTCTGGGGACTTTTAAGTTGGGCACTGAAGACACCTCAATTTCCCCCAAAACTTTAGAGCACAGTTTGGAACAGAGAATTCGCCTGTATGTTGAGGGGGAGTGAATTTCTCCAATCTTAATGTTATCCAGGGGGCCGCCTAAGTTGCCTTCTGAGGGTCCTGTGCGTAGATGTTTTTAATTCTACnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnGCGCTTTAACCCCTTTCAATTAGCCTGGGGATTCAAAGACTAAAGTTAAATCCGGCCATAAAGTTTATTGCTTCAGACTCACAAGCGGCTGAGAACAGTCCCGCCGAAATAAAAAGAACATGCAGGCAAACAGGGTTCAGGGCCTGGTCCCGGGTGCGGGGGAGGGGGTCCTGAACACCCCCCCACACCAGGGTGGGGATCCTTGGTCCTCAGGGTCCAGTGGGCGCTAGCAGCCCAGGATCCACCTTGCAACCCGGGGGCCCAGCCTGGAGGTGCAGCCCCAGCCTCGCCGGCCTCTGCCACCCTCCCGCTCTCGCGAGCTAGCCTGAAACCCGGCCCCGAAGGCCGCCGCCTCAATTCAGCCCTGCCAAATGACCCCGGCCCGCGAAGACATATTGCCACAGCCCCGTAAGGAATCCCGCCAGAGTCCGCCTCGGCCCTGCCCCGGCCTTTCTTTCAAACTCCTGAGCGCAnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnACTGTCTCCCAGCCCCGACCCCAGGGCTCCGCGACCCCCAGGAGCTGGCCCCGGCCGGCCCAGCAATTGCGCGGGGGACTGGGGGTGCGGCCCTGCCAGGTCCCCACACACAGGCCCATTCGCACACAAAAATCATCTTTTTGCACGCCGGCGGGAGCAGCGGAAGTCATTAACATCCGCGGTTGTGCTGCAATTAAAGTTAGGCCTGGGGATGCGGCGCGGCCACAGGCGCTGCTCACTCTGCTGCCTCCGCAGAGTTGGCTCCTGGCGCTGCTCTTTTGGGCAGAGGGAAAGTTTGCTCTGCCTTTTCGAATTCAGAGGCAGCCTGAGTTATTGAACCnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnTTTCCAAAGTACAAATAAACTTGAAAGCGCTCAGGAGGCGAGCTTACCTTAACTCGGAGGGAGCCATTTTTCAGAGAGTTTTGAGAACTTGTGGTTTGGACACTTCTGGACCTAAAATTGACAGTTTGAATGGCCAGGCGGCACACGTAGCCTGCAAAAGAGTCAAATGGAGTCCAGCGTTAGTGAGATTATATGTTATGTGGTATATAATGTTGGATGTCAACTCCCCAAAACCATAAAACTTACTTTAATGGCCCCACGTGACGTTTTATAGCCAGTGAGCCGATCTGTCTGTGCTATGGATGATTTTACGATCTAATTCATAGACAAAACCCTATTCATTTGGCACCCAAATGTCATATAGCCGGAACTGGGGCTTATAAAGTTTACTGTTTTATAACTTTTAAAAGGAAAGACGGCATCAGTGTAAGCAGTCGGTAAATGTGCAAATCTCTAGTTGCGCTTTAGCTGCTCTGAGGAGTTTCCCAATCGAGCTAGGATGGGGTAAGTACCTTCAATTTGTAGCAAATTAATTGTAGCAAAAGAAGCCAACTGGGTCCCGGGTGAAGAGTGGGGAAGGGGTGCTGGGATGGGTTAAGGGCAGAGGGTTTGGGGTCCACAGACAGACATAGCAGCGTCTTCAGCAAGTGGAGGCCTAGGACAGCCTTAGGAAAGAGGCAGGATCTGTGTGGCCTGAGGGCGGCTAACAAAGCCCTGGGTTTTTTCTCCTTTTTTCTTGCTCTTTCTCTCTTTTTTGTACCCAGCAAGTTAACTTGGTTTCCTCAGAGATGGACAGGGTGTTCTGGGGCTTTGGAACAGCCTACAGCTTTTTCCACCTTCTGCCCTGAACTTTGCAATGGGTCAGAGGTAGGGAAGCGATGGGACAGTGTTGGTATGAGGTCTCCCTGCACAGGTCATCTGCTCAGGTAGCCTCAGACCCAACAGCTTCCAAGACTGCACAGACAGACAGAAAAGCAGACAGAGCCGCTCACTATTTGGCACAAACCAGACCAAGAGAACTTACAATAGAAAGTTTATTTTTTGTTCCAGTCAGTATTTTTTCCTTnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnGCTGATCACAGTTTGCTTAAAACAGCCAGACTTGGACAATATTTGTAACTTTGTTCACAAAAACATACATCACTGAAGCTGCGCTTATAAGAGCCACTTCCAGAGTTCGTGCAAAGGGTCCTATAAAGGCACGCAGGGACACACCGCTTGGAGTCACAGTTTTCATCACAGAGTCACTAGTCACTACACGTCGAACAAGTTGTGTCTCATCAAGTCACCTCTACAACAGCATTAATTACACAAGGAATATAGGTAGTTTGAATAAAAATATCTTTAACAGCTTGGAGCTATTGAGACAGGAACACTTCCACGCACATGCACAGTTAAACAACTTGAGTGCAACACACAACATTGGCACTAAACGAGATTGAAGGGGGACTTTTTGTGTGTTTTTTTTTCTCTTTTCTTTTTTTGTTATAGTTACTTCAAGTAACACAGCTTGCTTCATATAAATAAGTTAAAACATCTATTTTTTTTCAAGACAAAGCCATTCAGGACAAAGAGATGAACAGAAAGCAGATCTACTTATACAGGCGCTATAATGGCAATAAACAGGCTCATGATTAAAAGATGAATTAGGGCAACGAGAACAGGGCTTCTTCACAGAAGGAACACAAGGGAGTTTCAGAAAGTCACCTTAGTACTGACACTACGCGGGATCCGCTAATACTGCTCAGTACTTTAAACGCTCAGATACTCAGGGACGGAAGGCCCCTCCTGCCGCGGCCATGCTCATGCTTTTCAGCTTATTATCTTTTTTCCACTTCATTCTCCGGTTTTGGAACCAGATTTTAATTTGTCTCTCGGAGAGGCAAAGAGCATGTGCTATTTCAATCCTCCTTCTGCGGGTCAGGTAACGGTTGAAGTGGAACTCCTTCTCCAGCTCCAGGGTCTGGTAGCGCGTGTAGGCCGTCCGGGCCCTTTTGCCTTCCGGGCCGCCTATGTTGTCTGCAATAGAAAAGTCAGCGGTTTAGCCACCAACTCCTGTCTTCCAAAGTCCGCCAGGGGGACAAGCTTGGGTCATGAGCAGGGAACCCAGGCGAAAAGCTCAACAAGTTCTGCCTACCAGCCCGCACACCCCTCCCGAATTTCCTTCTCTCTTCCTTTCTAGAAAGAAAACAATACGATTTGGACCCTGGGAACAATCTGCCCATCTGAGGCTGGGGCCGTGTCCCGGCGGACTCCGGCTTTCCCTGGCCCCTCTCCTGCCCCCTCCGCCCTGCCCCGGGCGCCCCGATCGGGAGGCACAGCCCTCCCAGGCTGCCCACCGCACAGAAACCCAGGAAGCAAGGCCCTTTCCTGAGCGCCCAAGTGGCCTTCGGGTCACCCTCCCTCAAAGTTCCAGCCCCGAGAGCCGCCTCCCGTTTCCAGCCTGCAGGGTTGGGGAGCCTGTTTTCTTTTTCTTCCCTTTCCTTCTCTCTCCCTCCTGCCCCCAAAATTCAGAATCCTGCAGGCTCTCGCCTCGATTCTTTCCCCCAAGCCCCTTTTCGGGGGCTGTAATTAGTAACGCTGTTTCCCCAGCGTAGCCCTCCTCATAAATTATCCGCCGTGACAAGCCCGATTCACGGCTGCTACAGCCATCCTCTACCTCTCTGCGCCTTGCTCGGCTGGCCTGACCCGGGAGCGCGTCCCAAGGCGTGGGGTTCCAGAGGGGTTTTTTGCTTCCTCCCCCTTCCAACGTCTAAACTGTCCCAGAGAACGCCCATTTCCCCCACTATTTGTGAGCGCAGGGTGCTCGCAAAGAAGAGGAGGAAGGAGGAAGGCAGGGGAGGGAGAACGGCAAGGAGAGCTCCGCAGGGCTGGGAGAAATGAGACCAAGAGAGACTGGGAGAGGGCGGCAGAGAAGAGAGGGGGGACCGAGAGCCGCGTCCCCGCGGTCGCGTGGATTTAGAAAAAGGCTGGCTTTACCATGACTTATGTGCAGCTTGCGCATCCAGGGGTAGATCTGGGGTTGGGCGGGCGGCGCCGGGCTCGGCTCGCTCTGCGCACTCGCCTGCTCGCTGCTGGCAGGGGCGTCCTCCTCGGCTCCGGACGCCGTGCCAACCCCCTCTCTGCTGCTGATGTGGGTGCTGCCGGCGTCGGCCGAGGCGCCGCTGGAGTTGCTTAGGGAGTTTTTCCCGCCGTGGTGGCTGTCGCTGCCGGGCGAGGGGGCCACGGCGGAGCAGGGCAGCGGATCGGGCTGAGGAGAGTGCGTGGACGTGGCCGGCTGGCTGTACCTGGGCTCGGCGGGCGCCGCGCTGGCGCTGGCAGCGTAGCTGCGGGCGCGCTCTCCGGAGCCAAAGTGGCCGGAGCCCGAGCGGCCGACGCTGAGATCCATGCCATTGTAGCCGTAGCCGTACCTGCCGGAGTGCATGCTCGCCGAGTCCCTGAATTGCTCGCTCACGGAACTATGATCTCCATAATTATGCAACTGGTAGTCCGGGCCATTTGGATAGCGACCGCAAAATGAGTTTACAAAATAAGAGCTCATTTGTTTTTTGATATGTGTGCTTGATTTGTGGCTCGCGGTCGTTTGTGCGTCTATAGCACCCTTGCACAATTTATGATGAATTATGGAAATGACTGGGACATGTACTTGGTTCCCTCCTACGTAGGCACCCAAATATGGGGTACGACTTCGAATCACGTGCTTTTGTTGTCCAGTCGTAAATCCTGCCTGATGACCTCTAGAGGTAAACTCGTGCACTAATAGGGGAGTTGGGTGGAGGCGAGGGGGGTnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnAGTTGCCGCCGTTCAGCCGGACTCGAGCGCCACCCGCTGGAGGCAGGGCTCATCGCCCAGCTTCCGACCGGGGGCTGCAAGGGCCGGGGTCGAATTGAGGTTACAGCCCATTATGGCAAAATTATTGCATTTCCCTCGCAGTTCCATTAGGATGTACCAATTGTTAGGCCGTCAGCTGCCGATCGCGCGCCCGGCGAGGATGCAGAGGATTGGGGGGAGGTGGTGACTTGCATTTTATTTACAACAACTTTATTTCCCCCGTTTTGCAGCCCCTCTTATTTTTGTGTCGAGGTTGGGGTCGGTACTGACCGTCCTGCCAGCAGCTCTGAATTTTGAAAATACAGATATCACCTTCGGGGAAGGGGGAAAGCCATTTAGCCAATTGGAGAAATAAATCCTGCCCGCAGCAGCAGCAGCTACAATTACGGCTCTGTTTTTGCGAGCGCATGAGGGACAGTGTCCCTGCCGCTCTTAAATGACAGGCGTCTATTAAAGATAGCTTTTGTGTAGTGTTTCTCCAAGGCGAGGTCAAATTCCATACACTTTTATAACCGTAGTCGATTTTTCTTTCGTGTGAATATGGTTTTCGTGTCATTAGTTTGCGATTTGATTTGCTTACGTATCCAGCCTGGAAAATCTTCATCACAGGGTCCGGTTCCTCGAGCCAGCCGGGCCCCAAGTCGGAGGGTTCTCCTTGAACCCAGCGAGTGGGCCCAGGCTCCCTGCAGCCACAGAGGCTGCCTGGGGTCTGGGGATCCGTGGGGCGGGTTACTGGGGTCTTGCTTAGACCTCCAGGAGTAAAATGAGGGCGATAATGGAAGCATTCCTTGGCAGTGCCTAGTATCTCTGTAGTTATTTTCCACGGCTCCGAAAGACTCAAGTAAATCACAAATATAGCTGAGAGGCAAGTGGAGTCTCCCCGCTGGAGGCCCGGCGTTGCAGGCGCCCCTGGCACGTCTGGAAGCCAGGACTCTGGCGGCTCCCATGGCCCTGGGCCCCTCGTTGGGTCCTGAACGCTGCTGTGGCGGCGACGCGGGCGCTATCGGAGGCTGGGAGCGGGAATCCGGAGCCGGGAGCCTACCCCGGGCTGTAATGTTCCACCCGCGCCCAGGTTAACTCGCCTCGGCTGAGGCTGCTTCTCTTCCACTGACGGTTGCACACGCGGGACCGAGAGACTGGGCTCTGTTGGGGCCCCCTTTGTTCCTCGAGCTTCCTTCCTGTTCTGGGAGGCGGCTTGGGAGGCCGCGACAAGGCCGGGCTCCAGCTCTTAGACCCCCTCTTTCCACTGGCCAGAGATGATTTGATGATGCCCTTCGGGACTTACTGGCGAGGGACTTAGGCAGAGACGCCCAGACACGAAACGGGGCTCGGCCCAGGGCTCTTTCCTCCCCAGCAGCCCCGCGTCCCGAGGTCGGGGAGCTCAGAGACACTAGCACAGGAGCCCCAGACGCATTCAGGGCGCACCCCAGAACTCCGGAGCCGGTTTGGGCATCCTTGTGGAGCGGGACTGGGTGTGTGCAGTGCGCCCCGCTCCACCGCTGGTATTGGCTGTGTGTGAGnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnAAGAAATAAATGCACAGACGCTTGCAAAGCTCCGGGCTCCCCTGAAGCTGCGGAAGCCCCCAGATGGGAGCAGGCGGGGAGAAAAGTTGGGGAACAGGCGAGGGCAAGGGGGCAAAGCCGAAGGAGGTTGCAGCGCTGGCCTGGTCCCTGCCCAGGCATCTACTCGCCCGCCTTTGCCTCTGAGTCCTCCCCGCTGGGCTGCGTGGAATTGATGAGCTTGTTTTCCTTTTTCCACTTCATGCGGCGGTTCTGGAACCAGATCTTGATCTGGCGCTCGGTGAGGCAGAGCGCGTTGGCGATCTCGATGCGGCGGCGCCGTGTCAGGTAGCGGTTGAAGTGGAACTCCTTCTCCAGCTCCAGTGTCTG";
- Sequence seq(s, reduced_dna_alphabet);
- string a = "HumanHXA5\n"
-">hg18_knownGene_NM_019102_0\n"
-"GGGTGCTATAGACGCACAAACGACCGCGAGCCACAAATCAAGCACACATATCAAAAAACAAATGAGCTCTTATTTTGTAAACTCATTTTGCGGTCGCTATCCAAATGGCCCGGACTACCAGTTGCATAATTATGGAGATCATAGTTCCGTGAGCGAGCAATTCAGGGACTCGGCGAGCATGCACTCCGGCAGGTACGGCTACGGCTACAATGGCATGGATCTCAGCGTCGGCCGCTCGGGCTCCGGCCACTTTGGCTCCGGAGAGCGCGCCCGCAGCTACGCTGCCAGCGCCAGCGCGGCGCCCGCCGAGCCCAGGTACAGCCAGCCGGCCACGTCCACGCACTCTCCTCAGCCCGATCCGCTGCCCTGCTCCGCCGTGGCCCCCTCGCCCGGCAGCGACAGCCACCACGGCGGGAAAAACTCCCTAAGCAACTCCAGCGGCGCCTCGGCCGACGCCGGCAGCACCCACATCAGCAGCAGAGAGGGGGTTGGCACGGCGTCCGGAGCCGAGGAGGACGCCCCTGCCAGCAGCGAGCAGGCGAGTGCGCAGAGCGAGCCGAGCCCGGCGCCGCCCGCCCAACCCCAGATCTACCCCTGGATGCGCAAGCTGCACATAAGTCATG\n"
-"\n"
-">hg18_knownGene_NM_019102_1\n"
-"ACAACATAGGCGGCCCGGAAGGCAAAAGGGCCCGGACGGCCTACACGCGCTACCAGACCCTGGAGCTGGAGAAGGAGTTCCACTTCAACCGTTACCTGACCCGCAGAAGGAGGATTGAAATAGCACATGCTCTTTGCCTCTCCGAGAGACAAATTAAAATCTGGTTCCAAAACCGGAGAATGAAGTGGAAAAAAGATAATAAGCTGAAAAGCATGAGCATGGCCGCGGCAGGAGGGGCCTTCCGTCCCTGAGTATCTGAGCGTTTAAAGTACTGAGCAGTATTAGCGGATCCCGCGTAGTGTCAGTACTAAGGTGACTTTCTGAAACTCCCTTGTGTTCCTTCTGTGAAGAAGCCCTGTTCTCGTTGCCCTAATTCATCTTTTAATCATGAGCCTGTTTATTGCCATTATAGCGCCTGTATAAGTAGATCTGCTTTCTGTTCATCTCTTTGTCCTGAATGGCTTTGTCTTGAAAAAAAATAGATGTTTTAACTTATTTATATGAAGCAAGCTGTGTTACTTGAAGTAACTATAACAAAAAAAGAAAAGAGAAAAAAAAACACACAAAAAGTCCCCCTTCAATCTCGTTTAGTGCCAATGTTGTGTGTTGCACTCAAGTTGTTTAACTGTGCATGTGCGTGGAAGTGTTCCTGTCTCAATAGCTCCAAGCTGTTAAAGATATTTTTATTCAAACTACCTATATTCCTTGT\n";
- stringstream annot(a);
+ string s = "AATTACACAAGGAATATAGGTAGTTTGAATAAAAATATCTTTAACAGCTTGGAGCTATTGAGACAGGAACACTTCCACGCACATGCACAGTTAAACAACTTGAGTGCAACACACAACATTGGCACTAAACGAGATTGAAGGGGGACTTTTTGTGTGTTTTTTTTTCTCTTTTCTTTTTTTGTTATAGTTACTTCAAGTAACACAGCTTGCTTCATATAAATAAGTTAAAACATCTATTTTTTTTCAAGACAAAGCCATTCAGGACAAAGAGATGAACAGAAAGCAGATCTACTTATACAGGCGCTATAATGGCAATAAACAGGCTCATGATTAAAAGATGAATTAGGGCAACGAGAACAGGGCTTCTTCACAGAAGGAACACAAGGGAGTTTCAGAAAGTCACCTTAGTACTGACACTACGCGGGATCCGCTAATACTGCTCAGTACTTTAAACGCTCAGATACTCAGGGACGGAAGGCCCCTCCTGCCGCGGCCATGCTCATGCTTTTCAGCTTATTATCTTTTTTCCACTTCATTCTCCGGTTTTGGAACCAGATTTTAATTTGTCTCTCGGAGAGGCAAAGAGCATGTGCTATTTCAATCCTCCTTCTGCGGGTCAGGTAACGGTTGAAGTGGAACTCCTTCTCCAGCTCCAGGGTCTGGTAGCGCGTGTAGGCCGTCCGGGCCCTTTTGCCTTCCGGGCCGCCTATGTTGTCTGCAATAGAAAAGTCAGCGGTTTAGCCACCAACTCCTGTCTTCCAAAGTCCGCCAGGGGGACAAGCTTGGGTCATGAGCAGGGAACCCAGGCGAAAAGCTCAACAAGTTCTGCCTACCAGCCCGCACACCCCTCCCGAATTTCCTTCTCTCTTCCTTTCTAGAAAGAAAACAATACGATTTGGACCCTGGGAACAATCTGCCCATCTGAGGCTGGGGCCGTGTCCCGGCGGACTCCGGCTTTCCCTGGCCCCTCTCCTGCCCCCTCCGCCCTGCCCCGGGCGCCCCGATCGGGAGGCACAGCCCTCCCAGGCTGCCCACCGCACAGAAACCCAGGAAGCAAGGCCCTTTCCTGAGCGCCCAAGTGGCCTTCGGGTCACCCTCCCTCAAAGTTCCAGCCCCGAGAGCCGCCTCCCGTTTCCAGCCTGCAGGGTTGGGGAGCCTGTTTTCTTTTTCTTCCCTTTCCTTCTCTCTCCCTCCTGCCCCCAAAATTCAGAATCCTGCAGGCTCTCGCCTCGATTCTTTCCCCCAAGCCCCTTTTCGGGGGCTGTAATTAGTAACGCTGTTTCCCCAGCGTAGCCCTCCTCATAAATTATCCGCCGTGACAAGCCCGATTCACGGCTGCTACAGCCATCCTCTACCTCTCTGCGCCTTGCTCGGCTGGCCTGACCCGGGAGCGCGTCCCAAGGCGTGGGGTTCCAGAGGGGTTTTTTGCTTCCTCCCCCTTCCAACGTCTAAACTGTCCCAGAGAACGCCCATTTCCCCCACTATTTGTGAGCGCAGGGTGCTCGCAAAGAAGAGGAGGAAGGAGGAAGGCAGGGGAGGGAGAACGGCAAGGAGAGCTCCGCAGGGCTGGGAGAAATGAGACCAAGAGAGACTGGGAGAGGGCGGCAGAGAAGAGAGGGGGGACCGAGAGCCGCGTCCCCGCGGTCGCGTGGATTTAGAAAAAGGCTGGCTTTACCATGACTTATGTGCAGCTTGCGCATCCAGGGGTAGATCTGGGGTTGGGCGGGCGGCGCCGGGCTCGGCTCGCTCTGCGCACTCGCCTGCTCGCTGCTGGCAGGGGCGTCCTCCTCGGCTCCGGACGCCGTGCCAACCCCCTCTCTGCTGCTGATGTGGGTGCTGCCGGCGTCGGCCGAGGCGCCGCTGGAGTTGCTTAGGGAGTTTTTCCCGCCGTGGTGGCTGTCGCTGCCGGGCGAGGGGGCCACGGCGGAGCAGGGCAGCGGATCGGGCTGAGGAGAGTGCGTGGACGTGGCCGGCTGGCTGTACCTGGGCTCGGCGGGCGCCGCGCTGGCGCTGGCAGCGTAGCTGCGGGCGCGCTCTCCGGAGCCAAAGTGGCCGGAGCCCGAGCGGCCGACGCTGAGATCCATGCCATTGTAGCCGTAGCCGTACCTGCCGGAGTGCATGCTCGCCGAGTCCCTGAATTGCTCGCTCACGGAACTATGATCTCCATAATTATGCAACTGGTAGTCCGGGCCATTTGGATAGCGACCGCAAAATGAGTTTACAAAATAAGAGCTCATTTGTTTTTTGATATGTGTGCTTGATTTGTGGCTCGCGGTCGTTTGTGCGTCTATAGCACCCTT";
+ std::string species = "HumanHXA5\n";
+ std::string header0 = ">hg18_knownGene_NM_019102_0\n";
+ std::string str0 = "GGGTGCTATAGACGCACAAACGACCGCGAGCCACAAATCAAGCACACATATCAAAAAACAAATGAGCTCTTATTTTGTAAACTCATTTTGCGGTCGCTATCCAAATGGCCCGGACTACCAGTTGCATAATTATGGAGATCATAGTTCCGTGAGCGAGCAATTCAGGGACTCGGCGAGCATGCACTCCGGCAGGTACGGCTACGGCTACAATGGCATGGATCTCAGCGTCGGCCGCTCGGGCTCCGGCCACTTTGGCTCCGGAGAGCGCGCCCGCAGCTACGCTGCCAGCGCCAGCGCGGCGCCCGCCGAGCCCAGGTACAGCCAGCCGGCCACGTCCACGCACTCTCCTCAGCCCGATCCGCTGCCCTGCTCCGCCGTGGCCCCCTCGCCCGGCAGCGACAGCCACCACGGCGGGAAAAACTCCCTAAGCAACTCCAGCGGCGCCTCGGCCGACGCCGGCAGCACCCACATCAGCAGCAGAGAGGGGGTTGGCACGGCGTCCGGAGCCGAGGAGGACGCCCCTGCCAGCAGCGAGCAGGCGAGTGCGCAGAGCGAGCCGAGCCCGGCGCCGCCCGCCCAACCCCAGATCTACCCCTGGATGCGCAAGCTGCACATAAGTCATG";
+ std::string header1 = ">hg18_knownGene_NM_019102_1\n";
+ std::string str1 = "ACAACATAGGCGGCCCGGAAGGCAAAAGGGCCCGGACGGCCTACACGCGCTACCAGACCCTGGAGCTGGAGAAGGAGTTCCACTTCAACCGTTACCTGACCCGCAGAAGGAGGATTGAAATAGCACATGCTCTTTGCCTCTCCGAGAGACAAATTAAAATCTGGTTCCAAAACCGGAGAATGAAGTGGAAAAAAGATAATAAGCTGAAAAGCATGAGCATGGCCGCGGCAGGAGGGGCCTTCCGTCCCTGAGTATCTGAGCGTTTAAAGTACTGAGCAGTATTAGCGGATCCCGCGTAGTGTCAGTACTAAGGTGACTTTCTGAAACTCCCTTGTGTTCCTTCTGTGAAGAAGCCCTGTTCTCGTTGCCCTAATTCATCTTTTAATCATGAGCCTGTTTATTGCCATTATAGCGCCTGTATAAGTAGATCTGCTTTCTGTTCATCTCTTTGTCCTGAATGGCTTTGTCTTGAAAAAAAATAGATGTTTTAACTTATTTATATGAAGCAAGCTGTGTTACTTGAAGTAACTATAACAAAAAAAGAAAAGAGAAAAAAAAACACACAAAAAGTCCCCCTTCAATCTCGTTTAGTGCCAATGTTGTGTGTTGCACTCAAGTTGTTTAACTGTGCATGTGCGTGGAAGTGTTCCTGTCTCAATAGCTCCAAGCTGTTAAAGATATTTTTATTCAAACTACCTATATTCCTTGT";
+ stringstream annot;
+ annot << species
+ << header0
+ << str0 << std::endl
+ << std::endl
+ << header1
+ << str1;
+ // need to convert strings to sequences for reverse complementing
+ Sequence seq0(str0, reduced_dna_alphabet);
+ Sequence seq1(str1, reduced_dna_alphabet);
+
+ Sequence annotated_seq(s, reduced_dna_alphabet);
+ annotated_seq.load_annot(annot, 0, 0);
+
+ SeqSpanRefList annots_list = annotated_seq.annotations();
+ // both sequences were found
+ BOOST_REQUIRE_EQUAL( annots_list.size(), 2 );
- seq.load_annot(annot, 0, 0);
+ std::vector<SeqSpanRef> annots(annots_list.begin(), annots_list.end());
+ // are they the same sequence?
+ BOOST_CHECK_EQUAL( annots[0]->size(), seq0.size());
+ BOOST_CHECK_EQUAL( annots[0]->sequence(), seq0.rev_comp() );
+ // this should hopefully catch the case when my hack in
+ // sequence.cpp::push_back_seq::operator() is no longer needed.
+ // spirit (or my grammar was duplicating the last char,
+ // the hack removes the duplicate. but if what ever's causing
+ // the dup gets fixed actual meaningful data will be being removed.
+ // see mussa ticket:265 for more information
+ BOOST_CHECK_EQUAL( annots[1]->size(), seq1.size());
+ BOOST_CHECK_EQUAL( annots[1]->sequence(), seq1.rev_comp() );
- BOOST_CHECK_EQUAL( seq.annotations().size(), 2 );
}
BOOST_AUTO_TEST_CASE( subseq_annotation_test )