}
}
-void Sequence::load_fasta(std::iostream& file,
+void Sequence::load_fasta(std::istream& file,
int seq_num, int start_index, int end_index)
{
load_fasta(file, alphabet, seq_num, start_index, end_index);
}
void
-Sequence::load_fasta(std::iostream& data_file, alphabet_ref a,
+Sequence::load_fasta(std::istream& data_file, alphabet_ref a,
int seq_num,
int start_index, int end_index)
{
std::string rc_map = create_reverse_map();
// reverse and convert
- seq_string::const_reverse_iterator seq_i;
- seq_string::const_reverse_iterator seq_end = seq->rend();
- for(seq_i = seq->rbegin();
+ Sequence::const_reverse_iterator seq_i;
+ Sequence::const_reverse_iterator seq_end = rend();
+ for(seq_i = rbegin();
seq_i != seq_end;
++seq_i)
{
}
}
+Sequence::const_reverse_iterator Sequence::rbegin() const
+{
+ if (seq and seq_count != 0)
+ return seq->rbegin()+(seq->size()-(seq_start+seq_count));
+ else
+ return Sequence::const_reverse_iterator();
+}
+
+Sequence::const_reverse_iterator Sequence::rend() const
+{
+ if (seq and seq_count != 0) {
+ return rbegin() + seq_count;
+ } else {
+ return Sequence::const_reverse_iterator();
+ }
+}
+
bool Sequence::empty() const
{
return (seq_count == 0) ? true : false;
size_type size() const;
//! alias for size (used by string)
size_type length() const;
+ //! reverse iterator
+ const_reverse_iterator rbegin() const;
+ //! reverse end iterator
+ const_reverse_iterator rend() const;
+ //! is our sequence empty?
//! start position relative to "base" sequence
size_type start() const;
//! one past the last position relative to "base" sequence
alphabet_ref a,
int seq_num=1,
int start_index=0, int end_index=0);
- void load_fasta(std::iostream& file,
+ void load_fasta(std::istream& file,
int seq_num=1, int start_index=0, int end_index=0);
//! load sequence from stream
//! \throw mussa_load_error
//! \throw sequence_empty_error
//! \throw sequence_empty_file_error
- void load_fasta(std::iostream& file,
+ void load_fasta(std::istream& file,
alphabet_ref a,
int seq_num=1,
int start_index=0, int end_index=0);
sequence_invalid_load_error);
}
+BOOST_AUTO_TEST_CASE( sequence_load_multiple_sequences_one_fasta )
+{
+ std::string fasta_file(
+ ">gi|10129974|gb|AF188002.1|AF188002\n"
+ "AAAAGGCTCCTGTCATATTGTGTCCTGCTCTGGTCTGC\n"
+ ">gi|180579|gb|M21487.1|HUMCKMM1\n"
+ "CGCCGAGAGCGCTTGCTCTGCCCAGATCTCGGCGAGTC\n"
+ ">gi|1621|emb|X55146.1|OCMCK1\n"
+ "CTCCCTGAGGGGAGTGCCCCGCTTAGCCC\n"
+ );
+ istringstream seq1_file(fasta_file);
+ Sequence seq1;
+ seq1.load_fasta(seq1_file, 1, 0, 0);
+ BOOST_CHECK_EQUAL(seq1.get_sequence(), "AAAAGGCTCCTGTCATATTGTGTCCTGCTCTGGTCTGC");
+
+ istringstream seq2_file(fasta_file);
+ Sequence seq2;
+ seq2.load_fasta(seq2_file, 2, 0, 0);
+ BOOST_CHECK_EQUAL(seq2.get_sequence(), "CGCCGAGAGCGCTTGCTCTGCCCAGATCTCGGCGAGTC");
+
+ istringstream seq3_file(fasta_file);
+ Sequence seq3;
+ seq3.load_fasta(seq3_file, 3, 0, 0);
+ BOOST_CHECK_EQUAL(seq3.get_sequence(), "CTCCCTGAGGGGAGTGCCCCGCTTAGCCC");
+}
+
BOOST_AUTO_TEST_CASE( sequence_reverse_complement )
{
std::string iupac_symbols("AaCcGgTtRrYySsWwKkMmBbDdHhVvNn-~.?");
BOOST_CHECK_EQUAL(rna_seq, rna_seq.rev_comp().rev_comp());
}
+BOOST_AUTO_TEST_CASE( sequence_reverse_complement_subseq )
+{
+ std::string dna_str("AAAAAAAAAAGGGGGGGGGGG");
+ Sequence seq(dna_str, Sequence::reduced_dna_alphabet);
+ Sequence subseq = seq.subseq(8,4);
+ BOOST_CHECK_EQUAL( subseq, "AAGG");
+ Sequence rev_subseq = subseq.rev_comp();
+ BOOST_CHECK_EQUAL( rev_subseq.size(), subseq.size() );
+ BOOST_CHECK_EQUAL( rev_subseq.get_sequence(), "CCTT");
+}
+
+BOOST_AUTO_TEST_CASE( sequence_reverse_iterator )
+{
+ std::string dna_str("AAAAAAAAAAGGGGGGGGGGG");
+ std::string dna_str_reversed(dna_str.rbegin(), dna_str.rend());
+ Sequence seq(dna_str);
+ std::string seq_reversed(seq.rbegin(), seq.rend());
+ BOOST_CHECK_EQUAL(seq_reversed, dna_str_reversed);
+
+ std::string substr = dna_str.substr(8,4);
+ Sequence subseq = seq.subseq(8,4);
+ BOOST_CHECK_EQUAL(substr, subseq);
+
+ std::string substr_reversed(substr.rbegin(), substr.rend());
+ std::string subseq_reversed(subseq.rbegin(), subseq.rend());
+ BOOST_CHECK_EQUAL(substr_reversed, subseq_reversed);
+}
+
+BOOST_AUTO_TEST_CASE( sequence_empty_reverse_iterator)
+{
+ // so what happens with reverse interators when we have no sequence?
+ Sequence seq1;
+ Sequence seq2;
+ Sequence seq3("AGCT");
+
+ // all the empty sequences should have equal iterators
+ BOOST_CHECK(seq1.rbegin() == seq1.rend());
+ BOOST_CHECK(seq1.rbegin() == seq2.rend());
+
+ // none of the seq1 iterators should equal any of the seq3 iterators
+ BOOST_CHECK(seq1.rbegin() != seq3.rbegin());
+ BOOST_CHECK(seq1.rbegin() != seq3.rend());
+ BOOST_CHECK(seq1.rend() != seq3.rbegin());
+ BOOST_CHECK(seq1.rend() != seq3.rend());
+
+ // seq3 iterators should work
+ BOOST_CHECK(seq3.rbegin() != seq3.rend());
+
+}
+
BOOST_AUTO_TEST_CASE( annotation_load )
{
string annot_data = "human\n"