From: Diane Trout <diane@caltech.edu>
Date: Thu, 19 Oct 2006 00:58:47 +0000 (+0000)
Subject: Sequence::rev_comp works on subsequences
X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=mussa.git;a=commitdiff_plain;h=f2459784ce26346876ba2ec76475a579051bbd5c

Sequence::rev_comp works on subsequences
ticket:197
Sequence::rev_comp when called on a Sequence which contained a subsequence
was actually reversing the entire sequence and not just the selected region.

To fix this I added rbegin and rend which return reverse iterators that
cover the subseq range and updated rev_comp to use them.

There's also some extra sequence unittests to make sure that rbegin/rend
work correctly. (and as a bonus loading several sequences out of one fasta
file works).
---

diff --git a/alg/sequence.cpp b/alg/sequence.cpp
index 3ac4dd0..9abbbcd 100644
--- a/alg/sequence.cpp
+++ b/alg/sequence.cpp
@@ -197,14 +197,14 @@ void Sequence::load_fasta(fs::path file_path, alphabet_ref a,
   }
 }
 
-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)
 {
@@ -580,9 +580,9 @@ Sequence Sequence::rev_comp() const
   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)
   {
@@ -711,6 +711,23 @@ Sequence::const_iterator Sequence::end() const
   }
 }
 
+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;
diff --git a/alg/sequence.hpp b/alg/sequence.hpp
index 20bf018..6365ea7 100644
--- a/alg/sequence.hpp
+++ b/alg/sequence.hpp
@@ -160,6 +160,11 @@ public:
   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
@@ -202,13 +207,13 @@ public:
                   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);
diff --git a/alg/test/test_sequence.cpp b/alg/test/test_sequence.cpp
index 48492f7..6317144 100644
--- a/alg/test/test_sequence.cpp
+++ b/alg/test/test_sequence.cpp
@@ -258,6 +258,32 @@ BOOST_AUTO_TEST_CASE( sequence_load_fasta_default )
                     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-~.?");
@@ -287,6 +313,56 @@ BOOST_AUTO_TEST_CASE( sequence_reverse_complement_rna )
   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"