add fasta file format output capability with unit tests

include/boost/bioseq/io_formats/fasta.hpp

@@ -34,7 +34,18 @@ public:
 
 private:
     virtual void do_print(std::basic_ostream<CharT,Traits>& out, const SeqT& s)
-    {}
+    {
+        out << '>' << s.long_name();
+
+        for (size_t i = 0; i < s.size(); ++i)
+        {
+            if (0 == i % 70)
+                out << std::endl;
+            out << s[i];
+        }
+
+        out << std::endl;
+    }
 
     virtual void do_scan(std::basic_istream<CharT,Traits>& in, SeqT& s)
     {

test/test_io_fasta.cpp

@@ -15,7 +15,7 @@
 #define BOOST_TEST_MODULE TestIOFasta
 #include <boost/mpl/list.hpp>
 #include <boost/test/unit_test.hpp>
-// #include <boost/test/output_test_stream.hpp>
+#include <boost/test/output_test_stream.hpp>
 // #if (BOOST_VERSION >= 105900)
 // #   include <boost/test/unit_test_parameters.hpp>
 // #else
@@ -35,27 +35,28 @@
 #include <boost/bioseq/components/description.hpp>
 #include <boost/bioseq/io_formats/fasta.hpp>
 
-namespace bioseq = boost::bioseq;
+using boost::test_tools::output_test_stream;
+namespace bsq = boost::bioseq;
 
 // preparing str_seq type
 template<class CharT, class AllocatorT> using bs_string
 =   std::basic_string<CharT, std::char_traits<CharT>, AllocatorT>;
 
-typedef bioseq::sequence_host
+typedef bsq::sequence_host
 <
     char
 ,   std::allocator
 ,   bs_string
-,   bioseq::component::name<>
-,   bioseq::component::description<>
+,   bsq::component::name<>
+,   bsq::component::description<>
 >   str_seq;
 
-typedef bioseq::ioformat
+typedef bsq::ioformat
 <
     char
 ,   std::char_traits<char>
 ,   str_seq
-,   bioseq::fasta_format
+,   bsq::fasta_format
 >   frmt1;
 
 #if BOOST_WORKAROUND(BOOST_GCC, < 70000)
@@ -63,24 +64,24 @@ typedef bioseq::ioformat
     template<> struct io_format_traits<str_seq> { typedef frmt1 type; };
     }}
 #else
-    template<> struct bioseq::io_format_traits<str_seq> { typedef frmt1 type; };
+    template<> struct bsq::io_format_traits<str_seq> { typedef frmt1 type; };
 #endif  // BOOST_GCC < 70000
 
 // preparing vec_seq type
-typedef bioseq::sequence_host
+typedef bsq::sequence_host
 <
     char
 ,   std::allocator
 ,   std::vector
-,   bioseq::component::name<>
-,   bioseq::component::description<>
+,   bsq::component::name<>
+,   bsq::component::description<>
 >   vec_seq;
 
-typedef bioseq::ioformat
+typedef bsq::ioformat
 <   char
 ,   std::char_traits<char>
 ,   vec_seq
-,   bioseq::fasta_format
+,   bsq::fasta_format
 >   frmt2;
 
 #if BOOST_WORKAROUND(BOOST_GCC, < 70000)
@@ -88,7 +89,7 @@ typedef bioseq::ioformat
     template<> struct io_format_traits<vec_seq> { typedef frmt2 type; };
     }}
 #else
-    template<> struct bioseq::io_format_traits<vec_seq> { typedef frmt2 type; };
+    template<> struct bsq::io_format_traits<vec_seq> { typedef frmt2 type; };
 #endif  // BOOST_GCC < 70000
 
 
@@ -97,38 +98,18 @@ typedef boost::mpl::list<vec_seq, str_seq> seq_types;
 
 BOOST_AUTO_TEST_CASE_TEMPLATE(read_single_fasta, T, seq_types)
 {
-    // auto start = std::chrono::high_resolution_clock::now();
-    // for (size_t i = 0; i < 1000; ++i)
-    // {
-        std::ifstream in(BOOST_BIOSEQ_TEST_DATA_PATH"/chrMT.fa");
-        T mt;
-        in >> mt;
-    // }
-    // auto d = std::chrono::duration_cast<std::chrono::milliseconds>(std::chrono::high_resolution_clock::now() - start);
-    // std::cout << "Elapsed time: " << d.count() << " ms" << std::endl;
-
-    BOOST_CHECK_EQUAL(mt[0], 'G');
-    BOOST_CHECK_EQUAL(mt[1], 'A');
-    BOOST_CHECK_EQUAL(mt[69], 'G');
-    BOOST_CHECK_EQUAL(mt[139], 'C');
-    BOOST_CHECK_EQUAL(mt[16566], 'A');
-    BOOST_CHECK_EQUAL(mt[16567], 'T');
-    BOOST_CHECK_EQUAL(mt[16568], 'G');
+    std::ifstream in(BOOST_BIOSEQ_TEST_DATA_PATH"/chrMT.fa");
+    T mt;
+    in >> mt;
 
     BOOST_CHECK( 16569 == mt.size() );
-
     BOOST_CHECK_EQUAL(mt.name(), "gi|113200490|gb|J01415.2|HUMMTCG");
     BOOST_CHECK_EQUAL(mt.description(), "Homo sapiens mitochondrion, complete genome");
     BOOST_CHECK_EQUAL(mt.long_name(), "gi|113200490|gb|J01415.2|HUMMTCG Homo sapiens mitochondrion, complete genome");
 
-    // BOOST_CHECK( mt.short_name() == "gi|113200490|gb|J01415.2|HUMMTCG" );
-    // BOOST_CHECK( mt.long_name()
-    // ==  "gi|113200490|gb|J01415.2|HUMMTCG "
-    //     "Homo sapiens mitochondrion, complete genome" );
-
-    // output_test_stream cout(BOOST_BIOSEQ_TEST_DATA_PATH"/chrMT.fa");
-    // cout << mt;
-    // BOOST_CHECK(cout.match_pattern());
+    output_test_stream cout(BOOST_BIOSEQ_TEST_DATA_PATH"/chrMT.fa");
+    cout << mt;
+    BOOST_CHECK(cout.match_pattern());
 }
 
 BOOST_AUTO_TEST_CASE_TEMPLATE(read_multi_fasta, T, seq_types)
@@ -162,6 +143,13 @@ BOOST_AUTO_TEST_CASE_TEMPLATE(read_multi_fasta, T, seq_types)
 
     BOOST_CHECK_EQUAL(reads[0].long_name(), "gi|406593966|ref|NC_018627.1|-40485/1");
 
+    output_test_stream cout(BOOST_BIOSEQ_TEST_DATA_PATH"/reads.fa");
+    for (const auto& read : reads)
+    {
+        cout << read;
+        BOOST_CHECK(cout.match_pattern());
+    }
+
     // T copy(reads[0]);
     // BOOST_CHECK_EQUAL(copy.name(), "gi|406593966|ref|NC_018627.1|-40485/1");
     // BOOST_CHECK_EQUAL(copy.data(), "ACACCAGAAGCATCGTCTGTTGTGGTGATATATGCGGGCTCTTCTGTTATCTCGTTAAGATCGAGATGGAGATTCTTTACTGAGATGTTGTTGGTAGTTTGAAACTTCGTCCCAGGATGCATGCAGAGTATAGATTGAAGATTTTCATCA");