[MISC] rename seqan3::{alignment => sam}_file_header*

include/seqan3/io/alignment_file/format_bam.hpp

@@ -103,7 +103,7 @@ class format_bam : private detail::format_sam_base
     void read_alignment_record(stream_type & stream,
                                alignment_file_input_options<seq_legal_alph_type> const & SEQAN3_DOXYGEN_ONLY(options),
                                ref_seqs_type & ref_seqs,
-                               alignment_file_header<ref_ids_type> & header,
+                               sam_file_header<ref_ids_type> & header,
                                seq_type & seq,
                                qual_type & qual,
                                id_type & id,
@@ -289,7 +289,7 @@ template <typename stream_type,     // constraints checked by file
 inline void format_bam::read_alignment_record(stream_type & stream,
                                               alignment_file_input_options<seq_legal_alph_type> const & SEQAN3_DOXYGEN_ONLY(options),
                                               ref_seqs_type & ref_seqs,
-                                              alignment_file_header<ref_ids_type> & header,
+                                              sam_file_header<ref_ids_type> & header,
                                               seq_type & seq,
                                               qual_type & qual,
                                               id_type & id,

include/seqan3/io/alignment_file/format_sam.hpp

@@ -189,7 +189,7 @@ class format_sam : private detail::format_sam_base
     void read_alignment_record(stream_type & stream,
                                alignment_file_input_options<seq_legal_alph_type> const & SEQAN3_DOXYGEN_ONLY(options),
                                ref_seqs_type & ref_seqs,
-                               alignment_file_header<ref_ids_type> & header,
+                               sam_file_header<ref_ids_type> & header,
                                seq_type & seq,
                                qual_type & qual,
                                id_type & id,
@@ -245,7 +245,7 @@ class format_sam : private detail::format_sam_base
     static constexpr std::string_view dummy{};
 
     //!\brief The default header for the alignment format.
-    alignment_file_header<> default_header{};
+    sam_file_header<> default_header{};
 
     //!\brief Tracks whether reference information (\@SR tag) were found in the SAM header
     bool ref_info_present_in_header{false};
@@ -384,7 +384,7 @@ template <typename stream_type,     // constraints checked by file
 inline void format_sam::read_alignment_record(stream_type & stream,
                                               alignment_file_input_options<seq_legal_alph_type> const & SEQAN3_DOXYGEN_ONLY(options),
                                               ref_seqs_type & ref_seqs,
-                                              alignment_file_header<ref_ids_type> & header,
+                                              sam_file_header<ref_ids_type> & header,
                                               seq_type & seq,
                                               qual_type & qual,
                                               id_type & id,

include/seqan3/io/alignment_file/format_sam_base.hpp

@@ -126,13 +126,13 @@ class format_sam_base
 
     template <typename stream_view_type, typename ref_ids_type, typename ref_seqs_type>
     void read_header(stream_view_type && stream_view,
-                     alignment_file_header<ref_ids_type> & hdr,
+                     sam_file_header<ref_ids_type> & hdr,
                      ref_seqs_type & /*ref_id_to_pos_map*/);
 
     template <typename stream_t, typename ref_ids_type>
     void write_header(stream_t & stream,
                       alignment_file_output_options const & options,
-                      alignment_file_header<ref_ids_type> & header);
+                      sam_file_header<ref_ids_type> & header);
 };
 
 /*!\brief Checks for known reference ids or adds a new reference is and assigns a reference id to `ref_id`.
@@ -455,7 +455,7 @@ inline void format_sam_base::read_field(stream_view_type && stream_view, std::op
  */
 template <typename stream_view_type, typename ref_ids_type, typename ref_seqs_type>
 inline void format_sam_base::read_header(stream_view_type && stream_view,
-                                         alignment_file_header<ref_ids_type> & hdr,
+                                         sam_file_header<ref_ids_type> & hdr,
                                          ref_seqs_type & /*ref_id_to_pos_map*/)
 {
     auto it = std::ranges::begin(stream_view);
@@ -569,7 +569,7 @@ inline void format_sam_base::read_header(stream_view_type && stream_view,
 
             case 'P': /* PG (program) tag */
             {
-                typename alignment_file_header<ref_ids_type>::program_info_t tmp{};
+                typename sam_file_header<ref_ids_type>::program_info_t tmp{};
 
                 parse_tag_value(tmp.id);                                // read required ID tag
 
@@ -650,7 +650,7 @@ inline void format_sam_base::read_header(stream_view_type && stream_view,
 template <typename stream_t, typename ref_ids_type>
 inline void format_sam_base::write_header(stream_t & stream,
                                           alignment_file_output_options const & options,
-                                          alignment_file_header<ref_ids_type> & header)
+                                          sam_file_header<ref_ids_type> & header)
 {
     // -----------------------------------------------------------------
     // Check Header

include/seqan3/io/alignment_file/header.hpp

@@ -6,7 +6,7 @@
 // -----------------------------------------------------------------------------------------------------
 
 /*!\file
- * \brief Provides the seqan3::alignment_file_header class.
+ * \brief Provides the seqan3::sam_file_header class.
  * \author Svenja Mehringer <svenja.mehringer AT fu-berlin.de>
  */
 
@@ -29,36 +29,36 @@ namespace seqan3
 //!\brief Stores the header information of alignment files.
 //!\ingroup alignment_file
 template <std::ranges::forward_range ref_ids_type = std::deque<std::string>>
-class alignment_file_header
+class sam_file_header
 {
 public:
     /*!\name Constructors, destructor and assignment
      * \{
      */
     //!\brief Default constructor is defaulted.
-    alignment_file_header() = default;
+    sam_file_header() = default;
     //!\brief Copy construction is defaulted.
-    alignment_file_header(alignment_file_header const &) = default;
+    sam_file_header(sam_file_header const &) = default;
     //!\brief Copy assignment is defaulted.
-    alignment_file_header & operator=(alignment_file_header const &) = default;
+    sam_file_header & operator=(sam_file_header const &) = default;
     //!\brief Move construction is defaulted.
-    alignment_file_header(alignment_file_header &&) = default;
+    sam_file_header(sam_file_header &&) = default;
     //!\brief Move assignment is defaulted.
-    alignment_file_header & operator=(alignment_file_header &&) = default;
+    sam_file_header & operator=(sam_file_header &&) = default;
     //!\brief Destructor is defaulted.
-    ~alignment_file_header() = default;
+    ~sam_file_header() = default;
 
     /*!\brief Construct from a range of reference ids which redirects the `ref_ids_ptr` member (non-owning).
      * \param[in] ref_ids The range over reference ids to redirect the pointer at.
      */
-    alignment_file_header(ref_ids_type & ref_ids) :
+    sam_file_header(ref_ids_type & ref_ids) :
         ref_ids_ptr{&ref_ids, ref_ids_deleter_noop}
     {}
 
     /*!\brief Construct from a rvalue range of reference ids which is moved into the `ref_ids_ptr` (owning).
      * \param[in] ref_ids The range over reference ids to own.
      */
-    alignment_file_header(ref_ids_type && ref_ids) :
+    sam_file_header(ref_ids_type && ref_ids) :
         ref_ids_ptr{new ref_ids_type{std::move(ref_ids)}, ref_ids_deleter_default}
     {}
     //!\}

include/seqan3/io/alignment_file/input.hpp

@@ -432,8 +432,8 @@ class alignment_file_input
     using e_value_type             = double;
     //!\brief The type of field::bitscore is fixed to double.
     using bitscore_type            = double;
-    //!\brief The type of field::header_ptr (default: alignment_file_header<typename traits_type::ref_ids>).
-    using header_type              = alignment_file_header<typename traits_type::ref_ids>;
+    //!\brief The type of field::header_ptr (default: sam_file_header<typename traits_type::ref_ids>).
+    using header_type              = sam_file_header<typename traits_type::ref_ids>;
 
 private:
     //!\brief The type of the aligned query sequence (second type of the pair of alignment_type).
@@ -488,7 +488,7 @@ class alignment_file_input
      *
      * There exists one more field for alignment files, the seqan3::field::header_ptr, but this field is mostly used
      * internally. Please see the seqan3::alignment_file_output::header member function for details on how to access
-     * the seqan3::alignment_file_header of the file.)
+     * the seqan3::sam_file_header of the file.)
      */
     using field_ids = fields<field::seq,
                              field::id,
@@ -825,7 +825,7 @@ class alignment_file_input
      *
      * \include test/snippet/io/alignment_file/alignment_file_input_get_header.cpp
      *
-     * \sa seqan3::alignment_file_header
+     * \sa seqan3::sam_file_header
      */
     header_type & header()
     {

include/seqan3/io/alignment_file/input_format_concept.hpp

@@ -77,7 +77,7 @@ SEQAN3_CONCEPT alignment_file_input_format =
               std::ifstream                                                       & stream,
               alignment_file_input_options<dna5>                                  & options,
               std::vector<dna5_vector>                                            & ref_sequences,
-              alignment_file_header<>                                             & header,
+              sam_file_header<>                                                   & header,
               dna5_vector                                                         & seq,
               std::vector<phred42>                                                & qual,
               std::string                                                         & id,
@@ -186,7 +186,7 @@ SEQAN3_CONCEPT alignment_file_input_format =
  * \param[in,out] stream      The input stream to read from.
  * \param[in]     options     File specific options passed to the format.
  * \param[out]    ref_seqs    The reference sequences to the corresponding alignments.
- * \param[out]    header      A pointer to the seqan3::alignment_file_header object.
+ * \param[out]    header      A pointer to the seqan3::sam_file_header object.
  * \param[out]    seq         The buffer for seqan3::field::seq input.
  * \param[out]    qual        The buffer for seqan3::field::qual input.
  * \param[out]    id          The buffer for seqan3::field::id input.

include/seqan3/io/alignment_file/output.hpp

@@ -687,7 +687,7 @@ class alignment_file_output
      *
      * \include test/snippet/io/alignment_file/alignment_file_output_set_header.cpp
      *
-     * \sa seqan3::alignment_file_header
+     * \sa seqan3::sam_file_header
      */
     auto & header()
     {
@@ -728,9 +728,9 @@ class alignment_file_output
     //!\}
 
     //!\brief The header type, which specilised with ref_ids_type if reference information are given.
-    using header_type = alignment_file_header<std::conditional_t<std::same_as<ref_ids_type, ref_info_not_given>,
-                                              std::vector<std::string>,
-                                              ref_ids_type>>;
+    using header_type = sam_file_header<std::conditional_t<std::same_as<ref_ids_type, ref_info_not_given>,
+                                        std::vector<std::string>,
+                                        ref_ids_type>>;
 
     //!\brief The file header object (will be set on construction).
     std::unique_ptr<header_type> header_ptr;
@@ -741,7 +741,7 @@ class alignment_file_output
     {
         assert(std::ranges::size(ref_ids) == std::ranges::size(ref_lengths));
 
-        header_ptr = std::make_unique<alignment_file_header<ref_ids_type>>(std::forward<ref_ids_type_>(ref_ids));
+        header_ptr = std::make_unique<sam_file_header<ref_ids_type>>(std::forward<ref_ids_type_>(ref_ids));
 
         for (int32_t idx = 0; idx < std::ranges::distance(ref_ids); ++idx)
         {

include/seqan3/io/alignment_file/output_format_concept.hpp

@@ -76,7 +76,7 @@ SEQAN3_CONCEPT alignment_file_output_format =
     requires (detail::alignment_file_output_format_exposer<t>                      & v,
               std::ofstream                                                        & stream,
               alignment_file_output_options                                        & options,
-              alignment_file_header<>                                              & header,
+              sam_file_header<>                                                    & header,
               dna5_vector                                                          & seq,
               std::vector<phred42>                                                 & qual,
               std::string                                                          & id,
@@ -125,7 +125,7 @@ SEQAN3_CONCEPT alignment_file_output_format =
 
 /*!\fn void write_alignment_record(stream_type                            &  stream,
                                    alignment_file_output_options const    &  options,
-                                   alignment_file_header<>                & header,
+                                   sam_file_header<>                      &  header,
                                    seq_type                               && seq,
                                    qual_type                              && qual,
                                    id_type                                && id,

include/seqan3/io/record.hpp

@@ -81,7 +81,7 @@ enum class field
     ref_id,         //!< The identifier of the (reference) sequence that seqan3::field::seq was aligned to.
     ref_seq,        //!< The (reference) "sequence" information, usually a range of nucleotides or amino acids.
     ref_offset,     //!< Sequence (seqan3::field::ref_seq) relative start position (0-based), unsigned value.
-    header_ptr,     //!< A pointer to the seqan3::alignment_file_header object storing header information.
+    header_ptr,     //!< A pointer to the seqan3::sam_file_header object storing header information.
 
     flag,           //!< The alignment flag (bit information), `uint16_t` value.
     mate,           //!< The mate pair information given as a std::tuple of reference name, offset and template length.

test/unit/io/alignment_file/alignment_file_format_test_template.hpp

@@ -38,7 +38,7 @@ struct alignment_file_data : public ::testing::Test
     {
         ref_sequences = std::vector<seqan3::dna5_vector>{ref_seq};
         ref_ids = std::vector<std::string>{ref_id};
-        header = seqan3::alignment_file_header{ref_ids};
+        header = seqan3::sam_file_header{ref_ids};
         header.ref_id_info.emplace_back(ref_seq.size(), "");
         header.ref_dict[header.ref_ids()[0]] = 0; // set up header which is otherwise done on file level
     }
@@ -128,7 +128,7 @@ struct alignment_file_data : public ::testing::Test
 
     std::vector<seqan3::dna5_vector> ref_sequences{};
     std::vector<std::string> ref_ids{};
-    seqan3::alignment_file_header<std::vector<std::string>> header{};
+    seqan3::sam_file_header<std::vector<std::string>> header{};
 };
 
 template <typename format_t>
@@ -497,7 +497,7 @@ TYPED_TEST_P(alignment_file_write, write_ref_id_with_different_types)
 
 TYPED_TEST_P(alignment_file_write, with_header)
 {
-    seqan3::alignment_file_header header{std::vector<std::string>{this->ref_id}};
+    seqan3::sam_file_header header{std::vector<std::string>{this->ref_id}};
     header.sorting = "unknown";
     header.grouping = "none";
     header.ref_id_info.push_back({this->ref_seq.size(), "AN:other_name"});

test/unit/io/alignment_file/alignment_file_output_test.cpp

@@ -384,7 +384,7 @@ TEST(row, print_header_in_record)
     std::vector<std::string> const ref_ids{"ref1", "ref2"};
     std::vector<int32_t>     const ref_len{234511, 243243};
 
-    seqan3::alignment_file_header header{ref_ids};
+    seqan3::sam_file_header header{ref_ids};
 
     header.ref_id_info.push_back({ref_len[0], ""});
     header.ref_id_info.push_back({ref_len[1], ""});

test/unit/io/alignment_file/format_bam_test.cpp

@@ -496,7 +496,7 @@ TEST_F(bam_format, too_long_cigar_string_write)
 
     std::ostringstream os{};
 
-    seqan3::alignment_file_header header{std::vector<std::string>{this->ref_id}};
+    seqan3::sam_file_header header{std::vector<std::string>{this->ref_id}};
     header.ref_id_info.push_back({ref.size(), ""});
     header.ref_dict[this->ref_id] = 0;