Use RAII in sequence_writer_t

UDC-GAC · Aug 29, 2024 · fd9e40c · fd9e40c
1 parent ff395d7
commit fd9e40c
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Showing 5 changed files with 32 additions and 22 deletions.
diff --git a/lib/PATO/sequence_loader.cpp b/lib/PATO/sequence_loader.cpp
@@ -22,8 +22,13 @@
 
 #include "sequence_loader.h"
 
-bool pato::sequence_loader_t::init(const seqan::CharString &file_name) {
-  return seqan::open(fasta_file, seqan::toCString(file_name));
+std::optional<pato::sequence_loader_t>
+pato::sequence_loader_t::create(const seqan::CharString &file_name) {
+  seqan::SeqFileIn *fasta_file{new seqan::SeqFileIn{}};
+  if (seqan::open(*fasta_file, seqan::toCString(file_name))) {
+    return pato::sequence_loader_t{fasta_file};
+  }
+  return std::nullopt;
 }
 
 static void crop_sequence_name(seqan::CharString &name) {
@@ -36,7 +41,7 @@ static void crop_sequence_name(seqan::CharString &name) {
 bool pato::sequence_loader_t::load_sequences(pato::triplex_vector_t &sequences,
                                              pato::name_vector_t &names,
                                              unsigned num_sequences) {
-  seqan::readRecords(names, sequences, fasta_file, num_sequences);
+  seqan::readRecords(names, sequences, *fasta_file, num_sequences);
   for (seqan::CharString &name : names) {
     crop_sequence_name(name);
   }

diff --git a/lib/PATO/sequence_loader.h b/lib/PATO/sequence_loader.h
@@ -26,19 +26,24 @@
 #include <PATO/options.h>
 #include <seqan/seq_io.h>
 
+#include <optional>
+
 #include "types.h"
 
 namespace pato {
 
 class sequence_loader_t {
 public:
-  // FIXME: Use RAII!
-  bool init(const seqan::CharString &file_name);
+  static std::optional<sequence_loader_t>
+  create(const seqan::CharString &file_name);
+
   bool load_sequences(triplex_vector_t &sequences, name_vector_t &names,
                       unsigned num_sequences);
 
 private:
-  seqan::SeqFileIn fasta_file;
+  sequence_loader_t(seqan::SeqFileIn *fasta_file_) : fasta_file{fasta_file_} {}
+
+  std::shared_ptr<seqan::SeqFileIn> fasta_file;
 };
 
 } // namespace pato

diff --git a/lib/PATO/tfo_finder.cpp b/lib/PATO/tfo_finder.cpp
@@ -221,8 +221,8 @@ void pato::find_tfo_motifs(pato::motif_vector_t &motifs,
 
 pato::find_tfo_motifs_result
 pato::find_tfo_motifs(const pato::options_t &opts) {
-  pato::sequence_loader_t sequence_loader;
-  if (!sequence_loader.init(opts.tfo_file)) {
+  auto sequence_loader = pato::sequence_loader_t::create(opts.tfo_file);
+  if (!sequence_loader) {
     return pato::find_tfo_motifs_result::cannot_open_tfo_file;
   }
 
@@ -233,8 +233,8 @@ pato::find_tfo_motifs(const pato::options_t &opts) {
 
   pato::name_vector_t tfo_names;
   pato::triplex_vector_t tfo_sequences;
-  sequence_loader.load_sequences(tfo_sequences, tfo_names,
-                                 std::numeric_limits<unsigned>::max());
+  sequence_loader->load_sequences(tfo_sequences, tfo_names,
+                                  std::numeric_limits<unsigned>::max());
   pato::motif_vector_t tfo_motifs;
   pato::motif_potential_vector_t tfo_potentials;
   pato::find_tfo_motifs(tfo_motifs, tfo_potentials, tfo_sequences, opts);

diff --git a/lib/PATO/tpx_finder.cpp b/lib/PATO/tpx_finder.cpp
@@ -269,12 +269,12 @@ static void match_tfo_tts_motifs(
 }
 
 pato::find_tpx_result pato::find_tpxes(const pato::options_t &opts) {
-  pato::sequence_loader_t tfo_sequence_loader;
-  if (!tfo_sequence_loader.init(opts.tfo_file)) {
+  auto tfo_sequence_loader = pato::sequence_loader_t::create(opts.tfo_file);
+  if (!tfo_sequence_loader) {
     return pato::find_tpx_result::cannot_open_tfo_file;
   }
-  pato::sequence_loader_t tts_sequence_loader;
-  if (!tts_sequence_loader.init(opts.tts_file)) {
+  auto tts_sequence_loader = pato::sequence_loader_t::create(opts.tts_file);
+  if (!tts_sequence_loader) {
     return pato::find_tpx_result::cannot_open_tts_file;
   }
 
@@ -285,8 +285,8 @@ pato::find_tpx_result pato::find_tpxes(const pato::options_t &opts) {
 
   pato::name_vector_t tfo_names;
   pato::triplex_vector_t tfo_sequences;
-  tfo_sequence_loader.load_sequences(tfo_sequences, tfo_names,
-                                     std::numeric_limits<unsigned>::max());
+  tfo_sequence_loader->load_sequences(tfo_sequences, tfo_names,
+                                      std::numeric_limits<unsigned>::max());
   pato::motif_vector_t tfo_motifs;
   pato::motif_potential_vector_t tfo_potentials;
   pato::find_tfo_motifs(tfo_motifs, tfo_potentials, tfo_sequences, opts);
@@ -304,8 +304,8 @@ pato::find_tpx_result pato::find_tpxes(const pato::options_t &opts) {
   pato::potential_map_t potentials;
 
   while (true) {
-    if (!tts_sequence_loader.load_sequences(tts_sequences, tts_names,
-                                            opts.chunk_size)) {
+    if (!tts_sequence_loader->load_sequences(tts_sequences, tts_names,
+                                             opts.chunk_size)) {
       break;
     }
 

diff --git a/lib/PATO/tts_finder.cpp b/lib/PATO/tts_finder.cpp
@@ -178,8 +178,8 @@ void pato::find_tts_motifs(pato::motif_vector_t &motifs,
 
 pato::find_tts_motifs_result
 pato::find_tts_motifs(const pato::options_t &opts) {
-  pato::sequence_loader_t sequence_loader;
-  if (!sequence_loader.init(opts.tts_file)) {
+  auto sequence_loader = pato::sequence_loader_t::create(opts.tts_file);
+  if (!sequence_loader) {
     return pato::find_tts_motifs_result::cannot_open_tts_file;
   }
 
@@ -194,8 +194,8 @@ pato::find_tts_motifs(const pato::options_t &opts) {
   pato::motif_potential_vector_t tts_potentials;
 
   while (true) {
-    if (!sequence_loader.load_sequences(tts_sequences, tts_names,
-                                        opts.chunk_size)) {
+    if (!sequence_loader->load_sequences(tts_sequences, tts_names,
+                                         opts.chunk_size)) {
       break;
     }
     pato::find_tts_motifs(tts_motifs, tts_potentials, tts_sequences, opts);