Fixed #573.

bbuchfink · Apr 19, 2022 · 69517b0 · 69517b0
1 parent e346524
commit 69517b0
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Showing 3 changed files with 8 additions and 26 deletions.
diff --git a/src/output/daa/daa_file.h b/src/output/daa/daa_file.h
@@ -16,9 +16,7 @@ You should have received a copy of the GNU General Public License
 along with this program.  If not, see <http://www.gnu.org/licenses/>.
 ****/
 
-#ifndef DAA_FILE_H_
-#define DAA_FILE_H_
-
+#pragma once
 #include <string>
 #include <exception>
 #include "../util/ptr_vector.h"
@@ -29,8 +27,6 @@ along with this program.  If not, see <http://www.gnu.org/licenses/>.
 #include "../basic/value.h"
 #include "../data/reference.h"
 
-using std::string;
-
 struct DAA_header1
 {
 	enum { VERSION = 1, COMPATIBILITY_VERSION = 0 };
@@ -222,5 +218,3 @@ struct DAA_file
 	vector<uint32_t> ref_len_;
 
 };
-
-#endif /* DAA_FILE_H_ */
diff --git a/src/output/daa/daa_record.cpp b/src/output/daa/daa_record.cpp
@@ -77,5 +77,6 @@ BinaryBuffer::Iterator& operator>>(BinaryBuffer::Iterator &it, DAA_query_record:
 	}
 	r.context().parse();
 	r.evalue = score_matrix.evalue(r.score, r.parent_.context[0].size(), r.subject_len);
+	r.bit_score = score_matrix.bitscore(r.score);
 	return it;
 }
diff --git a/src/output/daa/daa_record.h b/src/output/daa/daa_record.h
@@ -16,9 +16,7 @@ You should have received a copy of the GNU General Public License
 along with this program.  If not, see <http://www.gnu.org/licenses/>.
 ****/
 
-#ifndef DAA_RECORD_H_
-#define DAA_RECORD_H_
-
+#pragma once
 #include <limits>
 #include "daa_file.h"
 #include "../basic/packed_sequence.h"
@@ -28,16 +26,7 @@ along with this program.  If not, see <http://www.gnu.org/licenses/>.
 #include "../stats/score_matrix.h"
 #include "../basic/match.h"
 
-using std::string;
-using std::vector;
-
-/*void translate_query(const vector<Letter>& query, vector<Letter> *context)
-{
-	context[0] = query;
-	context[1] = Translator::reverse(query);
-}*/
-
-inline void translate_query(const vector<Letter>& query, vector<Letter> *context)
+inline void translate_query(const std::vector<Letter>& query, std::vector<Letter> *context)
 {
 	Translator::translate(query, context);
 }
@@ -126,10 +115,10 @@ struct DAA_query_record
 		return align_mode.query_translated ? source_seq.size() : context[0].size();
 	}
 
-	string query_name;
+	std::string query_name;
 	size_t query_num;
-	vector<Letter> source_seq;
-	vector<Letter> context[6];
+	std::vector<Letter> source_seq;
+	std::vector<Letter> context[6];
 	TranslatedSequence query_seq;
 
 private:
@@ -143,6 +132,4 @@ struct DAA_query_record
 
 };
 
-BinaryBuffer::Iterator& operator>>(BinaryBuffer::Iterator &it, DAA_query_record::Match &r);
-
-#endif /* DAA_RECORD_H_ */
+BinaryBuffer::Iterator& operator>>(BinaryBuffer::Iterator &it, DAA_query_record::Match &r);