Seqalign2

src/openms/include/OpenMS/ANALYSIS/ID/ConsensusIDAlgorithmPEPIons.h

@@ -69,7 +69,7 @@ namespace OpenMS
     void updateMembers_() override;
 
     /// Sequence similarity based on matching ions
-    double getSimilarity_(AASequence seq1, AASequence seq2) override;
+    double getSimilarity_(const AASequence& seq1, const AASequence& seq2) override;
 
   };
 

src/openms/include/OpenMS/ANALYSIS/ID/ConsensusIDAlgorithmPEPMatrix.h

@@ -68,7 +68,7 @@ namespace OpenMS
     ConsensusIDAlgorithmPEPMatrix& operator=(const ConsensusIDAlgorithmPEPMatrix&);
 
     /// Sequence similarity based on substitution matrix (ignores PTMs)
-    double getSimilarity_(AASequence seq1, AASequence seq2) override;
+    double getSimilarity_(const AASequence& seq1, const AASequence& seq2) override;
 
     // Docu in base class
     void updateMembers_() override;

src/openms/include/OpenMS/ANALYSIS/ID/ConsensusIDAlgorithmSimilarity.h

@@ -71,7 +71,7 @@ namespace OpenMS
 
        @return Similarity between two sequences in the range [0, 1]
     */
-    virtual double getSimilarity_(AASequence seq1, AASequence seq2) = 0;
+    virtual double getSimilarity_(const AASequence& seq1, const  AASequence& seq2) = 0;
 
   private:
     /// Not implemented

src/openms/source/ANALYSIS/ID/ConsensusIDAlgorithmPEPIons.cpp

@@ -66,12 +66,12 @@ namespace OpenMS
   }
 
 
-  double ConsensusIDAlgorithmPEPIons::getSimilarity_(AASequence seq1,
-                                                     AASequence seq2)
+  double ConsensusIDAlgorithmPEPIons::getSimilarity_(const AASequence& seq1,
+                                                     const AASequence& seq2)
   {
     if (seq1 == seq2) return 1.0;
-    // order of sequences matters for cache look-up:
-    if (seq2 < seq1) std::swap(seq1, seq2); // "operator>" not defined
+    // order of sequences matters for cache look-up:    
+    if (seq2 < seq1) getSimilarity_(seq2, seq1); // "operator>" not defined
     pair<AASequence, AASequence> seq_pair = make_pair(seq1, seq2);
     SimilarityCache::iterator pos = similarities_.find(seq_pair);
     if (pos != similarities_.end()) return pos->second; // score found in cache

src/openms/source/ANALYSIS/ID/ConsensusIDAlgorithmPEPMatrix.cpp

@@ -74,8 +74,8 @@ namespace OpenMS
     similarities_.clear();
   }
 
-  double ConsensusIDAlgorithmPEPMatrix::getSimilarity_(AASequence seq1,
-                                                       AASequence seq2)
+  double ConsensusIDAlgorithmPEPMatrix::getSimilarity_(const AASequence& seq1,
+                                                       const AASequence& seq2)
   {
     // here we cannot take modifications into account:
     String unmod_seq1 = seq1.toUnmodifiedString();

src/openms/source/FORMAT/FASTAFile.cpp

@@ -198,9 +198,9 @@ namespace OpenMS
     }
     ++entries_read_;
 
-    protein.identifier = std::move(id_);
-    protein.description = std::move(description_);
-    protein.sequence = std::move(seq_);
+    protein.identifier = id_;
+    protein.description = description_;
+    protein.sequence = seq_;
 
     return true;
   }