Fixed slight slowdown introduced in 2.1.0 revision

Author: agudys

.github/workflows/self-hosted.yml

@@ -399,7 +399,7 @@ jobs:
         
     - name: no refinement
       run: |
-        ./famsa-${{matrix.compiler}} -gt import upgma.dnd -refine_mode off ${INPUT} upgma.no_refine.fasta
+        ./famsa-${{matrix.compiler}} -gt import ${REF_DIR}/upgma.dnd -refine_mode off ${INPUT} upgma.no_refine.fasta
         cmp upgma.no_refine.fasta ${REF_DIR}/upgma.no_refine.fasta
         
     - name: profile-profile alignment

makefile

@@ -130,6 +130,7 @@ CXXFLAGS_NEON = $(CXXFLAGS) ${ABI_FLAG} -funroll-loops
 
 
 COMMON_OBJS := src/msa.o \
+	src/msa_refinement.o \
 	src/tree/AbstractTreeGenerator.o \
 	src/tree/Clustering.o \
 	src/tree/DistanceCalculator.o \

src/core/version.h

@@ -9,14 +9,17 @@ Authors: Sebastian Deorowicz, Agnieszka Debudaj-Grabysz, Adam Gudys
 #ifndef _VERSION_H
 #define _VERSION_H
 
-#define FAMSA_VER		"2.2.1"
-#define FAMSA_DATE		"2022-10-05"
+#define FAMSA_VER		"2.2.2"
+#define FAMSA_DATE		"2022-10-09"
 #define FAMSA_AUTHORS	"S. Deorowicz, A. Debudaj-Grabysz, A. Gudys"
 
 #endif
 
 /*
 Version history:
+2.2.2 (2022-10-09):
+- Fixed slowdown caused by the duplicate removal (feature added in 2.1.0).
+
 2.2.1 (2022-10-05):
 - Pairwise identity (-pid switch) properly calculated as the number of matching residues divided by the shorter sequence length.
 

src/famsa.vcxproj

@@ -268,6 +268,7 @@
       <EnableEnhancedInstructionSet Condition="'$(Configuration)|$(Platform)'=='Release|ARM64'">AdvancedVectorExtensions</EnableEnhancedInstructionSet>
     </ClCompile>
     <ClCompile Include="lcs\lcsbp_neon_intr.cpp" />
+    <ClCompile Include="msa_refinement.cpp" />
     <ClCompile Include="tree\AbstractTreeGenerator.cpp" />
     <ClCompile Include="tree\Clustering.cpp" />
     <ClCompile Include="tree\DistanceCalculator.cpp" />

src/famsa.vcxproj.filters

@@ -113,6 +113,7 @@
     <ClCompile Include="..\libs\mimalloc\static.cpp">
       <Filter>libraries</Filter>
     </ClCompile>
+    <ClCompile Include="msa_refinement.cpp" />
   </ItemGroup>
   <ItemGroup>
     <ClInclude Include="msa.h" />