Don't expose simd.h in any MMseqs2 header

Author: milot-mirdita

lib/simd/simd.h

@@ -2,6 +2,10 @@
 // optimze based on technolegy double, float and integer (32) SIMD instructions
 // writen by Martin Steinegger
 
+// #ifdef SIMD_H
+// #error "simd.h included multiple times in the same translation unit"
+// #endif
+
 #ifndef SIMD_H
 #define SIMD_H
 #include <cstdlib>

src/alignment/CMakeLists.txt

@@ -23,6 +23,7 @@ set(alignment_source_files
         alignment/PSSMCalculator.cpp
         alignment/StripedSmithWaterman.cpp
         alignment/BandedNucleotideAligner.cpp
+        alignment/DistanceCalculator.cpp
         alignment/rescorediagonal.cpp
         alignment/Fwbw.cpp
         PARENT_SCOPE

src/alignment/DistanceCalculator.cpp

@@ -0,0 +1,27 @@
+#include "DistanceCalculator.h"
+
+#include "simd.h"
+
+template<typename T>
+unsigned int DistanceCalculator::computeInverseHammingDistance(const T *seq1, const T *seq2, unsigned int length){
+    unsigned int diff = 0;
+    unsigned int simdBlock = length/(VECSIZE_INT*4);
+    simd_int * simdSeq1 = (simd_int *) seq1;
+    simd_int * simdSeq2 = (simd_int *) seq2;
+    for (unsigned int pos = 0; pos < simdBlock; pos++ ) {
+        simd_int seq1vec = simdi_loadu(simdSeq1+pos);
+        simd_int seq2vec = simdi_loadu(simdSeq2+pos);
+        // int _mm_movemask_epi8(__m128i a) creates 16-bit mask from most significant bits of
+        // the 16 signed or unsigned 8-bit integers in a and zero-extends the upper bits.
+        simd_int seqComparision = simdi8_eq(seq1vec, seq2vec);
+        int res = simdi8_movemask(seqComparision);
+        diff += __builtin_popcount(res);  // subtract positions that should not contribute to coverage
+    }
+    // compute missing rest
+    for (unsigned int pos = simdBlock*(VECSIZE_INT*4); pos < length; pos++ ) {
+        diff += (seq1[pos] == seq2[pos]);
+    }
+    return diff;
+}
+
+template unsigned int DistanceCalculator::computeInverseHammingDistance<char>(const char *seq1, const char *seq2, unsigned int length);

src/alignment/DistanceCalculator.h

@@ -5,7 +5,6 @@
 #include <cstring>
 #include <vector>
 
-#include "simd.h"
 #include "MathUtil.h"
 #include "BaseMatrix.h"
 #include "Parameters.h"
@@ -273,26 +272,7 @@ class DistanceCalculator {
 
 
     template<typename T>
-    static unsigned int computeInverseHammingDistance(const T *seq1, const T *seq2, unsigned int length){
-        unsigned int diff = 0;
-        unsigned int simdBlock = length/(VECSIZE_INT*4);
-        simd_int * simdSeq1 = (simd_int *) seq1;
-        simd_int * simdSeq2 = (simd_int *) seq2;
-        for (unsigned int pos = 0; pos < simdBlock; pos++ ) {
-            simd_int seq1vec = simdi_loadu(simdSeq1+pos);
-            simd_int seq2vec = simdi_loadu(simdSeq2+pos);
-            // int _mm_movemask_epi8(__m128i a) creates 16-bit mask from most significant bits of
-            // the 16 signed or unsigned 8-bit integers in a and zero-extends the upper bits.
-            simd_int seqComparision = simdi8_eq(seq1vec, seq2vec);
-            int res = simdi8_movemask(seqComparision);
-            diff += __builtin_popcount(res);  // subtract positions that should not contribute to coverage
-        }
-        // compute missing rest
-        for (unsigned int pos = simdBlock*(VECSIZE_INT*4); pos < length; pos++ ) {
-            diff += (seq1[pos] == seq2[pos]);
-        }
-        return diff;
-    }
+    static unsigned int computeInverseHammingDistance(const T *seq1, const T *seq2, unsigned int length);
 
 
 

src/alignment/MultipleAlignment.cpp

@@ -1,6 +1,7 @@
 #include "MultipleAlignment.h"
 
 #include "Debug.h"
+#include "simd.h"
 #include "Sequence.h"
 #include "SubstitutionMatrix.h"
 #include "Util.h"