Fixed generic architecture.

bbuchfink · Oct 27, 2021 · c35483c · c35483c
1 parent a332de5
commit c35483c
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Showing 6 changed files with 20 additions and 24 deletions.
diff --git a/src/dp/score_vector_int16.h b/src/dp/score_vector_int16.h
@@ -206,30 +206,9 @@ struct ScoreVector<int16_t, DELTA>
 		data_(_mm_loadu_si128((const __m128i*)x))
 	{}
 
-	ScoreVector(unsigned a, uint64_t seq)
-	{
-		const uint16_t* row((uint16_t*)&score_matrix.matrix16()[a << 5]);
-		uint64_t b = uint64_t(row[seq & 0xff]);
-		seq >>= 8;
-		b |= uint64_t(row[seq & 0xff]) << 16;
-		seq >>= 8;
-		b |= uint64_t(row[seq & 0xff]) << 16 * 2;
-		seq >>= 8;
-		b |= uint64_t(row[seq & 0xff]) << 16 * 3;
-		seq >>= 8;
-		uint64_t c = uint64_t(row[seq & 0xff]);
-		seq >>= 8;
-		c |= uint64_t(row[seq & 0xff]) << 16;
-		seq >>= 8;
-		c |= uint64_t(row[seq & 0xff]) << 16 * 2;
-		seq >>= 8;
-		c |= uint64_t(row[seq & 0xff]) << 16 * 3;
-		data_ = _mm_set_epi64x(c, b);
-	}
-
+#ifdef __SSSE3__
 	ScoreVector(unsigned a, Register seq)
 	{
-#ifdef __SSSE3__
 		const __m128i *row = reinterpret_cast<const __m128i*>(&score_matrix.matrix8u()[a << 5]);
 
 		__m128i high_mask = _mm_slli_epi16(_mm_and_si128(seq, ::SIMD::_mm_set1_epi8('\x10')), 3);
@@ -242,8 +221,8 @@ struct ScoreVector<int16_t, DELTA>
 		__m128i s2 = _mm_shuffle_epi8(r2, seq_high);
 		data_ = _mm_and_si128(_mm_or_si128(s1, s2), ::SIMD::_mm_set1_epi16(255));
 		data_ = _mm_subs_epi16(data_, ::SIMD::_mm_set1_epi16(score_matrix.bias()));
-#endif
 	}
+#endif
 
 	ScoreVector operator+(const ScoreVector&rhs) const
 	{

diff --git a/src/dp/score_vector_int8.h b/src/dp/score_vector_int8.h
@@ -238,6 +238,7 @@ struct ScoreVector<int8_t, DELTA>
 		data_(_mm_loadu_si128(reinterpret_cast<const __m128i*>(s)))
 	{ }
 
+#ifdef __SSSE3__
 	ScoreVector(unsigned a, __m128i seq)
 	{
 		const __m128i* row = reinterpret_cast<const __m128i*>(&score_matrix.matrix8()[a << 5]);
@@ -252,6 +253,7 @@ struct ScoreVector<int8_t, DELTA>
 		__m128i s2 = _mm_shuffle_epi8(r2, seq_high);
 		data_ = _mm_or_si128(s1, s2);
 	}
+#endif
 
 	ScoreVector operator+(const ScoreVector&rhs) const
 	{

diff --git a/src/dp/swipe/banded_3frame_swipe.cpp b/src/dp/swipe/banded_3frame_swipe.cpp
@@ -425,6 +425,7 @@ list<Hsp> banded_3frame_swipe(
 		frameshift_penalty(score_matrix.frame_shift());
 
 	SwipeProfile<_sv> profile;
+	std::array<const int8_t*, 32> target_scores;
 	Score best[ScoreTraits<_sv>::CHANNELS];
 	int max_col[ScoreTraits<_sv>::CHANNELS];
 	for (int i = 0; i < ScoreTraits<_sv>::CHANNELS; ++i) {
@@ -443,7 +444,11 @@ list<Hsp> banded_3frame_swipe(
 		_sv vgap0, vgap1, vgap2, hgap, col_best;
 		vgap0 = vgap1 = vgap2 = col_best = ScoreTraits<_sv>::zero();
 
+#ifdef __SSSE3__
 		profile.set(targets.get());
+#else
+		profile.set(targets.get(target_scores.data()));
+#endif
 		for (int i = i0_; i <= i1_; ++i) {
 			hgap = it.hgap();
 			_sv next = cell_update<_sv>(it.sm3, it.sm4, it.sm2, profile.get(q[0][i]), extend_penalty, open_penalty, frameshift_penalty, hgap, vgap0, col_best);

diff --git a/src/dp/swipe/banded_swipe.h b/src/dp/swipe/banded_swipe.h
@@ -252,7 +252,11 @@ list<Hsp> swipe(const vector<DpTarget>::const_iterator subject_begin, const vect
 				profile.set(targets.get(target_scores.data()));
 		}
 		else {
+#ifdef __SSSE3__
 			profile.set(target_seqv);
+#else
+			profile.set(targets.get(target_scores.data()));
+#endif
 		}
 #ifdef DP_STAT
 		const uint64_t live = targets.live();

diff --git a/src/dp/swipe/full_swipe.h b/src/dp/swipe/full_swipe.h
@@ -162,7 +162,11 @@ list<Hsp> swipe(const It target_begin, const It target_end, std::atomic_size_t*
 				profile.set(targets.get(target_scores.data()));
 		}
 		else {
+#ifdef __SSSE3__
 			profile.set(target_seq_vector);
+#else
+			profile.set(targets.get(target_scores.data()));
+#endif
 		}
 
 #ifdef DP_STAT

diff --git a/src/dp/swipe/swipe.h b/src/dp/swipe/swipe.h
@@ -92,12 +92,14 @@ template<typename Sv>
 struct SwipeProfile
 {
 
+#ifdef __SSSE3__
 	inline void set(typename ScoreTraits<Sv>::Vector seq)
 	{
 		assert(sizeof(data_) / sizeof(Sv) >= value_traits.alphabet_size);
 		for (unsigned j = 0; j < AMINO_ACID_COUNT; ++j)
 			data_[j] = Sv(j, seq);
 	}
+#endif
 
 	inline const Sv& get(Letter i) const
 	{
@@ -166,7 +168,7 @@ struct SwipeProfile<int32_t>
 		for (int i = 0; i < 32; ++i)
 			row[i] = target_scores[0][i];
 	}
-	void set(const int32_t * *target_scores) {
+	void set(const int32_t** target_scores) {
 		for (int i = 0; i < 32; ++i)
 			row[i] = target_scores[0][i];
 	}