Search outparam

include/seqan3/search/fm_index/bi_fm_index_cursor.hpp

@@ -964,18 +964,85 @@ class bi_fm_index_cursor
     {
         assert(index != nullptr);
 
-        std::vector<std::pair<size_type, size_type>> occ;
+        std::vector<std::pair<size_type, size_type>> occ{};
         occ.reserve(count());
+
+        if (!count())
+            return occ; // empty result vector
+
+        // fill occ with locations in order to not allocate another vector
         for (size_type i = 0; i < count(); ++i)
+            occ.emplace_back(offset() - index->fwd_fm.index[fwd_lb + i], 0);
+        std::sort(occ.begin(), occ.end());
+
+        size_type seq_idx = index->fwd_fm.text_begin_rs.rank(occ[0].first + 1);
+        size_type seq_offset = index->fwd_fm.text_begin_ss.select(seq_idx);
+        size_type next_seq_offset = (seq_idx == index->fwd_fm.text_begin_rs.rank(index->size() - 1))
+                                        ? index->size() - 1
+                                        : index->fwd_fm.text_begin_ss.select(seq_idx + 1);
+
+        // replace first occurrence value with correct entries
+        occ[0].second = occ[0].first - seq_offset; // position in seq i
+        occ[0].first  = seq_idx - 1; // position in seq i
+
+        for (size_type i = 1; i < count(); ++i)
         {
-            size_type loc = offset() - index->fwd_fm.index[fwd_lb + i];
-            size_type sequence_rank = index->fwd_fm.text_begin_rs.rank(loc + 1);
-            size_type sequence_position = loc - index->fwd_fm.text_begin_ss.select(sequence_rank);
-            occ.emplace_back(sequence_rank - 1, sequence_position);
+            if (occ[i].first >= next_seq_offset)
+            {
+                seq_idx = index->fwd_fm.text_begin_rs.rank(occ[i].first + 1);
+                seq_offset = index->fwd_fm.text_begin_ss.select(seq_idx);
+            }
+
+            // replace occurrence values with correct entries
+            occ[i].second = occ[i].first - seq_offset; // position in seq i
+            occ[i].first  = seq_idx - 1; // position in seq i
         }
+
         return occ;
     }
 
+    //!\overload
+    void locate(std::vector<std::pair<size_type, size_type>> & occ) const
+    //!\cond
+        requires index_t::text_layout_mode == text_layout::collection
+    //!\endcond
+    {
+        assert(index != nullptr);
+        auto const start = occ.size();
+        occ.reserve(start + count());
+
+        if (!count())
+            return; // empty result vector
+
+        // fill occ with locations in order to not allocate another vector
+        for (size_type i = 0; i < count(); ++i)
+            occ.emplace_back(offset() - index->fwd_fm.index[fwd_lb + i], 0);
+        std::sort(occ.begin(), occ.end());
+
+        size_type seq_idx = index->fwd_fm.text_begin_rs.rank(occ[0].first + 1);
+        size_type seq_offset = index->fwd_fm.text_begin_ss.select(seq_idx);
+        size_type next_seq_offset = (seq_idx == index->fwd_fm.text_begin_rs.rank(index->fwd_fm.size() - 1))
+                                        ? index->fwd_fm.size() - 1
+                                        : index->fwd_fm.text_begin_ss.select(seq_idx + 1);
+
+        // replace first occurrence value with correct entries
+        occ[start].second = occ[start].first - seq_offset; // position in seq i
+        occ[start].first  = seq_idx - 1; // position in seq i
+
+        for (size_type i = 1; i < count(); ++i)
+        {
+            if (occ[start + i].first >= next_seq_offset)
+            {
+                seq_idx = index->fwd_fm.text_begin_rs.rank(occ[start + i].first + 1);
+                seq_offset = index->fwd_fm.text_begin_ss.select(seq_idx);
+            }
+
+            // replace occurrence values with correct entries
+            occ[start + i].second = occ[start + i].first - seq_offset; // position in seq i
+            occ[start + i].first  = seq_idx - 1; // position in seq i
+        }
+    }
+
     /*!\brief Locates the occurrences of the searched query in the text on demand, i.e. a ranges::view is returned
      *        and every position is located once it is accessed.
      * \returns Positions in the text.

include/seqan3/search/fm_index/fm_index_cursor.hpp

@@ -516,39 +516,69 @@ class fm_index_cursor
      *
      * Strong exception guarantee (no data is modified in case an exception is thrown).
      */
-    std::vector<size_type> locate() const
+    void locate(std::vector<size_type> & occ) const
     //!\cond
         requires index_t::text_layout_mode == text_layout::single
     //!\endcond
     {
         assert(index != nullptr);
-
-        std::vector<size_type> occ(count());
-        for (size_type i = 0; i < occ.size(); ++i)
+        occ.reserve(occ.size() + count());
+        for (size_type i = 0; i < count(); ++i)
         {
-            occ[i] = offset() - index->index[node.lb + i];
+            occ.push_back(offset() - index->index[node.lb + i]);
         }
-        return occ;
     }
 
     //!\overload
-    std::vector<std::pair<size_type, size_type>> locate() const
+    auto locate() const
+    {
+        using hit_t = std::conditional_t<index_t::text_layout_mode == text_layout::collection,
+                                         std::pair<size_type, size_type>,
+                                         size_type>;
+        std::vector<hit_t> occ{};
+        locate(occ);
+        return occ;
+    }
+
+    void locate(std::vector<std::pair<size_type, size_type>> & occ) const
     //!\cond
         requires index_t::text_layout_mode == text_layout::collection
     //!\endcond
     {
         assert(index != nullptr);
+        auto const start = occ.size();
+        occ.reserve(start + count());
+
+        if (!count())
+            return; // empty result vector
 
-        std::vector<std::pair<size_type, size_type>> occ;
-        occ.reserve(count());
+        // fill occ with locations in order to not allocate another vector
         for (size_type i = 0; i < count(); ++i)
+            occ.emplace_back(offset() - index->index[node.lb + i], 0);
+        std::sort(occ.begin(), occ.end());
+
+        size_type seq_idx = index->text_begin_rs.rank(occ[0].first + 1);
+        size_type seq_offset = index->text_begin_ss.select(seq_idx);
+        size_type next_seq_offset = (seq_idx == index->text_begin_rs.rank(index->size() - 1))
+                                        ? index->size() - 1
+                                        : index->text_begin_ss.select(seq_idx + 1);
+
+        // replace first occurrence value with correct entries
+        occ[start].second = occ[start].first - seq_offset; // position in seq i
+        occ[start].first  = seq_idx - 1; // position in seq i
+
+        for (size_type i = 1; i < count(); ++i)
         {
-            size_type loc = offset() - index->index[node.lb + i];
-            size_type sequence_rank = index->text_begin_rs.rank(loc + 1);
-            size_type sequence_position = loc - index->text_begin_ss.select(sequence_rank);
-            occ.emplace_back(sequence_rank - 1, sequence_position);
+            if (occ[start + i].first >= next_seq_offset)
+            {
+                seq_idx = index->text_begin_rs.rank(occ[start + i].first + 1);
+                seq_offset = index->text_begin_ss.select(seq_idx);
+            }
+
+            // replace occurrence values with correct entries
+            occ[start + i].second = occ[start + i].first - seq_offset; // position in seq i
+            occ[start + i].first  = seq_idx - 1; // position in seq i
         }
-        return occ;
     }
 
     /*!\brief Locates the occurrences of the searched query in the text on demand, i.e. a ranges::view is returned and

test/unit/search/fm_index_cursor/fm_index_cursor_collection_test_template.hpp

@@ -328,7 +328,7 @@ TYPED_TEST_P(fm_index_cursor_collection_test, lazy_locate)
     TypeParam it = TypeParam(fm);
     it.extend_right("ACG"_dna4);
 
-    EXPECT_TRUE(std::ranges::equal(it.locate(), it.lazy_locate()));
+    EXPECT_TRUE(std::ranges::equal(seqan3::uniquify(it.locate()), seqan3::uniquify(it.lazy_locate())));
 }
 
 TYPED_TEST_P(fm_index_cursor_collection_test, concept_check)