From df5a826d23e9de4fc2fe5a368b3da49b23eb5eea Mon Sep 17 00:00:00 2001
From: Simon Gene Gottlieb <simon@gottliebtfreitag.de>
Date: Fri, 14 Jul 2023 13:14:48 +0200
Subject: [PATCH] feat: FMIndex can use other CSA, and selectLeftCursor

---
 src/fmindex-collection/FMIndex.h              |  9 ++++----
 .../search/SearchNoErrors.h                   | 15 ++++++------
 src/fmindex-collection/search/SelectCursor.h  | 23 +++++++++++++++----
 3 files changed, 30 insertions(+), 17 deletions(-)

diff --git a/src/fmindex-collection/FMIndex.h b/src/fmindex-collection/FMIndex.h
index 8e9fa5bb..b44a6cb0 100644
--- a/src/fmindex-collection/FMIndex.h
+++ b/src/fmindex-collection/FMIndex.h
@@ -12,17 +12,16 @@
 
 namespace fmindex_collection {
 
-template <OccTable Table>
+template <OccTable Table, typename TCSA = CSA>
 struct FMIndex {
     static size_t constexpr Sigma = Table::Sigma;
 
     using TTable = Table;
 
     Table  occ;
-    CSA    csa;
+    TCSA   csa;
 
-
-    FMIndex(std::span<uint8_t const> bwt, CSA _csa)
+    FMIndex(std::span<uint8_t const> bwt, TCSA _csa)
         : occ{bwt}
         , csa{std::move(_csa)}
     {}
@@ -44,7 +43,7 @@ struct FMIndex {
         auto [bwt, csa] = [&, &inputText=inputText, &inputSizes=inputSizes] () {
             auto sa  = createSA(inputText, threadNbr);
             auto bwt = createBWT(inputText, sa);
-            auto csa = CSA{std::move(sa), samplingRate, inputSizes};
+            auto csa = TCSA{std::move(sa), samplingRate, inputSizes};
 
             return std::make_tuple(std::move(bwt), std::move(csa));
         }();
diff --git a/src/fmindex-collection/search/SearchNoErrors.h b/src/fmindex-collection/search/SearchNoErrors.h
index 9309e253..abec4a82 100644
--- a/src/fmindex-collection/search/SearchNoErrors.h
+++ b/src/fmindex-collection/search/SearchNoErrors.h
@@ -13,9 +13,9 @@
 
 namespace fmindex_collection::search_no_errors {
 
-template <typename index_t, Sequence query_t, typename delegate_t>
-void search(index_t const & index, query_t && query, delegate_t && delegate) {
-    using cursor_t = LeftBiFMIndexCursor<index_t>;
+template <typename index_t, Sequence query_t>
+auto search(index_t const & index, query_t && query) {
+    using cursor_t = select_left_cursor_t<index_t>;
     static_assert(not cursor_t::Reversed, "reversed fmindex is not supported");
 
     auto cur = cursor_t{index};
@@ -23,10 +23,10 @@ void search(index_t const & index, query_t && query, delegate_t && delegate) {
         auto r = query[query.size() - i - 1];
         cur = cur.extendLeft(r);
         if (cur.empty()) {
-            return;
+            return cur;
         }
     }
-    delegate(cur);
+    return cur;
 }
 
 template <typename index_t, Sequences queries_t, typename delegate_t>
@@ -34,9 +34,8 @@ void search(index_t const & index, queries_t && queries, delegate_t && delegate)
 
     for (size_t qidx{0}; qidx < queries.size(); ++qidx) {
         auto const& query = queries[qidx];
-        search(index, query, [&qidx, &delegate](auto cursor) {
-            delegate(qidx, cursor);
-        });
+        auto cursor = search(index, query);
+        delegate(qidx, cursor);
     }
 }
 
diff --git a/src/fmindex-collection/search/SelectCursor.h b/src/fmindex-collection/search/SelectCursor.h
index 894e9be3..a5b6da76 100644
--- a/src/fmindex-collection/search/SelectCursor.h
+++ b/src/fmindex-collection/search/SelectCursor.h
@@ -21,9 +21,9 @@ struct SelectIndexCursor<BiFMIndex<OccTable, TCSA>> {
     using cursor_t = BiFMIndexCursor<BiFMIndex<OccTable, TCSA>>;
 };
 
-template <typename OccTable>
-struct SelectIndexCursor<FMIndex<OccTable>> {
-    using cursor_t = FMIndexCursor<FMIndex<OccTable>>;
+template <typename OccTable, typename TCSA>
+struct SelectIndexCursor<FMIndex<OccTable, TCSA>> {
+    using cursor_t = FMIndexCursor<FMIndex<OccTable, TCSA>>;
 };
 
 template <typename OccTable, typename TCSA>
@@ -31,8 +31,23 @@ struct SelectIndexCursor<ReverseFMIndex<OccTable, TCSA>> {
     using cursor_t = ReverseFMIndexCursor<ReverseFMIndex<OccTable, TCSA>>;
 };
 
+template <typename Index>
+struct SelectLeftIndexCursor;
+
+template <typename OccTable, typename TCSA>
+struct SelectLeftIndexCursor<BiFMIndex<OccTable, TCSA>> {
+    using cursor_t = LeftBiFMIndexCursor<BiFMIndex<OccTable, TCSA>>;
+};
+
+template <typename OccTable, typename TCSA>
+struct SelectLeftIndexCursor<FMIndex<OccTable, TCSA>> {
+    using cursor_t = FMIndexCursor<FMIndex<OccTable, TCSA>>;
+};
+
+template <typename Index>
+using select_cursor_t      = typename SelectIndexCursor<Index>::cursor_t;
 
 template <typename Index>
-using select_cursor_t = typename SelectIndexCursor<Index>::cursor_t;
+using select_left_cursor_t = typename SelectLeftIndexCursor<Index>::cursor_t;
 
 }