feat: add unit tests for DenseCSA

SGSSGene · Nov 18, 2024 · 0a096b0 · 0a096b0
1 parent 0cc9928
commit 0a096b0
Showing 1 changed file with 75 additions and 0 deletions.
diff --git a/src/test_fmindex-collection/fmindex/checkCSA.cpp b/src/test_fmindex-collection/fmindex/checkCSA.cpp
@@ -4,6 +4,7 @@
 
 #include <catch2/catch_all.hpp>
 #include <fmindex-collection/suffixarray/CSA.h>
+#include <fmindex-collection/suffixarray/DenseCSA.h>
 #include <fmindex-collection/utils.h>
 
 TEST_CASE("check Compressed Suffix Array (CSA)", "[CSA]") {
@@ -73,6 +74,80 @@ TEST_CASE("check Compressed Suffix Array (CSA)", "[CSA]") {
     SECTION("sampling 8") {
         auto csa = fmindex_collection::CSA {sa, /*.samplingRate =*/ 8, inputSizes};
 
+        auto expected = std::vector<std::optional<std::tuple<size_t, size_t>>>(12);
+        expected[2] = {0, 0};
+        expected[3] = {1, 0};
+        check(csa, expected);
+    }
+}
+
+TEST_CASE("check Dense Compressed Suffix Array (DenseCSA)", "[DenseCSA]") {
+    // SA of 'Hello$World$':
+    //               S P  SA
+    // $Hello$World  1 5  11
+    // $World$Hello  0 5   5
+    // Hello$World$  0 0   0
+    // World$Hello$  1 0   6
+    // d$Hello$Worl  1 4  10
+    // ello$World$H  0 1   1
+    // ld$Hello$Wor  1 3   9
+    // llo$World$He  0 2   2
+    // lo$World$Hel  0 3   3
+    // o$World$Hell  0 4   4
+    // orld$Hello$W  1 1   7
+    // rld$Hello$Wo  1 2   8
+
+
+    auto [totalSize, input, inputSizes] = fmindex_collection::createSequences(fmindex_collection::test::createInputData({"Hello", "World"}));
+    auto sa                             = fmindex_collection::createSA64(input, 1);
+
+
+    auto check = [&](auto const& csa, auto const& expected) {
+        REQUIRE(sa.size() == expected.size());
+        for (size_t i{0}; i < sa.size(); ++i) {
+            REQUIRE(csa.value(i) == expected[i]);
+            if (expected[i]) {
+                CHECK(*csa.value(i) == *expected[i]);
+            }
+        }
+    };
+
+    SECTION("sampling 3") {
+        auto csa = fmindex_collection::DenseCSA {sa, /*.samplingRate =*/ 3, inputSizes};
+
+        auto expected = std::vector<std::optional<std::tuple<size_t, size_t>>>(12);
+        expected[2] = {0, 0};
+        expected[3] = {1, 0};
+        expected[6] = {1, 3};
+        expected[8] = {0, 3};
+        check(csa, expected);
+    }
+
+    SECTION("sampling 4") {
+        auto csa = fmindex_collection::DenseCSA {sa, /*.samplingRate =*/ 4, inputSizes};
+
+        auto expected = std::vector<std::optional<std::tuple<size_t, size_t>>>(12);
+        expected[2] = {0, 0};
+        expected[3] = {1, 0};
+        expected[4] = {1, 4};
+        expected[9] = {0, 4};
+        check(csa, expected);
+    }
+
+    SECTION("sampling 5") {
+        auto csa = fmindex_collection::DenseCSA {sa, /*.samplingRate =*/ 5, inputSizes};
+
+        auto expected = std::vector<std::optional<std::tuple<size_t, size_t>>>(12);
+        expected[0] = {1, 5};
+        expected[1] = {0, 5};
+        expected[2] = {0, 0};
+        expected[3] = {1, 0};
+        check(csa, expected);
+    }
+
+    SECTION("sampling 8") {
+        auto csa = fmindex_collection::DenseCSA {sa, /*.samplingRate =*/ 8, inputSizes};
+
         auto expected = std::vector<std::optional<std::tuple<size_t, size_t>>>(12);
         expected[2] = {0, 0};
         expected[3] = {1, 0};