[WIP] work in progress

seqan · Apr 8, 2020 · a04799c · a04799c
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -56,8 +56,6 @@ Note that 3.1.0 will be the first API stable release and interfaces in this rele
 
 * Added `seqan3::interleaved_bloom_filter`, a data structure that efficiently answers set-membership queries for
   multiple bins ([\#920](https://github.com/seqan/seqan3/pull/920)).
-*  The `extend_right()` function can now also handle `char const *`.
-  ([\#1588](https://github.com/seqan/seqan3/pull/1588)).
 
 ## API changes
 

diff --git a/test/unit/search/fm_index/bi_fm_index_aa27_test.cpp b/test/unit/search/fm_index/bi_fm_index_aa27_test.cpp
@@ -10,8 +10,6 @@
 #include "fm_index_collection_test_template.hpp"
 #include "fm_index_test_template.hpp"
 
-#include <seqan3/alphabet/aminoacid/aa27.hpp>
-
 using t1 = std::pair<seqan3::bi_fm_index<seqan3::aa27, seqan3::text_layout::single>,
                      seqan3::aa27_vector>;
 INSTANTIATE_TYPED_TEST_SUITE_P(aa27, fm_index_test, t1, );

diff --git a/test/unit/search/fm_index/bi_fm_index_char_test.cpp b/test/unit/search/fm_index/bi_fm_index_char_test.cpp
@@ -8,8 +8,6 @@
 #include "fm_index_collection_test_template.hpp"
 #include "fm_index_test_template.hpp"
 
-#include <seqan3/alphabet/adaptation/uint.hpp>
-
 using t1 = std::pair<seqan3::bi_fm_index<unsigned char, seqan3::text_layout::single>,
                      std::vector<unsigned char>>;
 INSTANTIATE_TYPED_TEST_SUITE_P(char, fm_index_test, t1, );

diff --git a/test/unit/search/fm_index/bi_fm_index_dna4_test.cpp b/test/unit/search/fm_index/bi_fm_index_dna4_test.cpp
@@ -10,8 +10,6 @@
 #include "fm_index_collection_test_template.hpp"
 #include "fm_index_test_template.hpp"
 
-#include <seqan3/alphabet/nucleotide/dna4.hpp>
-
 using t1 = std::pair<seqan3::bi_fm_index<seqan3::dna4, seqan3::text_layout::single>,
                      seqan3::dna4_vector>;
 INSTANTIATE_TYPED_TEST_SUITE_P(dna4, fm_index_test, t1, );

diff --git a/test/unit/search/fm_index/fm_index_dna4_test.cpp b/test/unit/search/fm_index/fm_index_dna4_test.cpp
@@ -11,9 +11,6 @@
 #include "fm_index_collection_test_template.hpp"
 #include "fm_index_test_template.hpp"
 
-#include <seqan3/alphabet/nucleotide/dna4.hpp>
-#include <seqan3/alphabet/nucleotide/dna5.hpp>
-
 using t1 = std::pair<seqan3::fm_index<seqan3::dna4, seqan3::text_layout::single>, seqan3::dna4_vector>;
 INSTANTIATE_TYPED_TEST_SUITE_P(dna4, fm_index_test, t1, );
 using t2 = std::pair<seqan3::fm_index<seqan3::dna4, seqan3::text_layout::collection>, std::vector<seqan3::dna4_vector>>;

diff --git a/test/unit/search/fm_index_cursor/fm_index_cursor_collection_test_template.hpp b/test/unit/search/fm_index_cursor/fm_index_cursor_collection_test_template.hpp
@@ -323,40 +323,35 @@ TYPED_TEST_P(fm_index_cursor_collection_test, lazy_locate)
 
 TYPED_TEST_P(fm_index_cursor_collection_test, locate_char_string)
 {
-    // test case for https://github.com/seqan/seqan3/issues/1473
-    std::string text = "How much wood would a woodchuck chuck?";
-    char const * wood = "wood";
-
-    // extend_right()
-    {
-        seqan3::fm_index index{text};
-        auto it1 = index.cursor();
-        auto it2 = index.cursor();
-
-        it1.extend_right("wood");
-        it2.extend_right(wood);
-
-        EXPECT_TRUE(std::ranges::equal(it1.locate(), it2.locate())); // [22,9] == [22,9]
-
-        seqan3::bi_fm_index b_index{text};
-        auto it3 = b_index.cursor();
-        auto it4 = b_index.cursor();
-
-        it3.extend_right("wood");
-        it4.extend_right(wood);
+    using alphabet_type = typename TestFixture::alphabet_type;
 
-        EXPECT_TRUE(std::ranges::equal(it3.locate(), it4.locate())); // [22,9] == [22,9]
-    }
-    // extend_left()
+    // test case for https://github.com/seqan/seqan3/issues/1473
+    if (std::is_same<alphabet_type, char>::value)
     {
-        seqan3::bi_fm_index b_index{text};
-        auto it3 = b_index.cursor();
-        auto it4 = b_index.cursor();
-
-        it3.extend_left("wood");
-        it4.extend_left(wood);
-
-        EXPECT_TRUE(std::ranges::equal(it3.locate(), it4.locate())); // [22,9] == [22,9]
+        char const * cg = "CG";
+
+        // extend_right()
+        {
+            typename TypeParam::index_type fm{this->text_col1}; // {"ACGACG", "ACGACG"}
+            TypeParam it1 = TypeParam(fm);
+            TypeParam it2 = TypeParam(fm);
+
+            it1.extend_right(cg);
+            it2.extend_right(seqan3::views::slice(this->text1, 1, 3));      // "CG"
+
+            // EXPECT_TRUE(std::ranges::equal(it1.locate(), it2.locate()));    // [(0,1),(0,4),(1,4),(1,1)]
+        }
+        // // extend_left()
+        // {
+        //     seqan3::bi_fm_index b_index{this->text_col1}; // {"ACGACG", "ACGACG"}
+        //     auto it3 = b_index.cursor();
+        //     auto it4 = b_index.cursor();
+
+        //     it3.extend_left("AC");
+        //     it4.extend_right(seqan3::views::slice(this->text1, 1, 3));      // "CG"
+
+        //     EXPECT_TRUE(std::ranges::equal(it3.locate(), it4.locate()));    // [(0,1),(0,4),(1,4),(1,1)]
+        // }
     }
 }