[MISC] rename seqan3::views::trim to seqan3::views::trim_quality

CHANGELOG.md

@@ -101,6 +101,7 @@ Note that 3.1.0 will be the first API stable release and interfaces in this rele
   ([\#1654](https://github.com/seqan/seqan3/pull/1654)).
 * Added `seqan3::views::minimiser_hash`, a view that computes the minimisers of a range of type seqan3::semialphabet.
   ([\#1721](https://https://github.com/seqan/seqan3/pull/1721)).
+* `seqan3::views:trim` has been renamed to `seqan3::views:trim_quality`.
 
 #### Search
 

doc/tutorial/ranges/index.md

@@ -235,7 +235,7 @@ We provide overview tables for all our view adaptors that document which concept
 ## Views in the standard library and in SeqAn
 
 The standard library in C++20 provides a number of useful views and SeqAn provides many views, as well.
-Most views provided by SeqAn3 are specific to biological operations, like seqan3::views::trim which trims sequences
+Most views provided by SeqAn3 are specific to biological operations, like seqan3::views::trim_quality which trims sequences
 based on the quality or seqan3::views::complement which generates the complement of a nucleotide sequence.
 But SeqAn3 also provides some general purpose views.
 

include/seqan3/range/views/all.hpp

@@ -33,7 +33,7 @@
 #include <seqan3/range/views/to_char.hpp>
 #include <seqan3/range/views/to_rank.hpp>
 #include <seqan3/range/views/translate.hpp>
-#include <seqan3/range/views/trim.hpp>
+#include <seqan3/range/views/trim_quality.hpp>
 
 /*!\defgroup views Views
  * \brief Views are "lazy range combinators" that offer modified views onto other ranges.
@@ -52,7 +52,7 @@
  *
  * See the \link range range module \endlink for how views relate to containers and decorators.
  *
- * Most views provided by SeqAn are specific to biological operations, like seqan3::views::trim which trims
+ * Most views provided by SeqAn are specific to biological operations, like seqan3::views::trim_quality which trims
  * sequences based on the quality or seqan3::views::complement which generates the complement of a nucleotide sequence.
  * But SeqAn also provides some general purpose views.
  *

include/seqan3/range/views/trim.hpp → include/seqan3/range/views/trim_quality.hpp

@@ -7,7 +7,7 @@
 
 /*!\file
  * \author Hannes Hauswedell <hannes.hauswedell AT fu-berlin.de>
- * \brief Provides seqan3::views::trim.
+ * \brief Provides seqan3::views::trim_quality.
  */
 
 #pragma once
@@ -20,7 +20,7 @@
 namespace seqan3::detail
 {
 
-/*!\brief The underlying type of seqan3::views::trim.
+/*!\brief The underlying type of seqan3::views::trim_quality.
  * \ingroup views
  *
  * Under the hood this delegates to views::take_until.
@@ -39,15 +39,15 @@ struct trim_fn
     }
 
     /*!\brief Trim based on minimum phred score.
-     * \tparam irng_t The type of the range being processed. See seqan3::views::trim for requirements.
+     * \tparam irng_t The type of the range being processed. See seqan3::views::trim_quality for requirements.
      * \param irange The range being processed.
      * \param threshold The minimum quality as a phred score [integral type].
      */
     template <std::ranges::input_range irng_t, typename threshold_t>
     constexpr auto operator()(irng_t && irange, threshold_t const threshold) const
     {
         static_assert(quality_alphabet<std::remove_reference_t<std::ranges::range_reference_t<irng_t>>>,
-                      "views::trim can only operate on ranges over seqan3::quality_alphabet.");
+                      "views::trim_quality can only operate on ranges over seqan3::quality_alphabet.");
         static_assert(std::same_as<remove_cvref_t<threshold_t>,
                      remove_cvref_t<std::ranges::range_reference_t<irng_t>>> ||
                       std::integral<remove_cvref_t<threshold_t>>,
@@ -90,7 +90,7 @@ namespace seqan3::views
  *
  * \details
  *
- * \header_file{seqan3/range/views/trim.hpp}
+ * \header_file{seqan3/range/views/trim_quality.hpp}
  *
  * This view can be used to do easy quality based trimming of sequences.
  *
@@ -126,7 +126,7 @@ namespace seqan3::views
  * \hideinitializer
  */
 
-inline constexpr auto trim = deep{seqan3::detail::trim_fn{}};
+inline constexpr auto trim_quality = deep{seqan3::detail::trim_fn{}};
 
 //!\}
 

test/snippet/range/views/trim_dna5q.cpp

@@ -4,7 +4,7 @@
 #include <seqan3/alphabet/nucleotide/dna5.hpp>
 #include <seqan3/alphabet/quality/aliases.hpp>
 #include <seqan3/alphabet/quality/phred42.hpp>
-#include <seqan3/range/views/trim.hpp>
+#include <seqan3/range/views/trim_quality.hpp>
 #include <seqan3/range/views/to_char.hpp>
 #include <seqan3/range/views/to.hpp>
 
@@ -23,14 +23,14 @@ int main()
                                    {'A'_dna5, '5'_phred42}};
 
     // trim by phred_value
-    auto v1 = vec | seqan3::views::trim(20u);
+    auto v1 = vec | seqan3::views::trim_quality(20u);
     assert((v1 | seqan3::views::to<std::vector>) == cmp);
 
     // trim by quality character; in this case the nucleotide part of the character is irrelevant
-    auto v2 = vec | seqan3::views::trim(seqan3::dna5q{'C'_dna5, '5'_phred42});
+    auto v2 = vec | seqan3::views::trim_quality(seqan3::dna5q{'C'_dna5, '5'_phred42});
     assert((v2 | seqan3::views::to<std::vector>) == cmp);
 
     // combinability
-    auto v3 = seqan3::views::trim(vec, 20u) | seqan3::views::to_char;
+    auto v3 = seqan3::views::trim_quality(vec, 20u) | seqan3::views::to_char;
     assert(std::ranges::equal(std::string{"AGGA"}, v3 | seqan3::views::to<std::string>));
 }

test/snippet/range/views/trim_phred42.cpp

@@ -2,7 +2,7 @@
 #include <vector>
 
 #include <seqan3/alphabet/quality/phred42.hpp>
-#include <seqan3/range/views/trim.hpp>
+#include <seqan3/range/views/trim_quality.hpp>
 #include <seqan3/range/views/to_char.hpp>
 
 int main()
@@ -11,14 +11,14 @@ int main()
                                      seqan3::phred42{20}, seqan3::phred42{10}};
 
     // trim by phred_value
-    auto v1 = vec | seqan3::views::trim(20u);                            // == ['I','I','?','5']
+    auto v1 = vec | seqan3::views::trim_quality(20u);                            // == ['I','I','?','5']
 
     // trim by quality character
-    auto v2 = vec | seqan3::views::trim(seqan3::phred42{40});            // == ['I','I']
+    auto v2 = vec | seqan3::views::trim_quality(seqan3::phred42{40});            // == ['I','I']
 
     // function syntax
-    auto v3 = seqan3::views::trim(vec, 20u);                             // == ['I','I','?','5']
+    auto v3 = seqan3::views::trim_quality(vec, 20u);                             // == ['I','I','?','5']
 
     // combinability
-    auto v4 = seqan3::views::trim(vec, 20u) | seqan3::views::to_char;    // == "II?5"
+    auto v4 = seqan3::views::trim_quality(vec, 20u) | seqan3::views::to_char;    // == "II?5"
 }

test/unit/range/views/view_trim_test.cpp

@@ -13,7 +13,7 @@
 #include <seqan3/range/concept.hpp>
 #include <seqan3/range/views/to_char.hpp>
 #include <seqan3/range/views/to.hpp>
-#include <seqan3/range/views/trim.hpp>
+#include <seqan3/range/views/trim_quality.hpp>
 #include <seqan3/std/ranges>
 
 using seqan3::operator""_dna5;
@@ -27,19 +27,19 @@ TEST(view_trim, standalone)
     std::vector<seqan3::phred42> cmp2{seqan3::phred42{40}, seqan3::phred42{40}};
 
     // trim by phred_value
-    auto v1 = vec | seqan3::views::trim(20u);                   // == ['I','I','?','5']
+    auto v1 = vec | seqan3::views::trim_quality(20u);                   // == ['I','I','?','5']
     EXPECT_EQ(v1 | seqan3::views::to<std::vector>, cmp1);
 
     // trim by quality character
-    auto v2 = vec | seqan3::views::trim(seqan3::phred42{40});   // == ['I','I']
+    auto v2 = vec | seqan3::views::trim_quality(seqan3::phred42{40});   // == ['I','I']
     EXPECT_EQ(v2 | seqan3::views::to<std::vector>, cmp2);
 
     // function syntax
-    auto v3 = seqan3::views::trim(vec, 20u);                    // == ['I','I','?','5']
+    auto v3 = seqan3::views::trim_quality(vec, 20u);                    // == ['I','I','?','5']
     EXPECT_EQ(v3 | seqan3::views::to<std::vector>, cmp1);
 
     // combinability
-    std::string v4 = seqan3::views::trim(vec, 20u) | seqan3::views::to_char | seqan3::views::to<std::string>; //=="II?5"
+    std::string v4 = seqan3::views::trim_quality(vec, 20u) | seqan3::views::to_char | seqan3::views::to<std::string>; //=="II?5"
     EXPECT_EQ("II?5", v4);
 }
 
@@ -58,19 +58,19 @@ TEST(view_trim, qualified)
                                     {'G'_dna5, seqan3::phred42{40}}};
 
     // trim by phred_value
-    auto v1 = vec | seqan3::views::trim(20u);
+    auto v1 = vec | seqan3::views::trim_quality(20u);
     EXPECT_EQ(v1 | seqan3::views::to<std::vector>, cmp1);
 
     // trim by quality character
-    auto v2 = vec | seqan3::views::trim(seqan3::dna5q{'C'_dna5, seqan3::phred42{40}});
+    auto v2 = vec | seqan3::views::trim_quality(seqan3::dna5q{'C'_dna5, seqan3::phred42{40}});
     EXPECT_EQ(v2 | seqan3::views::to<std::vector>, cmp2);
 
     // function syntax
-    auto v3 = seqan3::views::trim(vec, 20u);
+    auto v3 = seqan3::views::trim_quality(vec, 20u);
     EXPECT_EQ(v3 | seqan3::views::to<std::vector>, cmp1);
 
     // combinability
-    std::string v4 = seqan3::views::trim(vec, 20u) | seqan3::views::to_char | seqan3::views::to<std::string>;
+    std::string v4 = seqan3::views::trim_quality(vec, 20u) | seqan3::views::to_char | seqan3::views::to<std::string>;
     EXPECT_EQ("AGGA", v4);
 }
 
@@ -88,7 +88,7 @@ TEST(view_trim, concepts)
     EXPECT_TRUE((std::ranges::output_range<decltype(vec), seqan3::dna5q>));
     EXPECT_TRUE(std::ranges::sized_range<decltype(vec)>);
 
-    auto v1 = vec | seqan3::views::trim(20u);
+    auto v1 = vec | seqan3::views::trim_quality(20u);
     EXPECT_TRUE(std::ranges::input_range<decltype(v1)>);
     EXPECT_TRUE(std::ranges::forward_range<decltype(v1)>);
     EXPECT_TRUE(std::ranges::random_access_range<decltype(v1)>);