View¶

Meta-header for the view submodule .

Author: Hannes Hauswedell <hannes.hauswedell AT fu-berlin.de>

namespace view¶

The SeqAn3 namespace for views.

Since views often have name clashes with regular functions and ranges they are implemented in the sub namespace view.

See the view submodule of the range module for more details.

Provides seqan3::view::char_to.

Author: Hannes Hauswedell <hannes.hauswedell AT fu-berlin.de>

namespace view¶

The SeqAn3 namespace for views.

Since views often have name clashes with regular functions and ranges they are implemented in the sub namespace view.

See the view submodule of the range module for more details.

Variables

auto const char_to¶

A view over an alphabet, given a range of characters.

Return

A view over alphabet_type, created from it’s character representation.

View properties

view type: same input_range
value type: alphabet_type
const iterable: yes

Complexity

Linear in the size if the input range ( $O(n)$ ).

Exceptions

Strong exception guarantee (does not modify data).

Thread safety

Does not modify data.

Example

std::string s{"ACTTTGATAN"};
auto v1 = s | view::char_to<dna4>; // == "ACTTTGATAA"_dna4
auto v2 = s | view::char_to<dna5>; // == "ACTTTGATAN"_dna5

Template Parameters

alphabet_type: The type of the desired alphabet, must satisfy seqan3::alphabet_concept.

Parameters

input_range: The range you wish to convert, elements must be convertible to alphabet_type’s seqan3::underlying_char_t.

Provides seqan3::view::complement.

Author: Hannes Hauswedell <hannes.hauswedell AT fu-berlin.de>

namespace view

The SeqAn3 namespace for views.

Since views often have name clashes with regular functions and ranges they are implemented in the sub namespace view.

See the view submodule of the range module for more details.

Variables

auto const complement¶

A view that converts a range of nucleotides to their complement.

dna5_vector foo{"ACGTA"_dna5};

// pipe notation
auto v = foo | view::complement;                                  // == "TGCAT"

// function notation
dna5_vector v2(view::complement(foo));                            // == "TGCAT"

// generate the reverse complement:
dna5_vector v3 = foo | view::complement | ranges::view::reverse;  // == "TACGT"

View properties

view type: same as input_range
value type: remove_reference_t<value_type_t<input_range>>
const iterable: yes

Complexity

Linear in the size if the input range ( $O(n)$ ).

Exceptions

Strong exception guarantee (does not modify data).

Thread safety

Does not modify data.

Example

Parameters

input_range: The range you wish to convert, must satisfy seqan3::input_range_concept and the value_type must satisfy seqan3::nucleotide_concept.

Adaptation of the view concept from the Ranges TS.

Author: Hannes Hauswedell <hannes.hauswedell AT fu-berlin.de>

namespace seqan3¶

The main SeqAn3 namespace.

Helpers for seqan3::semi_alphabet_concept

These functions and metafunctions expose member variables and types so that they satisfy seqan3::semi_alphabet_concept.

Helpers for seqan3::alphabet_concept

These functions and metafunctions expose member variables and types so that they satisfy seqan3::alphabet_concept.

Helpers for seqan3::nucleotide_concept

These functions and metafunctions expose member variables and types so that they satisfy seqan3::nucleotide_concept.

Alphabet aliases

Other names (typedefs) for seqan3::nucl16

Range concepts

Adapted from the Ranges TS.

Container concepts

Container concepts as defined by the standard library (or very close).

Container-of-container concepts

Shortcuts for multi-dimensional container concepts.

Variables

concept bool seqan3::view_concept = range_concept<type> && (bool)ranges::View<type>()

Specifies the requirements of a Range type that has constant time copy, move and assignment operators.

See: http://en.cppreference.com/w/cpp/experimental/ranges/iterator/View

Provides seqan3::view::convert.

Author: Hannes Hauswedell <hannes.hauswedell AT fu-berlin.de>

namespace view

The SeqAn3 namespace for views.

Since views often have name clashes with regular functions and ranges they are implemented in the sub namespace view.

See the view submodule of the range module for more details.

Variables

auto const convert¶

A view that converts each element in the input range (implicitly or via static_cast).

Convert from int to bool:

// convert from int to bool
std::vector<int>  vec{7, 5, 0, 5, 0, 0, 4, 8, -3};

// pipe notation
auto v = vec | view::convert<bool>; // == [1, 1, 0, 1, 0, 0, 1, 1, 1];

// function notation and immediate conversion to vector again
std::vector<bool> v2(view::convert<bool>(vec));

// combinability
auto v3 = vec | view::convert<bool> | ranges::view::reverse; // == [1, 1, 1, 0, 0, 1, 0, 1, 1];

Return

A view with the value_type being out_t

View properties

view type: same input_range
value type: out_t
const iterable: yes

Complexity

Linear in the size if the input range ( $O(n)$ ).

Exceptions

Strong exception guarantee (does not modify data).

Thread safety

Does not modify data.

Example

Template Parameters

out_t: The type to convert to (must be given).

Parameters

input_range: The range you wish to convert, must satisfy seqan3::input_range_concept.

Convert from seqan3::nucl16 to seqan3::dna5:

nucl16_vector vec2{"ACYGTN"_nucl16};
auto v4 = vec2 | view::convert<dna5>; // == "ACNGTN"_dna5

Provides seqan3::view::rank_to.

Author: Hannes Hauswedell <hannes.hauswedell AT fu-berlin.de>

namespace view

The SeqAn3 namespace for views.

Since views often have name clashes with regular functions and ranges they are implemented in the sub namespace view.

See the view submodule of the range module for more details.

Variables

auto const rank_to¶

A view over an alphabet, given a range of ranks.

Return

A view over alphabet_type, created from it’s rank representation.

View properties

view type: same input_range
value type: alphabet_type
const iterable: yes

Complexity

Linear in the size if the input range ( $O(n)$ ).

Exceptions

Strong exception guarantee (does not modify data).

Thread safety

Does not modify data.

Example

std::vector<int> vec{0, 1, 3, 3, 3, 2, 0, 3, 0};
auto v1 = vec | view::rank_to<dna4>; // == "ACTTTGATA"_dna4
auto v2 = vec | view::rank_to<dna5>; // == "ACTTTGATA"_dna5

Template Parameters

alphabet_type: The type of the desired alphabet, must satisfy seqan3::alphabet_concept.

Parameters

input_range: The range you wish to convert, elements be must convertible to alphabet_type’s seqan3::underlying_rank_t.

Provides seqan3::view::to_char.

Author: Hannes Hauswedell <hannes.hauswedell AT fu-berlin.de>

namespace view

The SeqAn3 namespace for views.

Since views often have name clashes with regular functions and ranges they are implemented in the sub namespace view.

See the view submodule of the range module for more details.

Variables

auto const to_char¶

A view that calls seqan3::to_char() on each element in the input range.

Return

A view with the value_type being seqan3::underlying_char_t of the input alphabet.

View properties

view type: same input_range
value type: seqan3::underlying_char_t of the input’s value_type
const iterable: yes

Complexity

Linear in the size if the input range ( $O(n)$ ).

Exceptions

Strong exception guarantee (does not modify data).

Thread safety

Does not modify data.

Example

dna4_vector vec = "ACTTTGATA"_dna4;
auto v = vec | view::to_char;
std::cout << v << '\n'; // [A,C,T,T,T,G,A,T,A]

std::vector<illumina18> qvec{{0}, {7}, {5}, {3}, {7}, {4}, {30}, {16}, {23}};
auto v3 = qvec | view::to_char;
std::cout << v3 << '\n'; // [!,(,&,$,(,%,?,1,8]

std::vector<dna4q> qcvec{{dna4::C, 0}, {dna4::A, 7}, {dna4::G, 5}, {dna4::T, 3}, {dna4::G, 7}, {dna4::A, 4}, {dna4::C, 30}, {dna4::T, 16}, {dna4::A, 23}};
auto v4 = qcvec | view::to_char;
std::cout << v4 << '\n'; // [C,A,G,T,G,A,C,T,A]

Parameters

input_range: The range you wish to convert, must satisfy seqan3::input_range_concept and the value_type must satisfy seqan3::alphabet_concept.

Provides seqan3::view::to_rank.

Author: Hannes Hauswedell <hannes.hauswedell AT fu-berlin.de>

namespace view

The SeqAn3 namespace for views.

Since views often have name clashes with regular functions and ranges they are implemented in the sub namespace view.

See the view submodule of the range module for more details.

Variables

auto const to_rank¶

A view that calls seqan3::to_rank() on each element in the input range.

Return

A view with the value_type being seqan3::underlying_rank_t of the input alphabet.

View properties

view type: same input_range
value type: seqan3::underlying_rank_t of the input’s value_type
const iterable: yes

Complexity

Linear in the size if the input range ( $O(n)$ ).

Exceptions

Strong exception guarantee (does not modify data).

Thread safety

Does not modify data.

Example

dna4_vector vec = "ACTTTGATA"_dna4;
auto v = vec | view::to_rank | view::convert<unsigned>;
std::cout << v << '\n'; // [0,1,3,3,3,2,0,3,0]

std::vector<illumina18> qvec{{0}, {7}, {5}, {3}, {7}, {4}, {30}, {16}, {23}};
auto v3 = qvec | view::to_rank | view::convert<unsigned>;
std::cout << v3 << '\n'; // [0,7,5,3,7,4,30,16,23]

std::vector<dna4q> qcvec{{dna4::C, 0}, {dna4::A, 7}, {dna4::G, 5}, {dna4::T, 3}, {dna4::G, 7}, {dna4::A, 4}, {dna4::C, 30}, {dna4::T, 16}, {dna4::A, 23}};
auto v4 = qcvec | view::to_rank | view::convert<unsigned>;
std::cout << v4 << '\n'; // [1,28,22,15,30,16,121,67,92]

We also convert to unsigned here, because the seqan3::underlying_rank_t is often uint8_t which is often implemented as unsigned char and thus will not be printed as a number by default.

Parameters

input_range: The range you wish to convert, must satisfy seqan3::input_range_concept and the value_type must satisfy seqan3::alphabet_concept.