SeqAn3  3.0.2
The Modern C++ library for sequence analysis.
seqan3::fm_index_cursor< index_t > Class Template Reference

The SeqAn FM Index Cursor. More...

#include <seqan3/search/fm_index/fm_index_cursor.hpp>

+ Inheritance diagram for seqan3::fm_index_cursor< index_t >:

Public Member Functions

size_type count () const noexcept
 Counts the number of occurrences of the searched query in the text. More...
 
bool cycle_back () noexcept
 Tries to replace the rightmost character of the query by the next lexicographically larger character such that the query is found in the text. More...
 
bool extend_right () noexcept
 Tries to extend the query by the smallest possible character to the right such that the query is found in the text. More...
 
template<typename char_t >
bool extend_right (char_t const c) noexcept
 Tries to extend the query by the character c to the right. More...
 
template<std::ranges::range seq_t>
bool extend_right (seq_t &&seq) noexcept
 Tries to extend the query by seq to the right. More...
 
size_type last_rank () const noexcept
 Outputs the rightmost rank. More...
 
auto lazy_locate () const
 Locates the occurrences of the searched query in the text on demand, i.e. a ranges::view is returned and every position is located once it is accessed. More...
 
auto lazy_locate () const
 
std::vector< size_typelocate () const
 Locates the occurrences of the searched query in the text. More...
 
std::vector< std::pair< size_type, size_type > > locate () const
 
bool operator!= (fm_index_cursor const &rhs) const noexcept
 Compares two cursors. More...
 
bool operator== (fm_index_cursor const &rhs) const noexcept
 Compares two cursors. More...
 
template<std::ranges::range text_t>
auto path_label (text_t &&text) const noexcept
 Returns the searched query. More...
 
template<std::ranges::range text_t>
auto path_label (text_t &&text) const noexcept
 
size_type query_length () const noexcept
 Returns the length of the searched query. More...
 
Constructors, destructor and assignment
 fm_index_cursor () noexcept=default
 Default constructor. Accessing member functions on a default constructed object is undefined behavior. More...
 
 fm_index_cursor (fm_index_cursor const &) noexcept=default
 Defaulted.
 
fm_index_cursoroperator= (fm_index_cursor const &) noexcept=default
 Defaulted.
 
 fm_index_cursor (fm_index_cursor &&) noexcept=default
 Defaulted.
 
fm_index_cursoroperator= (fm_index_cursor &&) noexcept=default
 Defaulted.
 
 ~fm_index_cursor ()=default
 Defaulted.
 
 fm_index_cursor (index_t const &_index) noexcept
 Construct from given index.
 

Friends

template<typename _index_t >
class bi_fm_index_cursor
 

Member types

using index_type = index_t
 Type of the index.
 
using size_type = typename index_type::size_type
 Type for representing positions in the indexed text.
 

Detailed Description

template<typename index_t>
class seqan3::fm_index_cursor< index_t >

The SeqAn FM Index Cursor.

Template Parameters
index_tThe type of the underlying index; must model seqan3::fm_index_specialisation.

The cursor's interface provides searching a string from left to right in the indexed text. All methods modifying the cursor (e.g. extending by a character with extend_right()) return a bool value whether the operation was successful or not. In case of an unsuccessful operation the cursor remains unmodified, i.e. an cursor can never be in an invalid state except default constructed cursors that are always invalid.

The asymptotic running times for using the cursor depend on the SDSL index configuration. To determine the exact running times, you have to additionally look up the running times of the used traits (configuration).

Constructor & Destructor Documentation

◆ fm_index_cursor()

template<typename index_t >
seqan3::fm_index_cursor< index_t >::fm_index_cursor ( )
defaultnoexcept

Default constructor. Accessing member functions on a default constructed object is undefined behavior.

Defaulted.

Member Function Documentation

◆ count()

template<typename index_t >
size_type seqan3::fm_index_cursor< index_t >::count ( ) const
inlinenoexcept

Counts the number of occurrences of the searched query in the text.

Returns
Number of occurrences of the searched query in the text.

Complexity

Constant.

Exceptions

No-throw guarantee.

◆ cycle_back()

template<typename index_t >
bool seqan3::fm_index_cursor< index_t >::cycle_back ( )
inlinenoexcept

Tries to replace the rightmost character of the query by the next lexicographically larger character such that the query is found in the text.

Returns
true if there exists a query in the text where the rightmost character of the query is lexicographically larger than the current rightmost character of the query.

Example:

#include <vector>
int main()
{
using seqan3::operator""_dna4;
std::vector<seqan3::dna4> genome{"AATAATAAC"_dna4};
seqan3::fm_index index{genome}; // build the index
auto cur = index.begin(); // create a cursor
// cur.cycle_back(); // cycle_back on begin() is undefined behaviour!
cur.extend_right("AAC"_dna4); // search the sequence "AAC"
seqan3::debug_stream << cur.path_label(genome) << '\n'; // outputs "AAC"
seqan3::debug_stream << cur.last_rank() << '\n'; // outputs 1
cur.cycle_back(); // search the sequence "AAT"
seqan3::debug_stream << cur.path_label(genome) << '\n'; // outputs "AAT"
seqan3::debug_stream << cur.last_rank() << '\n'; // outputs 3
cur.cycle_back(); // "cur" doesn't change because the rightmost char
// is already the largest dna4 char.
seqan3::debug_stream << cur.path_label(genome) << '\n'; // outputs "AAT"
seqan3::debug_stream << cur.last_rank() << '\n'; // outputs 3
}

Complexity

$O(\Sigma) * O(T_{BACKWARD\_SEARCH})$

It scans linearly over the alphabet starting from the rightmost character until it finds the query with a larger rightmost character.

Exceptions

No-throw guarantee.

◆ extend_right() [1/3]

template<typename index_t >
bool seqan3::fm_index_cursor< index_t >::extend_right ( )
inlinenoexcept

Tries to extend the query by the smallest possible character to the right such that the query is found in the text.

Returns
true if the cursor could extend the query successfully.

Complexity

$O(\Sigma) * O(T_{BACKWARD\_SEARCH})$

It scans linearly over the alphabet until it finds the smallest character that is represented by an edge.

Exceptions

No-throw guarantee.

◆ extend_right() [2/3]

template<typename index_t >
template<typename char_t >
bool seqan3::fm_index_cursor< index_t >::extend_right ( char_t const  c)
inlinenoexcept

Tries to extend the query by the character c to the right.

Template Parameters
char_tType of the character needs to be convertible to the character type char_type of the index.
Parameters
[in]cCharacter to extend the query with to the right.
Returns
true if the cursor could extend the query successfully.

Complexity

$O(T_{BACKWARD\_SEARCH})$

Exceptions

No-throw guarantee.

◆ extend_right() [3/3]

template<typename index_t >
template<std::ranges::range seq_t>
bool seqan3::fm_index_cursor< index_t >::extend_right ( seq_t &&  seq)
inlinenoexcept

Tries to extend the query by seq to the right.

Template Parameters
seq_tThe type of range of the sequence to search; must model std::ranges::forward_range.
Parameters
[in]seqSequence to extend the query with to the right.
Returns
true if the cursor could extend the query successfully.

If extending fails in the middle of the sequence, all previous computations are rewound to restore the cursor's state before calling this method.

Complexity

$|seq| * O(T_{BACKWARD\_SEARCH})$

Exceptions

No-throw guarantee.

◆ last_rank()

template<typename index_t >
size_type seqan3::fm_index_cursor< index_t >::last_rank ( ) const
inlinenoexcept

Outputs the rightmost rank.

Returns
Rightmost rank.

Example:

#include <vector>
int main()
{
using seqan3::operator""_dna4;
std::vector<seqan3::dna4> genome{"AATAATAAC"_dna4};
seqan3::fm_index index{genome}; // build the index
auto cur = index.begin(); // create a cursor
// cur.cycle_back(); // cycle_back on begin() is undefined behaviour!
cur.extend_right("AAC"_dna4); // search the sequence "AAC"
seqan3::debug_stream << cur.path_label(genome) << '\n'; // outputs "AAC"
seqan3::debug_stream << cur.last_rank() << '\n'; // outputs 1
cur.cycle_back(); // search the sequence "AAT"
seqan3::debug_stream << cur.path_label(genome) << '\n'; // outputs "AAT"
seqan3::debug_stream << cur.last_rank() << '\n'; // outputs 3
cur.cycle_back(); // "cur" doesn't change because the rightmost char
// is already the largest dna4 char.
seqan3::debug_stream << cur.path_label(genome) << '\n'; // outputs "AAT"
seqan3::debug_stream << cur.last_rank() << '\n'; // outputs 3
}

Complexity

Constant.

Exceptions

No-throw guarantee.

◆ lazy_locate() [1/2]

template<typename index_t >
auto seqan3::fm_index_cursor< index_t >::lazy_locate ( ) const
inline

Locates the occurrences of the searched query in the text on demand, i.e. a ranges::view is returned and every position is located once it is accessed.

Returns
Positions in the text.

Complexity

$count() * O(T_{BACKWARD\_SEARCH} * SAMPLING\_RATE)$

Exceptions

Strong exception guarantee (no data is modified in case an exception is thrown).

◆ lazy_locate() [2/2]

template<typename index_t >
auto seqan3::fm_index_cursor< index_t >::lazy_locate ( ) const
inline

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

◆ locate() [1/2]

template<typename index_t >
std::vector<size_type> seqan3::fm_index_cursor< index_t >::locate ( ) const
inline

Locates the occurrences of the searched query in the text.

Returns
Positions in the text.

Complexity

$count() * O(T_{BACKWARD\_SEARCH} * SAMPLING\_RATE)$

Exceptions

Strong exception guarantee (no data is modified in case an exception is thrown).

◆ locate() [2/2]

template<typename index_t >
std::vector<std::pair<size_type, size_type> > seqan3::fm_index_cursor< index_t >::locate ( ) const
inline

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

◆ operator!=()

template<typename index_t >
bool seqan3::fm_index_cursor< index_t >::operator!= ( fm_index_cursor< index_t > const &  rhs) const
inlinenoexcept

Compares two cursors.

Parameters
[in]rhsOther cursor to compare it to.
Returns
true if the cursors are not equal, false otherwise.

Complexity

Constant.

Exceptions

No-throw guarantee.

◆ operator==()

template<typename index_t >
bool seqan3::fm_index_cursor< index_t >::operator== ( fm_index_cursor< index_t > const &  rhs) const
inlinenoexcept

Compares two cursors.

Parameters
[in]rhsOther cursor to compare it to.
Returns
true if both cursors are equal, false otherwise.

Complexity

Constant.

Exceptions

No-throw guarantee.

◆ path_label() [1/2]

template<typename index_t >
template<std::ranges::range text_t>
auto seqan3::fm_index_cursor< index_t >::path_label ( text_t &&  text) const
inlinenoexcept

Returns the searched query.

Template Parameters
text_tThe type of the text used to build the index; must model std::ranges::input_range.
Parameters
[in]textText that was used to build the index.
Returns
Searched query.

Complexity

$O(SAMPLING\_RATE * T_{BACKWARD\_SEARCH}) + query\_length()$

Exceptions

No-throw guarantee.

◆ path_label() [2/2]

template<typename index_t >
template<std::ranges::range text_t>
auto seqan3::fm_index_cursor< index_t >::path_label ( text_t &&  text) const
inlinenoexcept

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

◆ query_length()

template<typename index_t >
size_type seqan3::fm_index_cursor< index_t >::query_length ( ) const
inlinenoexcept

Returns the length of the searched query.

Returns
Length of query.

Complexity

Constant.

Exceptions

No-throw guarantee.


The documentation for this class was generated from the following file: