StringEnumerator - SeqAn API Documentation

# Class StringEnumerator
Class to enumerate all strings within a given edit/Hamming distance.

All Subcl's | HammingStringEnumerator, LevenshteinStringEnumerator
Defined in | <seqan/misc/edit_environment.h>
Signature | `template <typename TString, typename TSpec> class StringEnumerator<TString, TSpec>;`

## Template Parameters

`TString` | Type of the string to enumerate the environment of.
`TSpec` | Specialization tag.

## Member Function Overview

- `StringEnumerator::StringEnumerator(string[, minDist]);`
  Constructor

## Interface Function Overview

- `TIter begin(stringEnum[, tag]);`
  Return begin iterator.
- `TIter end(stringEnum[, tag]);`
  Return end iterator.
- `TSize length(stringEnum);`
  Return number of strings that will be enumerated.

## Interface Metafunction Overview

- `Difference<TStringEnumerator>::Type;`
  Returns difference type.
- `Host<TStringEnumerator>::Type;`
  Returns host type.
- `Position<TStringEnumerator, TSpec>::Type;`
  Returns iterator type.
- `Position<TStringEnumerator>::Type;`
  Returns position type.
- `Reference<TStringEnumerator>::Type;`
  Returns reference type of the enumerated strings.
- `Size<TStringEnumerator>::Type;`
  Returns size type.
- `Value<TStringEnumerator>::Type;`
  Return value type of the string to enumerate.

## Member Variable Overview

- `bool StringEnumerator::trim`
  Indicate whether to ignore substitutions in first or last character of string in Levenshtein mode (optimization for approximate search).

## Member Functions Detail

### `StringEnumerator::StringEnumerator(string[, minDist]);`

Constructor

#### Parameters

`string` | The string to use as the center. Types: `TString`.
`minDist` | The smallest distance to generate strings with. Type: `unsigned`. Default: 0

#### Data Races

If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.

## Interface Functions Detail

### `TIter begin(stringEnum[, tag]);`

Return begin iterator.

#### Parameters

`stringEnum` | StringEnumerator to query.
`tag` | Iterator tag to use.

#### Returns

`TIter` | Iterator to the first string in the enumerator.

#### Data Races

If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.

### `TIter end(stringEnum[, tag]);`

Return end iterator.

#### Parameters

`stringEnum` | StringEnumerator to query.
`tag` | Iterator tag to use.

#### Returns

`TIter` | End iterator for the string enumerator.

#### Data Races

If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.

### `TSize length(stringEnum);`

Return number of strings that will be enumerated.

#### Parameters

`stringEnum` | StringEnumerator to query.

#### Returns

`TSize` | The number of elements in the enumerator (Metafunction: Size).

#### Data Races

If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.

## Interface Metafunctions Detail

### `Difference<TStringEnumerator>::Type;`

Returns difference type.

### `Host<TStringEnumerator>::Type;`

Returns host type.

### `Position<TStringEnumerator, TSpec>::Type;`

Returns iterator type.

### `Position<TStringEnumerator>::Type;`

Returns position type.

### `Reference<TStringEnumerator>::Type;`

Returns reference type of the enumerated strings.

### `Size<TStringEnumerator>::Type;`

Returns size type.

### `Value<TStringEnumerator>::Type;`

Return value type of the string to enumerate.

## Member Variables Detail

### `bool StringEnumerator::trim`

Indicate whether to ignore substitutions in first or last character of string in Levenshtein mode (optimization for approximate search).

This is useful when searching for such enumerated strings in large texts. Patterns with substitutions in the first base would also be found.

#### Examples

    #include <iostream>

    #include <seqan/basic.h>
    #include <seqan/sequence.h>
    #include <seqan/stream.h>      // For printing SeqAn Strings.
    #include <seqan/misc/edit_environment.h>

    using namespace seqan;

    int main()
    {
        Dna5String original = "CGAT";

        // Enumerate neighbourhood using Hamming distance.
        typedef StringEnumerator<Dna5String, EditEnvironment<HammingDistance, 2> > THammingEnumerator;
        typedef Iterator<THammingEnumerator>::Type THammingIterator;
        std::cout << "Enumerating Hamming distance environment of " << original << " of distance 2\n";
        THammingEnumerator hammingEnumerator(original);
        for (THammingIterator itH = begin(hammingEnumerator); !atEnd(itH); goNext(itH))
            std::cout << *itH << '\n';

        // Enumerate neighbourhood using edit distance.
        typedef StringEnumerator<Dna5String, EditEnvironment<LevenshteinDistance, 2> > TEditEnumerator;
        typedef Iterator<TEditEnumerator>::Type TEditIterator;
        std::cout << "\nEnumerating edit distance environment of " << original << " of distance 1-2\n";
        TEditEnumerator editEnumerator(original);
        for (TEditIterator itE = begin(editEnumerator); !atEnd(itE); goNext(itE))
            std::cout << *itE << '\n';

        return 0;
    }

Demo: demos/dox/misc/enumerate_strings.cpp

    Enumerating Hamming distance environment of CGAT of distance 2
    AGAT
    CGAT
    GGAT
    TGAT
    NGAT
    CAAT
    CCAT
    CTAT
    CNAT
    CGCT
    CGGT
    CGTT
    CGNT
    CGAA
    CGAC
    CGAG
    CGAN
    AAAT
    ACAT
    ATAT
    ANAT
    GAAT
    GCAT
    GTAT
    GNAT
    TAAT
    TCAT
    TTAT
    TNAT
    NAAT
    NCAT
    NTAT
    NNAT
    AGCT
    AGGT
    AGTT
    AGNT
    GGCT
    GGGT
    GGTT
    GGNT
    TGCT
    TGGT
    TGTT
    TGNT
    NGCT
    NGGT
    NGTT
    NGNT
    AGAA
    AGAC
    AGAG
    AGAN
    GGAA
    GGAC
    GGAG
    GGAN
    TGAA
    TGAC
    TGAG
    TGAN
    NGAA
    NGAC
    NGAG
    NGAN
    CACT
    CAGT
    CATT
    CANT
    CCCT
    CCGT
    CCTT
    CCNT
    CTCT
    CTGT
    CTTT
    CTNT
    CNCT
    CNGT
    CNTT
    CNNT
    CAAA
    CAAC
    CAAG
    CAAN
    CCAA
    CCAC
    CCAG
    CCAN
    CTAA
    CTAC
    CTAG
    CTAN
    CNAA
    CNAC
    CNAG
    CNAN
    CGCA
    CGCC
    CGCG
    CGCN
    CGGA
    CGGC
    CGGG
    CGGN
    CGTA
    CGTC
    CGTG
    CGTN
    CGNA
    CGNC
    CGNG
    CGNN

    Enumerating edit distance environment of CGAT of distance 1-2
    CGAT
    CAAT
    CCAT
    CTAT
    CNAT
    CGCT
    CGGT
    CGTT
    CGNT
    GAT
    CAT
    CGT
    CGA
    CAGAT
    CCGAT
    CGGAT
    CTGAT
    CNGAT
    CGAAT
    CGCAT
    CGGAT
    CGTAT
    CGNAT
    CGAAT
    CGACT
    CGAGT
    CGATT
    CGANT
    CACT
    CAGT
    CATT
    CANT
    CCCT
    CCGT
    CCTT
    CCNT
    CTCT
    CTGT
    CTTT
    CTNT
    CNCT
    CNGT
    CNTT
    CNNT
    CAT
    CCT
    CTT
    CNT
    CAA
    CCA
    CTA
    CNA
    CGC
    CGG
    CGT
    CGN
    CAAAT
    CACAT
    CAGAT
    CATAT
    CANAT
    CCAAT
    CCCAT
    CCGAT
    CCTAT
    CCNAT
    CTAAT
    CTCAT
    CTGAT
    CTTAT
    CTNAT
    CNAAT
    CNCAT
    CNGAT
    CNTAT
    CNNAT
    CAAAT
    CAACT
    CAAGT
    CAATT
    CAANT
    CCAAT
    CCACT
    CCAGT
    CCATT
    CCANT
    CTAAT
    CTACT
    CTAGT
    CTATT
    CTANT
    CNAAT
    CNACT
    CNAGT
    CNATT
    CNANT
    CGCAT
    CGCCT
    CGCGT
    CGCTT
    CGCNT
    CGGAT
    CGGCT
    CGGGT
    CGGTT
    CGGNT
    CGTAT
    CGTCT
    CGTGT
    CGTTT
    CGTNT
    CGNAT
    CGNCT
    CGNGT
    CGNTT
    CGNNT
    GCT
    GGT
    GTT
    GNT
    AT
    GT
    GA
    CT
    CA
    CG
    GAAT
    GCAT
    GGAT
    GTAT
    GNAT
    GAAT
    GACT
    GAGT
    GATT
    GANT
    CAAT
    CACT
    CAGT
    CATT
    CANT
    CAGCT
    CAGGT
    CAGTT
    CAGNT
    CCGCT
    CCGGT
    CCGTT
    CCGNT
    CGGCT
    CGGGT
    CGGTT
    CGGNT
    CTGCT
    CTGGT
    CTGTT
    CTGNT
    CNGCT
    CNGGT
    CNGTT
    CNGNT
    CAGT
    CCGT
    CGGT
    CTGT
    CNGT
    CAGA
    CCGA
    CGGA
    CTGA
    CNGA
    CGAA
    CGCA
    CGGA
    CGTA
    CGNA
    CAAGAT
    CACGAT
    CAGGAT
    CATGAT
    CANGAT
    CCAGAT
    CCCGAT
    CCGGAT
    CCTGAT
    CCNGAT
    CGAGAT
    CGCGAT
    CGGGAT
    CGTGAT
    CGNGAT
    CTAGAT
    CTCGAT
    CTGGAT
    CTTGAT
    CTNGAT
    CNAGAT
    CNCGAT
    CNGGAT
    CNTGAT
    CNNGAT
    CAGAAT
    CAGCAT
    CAGGAT
    CAGTAT
    CAGNAT
    CCGAAT
    CCGCAT
    CCGGAT
    CCGTAT
    CCGNAT
    CGGAAT
    CGGCAT
    CGGGAT
    CGGTAT
    CGGNAT
    CTGAAT
    CTGCAT
    CTGGAT
    CTGTAT
    CTGNAT
    CNGAAT
    CNGCAT
    CNGGAT
    CNGTAT
    CNGNAT
    CAGAAT
    CAGACT
    CAGAGT
    CAGATT
    CAGANT
    CCGAAT
    CCGACT
    CCGAGT
    CCGATT
    CCGANT
    CGGAAT
    CGGACT
    CGGAGT
    CGGATT
    CGGANT
    CTGAAT
    CTGACT
    CTGAGT
    CTGATT
    CTGANT
    CNGAAT
    CNGACT
    CNGAGT
    CNGATT
    CNGANT
    CGAAAT
    CGACAT
    CGAGAT
    CGATAT
    CGANAT
    CGCAAT
    CGCCAT
    CGCGAT
    CGCTAT
    CGCNAT
    CGGAAT
    CGGCAT
    CGGGAT
    CGGTAT
    CGGNAT
    CGTAAT
    CGTCAT
    CGTGAT
    CGTTAT
    CGTNAT
    CGNAAT
    CGNCAT
    CGNGAT
    CGNTAT
    CGNNAT
    CGAAAT
    CGAACT
    CGAAGT
    CGAATT
    CGAANT
    CGCAAT
    CGCACT
    CGCAGT
    CGCATT
    CGCANT
    CGGAAT
    CGGACT
    CGGAGT
    CGGATT
    CGGANT
    CGTAAT
    CGTACT
    CGTAGT
    CGTATT
    CGTANT
    CGNAAT
    CGNACT
    CGNAGT
    CGNATT
    CGNANT
    CGAAAT
    CGAACT
    CGAAGT
    CGAATT
    CGAANT
    CGACAT
    CGACCT
    CGACGT
    CGACTT
    CGACNT
    CGAGAT
    CGAGCT
    CGAGGT
    CGAGTT
    CGAGNT
    CGATAT
    CGATCT
    CGATGT
    CGATTT
    CGATNT
    CGANAT
    CGANCT
    CGANGT
    CGANTT
    CGANNT

#### Dox Sources

    /*!
     * @class StringEnumerator
     *
     * @headerfile <seqan/misc/edit_environment.h>
     *
     * @brief Class to enumerate all strings within a given edit/Hamming distance.
     *
     * @signature template <typename TString, typename TSpec> class
     *            StringEnumerator<TString, TSpec>;
     *
     * @tparam TString Type of the string to enumerate the environment of.
     * @tparam TSpec Specialization tag.
     *
     * @mfn StringEnumerator#Value
     *
     * @brief Return value type of the string to enumerate.
     *
     * @signature Value<TStringEnumerator>::Type;
     *
     * @mfn StringEnumerator#Reference
     *
     * @brief Returns reference type of the enumerated strings.
     *
     * @signature Reference<TStringEnumerator>::Type;
     *
     * @mfn StringEnumerator#Size
     *
     * @brief Returns size type.
     *
     * @signature Size<TStringEnumerator>::Type;
     *
     * @mfn StringEnumerator#Difference
     *
     * @brief Returns difference type.
     *
     * @signature Difference<TStringEnumerator>::Type;
     *
     * @mfn StringEnumerator#Position
     *
     * @brief Returns position type.
     *
     * @signature Position<TStringEnumerator>::Type;
     *
     * @mfn StringEnumerator#Iterator
     *
     * @brief Returns iterator type.
     *
     * @signature Position<TStringEnumerator, TSpec>::Type;
     *
     * @mfn StringEnumerator#Host
     *
     * @brief Returns host type.
     *
     * @signature Host<TStringEnumerator>::Type;
     *
     * @fn StringEnumerator::StringEnumerator
     *
     * @brief Constructor
     *
     * @signature StringEnumerator::StringEnumerator(string[, minDist]);
     *
     * @param[in] string The string to use as the center. Types: <tt>TString</tt>.
     * @param[in] minDist The smallest distance to generate strings with. Type:
     *                    <tt>unsigned</tt>. Default: 0
     *
     * @var bool StringEnumerator::trim;
     *
     * @brief Indicate whether to ignore substitutions in first or last character of
     *        string in Levenshtein mode (optimization for approximate search).
     *
     * This is useful when searching for such enumerated strings in large texts.
     * Patterns with substitutions in the first base would also be found.
     *
     * @section Examples
     *
     * @include demos/dox/misc/enumerate_strings.cpp
     *
     * @include demos/dox/misc/enumerate_strings.cpp.stdout
     *
     *
     *
     * @fn StringEnumerator#begin
     *
     * @brief Return begin iterator.
     *
     * @signature TIter begin(stringEnum[, tag]);
     *
     * @param[in] stringEnum StringEnumerator to query.
     * @param[in] tag Iterator tag to use.
     *
     * @return TIter Iterator to the first string in the enumerator.
     *
     * @fn StringEnumerator#end
     *
     * @brief Return end iterator.
     *
     * @signature TIter end(stringEnum[, tag]);
     *
     * @param[in] stringEnum StringEnumerator to query.
     * @param[in] tag Iterator tag to use.
     *
     * @return TIter End iterator for the string enumerator.
     *
     * @fn StringEnumerator#length
     *
     * @brief Return number of strings that will be enumerated.
     *
     * @signature TSize length(stringEnum);
     *
     * @param[in] stringEnum StringEnumerator to query.
     *
     * @return TSize The number of elements in the enumerator (Metafunction: @link
     *               StringEnumerator#Size @endlink).
     */