Index - SeqAn API Documentation

# Class Index
Indices are data structures which contain preprocessing data of a fixed text (or set of texts). In combination with a Finder or an VSTreeIterator it allows fast dictionary look-up and advanced computations.

All Subcl's | FMIndex, IndexDfi, IndexEsa, IndexQGram, IndexSa, IndexWotd, OpenAddressingQGramIndex, PizzaChiliIndex
Defined in | <seqan/index.h>
Signature | `class Index<TText[, TSpec]>;`

## Template Parameters

`TSpec` | The index type.
`TText` | The text type. Types: String, StringSet

## Interface Function Overview

- `void clear(index);`
  Resets all fibres of an index.
- `TSize countSequences(index);`
  Return the number of sequences in an index' underlying text.
- `TFibre getFibre(index, fibreTag);`
  Returns a specific fibre of a container.
- `bool indexCreate(index, fibreTag[, algoTag]);`
  Creates a specific Fibre.
- `TFibre indexRawText(position, index);`
  Shortcut for `$getFibre(.., FibreRawText)`.
- `bool indexRequire(index, fibreTag);`
  On-demand creation of a specific Fibre.
- `bool indexSupplied(index, fibreTag);`
  Returns whether a specific Fibre is present.
- `TFibre indexText(index);`
  Shortcut for `getFibre(.., EsaText)`.
- `TSize length(index);`
  Returns the number of characters in the underlying text of the index.
- `bool open(index, fileName[, mode]);`
  This functions opens an index from disk.
- `TValue rawtextAt(position, index);`
  Shortcut for `value(indexRawText(..), ..)`.
- `bool save(index, fileName[, mode]);`
  This functions saves an index to disk.

## Interface Metafunction Overview

- `DefaultIndexCreator<TIndex, TFibre>::Type;`
  Default algorithm to create a demanded and not yet existing Fibre.
- `DefaultIndexSpec<TText>::Type;`
  Default Index specialization type.
- `DefaultIndexStringSpec<TIndex>::Type;`
  Default String specialization type of the Fibre of an Index.
- `GetVSTreeIteratorTraits<TIterator>::Type`
  Default behaviour of goNext when no second parameter is given.
- `Size<TIndex>::Type;`
  Returns the size type of an Index.

## Detailed Description

An index contains various arrays or objects, also called fibres (see Fibre). These fibres are created on demand depending on the requirements of an algorithm. To force the fibre creation you can use the function indexCreate. The list of fibres is available in Fibre

### Examples

The following code shows how to search for exact matches between the reference "tobeornottobe" and the pattern "to" with the means of a Finder.

    #include <seqan/index.h>

    using namespace seqan;

    int main()
    {
        typedef Index<CharString> TIndex;

        TIndex index("tobeornottobe");
        Finder<TIndex> finder(index);

        // The Finder object has a pointer to the first, current and last hit
        // Each consecutive call sets the current pointer to the appropriate hit
        while (find(finder, "to"))
            std::cout << "Hit at position: " << position(finder) << std::endl;

        return 0;
    }

Demo: demos/dox/index/finder.cpp

The result is as follows

    Hit at position: 9
    Hit at position: 0

This code shows how an index can be used with iterators to achieve a pre-order tree like traversal in DFS of the text "tobeornottobe". In order to do so a Top-Down History iterator is used.

    #include <seqan/index.h>

    using namespace seqan;

    int main()
    {
        typedef Index<CharString> TIndex;

        TIndex index("tobeornottobe");
        Iterator<TIndex, TopDown<ParentLinks<> > >::Type it(index);

        do
        {
            // Print the letters from the root to the current node
            std::cout << representative(it) << std::endl;

            if (!goDown(it) && !goRight(it))
                while (goUp(it) && !goRight(it))
                    ;
        }
        while (!isRoot(it));

        return 0;
    }

Demo: demos/dox/index/iterator.cpp

The result is as follows

    be
    beornottobe
    e
    eornottobe
    nottobe
    o
    obe
    obeornottobe
    ornottobe
    ottobe
    rnottobe
    t
    tobe
    tobeornottobe
    ttobe

Note that you can also use specialized iterators such as:

    Iterator<TIndex, TopDown<ParentLinks<PreOrder> > >::Type

or

    Iterator<TIndex, TopDown<ParentLinks<PostOrder> > >::Type

You can achieve a post-order traversal like this:

        Iterator<TIndex, TopDown<ParentLinks<Postorder> > >::Type it(index);

        goBegin(it);
        while (!atEnd(it))
        {
            std::cout << representative(it) << std::endl;
            ++it;
        }

Snippet from: demos/dox/index/iterator_short.cpp

The result is as follows

    beornottobe
    be
    eornottobe
    e
    nottobe
    obeornottobe
    obe
    ornottobe
    ottobe
    o
    rnottobe
    tobeornottobe
    tobe
    ttobe
    t

## Interface Functions Detail

### `void clear(index);`

Resets all fibres of an index.

#### Parameters

`index` | The index to be cleared.

#### Data Races

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

### `TSize countSequences(index);`

Return the number of sequences in an index' underlying text.

#### Parameters

`index` | The index to return the number of sequences of.

#### Returns

`TSize` | The number of sequences in the index' underlying text with TSize being the result Size.

#### Examples

The following example shows how to count characters of an index, determine the number of sequences involved and how to search for a pattern.

    #include <seqan/index.h>

    using namespace seqan;

    int main()
    {
        typedef StringSet<String<char> >    TText;
        typedef Index<TText>                TIndex;

        TText text;
        appendValue(text, "MISSISSIPPI");
        appendValue(text, "MYMISSISAHAPPY");

        TIndex index(text);
        Finder<TIndex> finder(index);

        std::cout << "The text has " << length(index) << " characters and consists of " << countSequences(index) <<
        " sequences." << std::endl;

        // The Finder object has a pointer to the first, current and last hit
        // Each consecutive call sets the current pointer to the appropriate hit
        while (find(finder, "MISS"))
            std::cout << "Hit at position: " << position(finder) << std::endl;

        return 0;
    }

Demo: demos/dox/index/length_countSequences.cpp

The output is as follows:

    The text has 25 characters and consists of 2 sequences.
    Hit at position: < 1 , 2 >
    Hit at position: < 0 , 0 >

#### Data Races

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

### `TFibre getFibre(index, fibreTag);`

Returns a specific fibre of a container.

#### Parameters

`index` | The container holding the fibre.
`fibreTag` | A tag that identifies the Fibre. Types: Index Esa Fibres, FM Index Fibres, Index Wotd Fibres, and Index QGram Fibres.

#### Returns

`TFibre` | A reference to the Fibre object.

#### Examples

The following example shows how to search for a pattern in a string.

    #include <seqan/index.h>

    using namespace seqan;

    int main()
    {
        typedef StringSet<String<char> >    TText;
        typedef Index<TText>                TIndex;
        typedef SAValue<TIndex>::Type       TSAValue;

        TText text;
        appendValue(text, "MISSISSIPPI");
        appendValue(text, "MYMISSISAHAPPY");

        TIndex index(text);
        Iterator<TIndex, TopDown<> >::Type it(index);

        goDown(it, "SSI");

        std::cout << "SSI occurs in " << getFrequency(it) << " sequences." << std::endl;

        // 1 alternative to print the location of hits
        String<TSAValue> saPositions = getOccurrences(it);
        for (unsigned i = 0; i < length(saPositions); ++i)
            std::cout << "Hit in sequence " << saPositions[i].i1 << " at position " << saPositions[i].i2 << std::endl;

        std::cout << "----------------------------" << std::endl;

        // 2 alternative to print the location of hits
        Pair<unsigned> hitInterval = range(it);
        for (; hitInterval.i1 < hitInterval.i2; ++hitInterval.i1)
            std::cout << "Hit in sequence " << getFibre(index, FibreSA())[hitInterval.i1].i1 <<
            " at position " << getFibre(index, FibreSA())[hitInterval.i1].i2 << std::endl;

        return 0;
    }

Demo: demos/dox/index/getOccurrences_getFrequency_range_getFibre.cpp

The output is as follows:

    SSI occurs in 2 sequences.
    Hit in sequence 0 at position 5
    Hit in sequence 1 at position 4
    Hit in sequence 0 at position 2
    ----------------------------
    Hit in sequence 0 at position 5
    Hit in sequence 1 at position 4
    Hit in sequence 0 at position 2

#### Data Races

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

#### See Also

- Fibre

### `bool indexCreate(index, fibreTag[, algoTag]);`

Creates a specific Fibre.

#### Parameters

`fibreTag` | A tag that identifies the Fibre
`algoTag` | A tag that identifies the algorithm which is used to create the fibre. Default: The result of DefaultIndexCreator.
`index` | The Index object holding the fibre.

#### Returns

`bool` | `true` on a success and false `otherwise`

`indexCreate` calls the fibre corresponding `createXXX(..)` function (e.g. createSuffixArray).

#### Data Races

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

### `TFibre indexRawText(position, index);`

Shortcut for `$getFibre(.., FibreRawText)`.

#### Parameters

`position` | A position in the array on which the value should be accessed.
`index` | The Index object.

#### Returns

`TFibre` | A reference or proxy to the value.

#### Data Races

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

### `bool indexRequire(index, fibreTag);`

On-demand creation of a specific Fibre.

#### Parameters

`index` | The Index object holding the fibre.
`fibreTag` | A tag that identifies the Fibre

#### Returns

`bool` | `true` on a successful creation.

If the fibre already exists (indexSupplied is true) then `indexRequire` does nothing. If the fibre doesn't exist then indexCreate is called to create it.

#### Examples

The following code shows how the BWT of an text can be computed.

    #include <seqan/index.h>

    using namespace seqan;

    int main()
    {
        Index<String<char> > index("MISSISSIPPI");

        // Because indices are build on demand we force the index creation here.
        indexRequire(index, FibreSA());

        std::cout << "BWT\tSuffices" << std::endl;

        for (unsigned i = 0; i < length(indexSA(index)); ++i)
        {
            unsigned textPos = (saAt(i, index) == 0) ? length(index) - 1 : saAt(i, index) - 1;
            std::cout << textAt(textPos, index) << "\t" << suffix(indexText(index), textPos) << std::endl;
        }
        return 0;
    }

Demo: demos/dox/index/textAt_indexText_saAt_indexRequire.cpp

The output is as follows:

    BWT	Suffices
    P	PI
    S	SIPPI
    S	SISSIPPI
    M	MISSISSIPPI
    I	I
    P	PPI
    I	IPPI
    S	SSIPPI
    S	SSISSIPPI
    I	ISSIPPI
    I	ISSISSIPPI

#### Data Races

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

### `bool indexSupplied(index, fibreTag);`

Returns whether a specific Fibre is present.

#### Parameters

`index` | The Index object holding the fibre.
`fibreTag` | A tag that identifies the Fibre Index Fibres.

#### Returns

`bool` | `true`, iff the fibre is present.

#### Data Races

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

### `TFibre indexText(index);`

Note.

The result of this function when used on an `Index<TText, FMIndex<TOccSpec, CompressText> > is not defined.`

Shortcut for `getFibre(.., EsaText)`.

#### Parameters

`index` | The Index object holding the fibre.

#### Returns

`TFibre` | A reference to the text of the index.

#### Examples

The following code shows how the BWT of a text can be computed.

    #include <seqan/index.h>

    using namespace seqan;

    int main()
    {
        Index<String<char> > index("MISSISSIPPI");

        // Because indices are build on demand we force the index creation here.
        indexRequire(index, FibreSA());

        std::cout << "BWT\tSuffices" << std::endl;

        for (unsigned i = 0; i < length(indexSA(index)); ++i)
        {
            unsigned textPos = (saAt(i, index) == 0) ? length(index) - 1 : saAt(i, index) - 1;
            std::cout << textAt(textPos, index) << "\t" << suffix(indexText(index), textPos) << std::endl;
        }
        return 0;
    }

Demo: demos/dox/index/textAt_indexText_saAt_indexRequire.cpp

The output is as follows:

    BWT	Suffices
    P	PI
    S	SIPPI
    S	SISSIPPI
    M	MISSISSIPPI
    I	I
    P	PPI
    I	IPPI
    S	SSIPPI
    S	SSISSIPPI
    I	ISSIPPI
    I	ISSISSIPPI

#### Data Races

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

### `TSize length(index);`

Returns the number of characters in the underlying text of the index.

#### Parameters

`index` | An index of a text.

#### Returns

`TSize` | Returns the number of characters in the raw underlying text of the index with TSize being the result of the Size meta-function of Index.

#### Examples

The following example shows how to count characters of an index, determine the number of sequences involved and how to search for a pattern.

    #include <seqan/index.h>

    using namespace seqan;

    int main()
    {
        typedef StringSet<String<char> >    TText;
        typedef Index<TText>                TIndex;

        TText text;
        appendValue(text, "MISSISSIPPI");
        appendValue(text, "MYMISSISAHAPPY");

        TIndex index(text);
        Finder<TIndex> finder(index);

        std::cout << "The text has " << length(index) << " characters and consists of " << countSequences(index) <<
        " sequences." << std::endl;

        // The Finder object has a pointer to the first, current and last hit
        // Each consecutive call sets the current pointer to the appropriate hit
        while (find(finder, "MISS"))
            std::cout << "Hit at position: " << position(finder) << std::endl;

        return 0;
    }

Demo: demos/dox/index/length_countSequences.cpp

The output is as follows:

    The text has 25 characters and consists of 2 sequences.
    Hit at position: < 1 , 2 >
    Hit at position: < 0 , 0 >

#### Data Races

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

### `bool open(index, fileName[, mode]);`

This functions opens an index from disk.

#### Parameters

`index` | The index to be opened.
`fileName` | C-style character string containing the file name.
`mode` | The combination of flags defining how the file should be opened.To open a file read-only, write-only or to read and write use `OPEN_RDONLY`, `OPEN_WRONLY`, or `OPEN_RDWR`.To create or overwrite a file add `OPEN_CREATE`.To append a file if existing add `OPEN_APPEND`.To circumvent problems, files are always opened in binary mode. Default: `OPEN_RDWR | OPEN_CREATE | OPEN_APPEND`.

#### Returns

`bool` | `true` on success and `false` otherwise.

#### Examples

The following code shows how the function open is used with indices.

    #include <seqan/index.h>

    using namespace seqan;

    int main()
    {
        typedef StringSet<String<char> >    TText;
        typedef Index<TText>                TIndex;

        TText text;
        appendValue(text, "MISSISSIPPI");
        appendValue(text, "MYMISSISAHAPPY");

        TIndex saveIndex(text);

        // Because indices are build on demand we fore the index creation here.
        indexCreate(saveIndex, FibreSA());

        const char * tempFileName = SEQAN_TEMP_FILENAME();
        std::cout << save(saveIndex, tempFileName) << std::endl;

        // In a different program
        TIndex openIndex;
        std::cout << open(openIndex, tempFileName) << std::endl;

        // clean up tmp directory (internal function)
        // only important when running seqan unit tests
        ClassTest::_deleteTempFile(ClassTest::_stripFileName(tempFileName));

        return 0;
    }

Demo: demos/dox/index/open_save.cpp

The output is as follows:

    1
    1

#### Data Races

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

### `TValue rawtextAt(position, index);`

Note.

The result of this function when used on an Index<TText, FMIndex<TOccSpec, Compress> > is not defined.

Shortcut for `value(indexRawText(..), ..)`.

#### Parameters

`index` | The Index object. Types: Index
`position` | A position in the array on which the value should be accessed.

#### Returns

`TValue` | A reference or proxy to the value. The type is the result if the meta-function Reference.

#### Data Races

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

### `bool save(index, fileName[, mode]);`

This functions saves an index to disk.

#### Parameters

`index` | The index to be opened.
`fileName` | C-style character string containing the file name.
`mode` | The combination of flags defining how the file should be opened.To open a file read-only, write-only or to read and write use `OPEN_RDONLY`, `OPEN_WRONLY`, or `OPEN_RDWR`.To create or overwrite a file add `OPEN_CREATE`.To append a file if existing add `OPEN_APPEND`.To circumvent problems, files are always opened in binary mode. Default: `OPEN_RDWR | OPEN_CREATE | OPEN_APPEND`.

#### Returns

`bool` | `true` on success and `false` otherwise.

#### Examples

The following code shows how the function save is used with indices.

    #include <seqan/index.h>

    using namespace seqan;

    int main()
    {
        typedef StringSet<String<char> >    TText;
        typedef Index<TText>                TIndex;

        TText text;
        appendValue(text, "MISSISSIPPI");
        appendValue(text, "MYMISSISAHAPPY");

        TIndex saveIndex(text);

        // Because indices are build on demand we fore the index creation here.
        indexCreate(saveIndex, FibreSA());

        const char * tempFileName = SEQAN_TEMP_FILENAME();
        std::cout << save(saveIndex, tempFileName) << std::endl;

        // In a different program
        TIndex openIndex;
        std::cout << open(openIndex, tempFileName) << std::endl;

        // clean up tmp directory (internal function)
        // only important when running seqan unit tests
        ClassTest::_deleteTempFile(ClassTest::_stripFileName(tempFileName));

        return 0;
    }

Demo: demos/dox/index/open_save.cpp

The output is as follows:

    1
    1

#### Data Races

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

## Interface Metafunctions Detail

### `DefaultIndexCreator<TIndex, TFibre>::Type;`

Note.

Advanced functionality, not commonly used.

Default algorithm to create a demanded and not yet existing Fibre.

#### Template Parameters

`TIndex` | An Index Type.
`TFibre` | A tag specifying the fibre (e.g. EsaSA).

#### Returns

`Type` | A tag specifying the default algorithm to create the fibre with.

### `DefaultIndexSpec<TText>::Type;`

Default Index specialization type.

#### Template Parameters

`TText` | The given text type.

#### Returns

`TReturn` | Currently the return type is IndexEsa.

#### Examples

The following will define `TIndex` to be of type IndexEsa, because the default index type for String or StringSet is IndexEsa.

    typedef DefaultIndexSpec<String<Dna> >::Type TIndex;

### `DefaultIndexStringSpec<TIndex>::Type;`

Deprecated.

Deprecated in favor of StringSpec.

Default String specialization type of the Fibre of an Index.

#### Template Parameters

`TIndex` | An Index Type.

#### Returns

`TReturn` | If the underlying text is a String or a set of Strings (see StringSet) the String's spec. type is returned.

#### Remarks

Most of the Index fibres are strings. The String specialization type is chosen by this meta-function.

### `GetVSTreeIteratorTraits<TIterator>::Type`

Default behaviour of goNext when no second parameter is given.

#### Template Parameters

`TIterator` | A VSTreeIterator.

#### Returns

`TReturn` | Postorder by default and Preorder if `TIterator` is `VSTree<TopDown<ParentLinks<> > >` or `VSTree<TopDown<ParentLinks<Preorder> > >`.

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

Returns the size type of an Index.

#### Template Parameters

`TIndex` | The Index specialization.

#### Returns

`Type` | The resulting size type of the index.

#### Dox Sources

    /*!
     * @class Index
     *
     * @headerfile <seqan/index.h>
     *
     * @brief Indices are data structures which contain preprocessing data of a
     *        fixed text (or set of texts). In combination with a @link Finder
     *        @endlink or an @link VSTreeIterator @endlink it allows fast dictionary
     *        look-up and advanced computations.
     *
     * @signature class Index<TText[, TSpec]>;
     *
     * @tparam TSpec The index type.
     * @tparam TText The text type. Types: @link String @endlink, @link StringSet
     *               @endlink
     *
     * An index contains various arrays or objects, also called fibres (see @link
     * Fibre @endlink). These fibres are created on demand depending on the
     * requirements of an algorithm. To force the fibre creation you can use the
     * function @link Index#indexCreate @endlink. The list of fibres is available in
     * @link Fibre @endlink
     *
     * @section Examples
     *
     * The following code shows how to search for exact matches between the
     * reference "tobeornottobe" and the pattern "to" with the means of a Finder.
     *
     * @include demos/dox/index/finder.cpp
     *
     * The result is as follows
     *
     * @include demos/dox/index/finder.cpp.stdout
     *
     * This code shows how an index can be used with iterators to achieve a pre-
     * order tree like traversal in DFS of the text "tobeornottobe". In order to do
     * so a Top-Down History iterator is used.
     *
     * @include demos/dox/index/iterator.cpp
     *
     * The result is as follows
     *
     * @include demos/dox/index/iterator.cpp.stdout
     *
     * Note that you can also use specialized iterators such as:
     *
     * @code{.cpp}
     * Iterator<TIndex, TopDown<ParentLinks<PreOrder> > >::Type
     * @endcode
     *
     *
     * or
     *
     * @code{.cpp}
     * Iterator<TIndex, TopDown<ParentLinks<PostOrder> > >::Type
     * @endcode
     *
     *
     * You can achieve a post-order traversal like this:
     *
     * @snippet demos/dox/index/iterator_short.cpp iteration
     *
     * The result is as follows
     *
     * @include demos/dox/index/iterator_short.cpp.stdout
     *
     *
     *
     * @mfn Index#GetVSTreeIteratorTraits
     *
     * @headerfile <seqan/index.h>
     *
     * @brief Default behaviour of @link InputIteratorConcept#goNext @endlink when
     *        no second parameter is given.
     *
     * @signature GetVSTreeIteratorTraits<TIterator>::Type
     *
     * @tparam TIterator A @link VSTreeIterator @endlink.
     *
     * @return TReturn @link DfsOrder#Postorder @endlink by default and @link
     *                 DfsOrder#Preorder @endlink if <tt>TIterator</tt> is
     *                 <tt>VSTree&lt;TopDown&lt;ParentLinks&lt;&gt; &gt; &gt;</tt>
     *                 or <tt>VSTree&lt;TopDown&lt;ParentLinks&lt;Preorder&gt; &gt;
     *                 &gt;</tt>.
     *
     * @mfn Index#DefaultIndexSpec
     *
     * @headerfile <seqan/index.h>
     *
     * @brief Default @link Index @endlink specialization type.
     *
     * @signature DefaultIndexSpec<TText>::Type;
     *
     * @tparam TText The given text type.
     *
     * @return TReturn Currently the return type is @link IndexEsa @endlink.
     *
     * @section Examples
     *
     * The following will define <tt>TIndex</tt> to be of type @link IndexEsa
     * @endlink, because the default index type for @link String @endlink or @link
     * StringSet @endlink is @link IndexEsa @endlink.
     *
     * @code{.cpp}
     * typedef DefaultIndexSpec<String<Dna> >::Type TIndex;
     * @endcode
     *
     *
     * @mfn Index#DefaultIndexStringSpec
     *
     * @headerfile <seqan/index.h>
     *
     * @brief Default @link String @endlink specialization type of the @link Fibre
     *        @endlink of an @link Index @endlink.
     *
     * @deprecated Deprecated in favor of StringSpec.
     *
     * @signature DefaultIndexStringSpec<TIndex>::Type;
     *
     * @tparam TIndex An @link Index @endlink Type.
     *
     * @return TReturn If the underlying text is a @link String @endlink or a set of
     *                 Strings (see @link StringSet @endlink) the String's spec.
     *                 type is returned.
     *
     * @section Remarks
     *
     * Most of the @link Index @endlink fibres are strings. The @link String
     * @endlink specialization type is chosen by this meta-function.
     *
     * @mfn Index#DefaultIndexCreator
     *
     * @headerfile <seqan/index.h>
     *
     * @brief Default algorithm to create a demanded and not yet existing @link
     *        Fibre @endlink.
     *
     * @note Advanced functionality, not commonly used.
     *
     * @signature DefaultIndexCreator<TIndex, TFibre>::Type;
     *
     * @tparam TIndex An @link Index @endlink Type.
     * @tparam TFibre A tag specifying the fibre (e.g. @link IndexEsaFibres#EsaSA
     *                @endlink).
     *
     * @return Type A tag specifying the default algorithm to create the fibre with.
     *
     * @mfn Index#Size
     *
     * @headerfile <seqan/index.h>
     *
     * @brief Returns the size type of an Index.
     *
     * @signature Size<TIndex>::Type;
     *
     * @tparam TIndex The Index specialization.
     *
     * @return Type The resulting size type of the index.
     *
     * @fn Index#clear
     *
     * @brief Resets all fibres of an index.
     *
     * @signature void clear(index);
     *
     * @param[in,out] index The index to be cleared.
     *
     * @fn Index#getFibre
     *
     * @headerfile <seqan/index.h>
     *
     * @brief Returns a specific fibre of a container.
     *
     * @signature TFibre getFibre(index, fibreTag);
     *
     * @param[in] index The container holding the fibre.
     * @param[in] fibreTag A tag that identifies the @link Fibre @endlink. Types:
     *                     @link IndexEsaFibres Index Esa Fibres @endlink, @link
     *                     FMIndexFibres FM Index Fibres @endlink, @link
     *                     WOTDIndexFibres Index Wotd Fibres @endlink, and @link
     *                     QGramIndexFibres Index QGram Fibres @endlink.
     *
     * @return TFibre A reference to the @link Fibre @endlink object.
     *
     * @section Examples
     *
     * The following example shows how to search for a pattern in a string.
     *
     * @include demos/dox/index/getOccurrences_getFrequency_range_getFibre.cpp
     *
     * The output is as follows:
     *
     * @include demos/dox/index/getOccurrences_getFrequency_range_getFibre.cpp.stdout
     *
     * @see Fibre
     *
     * @fn Index#length
     *
     * @headerfile <seqan/index.h>
     *
     * @brief Returns the number of characters in the underlying text of the index.
     *
     * @signature TSize length(index);
     *
     * @param[in] index An index of a text.
     *
     * @return TSize Returns the number of characters in the raw underlying text of
     *               the index with TSize being the result of the @link Size
     *               @endlink meta-function of @link Index @endlink.
     *
     * @section Examples
     *
     * The following example shows how to count characters of an index, determine
     * the number of sequences involved and how to search for a pattern.
     *
     * @include demos/dox/index/length_countSequences.cpp
     *
     * The output is as follows:
     *
     * @include demos/dox/index/length_countSequences.cpp.stdout
     *
     *
     *
     * @fn Index#countSequences
     *
     * @headerfile <seqan/index.h>
     *
     * @brief Return the number of sequences in an index' underlying text.
     *
     * @signature TSize countSequences(index);
     *
     * @param[in] index The index to return the number of sequences of.
     *
     * @return TSize The number of sequences in the index' underlying text with
     *               TSize being the result @link Size @endlink.
     *
     * @section Examples
     *
     * The following example shows how to count characters of an index, determine
     * the number of sequences involved and how to search for a pattern.
     *
     * @include demos/dox/index/length_countSequences.cpp
     *
     * The output is as follows:
     *
     * @code{.output}
     * The text has 25 characters and consists of 2 sequences.
     * Hit at position: < 1 , 2 >
     * Hit at position: < 0 , 0 >
     * @endcode
     *
     *
     * @fn Index#rawtextAt
     *
     * @headerfile <seqan/index.h>
     *
     * @brief Shortcut for <tt>value(indexRawText(..), ..)</tt>.
     *
     * @note The result of this function when used on an Index&lt;TText,
     *       FMIndex&lt;TOccSpec, Compress&gt; &gt; is not defined.
     *
     * @signature TValue rawtextAt(position, index);
     *
     * @param[in] index The @link Index @endlink object. Types: @link Index @endlink
     * @param[in] position A position in the array on which the value should be
     *                     accessed.
     *
     * @return TValue A reference or proxy to the value. The type is the result if
     *                the meta-function @link Reference @endlink.
     *
     * @fn Index#indexText
     *
     * @headerfile <seqan/index.h>
     *
     * @brief Shortcut for <tt>getFibre(.., EsaText)</tt>.
     *
     * @note The result of this function when used on an <tt>Index&lt;TText,
     *       FMIndex&lt;TOccSpec, CompressText&gt; &gt; is not defined.
     *
     * @signature TFibre indexText(index);
     *
     * @param[in] index The @link Index @endlink object holding the fibre.
     *
     * @return TFibre A reference to the text of the index.
     *
     * @section Examples
     *
     * The following code shows how the BWT of a text can be computed.
     *
     * @include demos/dox/index/textAt_indexText_saAt_indexRequire.cpp
     *
     * The output is as follows:
     *
     * @include demos/dox/index/textAt_indexText_saAt_indexRequire.cpp.stdout
     *
     *
     *
     * @fn Index#indexRawText
     *
     * @headerfile <seqan/index.h>
     *
     * @brief Shortcut for <tt>$getFibre(.., FibreRawText)</tt>.
     *
     * @signature TFibre indexRawText(position, index);
     *
     * @param[in] position A position in the array on which the value should be
     *                     accessed.
     * @param[in] index The @link Index @endlink object.
     *
     * @return TFibre A reference or proxy to the value.
     *
     * @fn Index#open
     *
     * @headerfile <seqan/index.h>
     *
     * @brief This functions opens an index from disk.
     *
     * @signature bool open(index, fileName[, mode]);
     *
     * @param[in,out] index The index to be opened.
     * @param[in] fileName C-style character string containing the file name.
     * @param[in] mode The combination of flags defining how the file should be
     *                 opened.To open a file read-only, write-only or to read and
     *                 write use <tt>OPEN_RDONLY</tt>, <tt>OPEN_WRONLY</tt>, or
     *                 <tt>OPEN_RDWR</tt>.To create or overwrite a file add
     *                 <tt>OPEN_CREATE</tt>.To append a file if existing add
     *                 <tt>OPEN_APPEND</tt>.To circumvent problems, files are always
     *                 opened in binary mode. Default: <tt>OPEN_RDWR | OPEN_CREATE |
     *                 OPEN_APPEND</tt>.
     *
     * @return bool <tt>true</tt> on success and <tt>false</tt> otherwise.
     *
     * @section Examples
     *
     * The following code shows how the function @link Index#open @endlink is used
     * with indices.
     *
     * @include demos/dox/index/open_save.cpp
     *
     * The output is as follows:
     *
     * @include demos/dox/index/open_save.cpp.stdout
     *
     *
     *
     * @fn Index#save
     *
     * @headerfile <seqan/index.h>
     *
     * @brief This functions saves an index to disk.
     *
     * @signature bool save(index, fileName[, mode]);
     *
     * @param[in,out] index The index to be opened.
     * @param[in] fileName C-style character string containing the file name.
     * @param[in] mode The combination of flags defining how the file should be
     *                 opened.To open a file read-only, write-only or to read and
     *                 write use <tt>OPEN_RDONLY</tt>, <tt>OPEN_WRONLY</tt>, or
     *                 <tt>OPEN_RDWR</tt>.To create or overwrite a file add
     *                 <tt>OPEN_CREATE</tt>.To append a file if existing add
     *                 <tt>OPEN_APPEND</tt>.To circumvent problems, files are always
     *                 opened in binary mode. Default: <tt>OPEN_RDWR | OPEN_CREATE |
     *                 OPEN_APPEND</tt>.
     *
     * @return bool <tt>true</tt> on success and <tt>false</tt> otherwise.
     *
     * @section Examples
     *
     * The following code shows how the function @link Index#save @endlink is used
     * with indices.
     *
     * @include demos/dox/index/open_save.cpp
     *
     * The output is as follows:
     *
     * @include demos/dox/index/open_save.cpp.stdout
     *
     *
     *
     * @fn Index#indexCreate
     *
     * @headerfile <seqan/index.h>
     *
     * @brief Creates a specific @link Fibre @endlink.
     *
     * @signature bool indexCreate(index, fibreTag[, algoTag]);
     *
     * @param[in] fibreTag A tag that identifies the @link Fibre @endlink
     * @param[in] algoTag A tag that identifies the algorithm which is used to
     *                    create the fibre. Default: The result of @link
     *                    Index#DefaultIndexCreator @endlink.
     * @param[in,out] index The @link Index @endlink object holding the fibre.
     *
     * @return bool <tt>true</tt> on a success and false <tt>otherwise</tt>
     *
     * <tt>indexCreate</tt> calls the fibre corresponding <tt>createXXX(..)</tt>
     * function (e.g. @link createSuffixArray @endlink).
     *
     * @fn Index#indexSupplied
     *
     * @headerfile <seqan/index.h>
     *
     * @brief Returns whether a specific @link Fibre @endlink is present.
     *
     * @signature bool indexSupplied(index, fibreTag);
     *
     * @param[in] index The @link Index @endlink object holding the fibre.
     * @param[in] fibreTag A tag that identifies the @link Fibre @endlink Index
     *                     Fibres.
     *
     * @return bool <tt>true</tt>, iff the fibre is present.
     *
     * @fn Index#indexRequire
     *
     * @headerfile <seqan/index.h>
     *
     * @brief On-demand creation of a specific @link Fibre @endlink.
     *
     * @signature bool indexRequire(index, fibreTag);
     *
     * @param[in,out] index The @link Index @endlink object holding the fibre.
     * @param[in] fibreTag A tag that identifies the @link Fibre @endlink
     *
     * @return bool <tt>true</tt> on a successful creation.
     *
     * If the fibre already exists (@link Index#indexSupplied @endlink is true) then
     * <tt>indexRequire</tt> does nothing. If the fibre doesn't exist then @link
     * Index#indexCreate @endlink is called to create it.
     *
     * @section Examples
     *
     * The following code shows how the BWT of an text can be computed.
     *
     * @include demos/dox/index/textAt_indexText_saAt_indexRequire.cpp
     *
     * The output is as follows:
     *
     * @include demos/dox/index/textAt_indexText_saAt_indexRequire.cpp.stdout
     */