VSTree Iterator - SeqAn API Documentation

# Spec VSTree Iterator
Abstract iterator for string trees, where string trees are trees constructed from a string.

Extends | Iter
All Extended | Iter
All Subcl's | BottomUpIterator, MaxRepeatsIterator, MultiMemsIterator, MumsIterator, SuperMaxRepeatsFastIterator, SuperMaxRepeatsIterator, TopDownHistoryIterator, TopDownIterator
All Impl'd | IteratorAssociatedTypesConcept
Defined in | <seqan/index.h>
Signature | `template <typename TContainer, typename TSpec> class Iter<TContainer, VSTree<TSpec> >;`

## Template Parameters

`TSpec` | The specialization type.
`TContainer` | Type of the container that can be iterated. Types: IndexDfi, IndexEsa, IndexWotd, FMIndex

## Member Function Overview

### Member Functions Inherited From Iter

- `Iter`

## Interface Function Overview

- `TAlign alignment(iterator);`
  Returns an alignment of the occurrences of the representative substring in the index text.
- `void assignProperty(pm, value(iterator), val)`
  Assigns a property to an item in the property map.
- `bool atEnd(iterator);`
  Determines whether an virtual string tree iterator is at the end position.
- `bool childrenAreLeaves(iterator);`
  Test whether iterator points to a node with only leaf-children.
- `TSize countChildren(iterator);`
  Count the number of children of a tree node.
- `TSize countOccurrences(iterator);`
  Returns the number of occurrences of representative substring in the index text.
- `int getFrequency(iterator);`
  Returns the number of sequences, which contain the representative as a substring.
- `TSAValue getOccurrence(iterator);`
  Returns an occurrence of the representative substring in the index text.
- `TInfix getOccurrences(iterator);`
  Returns all occurrences of the representative substring in the index text.
- `TReturn getOccurrencesBwt(iterator);`
  Returns the characters left beside all occurrence of the representative substring in the index text.
- `TValue getProperty(pm, value(iterator))`
  Get method for an item's property.
- `void goBegin(iterator);`
  Iterates to the first position of a container.
- `void goNext(it);`
  Go to next tree node.
- `void goRoot(iterator);`
  Move iterator to the root node.
- `bool isLeaf(iterator);`
  Test whether a tree iterator points to a leaf.
- `bool isLeftMaximal(iterator);`
  Test whether the occurrences of an iterator's representative mutually differ in the character left of the hits.
- `bool isPartiallyLeftExtensible(iterator);`
  Test whether the characters left of the two occurrences of representative are equal.
- `bool isRightTerminal(iterator);`
  Test whether iterator points to a suffix.
- `bool isRoot(iterator);`
  Test whether a tree iterator points to the root node.
- `bool isUnique(iterator);`
  Test whether the representative occurs only once in every sequence.
- `bool nodeHullPredicate(iterator);`
  If `false` this node and its subtree is concealed.
- `bool nodePredicate(iterator);`
  If `false` this node will be skipped during the bottom-up traversal.
- `TRef property(pm, value(iterator))`
  Accesses the property of an item in the property map.
- `TPair range(iterator);`
  Returns the suffix array interval borders of occurrences of representative substring in the index text.
- `TSize repLength(iterator);`
  Returns the length of the substring representing the path from root to `iterator` node.
- `TInfix representative(iterator);`
  Returns a substring representing the path from root to `iterator` node.
- `TDesc value(iterator);`
  Returns a vertex descriptor of the current node.

### Interface Functions Inherited From IteratorAssociatedTypesConcept

- `operator*`
- `value`
- `getValue`

## Interface Metafunction Overview

- `EdgeLabel<TSpec>::Type;`
  Type of a string representing the characters of edges.

### Interface Metafunctions Inherited From Iter

- `Container`
- `IterComplementConst`
- `IterMakeConst`
- `Spec`

### Interface Metafunctions Inherited From IteratorAssociatedTypesConcept

- `Difference`
- `GetValue`
- `Pointer`
- `Reference`
- `Value`

## Detailed Description

This iterator is a pointer to a node in the string tree of a given text. Depending on the index this can either be a suffix or prefix tree/trie. Every node can uniquely be mapped to an interval of suffices or prefixes.

Default virtual string tree iterators depending on the Index

IndexSa | Virtual suffix trie iterator
IndexEsa | Virtual suffix tree iterator
IndexWotd | Virtual suffix tree iterator
IndexDfi | Virtual suffix tree iterator
FMIndex | Virtual prefix trie iterator

### Examples

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 seqan2;

    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

## Interface Functions Detail

### `TAlign alignment(iterator);`

Note.

Internal function.

Returns an alignment of the occurrences of the representative substring in the index text.

#### Parameters

`iterator` | An iterator of a string tree.

#### Returns

`TAlign` | A local alignment corresponding to the seed of the `iterator`.``

The function representative must uniquely occur in every sequence (e.g. in Mums), otherwise the seed returned is one many. The return type is a Align object.

#### Data Races

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

### `void assignProperty(pm, value(iterator), val)`

Assigns a property to an item in the property map.

#### Parameters

`pm` | An PropertyMapConcept.
`iterator` | An iterator of a string tree. Types: VSTreeIterator
`val` | The new value, where the type of the new value must match the value type of the property map.

#### Data Races

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

### `bool atEnd(iterator);`

Determines whether an virtual string tree iterator is at the end position.

#### Parameters

`iterator` | An iterator.

#### Returns

`bool` | `true` if `iterator` points behind the last item of the container, otherwise `false`.

#### Examples

The following example shows the usage of the atEnd function.

    #include <seqan/index.h>

    using namespace seqan2;

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

        Iterator<TIndex, TopDown<ParentLinks<> > >::Type itDefault;
        itDefault = begin(index, TopDown<ParentLinks<> >());

        while (!atEnd(itDefault))
        {
            std::cout << representative(itDefault) << std::endl;
            goNext(itDefault);
        }

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

        Iterator<TIndex, TopDown<ParentLinks<Postorder> > >::Type itPostOrder;
        itPostOrder = begin(index, TopDown<ParentLinks<Postorder> >());

        while (!atEnd(itPostOrder))
        {
            std::cout << representative(itPostOrder) << std::endl;
            goNext(itPostOrder);
        }

        return 0;
    }

Demo: demos/dox/index/begin_atEnd_representative.cpp

#### Data Races

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

### `bool childrenAreLeaves(iterator);`

Test whether iterator points to a node with only leaf-children.

#### Parameters

`iterator` | An iterator of a suffix tree.

#### Returns

`bool` | `true` if `iterator` points to an inner node of the tree, whose children are leaves. Otherwise it is `false`.

#### Data Races

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

### `TSize countChildren(iterator);`

Count the number of children of a tree node.

#### Parameters

`iterator` | An iterator of a string tree.

#### Returns

`TSize` | The number of children of a tree node. The type is the result of Size of the index type of the iterator.

#### Examples

    // this code is in seqan/index/index_esa_stree.h

     typedef Index< String<char> > TMyIndex;
     TMyIndex myIndex(myString);

     Iterator< TMyIndex, TopDown<ParentLinks<PreorderEmptyEdges> > >::Type tdIterator(myIndex);
     Size<TMyIndex>::Type count;

     while (!atEnd(tdIterator)) {
     // We print out the representatives of all nodes that have more than 3 children and the number of occurrences.
     count = countChildren(tdIterator);
     if (count >= 3)
     {
         std::cout << "Representative " << representative(tdIterator) << " has " <<  count << " children  and " << countOccurrences(tdIterator) << " Occurrences " << std::endl;

         ++tdIterator;
     }

DemoIndexCountChildren

#### Data Races

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

### `TSize countOccurrences(iterator);`

Returns the number of occurrences of representative substring in the index text.

#### Parameters

`iterator` | An iterator of a string tree.

#### Returns

`TSize` | The number of positions where the representative of `iterator` occurs in the text. The return type is the result of the metafunction Size of the index type of the iterator.

The necessary index tables are built on-demand via indexRequire if index is not `const`.

#### Examples

    ///An example to demonstrate  the functions countChildren and countOccurrences
    #include <iostream>
    #include <seqan/index.h>

    using namespace seqan2;

    int main()
    {
        //We begin with a String to store our sequence.
        String<char> myString = "How many wood would a woodchuck chuck. A woodchuck chucks as much wood as a woodchuck could";

        //Then we create an Index of this StringSet.
        typedef Index<String<char> > TMyIndex;
        TMyIndex myIndex(myString);

        // We will use a TopDown Iterator that supports parent links, ommits
        // empty edges and traverses the index in preorder to print out the number of
        // children at each node (not the number of leafs in the subtree).
        Iterator<TMyIndex, TopDown<ParentLinks<PreorderEmptyEdges> > >::Type tdIterator(myIndex);
        Size<TMyIndex>::Type count;

        while (!atEnd(tdIterator))
        {
            //We print out the representatives of all nodes that have more than 3
            //children and the number of occurrences. Also, we print a message if a node
            //is a leaf.
            count = countChildren(tdIterator);
            if (count >= 3)
            {
                std::cout << "Representative " << representative(tdIterator) << " has " <<  count << " children and ";
                std::cout << countOccurrences(tdIterator) << " occurrences " << std::endl;
            }
            if (isLeaf(tdIterator))
                std::cout << "The node is a leaf " << std::endl;

            tdIterator++;
        }

        return 0;
    }

Demo: demos/dox/index/counting.cpp

The result is as follows:

    Representative  has 17 children and 91 occurrences
    Representative   has 5 children and 16 occurrences
    The node is a leaf
    The node is a leaf
    The node is a leaf
    The node is a leaf
    The node is a leaf
    The node is a leaf
    The node is a leaf
    The node is a leaf
    The node is a leaf
    The node is a leaf
    The node is a leaf
    The node is a leaf
    The node is a leaf
    The node is a leaf
    The node is a leaf
    The node is a leaf
    The node is a leaf
    The node is a leaf
    The node is a leaf
    Representative a has 3 children and 5 occurrences
    The node is a leaf
    The node is a leaf
    The node is a leaf
    The node is a leaf
    The node is a leaf
    Representative c has 3 children and 12 occurrences
    The node is a leaf
    Representative chuck has 3 children and 5 occurrences
    The node is a leaf
    The node is a leaf
    The node is a leaf
    The node is a leaf
    The node is a leaf
    Representative ck has 3 children and 5 occurrences
    The node is a leaf
    The node is a leaf
    The node is a leaf
    The node is a leaf
    The node is a leaf
    The node is a leaf
    Representative d has 3 children and 7 occurrences
    The node is a leaf
    The node is a leaf
    The node is a leaf
    The node is a leaf
    The node is a leaf
    The node is a leaf
    The node is a leaf
    The node is a leaf
    Representative huck has 3 children and 5 occurrences
    The node is a leaf
    The node is a leaf
    The node is a leaf
    The node is a leaf
    The node is a leaf
    Representative k has 3 children and 5 occurrences
    The node is a leaf
    The node is a leaf
    The node is a leaf
    The node is a leaf
    The node is a leaf
    The node is a leaf
    The node is a leaf
    The node is a leaf
    The node is a leaf
    The node is a leaf
    Representative o has 4 children and 13 occurrences
    The node is a leaf
    The node is a leaf
    The node is a leaf
    The node is a leaf
    The node is a leaf
    The node is a leaf
    The node is a leaf
    The node is a leaf
    The node is a leaf
    The node is a leaf
    The node is a leaf
    The node is a leaf
    The node is a leaf
    The node is a leaf
    The node is a leaf
    The node is a leaf
    The node is a leaf
    Representative uck has 3 children and 5 occurrences
    The node is a leaf
    The node is a leaf
    The node is a leaf
    The node is a leaf
    The node is a leaf
    The node is a leaf
    The node is a leaf
    The node is a leaf
    The node is a leaf
    The node is a leaf
    The node is a leaf
    The node is a leaf
    The node is a leaf
    The node is a leaf
    The node is a leaf

#### Data Races

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

### `int getFrequency(iterator);`

Returns the number of sequences, which contain the representative as a substring.

#### Parameters

`iterator` | An iterator of a suffix tree. Types: VSTreeIterator

#### Returns

`int` | The number of different sequences containing the representative.

#### Example

The following code how getFrequency is used. Note that the result of alternative 1 and 2 is the same, however alternative one copies a string which requires more memory.

    #include <seqan/index.h>

    using namespace seqan2;

    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

    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

- getOccurrences

### `TSAValue getOccurrence(iterator);`

Returns an occurrence of the representative substring in the index text.

#### Parameters

`iterator` | An iterator of a string tree.

#### Returns

`TSAValue` | A position where the representative of `iterator` occurs in the text. The return type is the result of the metafunction SAValue of the index type of the iterator.

#### Data Races

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

### `TInfix getOccurrences(iterator);`

Returns all occurrences of the representative substring in the index text.

#### Parameters

`iterator` | An iterator of a string tree.

#### Returns

`TInfix` | All positions where the representative of `iterator` occurs in the text. Type Infix<Fibre<TIndex, FibreSA>::Type>.

The necessary index tables are built on-demand via indexRequire if index is not `const`.

#### Example

DemoMummy DemoSupermaximalRepeats DemoMaximalUniqueMatches

#### Data Races

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

#### See Also

- getFrequency
- isLeftMaximal
- isPartiallyLeftExtensible
- isUnique
- orderOccurrences

### `TReturn getOccurrencesBwt(iterator);`

Returns the characters left beside all occurrence of the representative substring in the index text.

#### Parameters

`iterator` | An iterator of a suffix tree.

#### Returns

`TReturn` | All positions where the representative of `iterator` occurs in the text.

If `iterator`'s container type is `TIndex` the return type is `Infix<Fibre<TIndex, EsaBwt>::Type const>::Type`.

#### Data Races

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

### `TValue getProperty(pm, value(iterator))`

Get method for an item's property.

#### Parameters

`pm` | An PropertyMapConcept.
`iterator` | An iterator of a string tree. Types: VSTreeIterator

#### Returns

`TValue` | Reference to the item in the property map of type GetValue.

#### Data Races

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

### `void goBegin(iterator);`

Iterates to the first position of a container.

#### Parameters

`iterator` | Object that iterates through

This function is equivalent to `iterator = begin(container)`.

#### Data Races

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

#### See Also

- begin

### `void goNext(it);`

Go to next tree node.

#### Parameters

`it` | VSTreeIterator to advance.

#### Data Races

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

### `void goRoot(iterator);`

Move iterator to the root node.

#### Parameters

`iterator` | An iterator of a suffix tree.

#### Data Races

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

### `bool isLeaf(iterator);`

Test whether a tree iterator points to a leaf.

#### Parameters

`iterator` | An iterator of a tree.

#### Returns

`bool` | `true` if `iterator` points to a leaf of the tree, otherwise `false`.

DemoIndexCountChildren

#### Data Races

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

### `bool isLeftMaximal(iterator);`

Test whether the occurrences of an iterator's representative mutually differ in the character left of the hits.

#### Parameters

`iterator` | An iterator of a suffix tree.

#### Returns

`bool` | `true` if there are at least two different characters left of the occurrences, otherwise `false`.

#### Data Races

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

#### See Also

- getOccurrences

### `bool isPartiallyLeftExtensible(iterator);`

Test whether the characters left of the two occurrences of representative are equal.

#### Parameters

`iterator` | An iterator of a suffix tree.

#### Returns

`bool` | `true` if there are at least two different characters left of the occurrences, otherwise `false`.

#### Data Races

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

#### See Also

- getOccurrences

### `bool isRightTerminal(iterator);`

Test whether iterator points to a suffix.

#### Parameters

`iterator` | An iterator of a suffix tree.

#### Returns

`bool` | `true` if `iterator` points to the node representing a suffix, otherwise `false`.

Every leaf is also a right terminal (see isLeaf), but not vice versa.

#### Data Races

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

### `bool isRoot(iterator);`

Test whether a tree iterator points to the root node.

#### Parameters

`iterator` | An iterator of a tree.

#### Returns

`bool` | `true` if `iterator` points to the root of the tree, otherwise `false`.

#### Example

The following example shows the usage of the @Function.isRoot@ function.

    #include <seqan/index.h>

    using namespace seqan2;

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

        Iterator<TIndex, BottomUp<Postorder> >::Type itDefault;
        itDefault = begin(index, BottomUp<Postorder>());

        while (!isRoot(itDefault))
        {
            std::cout << representative(itDefault) << std::endl;
            goNext(itDefault);
        }

        return 0;
    }

Demo: demos/dox/index/begin_atEnd_representative_bottomUp.cpp

code{.output} output:AA ATAA A TAA TATAA TA @endcode

#### Data Races

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

### `bool isUnique(iterator);`

Test whether the representative occurs only once in every sequence.

#### Parameters

`iterator` | An iterator of a suffix tree.

#### Returns

`bool` | `true` if there are at least two different characters left of the occurrences, otherwise `false`.

#### Data Races

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

#### See Also

- getOccurrences

### `bool nodeHullPredicate(iterator);`

If `false` this node and its subtree is concealed.

#### Parameters

`iterator` | An iterator of a string tree.

#### Returns

`bool` | Returns whether or not a subtree is concealed.

DemoConstraintIterator

#### Data Races

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

### `bool nodePredicate(iterator);`

If `false` this node will be skipped during the bottom-up traversal.

#### Parameters

`iterator` | An iterator of a string tree.

#### Returns

`bool` | Returns whether or not the node will be skipped.

#### Data Races

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

#### See Also

- DemoConstraintIterator

### `TRef property(pm, value(iterator))`

Accesses the property of an item in the property map.

#### Parameters

`pm` | An PropertyMapConcept.
`iterator` | An iterator of a string tree. Types: VSTreeIterator

#### Returns

`TRef` | Reference to the item in the property map of type Reference.

#### Data Races

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

### `TPair range(iterator);`

Returns the suffix array interval borders of occurrences of representative substring in the index text.

#### Parameters

`iterator` | An iterator of a string tree/trie.

#### Returns

`TPair` | All positions where a substring occurs in the text are stored in a contiguous range of the suffix array. `range` returns begin and end position of this range for occurrences of representative. The type is Pair<Size< `TIndex`> > with TIndex being the index type of the iterator.``

The necessary index tables are built on-demand via indexRequire if index is not `const`.

#### Data Races

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

### `TSize repLength(iterator);`

Returns the length of the substring representing the path from root to `iterator` node.

#### Parameters

`iterator` | An iterator of a string tree. Types: VSTreeIterator

#### Returns

`TSize` | The length of the sequence returned by representative The return type is the result of the metafunction Size of the underlying index.

DemoMummy DemoSupermaximalRepeats DemoMaximalUniqueMatches

#### Data Races

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

### `TInfix representative(iterator);`

Returns a substring representing the path from root to `iterator` node.

#### Parameters

`iterator` | An iterator of a string tree.

#### Returns

`TInfix` | Infix<TSting> An InfixSegment of the text of an index. The type is `Infix<Fibre<TIndex, FibreText>::Type>::Type`.

#### Examples

DemoMummy DemoSupermaximalRepeats DemoConstraintIterator DemoMaximalRepeats DemoMaximalUniqueMatches

#### Data Races

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

### `TDesc value(iterator);`

Returns a vertex descriptor of the current node.

#### Parameters

`iterator` | An iterator of a string tree. Types: VSTreeIterator

#### Returns

`TDesc` | An object of type VertexDescriptor that uniquely identifies the current node. The vertex descriptor can be used to store node specific values in an PropertyMapConcept.

#### Data Races

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

## Interface Metafunctions Detail

### `EdgeLabel<TSpec>::Type;`

Type of a string representing the characters of edges.

#### Template Parameters

`TSpec` | Tag to specify the object of which the type of the edge labels is requested.

#### Returns

`Type` | of a string representing the characters of edges.

#### Dox Sources

    /*!
     * @class VSTreeIterator VSTree Iterator
     *
     * @extends Iter
     *
     * @headerfile <seqan/index.h>
     *
     * @brief Abstract iterator for string trees, where string trees are trees
     *        constructed from a string.
     *
     * @signature template <typename TContainer, typename TSpec> class
     *            Iter<TContainer, VSTree<TSpec> >;
     *
     * @tparam TSpec The specialization type.
     * @tparam TContainer Type of the container that can be iterated. Types: @link
     *                    IndexDfi @endlink, @link IndexEsa @endlink, @link
     *                    IndexWotd @endlink, @link FMIndex @endlink
     *
     * This iterator is a pointer to a node in the string tree of a given text.
     * Depending on the index this can either be a suffix or prefix tree/trie. Every
     * node can uniquely be mapped to an interval of suffices or prefixes.
     *
     * Default virtual string tree iterators depending on the @link Index @endlink
     *
     * <table border="1"> <tr> <td>IndexSa</td> <td>Virtual suffix trie
     * iterator</td> </tr> <tr> <td>IndexEsa</td> <td>Virtual suffix tree
     * iterator</td> </tr> <tr> <td>IndexWotd</td> <td>Virtual suffix tree
     * iterator</td> </tr> <tr> <td>IndexDfi</td> <td>Virtual suffix tree
     * iterator</td> </tr> <tr> <td>FMIndex</td> <td>Virtual prefix trie
     * iterator</td> </tr> </table>
     *
     * @section Examples
     *
     * 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
     *
     * @mfn VSTreeIterator#EdgeLabel
     *
     * @headerfile <seqan/index.h>
     *
     * @brief Type of a string representing the characters of edges.
     *
     * @signature EdgeLabel<TSpec>::Type;
     *
     * @tparam TSpec Tag to specify the object of which the type of the edge labels
     *               is requested.
     *
     * @return Type of a string representing the characters of edges.
     *
     * @fn VSTreeIterator#repLength
     *
     * @headerfile <seqan/index.h>
     *
     * @brief Returns the length of the substring representing the path from root to
     *        <tt>iterator</tt> node.
     *
     * @signature TSize repLength(iterator);
     *
     * @param[in] iterator An iterator of a string tree. Types: @link VSTreeIterator
     *                     @endlink
     *
     * @return TSize The length of the sequence returned by @link
     *               VSTreeIterator#representative @endlink The return type is the
     *               result of the metafunction @link Size @endlink of the
     *               underlying index.
     *
     * @link DemoMummy @endlink @link DemoSupermaximalRepeats @endlink @link
     * DemoMaximalUniqueMatches @endlink
     *
     * @fn VSTreeIterator#value
     *
     * @headerfile <seqan/index.h>
     *
     * @brief Returns a vertex descriptor of the current node.
     *
     * @signature TDesc value(iterator);
     *
     * @param[in] iterator An iterator of a string tree. Types: @link VSTreeIterator
     *                     @endlink
     *
     * @return TDesc An object of type @link StringTreeConcept#VertexDescriptor
     *               @endlink that uniquely identifies the current node. The vertex
     *               descriptor can be used to store node specific values in an
     *               @link PropertyMapConcept @endlink.
     *
     * @fn VSTreeIterator#assignProperty
     *
     * @brief Assigns a property to an item in the property map.
     *
     * @signature void assignProperty(pm, value(iterator), val)
     *
     * @param[in,out] pm An @link PropertyMapConcept @endlink.
     * @param[in] iterator An iterator of a string tree. Types: @link VSTreeIterator
     *                     @endlink
     * @param[in] val The new value, where the type of the new value must match the
     *                value type of the property map.
     *
     * @fn VSTreeIterator#property
     *
     * @brief Accesses the property of an item in the property map.
     *
     * @signature TRef property(pm, value(iterator))
     *
     * @param[in,out] pm An @link PropertyMapConcept @endlink.
     * @param[in] iterator An iterator of a string tree. Types: @link VSTreeIterator
     *                     @endlink
     *
     * @return TRef Reference to the item in the property map of type @link
     *              Reference @endlink.
     *
     * @fn VSTreeIterator#getProperty
     *
     * @brief Get method for an item's property.
     *
     * @signature TValue getProperty(pm, value(iterator))
     *
     * @param[in,out] pm An @link PropertyMapConcept @endlink.
     * @param[in] iterator An iterator of a string tree. Types: @link VSTreeIterator
     *                     @endlink
     *
     * @return TValue Reference to the item in the property map of type @link
     *                GetValue @endlink.
     *
     * @fn VSTreeIterator#getOccurrence
     *
     * @headerfile <seqan/index.h>
     *
     * @brief Returns an occurrence of the @link VSTreeIterator#representative
     *        @endlink substring in the index text.
     *
     * @signature TSAValue getOccurrence(iterator);
     *
     * @param[in] iterator An iterator of a string tree.
     *
     * @return TSAValue A position where the @link VSTreeIterator#representative
     *                  @endlink of <tt>iterator</tt> occurs in the text. The return
     *                  type is the result of the metafunction @link SAValue
     *                  @endlink of the index type of the iterator.
     *
     * @fn VSTreeIterator#countOccurrences
     *
     * @headerfile <seqan/index.h>
     *
     * @brief Returns the number of occurrences of @link
     *        VSTreeIterator#representative @endlink substring in the index text.
     *
     * @signature TSize countOccurrences(iterator);
     *
     * @param[in] iterator An iterator of a string tree.
     *
     * @return TSize The number of positions where the @link
     *               VSTreeIterator#representative @endlink of <tt>iterator</tt>
     *               occurs in the text. The return type is the result of the
     *               metafunction @link Size @endlink of the index type of the
     *               iterator.
     *
     * The necessary index tables are built on-demand via @link Index#indexRequire
     * @endlink if index is not <tt>const</tt>.
     *
     * @section Examples
     *
     * @include demos/dox/index/counting.cpp
     *
     * The result is as follows:
     *
     * @include demos/dox/index/counting.cpp.stdout
     *
     *
     *
     * @fn VSTreeIterator#range
     *
     * @headerfile <seqan/index.h>
     *
     * @brief Returns the suffix array interval borders of occurrences of @link
     *        VSTreeIterator#representative @endlink substring in the index text.
     *
     * @signature TPair range(iterator);
     *
     * @param[in] iterator An iterator of a string tree/trie.
     *
     * @return TPair All positions where a substring occurs in the text are stored
     *               in a contiguous range of the suffix array. <tt>range</tt>
     *               returns begin and end position of this range for occurrences of
     *               @link VSTreeIterator#representative @endlink. The type is @link
     *               Pair @endlink<@link Size @endlink< <tt>TIndex<tt> > > with
     *               TIndex being the index type of the iterator.
     *
     * The necessary index tables are built on-demand via @link Index#indexRequire
     * @endlink if index is not <tt>const</tt>.
     *
     * @fn VSTreeIterator#getOccurrences
     *
     * @headerfile <seqan/index.h>
     *
     * @brief Returns all occurrences of the @link VSTreeIterator#representative
     *        @endlink substring in the index text.
     *
     * @signature TInfix getOccurrences(iterator);
     *
     * @param[in] iterator An iterator of a string tree.
     *
     * @return TInfix All positions where the @link VSTreeIterator#representative
     *                @endlink of <tt>iterator</tt> occurs in the text. Type @link
     *                SegmentableConcept#Infix @endlink&lt;@link Fibre
     *                @endlink&lt;TIndex, FibreSA&gt;::Type&gt;.
     *
     * The necessary index tables are built on-demand via @link Index#indexRequire
     * @endlink if index is not <tt>const</tt>.
     *
     * @section Example
     *
     * @link DemoMummy @endlink @link DemoSupermaximalRepeats @endlink @link
     * DemoMaximalUniqueMatches @endlink
     *
     * @see VSTreeIterator#isUnique
     * @see VSTreeIterator#getFrequency
     * @see VSTreeIterator#isPartiallyLeftExtensible
     * @see VSTreeIterator#isLeftMaximal
     * @see orderOccurrences
     *
     * @fn VSTreeIterator#alignment
     *
     * @brief Returns an alignment of the occurrences of the @link
     *        VSTreeIterator#representative @endlink substring in the index text.
     *
     * @note Internal function.
     *
     * @signature TAlign alignment(iterator);
     *
     * @param[in] iterator An iterator of a string tree.
     *
     * @return TAlign A local alignment corresponding to the seed of the
     *                <tt>iterator<tt>.
     *
     * The function @link VSTreeIterator#representative @endlink must uniquely occur
     * in every sequence (e.g. in Mums), otherwise the seed returned is one many.
     * The return type is a @link Align @endlink object.
     *
     * @fn VSTreeIterator#getOccurrencesBwt
     *
     * @headerfile <seqan/index.h>
     *
     * @brief Returns the characters left beside all occurrence of the @link
     *        VSTreeIterator#representative @endlink substring in the index text.
     *
     * @signature TReturn getOccurrencesBwt(iterator);
     *
     * @param[in] iterator An iterator of a suffix tree.
     *
     * @return TReturn All positions where the @link VSTreeIterator#representative
     *                 @endlink of <tt>iterator</tt> occurs in the text.
     *
     * If <tt>iterator</tt>'s container type is <tt>TIndex</tt> the return type is
     * <tt>Infix<Fibre<TIndex, EsaBwt>::Type const>::Type</tt>.
     *
     * @fn VSTreeIterator#representative
     *
     * @headerfile <seqan/index.h>
     *
     * @brief Returns a substring representing the path from root to
     *        <tt>iterator</tt> node.
     *
     * @signature TInfix representative(iterator);
     *
     * @param[in] iterator An iterator of a string tree.
     *
     * @return TInfix Infix&lt;TSting&gt; An @link InfixSegment @endlink of the text
     *                of an index. The type is <tt>Infix&lt;Fibre&lt;TIndex,
     *                FibreText&gt;::Type&gt;::Type</tt>.
     *
     * @section Examples
     *
     * @link DemoMummy @endlink @link DemoSupermaximalRepeats @endlink @link
     * DemoConstraintIterator @endlink @link DemoMaximalRepeats @endlink @link
     * DemoMaximalUniqueMatches @endlink
     *
     * @fn VSTreeIterator#countChildren
     *
     * @headerfile <seqan/index.h>
     *
     * @brief Count the number of children of a tree node.
     *
     * @signature TSize countChildren(iterator);
     *
     * @param[in] iterator An iterator of a string tree.
     *
     * @return TSize The number of children of a tree node. The type is the result
     *               of @link Size @endlink of the index type of the iterator.
     *
     * @section Examples
     *
     * @code{.cpp}
     * // this code is in seqan/index/index_esa_stree.h
     *
     *  typedef Index< String<char> > TMyIndex;
     *  TMyIndex myIndex(myString);
     *
     *  Iterator< TMyIndex, TopDown<ParentLinks<PreorderEmptyEdges> > >::Type tdIterator(myIndex);
     *  Size<TMyIndex>::Type count;
     *
     *  while (!atEnd(tdIterator)) {
     *  // We print out the representatives of all nodes that have more than 3 children and the number of occurrences.
     *  count = countChildren(tdIterator);
     *  if (count >= 3)
     *  {
     *      std::cout << "Representative " << representative(tdIterator) << " has " <<  count << " children  and " << countOccurrences(tdIterator) << " Occurrences " << std::endl;
     *
     *      ++tdIterator;
     *  }
     * @endcode
     *
     *
     * @link DemoIndexCountChildren @endlink
     *
     * @fn VSTreeIterator#nodePredicate
     *
     * @headerfile <seqan/index.h>
     *
     * @brief If <tt>false</tt> this node will be skipped during the bottom-up
     *        traversal.
     *
     * @signature bool nodePredicate(iterator);
     *
     * @param[in] iterator An iterator of a string tree.
     *
     * @return bool Returns whether or not the node will be skipped.
     *
     * @see DemoConstraintIterator
     *
     * @fn VSTreeIterator#nodeHullPredicate
     *
     * @headerfile <seqan/index.h>
     *
     * @brief If <tt>false</tt> this node and its subtree is concealed.
     *
     * @signature bool nodeHullPredicate(iterator);
     *
     * @param[in] iterator An iterator of a string tree.
     *
     * @return bool Returns whether or not a subtree is concealed.
     *
     * @link DemoConstraintIterator @endlink
     *
     * @fn VSTreeIterator#goRoot
     *
     * @headerfile <seqan/index.h>
     *
     * @brief Move iterator to the root node.
     *
     * @signature void goRoot(iterator);
     *
     * @param[in,out] iterator An iterator of a suffix tree.
     *
     * @fn VSTreeIterator#goBegin
     *
     * @headerfile <seqan/index.h>
     *
     * @brief Iterates to the first position of a container.
     *
     * @signature void goBegin(iterator);
     *
     * @param[in,out] iterator Object that iterates through
     *
     * This function is equivalent to <tt>iterator = begin(container)</tt>.
     *
     * @see StringTreeConcept#begin
     *
     * @fn VSTreeIterator#goNext
     *
     * @brief Go to next tree node.
     *
     * @signature void goNext(it);
     *
     * @param[in,out] it VSTreeIterator to advance.
     *
     * @fn VSTreeIterator#atEnd
     *
     * @headerfile <seqan/index.h>
     *
     * @brief Determines whether an virtual string tree iterator is at the end
     *        position.
     *
     * @signature bool atEnd(iterator);
     *
     * @param[in] iterator An iterator.
     *
     * @return bool <tt>true</tt> if <tt>iterator</tt> points behind the last item
     *              of the container, otherwise <tt>false</tt>.
     *
     * @section Examples
     *
     * The following example shows the usage of the @link VSTreeIterator#atEnd
     * @endlink function.
     *
     * @include demos/dox/index/begin_atEnd_representative.cpp
     *
     * @fn VSTreeIterator#isRoot
     *
     * @headerfile <seqan/index.h>
     *
     * @brief Test whether a tree iterator points to the root node.
     *
     * @signature bool isRoot(iterator);
     *
     * @param[in] iterator An iterator of a tree.
     *
     * @return bool <tt>true</tt> if <tt>iterator</tt> points to the root of the
     *              tree, otherwise <tt>false</tt>.
     *
     * @section Example
     *
     * The following example shows the usage of the @Function.isRoot@ function.
     *
     * @include demos/dox/index/begin_atEnd_representative_bottomUp.cpp
     *
     * code{.output} output:AA ATAA A TAA TATAA TA @endcode
     *
     * @fn VSTreeIterator#isRightTerminal
     *
     * @headerfile <seqan/index.h>
     *
     * @brief Test whether iterator points to a suffix.
     *
     * @signature bool isRightTerminal(iterator);
     *
     * @param[in] iterator An iterator of a suffix tree.
     *
     * @return bool <tt>true</tt> if <tt>iterator</tt> points to the node
     *              representing a suffix, otherwise <tt>false</tt>.
     *
     * Every leaf is also a right terminal (see @link VSTreeIterator#isLeaf
     * @endlink), but not vice versa.
     *
     * @fn VSTreeIterator#isLeftMaximal
     *
     * @headerfile <seqan/index.h>
     *
     * @brief Test whether the occurrences of an iterator's @link
     *        VSTreeIterator#representative @endlink mutually differ in the
     *        character left of the hits.
     *
     * @signature bool isLeftMaximal(iterator);
     *
     * @param[in] iterator An iterator of a suffix tree.
     *
     * @return bool <tt>true</tt> if there are at least two different characters
     *              left of the occurrences, otherwise <tt>false</tt>.
     *
     * @see VSTreeIterator#getOccurrences
     *
     * @fn VSTreeIterator#isPartiallyLeftExtensible
     *
     * @headerfile <seqan/index.h>
     *
     * @brief Test whether the characters left of the two occurrences of @link
     *        VSTreeIterator#representative @endlink are equal.
     *
     * @signature bool isPartiallyLeftExtensible(iterator);
     *
     * @param[in] iterator An iterator of a suffix tree.
     *
     * @return bool <tt>true</tt> if there are at least two different characters
     *              left of the occurrences, otherwise <tt>false</tt>.
     *
     * @see VSTreeIterator#getOccurrences
     *
     * @fn VSTreeIterator#isUnique
     *
     * @headerfile <seqan/index.h>
     *
     * @brief Test whether the @link VSTreeIterator#representative @endlink occurs
     *        only once in every sequence.
     *
     * @signature bool isUnique(iterator);
     *
     * @param[in] iterator An iterator of a suffix tree.
     *
     * @return bool <tt>true</tt> if there are at least two different characters
     *              left of the occurrences, otherwise <tt>false</tt>.
     *
     * @see VSTreeIterator#getOccurrences
     *
     * @fn VSTreeIterator#getFrequency
     *
     * @headerfile <seqan/index.h>
     *
     * @brief Returns the number of sequences, which contain the @link
     *        VSTreeIterator#representative @endlink as a substring.
     *
     * @signature int getFrequency(iterator);
     *
     * @param[in] iterator An iterator of a suffix tree. Types: @link VSTreeIterator
     *                     @endlink
     *
     * @return int The number of different sequences containing the @link
     *             VSTreeIterator#representative @endlink.
     *
     * @section Example
     *
     * The following code how @link VSTreeIterator#getFrequency @endlink is used.
     * Note that the result of alternative 1 and 2 is the same, however alternative
     * one copies a string which requires more memory.
     *
     * @include demos/dox/index/getOccurrences_getFrequency_range_getFibre.cpp
     *
     * @code{.output}
     * 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
     * @endcode
     *
     *
     * @see VSTreeIterator#getOccurrences
     *
     * @fn VSTreeIterator#childrenAreLeaves
     *
     * @headerfile <seqan/index.h>
     *
     * @brief Test whether iterator points to a node with only leaf-children.
     *
     * @signature bool childrenAreLeaves(iterator);
     *
     * @param[in] iterator An iterator of a suffix tree.
     *
     * @return bool <tt>true</tt> if <tt>iterator</tt> points to an inner node of
     *              the tree, whose children are leaves. Otherwise it is
     *              <tt>false</tt>.
     *
     * @fn VSTreeIterator#isLeaf
     *
     * @headerfile <seqan/index.h>
     *
     * @brief Test whether a tree iterator points to a leaf.
     *
     * @signature bool isLeaf(iterator);
     *
     * @param[in] iterator An iterator of a tree.
     *
     * @return bool <tt>true</tt> if <tt>iterator</tt> points to a leaf of the tree,
     *              otherwise <tt>false</tt>.
     *
     * @link DemoIndexCountChildren @endlink
     */