AnnotationTree Iterator

Class Specialization

Iterator of the annotation tree represented by a FragmentStore.



IteratorAssociatedTypesConcept

Iter

RootedIteratorConcept

AnnotationTree Iterator

Iter<TFragmentStore, AnnotationTree<> >

Iterator<TFragmentStore, AnnotationTree<> >::Type

Include Headers

seqan/store.h

Parameters

TFragmentStore

A FragmentStore class.

Types: FragmentStore

Remarks

This iterator can move down, right, and up in the tree and supports a preorder dfs traversal via the functions goBegin, goNext, and atEnd. Preorder means that the iterator visits a node before its children.

To access the annotation, the iterator points to, use getAnnotation. The annotation id is returned by value.

Specialization of

Iter

Implements

RootedIteratorConcept, IteratorAssociatedTypesConcept

Metafunctions

Container	Type of the container given an iterator. (Iter)
Difference	Type of an object that stores the difference between two iterators. (Iter)
GetValue	Type for reading values. (Iter)
Iterator	Type of iterator objects that are used to traverse the container. (Iter)
Position	Type of an object that represents a position in a container. (Iter)
Reference	Reference type. (Iter)
Spec	The spec of a class. (Iter)
Value	Type of the items in the container or behind an iterator. (Iter)

Member Functions

AnnotationTree Iterator

Constructor

Functions

assignValue	Assigns value to item. (Iter)
assignValueByKey	Add or update a key-value pair of the current annotation.
atBegin	Determines whether an iterator is at the beginning position.
atEnd	Determines whether an iterator is at the end position.
atEndOfSequence	Returns true if the iterator is at the end of a sequence. (Iter)
clearValues	Clear all key-value pairs of the current annotation.
container	Container of an iterator. (Iter)
createLeftChild	Creates a new left-most child of the current node and returns an iterator to it.
createRightChild	Creates a new right-most child of the current node and returns an iterator to it.
createSibling	Creates a new right sibling of the current node and returns an iterator to it.
difference	The difference between two iterators. (Iter)
getAnnotation	Returns the current annotation.
getName	Returns the identifier of the current annotation.
getParentName	Returns the identifier of the parent node in the annotation tree of the current annotation.
getType	Returns the type name of the current annotation.
getUniqueName	Returns a unique name of the current annotation.
getValue	Access to the value. (Iter)
getValueByKey	Given a key, retrieve its value of the current annotation.
goBegin	Iterates to the first position of a container.
goDown	Move the iterator down to the left-most child in the annotation tree.
goEnd	Iterates to the last position of a container.
goFurther	Iterates some steps further. (Iter)
goNext	Iterates to next position.
goNextRight	Go to the next node in preorder DFS skipping the current node's subtree.
goNextUp	Go to the next node in preorder DFS skipping the subtrees of the current node and of all its siblings.
goPrevious	Iterates to pevious position. (Iter)
goRight	Move the iterator right to the next sibling in the annotation tree.
goRoot	Go to the root node in the annotation tree.
goTo	Moves the iterator to an arbitrary node given its annotationId.
goUp	Move the iterator up in the annotation tree.
isLastChild	Returns a boolean value that indicates whether the current node is the last child.
isLeaf	Test whether a tree iterator points to a leaf.
isRoot	Test whether a tree iterator points to the root node.
moveValue	Assigns value to item. (Iter)
nodeDown	Returns a new iterator to the first child node of the current annotation in the annotation tree.
nodeRight	Returns a new iterator to the right sibling of the current annotation in the annotation tree.
nodeUp	Returns a new iterator to the parent node of the current annotation in the annotation tree.
position	Position of an iterator. (Iter)
setName	Sets the identifier of the current annotation.
setType	Sets the type name of the current annotation.
value	Reference to the value. (Iter)

Examples

Typical annotation tree hierarchy.

A new annotation tree iterator can be instantiated as follows:

Iterator<FragmentStore<>, AnnotationTree<> >::Type it;
it = begin(store, AnnotationTree<>());

Or shorter (see AnnotationTree Iterator constructor):

Iterator<FragmentStore<>, AnnotationTree<> >::Type it(store);

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