Class Specialization
AnnotationTree Iterator
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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