Class Specialization
VSTree Iterator
Abstract iterator for suffix trees.

VSTree Iterator

BottomUp Iterator | TopDown Iterator

MaxRepeats Iterator | MultiMems Iterator | Mums Iterator
SuperMaxRepeats Iterator | SuperMaxRepeatsFast Iterator

TopDownHistory Iterator

Iter<TContainer, VSTree<TSpec> >
Include Headers
seqan/index.h
Parameters

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

Remarks
This iterator is a pointer to a node in the suffix tree (given by the enhanced suffix array IndexEsa). Every node can uniquely be mapped to an interval of the suffix array containing all suffixes of the node's subtree. This interval and some extra information constitute the VertexDescriptor returned by the value function of the iterator.
Specializations

BottomUp Iterator | Iterator for an efficient postorder depth-first search in a suffix tree.
TopDown Iterator | Iterator for suffix trees that can go down and right beginning from the root.

Functions

alignment | Returns an alignment of the occurences of the representative substring in the index text.
childrenAreLeaves | Test whether iterator points to a node with only leaf-children.
container | Container of an iterator.
countChildren | Count the number of children of a tree node.
countOccurrences | Returns the number of occurences of representative substring or a q-gram in the index text.
getFrequency | Returns the number of sequences, which contain the representative as a substring.
getOccurrence | Returns an occurence of the representative substring or a q-gram in the index text.
getOccurrences | Returns all occurences of the representative substring or a q-gram in the index text.
getOccurrencesBwt | Returns the characters left beside all occurence of the representative substring in the index text.
isLeaf | Test whether iterator points to a leaf.
isLeftMaximal | Test whether the occurences of an iterator's representative mutually differ in the character left of the hits.
isPartiallyLeftExtensible | Test whether the characters left of the two occurences of representative are equal.
isRightTerminal | Test whether iterator points to a suffix.
isRoot | Test whether iterator points to the root node.
isUnique | Test whether the representative occurs only once in every sequence.
nodeHullPredicate | If false this node and its subtree is concealed.
nodePredicate | If false this node will be skipped during the bottom-up traversal.
range | Returns the suffix array interval borders of occurences of representative substring or a q-gram in the index text.
repLength | Returns the length of the substring representing the path from root to iterator node.
representative | Returns a substring representing the path from root to iterator node.
value | Reference to the value.

SeqAn - Sequence Analysis Library - www.seqan.de

Page built @2012/03/14 16:34:52