Class Specialization
VSTree Iterator
Abstract iterator for suffix trees.
Iter<TContainer, VSTree<TSpec> >
Include Headers
seqan/index.h
Parameters
TContainer
Type of the container that can be iterated.
Metafunctions: Container
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 IteratorIterator for an efficient postorder depth-first search in a suffix tree.
TopDown IteratorIterator for suffix trees that can go down and right beginning from the root.
Functions
alignmentReturns an alignment of the occurences of the representative substring in the index text.
childrenAreLeavesTest whether iterator points to a node with only leaf-children.
containerContainer of an iterator.
countChildrenCount the number of children of a tree node.
countOccurrencesReturns the number of occurences of representative substring or a q-gram in the index text.
getFrequencyReturns the number of sequences, which contain the representative as a substring.
getOccurrenceReturns an occurence of the representative substring or a q-gram in the index text.
getOccurrencesReturns all occurences of the representative substring or a q-gram in the index text.
getOccurrencesBwtReturns the characters left beside all occurence of the representative substring in the index text.
isLeafTest whether iterator points to a leaf.
isLeftMaximalTest whether the occurences of an iterator's representative mutually differ in the character left of the hits.
isPartiallyLeftExtensibleTest whether the characters left of the two occurences of representative are equal.
isRightTerminalTest whether iterator points to a suffix.
isRootTest whether iterator points to the root node.
isUniqueTest whether the representative occurs only once in every sequence.
nodeHullPredicateIf false this node and its subtree is concealed.
nodePredicateIf false this node will be skipped during the bottom-up traversal.
rangeReturns the suffix array interval borders of occurences of representative substring or a q-gram in the index text.
repLengthReturns the length of the substring representing the path from root to iterator node.
representativeReturns a substring representing the path from root to iterator node.
valueReference to the value.
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