Class Specialization
TopDownHistory Iterator
Iterator for suffix trees that can go down, right, and up. Supports depth-first search.
Iterator<TContainer, TopDown< ParentLinks<TSpec> > >::Type
Iter<TContainer, VSTree< TopDown< ParentLinks<TSpec> > > >
Include Headers
seqan/index.h
Parameters
TContainer
Type of the container that can be iterated.
Metafunctions: Container
TSpec
The specialization type. Specifies the depth-first search mode.
Remarks
If not copy-constructed the TopDownHistory Iterator starts in the root node of the suffix tree. Depending on the depth-first search mode the root is not the first DFS node. To go to the first DFS node use goBegin.
Specialization of
Metafunctions
ContainerType of the container given an iterator. (Iter)
DifferenceType of an object that stores the difference between two iterators. (Iter)
GetValueType for reading values. (Iter)
IteratorType of iterator objects that are used to traverse the container. (Iter)
PositionType of an object that represents a position in a container. (Iter)
ReferenceReference type. (Iter)
SpecThe spec of a class. (Iter)
ValueType of the items in the container or behind an iterator. (Iter)
Member Functions
IteratorConstructor (TopDown Iterator)
Functions
alignmentReturns an alignment of the occurences of the representative substring in the index text. (VSTree Iterator)
assignValueAssigns value to item. (Iter)
atBeginDetermines whether an iterator is at the beginning position. (Iter)
atEndDetermines whether an iterator is at the end position.
atEndOfSequenceReturns true if the iterator is at the end of a sequence. (Iter)
childrenAreLeavesTest whether iterator points to a node with only leaf-children. (VSTree Iterator)
containerContainer of an iterator. (VSTree Iterator)
countChildrenCount the number of children of a tree node. (VSTree Iterator)
countOccurrencesReturns the number of occurences of representative substring or a q-gram in the index text. (VSTree Iterator)
differenceThe difference between two iterators. (Iter)
emptyParentEdgeReturns true iff the edge label from the iterator node to its parent is empty. (TopDown Iterator)
getFrequencyReturns the number of sequences, which contain the representative as a substring. (VSTree Iterator)
getOccurrenceReturns an occurence of the representative substring or a q-gram in the index text. (VSTree Iterator)
getOccurrencesReturns all occurences of the representative substring or a q-gram in the index text. Returns the number of occurrences of a specified character from the start to a specified position. (VSTree Iterator)
getOccurrencesBwtReturns the characters left beside all occurrence of the representative substring in the index text. (VSTree Iterator)
getValueAccess to the value. (Iter)
goBeginIterates to the first position of a container.
goDownIterates down one edge or a path in a tree. (TopDown Iterator)
goEndIterates to the last position of a container.
goFurtherIterates some steps further. (Iter)
goLeftChild (TopDown Iterator)
goNextIterates to next position.
goPreviousIterates to pevious position. (Iter)
goRightIterates to the next sibling in a tree. (TopDown Iterator)
goRootMove iterator to the root node. (TopDown Iterator)
goUpIterates up one edge to the parent in a tree.
isLeafTest whether a tree iterator points to a leaf. (VSTree Iterator)
isLeftMaximalTest whether the occurences of an iterator's representative mutually differ in the character left of the hits. (VSTree Iterator)
isPartiallyLeftExtensibleTest whether the characters left of the two occurences of representative are equal. (VSTree Iterator)
isRightTerminalTest whether iterator points to a suffix. (VSTree Iterator)
isRootTest whether a tree iterator points to the root node. (VSTree Iterator)
isUniqueTest whether the representative occurs only once in every sequence. (VSTree Iterator)
lcaReturns the last common ancestor of two tree nodes.
lcpReturns the length of the longest-common-prefix of two suffix tree nodes.
moveValueAssigns value to item. (Iter)
nodeDepthReturns the zero-based node depth of the iterator node.
nodeHullPredicateIf false this node and its subtree is concealed. (VSTree Iterator)
nodePredicateIf false this node will be skipped during the bottom-up traversal. (VSTree Iterator)
nodeUpReturns the vertex descriptor of the parent node. (TopDown Iterator)
parentEdgeFirstCharReturns the first character of the edge from an iterator node to its parent.
parentEdgeLabelReturns a substring representing the edge from an iterator node to its parent.
parentEdgeLengthReturns the length of the edge from the iterator node to its parent.
parentRepLengthReturns the length of the substring representing the path from root to iterator's parent node. (TopDown Iterator)
positionPosition of an iterator. (Iter)
rangeReturns the suffix array interval borders of occurences of representative substring or a q-gram in the index text. (VSTree Iterator)
repLengthReturns the length of the substring representing the path from root to iterator node. (VSTree Iterator)
representativeReturns a substring representing the path from root to iterator node. (VSTree Iterator)
valueReference to the value. (VSTree Iterator)
Example Programs
SeqAn - Sequence Analysis Library - www.seqan.de
 

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