Class Specialization
TopDown Iterator
Iterator for virtual trees that can go down and right beginning from the root.
Iterator<TContainer, TopDown<TSpec> >::Type
Iter<TContainer, VSTree< TopDown<TSpec> > >
Include Headers
seqan/index.h
Parameters
TContainer
Type of the container that can be iterated.
Metafunctions: Container
TSpec
The specialization type.
Remarks
If not copy-constructed the TopDown Iterator starts in the root node of the virtual tree.
Note that the virtual tree can either be a virtual suffix tree or a virtual prefix tree. The suffix tree is shown in Figure 1 and is implemented with the IndexDfi, IndexEsa and IndexWotd. In contrast the FMIndex implements a prefix trie shown in Figure 2.
Specialization of
Specializations
TopDownHistory IteratorString tree iterator that can go down, right, and up. Supports depth-first search.
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
Functions
alignmentReturns an alignment of the occurrences 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. (Iter)
atEndOfSequenceReturns true if the iterator is at the end of a sequence. (Iter)
beginReturns an iterator pointing to the root node of the virtual string tree/trie of an index. The only exception are Postorder iterators, where begin returns an iterator pointing to the leftmost node in the tree/trie. (VSTree Iterator)
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 occurrences 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.
getFrequencyReturns the number of sequences, which contain the representative as a substring. (VSTree Iterator)
getOccurrenceReturns an occurrence of the representative substring or a q-gram in the index text. (VSTree Iterator)
getOccurrencesReturns all occurrences of the representative substring or a q-gram in the index text. (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. (Iter)
goDownIterates down one edge or a path in a tree.
goEndIterates to the last position of a container. (Iter)
goFurtherIterates some steps further. (Iter)
goNextIterates to next position. (Iter)
goPreviousIterates to pevious position. (Iter)
goRightIterates to the next sibling in a tree.
goRootMove iterator to the root node.
isLeafTest whether a tree iterator points to a leaf. (VSTree Iterator)
isLeftMaximalTest whether the occurrences of an iterator's representative mutually differ in the character left of the hits. (VSTree Iterator)
isPartiallyLeftExtensibleTest whether the characters left of the two occurrences 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)
moveValueAssigns value to item. (Iter)
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.
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.
positionPosition of an iterator. (Iter)
rangeReturns the suffix array interval borders of occurrences 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)
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