| Class Specialization TopDownHistory Iterator String tree iterator that can go down, right, and up. Supports depth-first search.
IteratorAssociatedTypesConcept
Iter
VSTree Iterator
ForwardIteratorConcept | TopDown Iterator
TopDownHistory Iterator
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 Types: IndexDfi, IndexEsa, IndexWotd
TSpec | The specialization type. Specifies the depth-first search mode. Types: Postorder, PostorderEmptyEdges, Preorder, PreorderEmptyEdges
Remarks If not copy-constructed the TopDownHistory Iterator starts in the root node of the string 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. 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 TopDown Iterator Implements ForwardIteratorConcept, 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
Iterator | Constructor (TopDown Iterator)
Functions
alignment | Returns an alignment of the occurrences of the representative substring in the index text. (VSTree Iterator)
assignValue | Assigns value to item. (Iter)
atBegin | Determines whether an iterator is at the beginning position. (Iter)
atEnd | Determines whether an iterator is at the end position.
atEndOfSequence | Returns true if the iterator is at the end of a sequence. (Iter)
begin | Returns 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)
childrenAreLeaves | Test whether iterator points to a node with only leaf-children. (VSTree Iterator)
container | Container of an iterator. (VSTree Iterator)
countChildren | Count the number of children of a tree node. (VSTree Iterator)
countOccurrences | Returns the number of occurrences of representative substring or a q-gram in the index text. (VSTree Iterator)
difference | The difference between two iterators. (Iter)
emptyParentEdge | Returns true iff the edge label from the iterator node to its parent is empty. (TopDown Iterator)
getFrequency | Returns the number of sequences, which contain the representative as a substring. (VSTree Iterator)
getOccurrence | Returns an occurrence of the representative substring or a q-gram in the index text. (VSTree Iterator)
getOccurrences | Returns all occurrences of the representative substring or a q-gram in the index text. (VSTree Iterator)
getOccurrencesBwt | Returns the characters left beside all occurrence of the representative substring in the index text. (VSTree Iterator)
getValue | Access to the value. (Iter)
goBegin | Iterates to the first position of a container.
goDown | Iterates down one edge or a path in a tree. (TopDown Iterator)
goEnd | Iterates to the last position of a container.
goFurther | Iterates some steps further. (Iter)
goNext | Iterates to next position.
goPrevious | Iterates to pevious position. (Iter)
goRight | Iterates to the next sibling in a tree. (TopDown Iterator)
goRoot | Move iterator to the root node. (TopDown Iterator)
goUp | Iterates up one edge to the parent in a tree.
isLeaf | Test whether a tree iterator points to a leaf. (VSTree Iterator)
isLeftMaximal | Test whether the occurrences of an iterator's representative mutually differ in the character left of the hits. (VSTree Iterator)
isPartiallyLeftExtensible | Test whether the characters left of the two occurrences of representative are equal. (VSTree Iterator)
isRightTerminal | Test whether iterator points to a suffix. (VSTree Iterator)
isRoot | Test whether a tree iterator points to the root node. (VSTree Iterator)
isUnique | Test whether the representative occurs only once in every sequence. (VSTree Iterator)
lca | Returns the last common ancestor of two tree nodes.
lcp | Returns the length of the longest-common-prefix of two suffix tree nodes.
moveValue | Assigns value to item. (Iter)
nodeDepth | Returns the zero-based node depth of the iterator node.
nodeHullPredicate | If false this node and its subtree is concealed. (VSTree Iterator)
nodePredicate | If false this node will be skipped during the bottom-up traversal. (VSTree Iterator)
nodeUp | Returns the vertex descriptor of the parent node. (TopDown Iterator)
parentEdgeFirstChar | Returns the first character of the edge from an iterator node to its parent. (TopDown Iterator)
parentEdgeLabel | Returns a substring representing the edge from an iterator node to its parent. (TopDown Iterator)
parentEdgeLength | Returns the length of the edge from the iterator node to its parent. (TopDown Iterator)
parentRepLength | Returns the length of the substring representing the path from root to iterator's parent node. (TopDown Iterator)
position | Position of an iterator. (Iter)
range | Returns the suffix array interval borders of occurrences of representative substring or a q-gram in the index text. (VSTree Iterator)
repLength | Returns the length of the substring representing the path from root to iterator node. (VSTree Iterator)
representative | Returns a substring representing the path from root to iterator node. (VSTree Iterator)
value | Reference to the value. (VSTree Iterator)
Example Programs Constraint Iterator SeqAn - Sequence Analysis Library - www.seqan.de

Page built @2014/10/13 16:13:00