MaxRepeats Iterator

Class Specialization

MaxRepeats Iterator

Iterator to search for all maximal repeats.



Iterator		VSTree Iterator

BottomUp Iterator

MaxRepeats Iterator

Iterator<TContainer, MaxRepeats>::Type

Iter<TContainer, VSTree< BottomUp<MaxRepeats> > >

Include Headers

seqan/index.h

Parameters

TContainer

Type of an index that can be iterated with a bottom-up iterator.

Metafunctions: Container

Types: IndexEsa

Specialization of

BottomUp Iterator

Implements

Iterator

Member Functions

Iterator	Constructor (BottomUp Iterator)
Iterator	Constructor

Functions

alignment	Returns an alignment of the occurences of the representative substring in the index text. (VSTree Iterator)
assignValue	Assigns value to item. (Iterator)
atBegin	Determines whether an iterator is at the beginning position. (Iterator)
atEnd	Determines whether an iterator is at the end position. (BottomUp Iterator)
atEnd	Determines whether an iterator is at the end position. (BottomUp Iterator)
begin	The begin of a container.
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 occurences of representative substring or a q-gram in the index text. (VSTree Iterator)
end	The end of a container.
getFrequency	Returns the number of sequences, which contain the representative as a substring. (VSTree Iterator)
getOccurrence	Returns an occurence of the representative substring or a q-gram in the index text. (VSTree Iterator)
getOccurrences	Returns all occurences of the representative substring or a q-gram in the index text. (VSTree Iterator)
getOccurrencesBwt	Returns the characters left beside all occurence of the representative substring in the index text. (VSTree Iterator)
getValue	Access to the value. (Iterator)
goBegin	Iterates to the first position of a container. (BottomUp Iterator)
goBegin	Iterates to the first position of a container. (BottomUp Iterator)
goEnd	Iterates to the last position of a container. (BottomUp Iterator)
goEnd	Iterates to the last position of a container. (BottomUp Iterator)
goFurther	Iterates some steps further. (Iterator)
goNext	Iterates to next position. (BottomUp Iterator)
goNext	Iterates to next position. (BottomUp Iterator)
goPrevious	Iterates to pevious position. (Iterator)
isLeaf	Test whether iterator points to a leaf. (VSTree Iterator)
isLeftMaximal	Test whether the occurences 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 occurences of representative are equal. (VSTree Iterator)
isRightTerminal	Test whether iterator points to a suffix. (VSTree Iterator)
isRoot	Test whether iterator points to the root node. (VSTree Iterator)
isUnique	Test whether the representative occurs only once in every sequence. (VSTree Iterator)
length	The number of items/characters.
moveValue	Assigns value to item. (Iterator)
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)
position	Position of an iterator. (Iterator)
range	Returns the suffix array interval borders of occurences 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)
value	Reference to the value. (VSTree Iterator)

Example Programs

Maximal Repeats

SeqAn - Sequence Analysis Library - www.seqan.de