Shape

Class

Shape

Stores hash value and shape for an ungapped or gapped q-gram.

Shape


GappedShape	GenericShape	OneGappedShape	SimpleShape	UngappedShape

Shape<TValue, TSpec>

Parameters

TValue	The Value type of the string the shape is applied to (e.g. Dna).
TSpec	The specializing type. Default: SimpleShape, for ungapped q-grams.

Remarks

The ValueSize of Shape is the ValueSize of TValue which is the alphabet size.

To get the span or the weight of a shape call length or weight.

Specializations

GappedShape	A fixed gapped shape.
GenericShape	A variable gapped shape.
OneGappedShape	A variable shape with one optional gap.
SimpleShape	A variable length ungapped shape (also called q-gram or k-mer).
UngappedShape	A fixed length ungapped shape (also called q-gram or k-mer).

Metafunctions

Host	Type of the object a given object depends on.
LENGTH	Number of elements in a fixed-size container.
Size	Type of an object that is suitable to hold size information.
Value	Type of the items in the container.
ValueSize	Number of different values a value type object can have.
WEIGHT	Number of relevant positions in a shape.
WEIGHT	Number of relevant positions in a shape.

Member Functions

Shape

Constructor

Functions

countOccurrences	Returns the number of occurences of representative substring or a q-gram in the index text.
countOccurrencesMultiple	Returns the number of occurences of a q-gram for every sequence of a StringSet .
createCountArray	Builds an index on a StringSet storing how often a q-gram occurs in each sequence.
createQGramIndex	Builds a q-gram index on a sequence.
createQGramIndexDirOnly	Builds the directory of a q-gram index on a sequence.
createQGramIndexSAOnly	Builds the suffix array of a q-gram index on a sequence.
getOccurrence	Returns an occurence of the representative substring or a q-gram in the index text.
getOccurrences	Returns all occurences of the representative substring or a q-gram in the index text.
hash	Computes a (lower) hash value for a shape applied to a sequence.
hash2	Computes an unique hash value of a shape applied to a sequence, even if the sequence is shorter than the shape span
hash2Next	Computes a unique hash value for the adjacent shape, even if it is shorter than q.
hash2Upper	Computes an upper unique hash value of a shape applied to a sequence, even if the sequence is shorter than the shape span.
hashNext	Computes the hash value for the adjacent shape.
hashUpper	Computes an upper hash value for a shape applied to a sequence.
indexShape	Shortcut for getFibre(.., QGramShape).
length	The number of items/characters.
length	The number of items/characters.
range	Returns the suffix array interval borders of occurences of representative substring or a q-gram in the index text.
shapeToString	Converts a given shape into a sequence of '1' (relevant position) and '0' (irrelevant position).
value	Reference to the value.
weight	Number of relevant positions in a shape.

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