Class
Shape
Stores hash value and shape for an ungapped or gapped q-gram.
Parameters
The Value type of the string the shape is applied to (e.g. | |
The specializing type. Default: SimpleShape, for ungapped q-grams. |
Remarks
Specializations
| A fixed gapped shape. | |
| A variable gapped shape. | |
| A variable shape with one optional gap. | |
| A variable length ungapped shape (also called q-gram or k-mer). | |
| A fixed length ungapped shape (also called q-gram or k-mer). |
Metafunctions
| Type of the object a given object depends on. | |
| Number of elements in a fixed-size container. | |
| Type of an object that is suitable to hold size information. | |
| Type of the items in the container. | |
| Number of different values a value type object can have. | |
| Number of relevant positions in a shape. | |
| Number of relevant positions in a shape. |
Member Functions
| Constructor |
Functions
| Returns the number of occurences of representative substring or a q-gram in the index text. | |
| Returns the number of occurences of a q-gram for every sequence of a StringSet . | |
| Builds an index on a StringSet storing how often a q-gram occurs in each sequence. | |
| Builds a q-gram index on a sequence. | |
| Builds the directory of a q-gram index on a sequence. | |
| Builds the suffix array of a q-gram index on a sequence. | |
| Returns an occurence of the representative substring or a q-gram in the index text. | |
| Returns all occurences of the representative substring or a q-gram in the index text. | |
| Computes a (lower) hash value for a shape applied to a sequence. | |
| Computes an unique hash value of a shape applied to a sequence, even if the sequence is shorter than the shape span | |
| Computes a unique hash value for the adjacent shape, even if it is shorter than q. | |
| Computes an upper unique hash value of a shape applied to a sequence, even if the sequence is shorter than the shape span. | |
| Computes the hash value for the adjacent shape. | |
| Computes an upper hash value for a shape applied to a sequence. | |
| Shortcut for | |
| The number of items/characters. | |
| The number of items/characters. | |
| Returns the suffix array interval borders of occurences of representative substring or a q-gram in the index text. | |
| Converts a given shape into a sequence of '1' (relevant position) and '0' (irrelevant position). | |
| Reference to the value. | |
| Number of relevant positions in a shape. |
SeqAn - Sequence Analysis Library - www.seqan.de
