Class Specialization
SimpleShape
A variable length ungapped shape (also called q-gram or k-mer).
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SimpleShape | |||||||
Include Headers
seqan/index.h
Parameters
The Value type of the string the shape is applied to (e.g. |
Remarks
A SimpleShape must be resized first to a valid length. To do so, call resize.
Specialization of
Metafunctions
| Type of the object a given object depends on. (Shape) | |
| Number of elements in a fixed-size container. (Shape) | |
| Type of an object that is suitable to hold size information. (Shape) | |
| Type of the items in the container or behind an iterator. (Shape) | |
| Number of different values a value type object can have. (Shape) | |
| Number of relevant positions in a shape. (Shape) |
Functions
| Returns the number of occurrences of representative substring or a q-gram in the index text. (Shape) | |
| Returns the number of occurrences of a q-gram for every sequence of a StringSet . (Shape) | |
| Builds an index on a StringSet storing how often a q-gram occurs in each sequence. (Shape) | |
| Builds a q-gram index on a sequence. (Shape) | |
| Builds the directory of a q-gram index on a sequence. (Shape) | |
| Builds the suffix array of a q-gram index on a sequence. (Shape) | |
| Returns an occurrence of the representative substring or a q-gram in the index text. (Shape) | |
| Returns all occurrences of the representative substring or a q-gram in the index text. (Shape) | |
| Computes a (lower) hash value for a shape applied to a sequence. (Shape) | |
| Computes an unique hash value of a shape applied to a sequence, even if the sequence is shorter than the shape span (Shape) | |
| Computes a unique hash value for the adjacent shape, even if it is shorter than q. (Shape) | |
| Computes an upper unique hash value of a shape applied to a sequence, even if the sequence is shorter than the shape span. (Shape) | |
| Computes the hash value for the adjacent shape. (Shape) | |
| Computes an upper hash value for a shape applied to a sequence. (Shape) | |
| Shortcut for | |
| The number of items/characters. (Shape) | |
| Returns the suffix array interval borders of occurrences of representative substring or a q-gram in the index text. (Shape) | |
| Resizes a container. If the new length exceeds the old length the new elements are filled with copies of | |
| Reverse an object/container in-place. | |
| Converts a given shape into a sequence of '1' (relevant position) and '0' (irrelevant position). (Shape) | |
| Takes a shape given as a string of '1' (relevant position) and '0' (irrelevant position) and converts it into a Shape object. | |
| Reference to the value. (Shape) | |
| Number of relevant positions in a shape. (Shape) |
See Also
SeqAn - Sequence Analysis Library - www.seqan.de