Class Specialization
ArrayGaps
Stores length of gap- and non-gapped runs in an array.
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Include Headers
seqan/align.h
Parameters
Type of the ungapped sequence. Metafunctions: Source |
Specialization of
Implements
Metafunctions
| Type for reading values. (Gaps) | |
| Determines whether a container stores its elements in sequential order. (Gaps) | |
| Type of iterator objects that are used to traverse the container. (Gaps) | |
| Type of an object that represents a position in a container. (Gaps) | |
| Reference type. (Gaps) | |
| Type of an object that is suitable to hold size information. (Gaps) | |
| Return underlying sequence of Gaps/Alignments. (Gaps) | |
| Type of the items in the container or behind an iterator. (Gaps) |
Functions
| Assign the source of a Gaps object, copying data. (Gaps) | |
| Assigns value to item. (ContainerConcept) | |
| The last item in container. (ContainerConcept) | |
| Computes the best global pairwise alignment between two sequences given a non-empty seed chain. (Gaps) | |
| The begin of a container. (ContainerConcept) | |
| Begin position of object in host. (ContainerConcept) | |
| Clear clipping from Gaps object. (Gaps) | |
| Clear gaps and clipping from Gaps object. (Gaps) | |
| Return the begin position of the clipping in the unclipped gapped sequence. (Gaps) | |
| Return the end position of the clipping in the unclipped gapped sequence. (Gaps) | |
| The end of a container. (ContainerConcept) | |
| End position of object in host. (ContainerConcept) | |
| The first item in container. (ContainerConcept) | |
| Access to the value. (ContainerConcept) | |
| Computes the best global pairwise alignment. (Gaps) | |
| Insert one gap into a gapped sequence. (Gaps) | |
| Insert multiple gaps into a gapped sequence. (Gaps) | |
| Query whether a given clipped view position is a gap. (Gaps) | |
| The number of items/characters. (ContainerConcept) | |
| Computes the best pairwise local alignment using the Smith-Waterman algorithm. (Gaps) | |
| Assigns value to item. (ContainerConcept) | |
| Compute next suboptimal local alignment. (Gaps) | |
| Position of an iterator. (ContainerConcept) | |
| Remove one gap from a gapped sequence. (Gaps) | |
| Remove multiple gaps from a gapped sequence. (Gaps) | |
| Set the begin position of the clipped gapped sequence, given a source position. (Gaps) | |
| Sets the begin position of the clipping. (Gaps) | |
| Sets the end position of the clipping. (Gaps) | |
| Set the end position of the clipped gapped sequence, given a source position. (Gaps) | |
| Set the source of a Gaps object, do not copy if possible. (Gaps) | |
| Return underlying object. (Gaps) | |
| Compute split alignments. (Gaps) | |
| Transforms view to source position, if the view position is a gap, the original position of the next non-gap entry is returned. (Gaps) | |
| Transforms source to view position. (Gaps) | |
| Return length of the gapped sequence without clipping. (Gaps) |
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