| Class Specialization ArrayGaps Stores length of gap- and non-gapped runs in an array.
SequenceConcept
Gaps
ArrayGaps
Gaps<TSequence, ArrayGaps> Include Headers seqan/align.h Parameters
TSequence | Type of the ungapped sequence. Metafunctions: Source
Specialization of Gaps Implements SequenceConcept Metafunctions
GetValue | Type for reading values. (Gaps)
IsSequence | Determines whether a container stores its elements in sequential order. (Gaps)
Iterator | Type of iterator objects that are used to traverse the container. (Gaps)
Position | Type of an object that represents a position in a container. (Gaps)
Reference | Reference type. (Gaps)
Size | Type of an object that is suitable to hold size information. (Gaps)
Source | Return underlying sequence of Gaps/Alignments. (Gaps)
Value | Type of the items in the container or behind an iterator. (Gaps)
Member Functions
Gaps | Constructor (Gaps)
Functions
assignSource | Assign the source of a Gaps object, copying data. (Gaps)
assignValue | Assigns value to item. (ContainerConcept)
back | The last item in container. (ContainerConcept)
bandedChainAlignment | Computes the best global pairwise alignment between two sequences given a non-empty seed chain. (Gaps)
begin | The begin of a container. (ContainerConcept)
beginPosition | Begin position of object in host. (ContainerConcept)
clearClipping | Clear clipping from Gaps object. (Gaps)
clearGaps | Clear gaps and clipping from Gaps object. (Gaps)
clippedBeginPosition | Return the begin position of the clipping in the unclipped gapped sequence. (Gaps)
clippedEndPosition | Return the end position of the clipping in the unclipped gapped sequence. (Gaps)
end | The end of a container. (ContainerConcept)
endPosition | End position of object in host. (ContainerConcept)
front | The first item in container. (ContainerConcept)
getValue | Access to the value. (ContainerConcept)
globalAlignment | Computes the best global pairwise alignment. (Gaps)
insertGap | Insert one gap into a gapped sequence. (Gaps)
insertGaps | Insert multiple gaps into a gapped sequence. (Gaps)
isGap | Query whether a given clipped view position is a gap. (Gaps)
length | The number of items/characters. (ContainerConcept)
localAlignment | Computes the best pairwise local alignment using the Smith-Waterman algorithm. (Gaps)
moveValue | Assigns value to item. (ContainerConcept)
nextLocalAlignment | Compute next suboptimal local alignment. (Gaps)
position | Position of an iterator. (ContainerConcept)
removeGap | Remove one gap from a gapped sequence. (Gaps)
removeGaps | Remove multiple gaps from a gapped sequence. (Gaps)
setBeginPosition | Set the begin position of the clipped gapped sequence, given a source position. (Gaps)
setClippedBeginPosition | Sets the begin position of the clipping. (Gaps)
setClippedEndPosition | Sets the end position of the clipping. (Gaps)
setEndPosition | Set the end position of the clipped gapped sequence, given a source position. (Gaps)
setSource | Set the source of a Gaps object, do not copy if possible. (Gaps)
source | Return underlying object. (Gaps)
splitAlignment | Compute split alignments. (Gaps)
toSourcePosition | Transforms view to source position, if the view position is a gap, the original position of the next non-gap entry is returned. (Gaps)
toViewPosition | Transforms source to view position. (Gaps)
unclippedLength | Return length of the gapped sequence without clipping. (Gaps)
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