Class Specialization
Stores gaps anchors of the first characters behind gaps.
Gaps<TSource, AnchorGaps<TGapAnchors> >
Include Headers
Type of the ungapped sequence.
Metafunctions: Source
Type of the sequence of gap anchors, e.g. a string of Class.GapAnchor.
Specialization of
GetValueType for reading values. (Gaps)
IsSequenceDetermines whether a container stores its elements in sequential order. (Gaps)
IteratorType of iterator objects that are used to traverse the container. (Gaps)
PositionType of an object that represents a position in a container. (Gaps)
ReferenceReference type. (Gaps)
SizeType of an object that is suitable to hold size information. (Gaps)
SourceReturn underlying sequence of Gaps/Alignments. (Gaps)
ValueType of the items in the container or behind an iterator. (Gaps)
Member Functions
GapsConstructor (Gaps)
assignSourceAssign the source of a Gaps object, copying data. (Gaps)
assignValueAssigns value to item. (ContainerConcept)
backThe last item in container. (ContainerConcept)
bandedChainAlignmentComputes the best global pairwise alignment between two sequences given a non-empty seed chain. (Gaps)
beginThe begin of a container. (ContainerConcept)
beginPositionBegin position of object in host. (ContainerConcept)
clearClippingClear clipping from Gaps object. (Gaps)
clearGapsClear gaps and clipping from Gaps object. (Gaps)
clippedBeginPositionReturn the begin position of the clipping in the unclipped gapped sequence. (Gaps)
clippedEndPositionReturn the end position of the clipping in the unclipped gapped sequence. (Gaps)
endThe end of a container. (ContainerConcept)
endPositionEnd position of object in host. (ContainerConcept)
frontThe first item in container. (ContainerConcept)
getValueAccess to the value. (ContainerConcept)
globalAlignmentComputes the best global pairwise alignment. (Gaps)
insertGapInsert one gap into a gapped sequence. (Gaps)
insertGapsInsert multiple gaps into a gapped sequence. (Gaps)
isGapQuery whether a given clipped view position is a gap. (Gaps)
lengthThe number of items/characters. (ContainerConcept)
localAlignmentComputes the best pairwise local alignment using the Smith-Waterman algorithm. (Gaps)
moveValueAssigns value to item. (ContainerConcept)
nextLocalAlignmentCompute next suboptimal local alignment. (Gaps)
positionPosition of an iterator. (ContainerConcept)
positionGapToSeqConvert from gap-space in the global alignment to the sequence-space on the reference.
positionSeqToGapConvert from sequence space on the reference to gap space in the global alignment.
removeGapRemove one gap from a gapped sequence. (Gaps)
removeGapsRemove multiple gaps from a gapped sequence. (Gaps)
setBeginPositionSet the begin position of the clipped gapped sequence, given a source position. (Gaps)
setClippedBeginPositionSets the begin position of the clipping. (Gaps)
setClippedEndPositionSets the end position of the clipping. (Gaps)
setEndPositionSet the end position of the clipped gapped sequence, given a source position. (Gaps)
setSourceSet the source of a Gaps object, do not copy if possible. (Gaps)
sourceReturn underlying object. (Gaps)
splitAlignmentCompute split alignments. (Gaps)
toSourcePositionTransforms view to source position, if the view position is a gap, the original position of the next non-gap entry is returned. (Gaps)
toViewPositionTransforms source to view position. (Gaps)
unclippedLengthReturn length of the gapped sequence without clipping. (Gaps)
SeqAn - Sequence Analysis Library -

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