Gaps

Class

Gaps

Stores the gaps in a gapped sequences.

Gaps


AnchorGaps	ArrayGaps	SumlistGaps

Gaps<TSource, TSpec>

Include Headers

seqan/align.h

Parameters

TSource	Type of the ungapped sequence. Metafunctions: Source
TSpec	The specializing type. Metafunctions: Spec

Remarks

The gaps are stored separately from the sequence. The ungapped sequence is called the source of the gaps object. Gaps either stores the source (then it is the owner of the source), or refers to an external source (then it is dependent).

Specializations

AnchorGaps	Stores gaps anchors of the first characters behind gaps.
ArrayGaps	Stores gaps sizes in an array.
SumlistGaps	Stores gaps in a Sumlist.

Metafunctions

GetSource	The type returned by the source function.
GetValue	Type for reading values.
Iterator	Type of iterator objects that are used to traverse the container.
Position	Type of an object that represents a position in a container.
Reference	Reference type.
Source	The underlying sequence for alignments or gaps data structures.
Spec	The spec of a class.
Value	Type of the items in the container.

Functions

assignSource	Assigns the source to a new value.
begin	The begin of a container.
clearGaps	Remove blanks from a gapped sequence.
clippedBeginPosition	Begin position of the source segment.
clippedEndPosition	Position of the end of the source segment.
countCharacters	Count characters at a specific position in a gapped sequence.
countGaps	Count blanks at a specific position in a gapped sequence.
createSource	Creates a new source.
dependentSource	Test if object depends from it's source.
detach	Makes an object independent from other objects.
emptySource	Test if there is a source.
end	The end of a container.
getValue	Access to the value.
id	A value that identifies the underlying sequence.
insertGap	Insert one blank into a gapped sequence.
insertGaps	Insert blanks into a gapped sequence.
isGap	Test a gapped sequence for gaps at a specific position.
length	The number of items/characters.
length	The number of items/characters.
moveSource	Moves the source to a new value.
removeGap	Removes one blank from a gapped sequence.
removeGaps	Removes blanks from a gapped sequence.
setSource	Let an external object be the source.
source	The source of an object.
sourceBegin	Begin of the source segment.
sourceEnd	End of the source segment.
sourceLength	Length of the source.
sourceSegment	The used part of the source.
toSourcePosition	Transforms view to source position, if the view position is a gap, the original position of the next non-gap entry is returned.
toViewPosition	Transforms source to view position.
value	Reference to the value.

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