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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