Gaps

Class

Gaps

Stores the gaps in a gapped sequences.

Gaps<TSource, TSpec>

Parameters

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

Metafunctions

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.
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.
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.
sourceSegment	The used part of the source.
value	Reference to the value.

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).

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