| Class Gaps Stores the gaps in a gapped sequences.
Gaps
ArrayGaps | SequenceGaps | SumlistGaps
Gaps<TSource, TSpec> Parameters
TSource | Type of the ungapped sequence. Metafunctions: Source
TSpec | The specializing type. Metafunctions: Spec
Specializations
ArrayGaps | Stores gaps sizes in an array.
SequenceGaps | Stores gapped sequences as sequences including blank signs.
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.
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.
sourceLength | Length of the source.
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). SeqAn - Sequence Analysis Library - www.seqan.de