Class Specialization
SumlistGaps
Stores gaps in a Sumlist.

Gaps

SumlistGaps

Gaps<TSource, SumlistGaps>
Include Headers
seqan/align.h
Parameters

TSource | Type of the ungapped sequence. Metafunctions: Source

Specialization of
Gaps
Metafunctions

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

Functions

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

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