Class DPBandConfig
Simple class to configure banded alignments.

Defined in <seqan/align.h>
Signature template <typename TSwitch> class DPBandConfig<TSwitch>;

Template Parameters

TSwitch Tag to switch between banded and unbanded alignments. One of DPBandSwitch. Defaults to BandOff.

Member Function Overview

Interface Function Overview

Interface Metafunction Overview

Detailed Description

To compute banded alignments use DPBand as a shortcut for the DPBandConfig with band switched on.

Member Functions Detail

DPBandConfig<TSwitch>(); DPBandConfig<BandOn>(lowerDiag, upperDiag);

Constructor.

Template Parameters

TSwitch Tag to switch between banded and unbanded alignments. One of DPBandSwitch. The second constructor is only supported when DPBandConfig is specialized with BandOn.

Parameters

lowerDiag The value for the lower diagonal of the band.
upperDiag The value for the upper diagonal of the band.

A negative value for the diagonals indicates an intersection of the diagonal with the vertical sequence (y-axis) and a positive value indicates an intersection with the horizontal sequence (x-axis). The value of the lower diagonal has to compare less or equal to the value of the upper diagonal.

Data Races

Thread safety unknown!

Interface Functions Detail

TSize bandSize(obj);

Note.

If the band is switched off this function always returns 0.

Returns the size of the band.

Parameters

obj The object of type DPBandConfig to query the band size for.

Returns

TSize The number of diagonals covered by the band.

Data Races

Thread safety unknown!

TPosition lowerDiagonal(obj);

Note.

If the band is switched off this function always returns 0.

Returns the value of the lower diagonal.

Parameters

obj The object of type DPBandConfig to query the lower diagonal for.

Returns

TPosition The value of the lower diagonal.

Data Races

Thread safety unknown!

setLowerDiagonal(obj, val);

Note.

If the band is switched off, this function defaults to no-op.

Sets the value of the lower diagonal.

Parameters

obj The object of type DPBandConfig to set the lower diagonal for.
val The new value for the lower diagonal.

Data Races

Thread safety unknown!

setUpperDiagonal(obj, val);

Note.

If the band is switched off, this function defaults to no-op.

Sets the value of the upper diagonal.

Parameters

obj The object of type DPBandConfig to set the upper diagonal for.
val The new value for the upper diagonal.

Data Races

Thread safety unknown!

TPosition upperDiagonal(obj);

Note.

If the band is switched off this function always returns 0.

Returns the value of the upper diagonal.

Parameters

obj The object of type DPBandConfig to query the upper diagonal for.

Returns

TPosition The value of the upper diagonal.

Data Races

Thread safety unknown!

Interface Metafunctions Detail

typename Position<T>::Type;

Metafunction returning the position type.

Template Parameters

T The type DPBandConfig to query the position type for.

Returns

TPosition The position type.

typename Size<T>::Type;

Metafunction returning the size type.

Template Parameters

T The type DPBandConfig to query the size type for.

Returns

TSize The size type.