Class
DPBandConfigSimple class to configure banded alignments.
Simple class to configure banded alignments.
Defined in | <seqan/align.h> |
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Signature |
template <typename TSwitch>
class DPBandConfig<TSwitch>;
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Template Parameters
TSwitch |
Tag to switch between banded and unbanded alignments. One of DPBandSwitch. Defaults to BandOff. |
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Member Function Overview
Interface Function Overview
-
TSize bandSize(obj);
Returns the size of the band. -
TPosition lowerDiagonal(obj);
Returns the value of the lower diagonal. -
setLowerDiagonal(obj, val);
Sets the value of the lower diagonal. -
setUpperDiagonal(obj, val);
Sets the value of the upper diagonal. -
TPosition upperDiagonal(obj);
Returns the value of the upper diagonal.
Interface Metafunction Overview
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typename Position<T>::Type;
Metafunction returning the position type. -
typename Size<T>::Type;
Metafunction returning the size type.
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. |
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Parameters
lowerDiag
|
The value for the lower diagonal of the band. |
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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
If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.
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. |
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Returns
TSize |
The number of diagonals covered by the band. |
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Data Races
If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.
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. |
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Returns
TPosition |
The value of the lower diagonal. |
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Data Races
If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.
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. |
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val
|
The new value for the lower diagonal. |
Data Races
If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.
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. |
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val
|
The new value for the upper diagonal. |
Data Races
If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.
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. |
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Returns
TPosition |
The value of the upper diagonal. |
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Data Races
If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.