public class SmithWaterman extends NeedlemanWunsch
pairwiseAlignment
of this class. It
uses affine gap penalties if and only if the expenses of a delete or insert
operation are unequal to the expenses of gap extension. This uses
significantly more memory (four times as much) and increases the runtime if
swapping is performed.alignment, CostMatrix, pairalign, subMatrix
Constructor and Description |
---|
SmithWaterman(short match,
short replace,
short insert,
short delete,
short gapExtend,
SubstitutionMatrix matrix)
Constructs the new SmithWaterman alignment object.
|
Modifier and Type | Method and Description |
---|---|
int |
pairwiseAlignment(SymbolList query,
SymbolList subject)
Overrides the method inherited from the NeedlemanWunsch and performs only a
local alignment.
|
void |
setDelete(short del)
Overrides the method inherited from the NeedlemanWunsch and sets the
penalty for a delete operation to the specified value.
|
void |
setGapExt(short ge)
Overrides the method inherited from the NeedlemanWunsch and sets the
penalty for an extension of any gap (insert or delete) to the specified
value.
|
void |
setInsert(short ins)
Overrides the method inherited from the NeedlemanWunsch and sets the
penalty for an insert operation to the specified value.
|
void |
setMatch(short ma)
Overrides the method inherited from the NeedlemanWunsch and sets the
penalty for a match operation to the specified value.
|
void |
setReplace(short rep)
Overrides the method inherited from the NeedlemanWunsch and sets the
penalty for a replace operation to the specified value.
|
alignAll, getAlignment, getAlignmentString, getDelete, getEditDistance, getGapExt, getInsert, getMatch, getReplace, min, printAlignment, printCostMatrix, setSubstitutionMatrix
formatOutput
public SmithWaterman(short match, short replace, short insert, short delete, short gapExtend, SubstitutionMatrix matrix)
SubstitutionMatrix
equals the alphabet of both the query and the target Sequence
.
The alignment parameters here are expenses and not scores as they are in
the NeedlemanWunsch
object. scores are just given by
multiplying the expenses with (-1)
. For example you could
use parameters like "-2, 5, 3, 3, 0". If the expenses for gap extension are
equal to the cost of starting a gap (delete or insert), no affine gap
penalties are used, which saves memory.match
- expenses for a matchreplace
- expenses for a replace operationinsert
- expenses for a gap opening in the query sequencedelete
- expenses for a gap opening in the target sequencegapExtend
- expenses for the extension of a gap which was started earlier.matrix
- the SubstitutionMatrix
object to use.public void setInsert(short ins)
setInsert
in class NeedlemanWunsch
ins
- costs for a single insert operationpublic void setDelete(short del)
setDelete
in class NeedlemanWunsch
del
- costs for a single deletion operationpublic void setGapExt(short ge)
setGapExt
in class NeedlemanWunsch
ge
- costs for any gap extensionpublic void setMatch(short ma)
setMatch
in class NeedlemanWunsch
ma
- costs for a single match operationpublic void setReplace(short rep)
setReplace
in class NeedlemanWunsch
rep
- costs for a single replace operationpublic int pairwiseAlignment(SymbolList query, SymbolList subject) throws BioRuntimeException
pairwiseAlignment
in class NeedlemanWunsch
BioRuntimeException
SequenceAlignment.pairwiseAlignment(org.biojava.bio.symbol.SymbolList,
org.biojava.bio.symbol.SymbolList)