org.biojava.bio.alignment
Class SmithWaterman

java.lang.Object
  org.biojava.bio.alignment.SequenceAlignment
      org.biojava.bio.alignment.NeedlemanWunsch
          org.biojava.bio.alignment.SmithWaterman

public class SmithWaterman
extends NeedlemanWunsch

Smith and Waterman developed an efficient dynamic programing algorithm to perform local sequence alignments, which returns the most conserved region of two sequences (longes common substring with modifications). This algorithm is performed by the method 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 swaping is performed.

Since:

1.5

Author:

Andreas Dräger, Gero Greiner

Field Summary

Fields inherited from class org.biojava.bio.alignment.NeedlemanWunsch

alignment, CostMatrix, pairalign, subMatrix

Constructor Summary

SmithWaterman(double match, double replace, double insert, double delete, double gapExtend, SubstitutionMatrix matrix)
Constructs the new SmithWaterman alignment object.

Method Summary

double	pairwiseAlignment(Sequence query, Sequence subject) Overrides the method inherited from the NeedlemanWunsch and performs only a local alignment.
void	setDelete(double del) Overrides the method inherited from the NeedlemanWunsch and sets the penalty for a delete operation to the specified value.
void	setGapExt(double 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(double ins) Overrides the method inherited from the NeedlemanWunsch and sets the penalty for an insert operation to the specified value.
void	setMatch(double ma) Overrides the method inherited from the NeedlemanWunsch and sets the penalty for a match operation to the specified value.
void	setReplace(double rep) Overrides the method inherited from the NeedlemanWunsch and sets the penalty for a replace operation to the specified value.

Methods inherited from class org.biojava.bio.alignment.NeedlemanWunsch

alignAll, getAlignment, getAlignmentString, getDelete, getEditDistance, getGapExt, getInsert, getMatch, getReplace, min, printAlignment, printCostMatrix, setSubstitutionMatrix

Methods inherited from class org.biojava.bio.alignment.SequenceAlignment

formatOutput

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

SmithWaterman

public SmithWaterman(double match,
                     double replace,
                     double insert,
                     double delete,
                     double gapExtend,
                     SubstitutionMatrix matrix)

Constructs the new SmithWaterman alignment object. Alignments are only performed, if the alphabet of the given SubstitutionMatrix equals the alpabet 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 multipliing 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.

Parameters:

match - expenses for a match

replace - expenses for a replace operation

insert - expenses for a gap opening in the query sequence

delete - expenses for a gap opening in the target sequence

gapExtend - expenses for the extension of a gap which was started earlier.

matrix - the SubstitutionMatrix object to use.

Method Detail

setInsert

public void setInsert(double ins)

Overrides the method inherited from the NeedlemanWunsch and sets the penalty for an insert operation to the specified value. Reason: internaly scores are used instead of penalties so that the value is muliplied with -1.

Overrides:

setInsert in class NeedlemanWunsch

Parameters:

ins - costs for a single insert operation

setDelete

public void setDelete(double del)

Overrides the method inherited from the NeedlemanWunsch and sets the penalty for a delete operation to the specified value. Reason: internaly scores are used instead of penalties so that the value is muliplied with -1.

Overrides:

setDelete in class NeedlemanWunsch

Parameters:

del - costs for a single deletion operation

setGapExt

public void setGapExt(double 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. Reason: internaly scores are used instead of penalties so that the value is muliplied with -1.

Overrides:

setGapExt in class NeedlemanWunsch

Parameters:

ge - costs for any gap extension

setMatch

public void setMatch(double ma)

Overrides the method inherited from the NeedlemanWunsch and sets the penalty for a match operation to the specified value. Reason: internaly scores are used instead of penalties so that the value is muliplied with -1.

Overrides:

setMatch in class NeedlemanWunsch

Parameters:

ma - costs for a single match operation

setReplace

public void setReplace(double rep)

Overrides the method inherited from the NeedlemanWunsch and sets the penalty for a replace operation to the specified value. Reason: internaly scores are used instead of penalties so that the value is muliplied with -1.

Overrides:

setReplace in class NeedlemanWunsch

Parameters:

rep - costs for a single replace operation

pairwiseAlignment

public double pairwiseAlignment(Sequence query,
                                Sequence subject)
                         throws BioRuntimeException

Overrides the method inherited from the NeedlemanWunsch and performs only a local alignment. It finds only the longest common subsequence. This is good for the beginning, but it might be better to have a system to find more than only one hit within the score matrix. Therfore one should only define the k-th best hit, where k is somehow related to the number of hits.

Overrides:

pairwiseAlignment in class NeedlemanWunsch

Returns:

score of the alignment or the distance.

Throws:

BioRuntimeException

See Also:

SequenceAlignment.pairwiseAlignment(org.biojava.bio.seq.Sequence, org.biojava.bio.seq.Sequence)