Package org.biojava.bio.alignment

Class AlignmentAlgorithm

java.lang.Object

org.biojava.bio.alignment.AlignmentAlgorithm

Direct Known Subclasses:

NeedlemanWunsch, SmithWaterman

public abstract class AlignmentAlgorithm
extends Object

This Interface provides methods for the alignment of bio-sequences.

Author:

Andreas Dräger , Mark Schreiber

Constructor Summary

Constructors

Constructor	Description
AlignmentAlgorithm()

Method Summary

Modifier and Type	Method	Description
List<AlignmentPair>	alignAll(SequenceIterator source, SequenceDB subjectDB)
abstract AlignmentPair	pairwiseAlignment(SymbolList query, SymbolList subject)	Performs a pairwise sequence alignment of the two given sequences.

Methods inherited from class java.lang.Object

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

Constructor Detail

AlignmentAlgorithm

public AlignmentAlgorithm()

Method Detail

alignAll

public List<AlignmentPair> alignAll(SequenceIterator source,
                                    SequenceDB subjectDB)
                             throws Exception

Parameters:

source - a SequenceIterator containing a set of sequences to be aligned with

subjectDB - the SequenceDB containing another set of sequences.

Returns:

a list containing the results of all single alignments performed by this method.

Throws:

NoSuchElementException

Exception

pairwiseAlignment

public abstract AlignmentPair pairwiseAlignment(SymbolList query,
                                                SymbolList subject)
                                         throws Exception

Performs a pairwise sequence alignment of the two given sequences.

Parameters:

query -

subject -

Returns:

score of the alignment or the distance.

Throws:

Exception