edu.rit.compbio.seq

Class ProteinLocalAlignmentSeq

java.lang.Object

edu.rit.compbio.seq.ProteinLocalAlignment

edu.rit.compbio.seq.ProteinLocalAlignmentSeq

public class ProteinLocalAlignmentSeq
extends ProteinLocalAlignment

Class ProteinLocalAlignmentSeq provides an object that does local alignments of ProteinSequences. For further information, see the base class ProteinLocalAlignment.

The align() method is designed to be executed by a single thread. Thus, this class is suitable for use in a sequential program or one process of a cluster parallel program.

Constructor Summary

Constructors

Constructor and Description
ProteinLocalAlignmentSeq() Construct a new protein sequence local alignment object.

Method Summary

Modifier and Type	Method and Description
Alignment	align() Align the query sequence and the subject sequence.

Methods inherited from class edu.rit.compbio.seq.ProteinLocalAlignment

setGapExistencePenalty, setGapExtensionPenalty, setQuerySequence, setSubjectSequence, setSubstitutionMatrix

Methods inherited from class java.lang.Object

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

Constructor Detail

ProteinLocalAlignmentSeq

public ProteinLocalAlignmentSeq()

Construct a new protein sequence local alignment object.

Method Detail

align

public Alignment align()

Align the query sequence and the subject sequence.

Specified by:

align in class ProteinLocalAlignment

Returns:

Alignment.