edu.rit.compbio.seq

Class ProteinLocalAlignmentSmp

java.lang.Object

edu.rit.compbio.seq.ProteinLocalAlignment

edu.rit.compbio.seq.ProteinLocalAlignmentSmp

public class ProteinLocalAlignmentSmp
extends ProteinLocalAlignment

Class ProteinLocalAlignmentSmp 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 ParallelTeam of threads. Thus, this class is suitable for use in an SMP parallel program or a hybrid parallel program.

As an example of how the computation is performed in parallel while obeying the sequential dependencies in the Smith-Waterman algorithm, suppose the query sequence has 100 elements, the subject sequence has 500 elements, and the parallel team has 4 threads. The 500 columns of the scoring matrix S are partitioned equally among the threads: thread 0 gets columns 1..125, thread 1 gets columns 126..250, thread 2 gets columns 251..375, thread 3 gets columns 376..500. Then S is computed in parallel in a series of rounds:

Round:	Thread 0 computes:	Thread 1 computes:	Thread 2 computes:	Thread 3 computes:
1	S[1][1..125]	—	—	—
2	S[2][1..125]	S[1][126..250]	—	—
3	S[3][1..125]	S[2][126..250]	S[1][251..375]	—
4	S[4][1..125]	S[3][126..250]	S[2][251..375]	S[1][376..500]
5	S[5][1..125]	S[4][126..250]	S[3][251..375]	S[2][376..500]
…	…	…	…	…
99	S[99][1..125]	S[98][126..250]	S[97][251..375]	S[96][376..500]
100	S[100][1..125]	S[99][126..250]	S[98][251..375]	S[97][376..500]
101	—	S[100][126..250]	S[99][251..375]	S[98][376..500]
102	—	—	S[100][251..375]	S[99][376..500]
103	—	—	—	S[100][376..500]

After a short startup period, all columns of S are being computed in parallel, with different threads working on different rows so as to obey the sequential dependencies. For example, S[4][126] is computed (by thread 1 in round 5) after S[3][125] (by thread 0 in round 3), S[3][126] (by thread 1 in round 4), and S[4][125] (by thread 0 in round 4).

Constructor Summary

Constructors

Constructor and Description
ProteinLocalAlignmentSmp(ParallelTeam team) 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

ProteinLocalAlignmentSmp

public ProteinLocalAlignmentSmp(ParallelTeam team)

Construct a new protein sequence local alignment object.

Parameters:

team - Parallel thread team that will compute the alignment.

Throws:

java.lang.NullPointerException - (unchecked exception) Thrown if team is null.

Method Detail

align

public Alignment align()
                throws java.lang.Exception

Align the query sequence and the subject sequence. The parallel thread team specified to the constructor computes the alignment in parallel.

Specified by:

align in class ProteinLocalAlignment

Returns:

Alignment.

Throws:

java.lang.Exception - Thrown if an error occurred.