com.milaboratory.core.alignment

Class BandedAligner

java.lang.Object

com.milaboratory.core.alignment.BandedAligner

public class BandedAligner
extends Object

Author:

Dmitry Bolotin, Stanislav Poslavsky

Constructor Summary

Constructors

Constructor and Description
BandedAligner()

Method Summary

Methods

Modifier and Type	Method and Description
static Alignment<NucleotideSequence>	alignGlobal(AlignmentScoring<NucleotideSequence> scoring, NucleotideSequence seq1, NucleotideSequence seq2, int offset1, int length1, int offset2, int length2, int width) Classical Banded Alignment.

Methods inherited from class java.lang.Object

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

Constructor Detail

BandedAligner

public BandedAligner()

Method Detail

alignGlobal

public static Alignment<NucleotideSequence> alignGlobal(AlignmentScoring<NucleotideSequence> scoring,
                                        NucleotideSequence seq1,
                                        NucleotideSequence seq2,
                                        int offset1,
                                        int length1,
                                        int offset2,
                                        int length2,
                                        int width)

Classical Banded Alignment. Both sequences must be highly similar. Align 2 sequence completely (i.e. while first sequence will be aligned against whole second sequence).

Parameters:

scoring - scoring system

seq1 - first sequence

seq2 - second sequence

offset1 - offset in first sequence

length1 - length of first sequence's part to be aligned

offset2 - offset in second sequence

length2 - length of second sequence's part to be aligned

width - width of banded alignment matrix. In other terms max allowed number of indels