PairwiseAlignment (biojava 4.2.1 API)

public class PairwiseAlignment
extends Object

Constructors
Constructor and Description
`PairwiseAlignment(SequenceAlignmentCluster cluster1, SequenceAlignmentCluster cluster2)`

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`int[][][]`	`getAlignment()`
`double`	`getAlignmentLengthFraction()`
`SequenceAlignmentCluster`	`getCluster1()`
`SequenceAlignmentCluster`	`getCluster2()`
`double`	`getRmsd()`
`double`	`getSequenceIdentity()`
`void`	`setAlignment(int[][][] alignment)`
`void`	`setAlignmentLengthFraction(double alignmentLengthFraction)`
`void`	`setRmsd(double rmsd)`
`void`	`setSequenceIdentity(double sequenceIdentity)`
`String`	`toString()`

public PairwiseAlignment(SequenceAlignmentCluster cluster1,
                         SequenceAlignmentCluster cluster2)

public SequenceAlignmentCluster getCluster1()

public SequenceAlignmentCluster getCluster2()

public double getAlignmentLengthFraction()

public void setAlignmentLengthFraction(double alignmentLengthFraction)

public void setSequenceIdentity(double sequenceIdentity)

public void setAlignment(int[][][] alignment)

Class PairwiseAlignment