com.milaboratory.core.alignment

Class BandedMatrix

java.lang.Object

com.milaboratory.core.alignment.BandedMatrix

All Implemented Interfaces:

Serializable

public final class BandedMatrix
extends Object
implements Serializable

BandedMatrix - class which used to store alignment matrix for BandedLinearAligner.

It stores only main diagonal values as well as values of diagonal which are closed to main one (it's defined by #rowFactor and #columnDelta)

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
static int	DEFAULT_VALUE Value of empty cell

Constructor Summary

Constructors

Constructor and Description
BandedMatrix(CachedIntArray cachedArray, int size1, int size2, int width)

Method Summary

Methods

Modifier and Type	Method and Description
int	get(int i, int j)
int	getColumnDelta()
int	getRowFactor()
void	set(int i, int j, int value)
String	toString()

Methods inherited from class java.lang.Object

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

Field Detail

DEFAULT_VALUE

public static final int DEFAULT_VALUE

Value of empty cell

See Also:

Constant Field Values

Constructor Detail

BandedMatrix

public BandedMatrix(CachedIntArray cachedArray,
            int size1,
            int size2,
            int width)

Method Detail

getRowFactor

public int getRowFactor()

getColumnDelta

public int getColumnDelta()

get

public int get(int i,
      int j)

set

public void set(int i,
       int j,
       int value)

toString

public String toString()

Overrides:

toString in class Object