org.biojava.bio.symbol

Class SimpleGappedSymbolList.Block

java.lang.Object

org.biojava.bio.symbol.SimpleGappedSymbolList.Block

All Implemented Interfaces:

Serializable

Enclosing class:

SimpleGappedSymbolList

protected static final class SimpleGappedSymbolList.Block
extends Object
implements Serializable

An aligned block.

The alignment is actualy stoored as a list of these objects. Each block is contiguous with the next in the source fields, but may be gapped in the view fields.

Author:

Matthew Pocock

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
int	sourceEnd
int	sourceStart
int	viewEnd
int	viewStart

Constructor Summary

Constructors

Constructor and Description
SimpleGappedSymbolList.Block(int sourceStart, int sourceEnd, int viewStart, int viewEnd)
SimpleGappedSymbolList.Block(SimpleGappedSymbolList.Block block)

Method Summary

Methods

Modifier and Type	Method and Description
boolean	isSane()
String	toString()

Methods inherited from class java.lang.Object

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

Field Detail

sourceStart

public int sourceStart

sourceEnd

public int sourceEnd

viewStart

public int viewStart

viewEnd

public int viewEnd

Constructor Detail

SimpleGappedSymbolList.Block

public SimpleGappedSymbolList.Block(SimpleGappedSymbolList.Block block)

SimpleGappedSymbolList.Block

public SimpleGappedSymbolList.Block(int sourceStart,
                            int sourceEnd,
                            int viewStart,
                            int viewEnd)

Method Detail

isSane

public boolean isSane()

toString

public String toString()

Overrides:

toString in class Object