org.utgenome.gwt.utgb.client.bio
Class CIGAR

java.lang.Object
  org.utgenome.gwt.utgb.client.bio.CIGAR

All Implemented Interfaces:

Serializable, Iterable<CIGAR.Element>

public class CIGAR
extends Object
implements Serializable, Iterable<CIGAR.Element>

CIGAR string (in SAM format) management utility

Author:

leo

See Also:

Serialized Form

Nested Class Summary

static class	CIGAR.Element
static class	CIGAR.Type

Constructor Summary

CIGAR()
Creates an empty CIGAR

CIGAR(String cigarString)

Method Summary

void	add(int length, CIGAR.Type type)
CIGAR.Element	get(int index)
List<CIGAR.Element>	getElements()
Iterator<CIGAR.Element>	iterator()
int	size() Return the number of CIGAR elements
String	toCIGARString()
String	toString()

Methods inherited from class java.lang.Object

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

Constructor Detail

CIGAR

public CIGAR()

Creates an empty CIGAR

CIGAR

public CIGAR(String cigarString)
      throws UTGBClientException

Throws:

UTGBClientException

Method Detail

add

public void add(int length,
                CIGAR.Type type)

size

public int size()

Return the number of CIGAR elements

Returns:

get

public CIGAR.Element get(int index)

getElements

public List<CIGAR.Element> getElements()

toCIGARString

public String toCIGARString()

toString

public String toString()

Overrides:

toString in class Object

iterator

public Iterator<CIGAR.Element> iterator()

Specified by:

iterator in interface Iterable<CIGAR.Element>