Package org.broadinstitute.hellbender.tools

Class LocalAssembler.PathPartGap

java.lang.Object

org.broadinstitute.hellbender.tools.LocalAssembler.PathPartGap

All Implemented Interfaces:

LocalAssembler.PathPart

Enclosing class:

LocalAssembler

public static final class LocalAssembler.PathPartGap
extends Object
implements LocalAssembler.PathPart

A part of a path that isn't present in the graph.

Constructor Summary

Constructors

Constructor	Description
PathPartGap(LocalAssembler.KmerAdjacency kmer)

Method Summary

Modifier and Type	Method	Description
void	extend(char call)
LocalAssembler.Contig	getContig()
char	getFirstCall()
char	getLastCall()
int	getLength()
CharSequence	getSequence()
int	getStart()
int	getStop()
boolean	isGap()
LocalAssembler.PathPart	rc()

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.broadinstitute.hellbender.tools.LocalAssembler.PathPart

startsAtBeginning, stopsAtEnd

Constructor Details

PathPartGap

public PathPartGap(LocalAssembler.KmerAdjacency kmer)

Method Details

getContig

public LocalAssembler.Contig getContig()

Specified by:

getContig in interface LocalAssembler.PathPart

getSequence

public CharSequence getSequence()

Specified by:

getSequence in interface LocalAssembler.PathPart

extend

public void extend(char call)

Specified by:

extend in interface LocalAssembler.PathPart

getStart

public int getStart()

Specified by:

getStart in interface LocalAssembler.PathPart

getStop

public int getStop()

Specified by:

getStop in interface LocalAssembler.PathPart

isGap

public boolean isGap()

Specified by:

isGap in interface LocalAssembler.PathPart

getLength

public int getLength()

Specified by:

getLength in interface LocalAssembler.PathPart

rc

public LocalAssembler.PathPart rc()

Specified by:

rc in interface LocalAssembler.PathPart

getFirstCall

public char getFirstCall()

Specified by:

getFirstCall in interface LocalAssembler.PathPart

getLastCall

public char getLastCall()

Specified by:

getLastCall in interface LocalAssembler.PathPart