org.dishevelled.bio.assembly.gfa1

Class Gfa1Reader

java.lang.Object

org.dishevelled.bio.assembly.gfa1.Gfa1Reader

@Immutable
public final class Gfa1Reader
extends Object

Graphical Fragment Assembly (GFA) 1.0 reader.

Author:

Michael Heuer

Method Summary

Modifier and Type	Method and Description
static Iterable<Header>	header(Readable readable) Read zero or more GFA 1.0 header records from the specified readable.
static Iterable<Gfa1Record>	read(Readable readable) Read zero or more GFA 1.0 records from the specified readable.
static Iterable<Segment>	segments(Readable readable) Read zero or more GFA 1.0 segment records from the specified readable.
static void	stream(Readable readable, Gfa1Listener listener) Stream zero or more GFA 1.0 records from the specified readable.

Methods inherited from class java.lang.Object

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

Method Detail

read

public static Iterable<Gfa1Record> read(Readable readable)
                                 throws IOException

Read zero or more GFA 1.0 records from the specified readable.

Parameters:

readable - readable to read from, must not be null

Returns:

zero or more GFA 1.0 records read from the specified readable

Throws:

IOException - if an I/O error occurs

header

public static Iterable<Header> header(Readable readable)
                               throws IOException

Read zero or more GFA 1.0 header records from the specified readable. Only header records at the head of the readable (i.e. those before any containment, link, path, segment, or traversal records) will be returned.

Parameters:

readable - readable to read from, must not be null

Returns:

zero or more GFA 1.0 header records read from the specified readable

Throws:

IOException - if an I/O error occurs

segments

public static Iterable<Segment> segments(Readable readable)
                                  throws IOException

Read zero or more GFA 1.0 segment records from the specified readable. Only segment records at the head of the readable (i.e. those before any containment, link, path, or traversal records) will be returned.

Parameters:

readable - readable to read from, must not be null

Returns:

zero or more GFA 1.0 segment records read from the specified readable

Throws:

IOException - if an I/O error occurs

stream

public static void stream(Readable readable,
                          Gfa1Listener listener)
                   throws IOException

Stream zero or more GFA 1.0 records from the specified readable.

Parameters:

readable - readable to stream from, must not be null

listener - event based listener callback, must not be null

Throws:

IOException - if an I/O error occurs