org.dishevelled.bio.tools

Class RenameReferences

java.lang.Object

org.dishevelled.bio.tools.RenameReferences

All Implemented Interfaces:

Callable<Integer>

Deprecated.

by RenameGff3References in version 2.1, to be removed in 3.0

public final class RenameReferences
extends Object
implements Callable<Integer>

Rename references in GFF3 files.

Author:

Michael Heuer

Constructor Summary

Constructors

Constructor and Description
RenameReferences(boolean chr, File inputGff3File, File outputGff3File) Deprecated. Rename references in GFF3 files.
RenameReferences(boolean chr, Path inputGff3Path, File outputGff3File) Deprecated. Rename references in GFF3 files.

Method Summary

Modifier and Type	Method and Description
(package private) static String	addChr(String seqid) Deprecated.
Integer	call() Deprecated.
static void	main(String[] args) Deprecated. Main.
(package private) static String	removeChr(String seqid) Deprecated.
(package private) String	rename(String seqid) Deprecated.

Methods inherited from class java.lang.Object

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

Constructor Detail

RenameReferences

public RenameReferences(boolean chr,
                        File inputGff3File,
                        File outputGff3File)

Deprecated.

Rename references in GFF3 files.

Parameters:

chr - true to add "chr" to chromosome names

inputGff3File - input GFF3 file, if any

outputGff3File - output GFF3 file, if any

RenameReferences

public RenameReferences(boolean chr,
                        Path inputGff3Path,
                        File outputGff3File)

Deprecated.

Rename references in GFF3 files.

Parameters:

chr - true to add "chr" to chromosome names

inputGff3Path - input GFF3 path, if any

outputGff3File - output GFF3 file, if any

Since:

2.1

Method Detail

call

public Integer call()
             throws Exception

Deprecated.

Specified by:

call in interface Callable<Integer>

Throws:

Exception

addChr

static String addChr(String seqid)

Deprecated.

removeChr

static String removeChr(String seqid)

Deprecated.

rename

String rename(String seqid)

Deprecated.

main

public static void main(String[] args)

Deprecated.

Main.

Parameters:

args - command line args