org.dishevelled.bio.tools

Class ExportSegments

java.lang.Object

org.dishevelled.bio.tools.ExportSegments

All Implemented Interfaces:

Callable<Integer>

public final class ExportSegments
extends Object
implements Callable<Integer>

Export assembly segment sequences in GFA 1.0 format to FASTA format.

Since:

2.1

Author:

Michael Heuer

Field Summary

Fields

Modifier and Type	Field and Description
(package private) static int	DEFAULT_LINE_WIDTH

Constructor Summary

Constructors

Constructor and Description
ExportSegments(File inputGfa1File, File outputFastaFile, int lineWidth) Export assembly segment sequences in GFA 1.0 format to FASTA format.
ExportSegments(Path inputGfa1Path, File outputFastaFile, int lineWidth) Export assembly segment sequences in GFA 1.0 format to FASTA format.

Method Summary

Modifier and Type	Method and Description
Integer	call()
(package private) static String	describeSegment(Segment segment)
static void	main(String[] args) Main.

Methods inherited from class java.lang.Object

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

Field Detail

DEFAULT_LINE_WIDTH

static final int DEFAULT_LINE_WIDTH

See Also:

Constant Field Values

Constructor Detail

ExportSegments

public ExportSegments(File inputGfa1File,
                      File outputFastaFile,
                      int lineWidth)

Export assembly segment sequences in GFA 1.0 format to FASTA format.

Parameters:

inputGfa1File - input GFA 1.0 file, if any

outputFastaFile - output FASTA file, if any

lineWidth - line width

ExportSegments

public ExportSegments(Path inputGfa1Path,
                      File outputFastaFile,
                      int lineWidth)

Export assembly segment sequences in GFA 1.0 format to FASTA format.

Parameters:

inputGfa1Path - input GFA 1.0 path, if any

outputFastaFile - output FASTA file, if any

lineWidth - line width

Since:

2.1

Method Detail

call

public Integer call()
             throws Exception

Specified by:

call in interface Callable<Integer>

Throws:

Exception

describeSegment

static String describeSegment(Segment segment)

main

public static void main(String[] args)

Main.

Parameters:

args - command line args