org.dishevelled.bio.tools

Class CreateSequenceDictionary

java.lang.Object

org.dishevelled.bio.tools.CreateSequenceDictionary

All Implemented Interfaces:

Callable<Integer>

public final class CreateSequenceDictionary
extends Object
implements Callable<Integer>

Create a SequenceDictionary from DNA sequences in FASTA format.

Since:

2.1

Author:

Michael Heuer

Constructor Summary

Constructors

Constructor and Description
CreateSequenceDictionary(File inputFastaFile, File outputSequenceDictionaryFile) Create a SequenceDictionary from DNA sequences in FASTA format.
CreateSequenceDictionary(Path inputFastaPath, File outputSequenceDictionaryFile) Create a SequenceDictionary from DNA sequences in FASTA format.
CreateSequenceDictionary(URL url, File inputFastaFile, File outputSequenceDictionaryFile) Create a SequenceDictionary from DNA sequences in FASTA format with the specified URL.
CreateSequenceDictionary(URL url, Path inputFastaPath, File outputSequenceDictionaryFile) Create a SequenceDictionary from DNA sequences in FASTA format with the specified URL.

Method Summary

Modifier and Type	Method and Description
Integer	call()
static void	main(String[] args) Main.

Methods inherited from class java.lang.Object

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

Constructor Detail

CreateSequenceDictionary

public CreateSequenceDictionary(File inputFastaFile,
                                File outputSequenceDictionaryFile)

Create a SequenceDictionary from DNA sequences in FASTA format.

Parameters:

inputFastaFile - input FASTA file, if any

outputSequenceDictionaryFile - output SequenceDictionary .dict file, if any

CreateSequenceDictionary

public CreateSequenceDictionary(Path inputFastaPath,
                                File outputSequenceDictionaryFile)

Create a SequenceDictionary from DNA sequences in FASTA format.

Parameters:

inputFastaPath - input FASTA path, if any

outputSequenceDictionaryFile - output SequenceDictionary .dict file, if any

Since:

2.1

CreateSequenceDictionary

public CreateSequenceDictionary(URL url,
                                File inputFastaFile,
                                File outputSequenceDictionaryFile)

Create a SequenceDictionary from DNA sequences in FASTA format with the specified URL.

Parameters:

url - URL, if any

inputFastaFile - input FASTA file, if any

outputSequenceDictionaryFile - output SequenceDictionary .dict file, if any

Since:

2.1

CreateSequenceDictionary

public CreateSequenceDictionary(URL url,
                                Path inputFastaPath,
                                File outputSequenceDictionaryFile)

Create a SequenceDictionary from DNA sequences in FASTA format with the specified URL.

Parameters:

url - URL, if any

inputFastaPath - input FASTA path, if any

outputSequenceDictionaryFile - output SequenceDictionary .dict file, if any

Since:

2.1

Method Detail

call

public Integer call()
             throws Exception

Specified by:

call in interface Callable<Integer>

Throws:

Exception

main

public static void main(String[] args)

Main.

Parameters:

args - command line args