org.forester.io.parsers

Class FastaParser

java.lang.Object

org.forester.io.parsers.FastaParser

public class FastaParser
extends Object

Field Summary

Fields

Modifier and Type	Field and Description
static Pattern	FASTA_DESC_LINE

Constructor Summary

Constructors

Constructor and Description
FastaParser()

Method Summary

Modifier and Type	Method and Description
static boolean	isLikelyFasta(File f)
static boolean	isLikelyFasta(InputStream is)
static void	main(String[] args)
static List<MolecularSequence>	parse(File f)
static List<MolecularSequence>	parse(InputStream is)
static Msa	parseMsa(byte[] bytes)
static Msa	parseMsa(File f)
static Msa	parseMsa(InputStream is)
static Msa	parseMsa(String s)

Methods inherited from class java.lang.Object

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

Field Detail

FASTA_DESC_LINE

public static final Pattern FASTA_DESC_LINE

Constructor Detail

FastaParser

public FastaParser()

Method Detail

main

public static void main(String[] args)

isLikelyFasta

public static boolean isLikelyFasta(File f)
                             throws IOException

Throws:

IOException

isLikelyFasta

public static boolean isLikelyFasta(InputStream is)
                             throws IOException

Throws:

IOException

parseMsa

public static Msa parseMsa(File f)
                    throws IOException

Throws:

IOException

parseMsa

public static Msa parseMsa(InputStream is)
                    throws IOException

Throws:

IOException

parseMsa

public static Msa parseMsa(String s)
                    throws IOException

Throws:

IOException

parseMsa

public static Msa parseMsa(byte[] bytes)
                    throws IOException

Throws:

IOException

parse

public static List<MolecularSequence> parse(File f)
                                     throws IOException

Throws:

IOException

parse

public static List<MolecularSequence> parse(InputStream is)
                                     throws IOException

Throws:

IOException