org.forester.io.parsers
Class FastaParser

java.lang.Object
  org.forester.io.parsers.FastaParser

public class FastaParser
extends java.lang.Object

Field Summary

static java.util.regex.Pattern

FASTA_DESC_LINE

Constructor Summary

FastaParser()

Method Summary

static boolean	isLikelyFasta(java.io.InputStream is)
static void	main(java.lang.String[] args)
static java.util.List<Sequence>	parse(java.io.File f)
static java.util.List<Sequence>	parse(java.io.InputStream is)
static Msa	parseMsa(byte[] bytes)
static Msa	parseMsa(java.io.File f)
static Msa	parseMsa(java.io.InputStream is)
static Msa	parseMsa(java.lang.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 java.util.regex.Pattern FASTA_DESC_LINE

Constructor Detail

FastaParser

public FastaParser()

Method Detail

main

public static void main(java.lang.String[] args)

isLikelyFasta

public static boolean isLikelyFasta(java.io.InputStream is)
                             throws java.io.IOException

Throws:

java.io.IOException

parseMsa

public static Msa parseMsa(java.io.File f)
                    throws java.io.IOException

Throws:

java.io.IOException

parseMsa

public static Msa parseMsa(java.io.InputStream is)
                    throws java.io.IOException

Throws:

java.io.IOException

parseMsa

public static Msa parseMsa(java.lang.String s)
                    throws java.io.IOException

Throws:

java.io.IOException

parseMsa

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

Throws:

java.io.IOException

parse

public static java.util.List<Sequence> parse(java.io.File f)
                                      throws java.io.IOException

Throws:

java.io.IOException

parse

public static java.util.List<Sequence> parse(java.io.InputStream is)
                                      throws java.io.IOException

Throws:

java.io.IOException