org.biojava3.core.sequence.io
Class FastaReaderHelper

java.lang.Object
  org.biojava3.core.sequence.io.FastaReaderHelper

public class FastaReaderHelper
extends Object

Author:

Scooter Willis

Constructor Summary

FastaReaderHelper()

Method Summary

static void	main(String[] args)
static LinkedHashMap<String,DNASequence>	readFastaDNASequence(File file)
static LinkedHashMap<String,DNASequence>	readFastaDNASequence(InputStream inStream) Read a fasta DNA sequence
static LinkedHashMap<String,ProteinSequence>	readFastaProteinSequence(File file) Read a fasta file containing amino acids with setup that would handle most cases.
static LinkedHashMap<String,ProteinSequence>	readFastaProteinSequence(InputStream inStream) Read a fasta file containing amino acids with setup that would handle most cases.

Methods inherited from class java.lang.Object

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

Constructor Detail

FastaReaderHelper

public FastaReaderHelper()

Method Detail

readFastaProteinSequence

public static LinkedHashMap<String,ProteinSequence> readFastaProteinSequence(File file)
                                                                      throws Exception

Read a fasta file containing amino acids with setup that would handle most cases.

Parameters:

file -

Returns:

Throws:

Exception

readFastaProteinSequence

public static LinkedHashMap<String,ProteinSequence> readFastaProteinSequence(InputStream inStream)
                                                                      throws Exception

Read a fasta file containing amino acids with setup that would handle most cases. User is responsible for closing InputStream because you opened it

Parameters:

inStream -

Returns:

Throws:

Exception

readFastaDNASequence

public static LinkedHashMap<String,DNASequence> readFastaDNASequence(InputStream inStream)
                                                              throws Exception

Read a fasta DNA sequence

Parameters:

inStream -

Returns:

Throws:

Exception

readFastaDNASequence

public static LinkedHashMap<String,DNASequence> readFastaDNASequence(File file)
                                                              throws Exception

Parameters:

file -

Returns:

Throws:

Exception

main

public static void main(String[] args)
                 throws Exception

Throws:

Exception