org.biojava3.core.sequence.io

Class FastaReader<S extends Sequence<?>,C extends Compound>

java.lang.Object

org.biojava3.core.sequence.io.FastaReader<S,C>

public class FastaReader<S extends Sequence<?>,C extends Compound>
extends Object

Use FastaReaderHelper as an example of how to use this class where FastaReaderHelper should be the primary class used to read Fasta files

Author:

Scooter Willis

Constructor Summary

Constructors

Constructor and Description
FastaReader(File file, FastaHeaderParserInterface<S,C> headerParser, SequenceCreatorInterface<C> sequenceCreator) If you are going to use the FileProxyProteinSequenceCreator then you need to use this constructor because we need details about the location of the file.
FastaReader(InputStream is, FastaHeaderParserInterface<S,C> headerParser, SequenceCreatorInterface<C> sequenceCreator) If you are going to use FileProxyProteinSequenceCreator then do not use this constructor because we need details about local file offsets for quick reads.

Method Summary

Methods

Modifier and Type	Method and Description
static void	main(String[] args)
LinkedHashMap<String,S>	process() The parsing is done in this method

Methods inherited from class java.lang.Object

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

Constructor Detail

FastaReader

public FastaReader(InputStream is,
           FastaHeaderParserInterface<S,C> headerParser,
           SequenceCreatorInterface<C> sequenceCreator)

If you are going to use FileProxyProteinSequenceCreator then do not use this constructor because we need details about local file offsets for quick reads. InputStreams does not give you the name of the stream to access quickly via file seek. A seek in an inputstream is forced to read all the data so you don't gain anything.

Parameters:

br -

headerParser -

sequenceCreator -

FastaReader

public FastaReader(File file,
           FastaHeaderParserInterface<S,C> headerParser,
           SequenceCreatorInterface<C> sequenceCreator)
            throws FileNotFoundException

If you are going to use the FileProxyProteinSequenceCreator then you need to use this constructor because we need details about the location of the file.

Parameters:

file -

headerParser -

sequenceCreator -

Throws:

FileNotFoundException - if the file does not exist, is a directory rather than a regular file, or for some other reason cannot be opened for reading.

SecurityException - if a security manager exists and its checkRead method denies read access to the file.

Method Detail

process

public LinkedHashMap<String,S> process()
                                                    throws IOException

The parsing is done in this method

Returns:

Throws:

IOException - if an error occurs reading the input file

main

public static void main(String[] args)