org.expasy.mzjava.proteomics.io.mol

Class FastaProteinReader

java.lang.Object

org.expasy.mzjava.proteomics.io.mol.FastaProteinReader

All Implemented Interfaces:

IterativeReader<Protein>

public class FastaProteinReader
extends Object
implements IterativeReader<Protein>

A reader for FASTA formatted files. Information from the FASTA header can be extracted by adding an implementation of FastaHeaderParser. To make the header parser available automatically register the FastaHeaderParser as a @ServiceProvider(service = FastaHeaderParser.class). See UniprotFastaHeaderParser for an example.

Version:

sqrt -1

Author:

Oliver Horlacher

Field Summary

Fields inherited from interface org.expasy.mzjava.core.io.IterativeReader

EMPTY_READER

Constructor Summary

Constructors

Constructor and Description
FastaProteinReader(File file) Constructs a FastaReader that reads from a file.
FastaProteinReader(Reader reader) Construct a FastaReader that reads from a Reader

Method Summary

Methods

Modifier and Type	Method and Description
void	addHeaderParser(FastaHeaderParser parser) Add a header parser
void	close() Closes the reader and releases any system resources associated with it.
boolean	hasNext() Returns true if the reader has more elements.
Protein	next() Returns the next element in the reader.
protected void	parseHeader(String header, Protein.Builder builder)

Methods inherited from class java.lang.Object

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

Constructor Detail

FastaProteinReader

public FastaProteinReader(Reader reader)

Construct a FastaReader that reads from a Reader

Parameters:

reader - the reader to read from

FastaProteinReader

public FastaProteinReader(File file)
                   throws FileNotFoundException

Constructs a FastaReader that reads from a file.

Parameters:

file - the file to read

Throws:

FileNotFoundException

Method Detail

addHeaderParser

public void addHeaderParser(FastaHeaderParser parser)

Add a header parser

Parameters:

parser - the parser to add

hasNext

public boolean hasNext()

Description copied from interface: IterativeReader

Returns true if the reader has more elements. (In other words, returns true if IterativeReader.next() would return an element rather than throwing an exception.)

Specified by:

hasNext in interface IterativeReader<Protein>

Returns:

true if the reader has more elements

next

public Protein next()
             throws IOException

Description copied from interface: IterativeReader

Returns the next element in the reader.

Specified by:

next in interface IterativeReader<Protein>

Returns:

the next element in the iteration

Throws:

IOException - if there is an io exception

close

public void close()
           throws IOException

Description copied from interface: IterativeReader

Closes the reader and releases any system resources associated with it. Once the reader has been closed, further hasNext() or next() invocations will throw an IOException. Closing a previously closed reader has no effect.

Specified by:

close in interface IterativeReader<Protein>

Throws:

IOException - If an I/O error occurs

parseHeader

protected void parseHeader(String header,
               Protein.Builder builder)