org.expasy.mzjava.core.mol.polymer.prot

Class BioJavaFastaProteinReader

java.lang.Object

org.expasy.mzjava.core.mol.polymer.prot.BioJavaFastaProteinReader

All Implemented Interfaces:

IterativeReader<Protein>

public class BioJavaFastaProteinReader
extends Object
implements IterativeReader<Protein>

A Protein reader based on biojava3 FastaReader object.

Author:

fnikitin Date: 1/13/14

Field Summary

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

EMPTY_READER

Constructor Summary

Constructors

Constructor and Description
BioJavaFastaProteinReader(File file)
BioJavaFastaProteinReader(InputStream is)

Method Summary

Methods

Modifier and Type	Method and Description
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.

Methods inherited from class java.lang.Object

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

Constructor Detail

BioJavaFastaProteinReader

public BioJavaFastaProteinReader(File file)

BioJavaFastaProteinReader

public BioJavaFastaProteinReader(InputStream is)

Method Detail

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