com.compomics.util.experiment.identification.protein_sequences

Class SequenceFactory.ProteinIterator

java.lang.Object

com.compomics.util.experiment.identification.protein_sequences.SequenceFactory.ProteinIterator

Enclosing class:

SequenceFactory

public class SequenceFactory.ProteinIterator
extends Object

Convenience iterator iterating all proteins in a FASTA file without using index or cache.

Constructor Summary

Constructors

Constructor and Description
ProteinIterator(File file, boolean targetOnly) Constructor.

Method Summary

Modifier and Type	Method and Description
void	close() Closes the connection to the file.
Protein	getNextProtein() Returns the next protein.
boolean	hasNext() Returns true if there is another protein.

Methods inherited from class java.lang.Object

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

Constructor Detail

ProteinIterator

public ProteinIterator(File file,
                       boolean targetOnly)
                throws FileNotFoundException

Constructor.

Parameters:

targetOnly - if true only target proteins will be iterated

file - the FASTA file.

Throws:

FileNotFoundException - if a FileNotFoundException occurs

Method Detail

hasNext

public boolean hasNext()
                throws IOException

Returns true if there is another protein.

Returns:

true if there is another protein

Throws:

IOException - if an IOException occurs

getNextProtein

public Protein getNextProtein()

Returns the next protein.

Returns:

the next protein

close

public void close()
           throws IOException

Closes the connection to the file.

Throws:

IOException - if an IOException occurs