Package com.compomics.util.experiment.io.mass_spectrometry.mzml

Class MzmlFileIterator

java.lang.Object

com.compomics.util.experiment.io.mass_spectrometry.mzml.MzmlFileIterator

All Implemented Interfaces:

MsFileIterator, AutoCloseable

public class MzmlFileIterator
extends Object
implements MsFileIterator

An iterator of the spectra in an mzml file. Based on code from jmzML.

Author:

Harald Barsnes

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static enum	MzmlFileIterator.Precision	The supported precision types for the binary data as defined in the mzML specifications and the PSI-MS ontology.

Constructor Summary

Constructors

Constructor	Description
MzmlFileIterator(File mzmlFile, WaitingHandler waitingHandler)	Constructor.

Method Summary

Modifier and Type	Method	Description
void	close()
Number[]	getBinaryDataAsNumberArray(String compression, MzmlFileIterator.Precision precision, byte[] binary)	Retrieve the binary data as an array of numeric values.
Spectrum	getSpectrum()	Returns the spectrum corresponding to the title returned by the last call to the next() method.
boolean	needsUncompressing(String compression)	Reads true if the binary data is compressed.
String	next()	Returns the title of the next spectrum, null if none.

Methods inherited from class java.lang.Object

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

Constructor Details

MzmlFileIterator

public MzmlFileIterator(File mzmlFile,
 WaitingHandler waitingHandler)

Constructor.

Parameters:

mzmlFile - the mzml file to go through

waitingHandler - the waiting handler

Method Details

next

public String next()

Description copied from interface: MsFileIterator

Returns the title of the next spectrum, null if none.

Specified by:

next in interface MsFileIterator

Returns:

The title of the next spectrum.

getSpectrum

public Spectrum getSpectrum()

Description copied from interface: MsFileIterator

Returns the spectrum corresponding to the title returned by the last call to the next() method.

Specified by:

getSpectrum in interface MsFileIterator

Returns:

The spectrum corresponding to the title returned by the last call to the next() method.

close

public void close()

Specified by:

close in interface AutoCloseable

Specified by:

close in interface MsFileIterator

needsUncompressing

public boolean needsUncompressing(String compression)

Reads true if the binary data is compressed.

Parameters:

compression - the compression level

Returns:

true if the data is compressed

getBinaryDataAsNumberArray

public Number[] getBinaryDataAsNumberArray(String compression,
 MzmlFileIterator.Precision precision,
 byte[] binary)

Retrieve the binary data as an array of numeric values.

Parameters:

compression - the compression accession number

precision - the precision type

binary - the binary data, base64 encoded

Returns:

a Number array representation of the binary data