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
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Nested Class Summary
Nested Classes Modifier and Type Class Description static class
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.
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Constructor Details
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MzmlFileIterator
Constructor.- Parameters:
mzmlFile
- the mzml file to go throughwaitingHandler
- the waiting handler
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Method Details
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next
Description copied from interface:MsFileIterator
Returns the title of the next spectrum, null if none.- Specified by:
next
in interfaceMsFileIterator
- Returns:
- The title of the next spectrum.
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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 interfaceMsFileIterator
- Returns:
- The spectrum corresponding to the title returned by the last call to the next() method.
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close
public void close()- Specified by:
close
in interfaceAutoCloseable
- Specified by:
close
in interfaceMsFileIterator
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needsUncompressing
Reads true if the binary data is compressed.- Parameters:
compression
- the compression level- Returns:
- true if the data is compressed
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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 numberprecision
- the precision typebinary
- the binary data, base64 encoded- Returns:
- a Number array representation of the binary data
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