org.expasy.mzjava.proteomics.io.ms.spectrum

Class DtaReader

java.lang.Object

org.expasy.mzjava.core.io.ms.spectrum.AbstractMsReader<PeakAnnotation,MsnSpectrum>

org.expasy.mzjava.proteomics.io.ms.spectrum.DtaReader

All Implemented Interfaces:

IterativeReader<MsnSpectrum>

public final class DtaReader
extends AbstractMsReader<PeakAnnotation,MsnSpectrum>

A simple DTA reader.

http://www.matrixscience.com/help/data_file_help.html#DTA

Version:

1.0

Author:

nikitin, Oliver Horlacher

Nested Class Summary

Nested classes/interfaces inherited from class org.expasy.mzjava.core.io.ms.spectrum.AbstractMsReader

AbstractMsReader.ParseContext

Field Summary

Fields inherited from class org.expasy.mzjava.core.io.ms.spectrum.AbstractMsReader

acceptUnsortedSpectra, precision

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

EMPTY_READER

Constructor Summary

Constructors

Constructor and Description
DtaReader(File file, PeakList.Precision precision)
DtaReader(Reader reader, PeakList.Precision precision)
DtaReader(Reader reader, URI spectraSource, PeakList.Precision precision)
DtaReader(Reader reader, URI spectraSource, PeakList.Precision precision, PeakProcessorChain<PeakAnnotation> processorChain)

Method Summary

Methods

Modifier and Type	Method and Description
MsnSpectrum	next() Overridden so that the compiler knows that MsnSpectra are returned by next().
protected String	parseHeader(AbstractMsReader.ParseContext context) This is called on reader initialization.
protected MsnSpectrum	parseNextEntry(AbstractMsReader.ParseContext context)

Methods inherited from class org.expasy.mzjava.core.io.ms.spectrum.AbstractMsReader

acceptUnsortedSpectra, addPeaksToSpectrum, addPeakToSpectrum, close, getContext, getHeader, hasNext, init

Methods inherited from class java.lang.Object

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

Constructor Detail

DtaReader

public DtaReader(File file,
         PeakList.Precision precision)
          throws IOException

Throws:

IOException

DtaReader

public DtaReader(Reader reader,
         PeakList.Precision precision)
          throws IOException

Throws:

IOException

DtaReader

public DtaReader(Reader reader,
         URI spectraSource,
         PeakList.Precision precision)
          throws IOException

Throws:

IOException

DtaReader

public DtaReader(Reader reader,
         URI spectraSource,
         PeakList.Precision precision,
         PeakProcessorChain<PeakAnnotation> processorChain)
          throws IOException

Throws:

IOException

Method Detail

parseHeader

protected String parseHeader(AbstractMsReader.ParseContext context)
                      throws IOException

Description copied from class: AbstractMsReader

This is called on reader initialization. Subclasses should parse any information that occurs before the first spectrum. The information can returned as a string

Specified by:

parseHeader in class AbstractMsReader<PeakAnnotation,MsnSpectrum>

Parameters:

context - the parser context

Returns:

the data that is before the first spectrum

Throws:

IOException

parseNextEntry

protected MsnSpectrum parseNextEntry(AbstractMsReader.ParseContext context)
                              throws IOException

Specified by:

parseNextEntry in class AbstractMsReader<PeakAnnotation,MsnSpectrum>

Returns:

the next T-object or null if no more object to read.

Throws:

IOException

next

public MsnSpectrum next()
                 throws IOException

Overridden so that the compiler knows that MsnSpectra are returned by next(). If this method is missing the compiler thinks Spectrum are returned

Specified by:

next in interface IterativeReader<MsnSpectrum>

Overrides:

next in class AbstractMsReader<PeakAnnotation,MsnSpectrum>

Returns:

the next element in the iteration

Throws:

IOException - if there is an io exception