org.expasy.mzjava.core.io.ms.spectrum

Class AbstractMsReader<A extends PeakAnnotation,S extends Spectrum<A>>

java.lang.Object

org.expasy.mzjava.core.io.ms.spectrum.AbstractMsReader<A,S>

All Implemented Interfaces:

IterativeReader<S>

Direct Known Subclasses:

AbstractMgfReader, DtaReader, MsLibReader, MzxmlReader

public abstract class AbstractMsReader<A extends PeakAnnotation,S extends Spectrum<A>>
extends Object
implements IterativeReader<S>

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	AbstractMsReader.ParseContext

Field Summary

Fields

Modifier and Type	Field and Description
protected boolean	acceptUnsortedSpectra
protected PeakList.Precision	precision

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

EMPTY_READER

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	AbstractMsReader(Reader reader, URI source, PeakList.Precision precision, PeakProcessorChain<A> processorChain)

Method Summary

Methods

Modifier and Type	Method and Description
void	acceptUnsortedSpectra()
protected void	addPeaksToSpectrum(S spectrum, double[] mzs, double[] intensities, int size) Potentially non-order add peaks to spectrum.
protected int	addPeakToSpectrum(Spectrum<A> spectrum, double mz, double intensity, AbstractMsReader.ParseContext context) Potentially non-order add peak to spectrum.
void	close() Closes the reader and releases any system resources associated with it.
AbstractMsReader.ParseContext	getContext()
String	getHeader()
boolean	hasNext() Returns true if the reader has more elements.
protected void	init(AbstractMsReader.ParseContext parseContext)
S	next() Returns the next element in the reader.
protected abstract String	parseHeader(AbstractMsReader.ParseContext context) This is called on reader initialization.
protected abstract S	parseNextEntry(AbstractMsReader.ParseContext context)

Methods inherited from class java.lang.Object

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

Field Detail

precision

protected final PeakList.Precision precision

acceptUnsortedSpectra

protected boolean acceptUnsortedSpectra

Constructor Detail

AbstractMsReader

protected AbstractMsReader(Reader reader,
                URI source,
                PeakList.Precision precision,
                PeakProcessorChain<A> processorChain)
                    throws IOException

Throws:

IOException

Method Detail

init

protected void init(AbstractMsReader.ParseContext parseContext)
             throws IOException

Throws:

IOException

parseNextEntry

protected abstract S parseNextEntry(AbstractMsReader.ParseContext context)
                                                 throws IOException

Returns:

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

Throws:

IOException

getContext

public AbstractMsReader.ParseContext getContext()

Returns:

the context

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<S extends Spectrum<A>>

Returns:

true if the reader has more elements

next

public S next()
                           throws IOException

Description copied from interface: IterativeReader

Returns the next element in the reader.

Specified by:

next in interface IterativeReader<S extends Spectrum<A>>

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<S extends Spectrum<A>>

Throws:

IOException - If an I/O error occurs

acceptUnsortedSpectra

public void acceptUnsortedSpectra()

parseHeader

protected abstract String parseHeader(AbstractMsReader.ParseContext context)
                               throws IOException

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

Parameters:

context - the parser context

Returns:

the data that is before the first spectrum

Throws:

IOException

getHeader

public String getHeader()

addPeaksToSpectrum

protected void addPeaksToSpectrum(S spectrum,
                      double[] mzs,
                      double[] intensities,
                      int size)

Potentially non-order add peaks to spectrum.

Parameters:

spectrum - the spectrum to add peaks into.

mzs - the peak's m/zs.

intensities - the peak's intensities.

size - the spectrum size

Throws:

UnsortedPeakListException - if reader is not allowed to add unsorted peaklists.

addPeakToSpectrum

protected int addPeakToSpectrum(Spectrum<A> spectrum,
                    double mz,
                    double intensity,
                    AbstractMsReader.ParseContext context)

Potentially non-order add peak to spectrum.

Parameters:

spectrum - the spectrum to add peak into.

mz - the peak's m/z.

intensity - the peak's intensity.

context - the parse context

Returns:

the index at which the peak was added

Throws:

UnsortedPeakListException - if reader is not allowed to add unsorted peaklists.