org.expasy.mzjava.proteomics.avro.io

Class PeptideSpectrumReader

java.lang.Object

org.expasy.mzjava.avro.io.AvroIO<AbstractAvroReader>

org.expasy.mzjava.avro.io.AbstractAvroReader<PL>

org.expasy.mzjava.avro.io.AbstractPeakListReader<PepFragAnnotation,PeptideSpectrum>

org.expasy.mzjava.proteomics.avro.io.PeptideSpectrumReader

All Implemented Interfaces:

AvroExternalizable, AvroReader<PeptideSpectrum>

public class PeptideSpectrumReader
extends AbstractPeakListReader<PepFragAnnotation,PeptideSpectrum>

Version:

sqrt -1

Author:

Oliver Horlacher

Field Summary

Fields inherited from class org.expasy.mzjava.avro.io.AbstractPeakListReader

handleAnnotations, peakProcessorList, precisionOverride

Constructor Summary

Constructors

Constructor and Description
PeptideSpectrumReader()
PeptideSpectrumReader(com.google.common.base.Optional<PeakList.Precision> precisionOverride, List<PeakProcessor<PepFragAnnotation,PepFragAnnotation>> peakProcessors)

Method Summary

Methods

Modifier and Type	Method and Description
protected void	createRecordFields(List<org.apache.avro.Schema.Field> fields) Create a list containing the Schema.Fields for the fields that this class writes
Class	getObjectClass()
protected PeptideSpectrum	newPeakList(PeakList.Precision precision, double constantIntensity)
PeptideSpectrum	read(org.apache.avro.io.Decoder in) Read the object from the decoder

Methods inherited from class org.expasy.mzjava.avro.io.AbstractAvroReader

getRecordName, getRecordNameSpace, readArray, readMap, readMap, readMap, readOptional, readStringArray, readUnion, readUnionArray

Methods inherited from class org.expasy.mzjava.avro.io.AvroIO

createEnumSchema, createSchema, createSchemaField, createUnionSchema, createUnionSchema, getRecordDoc, getUnion, registerUnion, rewriteNameSpace

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.expasy.mzjava.avro.io.AvroExternalizable

createSchema

Constructor Detail

PeptideSpectrumReader

public PeptideSpectrumReader()

PeptideSpectrumReader

public PeptideSpectrumReader(com.google.common.base.Optional<PeakList.Precision> precisionOverride,
                     List<PeakProcessor<PepFragAnnotation,PepFragAnnotation>> peakProcessors)

Method Detail

getObjectClass

public Class getObjectClass()

newPeakList

protected PeptideSpectrum newPeakList(PeakList.Precision precision,
                          double constantIntensity)

Specified by:

newPeakList in class AbstractPeakListReader<PepFragAnnotation,PeptideSpectrum>

read

public PeptideSpectrum read(org.apache.avro.io.Decoder in)
                     throws IOException

Description copied from interface: AvroReader

Read the object from the decoder

Specified by:

read in interface AvroReader<PeptideSpectrum>

Overrides:

read in class AbstractPeakListReader<PepFragAnnotation,PeptideSpectrum>

Parameters:

in - the decoder

Returns:

the read object

Throws:

IOException

createRecordFields

protected void createRecordFields(List<org.apache.avro.Schema.Field> fields)

Description copied from class: AvroIO

Create a list containing the Schema.Fields for the fields that this class writes

Overrides:

createRecordFields in class AbstractPeakListReader<PepFragAnnotation,PeptideSpectrum>

Parameters:

fields - the list to add the fields to