org.expasy.mzjava.proteomics.avro.io

Class PeptideConsensusSpectrumReader

java.lang.Object

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

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

org.expasy.mzjava.avro.io.AbstractPeakListReader<PepLibPeakAnnotation,PeptideConsensusSpectrum>

org.expasy.mzjava.proteomics.avro.io.PeptideConsensusSpectrumReader

All Implemented Interfaces:

AvroExternalizable, AvroReader<PeptideConsensusSpectrum>

public class PeptideConsensusSpectrumReader
extends AbstractPeakListReader<PepLibPeakAnnotation,PeptideConsensusSpectrum>

Version:

sqrt -1

Author:

Oliver Horlacher

Field Summary

Fields

Modifier and Type	Field and Description
protected PeptideReader	peptideReader
protected PeakReader	precursorReader
protected RetentionTimeDiscreteReader	rtReader
protected UUIDReader	uuidReader

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

handleAnnotations, peakProcessorList, precisionOverride

Constructor Summary

Constructors

Constructor and Description
PeptideConsensusSpectrumReader()
PeptideConsensusSpectrumReader(com.google.common.base.Optional<PeakList.Precision> precisionOverride, List<PeakProcessor<PepLibPeakAnnotation,PepLibPeakAnnotation>> 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 PeptideConsensusSpectrum	newPeakList(PeakList.Precision precision, double constantIntensity)
PeptideConsensusSpectrum	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

Field Detail

precursorReader

protected final PeakReader precursorReader

peptideReader

protected final PeptideReader peptideReader

uuidReader

protected final UUIDReader uuidReader

rtReader

protected final RetentionTimeDiscreteReader rtReader

Constructor Detail

PeptideConsensusSpectrumReader

public PeptideConsensusSpectrumReader()

PeptideConsensusSpectrumReader

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

Method Detail

getObjectClass

public Class getObjectClass()

newPeakList

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

Specified by:

newPeakList in class AbstractPeakListReader<PepLibPeakAnnotation,PeptideConsensusSpectrum>

read

public PeptideConsensusSpectrum 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<PeptideConsensusSpectrum>

Overrides:

read in class AbstractPeakListReader<PepLibPeakAnnotation,PeptideConsensusSpectrum>

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<PepLibPeakAnnotation,PeptideConsensusSpectrum>

Parameters:

fields - the list to add the fields to