org.expasy.mzjava.avro.io

Class AbstractPeakListReader<A extends PeakAnnotation,PL extends PeakList<A>>

java.lang.Object

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

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

org.expasy.mzjava.avro.io.AbstractPeakListReader<A,PL>

All Implemented Interfaces:

AvroExternalizable, AvroReader<PL>

Direct Known Subclasses:

MsnSpectrumReader, PeakListReader, PeptideConsensusSpectrumReader, PeptideSpectrumReader

public abstract class AbstractPeakListReader<A extends PeakAnnotation,PL extends PeakList<A>>
extends AbstractAvroReader<PL>

Version:

sqrt -1

Author:

Oliver Horlacher

Field Summary

Fields

Modifier and Type	Field and Description
protected boolean	handleAnnotations
protected List<PeakProcessor<A,A>>	peakProcessorList
protected com.google.common.base.Optional<PeakList.Precision>	precisionOverride

Constructor Summary

Constructors

Constructor and Description
AbstractPeakListReader(AbstractAvroReader<? extends A>[] annotationReaders, com.google.common.base.Optional<PeakList.Precision> precisionOverride, List<PeakProcessor<A,A>> peakProcessorList)

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
protected abstract PL	newPeakList(PeakList.Precision precision, double constantIntensity)
PL	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, getObjectClass

Field Detail

precisionOverride

protected final com.google.common.base.Optional<PeakList.Precision> precisionOverride

peakProcessorList

protected final List<PeakProcessor<A extends PeakAnnotation,A extends PeakAnnotation>> peakProcessorList

handleAnnotations

protected final boolean handleAnnotations

Constructor Detail

AbstractPeakListReader

public AbstractPeakListReader(AbstractAvroReader<? extends A>[] annotationReaders,
                      com.google.common.base.Optional<PeakList.Precision> precisionOverride,
                      List<PeakProcessor<A,A>> peakProcessorList)

Method Detail

read

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

Description copied from interface: AvroReader

Read the object from the decoder

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

Specified by:

createRecordFields in class AvroIO<AbstractAvroReader>

Parameters:

fields - the list to add the fields to

newPeakList

protected abstract PL newPeakList(PeakList.Precision precision,
             double constantIntensity)