Uses of Class
org.expasy.mzjava.core.ms.spectrum.MsnSpectrum

Packages that use MsnSpectrum

Package	Description
org.expasy.mzjava.avro.io
org.expasy.mzjava.core.io.ms.spectrum
org.expasy.mzjava.core.io.ms.spectrum.mgf
org.expasy.mzjava.core.ms.spectrum
org.expasy.mzjava.external.io.ms.spectrum
org.expasy.mzjava.external.io.ms.spectrum.mzml
org.expasy.mzjava.hadoop.io
org.expasy.mzjava.proteomics.io.ms.ident
org.expasy.mzjava.proteomics.io.ms.spectrum
org.expasy.mzjava.proteomics.ms.ident
org.expasy.mzjava.spark
org.expasy.mzjava.utils.function

Uses of MsnSpectrum in org.expasy.mzjava.avro.io

Methods in org.expasy.mzjava.avro.io that return MsnSpectrum

Modifier and Type	Method and Description
protected MsnSpectrum	MsnSpectrumReader.newPeakList(PeakList.Precision precision, double constantIntensity)
MsnSpectrum	MsnSpectrumReader.read(org.apache.avro.io.Decoder in)

Methods in org.expasy.mzjava.avro.io with parameters of type MsnSpectrum

Modifier and Type	Method and Description
void	MsnSpectrumMetaDataReader.setValues(MsnSpectrum spectrum)
void	MsnSpectrumWriter.write(MsnSpectrum spectrum, org.apache.avro.io.Encoder out)
void	MsnSpectrumMetaDataWriter.writeMetaData(MsnSpectrum spectrum, org.apache.avro.io.Encoder out)

Constructor parameters in org.expasy.mzjava.avro.io with type arguments of type MsnSpectrum

Constructor and Description
MsnSpectrumMetaDataReader(AbstractAvroReader<? extends MsnSpectrum> reader)

Uses of MsnSpectrum in org.expasy.mzjava.core.io.ms.spectrum

Methods in org.expasy.mzjava.core.io.ms.spectrum that return MsnSpectrum

Modifier and Type	Method and Description
protected MsnSpectrum	MgfReader.newSpectrum(AbstractMsReader.ParseContext context, PeakList.Precision precision)
protected MsnSpectrum	MzxmlReader.newSpectrum(StartElement scanElement, AbstractMsReader.ParseContext context) Create a spectrum
MsnSpectrum	MgfReader.next() Overridden so that the compiler knows that MsnSpectra are returned by next().
MsnSpectrum	MzxmlReader.next()
protected MsnSpectrum	MzxmlReader.parseNextEntry(AbstractMsReader.ParseContext context)

Methods in org.expasy.mzjava.core.io.ms.spectrum that return types with arguments of type MsnSpectrum

Modifier and Type	Method and Description
com.google.common.base.Optional<MsnSpectrum>	MgfParameters.getHeaderData()

Methods in org.expasy.mzjava.core.io.ms.spectrum with parameters of type MsnSpectrum

Modifier and Type	Method and Description
protected void	MzxmlReader.consistencyChecks(MsnSpectrum spectrum) Check for all spectrum consistencies
protected int[]	MgfWriter.extractChargeList(PeakList peakList, MsnSpectrum metaData)
protected List<RetentionTime>	MgfWriter.extractRetentionTime(MsnSpectrum spectrum)
protected List<ScanNumber>	MgfWriter.extractScanNumbers(MsnSpectrum spectrum)
protected String	MgfWriter.extractTitle(MsnSpectrum spectrum)
protected boolean	MgfReader.parseTitleTag(String value, MsnSpectrum spectrum)
protected void	MgfReader.setRetentionTimes(MsnSpectrum spectrum, RetentionTimeList retentionTimeList)
protected void	MgfReader.setScanNumbers(MsnSpectrum spectrum, ScanNumberList scanNumbers)
void	MgfWriter.write(MsnSpectrum peakList)

Constructors in org.expasy.mzjava.core.io.ms.spectrum with parameters of type MsnSpectrum

Constructor and Description
MgfParameters(PeakList.Precision precision, MsnSpectrum headerData)

Constructor parameters in org.expasy.mzjava.core.io.ms.spectrum with type arguments of type MsnSpectrum

Constructor and Description
MgfParameters(NumberFormat mzFormat, NumberFormat intensityFormat, com.google.common.base.Optional<MsnSpectrum> headerData)

Uses of MsnSpectrum in org.expasy.mzjava.core.io.ms.spectrum.mgf

Methods in org.expasy.mzjava.core.io.ms.spectrum.mgf with parameters of type MsnSpectrum

Modifier and Type	Method and Description
boolean	ThermoFisherOrbitrapTitleParser.parseTitle(String title, MsnSpectrum spectrum)
boolean	TitleParser.parseTitle(String title, MsnSpectrum spectrum)
boolean	DelegatingRegexTitleParser.parseTitle(String title, MsnSpectrum spectrum)
boolean	AnalystTitleParser.parseTitle(String title, MsnSpectrum spectrum)
boolean	RegexScanNumTitleParser.parseTitle(String title, MsnSpectrum spectrum)

Uses of MsnSpectrum in org.expasy.mzjava.core.ms.spectrum

Methods in org.expasy.mzjava.core.ms.spectrum that return MsnSpectrum

Modifier and Type	Method and Description
MsnSpectrum	MsnSpectrum.copy(com.google.common.base.Function<Double,Double> rtCorrFct)
MsnSpectrum	MsnSpectrum.copy(PeakProcessor<PeakAnnotation,PeakAnnotation> peakProcessor)
MsnSpectrum	MsnSpectrum.copy(PeakProcessor<PeakAnnotation,PeakAnnotation> peakProcessor, com.google.common.base.Function<Double,Double> rtCorrFct)
MsnSpectrum	MsnSpectrum.copy(PeakProcessorChain<PeakAnnotation> peakProcessorChain)
MsnSpectrum	MsnSpectrum.copy(PeakProcessorChain<PeakAnnotation> peakProcessorChain, com.google.common.base.Function<Double,Double> rtCorrFct)

Constructors in org.expasy.mzjava.core.ms.spectrum with parameters of type MsnSpectrum

Constructor and Description
MsnSpectrum(MsnSpectrum src, PeakProcessor<PeakAnnotation,PeakAnnotation> peakProcessor) Copy constructor
MsnSpectrum(MsnSpectrum src, PeakProcessor<PeakAnnotation,PeakAnnotation> peakProcessor, com.google.common.base.Function<Double,Double> rtCorrFct) Copy constructor
MsnSpectrum(MsnSpectrum src, PeakProcessorChain<PeakAnnotation> peakProcessorChain) Copy constructor
MsnSpectrum(MsnSpectrum src, PeakProcessorChain<PeakAnnotation> peakProcessorChain, com.google.common.base.Function<Double,Double> rtCorrFct) Copy constructor

Uses of MsnSpectrum in org.expasy.mzjava.external.io.ms.spectrum

Methods in org.expasy.mzjava.external.io.ms.spectrum with parameters of type MsnSpectrum

Modifier and Type	Method and Description
void	ConsistencyChecker.checkConsistencies(MsnSpectrum spectrum, uk.ac.ebi.jmzml.model.mzml.Spectrum expectedValueContainer) Check strict and tolerant consistencies on spectrum
boolean	ConsistencyCheck.checkConsistency(MsnSpectrum observedValueContainer, uk.ac.ebi.jmzml.model.mzml.Spectrum expectedValueContainer, float delta) Check consistency
com.google.common.base.Optional<Double>	ConsistencyCheck.getObservedValue(MsnSpectrum spectrum) Get observed value from an MsnSpectrum
String	ConsistencyCheck.onFailSendWarning(MsnSpectrum observedValueContainer, uk.ac.ebi.jmzml.model.mzml.Spectrum expectedValueContainer) Send warning when check fails
ConsistencyCheckException	ConsistencyCheck.onFailThrowException(MsnSpectrum observedValueContainer, uk.ac.ebi.jmzml.model.mzml.Spectrum expectedValueContainer) Throw a ConsistencyCheckException when check fails

Uses of MsnSpectrum in org.expasy.mzjava.external.io.ms.spectrum.mzml

Classes in org.expasy.mzjava.external.io.ms.spectrum.mzml with type parameters of type MsnSpectrum

Modifier and Type	Class and Description
class	EbiMzmlReader<S extends MsnSpectrum> EbiMzmlReader is a wrapper over jmzml reader provided by EBI (https://code.google.com/p/jmzml/) that fully support mzML 1.1.0 specifications (http://www.psidev.info/mzml_1_0_0%20).

Methods in org.expasy.mzjava.external.io.ms.spectrum.mzml with type parameters of type MsnSpectrum

Modifier and Type	Method and Description
static <S extends MsnSpectrum> EbiMzmlReader	EbiMzmlReader.newStrictReader(uk.ac.ebi.jmzml.xml.io.MzMLUnmarshaller unmarshaller, PeakList.Precision precision, PeakProcessorChain<PeakAnnotation> processorChain)
static <S extends MsnSpectrum> EbiMzmlReader	EbiMzmlReader.newTolerantReader(uk.ac.ebi.jmzml.xml.io.MzMLUnmarshaller unmarshaller, PeakList.Precision precision, PeakProcessorChain<PeakAnnotation> processorChain)

Methods in org.expasy.mzjava.external.io.ms.spectrum.mzml with parameters of type MsnSpectrum

Modifier and Type	Method and Description
boolean	MzmlConsistencyCheck.checkConsistency(MsnSpectrum observedValueContainer, uk.ac.ebi.jmzml.model.mzml.Spectrum expectedValueContainer, float delta)
boolean	MzmlSpectrumCheck.checkConsistency(MsnSpectrum msnSpectrum, uk.ac.ebi.jmzml.model.mzml.Spectrum mzXmlSpectrum, float delta)
com.google.common.base.Optional<Double>	TicCheck.getObservedValue(MsnSpectrum observedValueContainer)
com.google.common.base.Optional<Double>	MzmlConsistencyCheck.getObservedValue(MsnSpectrum observedValueContainer)
com.google.common.base.Optional<Double>	FirstMzCheck.getObservedValue(MsnSpectrum spectrum)
com.google.common.base.Optional<Double>	LastMzCheck.getObservedValue(MsnSpectrum spectrum)
String	MzmlConsistencyCheck.onFailSendWarning(MsnSpectrum observedValueContainer, uk.ac.ebi.jmzml.model.mzml.Spectrum expectedValueContainer)
String	MzmlSpectrumCheck.onFailSendWarning(MsnSpectrum observedValueContainer, uk.ac.ebi.jmzml.model.mzml.Spectrum expectedValueContainer)
ConsistencyCheckException	MzmlConsistencyCheck.onFailThrowException(MsnSpectrum observedValueContainer, uk.ac.ebi.jmzml.model.mzml.Spectrum expectedValueContainer)
ConsistencyCheckException	MzmlSpectrumCheck.onFailThrowException(MsnSpectrum observedValueContainer, uk.ac.ebi.jmzml.model.mzml.Spectrum expectedValueContainer)

Uses of MsnSpectrum in org.expasy.mzjava.hadoop.io

Methods in org.expasy.mzjava.hadoop.io that return types with arguments of type MsnSpectrum

Modifier and Type	Method and Description
static HadoopSpectraReader<PeakAnnotation,MsnSpectrum>	HadoopSpectraReader.msnReader(File file)
static HadoopSpectraWriter<MsnSpectrum>	HadoopSpectraWriter.msnWriter(File file)

Uses of MsnSpectrum in org.expasy.mzjava.proteomics.io.ms.ident

Methods in org.expasy.mzjava.proteomics.io.ms.ident with parameters of type MsnSpectrum

Modifier and Type	Method and Description
void	PepXmlWriter.add(MsnSpectrum spectrum, List<PeptideMatch> peptideMatchList) Collect the list of peptide identifications for the given spectrum
void	PepXmlWriter.add(MsnSpectrum spectrum, PeptideMatch... peptideMatch) Collect the list of peptide identifications for the given spectrum
protected String	PepXmlWriter.buildSpectrumQuerySpectrumAttribute(MsnSpectrum spectrum) Format MsnSpectrum id for element spectrum attribute of spectrum_query element.
static String	PepXmlWriter.toDefaultSpectrumQuerySpectrumAttribute(MsnSpectrum spectrum) Create the following spectrum format 'basename.scanNumberStart.scanNumberEnd.charge' or 'basename.scanNumberIndex.scanNumberIndex.charge' if no scan numbers
protected MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery	PepXmlWriter.toSpectrumQuery(MsnSpectrum spectrum) Convert MsnSpectrum to PepXml element SpectrumQuery

Uses of MsnSpectrum in org.expasy.mzjava.proteomics.io.ms.spectrum

Methods in org.expasy.mzjava.proteomics.io.ms.spectrum that return MsnSpectrum

Modifier and Type	Method and Description
MsnSpectrum	DtaReader.next() Overridden so that the compiler knows that MsnSpectra are returned by next().
protected MsnSpectrum	DtaReader.parseNextEntry(AbstractMsReader.ParseContext context)

Methods in org.expasy.mzjava.proteomics.io.ms.spectrum that return types with arguments of type MsnSpectrum

Modifier and Type	Method and Description
static IterativeReader<MsnSpectrum>	MsReaderFactory.newMsnSpectraReader(File file, PeakList.Precision precision)

Uses of MsnSpectrum in org.expasy.mzjava.proteomics.ms.ident

Methods in org.expasy.mzjava.proteomics.ms.ident with parameters of type MsnSpectrum

Modifier and Type	Method and Description
List<PeptideMatch>	ScanNumberSearchResultMap.getResults(MsnSpectrum spectrum)
List<PeptideMatch>	TitleSearchResultMap.getResults(MsnSpectrum spectrum)
List<PeptideMatch>	ScanNumberIndexSearchResultMap.getResults(MsnSpectrum spectrum)
abstract List<PeptideMatch>	SearchResultMap.getResults(MsnSpectrum spectrum)

Uses of MsnSpectrum in org.expasy.mzjava.spark

Methods in org.expasy.mzjava.spark that return types with arguments of type MsnSpectrum

Modifier and Type	Method and Description
static org.apache.spark.api.java.JavaRDD<MsnSpectrum>	MzJavaSparkUtils.msnSpectra(org.apache.spark.api.java.JavaSparkContext sc, String queryPath)

Uses of MsnSpectrum in org.expasy.mzjava.utils.function

Methods in org.expasy.mzjava.utils.function with type parameters of type MsnSpectrum

Modifier and Type	Method and Description
<PL extends MsnSpectrum> List<List<PL>>	RetentionTimeSplitter.split(List<PL> input)