Uses of Interface
org.expasy.mzjava.core.io.IterativeReader

Packages that use IterativeReader

Package	Description
org.expasy.mzjava.app.io
org.expasy.mzjava.core.io
org.expasy.mzjava.core.io.ms.spectrum
org.expasy.mzjava.core.mol.polymer.prot
org.expasy.mzjava.external.io.ms.spectrum.mzml
org.expasy.mzjava.hadoop.io
org.expasy.mzjava.proteomics.io.mol
org.expasy.mzjava.proteomics.io.ms.spectrum
org.expasy.mzjava.proteomics.ms.dbsearch

Uses of IterativeReader in org.expasy.mzjava.app.io

Classes in org.expasy.mzjava.app.io that implement IterativeReader

Modifier and Type	Class and Description
class	MonitoredIterativeReader<T> MonitoredIterativeReader monitors the progression of IterativeReader reads.

Constructors in org.expasy.mzjava.app.io with parameters of type IterativeReader

Constructor and Description
MonitoredIterativeReader(IterativeReader<T> reader)
MonitoredIterativeReader(IterativeReader<T> reader, ConsoleProgressBar.View view)

Uses of IterativeReader in org.expasy.mzjava.core.io

Classes in org.expasy.mzjava.core.io that implement IterativeReader

Modifier and Type	Class and Description
class	ConcatIterativeReader<T> Combines multiple IterativeReaders into a single IterativeReader.

Fields in org.expasy.mzjava.core.io declared as IterativeReader

Modifier and Type	Field and Description
static IterativeReader<Object>	IterativeReader.EMPTY_READER The empty IterativeReader.

Methods in org.expasy.mzjava.core.io that return IterativeReader

Modifier and Type	Method and Description
static <T> IterativeReader<T>	IterativeReaders.empty()
static <T> IterativeReader<T>	IterativeReaders.fromCollection(Collection<T> collection)
static <T> IterativeReader<T>	IterativeReaders.fromIterator(Iterator<T> it)

Methods in org.expasy.mzjava.core.io with parameters of type IterativeReader

Modifier and Type	Method and Description
static <T> List<T>	IterativeReaders.toArrayList(IterativeReader<T> reader)

Constructors in org.expasy.mzjava.core.io with parameters of type IterativeReader

Constructor and Description
ConcatIterativeReader(IterativeReader<T>... readers) Create an IterativeReader that iterates over the readers in readers

Constructor parameters in org.expasy.mzjava.core.io with type arguments of type IterativeReader

Constructor and Description
ConcatIterativeReader(Collection<IterativeReader<T>> inputs) Create an IterativeReader that iterates over the readers in inputs

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

Classes in org.expasy.mzjava.core.io.ms.spectrum that implement IterativeReader

Modifier and Type	Class and Description
class	AbstractMgfReader<A extends PeakAnnotation,S extends Spectrum<A>> To extend how the TITLE line is handled add more TitleParser instances using addTitleParser
class	AbstractMsReader<A extends PeakAnnotation,S extends Spectrum<A>>
class	MgfReader
class	MzxmlReader

Uses of IterativeReader in org.expasy.mzjava.core.mol.polymer.prot

Classes in org.expasy.mzjava.core.mol.polymer.prot that implement IterativeReader

Modifier and Type	Class and Description
class	BioJavaFastaProteinReader A Protein reader based on biojava3 FastaReader object.

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

Classes in org.expasy.mzjava.external.io.ms.spectrum.mzml that implement IterativeReader

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).

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

Classes in org.expasy.mzjava.hadoop.io that implement IterativeReader

Modifier and Type	Class and Description
class	HadoopSpectraReader<A extends PeakAnnotation,S extends Spectrum<A>>

Uses of IterativeReader in org.expasy.mzjava.proteomics.io.mol

Classes in org.expasy.mzjava.proteomics.io.mol that implement IterativeReader

Modifier and Type	Class and Description
class	FastaProteinReader A reader for FASTA formatted files.

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

Classes in org.expasy.mzjava.proteomics.io.ms.spectrum that implement IterativeReader

Modifier and Type	Class and Description
class	DtaReader A simple DTA reader.
class	MsLibReader
class	MspReader An IterativeReader that can read nist msp files.
class	SptxtReader

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

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

Uses of IterativeReader in org.expasy.mzjava.proteomics.ms.dbsearch

Methods in org.expasy.mzjava.proteomics.ms.dbsearch with parameters of type IterativeReader

Modifier and Type	Method and Description
PeptideSpectrumDB.DigestDSL	PeptideSpectrumDB.DigestSourceDSL.setProteinSource(IterativeReader<Protein> reader) Set the IterativeReader reader as the protein source.

Constructors in org.expasy.mzjava.proteomics.ms.dbsearch with parameters of type IterativeReader

Constructor and Description
ArrayDigestDB.Builder(IterativeReader<Protein> reader, Protease protease, int missedCleavages) Create a bulder that build a ArrayDigestDB that digests proteins from the reader using the protease with missedCleavages missed cleavages.
ArrayDigestDB(IterativeReader<Protein> proteinReader, ProteinDigester proteinDigester, DigestDB.AmbiguousAminoAcidAction ambiguousAminoAcidAction) Construct a new ArrayDigestDB.