Uses of Interface
com.compomics.util.waiting.WaitingHandler

Packages that use WaitingHandler

Package	Description
com.compomics.cli.fasta	Command line for the handling of fasta files.
com.compomics.software.autoupdater	Classes related to auto updating compomics-utilities tools.
com.compomics.util.db.object	This package contains the classes relative to the object database.
com.compomics.util.experiment.biology.genes	Classes related to genes.
com.compomics.util.experiment.biology.genes.ensembl	Classes for the handling of Ensembl data.
com.compomics.util.experiment.biology.genes.go	Classes for the handling of GO terms.
com.compomics.util.experiment.identification	Experiment classes related to identifications.
com.compomics.util.experiment.identification.features	Classes for the generation of identification features.
com.compomics.util.experiment.identification.matches_iterators	Identification match iterators.
com.compomics.util.experiment.identification.peptide_inference	Classes related to peptide inference.
com.compomics.util.experiment.identification.protein_inference.fm_index	Protein sequence database indexing classes based on Burrows-Wheeler transform.
com.compomics.util.experiment.io.biology.protein	Experiment IO classes for biological resources.
com.compomics.util.experiment.io.biology.protein.converters	Fasta file converters.
com.compomics.util.experiment.io.biology.protein.iterators	Fasta file iterators.
com.compomics.util.experiment.io.identification	Experiment identification classes.
com.compomics.util.experiment.io.identification.idfilereaders	Experiment classes related to reading search engine files.
com.compomics.util.experiment.io.mass_spectrometry	Classes for the handling of mass spectrometry files.
com.compomics.util.experiment.io.mass_spectrometry.cms	Classes for the handling of Compomics mass spectrometry (cms) files.
com.compomics.util.experiment.io.mass_spectrometry.mgf	Classes for the handling of mgf files.
com.compomics.util.experiment.io.mass_spectrometry.mzml	Classes for the handling of mzml files.
com.compomics.util.experiment.quantification.spectrumcounting	Experiment classes related to spectrum counting.
com.compomics.util.gui.tablemodels	Self updating table model classes.
com.compomics.util.gui.waiting.waitinghandlers	Waiting handler classes.
com.compomics.util.io	Classes related to input/output.
com.compomics.util.io.compression	Classes related to file compression.
com.compomics.util.math.clustering	Basic clustering functions.
com.compomics.util.pdbfinder	Classes for mapping between UniProt accession numbers and PDB structures.

Uses of WaitingHandler in com.compomics.cli.fasta

Constructors in com.compomics.cli.fasta with parameters of type WaitingHandler

Modifier	Constructor	Description
	FastaParametersInputBean(org.apache.commons.cli.CommandLine aLine, File fastaFile, WaitingHandler waitingHandler)	Parses all the arguments from a command line.

Uses of WaitingHandler in com.compomics.software.autoupdater

Methods in com.compomics.software.autoupdater with parameters of type WaitingHandler

Modifier and Type	Method	Description
static void	DownloadLatestZipFromRepo.downloadLatestZipFromRepo(File downloadFolder, String toolName, String groupId, String artifactId, String iconName, String[] args, URL jarRepository, boolean startDownloadedVersion, boolean addDesktopIcon, FileDAO fileDAO, WaitingHandler waitingHandler)	Retrieves the latest version of a Maven jar file from a Maven repository.
static void	DownloadLatestZipFromRepo.downloadLatestZipFromRepo(URL jarPath, String toolName, boolean deleteOldFiles, boolean startDownloadedVersion, boolean addDesktopIcon, WaitingHandler waitingHandler)	Downloads the latest deploy from the genesis Maven repository of the artifact and starts it without arguments.
static void	DownloadLatestZipFromRepo.downloadLatestZipFromRepo(URL jarPath, String toolName, boolean deleteOldFiles, boolean addDesktopIcon, String[] args, URL jarRepository, WaitingHandler waitingHandler)	Downloads the latest zip archive of the jar in the URL from a given jarRepository.
static void	DownloadLatestZipFromRepo.downloadLatestZipFromRepo(URL jarPath, String toolName, boolean deleteOldFiles, String[] args, boolean startDownloadedVersion, boolean addDesktopIcon, WaitingHandler waitingHandler)	Downloads the latest zip archive of the jar in the URL from the genesis Maven repository.
static void	DownloadLatestZipFromRepo.downloadLatestZipFromRepo(URL jarPath, String toolName, boolean deleteOldFiles, String iconName, String[] args, URL jarRepository, boolean startDownloadedVersion, boolean addDesktopIcon, FileDAO fileDAO, WaitingHandler waitingHandler)	Retrieves the latest version of a Maven jar file from a Maven repository.
static void	DownloadLatestZipFromRepo.downloadLatestZipFromRepo(URL jarPath, String toolName, boolean deleteOldFiles, String iconName, String[] args, URL jarRepository, boolean startDownloadedVersion, boolean addDesktopIcon, WaitingHandler waitingHandler)	Retrieves the latest version of a Maven jar file from a Maven repository, also checks if the environment is headless or not.
boolean	FileDAO.unGzipAndUntarFile(GZIPInputStream in, File fileLocationOnDiskToDownloadTo, WaitingHandler waitingHandler)	Untars and ungzips a .tar.gz file.

Uses of WaitingHandler in com.compomics.util.db.object

Methods in com.compomics.util.db.object with parameters of type WaitingHandler

Modifier and Type	Method	Description
void	ObjectsDB.insertObjects(HashMap<Long,Object> objects, WaitingHandler waitingHandler, boolean displayProgress)	Inserts a set of objects in the given table.
void	ObjectsDB.loadObjects(Class className, WaitingHandler waitingHandler, boolean displayProgress)	Loads all objects from a given class.
void	ObjectsDB.loadObjects(Collection<Long> keys, WaitingHandler waitingHandler, boolean displayProgress)	Loads objects from a table in the cache.
void	ObjectsDB.lock(WaitingHandler waitingHandler)	Locking the db for storing.
void	ObjectsDB.removeObjects(Collection<Long> keys, WaitingHandler waitingHandler, boolean displayProgress)	Removing an object from the cache and database.
ArrayList<Object>	ObjectsDB.retrieveObjects(Class className, WaitingHandler waitingHandler, boolean displayProgress)	Retrieves all objects from a given class.
ArrayList<Object>	ObjectsDB.retrieveObjects(Collection<Long> keys, WaitingHandler waitingHandler, boolean displayProgress)	Retrieves some objects from the database or cache.
void	ObjectsCache.saveCache(WaitingHandler waitingHandler, boolean emptyCache)	Saves the cache content to the database.
void	ObjectsCache.saveObjects(int numLastEntries, WaitingHandler waitingHandler, boolean clearEntries)	Saves entries in the database if modified.

Uses of WaitingHandler in com.compomics.util.experiment.biology.genes

Methods in com.compomics.util.experiment.biology.genes with parameters of type WaitingHandler

Modifier and Type	Method	Description
boolean	ProteinGeneDetailsProvider.downloadGeneMappings(String ensemblType, String ensemblSchemaName, String ensemblDatasetName, String ensemblVersion, WaitingHandler waitingHandler)	Download the gene mappings.
boolean	ProteinGeneDetailsProvider.downloadGeneSequences(File destinationFile, String ensemblType, String ensemblSchemaName, String ensemblDbName, WaitingHandler waitingHandler)	Download the gene sequences mappings.
boolean	ProteinGeneDetailsProvider.downloadGoMappings(String ensemblType, String ensemblSchemaName, String ensemblDbName, boolean swissProtMapping, WaitingHandler waitingHandler)	Download the GO mappings.
boolean	ProteinGeneDetailsProvider.downloadMappings(WaitingHandler waitingHandler, String speciesName, String ensemblDatasetName, EnsemblSpecies.EnsemblDivision ensemblDivision)	Try to download the gene and GO mappings for the currently selected species.
GeneMaps	ProteinGeneDetailsProvider.getGeneMaps(GeneParameters genePreferences, FastaSummary fastaSummary, SequenceProvider sequenceProvider, ProteinDetailsProvider proteinDetailsProvider, WaitingHandler waitingHandler)	Returns the gene maps for the given proteins.
boolean	ProteinGeneDetailsProvider.queryEnsembl(String requestXml, File destinationFile, String ensemblType, WaitingHandler waitingHandler)	Sends an XML query to Ensembl and writes the result in a text file.
boolean	ProteinGeneDetailsProvider.queryEnsembl(String requestXml, String waitingText, File destinationFile, String ensemblType, WaitingHandler waitingHandler)	Sends an XML query to Ensembl and writes the result in a text file.

Uses of WaitingHandler in com.compomics.util.experiment.biology.genes.ensembl

Methods in com.compomics.util.experiment.biology.genes.ensembl with parameters of type WaitingHandler

Modifier and Type	Method	Description
void	GeneMapping.importFromFile(File file, WaitingHandler waitingHandler)	Reads go mappings from a BioMart file.

Uses of WaitingHandler in com.compomics.util.experiment.biology.genes.go

Methods in com.compomics.util.experiment.biology.genes.go with parameters of type WaitingHandler

Modifier and Type	Method	Description
void	GoDomains.loadMappingFromFile(File file, WaitingHandler waitingHandler)	Reads GO mappings from a file.
void	GoMapping.loadMappingsFromFile(File file, WaitingHandler waitingHandler)	Reads go mappings from a BioMart file.

Uses of WaitingHandler in com.compomics.util.experiment.identification

Methods in com.compomics.util.experiment.identification with parameters of type WaitingHandler

Modifier and Type	Method	Description
void	Identification.addObjects(HashMap<Long,Object> objects, WaitingHandler waitingHandler, boolean displayProgress)	Adds a list of objects into the database.
void	Identification.addSpectrumMatches(HashMap<Long,Object> spectrumMatches, WaitingHandler waitingHandler, boolean displayProgress)	Adds a spectrum matches into the database.
PeptideMatchesIterator	Identification.getPeptideMatchesIterator(long[] peptideKeys, WaitingHandler waitingHandler)	Returns a peptide matches iterator for a given key list.
PeptideMatchesIterator	Identification.getPeptideMatchesIterator(WaitingHandler waitingHandler)	Returns a peptide matches iterator for all PeptideMatches.
ProteinMatchesIterator	Identification.getProteinMatchesIterator(long[] proteinKeys, WaitingHandler waitingHandler)	Returns a protein matches iterator for a given key list.
ProteinMatchesIterator	Identification.getProteinMatchesIterator(WaitingHandler waitingHandler)	Returns a protein matches iterator for all PeptideMatches.
SpectrumMatchesIterator	Identification.getSpectrumMatchesIterator(long[] spectrumMatches, WaitingHandler waitingHandler)	Returns a spectrum matches iterator for a given key list.
SpectrumMatchesIterator	Identification.getSpectrumMatchesIterator(WaitingHandler waitingHandler)	Returns a spectrum matches iterator for all SpectrumMatches.
SpectrumMatchesIterator	Identification.getSpectrumMatchesIterator(WaitingHandler waitingHandler, String filters)	Returns a psm iterator for all SpectrumMatches.
void	Identification.loadObjects(Class className, WaitingHandler waitingHandler, boolean displayProgress)	Loads all objects of the class in cache.
void	Identification.loadObjects(ArrayList<Long> keyList, WaitingHandler waitingHandler, boolean displayProgress)	Loads all objects of given keys in cache.
void	Identification.removeObjects(ArrayList<Long> keys, WaitingHandler waitingHandler, boolean displayProgress)	Remove a list of objects from the database.
ArrayList<Object>	Identification.retrieveObjects(Class className, WaitingHandler waitingHandler, boolean displayProgress)	Returns an array of all objects of a given class
ArrayList<Object>	Identification.retrieveObjects(Collection<Long> keyList, WaitingHandler waitingHandler, boolean displayProgress)	Returns an array of all objects of a given list of keys

Uses of WaitingHandler in com.compomics.util.experiment.identification.features

Methods in com.compomics.util.experiment.identification.features with parameters of type WaitingHandler

Modifier and Type	Method	Description
int	IdentificationFeaturesGenerator.getNValidatedProteinGroups(long peptideKey, WaitingHandler waitingHandler)	Indicates whether a peptide is found in a single protein match.
long[]	IdentificationFeaturesGenerator.getProcessedProteinKeys(WaitingHandler waitingHandler, FilterParameters filterPreferences, boolean forceUpdate)	Returns the sorted list of protein keys.
long[]	IdentificationFeaturesGenerator.getProteinKeys(WaitingHandler waitingHandler, FilterParameters filterPreferences)	Returns the ordered protein keys to display when no filtering is applied.
long[]	IdentificationFeaturesGenerator.getValidatedProteins(WaitingHandler waitingHandler, FilterParameters filterPreferences)	Returns the list of validated protein keys.

Uses of WaitingHandler in com.compomics.util.experiment.identification.matches_iterators

Constructors in com.compomics.util.experiment.identification.matches_iterators with parameters of type WaitingHandler

Modifier	Constructor	Description
	MatchesIterator(long[] keys, Class className, Identification identification, WaitingHandler waitingHandler, boolean displayProgress, String filters)	Constructor.
	MatchesIterator(Class className, Identification identification, WaitingHandler waitingHandler, boolean displayProgress)	Constructor.
	PeptideMatchesIterator(long[] keys, Identification identification, WaitingHandler waitingHandler, boolean displayProgress)	Constructor.
	PeptideMatchesIterator(Identification identification, WaitingHandler waitingHandler, boolean displayProgress)	Constructor.
	ProteinMatchesIterator(long[] keys, Identification identification, WaitingHandler waitingHandler, boolean displayProgress)	Constructor.
	ProteinMatchesIterator(Identification identification, WaitingHandler waitingHandler, boolean displayProgress)	Constructor.
	SpectrumMatchesIterator(long[] keys, Identification identification, WaitingHandler waitingHandler, boolean displayProgress)	Constructor.
	SpectrumMatchesIterator(long[] keys, Identification identification, WaitingHandler waitingHandler, boolean displayProgress, String filters)	Constructor.
	SpectrumMatchesIterator(Identification identification, WaitingHandler waitingHandler, boolean displayProgress)	Constructor.

Uses of WaitingHandler in com.compomics.util.experiment.identification.peptide_inference

Methods in com.compomics.util.experiment.identification.peptide_inference with parameters of type WaitingHandler

Modifier and Type	Method	Description
void	PeptideInference.peptideInference(Identification identification, IdentificationParameters identificationParameters, SequenceProvider sequenceProvider, ModificationProvider modificationProvider, WaitingHandler waitingHandler)	Infers the PTM localization and its confidence for the best match of every spectrum.

Uses of WaitingHandler in com.compomics.util.experiment.identification.protein_inference.fm_index

Methods in com.compomics.util.experiment.identification.protein_inference.fm_index with parameters of type WaitingHandler

Modifier and Type	Method	Description
void	WaveletTree.createWaveletTreeHuffman(byte[] text, WaitingHandler waitingHandler, WaveletTree.HuffmanNode root)	Create wavelet tree huffman.

Constructors in com.compomics.util.experiment.identification.protein_inference.fm_index with parameters of type WaitingHandler

Modifier	Constructor	Description
	FMIndex(File fastaFile, FastaParameters fastaParameters, WaitingHandler waitingHandler, boolean displayProgress, PeptideVariantsParameters peptideVariantsPreferences, SearchParameters searchParameters)	Constructor.
	FMIndex(File fastaFile, FastaParameters fastaParameters, WaitingHandler waitingHandler, boolean displayProgress, IdentificationParameters identificationParameters)	Constructor.
	WaveletTree(byte[] text, long[] aAlphabet, WaitingHandler waitingHandler)	Constructor.
	WaveletTree(byte[] text, WaitingHandler waitingHandler, WaveletTree.HuffmanNode root)	Constructor.

Uses of WaitingHandler in com.compomics.util.experiment.io.biology.protein

Methods in com.compomics.util.experiment.io.biology.protein with parameters of type WaitingHandler

Modifier and Type	Method	Description
static FastaSummary	FastaSummary.getSummary(String fastaFile, FastaParameters fastaParameters, boolean alwaysCreateNew, WaitingHandler waitingHandler)	Gathers summary data on the FASTA file content.
static FastaSummary	FastaSummary.getSummary(String fastaFile, FastaParameters fastaParameters, WaitingHandler waitingHandler)	Gathers summary data on the FASTA file content.
static FastaParameters	FastaParameters.inferParameters(String fastaFilePath, WaitingHandler waitingHandler)	Infers the parameters used to parse the file.

Uses of WaitingHandler in com.compomics.util.experiment.io.biology.protein.converters

Methods in com.compomics.util.experiment.io.biology.protein.converters with parameters of type WaitingHandler

Modifier and Type	Method	Description
static void	DecoyConverter.appendDecoySequences(File fastaIn, File fastaOut, FastaParameters fastaParameters, WaitingHandler waitingHandler)	Appends decoy sequences to the provided FASTA file.
static void	GenericFastaConverter.convertFile(File fastaIn, File fastaOut, WaitingHandler waitingHandler)	Appends decoy sequences to the provided FASTA file.

Uses of WaitingHandler in com.compomics.util.experiment.io.biology.protein.iterators

Methods in com.compomics.util.experiment.io.biology.protein.iterators with parameters of type WaitingHandler

Modifier and Type	Method	Description
String	HeaderIterator.getNextHeader(WaitingHandler waitingHandler)	Returns the next header.Null if none.

Uses of WaitingHandler in com.compomics.util.experiment.io.identification

Methods in com.compomics.util.experiment.io.identification with parameters of type WaitingHandler

Modifier and Type	Method	Description
ArrayList<SpectrumMatch>	IdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider, WaitingHandler waitingHandler, SearchParameters searchParameters)	Retrieves all the spectrum matches from an identification file as a list of spectrum matches, one spectrum match per spectrum.
ArrayList<SpectrumMatch>	IdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider, WaitingHandler waitingHandler, SearchParameters searchParameters, SequenceMatchingParameters sequenceMatchingPreferences, boolean expandAaCombinations)	Retrieves all the spectrum matches from an identification file as a list of spectrum matches, one spectrum match per spectrum.It is very important to close the file reader after creation.

Constructors in com.compomics.util.experiment.io.identification with parameters of type WaitingHandler

Modifier	Constructor	Description
	MzIdentMLIdfileSearchParametersConverter(File mzIdentMLFile, SearchParameters searchParameters, String species, WaitingHandler waitingHandler)	Constructor.

Uses of WaitingHandler in com.compomics.util.experiment.io.identification.idfilereaders

Methods in com.compomics.util.experiment.io.identification.idfilereaders with parameters of type WaitingHandler

Modifier and Type	Method	Description
ArrayList<SpectrumMatch>	AndromedaIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider, WaitingHandler waitingHandler, SearchParameters searchParameters)
ArrayList<SpectrumMatch>	AndromedaIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider, WaitingHandler waitingHandler, SearchParameters searchParameters, SequenceMatchingParameters sequenceMatchingPreferences, boolean expandAaCombinations)
ArrayList<SpectrumMatch>	CossIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider, WaitingHandler waitingHandler, SearchParameters searchParameters)
ArrayList<SpectrumMatch>	CossIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider, WaitingHandler waitingHandler, SearchParameters searchParameters, SequenceMatchingParameters sequenceMatchingPreferences, boolean expandAaCombinations)
ArrayList<SpectrumMatch>	DirecTagIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider, WaitingHandler waitingHandler, SearchParameters searchParameters)
ArrayList<SpectrumMatch>	DirecTagIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider, WaitingHandler waitingHandler, SearchParameters searchParameters, SequenceMatchingParameters sequenceMatchingPreferences, boolean expandAaCombinations)
ArrayList<SpectrumMatch>	MascotIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider, WaitingHandler waitingHandler, SearchParameters searchParameters)
ArrayList<SpectrumMatch>	MascotIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider, WaitingHandler waitingHandler, SearchParameters searchParameters, SequenceMatchingParameters sequenceMatchingPreferences, boolean expandAaCombinations)
ArrayList<SpectrumMatch>	MsAmandaIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider, WaitingHandler waitingHandler, SearchParameters searchParameters)
ArrayList<SpectrumMatch>	MsAmandaIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider, WaitingHandler waitingHandler, SearchParameters searchParameters, SequenceMatchingParameters sequenceMatchingPreferences, boolean expandAaCombinations)
ArrayList<SpectrumMatch>	MzIdentMLIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider, WaitingHandler waitingHandler, SearchParameters searchParameters)
ArrayList<SpectrumMatch>	MzIdentMLIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider, WaitingHandler waitingHandler, SearchParameters searchParameters, SequenceMatchingParameters sequenceMatchingPreferences, boolean expandAaCombinations)
ArrayList<SpectrumMatch>	NovorIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider, WaitingHandler waitingHandler, SearchParameters searchParameters)
ArrayList<SpectrumMatch>	NovorIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider, WaitingHandler waitingHandler, SearchParameters searchParameters, SequenceMatchingParameters sequenceMatchingPreferences, boolean expandAaCombinations)
ArrayList<SpectrumMatch>	OnyaseIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider, WaitingHandler waitingHandler, SearchParameters searchParameters)
ArrayList<SpectrumMatch>	OnyaseIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider, WaitingHandler waitingHandler, SearchParameters searchParameters, SequenceMatchingParameters sequenceMatchingPreferences, boolean expandAaCombinations)
ArrayList<SpectrumMatch>	PepNovoIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider, WaitingHandler waitingHandler, SearchParameters searchParameters)
ArrayList<SpectrumMatch>	PepNovoIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider, WaitingHandler waitingHandler, SearchParameters searchParameters, SequenceMatchingParameters sequenceMatchingPreferences, boolean expandAaCombinations)
ArrayList<SpectrumMatch>	PepxmlIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider, WaitingHandler waitingHandler, SearchParameters searchParameters)
ArrayList<SpectrumMatch>	PepxmlIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider, WaitingHandler waitingHandler, SearchParameters searchParameters, SequenceMatchingParameters sequenceMatchingPreferences, boolean expandAaCombinations)
ArrayList<SpectrumMatch>	PNovoIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider, WaitingHandler waitingHandler, SearchParameters searchParameters)
ArrayList<SpectrumMatch>	PNovoIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider, WaitingHandler waitingHandler, SearchParameters searchParameters, SequenceMatchingParameters sequenceMatchingPreferences, boolean expandAaCombinations)
ArrayList<SpectrumMatch>	SageIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider, WaitingHandler waitingHandler, SearchParameters searchParameters)
ArrayList<SpectrumMatch>	SageIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider, WaitingHandler waitingHandler, SearchParameters searchParameters, SequenceMatchingParameters sequenceMatchingPreferences, boolean expandAaCombinations)
ArrayList<SpectrumMatch>	TideIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider, WaitingHandler waitingHandler, SearchParameters searchParameters)
ArrayList<SpectrumMatch>	TideIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider, WaitingHandler waitingHandler, SearchParameters searchParameters, SequenceMatchingParameters sequenceMatchingPreferences, boolean expandAaCombinations)
ArrayList<SpectrumMatch>	XTandemIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider, WaitingHandler waitingHandler, SearchParameters searchParameters)
ArrayList<SpectrumMatch>	XTandemIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider, WaitingHandler waitingHandler, SearchParameters searchParameters, SequenceMatchingParameters sequenceMatchingPreferences, boolean expandAaCombinations)

Constructors in com.compomics.util.experiment.io.identification.idfilereaders with parameters of type WaitingHandler

Modifier	Constructor	Description
	CossIdfileReader(File cossTsvFile, WaitingHandler waitingHandler)	Constructor for a COSS tsv result file reader.
	MascotIdfileReader(File inputFile, WaitingHandler waitingHandler)	Constructor for an Mascot dat csv result file reader.
	MsAmandaIdfileReader(File msAmandaCsvFile, WaitingHandler waitingHandler)	Constructor for an MS Amanda csv result file reader.
	MzIdentMLIdfileReader(File mzIdentMLFile, WaitingHandler waitingHandler)	Constructor for an mzIdentML result file reader.
	NovorIdfileReader(File novorCsvFile, WaitingHandler waitingHandler)	Constructor for an Novor csv result file reader.
	SageIdfileReader(File sageTsvFile, WaitingHandler waitingHandler)	Constructor for a Sage tsv file reader.
	TideIdfileReader(File tideTsvFile, WaitingHandler waitingHandler)	Constructor for an Tide tsv result file reader.
	XTandemIdfileReader(File inputFile, WaitingHandler waitingHandler)	Constructor for an X!Tandem xml result file reader.

Uses of WaitingHandler in com.compomics.util.experiment.io.mass_spectrometry

Methods in com.compomics.util.experiment.io.mass_spectrometry with parameters of type WaitingHandler

Modifier and Type	Method	Description
static MsFileIterator	MsFileIterator.getMsFileIterator(File file, WaitingHandler waitingHandler)	Returns the file reader for the given mass spectrometry file based on its extension.
void	MsFileHandler.register(File msFile, WaitingHandler waitingHandler)	Registers a mass spectrometry file and enables querying its spectra.If the file is not a cms file, a cms file will be created along with the ms file.
void	MsFileHandler.register(File msFile, File cmsFolder, WaitingHandler waitingHandler)	Registers a mass spectrometry file and enables querying its spectra.
static void	MsFileExporter.writeAplFile(SpectrumProvider spectrumProvider, boolean includeAllSpectrumLevels, String fileNameWithoutExtension, File destinationFile, SearchParameters searchParameters, WaitingHandler waitingHandler)	Writes the spectra of a file in the Andromeda peak list (apl) format.
static void	MsFileExporter.writeMgfFile(SpectrumProvider spectrumProvider, boolean includeAllSpectrumLevels, String fileNameWithoutExtension, File destinationFile, WaitingHandler waitingHandler)	Writes the spectra of a file in the Mascot Generic File (mgf) format.
static void	MsFileExporter.writeMs2File(SpectrumProvider spectrumProvider, boolean includeAllSpectrumLevels, String fileNameWithoutExtension, File destinationFile, WaitingHandler waitingHandler)	Writes the spectra of a file in the ms2 format.
static void	MsFileExporter.writeMsFile(SpectrumProvider spectrumProvider, boolean includeAllSpectrumLevels, String fileNameWithoutExtension, File destinationFile, MsFileExporter.Format format, SearchParameters searchParameters, WaitingHandler waitingHandler)	Writes the spectra of a file in the given format.

Uses of WaitingHandler in com.compomics.util.experiment.io.mass_spectrometry.cms

Constructors in com.compomics.util.experiment.io.mass_spectrometry.cms with parameters of type WaitingHandler

Modifier	Constructor	Description
	CmsFileIterator(File file, WaitingHandler waitingHandler)	Constructor.
	CmsFileReader(File file, WaitingHandler waitingHandler)	Constructor allocating for single thread usage.

Uses of WaitingHandler in com.compomics.util.experiment.io.mass_spectrometry.mgf

Methods in com.compomics.util.experiment.io.mass_spectrometry.mgf with parameters of type WaitingHandler

Modifier and Type	Method	Description
static void	MgfFileUtils.addMissingPrecursorCharges(File mgfFile, WaitingHandler waitingHandler)	Add missing precursor charges.
static void	MgfFileUtils.addMissingSpectrumTitles(File mgfFile, WaitingHandler waitingHandler)	Adds missing spectrum titles.
static MgfIndex	IndexedMgfReader.getMgfIndex(File mgfFile, WaitingHandler waitingHandler)	Returns the index of all spectra in the given MGF file.
static void	MgfFileUtils.removeDuplicateSpectrumTitles(File mgfFile, WaitingHandler waitingHandler)	Removes duplicate spectrum titles (the first occurrence is kept).
static void	MgfFileUtils.removeZeroes(File mgfFile, WaitingHandler waitingHandler)	Removes zero intensity peaks.
static void	MgfFileUtils.renameDuplicateSpectrumTitles(File mgfFile, WaitingHandler waitingHandler)	Renames duplicate spectrum titles.
static ArrayList<MgfIndex>	MgfFileUtils.splitFile(File mgfFile, int nSpectra, WaitingHandler waitingHandler)	Splits an mgf file into smaller ones and returns the indexes of the generated files.

Constructors in com.compomics.util.experiment.io.mass_spectrometry.mgf with parameters of type WaitingHandler

Modifier	Constructor	Description
	MgfFileIterator(File mgfFile, WaitingHandler waitingHandler)	Constructor.

Uses of WaitingHandler in com.compomics.util.experiment.io.mass_spectrometry.mzml

Constructors in com.compomics.util.experiment.io.mass_spectrometry.mzml with parameters of type WaitingHandler

Modifier	Constructor	Description
	MzmlFileIterator(File mzmlFile, WaitingHandler waitingHandler)	Constructor.

Uses of WaitingHandler in com.compomics.util.experiment.quantification.spectrumcounting

Methods in com.compomics.util.experiment.quantification.spectrumcounting with parameters of type WaitingHandler

Modifier and Type	Method	Description
void	ScalingFactorsEstimators.estimateScalingFactors(Identification identification, Metrics metrics, SequenceProvider sequenceProvider, IdentificationFeaturesGenerator identificationFeaturesGenerator, WaitingHandler waitingHandler, ExceptionHandler exceptionHandler, ProcessingParameters processingParameters)	Estimates the scaling factors and stores them in the given metrics.

Uses of WaitingHandler in com.compomics.util.gui.tablemodels

Methods in com.compomics.util.gui.tablemodels with parameters of type WaitingHandler

Modifier and Type	Method	Description
protected abstract int	SelfUpdatingTableModel.loadDataForRows(ArrayList<Integer> indexes, WaitingHandler waitingHandler)	Loads the data needed for objects at rows of the given view indexes.

Uses of WaitingHandler in com.compomics.util.gui.waiting.waitinghandlers

Classes in com.compomics.util.gui.waiting.waitinghandlers that implement WaitingHandler

Modifier and Type	Class	Description
class	ProgressDialogX	A dialog for displaying information about progress.
class	WaitingDialog	A dialog displaying progress details.
class	WaitingHandlerCLIImpl	This class is an implementation of the WaitingHandler interface to be used when operating through the Command Line Interface.
class	WaitingHandlerDummy	This class is an implementation of the WaitingHandler interface to be used when a process can be canceled, but no monitoring is needed.

Uses of WaitingHandler in com.compomics.util.io

Methods in com.compomics.util.io with parameters of type WaitingHandler

Modifier and Type	Method	Description
static File	IoUtil.saveUrl(File saveFile, String targetUrlAsString, int fileSizeInBytes, String userName, String password, WaitingHandler waitingHandler)	Save a file from a URL.

Uses of WaitingHandler in com.compomics.util.io.compression

Methods in com.compomics.util.io.compression with parameters of type WaitingHandler

Modifier and Type	Method	Description
static void	ZipUtils.addFileToZip(File file, ZipOutputStream out, WaitingHandler waitingHandler, long totalUncompressedFileSize)	Adds a new file to the zip stream.
static void	ZipUtils.addFileToZip(String subDirectory, File file, ZipOutputStream out, WaitingHandler waitingHandler, long totalUncompressedFileSize)	Adds a new file to the zip stream.
static void	TarUtils.addFolderContent(org.apache.commons.compress.archivers.ArchiveOutputStream tarOutput, File folder, WaitingHandler waitingHandler)	Add content to the tar file.
static void	ZipUtils.addToZip(File file, String subDirectory, ZipOutputStream out, WaitingHandler waitingHandler, long totalUncompressedFileSize)	Adds a new file to the zip stream.
static void	ZipUtils.addToZip(File file, ZipOutputStream out, WaitingHandler waitingHandler, long totalUncompressedFileSize)	Adds a new file to the zip stream.
static void	TarUtils.extractFile(File tarFile, WaitingHandler waitingHandler)	Extracts files from a tar.
static void	TarUtils.extractFile(File tarFile, File destinationFolder, WaitingHandler waitingHandler)	Extracts files from a tar.
static void	TarUtils.tarFolder(File folder, File destinationFile, WaitingHandler waitingHandler)	Tar a given folder to a file.
static void	TarUtils.tarFolderContent(File folder, File destinationFile, HashSet<String> exceptionsPaths, WaitingHandler waitingHandler)	Tar the content of a given folder to a file.
static void	ZipUtils.unzip(File zipFile, File destinationFolder, WaitingHandler waitingHandler)	Unzips the content of an archive into a given folder.
static void	ZipUtils.zip(File originFile, File destinationFile, WaitingHandler waitingHandler, long totalUncompressedFileSize)	Zips a file.

Uses of WaitingHandler in com.compomics.util.math.clustering

Methods in com.compomics.util.math.clustering with parameters of type WaitingHandler

Modifier and Type	Method	Description
void	KMeansClustering.kMeanCluster(WaitingHandler waitingHandler)	Run the k-means clustering.

Uses of WaitingHandler in com.compomics.util.pdbfinder

Constructors in com.compomics.util.pdbfinder with parameters of type WaitingHandler

Modifier	Constructor	Description
	FindPdbForUniprotAccessions(String aProteinAccession, WaitingHandler aWaitingHandler)	Constructor.