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

Packages that use WaitingHandler

Package	Description
com.compomics.software.autoupdater	Classes related to auto updating compomics-utilities tools.
com.compomics.util	General utilities classes.
com.compomics.util.db	Database related classes.
com.compomics.util.experiment.biology	Experiment classes related to biological entities.
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.matches_iterators	Identification match iterators.
com.compomics.util.experiment.identification.protein_inference.proteintree	Protein sequence database indexing classes.
com.compomics.util.experiment.identification.protein_sequences	Protein sequence handling related classes.
com.compomics.util.experiment.io.identifications	Experiment identification classes.
com.compomics.util.experiment.io.identifications.idfilereaders	Experiment classes related to reading search engine files.
com.compomics.util.experiment.io.massspectrometry	Reading and indexing of mgf files.
com.compomics.util.experiment.massspectrometry	Experiment classes related to spectra.
com.compomics.util.gui.tablemodels	Self updating table model classes.
com.compomics.util.gui.waiting.waitinghandlers	Waiting handler classes.
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.
com.compomics.util.protein_sequences_manager	Classes used for the management of FASTA files.

Uses of WaitingHandler in com.compomics.software.autoupdater

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

Modifier and Type	Method and 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

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

Modifier and Type	Method and Description
static File	Util.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.db

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

Modifier and Type	Method and Description
void	ObjectsDB.insertObjects(String tableName, HashMap<String,Object> objects, WaitingHandler waitingHandler) Inserts a set of objects in the given table.
void	ObjectsDB.insertObjects(String tableName, HashMap<String,Object> objects, WaitingHandler waitingHandler, boolean allNewObjects) Inserts a set of objects in the given table.
void	ObjectsDB.loadObjects(String tableName, ArrayList<String> keys, WaitingHandler waitingHandler, boolean displayProgress) Loads some objects from a table in the cache.
void	ObjectsDB.loadObjects(String tableName, WaitingHandler waitingHandler, boolean displayProgress) Loads all objects from a table in the cache.
void	ObjectsCache.reduceMemoryConsumption(double share, WaitingHandler waitingHandler) Reduces the memory consumption by saving the given share of hits.
void	ObjectsCache.saveCache(WaitingHandler waitingHandler, boolean emptyCache) Saves the cache content in the database.
void	ObjectsCache.saveObjects(ArrayList<String> entryKeys, WaitingHandler waitingHandler) Saves an entry in the database if modified and clears it from the cache.
void	ObjectsCache.saveObjects(ArrayList<String> entryKeys, WaitingHandler waitingHandler, boolean clearEntries) Saves an entry in the database if modified.

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

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

Modifier and Type	Method and Description
ArrayList<String>	Peptide.getParentProteinsCreateTree(SequenceMatchingPreferences sequenceMatchingPreferences, WaitingHandler waitingHandler, ExceptionHandler exceptionHandler) Returns the parent proteins and remaps the peptide to the protein if no protein mapping was set using the default protein tree of the sequence factory.

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 and Description
void	GeneFactory.downloadGeneMappings(String ensemblType, String ensemblSchemaName, String ensemblDatasetName, String ensemblVersion, WaitingHandler waitingHandler) Download the gene mappings.
boolean	GeneFactory.downloadGeneSequences(File destinationFile, String ensemblType, String ensemblSchemaName, String ensemblDbName, WaitingHandler waitingHandler) Download the gene sequences mappings.
boolean	GeneFactory.downloadGoMappings(String ensemblType, String ensemblSchemaName, String ensemblDbName, boolean swissProtMapping, WaitingHandler waitingHandler) Download the GO mappings.
boolean	GeneFactory.downloadMappings(WaitingHandler waitingHandler, Integer taxon) Try to download the gene and GO mappings for the currently selected species.
GeneMaps	GeneFactory.getGeneMaps(GenePreferences genePreferences, WaitingHandler waitingHandler) Returns the gene maps for the FASTA file loaded in the factory.
boolean	GeneFactory.queryEnsembl(String requestXml, File destinationFile, String ensemblType, WaitingHandler waitingHandler) Sends an XML query to Ensembl and writes the result in a text file.
boolean	GeneFactory.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 and 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 and Description
void	GoDomains.laodMappingFromFile(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 and Description
void	Identification.buildPeptidesAndProteins(WaitingHandler waitingHandler, SequenceMatchingPreferences sequenceMatchingPreferences) Creates the peptides and protein instances based on the spectrum matches.
PeptideMatchesIterator	Identification.getPeptideMatchesIterator(ArrayList<String> peptideKeys, ArrayList<UrParameter> peptideParameters, boolean loadPsms, ArrayList<UrParameter> psmParameters, WaitingHandler waitingHandler) Returns a peptide matches iterator.
PeptideMatchesIterator	Identification.getPeptideMatchesIterator(ArrayList<UrParameter> peptideParameters, boolean loadPsms, ArrayList<UrParameter> psmParameters, WaitingHandler waitingHandler) Returns a peptide matches iterator iterating all peptides.
ProteinMatchesIterator	Identification.getProteinMatchesIterator(ArrayList<String> proteinKeys, ArrayList<UrParameter> proteinParameters, boolean loadPeptides, ArrayList<UrParameter> peptideParameters, boolean loadPsms, ArrayList<UrParameter> psmParameters, WaitingHandler waitingHandler) Returns a protein matches iterator.
ProteinMatchesIterator	Identification.getProteinMatchesIterator(ArrayList<UrParameter> proteinParameters, boolean loadPeptides, ArrayList<UrParameter> peptideParameters, boolean loadPsms, ArrayList<UrParameter> psmParameters, WaitingHandler waitingHandler) Returns a protein matches iterator iterating all protein matches.
PsmIterator	Identification.getPsmIterator(ArrayList<String> spectrumKeys, ArrayList<UrParameter> psmParameters, boolean loadAssumptions, WaitingHandler waitingHandler) Returns a PSM iterator.
PsmIterator	Identification.getPsmIterator(ArrayList<String> spectrumKeys, boolean loadAssumptions, WaitingHandler waitingHandler) Returns a PSM iterator.
PsmIterator	Identification.getPsmIterator(boolean loadAssumptions, ArrayList<UrParameter> psmParameters, WaitingHandler waitingHandler) Returns a PSM iterator iterating all PSMs in a file.
PsmIterator	Identification.getPsmIterator(String spectrumFile, ArrayList<String> spectrumKeys, ArrayList<UrParameter> psmParameters, boolean loadAssumptions, WaitingHandler waitingHandler) Returns a PSM iterator.
PsmIterator	Identification.getPsmIterator(String spectrumFile, ArrayList<UrParameter> psmParameters, boolean loadAssumptions, WaitingHandler waitingHandler) Returns a PSM iterator iterating all PSMs in a file.
PsmIterator	Identification.getPsmIterator(String spectrumFile, boolean loadAssumptions, WaitingHandler waitingHandler) Returns a PSM iterator iterating all PSMs in a file.
void	IdentificationDB.loadAssumptions(ArrayList<String> spectrumKeys, WaitingHandler waitingHandler, boolean displayProgress) Loads all assumptions of the given spectra in the cache of the database.
void	Identification.loadAssumptions(ArrayList<String> spectrumKeys, WaitingHandler waitingHandler, boolean displayProgress) Loads the assumptions of the spectrum matches indicated by the given keys in the cache of the database.
void	IdentificationDB.loadAssumptions(String fileName, WaitingHandler waitingHandler, boolean displayProgress) Loads all assumptions of the given file in the cache of the database.
void	Identification.loadAssumptions(String fileName, WaitingHandler waitingHandler, boolean displayProgress) Loads all spectrum matches of the file in the cache of the database.
void	IdentificationDB.loadPeptideMatches(ArrayList<String> peptideKeys, WaitingHandler waitingHandler, boolean displayProgress) Loads the desired peptide matches of the given type in the cache of the database.
void	Identification.loadPeptideMatches(ArrayList<String> peptideKeys, WaitingHandler waitingHandler, boolean displayProgress) Loads the desired peptide matches of the given type in the cache of the database.
void	IdentificationDB.loadPeptideMatches(WaitingHandler waitingHandler, boolean displayProgress) Loads all peptide matches in the cache of the database.
void	Identification.loadPeptideMatches(WaitingHandler waitingHandler, boolean displayProgress) Loads all peptide matches in the cache of the database.
void	IdentificationDB.loadPeptideMatchParameters(ArrayList<String> peptideKeys, UrParameter urParameter, WaitingHandler waitingHandler, boolean displayProgress) Loads the desired peptide match parameters of the given type in the cache of the database.
void	Identification.loadPeptideMatchParameters(ArrayList<String> peptideKeys, UrParameter urParameter, WaitingHandler waitingHandler, boolean displayProgress) Loads the desired peptide match parameters of the given type in the cache of the database.
void	IdentificationDB.loadPeptideMatchParameters(UrParameter urParameter, WaitingHandler waitingHandler, boolean displayProgress) Loads all peptide match parameters of the given type in the cache of the database.
void	Identification.loadPeptideMatchParameters(UrParameter urParameter, WaitingHandler waitingHandler, boolean displayProgress) Loads all peptide match parameters of the given type in the cache of the database.
void	IdentificationDB.loadProteinMatches(ArrayList<String> proteinKeys, WaitingHandler waitingHandler, boolean displayProgress) Loads the desired protein matches of the given type in the cache of the database.
void	Identification.loadProteinMatches(ArrayList<String> proteinKeys, WaitingHandler waitingHandler, boolean displayProgress) Loads the desired protein matches of the given type in the cache of the database.
void	IdentificationDB.loadProteinMatches(WaitingHandler waitingHandler, boolean displayProgress) Loads all protein matches in the cache of the database.
void	Identification.loadProteinMatches(WaitingHandler waitingHandler, boolean displayProgress) Loads all protein matches in the cache of the database.
void	IdentificationDB.loadProteinMatchParameters(ArrayList<String> proteinKeys, UrParameter urParameter, WaitingHandler waitingHandler, boolean displayProgress) Loads the desired protein match parameters of the given type in the cache of the database.
void	Identification.loadProteinMatchParameters(ArrayList<String> proteinKeys, UrParameter urParameter, WaitingHandler waitingHandler, boolean displayProgress) Loads the desired protein match parameters of the given type in the cache of the database.
void	IdentificationDB.loadProteinMatchParameters(UrParameter urParameter, WaitingHandler waitingHandler, boolean displayProgress) Loads all protein match parameters of the given type in the cache of the database.
void	Identification.loadProteinMatchParameters(UrParameter urParameter, WaitingHandler waitingHandler, boolean displayProgress) Loads all protein match parameters of the given type in the cache of the database.
void	IdentificationDB.loadRawAssumptions(ArrayList<String> spectrumKeys, WaitingHandler waitingHandler, boolean displayProgress) Loads all raw assumptions of the given spectra in the cache of the database.
void	IdentificationDB.loadRawAssumptions(String fileName, WaitingHandler waitingHandler, boolean displayProgress) Loads all raw assumptions of the given file in the cache of the database.
void	Identification.loadRawAssumptions(String fileName, WaitingHandler waitingHandler, boolean displayProgress) Loads the raw assumptions of the spectrum matches indicated by the given keys in the cache of the database.
void	IdentificationDB.loadSpectrumMatches(ArrayList<String> spectrumKeys, WaitingHandler waitingHandler, boolean displayProgress) Loads all given spectrum matches in the cache of the database.
void	Identification.loadSpectrumMatches(ArrayList<String> spectrumKeys, WaitingHandler waitingHandler, boolean displayProgress) Loads the spectrum matches corresponding to the given keys in cache.
void	IdentificationDB.loadSpectrumMatches(String fileName, WaitingHandler waitingHandler, boolean displayProgress) Loads all spectrum matches of the given file in the cache of the database.
void	Identification.loadSpectrumMatches(String fileName, WaitingHandler waitingHandler, boolean displayProgress) Loads all spectrum matches of the file in cache.
void	IdentificationDB.loadSpectrumMatchParameters(ArrayList<String> spectrumKeys, UrParameter urParameter, WaitingHandler waitingHandler, boolean displayProgress) Loads all desired spectrum match parameters in the cache of the database.
void	Identification.loadSpectrumMatchParameters(ArrayList<String> spectrumKeys, UrParameter urParameter, WaitingHandler waitingHandler, boolean displayProgress) Loads all desired spectrum match parameters in the cache of the database.
void	IdentificationDB.loadSpectrumMatchParameters(String fileName, UrParameter urParameter, WaitingHandler waitingHandler, boolean displayProgress) Loads all spectrum match parameters of the given type in the cache of the database.
void	Identification.loadSpectrumMatchParameters(String fileName, UrParameter urParameter, WaitingHandler waitingHandler, boolean displayProgress) Loads all spectrum match parameters of the given type in the cache of the database

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

Constructor and Description
PeptideMatchesIterator(ArrayList<String> peptideKeys, Identification identification, ArrayList<UrParameter> peptideParameters, boolean loadPsms, ArrayList<UrParameter> psmParameters, WaitingHandler waitingHandler) Constructor.
PeptideMatchesIterator(ArrayList<String> peptideKeys, Identification identification, ArrayList<UrParameter> peptideParameters, WaitingHandler waitingHandler) Constructor.
PeptideMatchesIterator(Identification identification, ArrayList<UrParameter> peptideParameters, boolean loadPsms, ArrayList<UrParameter> psmParameters, WaitingHandler waitingHandler) Constructor.
ProteinMatchesIterator(ArrayList<String> proteinKeys, Identification identification, ArrayList<UrParameter> proteinParameters, boolean loadPeptides, ArrayList<UrParameter> peptideParameters, boolean loadPsms, ArrayList<UrParameter> psmParameters, WaitingHandler waitingHandler) Constructor.
ProteinMatchesIterator(Identification identification, ArrayList<UrParameter> proteinParameters, boolean loadPeptides, ArrayList<UrParameter> peptideParameters, boolean loadPsms, ArrayList<UrParameter> psmParameters, WaitingHandler waitingHandler) Constructor for an iterator iterating all protein keys.
PsmIterator(ArrayList<String> spectrumKeys, Identification identification, ArrayList<UrParameter> psmParameters, boolean loadAssumptions, WaitingHandler waitingHandler) Constructor.
PsmIterator(ArrayList<String> spectrumKeys, Identification identification, boolean loadAssumptions, WaitingHandler waitingHandler) Constructor.
PsmIterator(Identification identification, ArrayList<UrParameter> psmParameters, boolean loadAssumptions, WaitingHandler waitingHandler) Constructor.
PsmIterator(Identification identification, boolean loadAssumptions, WaitingHandler waitingHandler) Constructor.
PsmIterator(String spectrumFile, ArrayList<String> spectrumKeys, Identification identification, ArrayList<UrParameter> psmParameters, boolean loadAssumptions, WaitingHandler waitingHandler) Constructor.
PsmIterator(String spectrumFile, ArrayList<String> spectrumKeys, Identification identification, boolean loadAssumptions, WaitingHandler waitingHandler) Constructor.
PsmIterator(String spectrumFile, Identification identification, ArrayList<UrParameter> psmParameters, boolean loadAssumptions, WaitingHandler waitingHandler) Constructor.
PsmIterator(String spectrumFile, Identification identification, boolean loadAssumptions, ArrayList<UrParameter> psmParameters, WaitingHandler waitingHandler) Constructor.
PsmIterator(String spectrumFile, Identification identification, boolean loadAssumptions, WaitingHandler waitingHandler) Constructor.

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

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

Modifier and Type	Method and Description
void	ProteinTree.initiateTree(int initialTagSize, int maxNodeSize, int maxPeptideSize, Enzyme enzyme, WaitingHandler waitingHandler, ExceptionHandler exceptionHandler, boolean printExpectedImportTime, boolean displayProgress, int nThreads) Initiates the tree.
void	ProteinTree.initiateTree(int initialTagSize, int maxNodeSize, int maxPeptideSize, WaitingHandler waitingHandler, ExceptionHandler exceptionHandler, boolean printExpectedImportTime, boolean displayProgress, int nThreads) Initiates the tree.
void	ProteinTreeComponentsFactory.loadNodes(ArrayList<String> tags, WaitingHandler waitingHandler) Loads nodes in the cache.
void	ProteinTreeComponentsFactory.saveNodes(HashMap<String,Object> nodes, WaitingHandler waitingHandler) Adds nodes to the database.

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

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

Modifier and Type	Method and Description
void	SequenceFactory.appendDecoySequences(File destinationFile, WaitingHandler waitingHandler) Appends decoy sequences to the desired file while displaying progress.
ProteinTree	SequenceFactory.getDefaultProteinTree(int nThreads, WaitingHandler waitingHandler, ExceptionHandler exceptionHandler) Returns the default protein tree corresponding to the database loaded in factory, creates a new one if none found.
ProteinTree	SequenceFactory.getDefaultProteinTree(int nThreads, WaitingHandler waitingHandler, ExceptionHandler exceptionHandler, boolean displayProgress) Returns the default protein tree corresponding to the database loaded in factory, creates a new one if none found.
ProteinTree	SequenceFactory.getDefaultProteinTree(WaitingHandler waitingHandler, ExceptionHandler exceptionHandler) Returns the default protein tree corresponding to the database loaded in factory, creates a new one if none found.
static FastaIndex	SequenceFactory.getFastaIndex(File fastaFile, boolean overwrite, WaitingHandler waitingHandler) Returns the file index of the given FASTA file.
void	SequenceFactory.loadFastaFile(File fastaFile, WaitingHandler waitingHandler) Loads a new FASTA file in the factory.

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

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

Modifier and Type	Method and Description
LinkedList<SpectrumMatch>	IdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler, SearchParameters searchParameters) Retrieves all the identifications from an identification file as a list of spectrum matches It is very important to close the file reader after creation.
LinkedList<SpectrumMatch>	IdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler, SearchParameters searchParameters, SequenceMatchingPreferences sequenceMatchingPreferences, boolean expandAaCombinations) Retrieves all the identifications from an identification file as a list of spectrum matches It is very important to close the file reader after creation.
static String	MzIdentMLIdfileSearchParametersConverter.getSearchParameters(File mzIdentMLFile, SearchParameters searchParameters, String species, WaitingHandler waitingHandler) Constructor.

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

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

Modifier and Type	Method and Description
LinkedList<SpectrumMatch>	TideIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler, SearchParameters searchParameters)
LinkedList<SpectrumMatch>	PNovoIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler, SearchParameters searchParameters)
LinkedList<SpectrumMatch>	PepxmlIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler, SearchParameters searchParameters)
LinkedList<SpectrumMatch>	PepNovoIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler, SearchParameters searchParameters)
LinkedList<SpectrumMatch>	NovorIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler, SearchParameters searchParameters)
LinkedList<SpectrumMatch>	MzIdentMLIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler, SearchParameters searchParameters)
LinkedList<SpectrumMatch>	MsAmandaIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler, SearchParameters searchParameters)
LinkedList<SpectrumMatch>	DirecTagIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler, SearchParameters searchParameters)
LinkedList<SpectrumMatch>	AndromedaIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler, SearchParameters searchParameters)
LinkedList<SpectrumMatch>	TideIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler, SearchParameters searchParameters, SequenceMatchingPreferences sequenceMatchingPreferences, boolean expandAaCombinations)
LinkedList<SpectrumMatch>	PNovoIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler, SearchParameters searchParameters, SequenceMatchingPreferences sequenceMatchingPreferences, boolean expandAaCombinations)
LinkedList<SpectrumMatch>	PepxmlIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler, SearchParameters searchParameters, SequenceMatchingPreferences sequenceMatchingPreferences, boolean expandAaCombinations)
LinkedList<SpectrumMatch>	PepNovoIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler, SearchParameters searchParameters, SequenceMatchingPreferences sequenceMatchingPreferences, boolean expandAaCombinations)
LinkedList<SpectrumMatch>	NovorIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler, SearchParameters searchParameters, SequenceMatchingPreferences sequenceMatchingPreferences, boolean expandAaCombinations)
LinkedList<SpectrumMatch>	MzIdentMLIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler, SearchParameters searchParameters, SequenceMatchingPreferences sequenceMatchingPreferences, boolean expandAaCombinations)
LinkedList<SpectrumMatch>	MsAmandaIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler, SearchParameters searchParameters, SequenceMatchingPreferences sequenceMatchingPreferences, boolean expandAaCombinations)
LinkedList<SpectrumMatch>	DirecTagIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler, SearchParameters searchParameters, SequenceMatchingPreferences sequenceMatchingPreferences, boolean expandAaCombinations)
LinkedList<SpectrumMatch>	AndromedaIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler, SearchParameters searchParameters, SequenceMatchingPreferences sequenceMatchingPreferences, boolean expandAaCombinations)

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

Constructor and Description
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.
PepNovoIdfileReader(File identificationFile, WaitingHandler waitingHandler) Constructor, initiate the parser.
PNovoIdfileReader(File identificationFile, WaitingHandler waitingHandler) Constructor, initiate the parser.
TideIdfileReader(File tideTsvFile, WaitingHandler waitingHandler) Constructor for an Tide tsv result file reader.

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

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

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

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

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

Modifier and Type	Method and Description
void	SpectrumFactory.addSpectra(File spectrumFile, WaitingHandler waitingHandler) Add spectra to the factory.

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 and Description
protected abstract void	SelfUpdatingTableModel.loadDataForColumn(int column, WaitingHandler waitingHandler) Loads the data for a column.
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 and 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.compression

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

Modifier and Type	Method and 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, File destinationFolder, WaitingHandler waitingHandler) Extracts files from a tar.
static void	TarUtils.extractFile(File tarFile, 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 and 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

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

Uses of WaitingHandler in com.compomics.util.protein_sequences_manager

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

Modifier and Type	Method and Description
void	ProteinSequencesManager.addFastaFile(File fastaFile, SequenceInputType sequenceInputType, WaitingHandler waitingHandler) Adds a FASTA file to the working folder.