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

Packages that use WaitingHandler
com.compomics.util.db This package contains database related classes. 
com.compomics.util.experiment.annotation.gene   
com.compomics.util.experiment.annotation.go   
com.compomics.util.experiment.identification This package contains experiment classes related to identifications. 
com.compomics.util.experiment.identification.protein_inference.proteintree   
com.compomics.util.experiment.io.identifications   
com.compomics.util.experiment.io.identifications.idfilereaders This package contains experiment classes related to reading search engine files. 
com.compomics.util.experiment.io.massspectrometry   
com.compomics.util.experiment.massspectrometry This package contains experiment classes related to spectra. 
com.compomics.util.experiment.quantification This package contains experiment classes related to quantification. 
com.compomics.util.gui.tablemodels   
com.compomics.util.gui.waiting.waitinghandlers   
com.compomics.util.io This package contains classes related to input/output. 
com.compomics.util.preferences   
 

Uses of WaitingHandler in com.compomics.util.db
 

Methods in com.compomics.util.db with parameters of type WaitingHandler
 void ObjectsDB.insertObjects(String tableName, HashMap<String,Object> objects, WaitingHandler waitingHandler)
          Inserts a set of objects in the given table.
 void ObjectsDB.loadObjects(String tableName, ArrayList<String> keys, WaitingHandler waitingHandler)
          Loads some objects from a table in the cache.
 void ObjectsDB.loadObjects(String tableName, WaitingHandler waitingHandler)
          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.annotation.gene
 

Methods in com.compomics.util.experiment.annotation.gene with parameters of type WaitingHandler
 void GeneFactory.initialize(File file, WaitingHandler waitingHandler)
          Initializes the factory on the given file.
 

Uses of WaitingHandler in com.compomics.util.experiment.annotation.go
 

Methods in com.compomics.util.experiment.annotation.go with parameters of type WaitingHandler
 void GOFactory.initialize(File file, WaitingHandler waitingHandler)
          Initializes the factory on the given file
 

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

Methods in com.compomics.util.experiment.identification with parameters of type WaitingHandler
 void SequenceFactory.appendDecoySequences(File destinationFile, WaitingHandler waitingHandler)
          Appends decoy sequences to the desired file while displaying progress.
 void Identification.buildPeptidesAndProteins(WaitingHandler waitingHandler)
          Creates the peptides and protein instances based on the spectrum matches.
 void Identification.convert(WaitingHandler waitingHandler, String newDirectory, String newName, ObjectsCache objectsCache, File directory)
          Converts a serialization based structure into a database based one.
 void SequenceFactory.loadFastaFile(File fastaFile, WaitingHandler waitingHandler)
          Loads a new FASTA file in the factory.
 void IdentificationDB.loadPeptideMatches(ArrayList<String> peptideKeys, WaitingHandler waitingHandler)
          Loads the desired peptide matches of the given type in the cache of the database.
 void Identification.loadPeptideMatches(ArrayList<String> peptideKeys, WaitingHandler waitingHandler)
          Loads the desired peptide matches of the given type in the cache of the database.
 void IdentificationDB.loadPeptideMatches(WaitingHandler waitingHandler)
          Loads all peptide matches in the cache of the database.
 void Identification.loadPeptideMatches(WaitingHandler waitingHandler)
          Loads all peptide matches in the cache of the database.
 void IdentificationDB.loadPeptideMatchParameters(ArrayList<String> peptideKeys, UrParameter urParameter, WaitingHandler waitingHandler)
          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)
          Loads the desired peptide match parameters of the given type in the cache of the database.
 void IdentificationDB.loadPeptideMatchParameters(UrParameter urParameter, WaitingHandler waitingHandler)
          Loads all peptide match parameters of the given type in the cache of the database.
 void Identification.loadPeptideMatchParameters(UrParameter urParameter, WaitingHandler waitingHandler)
          Loads all peptide match parameters of the given type in the cache of the database.
 void IdentificationDB.loadProteinMatches(ArrayList<String> proteinKeys, WaitingHandler waitingHandler)
          Loads the desired protein matches of the given type in the cache of the database.
 void Identification.loadProteinMatches(ArrayList<String> proteinKeys, WaitingHandler waitingHandler)
          Loads the desired protein matches of the given type in the cache of the database.
 void IdentificationDB.loadProteinMatches(WaitingHandler waitingHandler)
          Loads all protein matches in the cache of the database.
 void Identification.loadProteinMatches(WaitingHandler waitingHandler)
          Loads all protein matches in the cache of the database.
 void IdentificationDB.loadProteinMatchParameters(ArrayList<String> proteinKeys, UrParameter urParameter, WaitingHandler waitingHandler)
          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)
          Loads the desired protein match parameters of the given type in the cache of the database.
 void IdentificationDB.loadProteinMatchParameters(UrParameter urParameter, WaitingHandler waitingHandler)
          Loads all protein match parameters of the given type in the cache of the database.
 void Identification.loadProteinMatchParameters(UrParameter urParameter, WaitingHandler waitingHandler)
          Loads all protein match parameters of the given type in the cache of the database.
 void IdentificationDB.loadSpectrumMatches(ArrayList<String> spectrumKeys, WaitingHandler waitingHandler)
          Loads all given spectrum matches in the cache of the database.
 void Identification.loadSpectrumMatches(ArrayList<String> spectrumKeys, WaitingHandler waitingHandler)
          Loads the given spectrum matches in the cache of the database.
 void IdentificationDB.loadSpectrumMatches(String fileName, WaitingHandler waitingHandler)
          Loads all spectrum matches of the given file in the cache of the database.
 void Identification.loadSpectrumMatches(String fileName, WaitingHandler waitingHandler)
          Loads all spectrum matches of the file in the cache of the database
 void IdentificationDB.loadSpectrumMatchParameters(ArrayList<String> spectrumKeys, UrParameter urParameter, WaitingHandler waitingHandler)
          Loads all desired spectrum match parameters in the cache of the database.
 void Identification.loadSpectrumMatchParameters(ArrayList<String> spectrumKeys, UrParameter urParameter, WaitingHandler waitingHandler)
          Loads all desired spectrum match parameters in the cache of the database.
 void IdentificationDB.loadSpectrumMatchParameters(String fileName, UrParameter urParameter, WaitingHandler waitingHandler)
          Loads all spectrum match parameters of the given type in the cache of the database.
 void Identification.loadSpectrumMatchParameters(String fileName, UrParameter urParameter, WaitingHandler waitingHandler)
          Loads all spectrum match parameters of the given type in the cache of the database
 

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
 void ProteinTree.initiateTree(int initialTagSize, int maxNodeSize, Enzyme enzyme, WaitingHandler waitingHandler)
          Initiates the tree.
 void ProteinTree.initiateTree(int initialTagSize, int maxNodeSize, WaitingHandler waitingHandler)
          Initiates the tree.
 

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

Methods in com.compomics.util.experiment.io.identifications with parameters of type WaitingHandler
 HashSet<SpectrumMatch> IdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler)
          This methods 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.
 IdfileReader IdfileReaderFactory.getFileReader(File aFile, WaitingHandler waitingHandler)
          This method returns the proper identification file reader depending on the format of the provided file.
 

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
 HashSet<SpectrumMatch> AndromedaIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler)
           
 

Constructors in com.compomics.util.experiment.io.identifications.idfilereaders with parameters of type WaitingHandler
AndromedaIdfileReader(File resFile, WaitingHandler waitingHandler)
          Constructor for an Andromeda 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
static void MgfReader.fixDuplicateSpectrumTitles(File mgfFile, WaitingHandler waitingHandler)
          Fix duplicate spectrum titles.
static MgfIndex MgfReader.getIndexMap(File mgfFile, WaitingHandler waitingHandler)
          Returns the index of all spectra in the given MGF file.
 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.
static String MgfReader.validateSpectrumTitles(File mgfFile, WaitingHandler waitingHandler)
          Validates the spectrum titles, i.e., check for duplicate titles.
 

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

Methods in com.compomics.util.experiment.massspectrometry with parameters of type WaitingHandler
 void SpectrumFactory.addSpectra(File spectrumFile, WaitingHandler waitingHandler)
          Add spectra to the factory.
 

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

Methods in com.compomics.util.experiment.quantification with parameters of type WaitingHandler
 void Quantification.buildPeptidesAndProteinQuantifications(Identification identification, WaitingHandler waitingHandler)
          Creates the peptides and protein quantification instances based on the identification and the psm quantification.
 

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

Methods in com.compomics.util.gui.tablemodels with parameters of type WaitingHandler
protected abstract  void SelfUpdatingTableModel.loadDataForColumn(int column, WaitingHandler waitingHandler)
          Loads the data for a column.
 

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

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

Uses of WaitingHandler in com.compomics.util.io
 

Methods in com.compomics.util.io with parameters of type WaitingHandler
static void TarUtils.addFolderContent(org.apache.commons.compress.archivers.ArchiveOutputStream tarOutput, File folder, WaitingHandler waitingHandler)
          Add content to the tar file.
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 in a file.
 

Uses of WaitingHandler in com.compomics.util.preferences
 

Methods in com.compomics.util.preferences with parameters of type WaitingHandler
 void GenePreferences.downloadGeneMappings(String ensemblType, String ensemblSchemaName, String selectedSpecies, String ensemblVersion, WaitingHandler waitingHandler)
          Download the gene mappings.
 boolean GenePreferences.downloadGoMappings(String ensemblType, String ensemblSchemaName, String selectedSpecies, WaitingHandler waitingHandler)
          Download the GO mappings.
 boolean GenePreferences.loadGeneMappings(String jarFilePath, WaitingHandler waitingHandler)
          Imports the gene mappings.
 



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