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

Packages that use WaitingHandler
com.compomics.util.db This package contains database related classes. 
com.compomics.util.experiment.identification This package contains experiment classes related to identifications. 
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.waiting.waitinghandlers   
 

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 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.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 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
 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> XTandemIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler)
           
 HashSet<SpectrumMatch> OMSSAIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler)
           
 HashSet<SpectrumMatch> MascotIdfileReader.getAllSpectrumMatches(WaitingHandler 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 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.
 

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.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.
 



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