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Packages that use WaitingHandler | |
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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 | |
com.compomics.util.io | This package contains classes related to input/output. |
Uses of WaitingHandler in com.compomics.util.db |
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Methods in com.compomics.util.db with parameters of type WaitingHandler | |
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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.identification |
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Methods in com.compomics.util.experiment.identification with parameters of type WaitingHandler | |
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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)
Converts a serlialization 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(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(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.io.identifications |
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Methods in com.compomics.util.experiment.io.identifications with parameters of type WaitingHandler | |
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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 |
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Methods in com.compomics.util.experiment.io.identifications.idfilereaders with parameters of type WaitingHandler | |
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HashSet<SpectrumMatch> |
AndromedaIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler)
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Constructors in com.compomics.util.experiment.io.identifications.idfilereaders with parameters of type WaitingHandler | |
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AndromedaIdfileReader(File resFile,
WaitingHandler waitingHandler)
Constructor for an Andromeda result file reader. |
Uses of WaitingHandler in com.compomics.util.experiment.io.massspectrometry |
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Methods in com.compomics.util.experiment.io.massspectrometry with parameters of type WaitingHandler | |
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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 |
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Methods in com.compomics.util.experiment.massspectrometry with parameters of type WaitingHandler | |
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void |
SpectrumFactory.addSpectra(File spectrumFile,
WaitingHandler waitingHandler)
Add spectra to the factory. |
Uses of WaitingHandler in com.compomics.util.experiment.quantification |
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Methods in com.compomics.util.experiment.quantification with parameters of type WaitingHandler | |
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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 |
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Classes in com.compomics.util.gui.waiting.waitinghandlers that implement WaitingHandler | |
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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 |
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Methods in com.compomics.util.io with parameters of type WaitingHandler | |
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static void |
TarUtils.addFolderContent(org.apache.commons.compress.archivers.ArchiveOutputStream tarOutput,
File folder,
WaitingHandler waitingHandler)
Add content to the tar file. |
static void |
TarUtils.tarFolder(File folder,
File destinationFile,
WaitingHandler waitingHandler)
Tar a given folder in a file. |
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