Modifier and Type | Method and Description |
---|---|
void |
ObjectsDB.insertObjects(java.lang.String tableName,
java.util.HashMap<java.lang.String,java.lang.Object> objects,
WaitingHandler waitingHandler)
Inserts a set of objects in the given table.
|
void |
ObjectsDB.loadObjects(java.lang.String tableName,
java.util.ArrayList<java.lang.String> keys,
WaitingHandler waitingHandler)
Loads some objects from a table in the cache.
|
void |
ObjectsDB.loadObjects(java.lang.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(java.util.ArrayList<java.lang.String> entryKeys,
WaitingHandler waitingHandler)
Saves an entry in the database if modified and clears it from the cache.
|
void |
ObjectsCache.saveObjects(java.util.ArrayList<java.lang.String> entryKeys,
WaitingHandler waitingHandler,
boolean clearEntries)
Saves an entry in the database if modified.
|
Modifier and Type | Method and Description |
---|---|
void |
GeneFactory.initialize(java.io.File file,
WaitingHandler waitingHandler)
Initializes the factory on the given file.
|
Modifier and Type | Method and Description |
---|---|
void |
GOFactory.initialize(java.io.File file,
WaitingHandler waitingHandler)
Initializes the factory on the given file
|
Modifier and Type | Method and Description |
---|---|
void |
SequenceFactory.appendDecoySequences(java.io.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,
java.lang.String newDirectory,
java.lang.String newName,
ObjectsCache objectsCache,
java.io.File directory)
Converts a serialization based structure into a database based one.
|
void |
SequenceFactory.loadFastaFile(java.io.File fastaFile,
WaitingHandler waitingHandler)
Loads a new FASTA file in the factory.
|
void |
IdentificationDB.loadPeptideMatches(java.util.ArrayList<java.lang.String> peptideKeys,
WaitingHandler waitingHandler)
Loads the desired peptide matches of the given type in the cache of the
database.
|
void |
Identification.loadPeptideMatches(java.util.ArrayList<java.lang.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(java.util.ArrayList<java.lang.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(java.util.ArrayList<java.lang.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(java.util.ArrayList<java.lang.String> proteinKeys,
WaitingHandler waitingHandler)
Loads the desired protein matches of the given type in the cache of the
database.
|
void |
Identification.loadProteinMatches(java.util.ArrayList<java.lang.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(java.util.ArrayList<java.lang.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(java.util.ArrayList<java.lang.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(java.util.ArrayList<java.lang.String> spectrumKeys,
WaitingHandler waitingHandler)
Loads all given spectrum matches in the cache of the database.
|
void |
Identification.loadSpectrumMatches(java.util.ArrayList<java.lang.String> spectrumKeys,
WaitingHandler waitingHandler)
Loads the given spectrum matches in the cache of the database.
|
void |
IdentificationDB.loadSpectrumMatches(java.lang.String fileName,
WaitingHandler waitingHandler)
Loads all spectrum matches of the given file in the cache of the
database.
|
void |
Identification.loadSpectrumMatches(java.lang.String fileName,
WaitingHandler waitingHandler)
Loads all spectrum matches of the file in the cache of the database
|
void |
IdentificationDB.loadSpectrumMatchParameters(java.util.ArrayList<java.lang.String> spectrumKeys,
UrParameter urParameter,
WaitingHandler waitingHandler)
Loads all desired spectrum match parameters in the cache of the database.
|
void |
Identification.loadSpectrumMatchParameters(java.util.ArrayList<java.lang.String> spectrumKeys,
UrParameter urParameter,
WaitingHandler waitingHandler)
Loads all desired spectrum match parameters in the cache of the database.
|
void |
IdentificationDB.loadSpectrumMatchParameters(java.lang.String fileName,
UrParameter urParameter,
WaitingHandler waitingHandler)
Loads all spectrum match parameters of the given type in the cache of the
database.
|
void |
Identification.loadSpectrumMatchParameters(java.lang.String fileName,
UrParameter urParameter,
WaitingHandler waitingHandler)
Loads all spectrum match parameters of the given type in the cache of the
database
|
Modifier and Type | Method and Description |
---|---|
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.
|
Modifier and Type | Method and Description |
---|---|
java.util.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(java.io.File aFile,
WaitingHandler waitingHandler)
This method returns the proper identification file reader depending on
the format of the provided file.
|
Modifier and Type | Method and Description |
---|---|
java.util.HashSet<SpectrumMatch> |
AndromedaIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler) |
Constructor and Description |
---|
AndromedaIdfileReader(java.io.File resFile,
WaitingHandler waitingHandler)
Constructor for an Andromeda result file reader.
|
Modifier and Type | Method and Description |
---|---|
static void |
MgfReader.fixDuplicateSpectrumTitles(java.io.File mgfFile,
WaitingHandler waitingHandler)
Fix duplicate spectrum titles.
|
static MgfIndex |
MgfReader.getIndexMap(java.io.File mgfFile,
WaitingHandler waitingHandler)
Returns the index of all spectra in the given MGF file.
|
java.util.ArrayList<MgfIndex> |
MgfReader.splitFile(java.io.File mgfFile,
int nSpectra,
WaitingHandler waitingHandler)
Splits an mgf file into smaller ones and returns the indexes of the
generated files.
|
static java.lang.String |
MgfReader.validateSpectrumTitles(java.io.File mgfFile,
WaitingHandler waitingHandler)
Validates the spectrum titles, i.e., check for duplicate titles.
|
Modifier and Type | Method and Description |
---|---|
void |
SpectrumFactory.addSpectra(java.io.File spectrumFile,
WaitingHandler waitingHandler)
Add spectra to the factory.
|
Modifier and Type | Method and Description |
---|---|
void |
Quantification.buildPeptidesAndProteinQuantifications(Identification identification,
WaitingHandler waitingHandler)
Creates the peptides and protein quantification instances based on the
identification and the psm quantification.
|
Modifier and Type | Method and Description |
---|---|
protected abstract void |
SelfUpdatingTableModel.loadDataForColumn(int column,
WaitingHandler waitingHandler)
Loads the data for a column.
|
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.
|
Modifier and Type | Method and Description |
---|---|
static void |
TarUtils.addFolderContent(org.apache.commons.compress.archivers.ArchiveOutputStream tarOutput,
java.io.File folder,
WaitingHandler waitingHandler)
Add content to the tar file.
|
static void |
TarUtils.extractFile(java.io.File tarFile,
WaitingHandler waitingHandler)
Extracts files from a tar.
|
static void |
TarUtils.tarFolder(java.io.File folder,
java.io.File destinationFile,
WaitingHandler waitingHandler)
Tar a given folder in a file.
|
Modifier and Type | Method and Description |
---|---|
void |
GenePreferences.downloadGeneMappings(java.lang.String ensemblType,
java.lang.String ensemblSchemaName,
java.lang.String selectedSpecies,
java.lang.String ensemblVersion,
WaitingHandler waitingHandler)
Download the gene mappings.
|
boolean |
GenePreferences.downloadGoMappings(java.lang.String ensemblType,
java.lang.String ensemblSchemaName,
java.lang.String selectedSpecies,
WaitingHandler waitingHandler)
Download the GO mappings.
|
boolean |
GenePreferences.loadGeneMappings(java.lang.String jarFilePath,
WaitingHandler waitingHandler)
Imports the gene mappings.
|
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