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.insertObjects(java.lang.String tableName,
java.util.HashMap<java.lang.String,java.lang.Object> objects,
WaitingHandler waitingHandler,
boolean allNewObjects)
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.
|
ProteinTree |
SequenceFactory.getDefaultProteinTree(WaitingHandler waitingHandler)
Returns the default protein tree corresponding to the database loaded in
factory.
|
ProteinTree |
SequenceFactory.getDefaultProteinTree(WaitingHandler waitingHandler,
boolean displayProgress)
Returns the default protein tree corresponding to the database loaded in
factory
|
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,
int maxPeptideSize,
Enzyme enzyme,
WaitingHandler waitingHandler,
boolean printExpectedImportTime,
boolean displayProgress)
Initiates the tree.
|
void |
ProteinTree.initiateTree(int initialTagSize,
int maxNodeSize,
int maxPeptideSize,
WaitingHandler waitingHandler,
boolean printExpectedImportTime,
boolean displayProgress)
Initiates the tree.
|
Modifier and Type | Field and Description |
---|---|
protected WaitingHandler |
ProteinTree.SequenceIndexer.waitingHandler
The waiting handler.
|
protected WaitingHandler |
ProteinTree.RawNodeProcessor.waitingHandler
The waiting handler
|
Modifier and Type | Method and Description |
---|---|
protected void |
ProteinTree.importDb(int initialTagSize,
int maxNodeSize,
int maxPeptideSize,
Enzyme enzyme,
WaitingHandler waitingHandler,
boolean printExpectedImportTime,
boolean displayProgress)
Imports the db which is in the sequence factory into the tree and saves
it in the nodeFactory.
|
void |
ProteinTree.initiateTree(int initialTagSize,
int maxNodeSize,
int maxPeptideSize,
Enzyme enzyme,
WaitingHandler waitingHandler,
boolean printExpectedImportTime,
boolean displayProgress)
Initiates the tree.
|
void |
ProteinTree.initiateTree(int initialTagSize,
int maxNodeSize,
int maxPeptideSize,
WaitingHandler waitingHandler,
boolean printExpectedImportTime,
boolean displayProgress)
Initiates the tree.
|
protected void |
ProteinTree.loadTags(java.util.ArrayList<java.lang.String> tags,
java.util.ArrayList<java.lang.String> accessions,
WaitingHandler waitingHandler,
int initialTagSize,
int maxNodeSize,
int maxPeptideSize,
Enzyme enzyme,
java.util.ArrayList<java.lang.String> loadedAccessions,
boolean displayProgress)
Loads the tags found in the given proteins in the tree and saves the end
nodes in the NodeFactory if not null.
|
Constructor and Description |
---|
ProteinTree.RawNodeProcessor(java.util.concurrent.BlockingQueue<java.lang.String> tagQueue,
int maxNodeSize,
int maxPeptideSize,
WaitingHandler waitingHandler,
boolean displayProgress)
Constructor.
|
ProteinTree.SequenceIndexer(java.util.concurrent.BlockingQueue<Protein> proteinQueue,
java.util.ArrayList<java.lang.String> tags,
int initialTagSize,
Enzyme enzyme,
WaitingHandler waitingHandler,
boolean displayProgress)
Constructor.
|
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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