Package | Description |
---|---|
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.
|
Modifier and Type | Method and Description |
---|---|
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.
|
Modifier and Type | Method and Description |
---|---|
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(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
|
Modifier and Type | Method and Description |
---|---|
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.
|
Modifier and Type | Method and Description |
---|---|
HashSet<SpectrumMatch> |
AndromedaIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler) |
Constructor and Description |
---|
AndromedaIdfileReader(File resFile,
WaitingHandler waitingHandler)
Constructor for an Andromeda result file reader.
|
Modifier and Type | Method and Description |
---|---|
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.
|
Modifier and Type | Method and Description |
---|---|
void |
SpectrumFactory.addSpectra(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 | 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,
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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