Package | Description |
---|---|
com.compomics.software.autoupdater | |
com.compomics.util.db |
This package contains database related classes.
|
com.compomics.util.experiment.annotation.gene | |
com.compomics.util.experiment.annotation.go | |
com.compomics.util.experiment.identification |
This package contains experiment classes related to identifications.
|
com.compomics.util.experiment.identification.protein_inference.proteintree | |
com.compomics.util.experiment.io.identifications | |
com.compomics.util.experiment.io.identifications.idfilereaders |
This package contains experiment classes related to reading search engine files.
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com.compomics.util.experiment.io.massspectrometry | |
com.compomics.util.experiment.massspectrometry |
This package contains experiment classes related to spectra.
|
com.compomics.util.gui.tablemodels | |
com.compomics.util.gui.waiting.waitinghandlers | |
com.compomics.util.io |
This package contains classes related to input/output.
|
com.compomics.util.preferences |
Modifier and Type | Method and Description |
---|---|
static void |
DownloadLatestZipFromRepo.downloadLatestZipFromRepo(URL jarPath,
String toolName,
boolean deleteOldFiles,
boolean startDownloadedVersion,
boolean addDesktopIcon,
WaitingHandler waitingHandler)
Downloads the latest deploy from the genesis maven repository of the
artifact and starts it without arguments.
|
static void |
DownloadLatestZipFromRepo.downloadLatestZipFromRepo(URL jarPath,
String toolName,
boolean deleteOldFiles,
boolean addDesktopIcon,
String[] args,
URL jarRepository,
WaitingHandler waitingHandler)
Downloads the latest zip archive of the jar in the url from a given
jarRepository.
|
static void |
DownloadLatestZipFromRepo.downloadLatestZipFromRepo(URL jarPath,
String toolName,
boolean deleteOldFiles,
String[] args,
boolean startDownloadedVersion,
boolean addDesktopIcon,
WaitingHandler waitingHandler)
Downloads the latest zip archive of the jar in the url from the genesis
maven repo.
|
static void |
DownloadLatestZipFromRepo.downloadLatestZipFromRepo(URL jarPath,
String toolName,
boolean deleteOldFiles,
String iconName,
String[] args,
URL jarRepository,
boolean startDownloadedVersion,
boolean addDesktopIcon,
FileDAO fileDAO,
WaitingHandler waitingHandler)
Retrieves the latest version of a maven jar file from a maven repository.
|
static void |
DownloadLatestZipFromRepo.downloadLatestZipFromRepo(URL jarPath,
String toolName,
boolean deleteOldFiles,
String iconName,
String[] args,
URL jarRepository,
boolean startDownloadedVersion,
boolean addDesktopIcon,
WaitingHandler waitingHandler)
Retrieves the latest version of a maven jar file from a maven repository,
also checks if the environment is headless or not.
|
boolean |
FileDAO.unGzipAndUntarFile(GZIPInputStream in,
File fileLocationOnDiskToDownloadTo,
WaitingHandler waitingHandler)
Untars and ungzips a .tar.gz file.
|
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.insertObjects(String tableName,
HashMap<String,Object> objects,
WaitingHandler waitingHandler,
boolean allNewObjects)
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 |
GeneFactory.initialize(File file,
WaitingHandler waitingHandler)
Initializes the factory on the given file.
|
Modifier and Type | Method and Description |
---|---|
void |
GOFactory.initialize(File file,
WaitingHandler waitingHandler)
Initializes the factory on the given file
|
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,
AminoAcidPattern.MatchingType matchingType,
Double massTolerance)
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.
|
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(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(ArrayList<String> proteinKeys,
WaitingHandler waitingHandler)
Loads the desired protein matches of the given type in the cache of the
database.
|
void |
Identification.loadProteinMatches(ArrayList<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(ArrayList<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(ArrayList<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(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 |
---|---|
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.
|
void |
ProteinTreeComponentsFactory.saveNodes(HashMap<String,Object> nodes,
WaitingHandler waitingHandler)
Adds nodes to the database.
|
void |
ProteinTreeComponentsFactory.saveProteinLengths(HashMap<String,Object> lengths,
WaitingHandler waitingHandler)
Adds a protein length to 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.
|
Modifier and Type | Method and Description |
---|---|
HashSet<SpectrumMatch> |
PepNovoIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler) |
HashSet<SpectrumMatch> |
MzIdentMLIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler) |
HashSet<SpectrumMatch> |
MsAmandaIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler) |
HashSet<SpectrumMatch> |
DirecTagIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler) |
HashSet<SpectrumMatch> |
AndromedaIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler) |
Constructor and Description |
---|
AndromedaIdfileReader(File resFile,
WaitingHandler waitingHandler)
Constructor for an Andromeda result file reader.
|
MsAmandaIdfileReader(File msAmandaCsvFile,
WaitingHandler waitingHandler)
Constructor for an MS Amanda csv result file reader.
|
MzIdentMLIdfileReader(File mzIdentMLFile,
WaitingHandler waitingHandler)
Constructor for an mzIdentML result file reader.
|
PepNovoIdfileReader(File identificationFile,
WaitingHandler waitingHandler)
Constructor, initiate the parser.
|
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.
|
static void |
MgfReader.removeDuplicateSpectrumTitles(File mgfFile,
WaitingHandler waitingHandler)
Removes duplicate spectrum titles (the first occurrence is kept).
|
static void |
MgfReader.renameDuplicateSpectrumTitles(File mgfFile,
WaitingHandler waitingHandler)
Renames duplicate spectrum titles.
|
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 |
---|---|
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,
File folder,
WaitingHandler waitingHandler)
Add content to the tar file.
|
static void |
TarUtils.extractFile(File tarFile,
File destinationFolder,
String backwardCompatibilityCorrection,
WaitingHandler waitingHandler)
Extracts files from a tar.
|
static void |
TarUtils.extractFile(File tarFile,
File destinationFolder,
WaitingHandler waitingHandler)
Extracts files from a tar.
|
static void |
TarUtils.extractFile(File tarFile,
WaitingHandler waitingHandler)
Extracts files from a tar.
|
static void |
TarUtils.tarFolder(File folder,
File destinationFile,
WaitingHandler waitingHandler)
Tar a given folder in a file.
|
Modifier and Type | Method and Description |
---|---|
void |
GenePreferences.downloadGeneMappings(String ensemblType,
String ensemblSchemaName,
String selectedSpecies,
String ensemblVersion,
WaitingHandler waitingHandler)
Download the gene mappings.
|
boolean |
GenePreferences.downloadGoMappings(String ensemblType,
String ensemblSchemaName,
String selectedSpecies,
WaitingHandler waitingHandler)
Download the GO mappings.
|
boolean |
GenePreferences.loadGeneMappings(String jarFilePath,
WaitingHandler waitingHandler)
Imports the gene mappings.
|
Copyright © 2014. All rights reserved.