Package | Description |
---|---|
com.compomics.software.autoupdater |
Classes related to auto updating compomics-utilities tools.
|
com.compomics.util |
General utilities classes.
|
com.compomics.util.db |
Database related classes.
|
com.compomics.util.experiment.annotation.gene |
MSExperiment main class and all sub-classes useful for the modeling of an experiment.
|
com.compomics.util.experiment.annotation.go |
GO factory classes.
|
com.compomics.util.experiment.biology |
Experiment classes related to biological entities.
|
com.compomics.util.experiment.identification |
Experiment classes related to identifications.
|
com.compomics.util.experiment.identification.matches_iterators |
Identification match iterators.
|
com.compomics.util.experiment.identification.protein_inference.proteintree |
Peptide to protein mapping classes.
|
com.compomics.util.experiment.io.identifications |
Experiment identification classes.
|
com.compomics.util.experiment.io.identifications.idfilereaders |
Experiment classes related to reading search engine files.
|
com.compomics.util.experiment.io.massspectrometry |
Reading and indexing of mgf files.
|
com.compomics.util.experiment.massspectrometry |
Experiment classes related to spectra.
|
com.compomics.util.gui.tablemodels |
Self updating table model classes.
|
com.compomics.util.gui.waiting.waitinghandlers |
Waiting handler classes.
|
com.compomics.util.io.compression |
Classes related to file compression.
|
com.compomics.util.pdbfinder |
Classes for mapping between UniProt accession numbers and PDB structures.
|
com.compomics.util.preferences |
Utilities preferences classes.
|
com.compomics.util.protein_sequences_manager |
Classes used for the management of FASTA files.
|
Modifier and Type | Method and Description |
---|---|
static void |
DownloadLatestZipFromRepo.downloadLatestZipFromRepo(File downloadFolder,
String toolName,
String groupId,
String artifactId,
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,
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 repository.
|
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 |
---|---|
static File |
Util.saveUrl(File saveFile,
String targetUrlAsString,
int fileSizeInBytes,
String userName,
String password,
WaitingHandler waitingHandler)
Save a file from a URL.
|
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,
boolean displayProgress)
Loads some objects from a table in the cache.
|
void |
ObjectsDB.loadObjects(String tableName,
WaitingHandler waitingHandler,
boolean displayProgress)
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 |
---|---|
ArrayList<String> |
Peptide.getParentProteinsCreateTree(SequenceMatchingPreferences sequenceMatchingPreferences,
WaitingHandler waitingHandler,
ExceptionHandler exceptionHandler)
Returns the parent proteins and remaps the peptide to the protein if no
protein mapping was set using the default protein tree of the sequence
factory.
|
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,
SequenceMatchingPreferences sequenceMatchingPreferences)
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(int nThreads,
WaitingHandler waitingHandler,
ExceptionHandler exceptionHandler)
Returns the default protein tree corresponding to the database loaded in
factory, creates a new one if none found.
|
ProteinTree |
SequenceFactory.getDefaultProteinTree(int nThreads,
WaitingHandler waitingHandler,
ExceptionHandler exceptionHandler,
boolean displayProgress)
Returns the default protein tree corresponding to the database loaded in
factory, creates a new one if none found.
|
ProteinTree |
SequenceFactory.getDefaultProteinTree(WaitingHandler waitingHandler,
ExceptionHandler exceptionHandler)
Returns the default protein tree corresponding to the database loaded in
factory, creates a new one if none found.
|
static FastaIndex |
SequenceFactory.getFastaIndex(File fastaFile,
boolean overwrite,
WaitingHandler waitingHandler)
Returns the file index of the given fasta file.
|
PeptideMatchesIterator |
Identification.getPeptideMatchesIterator(ArrayList<String> peptideKeys,
ArrayList<UrParameter> peptideParameters,
boolean loadPsms,
ArrayList<UrParameter> psmParameters,
WaitingHandler waitingHandler)
Returns a peptide matches iterator.
|
PeptideMatchesIterator |
Identification.getPeptideMatchesIterator(ArrayList<UrParameter> peptideParameters,
boolean loadPsms,
ArrayList<UrParameter> psmParameters,
WaitingHandler waitingHandler)
Returns a peptide matches iterator iterating all peptides.
|
ProteinMatchesIterator |
Identification.getProteinMatchesIterator(ArrayList<String> proteinKeys,
ArrayList<UrParameter> proteinParameters,
boolean loadPeptides,
ArrayList<UrParameter> peptideParameters,
boolean loadPsms,
ArrayList<UrParameter> psmParameters,
WaitingHandler waitingHandler)
Returns a protein matches iterator.
|
ProteinMatchesIterator |
Identification.getProteinMatchesIterator(ArrayList<UrParameter> proteinParameters,
boolean loadPeptides,
ArrayList<UrParameter> peptideParameters,
boolean loadPsms,
ArrayList<UrParameter> psmParameters,
WaitingHandler waitingHandler)
Returns a protein matches iterator iterating all protein matches.
|
PsmIterator |
Identification.getPsmIterator(ArrayList<String> spectrumKeys,
ArrayList<UrParameter> psmParameters,
boolean loadAssumptions,
WaitingHandler waitingHandler)
Returns a PSM iterator.
|
PsmIterator |
Identification.getPsmIterator(ArrayList<String> spectrumKeys,
boolean loadAssumptions,
WaitingHandler waitingHandler)
Returns a PSM iterator.
|
PsmIterator |
Identification.getPsmIterator(boolean loadAssumptions,
ArrayList<UrParameter> psmParameters,
WaitingHandler waitingHandler)
Returns a PSM iterator iterating all PSMs in a file.
|
PsmIterator |
Identification.getPsmIterator(String spectrumFile,
ArrayList<String> spectrumKeys,
ArrayList<UrParameter> psmParameters,
boolean loadAssumptions,
WaitingHandler waitingHandler)
Returns a PSM iterator.
|
PsmIterator |
Identification.getPsmIterator(String spectrumFile,
ArrayList<UrParameter> psmParameters,
boolean loadAssumptions,
WaitingHandler waitingHandler)
Returns a PSM iterator iterating all PSMs in a file.
|
PsmIterator |
Identification.getPsmIterator(String spectrumFile,
boolean loadAssumptions,
WaitingHandler waitingHandler)
Returns a PSM iterator iterating all PSMs in a file.
|
void |
IdentificationDB.loadAssumptions(ArrayList<String> spectrumKeys,
WaitingHandler waitingHandler,
boolean displayProgress)
Loads all assumptions of the given spectra in the cache of the database.
|
void |
Identification.loadAssumptions(ArrayList<String> spectrumKeys,
WaitingHandler waitingHandler,
boolean displayProgress)
Loads the given spectrum matches in the cache of the database.
|
void |
IdentificationDB.loadAssumptions(String fileName,
WaitingHandler waitingHandler,
boolean displayProgress)
Loads all assumptions of the given file in the cache of the database.
|
void |
Identification.loadAssumptions(String fileName,
WaitingHandler waitingHandler,
boolean displayProgress)
Loads all spectrum matches of the file in the cache of the database.
|
void |
SequenceFactory.loadFastaFile(File fastaFile,
WaitingHandler waitingHandler)
Loads a new FASTA file in the factory.
|
void |
IdentificationDB.loadPeptideMatches(ArrayList<String> peptideKeys,
WaitingHandler waitingHandler,
boolean displayProgress)
Loads the desired peptide matches of the given type in the cache of the
database.
|
void |
Identification.loadPeptideMatches(ArrayList<String> peptideKeys,
WaitingHandler waitingHandler,
boolean displayProgress)
Loads the desired peptide matches of the given type in the cache of the
database.
|
void |
IdentificationDB.loadPeptideMatches(WaitingHandler waitingHandler,
boolean displayProgress)
Loads all peptide matches in the cache of the database.
|
void |
Identification.loadPeptideMatches(WaitingHandler waitingHandler,
boolean displayProgress)
Loads all peptide matches in the cache of the database.
|
void |
IdentificationDB.loadPeptideMatchParameters(ArrayList<String> peptideKeys,
UrParameter urParameter,
WaitingHandler waitingHandler,
boolean displayProgress)
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,
boolean displayProgress)
Loads the desired peptide match parameters of the given type in the cache
of the database.
|
void |
IdentificationDB.loadPeptideMatchParameters(UrParameter urParameter,
WaitingHandler waitingHandler,
boolean displayProgress)
Loads all peptide match parameters of the given type in the cache of the
database.
|
void |
Identification.loadPeptideMatchParameters(UrParameter urParameter,
WaitingHandler waitingHandler,
boolean displayProgress)
Loads all peptide match parameters of the given type in the cache of the
database.
|
void |
IdentificationDB.loadProteinMatches(ArrayList<String> proteinKeys,
WaitingHandler waitingHandler,
boolean displayProgress)
Loads the desired protein matches of the given type in the cache of the
database.
|
void |
Identification.loadProteinMatches(ArrayList<String> proteinKeys,
WaitingHandler waitingHandler,
boolean displayProgress)
Loads the desired protein matches of the given type in the cache of the
database.
|
void |
IdentificationDB.loadProteinMatches(WaitingHandler waitingHandler,
boolean displayProgress)
Loads all protein matches in the cache of the database.
|
void |
Identification.loadProteinMatches(WaitingHandler waitingHandler,
boolean displayProgress)
Loads all protein matches in the cache of the database.
|
void |
IdentificationDB.loadProteinMatchParameters(ArrayList<String> proteinKeys,
UrParameter urParameter,
WaitingHandler waitingHandler,
boolean displayProgress)
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,
boolean displayProgress)
Loads the desired protein match parameters of the given type in the cache
of the database.
|
void |
IdentificationDB.loadProteinMatchParameters(UrParameter urParameter,
WaitingHandler waitingHandler,
boolean displayProgress)
Loads all protein match parameters of the given type in the cache of the
database.
|
void |
Identification.loadProteinMatchParameters(UrParameter urParameter,
WaitingHandler waitingHandler,
boolean displayProgress)
Loads all protein match parameters of the given type in the cache of the
database.
|
void |
IdentificationDB.loadSpectrumMatches(ArrayList<String> spectrumKeys,
WaitingHandler waitingHandler,
boolean displayProgress)
Loads all given spectrum matches in the cache of the database.
|
void |
Identification.loadSpectrumMatches(ArrayList<String> spectrumKeys,
WaitingHandler waitingHandler,
boolean displayProgress)
Loads the given spectrum matches in the cache of the database.
|
void |
IdentificationDB.loadSpectrumMatches(String fileName,
WaitingHandler waitingHandler,
boolean displayProgress)
Loads all spectrum matches of the given file in the cache of the
database.
|
void |
Identification.loadSpectrumMatches(String fileName,
WaitingHandler waitingHandler,
boolean displayProgress)
Loads all assumptions of all spectrum matches of the file in the cache of
the database.
|
void |
IdentificationDB.loadSpectrumMatchParameters(ArrayList<String> spectrumKeys,
UrParameter urParameter,
WaitingHandler waitingHandler,
boolean displayProgress)
Loads all desired spectrum match parameters in the cache of the database.
|
void |
Identification.loadSpectrumMatchParameters(ArrayList<String> spectrumKeys,
UrParameter urParameter,
WaitingHandler waitingHandler,
boolean displayProgress)
Loads all desired spectrum match parameters in the cache of the database.
|
void |
IdentificationDB.loadSpectrumMatchParameters(String fileName,
UrParameter urParameter,
WaitingHandler waitingHandler,
boolean displayProgress)
Loads all spectrum match parameters of the given type in the cache of the
database.
|
void |
Identification.loadSpectrumMatchParameters(String fileName,
UrParameter urParameter,
WaitingHandler waitingHandler,
boolean displayProgress)
Loads all spectrum match parameters of the given type in the cache of the
database
|
Constructor and Description |
---|
PeptideMatchesIterator(ArrayList<String> peptideKeys,
Identification identification,
ArrayList<UrParameter> peptideParameters,
boolean loadPsms,
ArrayList<UrParameter> psmParameters,
WaitingHandler waitingHandler)
Constructor.
|
PeptideMatchesIterator(ArrayList<String> peptideKeys,
Identification identification,
ArrayList<UrParameter> peptideParameters,
WaitingHandler waitingHandler)
Constructor.
|
PeptideMatchesIterator(Identification identification,
ArrayList<UrParameter> peptideParameters,
boolean loadPsms,
ArrayList<UrParameter> psmParameters,
WaitingHandler waitingHandler)
Constructor.
|
ProteinMatchesIterator(ArrayList<String> proteinKeys,
Identification identification,
ArrayList<UrParameter> proteinParameters,
boolean loadPeptides,
ArrayList<UrParameter> peptideParameters,
boolean loadPsms,
ArrayList<UrParameter> psmParameters,
WaitingHandler waitingHandler)
Constructor.
|
ProteinMatchesIterator(Identification identification,
ArrayList<UrParameter> proteinParameters,
boolean loadPeptides,
ArrayList<UrParameter> peptideParameters,
boolean loadPsms,
ArrayList<UrParameter> psmParameters,
WaitingHandler waitingHandler)
Constructor for an iterator iterating all protein keys.
|
PsmIterator(ArrayList<String> spectrumKeys,
Identification identification,
ArrayList<UrParameter> psmParameters,
boolean loadAssumptions,
WaitingHandler waitingHandler)
Constructor.
|
PsmIterator(ArrayList<String> spectrumKeys,
Identification identification,
boolean loadAssumptions,
WaitingHandler waitingHandler)
Constructor.
|
PsmIterator(Identification identification,
ArrayList<UrParameter> psmParameters,
boolean loadAssumptions,
WaitingHandler waitingHandler)
Constructor.
|
PsmIterator(Identification identification,
boolean loadAssumptions,
WaitingHandler waitingHandler)
Constructor.
|
PsmIterator(String spectrumFile,
ArrayList<String> spectrumKeys,
Identification identification,
ArrayList<UrParameter> psmParameters,
boolean loadAssumptions,
WaitingHandler waitingHandler)
Constructor.
|
PsmIterator(String spectrumFile,
ArrayList<String> spectrumKeys,
Identification identification,
boolean loadAssumptions,
WaitingHandler waitingHandler)
Constructor.
|
PsmIterator(String spectrumFile,
Identification identification,
ArrayList<UrParameter> psmParameters,
boolean loadAssumptions,
WaitingHandler waitingHandler)
Constructor.
|
PsmIterator(String spectrumFile,
Identification identification,
boolean loadAssumptions,
ArrayList<UrParameter> psmParameters,
WaitingHandler waitingHandler)
Constructor.
|
PsmIterator(String spectrumFile,
Identification identification,
boolean loadAssumptions,
WaitingHandler waitingHandler)
Constructor.
|
Modifier and Type | Method and Description |
---|---|
void |
ProteinTree.initiateTree(int initialTagSize,
int maxNodeSize,
int maxPeptideSize,
Enzyme enzyme,
WaitingHandler waitingHandler,
ExceptionHandler exceptionHandler,
boolean printExpectedImportTime,
boolean displayProgress,
int nThreads)
Initiates the tree.
|
void |
ProteinTree.initiateTree(int initialTagSize,
int maxNodeSize,
int maxPeptideSize,
WaitingHandler waitingHandler,
ExceptionHandler exceptionHandler,
boolean printExpectedImportTime,
boolean displayProgress,
int nThreads)
Initiates the tree.
|
void |
ProteinTreeComponentsFactory.loadNodes(ArrayList<String> tags,
WaitingHandler waitingHandler)
Loads nodes in the cache.
|
void |
ProteinTreeComponentsFactory.saveNodes(HashMap<String,Object> nodes,
WaitingHandler waitingHandler)
Adds nodes to the database.
|
Modifier and Type | Method and Description |
---|---|
LinkedList<SpectrumMatch> |
IdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler,
SearchParameters searchParameters)
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.
|
LinkedList<SpectrumMatch> |
IdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler,
SearchParameters searchParameters,
SequenceMatchingPreferences sequenceMatchingPreferences,
boolean expandAaCombinations)
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.
|
static String |
MzIdentMLIdfileSearchParametersConverter.getSearchParameters(File mzIdentMLFile,
SearchParameters searchParameters,
String species,
WaitingHandler waitingHandler)
Constructor.
|
Modifier and Type | Method and Description |
---|---|
LinkedList<SpectrumMatch> |
TideIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler,
SearchParameters searchParameters) |
LinkedList<SpectrumMatch> |
PNovoIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler,
SearchParameters searchParameters) |
LinkedList<SpectrumMatch> |
PepxmlIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler,
SearchParameters searchParameters) |
LinkedList<SpectrumMatch> |
PepNovoIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler,
SearchParameters searchParameters) |
LinkedList<SpectrumMatch> |
MzIdentMLIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler,
SearchParameters searchParameters) |
LinkedList<SpectrumMatch> |
MsAmandaIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler,
SearchParameters searchParameters) |
LinkedList<SpectrumMatch> |
DirecTagIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler,
SearchParameters searchParameters) |
LinkedList<SpectrumMatch> |
AndromedaIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler,
SearchParameters searchParameters) |
LinkedList<SpectrumMatch> |
TideIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler,
SearchParameters searchParameters,
SequenceMatchingPreferences sequenceMatchingPreferences,
boolean expandAaCombinations) |
LinkedList<SpectrumMatch> |
PNovoIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler,
SearchParameters searchParameters,
SequenceMatchingPreferences sequenceMatchingPreferences,
boolean expandAaCombinations) |
LinkedList<SpectrumMatch> |
PepxmlIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler,
SearchParameters searchParameters,
SequenceMatchingPreferences sequenceMatchingPreferences,
boolean expandAaCombinations) |
LinkedList<SpectrumMatch> |
PepNovoIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler,
SearchParameters searchParameters,
SequenceMatchingPreferences sequenceMatchingPreferences,
boolean expandAaCombinations) |
LinkedList<SpectrumMatch> |
MzIdentMLIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler,
SearchParameters searchParameters,
SequenceMatchingPreferences sequenceMatchingPreferences,
boolean expandAaCombinations) |
LinkedList<SpectrumMatch> |
MsAmandaIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler,
SearchParameters searchParameters,
SequenceMatchingPreferences sequenceMatchingPreferences,
boolean expandAaCombinations) |
LinkedList<SpectrumMatch> |
DirecTagIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler,
SearchParameters searchParameters,
SequenceMatchingPreferences sequenceMatchingPreferences,
boolean expandAaCombinations) |
LinkedList<SpectrumMatch> |
AndromedaIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler,
SearchParameters searchParameters,
SequenceMatchingPreferences sequenceMatchingPreferences,
boolean expandAaCombinations) |
Constructor and Description |
---|
AndromedaIdfileReader(File resultsFile,
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.
|
PNovoIdfileReader(File identificationFile,
WaitingHandler waitingHandler)
Constructor, initiate the parser.
|
TideIdfileReader(File tideTsvFile,
WaitingHandler waitingHandler)
Constructor for an Tide tsv result file reader.
|
Modifier and Type | Method and Description |
---|---|
static void |
MgfReader.addMissingSpectrumTitles(File mgfFile,
WaitingHandler waitingHandler)
Adds missing spectrum titles.
|
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.
|
protected abstract int |
SelfUpdatingTableModel.loadDataForRows(ArrayList<Integer> indexes,
WaitingHandler waitingHandler)
Loads the data needed for objects at rows of the given view indexes.
|
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.
|
class |
WaitingHandlerDummy
This class is an implementation of the WaitingHandler interface to be used
when a process can be canceled, but no monitoring is needed.
|
Modifier and Type | Method and Description |
---|---|
static void |
ZipUtils.addFileToZip(File file,
ZipOutputStream out,
WaitingHandler waitingHandler,
long totalUncompressedFileSize)
Adds a new file to the zip stream.
|
static void |
ZipUtils.addFileToZip(String subDirectory,
File file,
ZipOutputStream out,
WaitingHandler waitingHandler,
long totalUncompressedFileSize)
Adds a new file to the zip stream.
|
static void |
TarUtils.addFolderContent(org.apache.commons.compress.archivers.ArchiveOutputStream tarOutput,
File folder,
WaitingHandler waitingHandler)
Add content to the tar file.
|
static void |
ZipUtils.addToZip(File file,
String subDirectory,
ZipOutputStream out,
WaitingHandler waitingHandler,
long totalUncompressedFileSize)
Adds a new file to the zip stream.
|
static void |
ZipUtils.addToZip(File file,
ZipOutputStream out,
WaitingHandler waitingHandler,
long totalUncompressedFileSize)
Adds a new file to the zip stream.
|
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 to a file.
|
static void |
ZipUtils.unzip(File zipFile,
File destinationFolder,
WaitingHandler waitingHandler)
Unzips the content of an archive into a given folder.
|
static void |
ZipUtils.zip(File originFile,
File destinationFile,
WaitingHandler waitingHandler,
long totalUncompressedFileSize)
Zips a file.
|
Constructor and Description |
---|
FindPdbForUniprotAccessions(String aProteinAccession,
WaitingHandler aWaitingHandler)
Constructor.
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Modifier and Type | Method and Description |
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void |
GenePreferences.downloadGeneMappings(String ensemblType,
String ensemblSchemaName,
String selectedSpecies,
String ensemblVersion,
WaitingHandler waitingHandler)
Download the gene mappings.
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boolean |
GenePreferences.downloadGeneSequences(File destinationFile,
String ensemblType,
String ensemblSchemaName,
String selectedSpecies,
WaitingHandler waitingHandler)
Download the gene sequences mappings.
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boolean |
GenePreferences.downloadGoMappings(String ensemblType,
String ensemblSchemaName,
String selectedSpecies,
boolean swissProtMapping,
WaitingHandler waitingHandler)
Download the GO mappings.
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boolean |
GenePreferences.downloadMappings(WaitingHandler waitingHandler,
String currentEnsemblSpeciesType,
String selectedSpecies,
boolean commandLine)
Try to download the gene and GO mappings for the currently selected
species.
|
boolean |
GenePreferences.loadGeneMappings(String jarFilePath,
WaitingHandler waitingHandler)
Imports the gene mappings.
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boolean |
GenePreferences.queryEnsembl(String requestXml,
File destinationFile,
String ensemblType,
WaitingHandler waitingHandler)
Sends an XML query to Ensembl and writes the result in a text file.
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boolean |
GenePreferences.queryEnsembl(String requestXml,
String waitingText,
File destinationFile,
String ensemblType,
WaitingHandler waitingHandler)
Sends an XML query to Ensembl and writes the result in a text file.
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Modifier and Type | Method and Description |
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static void |
ProteinSequencesManager.addUserFastaFile(File userFastaFile,
WaitingHandler waitingHandler)
Adds a user FASTA file to the folder.
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