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Methods in com.compomics.software.autoupdater with parameters of type WaitingHandler
Modifier and Type |
Method |
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.
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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.
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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.
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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.
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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.
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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.
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boolean |
FileDAO.unGzipAndUntarFile(GZIPInputStream in,
File fileLocationOnDiskToDownloadTo,
WaitingHandler waitingHandler) |
Untars and ungzips a .tar.gz file.
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Methods in com.compomics.util.db.object with parameters of type WaitingHandler
Modifier and Type |
Method |
Description |
void |
ObjectsDB.insertObjects(HashMap<Long,Object> objects,
WaitingHandler waitingHandler,
boolean displayProgress) |
Inserts a set of objects in the given table.
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void |
ObjectsDB.loadObjects(Class className,
WaitingHandler waitingHandler,
boolean displayProgress) |
Loads all objects from a given class.
|
void |
ObjectsDB.loadObjects(Collection<Long> keys,
WaitingHandler waitingHandler,
boolean displayProgress) |
Loads objects from a table in the cache.
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void |
ObjectsDB.lock(WaitingHandler waitingHandler) |
Locking the db for storing.
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void |
ObjectsDB.removeObjects(Collection<Long> keys,
WaitingHandler waitingHandler,
boolean displayProgress) |
Removing an object from the cache and database.
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ArrayList<Object> |
ObjectsDB.retrieveObjects(Class className,
WaitingHandler waitingHandler,
boolean displayProgress) |
Retrieves all objects from a given class.
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ArrayList<Object> |
ObjectsDB.retrieveObjects(Collection<Long> keys,
WaitingHandler waitingHandler,
boolean displayProgress) |
Retrieves some objects from the database or cache.
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void |
ObjectsCache.saveCache(WaitingHandler waitingHandler,
boolean emptyCache) |
Saves the cache content in the database.
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void |
ObjectsCache.saveObjects(int numLastEntries,
WaitingHandler waitingHandler,
boolean clearEntries) |
Saves an entry in the database if modified.
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Methods in com.compomics.util.experiment.biology.genes with parameters of type WaitingHandler
Modifier and Type |
Method |
Description |
void |
ProteinGeneDetailsProvider.downloadGeneMappings(String ensemblType,
String ensemblSchemaName,
String ensemblDatasetName,
String ensemblVersion,
WaitingHandler waitingHandler) |
Download the gene mappings.
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boolean |
ProteinGeneDetailsProvider.downloadGeneSequences(File destinationFile,
String ensemblType,
String ensemblSchemaName,
String ensemblDbName,
WaitingHandler waitingHandler) |
Download the gene sequences mappings.
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boolean |
ProteinGeneDetailsProvider.downloadGoMappings(String ensemblType,
String ensemblSchemaName,
String ensemblDbName,
boolean swissProtMapping,
WaitingHandler waitingHandler) |
Download the GO mappings.
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boolean |
ProteinGeneDetailsProvider.downloadMappings(WaitingHandler waitingHandler,
Integer taxon) |
Try to download the gene and GO mappings for the currently selected
species.
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GeneMaps |
ProteinGeneDetailsProvider.getGeneMaps(GeneParameters genePreferences,
FastaSummary fastaSummary,
SequenceProvider sequenceProvider,
ProteinDetailsProvider proteinDetailsProvider,
WaitingHandler waitingHandler) |
Returns the gene maps for the given proteins.
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boolean |
ProteinGeneDetailsProvider.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 |
ProteinGeneDetailsProvider.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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Methods in com.compomics.util.experiment.identification with parameters of type WaitingHandler
Modifier and Type |
Method |
Description |
void |
Identification.addObjects(HashMap<Long,Object> objects,
WaitingHandler waitingHandler,
boolean displayProgress) |
Adds a list of objects into the database.
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void |
Identification.addSpectrumMatches(HashMap<Long,Object> spectrumMatches,
WaitingHandler waitingHandler,
boolean displayProgress) |
Adds a spectrum matches into the database.
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PeptideMatchesIterator |
Identification.getPeptideMatchesIterator(long[] peptideKeys,
WaitingHandler waitingHandler) |
Returns a peptide matches iterator for a given key list.
|
PeptideMatchesIterator |
Identification.getPeptideMatchesIterator(WaitingHandler waitingHandler) |
Returns a peptide matches iterator for all PeptideMatches.
|
ProteinMatchesIterator |
Identification.getProteinMatchesIterator(long[] proteinKeys,
WaitingHandler waitingHandler) |
Returns a protein matches iterator for a given key list.
|
ProteinMatchesIterator |
Identification.getProteinMatchesIterator(WaitingHandler waitingHandler) |
Returns a protein matches iterator for all PeptideMatches.
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SpectrumMatchesIterator |
Identification.getSpectrumMatchesIterator(long[] spectrumMatches,
WaitingHandler waitingHandler) |
Returns a spectrum matches iterator for a given key list.
|
SpectrumMatchesIterator |
Identification.getSpectrumMatchesIterator(WaitingHandler waitingHandler) |
Returns a spectrum matches iterator for all SpectrumMatches.
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SpectrumMatchesIterator |
Identification.getSpectrumMatchesIterator(WaitingHandler waitingHandler,
String filters) |
Returns a psm iterator for all SpectrumMatches.
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void |
Identification.loadObjects(Class className,
WaitingHandler waitingHandler,
boolean displayProgress) |
Loads all objects of the class in cache.
|
void |
Identification.loadObjects(ArrayList<Long> keyList,
WaitingHandler waitingHandler,
boolean displayProgress) |
Loads all objects of given keys in cache.
|
void |
Identification.removeObjects(ArrayList<Long> keys,
WaitingHandler waitingHandler,
boolean displayProgress) |
Remove a list of objects from the database.
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ArrayList<Object> |
Identification.retrieveObjects(Class className,
WaitingHandler waitingHandler,
boolean displayProgress) |
Returns an array of all objects of a given class
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ArrayList<Object> |
Identification.retrieveObjects(Collection<Long> keyList,
WaitingHandler waitingHandler,
boolean displayProgress) |
Returns an array of all objects of a given list of keys
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Constructors in com.compomics.util.experiment.identification.matches_iterators with parameters of type WaitingHandler
Constructor |
Description |
MatchesIterator(long[] keys,
Class className,
Identification identification,
WaitingHandler waitingHandler,
boolean displayProgress,
String filters) |
Constructor.
|
MatchesIterator(Class className,
Identification identification,
WaitingHandler waitingHandler,
boolean displayProgress) |
Constructor.
|
PeptideMatchesIterator(long[] keys,
Identification identification,
WaitingHandler waitingHandler,
boolean displayProgress) |
Constructor.
|
PeptideMatchesIterator(Identification identification,
WaitingHandler waitingHandler,
boolean displayProgress) |
Constructor.
|
ProteinMatchesIterator(long[] keys,
Identification identification,
WaitingHandler waitingHandler,
boolean displayProgress) |
Constructor.
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ProteinMatchesIterator(Identification identification,
WaitingHandler waitingHandler,
boolean displayProgress) |
Constructor.
|
SpectrumMatchesIterator(long[] keys,
Identification identification,
WaitingHandler waitingHandler,
boolean displayProgress) |
Constructor.
|
SpectrumMatchesIterator(long[] keys,
Identification identification,
WaitingHandler waitingHandler,
boolean displayProgress,
String filters) |
Constructor.
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SpectrumMatchesIterator(Identification identification,
WaitingHandler waitingHandler,
boolean displayProgress) |
Constructor.
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Constructors in com.compomics.util.experiment.identification.protein_inference.fm_index with parameters of type WaitingHandler
Constructor |
Description |
FMIndex(File fastaFile,
FastaParameters fastaParameters,
WaitingHandler waitingHandler,
boolean displayProgress,
PeptideVariantsParameters peptideVariantsPreferences,
SearchParameters searchParameters) |
Constructor.
|
FMIndex(File fastaFile,
FastaParameters fastaParameters,
WaitingHandler waitingHandler,
boolean displayProgress,
IdentificationParameters identificationParameters) |
Constructor.
|
WaveletTree(byte[] text,
long[] aAlphabet,
WaitingHandler waitingHandler) |
Constructor.
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WaveletTree(byte[] text,
WaitingHandler waitingHandler,
WaveletTree.HuffmanNode root) |
Constructor.
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Methods in com.compomics.util.experiment.io.identification.idfilereaders with parameters of type WaitingHandler
Modifier and Type |
Method |
Description |
ArrayList<SpectrumMatch> |
AndromedaIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider,
WaitingHandler waitingHandler,
SearchParameters searchParameters) |
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ArrayList<SpectrumMatch> |
AndromedaIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider,
WaitingHandler waitingHandler,
SearchParameters searchParameters,
SequenceMatchingParameters sequenceMatchingPreferences,
boolean expandAaCombinations) |
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ArrayList<SpectrumMatch> |
CossIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider,
WaitingHandler waitingHandler,
SearchParameters searchParameters) |
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ArrayList<SpectrumMatch> |
CossIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider,
WaitingHandler waitingHandler,
SearchParameters searchParameters,
SequenceMatchingParameters sequenceMatchingPreferences,
boolean expandAaCombinations) |
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ArrayList<SpectrumMatch> |
DirecTagIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider,
WaitingHandler waitingHandler,
SearchParameters searchParameters) |
|
ArrayList<SpectrumMatch> |
DirecTagIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider,
WaitingHandler waitingHandler,
SearchParameters searchParameters,
SequenceMatchingParameters sequenceMatchingPreferences,
boolean expandAaCombinations) |
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ArrayList<SpectrumMatch> |
MascotIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider,
WaitingHandler waitingHandler,
SearchParameters searchParameters) |
|
ArrayList<SpectrumMatch> |
MascotIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider,
WaitingHandler waitingHandler,
SearchParameters searchParameters,
SequenceMatchingParameters sequenceMatchingPreferences,
boolean expandAaCombinations) |
|
ArrayList<SpectrumMatch> |
MsAmandaIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider,
WaitingHandler waitingHandler,
SearchParameters searchParameters) |
|
ArrayList<SpectrumMatch> |
MsAmandaIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider,
WaitingHandler waitingHandler,
SearchParameters searchParameters,
SequenceMatchingParameters sequenceMatchingPreferences,
boolean expandAaCombinations) |
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ArrayList<SpectrumMatch> |
MzIdentMLIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider,
WaitingHandler waitingHandler,
SearchParameters searchParameters) |
|
ArrayList<SpectrumMatch> |
MzIdentMLIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider,
WaitingHandler waitingHandler,
SearchParameters searchParameters,
SequenceMatchingParameters sequenceMatchingPreferences,
boolean expandAaCombinations) |
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ArrayList<SpectrumMatch> |
NovorIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider,
WaitingHandler waitingHandler,
SearchParameters searchParameters) |
|
ArrayList<SpectrumMatch> |
NovorIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider,
WaitingHandler waitingHandler,
SearchParameters searchParameters,
SequenceMatchingParameters sequenceMatchingPreferences,
boolean expandAaCombinations) |
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ArrayList<SpectrumMatch> |
OnyaseIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider,
WaitingHandler waitingHandler,
SearchParameters searchParameters) |
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ArrayList<SpectrumMatch> |
OnyaseIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider,
WaitingHandler waitingHandler,
SearchParameters searchParameters,
SequenceMatchingParameters sequenceMatchingPreferences,
boolean expandAaCombinations) |
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ArrayList<SpectrumMatch> |
PepNovoIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider,
WaitingHandler waitingHandler,
SearchParameters searchParameters) |
|
ArrayList<SpectrumMatch> |
PepNovoIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider,
WaitingHandler waitingHandler,
SearchParameters searchParameters,
SequenceMatchingParameters sequenceMatchingPreferences,
boolean expandAaCombinations) |
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ArrayList<SpectrumMatch> |
PepxmlIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider,
WaitingHandler waitingHandler,
SearchParameters searchParameters) |
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ArrayList<SpectrumMatch> |
PepxmlIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider,
WaitingHandler waitingHandler,
SearchParameters searchParameters,
SequenceMatchingParameters sequenceMatchingPreferences,
boolean expandAaCombinations) |
|
ArrayList<SpectrumMatch> |
PNovoIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider,
WaitingHandler waitingHandler,
SearchParameters searchParameters) |
|
ArrayList<SpectrumMatch> |
PNovoIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider,
WaitingHandler waitingHandler,
SearchParameters searchParameters,
SequenceMatchingParameters sequenceMatchingPreferences,
boolean expandAaCombinations) |
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ArrayList<SpectrumMatch> |
TideIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider,
WaitingHandler waitingHandler,
SearchParameters searchParameters) |
|
ArrayList<SpectrumMatch> |
TideIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider,
WaitingHandler waitingHandler,
SearchParameters searchParameters,
SequenceMatchingParameters sequenceMatchingPreferences,
boolean expandAaCombinations) |
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ArrayList<SpectrumMatch> |
XTandemIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider,
WaitingHandler waitingHandler,
SearchParameters searchParameters) |
|
ArrayList<SpectrumMatch> |
XTandemIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider,
WaitingHandler waitingHandler,
SearchParameters searchParameters,
SequenceMatchingParameters sequenceMatchingPreferences,
boolean expandAaCombinations) |
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Methods in com.compomics.util.experiment.io.mass_spectrometry with parameters of type WaitingHandler
Modifier and Type |
Method |
Description |
static MsFileIterator |
MsFileIterator.getMsFileIterator(File file,
WaitingHandler waitingHandler) |
Returns the file reader for the given mass spectrometry file based on its
extension.
|
void |
MsFileHandler.register(File msFile,
WaitingHandler waitingHandler) |
Registers a mass spectrometry file and enables querying its spectra.If
the file is not a cms file, a cms file will be created along with the ms
file.
|
void |
MsFileHandler.register(File msFile,
File cmsFolder,
WaitingHandler waitingHandler) |
Registers a mass spectrometry file and enables querying its spectra.If
the file is not a cms file, a cms file will be created in the cms folder
if not null, along the ms file otherwise.
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static void |
MsFileExporter.writeAplFile(SpectrumProvider spectrumProvider,
String fileNameWithoutExtension,
File destinationFile,
SearchParameters searchParameters,
WaitingHandler waitingHandler) |
Writes the spectra of a file in the Andromeda peak list (apl) format.
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static void |
MsFileExporter.writeMgfFile(SpectrumProvider spectrumProvider,
String fileNameWithoutExtension,
File destinationFile,
WaitingHandler waitingHandler) |
Writes the spectra of a file in the Mascot Generic File (mgf) format.
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static void |
MsFileExporter.writeMs2File(SpectrumProvider spectrumProvider,
String fileNameWithoutExtension,
File destinationFile,
WaitingHandler waitingHandler) |
Writes the spectra of a file in the ms2 format.
|
static void |
MsFileExporter.writeMsFile(SpectrumProvider spectrumProvider,
String fileNameWithoutExtension,
File destinationFile,
MsFileExporter.Format format,
SearchParameters searchParameters,
WaitingHandler waitingHandler) |
Writes the spectra of a file in the given format.
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Methods in com.compomics.util.io.compression with parameters of type WaitingHandler
Modifier and Type |
Method |
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,
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.tarFolder(File folder,
File destinationFile,
WaitingHandler waitingHandler) |
Tar a given folder to a file.
|
static void |
TarUtils.tarFolderContent(File folder,
File destinationFile,
HashSet<String> exceptionsPaths,
WaitingHandler waitingHandler) |
Tar the content of 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.
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