Constructor and Description |
---|
FastaParametersInputBean(org.apache.commons.cli.CommandLine aLine,
File fastaFile,
WaitingHandler waitingHandler)
Parses all the arguments from a command line.
|
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 |
---|---|
void |
ObjectsDB.insertObjects(HashMap<Long,Object> objects,
WaitingHandler waitingHandler,
boolean displayProgress)
Inserts a set of objects in the given table.
|
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.
|
void |
ObjectsDB.lock(WaitingHandler waitingHandler)
Locking the db for storing.
|
void |
ObjectsDB.removeObjects(Collection<Long> keys,
WaitingHandler waitingHandler,
boolean displayProgress)
Removing an object from the cache and database.
|
ArrayList<Object> |
ObjectsDB.retrieveObjects(Class className,
WaitingHandler waitingHandler,
boolean displayProgress)
Retrieves all objects from a given class.
|
ArrayList<Object> |
ObjectsDB.retrieveObjects(Collection<Long> keys,
WaitingHandler waitingHandler,
boolean displayProgress)
Retrieves some objects from the database or cache.
|
void |
ObjectsCache.saveCache(WaitingHandler waitingHandler,
boolean emptyCache)
Saves the cache content in the database.
|
void |
ObjectsCache.saveObjects(int numLastEntries,
WaitingHandler waitingHandler,
boolean clearEntries)
Saves an entry in the database if modified.
|
Modifier and Type | Method and Description |
---|---|
void |
ProteinGeneDetailsProvider.downloadGeneMappings(String ensemblType,
String ensemblSchemaName,
String ensemblDatasetName,
String ensemblVersion,
WaitingHandler waitingHandler)
Download the gene mappings.
|
boolean |
ProteinGeneDetailsProvider.downloadGeneSequences(File destinationFile,
String ensemblType,
String ensemblSchemaName,
String ensemblDbName,
WaitingHandler waitingHandler)
Download the gene sequences mappings.
|
boolean |
ProteinGeneDetailsProvider.downloadGoMappings(String ensemblType,
String ensemblSchemaName,
String ensemblDbName,
boolean swissProtMapping,
WaitingHandler waitingHandler)
Download the GO mappings.
|
boolean |
ProteinGeneDetailsProvider.downloadMappings(WaitingHandler waitingHandler,
Integer taxon)
Try to download the gene and GO mappings for the currently selected
species.
|
GeneMaps |
ProteinGeneDetailsProvider.getGeneMaps(GeneParameters genePreferences,
FastaSummary fastaSummary,
SequenceProvider sequenceProvider,
ProteinDetailsProvider proteinDetailsProvider,
WaitingHandler waitingHandler)
Returns the gene maps for the given proteins.
|
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.
|
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.
|
Modifier and Type | Method and Description |
---|---|
void |
GeneMapping.importFromFile(File file,
WaitingHandler waitingHandler)
Reads go mappings from a BioMart file.
|
Modifier and Type | Method and Description |
---|---|
void |
GoDomains.laodMappingFromFile(File file,
WaitingHandler waitingHandler)
Reads go mappings from a file.
|
void |
GoMapping.loadMappingsFromFile(File file,
WaitingHandler waitingHandler)
Reads go mappings from a BioMart file.
|
Modifier and Type | Method and Description |
---|---|
void |
Identification.addObjects(HashMap<Long,Object> objects,
WaitingHandler waitingHandler,
boolean displayProgress)
Adds a list of objects into the database.
|
void |
Identification.addSpectrumMatches(HashMap<Long,Object> spectrumMatches,
WaitingHandler waitingHandler,
boolean displayProgress)
Adds a spectrum matches into the database.
|
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.
|
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.
|
SpectrumMatchesIterator |
Identification.getSpectrumMatchesIterator(WaitingHandler waitingHandler,
String filters)
Returns a psm iterator for all SpectrumMatches.
|
void |
Identification.loadObjects(ArrayList<Long> keyList,
WaitingHandler waitingHandler,
boolean displayProgress)
Loads all objects of given keys in cache.
|
void |
Identification.loadObjects(Class className,
WaitingHandler waitingHandler,
boolean displayProgress)
Loads all objects of the class in cache.
|
void |
Identification.removeObjects(ArrayList<Long> keys,
WaitingHandler waitingHandler,
boolean displayProgress)
Remove a list of objects from the database.
|
ArrayList<Object> |
Identification.retrieveObjects(Class className,
WaitingHandler waitingHandler,
boolean displayProgress)
Returns an array of all objects of a given class
|
ArrayList<Object> |
Identification.retrieveObjects(Collection<Long> keyList,
WaitingHandler waitingHandler,
boolean displayProgress)
Returns an array of all objects of a given list of keys
|
Modifier and Type | Method and Description |
---|---|
int |
IdentificationFeaturesGenerator.getNValidatedProteinGroups(long peptideKey,
WaitingHandler waitingHandler)
Indicates whether a peptide is found in a single protein match.
|
long[] |
IdentificationFeaturesGenerator.getProcessedProteinKeys(WaitingHandler waitingHandler,
FilterParameters filterPreferences)
Returns the sorted list of protein keys.
|
long[] |
IdentificationFeaturesGenerator.getProteinKeys(WaitingHandler waitingHandler,
FilterParameters filterPreferences)
Returns the ordered protein keys to display when no filtering is applied.
|
long[] |
IdentificationFeaturesGenerator.getValidatedProteins(WaitingHandler waitingHandler,
FilterParameters filterPreferences)
Returns the list of validated protein keys.
|
Constructor and Description |
---|
MatchesIterator(Class className,
Identification identification,
WaitingHandler waitingHandler,
boolean displayProgress)
Constructor.
|
MatchesIterator(long[] keys,
Class className,
Identification identification,
WaitingHandler waitingHandler,
boolean displayProgress,
String filters)
Constructor.
|
PeptideMatchesIterator(Identification identification,
WaitingHandler waitingHandler,
boolean displayProgress)
Constructor.
|
PeptideMatchesIterator(long[] keys,
Identification identification,
WaitingHandler waitingHandler,
boolean displayProgress)
Constructor.
|
ProteinMatchesIterator(Identification identification,
WaitingHandler waitingHandler,
boolean displayProgress)
Constructor.
|
ProteinMatchesIterator(long[] keys,
Identification identification,
WaitingHandler waitingHandler,
boolean displayProgress)
Constructor.
|
SpectrumMatchesIterator(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.
|
Modifier and Type | Method and Description |
---|---|
void |
PeptideInference.peptideInference(Identification identification,
IdentificationParameters identificationParameters,
SequenceProvider sequenceProvider,
ModificationProvider modificationProvider,
WaitingHandler waitingHandler)
Infers the PTM localization and its confidence for the best match of
every spectrum.
|
Modifier and Type | Method and Description |
---|---|
void |
WaveletTree.createWaveletTreeHuffman(byte[] text,
WaitingHandler waitingHandler,
WaveletTree.HuffmanNode root)
Create wavelet tree huffman.
|
Constructor and Description |
---|
FMIndex(File fastaFile,
FastaParameters fastaParameters,
WaitingHandler waitingHandler,
boolean displayProgress,
IdentificationParameters identificationParameters)
Constructor.
|
FMIndex(File fastaFile,
FastaParameters fastaParameters,
WaitingHandler waitingHandler,
boolean displayProgress,
PeptideVariantsParameters peptideVariantsPreferences,
SearchParameters searchParameters)
Constructor.
|
WaveletTree(byte[] text,
long[] aAlphabet,
WaitingHandler waitingHandler)
Constructor.
|
WaveletTree(byte[] text,
WaitingHandler waitingHandler,
WaveletTree.HuffmanNode root)
Constructor.
|
Modifier and Type | Method and Description |
---|---|
static FastaSummary |
FastaSummary.getSummary(String fastaFile,
FastaParameters fastaParameters,
boolean alwaysCreateNew,
WaitingHandler waitingHandler)
Gathers summary data on the FASTA file content.
|
static FastaSummary |
FastaSummary.getSummary(String fastaFile,
FastaParameters fastaParameters,
WaitingHandler waitingHandler)
Gathers summary data on the FASTA file content.
|
static FastaParameters |
FastaParameters.inferParameters(String fastaFilePath,
WaitingHandler waitingHandler)
Infers the parameters used to parse the file.
|
Modifier and Type | Method and Description |
---|---|
static void |
DecoyConverter.appendDecoySequences(File fastaIn,
File fastaOut,
FastaParameters fastaParameters,
WaitingHandler waitingHandler)
Appends decoy sequences to the provided FASTA file.
|
static void |
GenericFastaConverter.convertFile(File fastaIn,
File fastaOut,
WaitingHandler waitingHandler)
Appends decoy sequences to the provided FASTA file.
|
Modifier and Type | Method and Description |
---|---|
String |
HeaderIterator.getNextHeader(WaitingHandler waitingHandler)
Returns the next header.Null if none.
|
Modifier and Type | Method and Description |
---|---|
ArrayList<SpectrumMatch> |
IdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider,
WaitingHandler waitingHandler,
SearchParameters searchParameters)
Retrieves all the spectrum matches from an identification file as a list
of spectrum matches, one spectrum match per spectrum.
|
ArrayList<SpectrumMatch> |
IdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider,
WaitingHandler waitingHandler,
SearchParameters searchParameters,
SequenceMatchingParameters sequenceMatchingPreferences,
boolean expandAaCombinations)
Retrieves all the spectrum matches from an identification file as a list
of spectrum matches, one spectrum match per spectrum.It is very important
to close the file reader after creation.
|
Constructor and Description |
---|
MzIdentMLIdfileSearchParametersConverter(File mzIdentMLFile,
SearchParameters searchParameters,
String species,
WaitingHandler waitingHandler)
Constructor.
|
Modifier and Type | Method and Description |
---|---|
ArrayList<SpectrumMatch> |
XTandemIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider,
WaitingHandler waitingHandler,
SearchParameters searchParameters) |
ArrayList<SpectrumMatch> |
TideIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider,
WaitingHandler waitingHandler,
SearchParameters searchParameters) |
ArrayList<SpectrumMatch> |
PNovoIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider,
WaitingHandler waitingHandler,
SearchParameters searchParameters) |
ArrayList<SpectrumMatch> |
PepxmlIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider,
WaitingHandler waitingHandler,
SearchParameters searchParameters) |
ArrayList<SpectrumMatch> |
PepNovoIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider,
WaitingHandler waitingHandler,
SearchParameters searchParameters) |
ArrayList<SpectrumMatch> |
OnyaseIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider,
WaitingHandler waitingHandler,
SearchParameters searchParameters) |
ArrayList<SpectrumMatch> |
NovorIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider,
WaitingHandler waitingHandler,
SearchParameters searchParameters) |
ArrayList<SpectrumMatch> |
MzIdentMLIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider,
WaitingHandler waitingHandler,
SearchParameters searchParameters) |
ArrayList<SpectrumMatch> |
MsAmandaIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider,
WaitingHandler waitingHandler,
SearchParameters searchParameters) |
ArrayList<SpectrumMatch> |
MascotIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider,
WaitingHandler waitingHandler,
SearchParameters searchParameters) |
ArrayList<SpectrumMatch> |
DirecTagIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider,
WaitingHandler waitingHandler,
SearchParameters searchParameters) |
ArrayList<SpectrumMatch> |
CossIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider,
WaitingHandler waitingHandler,
SearchParameters searchParameters) |
ArrayList<SpectrumMatch> |
AndromedaIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider,
WaitingHandler waitingHandler,
SearchParameters searchParameters) |
ArrayList<SpectrumMatch> |
XTandemIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider,
WaitingHandler waitingHandler,
SearchParameters searchParameters,
SequenceMatchingParameters sequenceMatchingPreferences,
boolean expandAaCombinations) |
ArrayList<SpectrumMatch> |
TideIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider,
WaitingHandler waitingHandler,
SearchParameters searchParameters,
SequenceMatchingParameters sequenceMatchingPreferences,
boolean expandAaCombinations) |
ArrayList<SpectrumMatch> |
PNovoIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider,
WaitingHandler waitingHandler,
SearchParameters searchParameters,
SequenceMatchingParameters sequenceMatchingPreferences,
boolean expandAaCombinations) |
ArrayList<SpectrumMatch> |
PepxmlIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider,
WaitingHandler waitingHandler,
SearchParameters searchParameters,
SequenceMatchingParameters sequenceMatchingPreferences,
boolean expandAaCombinations) |
ArrayList<SpectrumMatch> |
PepNovoIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider,
WaitingHandler waitingHandler,
SearchParameters searchParameters,
SequenceMatchingParameters sequenceMatchingPreferences,
boolean expandAaCombinations) |
ArrayList<SpectrumMatch> |
OnyaseIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider,
WaitingHandler waitingHandler,
SearchParameters searchParameters,
SequenceMatchingParameters sequenceMatchingPreferences,
boolean expandAaCombinations) |
ArrayList<SpectrumMatch> |
NovorIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider,
WaitingHandler waitingHandler,
SearchParameters searchParameters,
SequenceMatchingParameters sequenceMatchingPreferences,
boolean expandAaCombinations) |
ArrayList<SpectrumMatch> |
MzIdentMLIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider,
WaitingHandler waitingHandler,
SearchParameters searchParameters,
SequenceMatchingParameters sequenceMatchingPreferences,
boolean expandAaCombinations) |
ArrayList<SpectrumMatch> |
MsAmandaIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider,
WaitingHandler waitingHandler,
SearchParameters searchParameters,
SequenceMatchingParameters sequenceMatchingPreferences,
boolean expandAaCombinations) |
ArrayList<SpectrumMatch> |
MascotIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider,
WaitingHandler waitingHandler,
SearchParameters searchParameters,
SequenceMatchingParameters sequenceMatchingPreferences,
boolean expandAaCombinations) |
ArrayList<SpectrumMatch> |
DirecTagIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider,
WaitingHandler waitingHandler,
SearchParameters searchParameters,
SequenceMatchingParameters sequenceMatchingPreferences,
boolean expandAaCombinations) |
ArrayList<SpectrumMatch> |
CossIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider,
WaitingHandler waitingHandler,
SearchParameters searchParameters,
SequenceMatchingParameters sequenceMatchingPreferences,
boolean expandAaCombinations) |
ArrayList<SpectrumMatch> |
AndromedaIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider,
WaitingHandler waitingHandler,
SearchParameters searchParameters,
SequenceMatchingParameters sequenceMatchingPreferences,
boolean expandAaCombinations) |
Constructor and Description |
---|
CossIdfileReader(File cossTsvFile,
WaitingHandler waitingHandler)
Constructor for a COSS tsv result file reader.
|
MascotIdfileReader(File inputFile,
WaitingHandler waitingHandler)
Constructor for an Mascot dat csv 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.
|
NovorIdfileReader(File novorCsvFile,
WaitingHandler waitingHandler)
Constructor for an Novor csv result file reader.
|
TideIdfileReader(File tideTsvFile,
WaitingHandler waitingHandler)
Constructor for an Tide tsv result file reader.
|
XTandemIdfileReader(File inputFile,
WaitingHandler waitingHandler)
Constructor for an X!Tandem xml result file reader.
|
Modifier and Type | Method and 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,
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.
|
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.
|
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.
|
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.
|
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.
|
Constructor and Description |
---|
CmsFileIterator(File file,
WaitingHandler waitingHandler)
Constructor.
|
CmsFileReader(File file,
WaitingHandler waitingHandler)
Constructor allocating for single thread usage.
|
Modifier and Type | Method and Description |
---|---|
static void |
MgfFileUtils.addMissingPrecursorCharges(File mgfFile,
WaitingHandler waitingHandler)
Add missing precursor charges.
|
static void |
MgfFileUtils.addMissingSpectrumTitles(File mgfFile,
WaitingHandler waitingHandler)
Adds missing spectrum titles.
|
static MgfIndex |
IndexedMgfReader.getMgfIndex(File mgfFile,
WaitingHandler waitingHandler)
Returns the index of all spectra in the given MGF file.
|
static void |
MgfFileUtils.removeDuplicateSpectrumTitles(File mgfFile,
WaitingHandler waitingHandler)
Removes duplicate spectrum titles (the first occurrence is kept).
|
static void |
MgfFileUtils.removeZeroes(File mgfFile,
WaitingHandler waitingHandler)
Removes zero intensity peaks.
|
static void |
MgfFileUtils.renameDuplicateSpectrumTitles(File mgfFile,
WaitingHandler waitingHandler)
Renames duplicate spectrum titles.
|
static ArrayList<MgfIndex> |
MgfFileUtils.splitFile(File mgfFile,
int nSpectra,
WaitingHandler waitingHandler)
Splits an mgf file into smaller ones and returns the indexes of the
generated files.
|
Constructor and Description |
---|
MgfFileIterator(File mgfFile,
WaitingHandler waitingHandler)
Constructor.
|
Constructor and Description |
---|
MzmlFileIterator(File mzmlFile,
WaitingHandler waitingHandler)
Constructor.
|
Modifier and Type | Method and Description |
---|---|
void |
ScalingFactorsEstimators.estimateScalingFactors(Identification identification,
Metrics metrics,
SequenceProvider sequenceProvider,
IdentificationFeaturesGenerator identificationFeaturesGenerator,
WaitingHandler waitingHandler,
ExceptionHandler exceptionHandler,
ProcessingParameters processingParameters)
Estimates the scaling factors and stores them in the given metrics.
|
Modifier and Type | Method and Description |
---|---|
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 File |
IoUtil.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 |
---|---|
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,
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 |
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.
|
Modifier and Type | Method and Description |
---|---|
void |
KMeansClustering.kMeanCluster(WaitingHandler waitingHandler)
Run the k-means clustering.
|
Constructor and Description |
---|
FindPdbForUniprotAccessions(String aProteinAccession,
WaitingHandler aWaitingHandler)
Constructor.
|
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