io.repseq.core

Class VDJCLibraryRegistry

java.lang.Object

io.repseq.core.VDJCLibraryRegistry

public final class VDJCLibraryRegistry
extends Object

Registry of VDJCLibraries. Central storage for VDJCLibraries objects. VDJCLibraries can be created only using VDJCLibraryRegistry.

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static interface	VDJCLibraryRegistry.AliasResolver Interface implemented by VDJCLibraryRegistry.LibraryResolver if it can also resolve library name aliases
static class	VDJCLibraryRegistry.ClasspathLibraryResolver Load library data from {libraryName}.json files in specified folder.
static class	VDJCLibraryRegistry.FolderLibraryResolver Load library data from {libraryName}.json files in specified folder.
static interface	VDJCLibraryRegistry.LibraryNameListProvider Interface implemented by VDJCLibraryRegistry.LibraryResolver if it can provide list of all base library names it can resolve
static interface	VDJCLibraryRegistry.LibraryResolver Tries to resolve library name to array of VDJCLibraryData[] objects E.g.

Field Summary

Fields

Modifier and Type	Field and Description
static String	DEFAULT_LIBRARY_NAME Name or alias-name of default V, D, J, C gene library.

Constructor Summary

Constructors

Constructor and Description
VDJCLibraryRegistry() Creates new VDJCLibraryRegistry with default sequence resolver
VDJCLibraryRegistry(SequenceResolver sequenceResolver) Creates new VDJCLibraryRegistry with specific sequence resolver.

Method Summary

Methods

Modifier and Type	Method and Description
void	addClasspathResolver(String searchPath) Adds classpath resolver to search for libraries with {libraryName}.json names in the specified folder
void	addClasspathResolver(String searchPath, ClassLoader classLoader) Adds classpath resolver to search for libraries with {libraryName}.json names in the specified folder
void	addLibraryResolver(VDJCLibraryRegistry.LibraryResolver resolver) Register library resolver to be used for automatic load of libraries by name and species
void	addPathResolver(Path searchPath) Adds path resolver to search for libraries with {libraryName}.json[.gz] file names in specified folder.
void	addPathResolver(String searchPath) Adds path resolver to search for libraries with {libraryName}.json[.gz] file names in specified folder.
void	addPathResolverWithPartialSearch(Path searchPath) Adds path resolver to search for libraries with {libraryName}[.*].json[.gz] file names in specified folder.
void	addPathResolverWithPartialSearch(String searchPath) Adds path resolver to search for libraries with {libraryName}[.*].json[.gz] file names in specified folder.
static VDJCLibraryRegistry	createDefaultRegistry() Creates new instance of basic default registry
static VDJCLibraryRegistry	getDefault() Returns default VDJCLibraryRegistry.
static VDJCLibrary	getDefaultLibrary(long taxonId) Retrieves default library (see description for DEFAULT_LIBRARY_NAME) from default registry for the specified species.
static VDJCLibrary	getDefaultLibrary(String species) Retrieves default library (see description for DEFAULT_LIBRARY_NAME) from default registry for the specified species name.
VDJCGene	getGene(VDJCGeneId geneId) Return gene by it's global id.
VDJCLibrary	getLibrary(String libraryName, long taxonId) Returns library with specified name and specified species.
VDJCLibrary	getLibrary(String libraryName, String species) Returns library with specified name and specified species.
VDJCLibrary	getLibrary(VDJCLibraryId libraryId) Returns library with specified name and specified species.
List<VDJCLibraryRegistry.LibraryResolver>	getLibraryResolvers() Return the list of library resolvers used by this registry
Collection<VDJCLibrary>	getLoadedLibraries() Returns collection of libraries that are currently loaded by this registry.
List<VDJCLibrary>	getLoadedLibrariesByName(String libraryName) Returns list of libraries that are currently loaded by this registry and has specified name.
List<VDJCLibrary>	getLoadedLibrariesByNamePattern(Pattern libraryNamePattern) Returns list of libraries that are currently loaded by this registry and has specified name pattern.
SequenceResolver	getSequenceResolver() Return sequence resolver used by this registry
List<String>	getSpeciesNames(long taxonId) Returns list of known species names for a given taxon id.
void	loadAllLibraries() Load all possible libraries using all available resolvers (resolvers having such feature)
void	loadAllLibraries(String name) Try resolve library using all available resolvers, and register all resolved libraries
void	registerLibraries(Path file) Register libraries from specific file
void	registerLibraries(Path file, String name) Register libraries from specific file with specified name
void	registerLibraries(String file) Register libraries from specific file
void	registerLibraries(String file, String name) Register libraries from specific file with specified name
VDJCLibrary	registerLibrary(Path context, String name, VDJCLibraryData data) Creates and registers single library from VDJCLibraryData
static void	resetDefaultRegistry() Resets default VDJLibrary registry
static void	resetDefaultRegistry(SequenceResolver resolver) Resets default VDJLibrary registry and sets specific sequence resolver
long	resolveSpecies(String name) Resolves species name to taxon id
Long	tryResolveSpecies(String name) Try resolves species name to taxon id.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

DEFAULT_LIBRARY_NAME

public static final String DEFAULT_LIBRARY_NAME

Name or alias-name of default V, D, J, C gene library. Now it is built-in RepSeq.IO library, hosted at https://github.com/repseqio/library . This name is uset to retrive library by

See Also:

Constant Field Values

Constructor Detail

VDJCLibraryRegistry

public VDJCLibraryRegistry()

Creates new VDJCLibraryRegistry with default sequence resolver

VDJCLibraryRegistry

public VDJCLibraryRegistry(SequenceResolver sequenceResolver)

Creates new VDJCLibraryRegistry with specific sequence resolver.

Parameters:

sequenceResolver - sequece resolver or null to use default resolver

Method Detail

getSequenceResolver

public SequenceResolver getSequenceResolver()

Return sequence resolver used by this registry

Returns:

sequence resolver used by this registry

getLoadedLibraries

public Collection<VDJCLibrary> getLoadedLibraries()

Returns collection of libraries that are currently loaded by this registry.

Returns:

collection of libraries that are currently loaded by this registry

getLoadedLibrariesByName

public List<VDJCLibrary> getLoadedLibrariesByName(String libraryName)

Returns list of libraries that are currently loaded by this registry and has specified name.

Returns:

list of libraries that are currently loaded by this registry and has specified name

getLoadedLibrariesByNamePattern

public List<VDJCLibrary> getLoadedLibrariesByNamePattern(Pattern libraryNamePattern)

Returns list of libraries that are currently loaded by this registry and has specified name pattern.

Returns:

list of libraries that are currently loaded by this registry and has specified name pattern

resolveSpecies

public long resolveSpecies(String name)

Resolves species name to taxon id

Parameters:

name - species name

Returns:

taxon id

Throws:

IllegalArgumentException - if can't resolve

tryResolveSpecies

public Long tryResolveSpecies(String name)

Try resolves species name to taxon id. Return null if failed

Parameters:

name - species name

Returns:

taxon id or null if not found

getSpeciesNames

public List<String> getSpeciesNames(long taxonId)

Returns list of known species names for a given taxon id.

Parameters:

taxonId - taxon id

Returns:

list of known species names for a given taxon id

addLibraryResolver

public void addLibraryResolver(VDJCLibraryRegistry.LibraryResolver resolver)

Register library resolver to be used for automatic load of libraries by name and species

Parameters:

resolver - resolver to add

addPathResolver

public void addPathResolver(Path searchPath)

Adds path resolver to search for libraries with {libraryName}.json[.gz] file names in specified folder.

Parameters:

searchPath - path to search for {libraryName}.json[.gz] files

addPathResolverWithPartialSearch

public void addPathResolverWithPartialSearch(Path searchPath)

Adds path resolver to search for libraries with {libraryName}[.*].json[.gz] file names in specified folder.

Parameters:

searchPath - path to search for {libraryName}[.*].json[.gz] files

addPathResolverWithPartialSearch

public void addPathResolverWithPartialSearch(String searchPath)

Adds path resolver to search for libraries with {libraryName}[.*].json[.gz] file names in specified folder.

Parameters:

searchPath - path to search for {libraryName}[.*].json[.gz] files

addPathResolver

public void addPathResolver(String searchPath)

Adds path resolver to search for libraries with {libraryName}.json[.gz] file names in specified folder.

Parameters:

searchPath - path to search for {libraryName}.json files[.gz]

addClasspathResolver

public void addClasspathResolver(String searchPath)

Adds classpath resolver to search for libraries with {libraryName}.json names in the specified folder

Parameters:

searchPath - root address to search for {libraryName}.json files inn classpath

addClasspathResolver

public void addClasspathResolver(String searchPath,
                        ClassLoader classLoader)

Adds classpath resolver to search for libraries with {libraryName}.json names in the specified folder

Parameters:

searchPath - root address to search for {libraryName}.json files inn classpath

classLoader - class loader

getGene

public VDJCGene getGene(VDJCGeneId geneId)

Return gene by it's global id. Libraries may be loaded during gene resolution.

Parameters:

geneId - global gene id

Returns:

gene instance

Throws:

IllegalArgumentException - if gene or library not found

getLibrary

public VDJCLibrary getLibrary(String libraryName,
                     String species)

Returns library with specified name and specified species. If not opened yet, library will be loaded using library providers added to this registry.

Parameters:

libraryName - library name

species - species name

Returns:

library

Throws:

RuntimeException - if no library found

IllegalArgumentException - if species can't be resolved

getLibrary

public VDJCLibrary getLibrary(String libraryName,
                     long taxonId)

Returns library with specified name and specified species. If not opened yet, library will be loaded using library providers added to this registry.

Parameters:

libraryName - library name

taxonId - taxon id

Returns:

library

Throws:

RuntimeException - if no library found

getLibrary

public VDJCLibrary getLibrary(VDJCLibraryId libraryId)

Returns library with specified name and specified species. If not opened yet, library will be loaded using library providers added to this registry.

Parameters:

libraryId - identifier of the library

Returns:

library

Throws:

RuntimeException - if no library found or checksum check failed

loadAllLibraries

public void loadAllLibraries(String name)

Try resolve library using all available resolvers, and register all resolved libraries

Parameters:

name - library name

loadAllLibraries

public void loadAllLibraries()

Load all possible libraries using all available resolvers (resolvers having such feature)

registerLibrary

public VDJCLibrary registerLibrary(Path context,
                          String name,
                          VDJCLibraryData data)

Creates and registers single library from VDJCLibraryData

Parameters:

context - context to use for resolution of sequences

name - library name

data - library data

Returns:

created library

registerLibraries

public void registerLibraries(String file)

Register libraries from specific file

Parameters:

file - libraries json file

registerLibraries

public void registerLibraries(String file,
                     String name)

Register libraries from specific file with specified name

Parameters:

file - libraries json file

name - library name

registerLibraries

public void registerLibraries(Path file)

Register libraries from specific file

Parameters:

file - libraries json file

registerLibraries

public void registerLibraries(Path file,
                     String name)

Register libraries from specific file with specified name

Parameters:

file - libraries json file

name - library name

resetDefaultRegistry

public static void resetDefaultRegistry()

Resets default VDJLibrary registry

resetDefaultRegistry

public static void resetDefaultRegistry(SequenceResolver resolver)

Resets default VDJLibrary registry and sets specific sequence resolver

createDefaultRegistry

public static VDJCLibraryRegistry createDefaultRegistry()

Creates new instance of basic default registry

Returns:

new instance of basic default registry

getDefault

public static VDJCLibraryRegistry getDefault()

Returns default VDJCLibraryRegistry.

Returns:

default VDJCLibraryRegistry

getDefaultLibrary

public static VDJCLibrary getDefaultLibrary(String species)

Retrieves default library (see description for DEFAULT_LIBRARY_NAME) from default registry for the specified species name. Equivalent of calling: getDefault().getLibrary(DEFAULT_LIBRARY_NAME, species);

Parameters:

species - species name

Returns:

library

Throws:

IllegalArgumentException - if species can't be resolved

getDefaultLibrary

public static VDJCLibrary getDefaultLibrary(long taxonId)

Retrieves default library (see description for DEFAULT_LIBRARY_NAME) from default registry for the specified species. Equivalent of calling: getDefault().getLibrary(DEFAULT_LIBRARY_NAME, taxonId);

Parameters:

taxonId - taxon id

Returns:

library

getLibraryResolvers

public List<VDJCLibraryRegistry.LibraryResolver> getLibraryResolvers()

Return the list of library resolvers used by this registry

Returns:

list of library resolvers used by this registry