VDJCLibraryRegistry (repseqio 1.3.5 API)

java.lang.Object
- io.repseq.core.VDJCLibraryRegistry

```
public final class VDJCLibraryRegistry
extends java.lang.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 java.lang.String DEFAULT_LIBRARY_NAME
Name or alias-name of default V, D, J, C gene library.

Fields
Modifier and Type	Field and Description
`static java.lang.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

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`addClasspathResolver(java.lang.String searchPath)` Adds classpath resolver to search for libraries with {libraryName}.json names in the specified folder
`void`	`addClasspathResolver(java.lang.String searchPath, java.lang.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(java.nio.file.Path searchPath)` Adds path resolver to search for libraries with {libraryName}.json[.gz] file names in specified folder.
`void`	`addPathResolver(java.lang.String searchPath)` Adds path resolver to search for libraries with {libraryName}.json[.gz] file names in specified folder.
`void`	`addPathResolverWithPartialSearch(java.nio.file.Path searchPath)` Adds path resolver to search for libraries with {libraryName}[.*].json[.gz] file names in specified folder.
`void`	`addPathResolverWithPartialSearch(java.lang.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(java.lang.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(java.lang.String libraryName, long taxonId)` Returns library with specified name and specified species.
`VDJCLibrary`	`getLibrary(java.lang.String libraryName, java.lang.String species)` Returns library with specified name and specified species.
`VDJCLibrary`	`getLibrary(VDJCLibraryId libraryId)` Returns library with specified name and specified species.
`java.util.List<VDJCLibraryRegistry.LibraryResolver>`	`getLibraryResolvers()` Return the list of library resolvers used by this registry
`java.util.Collection<VDJCLibrary>`	`getLoadedLibraries()` Returns collection of libraries that are currently loaded by this registry.
`java.util.List<VDJCLibrary>`	`getLoadedLibrariesByName(java.lang.String libraryName)` Returns list of libraries that are currently loaded by this registry and has specified name.
`java.util.List<VDJCLibrary>`	`getLoadedLibrariesByNamePattern(java.util.regex.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
`java.util.List<java.lang.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(java.lang.String name)` Try resolve library using all available resolvers, and register all resolved libraries
`void`	`registerLibraries(java.nio.file.Path file)` Register libraries from specific file
`void`	`registerLibraries(java.nio.file.Path file, java.lang.String name)` Register libraries from specific file with specified name
`void`	`registerLibraries(java.lang.String file)` Register libraries from specific file
`void`	`registerLibraries(java.lang.String file, java.lang.String name)` Register libraries from specific file with specified name
`VDJCLibrary`	`registerLibrary(java.nio.file.Path context, java.lang.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(java.lang.String name)` Resolves species name to taxon id
`java.lang.Long`	`tryResolveSpecies(java.lang.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 java.lang.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 java.util.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 java.util.List<VDJCLibrary> getLoadedLibrariesByName(java.lang.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 java.util.List<VDJCLibrary> getLoadedLibrariesByNamePattern(java.util.regex.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(java.lang.String name)
```
    Resolves species name to taxon id
    
    Parameters:
    
    name - species name
    
    Returns:
    
    taxon id
    
    Throws:
    
    java.lang.IllegalArgumentException - if can't resolve
  - tryResolveSpecies
```
public java.lang.Long tryResolveSpecies(java.lang.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 java.util.List<java.lang.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(java.nio.file.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(java.nio.file.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(java.lang.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(java.lang.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(java.lang.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(java.lang.String searchPath,
                                 java.lang.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:
    
    java.lang.IllegalArgumentException - if gene or library not found
  - getLibrary
```
public VDJCLibrary getLibrary(java.lang.String libraryName,
                              java.lang.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:
    
    java.lang.RuntimeException - if no library found
    
    java.lang.IllegalArgumentException - if species can't be resolved
  - getLibrary
```
public VDJCLibrary getLibrary(java.lang.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:
    
    java.lang.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:
    
    java.lang.RuntimeException - if no library found or checksum check failed
  - loadAllLibraries
```
public void loadAllLibraries(java.lang.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(java.nio.file.Path context,
                                   java.lang.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(java.lang.String file)
```
    Register libraries from specific file
    
    Parameters:
    
    file - libraries json file
  - registerLibraries
```
public void registerLibraries(java.lang.String file,
                              java.lang.String name)
```
    Register libraries from specific file with specified name
    
    Parameters:
    
    file - libraries json file
    
    name - library name
  - registerLibraries
```
public void registerLibraries(java.nio.file.Path file)
```
    Register libraries from specific file
    
    Parameters:
    
    file - libraries json file
  - registerLibraries
```
public void registerLibraries(java.nio.file.Path file,
                              java.lang.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(java.lang.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:
    
    java.lang.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 java.util.List<VDJCLibraryRegistry.LibraryResolver> getLibraryResolvers()
```
    Return the list of library resolvers used by this registry
    
    Returns:
    
    list of library resolvers used by this registry

Class VDJCLibraryRegistry

Nested Class Summary

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

DEFAULT_LIBRARY_NAME

Constructor Detail

VDJCLibraryRegistry

VDJCLibraryRegistry

Method Detail

getSequenceResolver

getLoadedLibraries

getLoadedLibrariesByName

getLoadedLibrariesByNamePattern

resolveSpecies

tryResolveSpecies

getSpeciesNames

addLibraryResolver

addPathResolver

addPathResolverWithPartialSearch

addPathResolverWithPartialSearch

addPathResolver

addClasspathResolver

addClasspathResolver

getGene

getLibrary

getLibrary

getLibrary

loadAllLibraries

loadAllLibraries

registerLibrary

registerLibraries

registerLibraries

registerLibraries

registerLibraries

resetDefaultRegistry

resetDefaultRegistry

createDefaultRegistry

getDefault

getDefaultLibrary

getDefaultLibrary

getLibraryResolvers