Class PrefixManager

java.lang.Object
org.incenp.obofoundry.sssom.PrefixManager
public class PrefixManager extends Object
Helper class to shorten/expand identifiers based on a prefix map.

This class is used internally by the TSVReader and TSVWriter classes. It automatically handles the prefixes that the SSSOM specification considers “built-in”.

  • Constructor Details

    • PrefixManager

      public PrefixManager()
      Creates a new instance.

  • Method Details

    • add

      public void add(String prefixName, String prefix)
      Adds a new prefix.
      Parameters:
      prefixName - The short name of the prefix, as it would appear in a CURIE. It should not include the colon.
      prefix - The expanded URL prefix;

    • add

      public void add(Map<? extends String, ? extends String> map)
      Adds new prefixes.
      Parameters:
      map - A map associating prefix names to prefixes.

    • getPrefixMap

      public Map<String,String> getPrefixMap()
      Gets the underlying map of prefix names to URL prefixes.
      Returns:
      The prefix map used by this prefix manager.

    • getUnresolvedPrefixNames

      public Set<String> getUnresolvedPrefixNames()
      Gets the prefix names that this resolver could not expand.
      Returns:
      The set of all prefixes encountered in the lifetime of this object that could not be expanded because the prefix was unknown.

    • getUnshortenedIRIs

      public Set<String> getUnshortenedIRIs()
      Gets the IRIs that could not be shortened by shortenIdentifier(String) for lack of a suitable prefix declaration.
      Returns:
      The set of all IRIs encountered in the lifetime of this object that could not be shortened.

    • getPrefix

      public String getPrefix(String prefixName)
      Gets the prefix associated with the given prefix name.
      Parameters:
      prefixName - The name of the prefix to retrieve.
      Returns:
      The corresponding prefix, or null if the name is not the name of a registered prefix.

    • getPrefixName

      public String getPrefixName(String iri)
      Gets the name of the best (longest) prefix for a given identifier.
      Parameters:
      iri - The identifier for which to search the longest prefix.
      Returns:
      The name of the best prefix, or null if no registered prefix is suitable for the given identifier.

    • getLocalName

      public String getLocalName(String iri)
      Gets the local part of the shortened form of given identifier.
      Parameters:
      iri - The identifier for which to get the local part.
      Returns:
      The local name of the identifier, that is, everything after the longest matching prefix; or null if the original identifier could not be shortened.

    • shortenIdentifier

      public String shortenIdentifier(String iri)
      Shortens an identifier according to the prefix map.
      Parameters:
      iri - The identifier to shorten.
      Returns:
      The shortened identifier, or the original identifier if it could not be shortened.

    • shortenIdentifiers

      public List<String> shortenIdentifiers(List<String> iris)
      Shortens all identifiers in the given list. The original list is left untouched.
      Parameters:
      iris - The list of identifiers to shorten.
      Returns:
      A new list with the shortened identifiers.

    • shortenIdentifiers

      public List<String> shortenIdentifiers(List<String> iris, boolean inPlace)
      Shortens all identifiers in the given list.
      Parameters:
      iris - The list of identifiers to shorten.
      inPlace - If true, the original list is modified; otherwise it is left untouched and a new list is returned.
      Returns:
      A list with the shortened identifiers. If inPlace is true, this is the original list.

    • expandIdentifier

      public String expandIdentifier(String curie)
      Expands a shortened identifier into its long, canonical form.
      Parameters:
      curie - The short identifier to expand.
      Returns:
      The full-length identifier, or the original identifier if it was not in CURIE form or the prefix name is unknown.

    • expandIdentifiers

      public List<String> expandIdentifiers(List<String> curies)
      Expands all identifiers in the given list. The original list is left untouched.
      Parameters:
      curies - The list of short identifiers to expand.
      Returns:
      A new list with the expanded identifiers..

    • expandIdentifiers

      public List<String> expandIdentifiers(List<String> curies, boolean inPlace)
      Expands all identifiers in the given list.
      Parameters:
      curies - The list of short identifiers to expand.
      inPlace - If true, the original list is modified; otherwise it is left untouched and a new list is returned.
      Returns:
      A list with the expanded identifiers. If inPlace is true, this is the original list.