Class PassthroughIdentifier

java.lang.Object
org.biojava.nbio.structure.PassthroughIdentifier
All Implemented Interfaces:
Serializable, StructureIdentifier

public class PassthroughIdentifier extends Object implements StructureIdentifier
A stub StructureIdentifier, representing the full structure in all cases.
Author:
Spencer Bliven
See Also:
  • Constructor Details

    • PassthroughIdentifier

      public PassthroughIdentifier(String identifier)
  • Method Details

    • getIdentifier

      public String getIdentifier()
      Description copied from interface: StructureIdentifier
      Get the String form of this identifier. It is recommended that the #toString() method also return the identifier, for consistency during serialization.
      Specified by:
      getIdentifier in interface StructureIdentifier
      Returns:
      The String form of this identifier
    • toCanonical

      public SubstructureIdentifier toCanonical()
      Description copied from interface: StructureIdentifier
      Convert to a canonical SubstructureIdentifier.

      This allows all domains to be converted to a standard format String.

      Specified by:
      toCanonical in interface StructureIdentifier
      Returns:
      A SubstructureIdentifier without ranges (e.g. including all residues)
    • reduce

      public Structure reduce(Structure input) throws StructureException
      Description copied from interface: StructureIdentifier
      Takes a complete structure as input and reduces it to the substructure represented by this StructureIdentifier.

      The returned structure may be a shallow copy of the input, with shared Chains, Residues, etc.

      Specified by:
      reduce in interface StructureIdentifier
      Parameters:
      input - A full structure, e.g. as loaded from the PDB. The structure ID should match that returned by getPdbId(), if applicable.
      Returns:
      Throws:
      StructureException
      See Also:
      • StructureTools#getReducedStructure(Structure, String)
    • loadStructure

      public Structure loadStructure(AtomCache cache) throws StructureException, IOException
      Passthrough identifiers don't know how to load a structure
      Specified by:
      loadStructure in interface StructureIdentifier
      Returns:
      null
      Throws:
      StructureException - For errors loading and parsing the structure
      IOException - Errors reading the structure from disk