Package org.biojavax

Class SimpleCrossRef

All Implemented Interfaces:
Comparable, Annotatable, Changeable, CrossRef, RichAnnotatable

public class SimpleCrossRef extends Unchangeable implements CrossRef
A basic CrossRef implementation.
Since:
1.5
Author:
Richard Holland, Mark Schreiber, George Waldon (made Unchangeable)
  • Constructor Details

    • SimpleCrossRef

      public SimpleCrossRef(String dbname, String accession, int version)
      Creates a new instance of SimpleCrossRef with the values to use for the immutable database name, accession and version.
      Parameters:
      dbname - the dbname for this crossref.
      accession - the accession for this crossref.
      version - the version for this crossref.
    • SimpleCrossRef

      public SimpleCrossRef(String dbname, String accession, Integer version)
      Creates a new instance of SimpleCrossRef with the values to use for the immutable database name, accession and version. Identical to other dbname/accession/version constructor except the version is specified as an Integer object rather than an int primitive. Will throw an exception if version is null.
      Parameters:
      dbname - the dbname for this crossref.
      accession - the accession for this crossref.
      version - the version for this crossref.
    • SimpleCrossRef

      protected SimpleCrossRef()
  • Method Details

    • getAnnotation

      Should return the associated annotation object.
      Specified by:
      getAnnotation in interface Annotatable
      Returns:
      an Annotation object, never null
    • getRichAnnotation

      Return the associated annotation object.
      Specified by:
      getRichAnnotation in interface RichAnnotatable
      Returns:
      a RichAnnotation object, never null
    • getNoteSet

      public Set getNoteSet()
      Returns the set of notes associated with this object. Would normally delegate call to internal RichAnnotation instance.
      Specified by:
      getNoteSet in interface RichAnnotatable
      Returns:
      set a set of Note objects.
      See Also:
    • setNoteSet

      public void setNoteSet(Set notes)
      Clears the notes associated with this object and replaces them with the contents of this set. Would normally delegate call to internal RichAnnotation instance.
      Specified by:
      setNoteSet in interface RichAnnotatable
      Parameters:
      notes - the set of Note objects to replace the existing ones with.
      See Also:
    • getAccession

      public String getAccession()
      Returns the accession of the object that the crossref refers to.
      Specified by:
      getAccession in interface CrossRef
      Returns:
      Value of property accession.
    • getDbname

      public String getDbname()
      Returns the name of the database the cross reference refers to. This would normally be a namespace name, eg. 'gb' for GenBank.
      Specified by:
      getDbname in interface CrossRef
      Returns:
      Value of property dbname.
    • getVersion

      public int getVersion()
      Returns the version of the object that the crossref refers to.
      Specified by:
      getVersion in interface CrossRef
      Returns:
      Value of property version.
    • compareTo

      public int compareTo(Object o)
      Compares cross references first by database name, then by accession, then by version.
      Specified by:
      compareTo in interface Comparable
    • equals

      public boolean equals(Object obj)
      Equality is defined as having the same database name, accession and version.
      Overrides:
      equals in class Object
    • hashCode

      public int hashCode()
      Overrides:
      hashCode in class Object
    • toString

      public String toString()
      Form: "dbname:accession.version"
      Overrides:
      toString in class Object
    • getId

      public Integer getId()
      Gets the Hibernate ID. Should be used with caution.
      Returns:
      the Hibernate ID, if using Hibernate.
    • setId

      public void setId(Integer id)
      Sets the Hibernate ID. Should be used with caution.
      Parameters:
      id - the Hibernate ID, if using Hibernate.