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## org.biojavax.bio
Class SimpleBioEntry

    java.lang.Object
      org.biojava.utils.AbstractChangeable
          org.biojavax.bio.SimpleBioEntry

All Implemented Interfaces:
  Comparable, Annotatable, Changeable, BioEntry, RankedCrossRefable, RichAnnotatable

Direct Known Subclasses:
  ThinRichSequence

    public class SimpleBioEntry

extends AbstractChangeable
implements BioEntry

Reference implementation of a BioEntry object which has no features or sequence. Equality is the combination of namespace, name, accession and version.

Since:
  1.5
Author:
  Richard Holland, Mark Schreiber, George Waldon

Nested Class Summary

Nested classes/interfaces inherited from interface org.biojava.bio.Annotatable
`Annotatable.AnnotationForwarder`

Field Summary

Fields inherited from interface org.biojavax.bio.BioEntry
`COMMENT, DESCRIPTION, DIVISION, IDENTIFIER, RANKEDCROSSREF, RANKEDDOCREF, RELATIONS, SEQVERSION, TAXON`

Fields inherited from interface org.biojava.bio.Annotatable
`ANNOTATION`

Constructor Summary
`protected` | `SimpleBioEntry()`
`` | `SimpleBioEntry(Namespace ns, String name, String accession, int version)` Creates a new bioentry representing the sequence in the given namespace with the given name, accession and version.

Method Summary
`void` | `addComment(Comment comment)` Adds a comment instance to this bioentry.
`void` | `addRankedCrossRef(RankedCrossRef crossref)` Adds a ranked cross reference to the existing set.
`void` | `addRankedDocRef(RankedDocRef docref)` Adds a ranked docref instance to this bioentry.
`void` | `addRelationship(BioEntryRelationship relation)` Adds a relation instance to this bioentry.
`int` | `compareTo(Object o)` Bioentries are ordered first by namespace, then name, accession, and finally version.
`boolean` | `equals(Object obj)` Two bioentries are equal if they share the same namespace, name, accession and version.
`String` | `getAccession()` Returns the accession of this bioentry.
`Annotation` | `getAnnotation()` Should return the associated annotation object.
`Set` | `getComments()` Returns a set of all comments associated with this bioentry. Warning this method gives access to the original Collection not a copy.
`String` | `getDescription()` Returns a description of this sequence.
`String` | `getDivision()` Returns the division of this bioentry.
`Integer` | `getId()` Gets the Hibernate ID.
`String` | `getIdentifier()` Returns the identifier of this bioentry.
`String` | `getName()` Returns the name of this bioentry.
`Namespace` | `getNamespace()` Returns the namespace of this bioentry.
`Set` | `getNoteSet()` Returns the set of notes associated with this object. Warning this method gives access to the original Collection not a copy.
`Set` | `getRankedCrossRefs()` Returns the set of all ranked cross references associated with an object. Warning this method gives access to the original Collection not a copy.
`Set` | `getRankedDocRefs()` Returns a set of all bioentrydocrefs associated with this bioentry. Warning this method gives access to the original Collection not a copy.
`Set` | `getRelationships()` Returns a set of all relationships associated with this bioentry. Warning this method gives access to the original Collection not a copy.
`RichAnnotation` | `getRichAnnotation()` Return the associated annotation object.
`NCBITaxon` | `getTaxon()` Gets the taxon associated with this bioentry.
`int` | `getVersion()` Gets the version of this bioentry.
`int` | `hashCode()`
`void` | `removeComment(Comment comment)` Removes a comment instance from this bioentry.
`void` | `removeRankedCrossRef(RankedCrossRef crossref)` Removes a ranked cross reference from the existing set.
`void` | `removeRankedDocRef(RankedDocRef docref)` Removes a ranked docref instance from this bioentry.
`void` | `removeRelationship(BioEntryRelationship relation)` Removes a relation instance from this bioentry.
`void` | `setDescription(String description)` Sets the description for this bioentry.
`void` | `setDivision(String division)` Sets the division of this bioentry.
`void` | `setId(Integer id)` Sets the Hibernate ID.
`void` | `setIdentifier(String identifier)` Sets the identifier of this bioentry.
`void` | `setNoteSet(Set notes)` Clears the notes associated with this object and replaces them with the contents of this set. Warning this method gives access to the original Collection not a copy.
`void` | `setRankedCrossRefs(Set rankedcrossrefs)` Sets the ranked cross references associated with an object.
`void` | `setTaxon(NCBITaxon taxon)` Sets the taxon for this bioentry.
`String` | `toString()` Form: namespace:name/accession.version

Methods inherited from class org.biojava.utils.AbstractChangeable
`addChangeListener, addChangeListener, generateChangeSupport, getChangeSupport, hasListeners, hasListeners, isUnchanging, removeChangeListener, removeChangeListener`

Methods inherited from class java.lang.Object
`clone, finalize, getClass, notify, notifyAll, wait, wait, wait`

Methods inherited from interface org.biojava.utils.Changeable
`addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener`

Constructor Detail

### SimpleBioEntry

    public SimpleBioEntry(Namespace ns,
                          String name,
                          String accession,
                          int version)

  Creates a new bioentry representing the sequence in the given namespace with the given name, accession and version. These properties are all immutable and non-nullable.

  Parameters:
    `ns` - The namespace for this new bioentry (not null).
    `name` - The name for this new bioentry (not null).
    `accession` - The accession for this new bioentry (not null).
    `version` - The version for this new bioentry.

### SimpleBioEntry

    protected SimpleBioEntry()

Method Detail

### getRankedCrossRefs

    public Set getRankedCrossRefs()

  Returns the set of all ranked cross references associated with an object. Warning this method gives access to the original Collection not a copy. This is required by Hibernate. If you modify the object directly the behaviour may be unpredictable.

  Specified by:
    `getRankedCrossRefs` in interface `RankedCrossRefable`
  Returns:
    a set of RankedCrossRef objects.

### setTaxon

    public void setTaxon(NCBITaxon taxon)
                  throws ChangeVetoException

  Sets the taxon for this bioentry. It may be null, in which case the taxon is unset.

  Specified by:
    `setTaxon` in interface `BioEntry`
  Parameters:
    `taxon` - New value of property taxon.
  Throws:
    `ChangeVetoException` - in case of objections.

### getAnnotation

    public Annotation getAnnotation()

  Should return the associated annotation object.

  Specified by:
    `getAnnotation` in interface `Annotatable`
  Returns:
    an Annotation object, never null

### getRichAnnotation

    public RichAnnotation 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. Warning this method gives access to the original Collection not a copy. This is required by Hibernate. If you modify the object directly the behaviour may be unpredictable.

  Specified by:
    `getNoteSet` in interface `RichAnnotatable`
  Returns:
    set a set of Note objects.
  See Also:
    `Note`

### setNoteSet

    public void setNoteSet(Set notes)
                    throws ChangeVetoException

  Clears the notes associated with this object and replaces them with the contents of this set. Would normally delegate call to internal RichAnnotation instance. Warning this method gives access to the original Collection not a copy. This is required by Hibernate. If you modify the object directly the behaviour may be unpredictable.

  Specified by:
    `setNoteSet` in interface `RichAnnotatable`
  Parameters:
    `notes` - the set of Note objects to replace the existing ones with.
  Throws:
    `ChangeVetoException` - if the set is null or contains any objects that are not Note objects.
  See Also:
    `Note`

### getComments

    public Set getComments()

  Returns a set of all comments associated with this bioentry. This set is not mutable. If no comments are associated, you will get back an empty set. Warning this method gives access to the original Collection not a copy. This is required by Hibernate. If you modify the object directly the behaviour may be unpredictable.

  Specified by:
    `getComments` in interface `BioEntry`
  Returns:
    a set of Comment objects.
  See Also:
    `Comment`

### getRankedDocRefs

    public Set getRankedDocRefs()

  Returns a set of all bioentrydocrefs associated with this bioentry. This set is not mutable. If no docrefs are associated, you will get back an empty set. Warning this method gives access to the original Collection not a copy. This is required by Hibernate. If you modify the object directly the behaviour may be unpredictable.

  Specified by:
    `getRankedDocRefs` in interface `BioEntry`
  Returns:
    a set of RankedDocRef objects.
  See Also:
    `RankedDocRef`

### getRelationships

    public Set getRelationships()

  Returns a set of all relationships associated with this bioentry. This set is not mutable. If no relationships are associated, you will get back an empty set. Warning this method gives access to the original Collection not a copy. This is required by Hibernate. If you modify the object directly the behaviour may be unpredictable.

  Specified by:
    `getRelationships` in interface `BioEntry`
  Returns:
    a set of BioEntryRelationship objects.
  See Also:
    `BioEntryRelationship`

### setIdentifier

    public void setIdentifier(String identifier)
                       throws ChangeVetoException

  Sets the identifier of this bioentry. Null is allowable.

  Specified by:
    `setIdentifier` in interface `BioEntry`
  Parameters:
    `identifier` - New value of property identifier.
  Throws:
    `ChangeVetoException` - in case of objections.

### setDivision

    public void setDivision(String division)
                     throws ChangeVetoException

  Sets the division of this bioentry. Null is allowable.

  Specified by:
    `setDivision` in interface `BioEntry`
  Parameters:
    `division` - New value of property division.
  Throws:
    `ChangeVetoException` - in case of objections.

### setDescription

    public void setDescription(String description)
                        throws ChangeVetoException

  Sets the description for this bioentry.

  Specified by:
    `setDescription` in interface `BioEntry`
  Parameters:
    `description` - New value of property description.
  Throws:
    `ChangeVetoException` - in case of objections.

### getAccession

    public String getAccession()

  Returns the accession of this bioentry. The accession is supposed to be an immutable property set by the constructor.

  Specified by:
    `getAccession` in interface `BioEntry`
  Returns:
    Value of property accession.

### getDescription

    public String getDescription()

  Returns a description of this sequence.

  Specified by:
    `getDescription` in interface `BioEntry`
  Returns:
    Value of property description.

### getDivision

    public String getDivision()

  Returns the division of this bioentry. Division relates to a division of the parent namespace.

  Specified by:
    `getDivision` in interface `BioEntry`
  Returns:
    Value of property division.

### getIdentifier

    public String getIdentifier()

  Returns the identifier of this bioentry.

  Specified by:
    `getIdentifier` in interface `BioEntry`
  Returns:
    Value of property identifier.

### getName

    public String getName()

  Returns the name of this bioentry. The name is supposed to be an immutable property set by the constructor.

  Specified by:
    `getName` in interface `BioEntry`
  Returns:
    Value of property name.

### getNamespace

    public Namespace getNamespace()

  Returns the namespace of this bioentry. The namespace is supposed to be an immutable property set by the constructor.

  Specified by:
    `getNamespace` in interface `BioEntry`
  Returns:
    the namespace of this bioentry.

### getTaxon

    public NCBITaxon getTaxon()

  Gets the taxon associated with this bioentry. It may be null.

  Specified by:
    `getTaxon` in interface `BioEntry`
  Returns:
    Value of property taxon.

### getVersion

    public int getVersion()

  Gets the version of this bioentry. Bioentries with no versions return 0. The version is supposed to be immutable and set only by the constructor.

  Specified by:
    `getVersion` in interface `BioEntry`
  Returns:
    Value of property version.

### equals

    public boolean equals(Object obj)

  Two bioentries are equal if they share the same namespace, name, accession and version.

  Overrides:
    `equals` in class `Object`

### compareTo

    public int compareTo(Object o)

  Bioentries are ordered first by namespace, then name, accession, and finally version.

  Specified by:
    `compareTo` in interface `Comparable`

### hashCode

    public int hashCode()

  Overrides:
    `hashCode` in class `Object`

### toString

    public String toString()

  Form: namespace:name/accession.version

  Overrides:
    `toString` in class `Object`

### addRankedCrossRef

    public void addRankedCrossRef(RankedCrossRef crossref)
                           throws ChangeVetoException

  Adds a ranked cross reference to the existing set. If already present, this call is ignored. Null values are not acceptable.

  Specified by:
    `addRankedCrossRef` in interface `RankedCrossRefable`
  Parameters:
    `crossref` - the ranked cross reference to add.
  Throws:
    `ChangeVetoException` - if the parameter is null.

### removeRankedCrossRef

    public void removeRankedCrossRef(RankedCrossRef crossref)
                              throws ChangeVetoException

  Removes a ranked cross reference from the existing set. If not present, this call is ignored. Null values are not acceptable.

  Specified by:
    `removeRankedCrossRef` in interface `RankedCrossRefable`
  Parameters:
    `crossref` - the ranked cross reference to remove.
  Throws:
    `ChangeVetoException` - if the parameter is null.

### addRankedDocRef

    public void addRankedDocRef(RankedDocRef docref)
                         throws ChangeVetoException

  Adds a ranked docref instance to this bioentry. Must not be null.

  Specified by:
    `addRankedDocRef` in interface `BioEntry`
  Parameters:
    `docref` - the item to add.
  Throws:
    `ChangeVetoException` - if it doesn't want to add it.

### removeRankedDocRef

    public void removeRankedDocRef(RankedDocRef docref)
                            throws ChangeVetoException

  Removes a ranked docref instance from this bioentry. If it was not found, nothing happens.

  Specified by:
    `removeRankedDocRef` in interface `BioEntry`
  Parameters:
    `docref` - the item to remove.
  Throws:
    `ChangeVetoException` - if it doesn't want to remove it.

### addComment

    public void addComment(Comment comment)
                    throws ChangeVetoException

  Adds a comment instance to this bioentry. Must not be null.

  Specified by:
    `addComment` in interface `BioEntry`
  Parameters:
    `comment` - the item to add.
  Throws:
    `ChangeVetoException` - if it doesn't want to add it.

### removeComment

    public void removeComment(Comment comment)
                       throws ChangeVetoException

  Removes a comment instance from this bioentry. If it wasn't present, it nothing will happen.

  Specified by:
    `removeComment` in interface `BioEntry`
  Parameters:
    `comment` - the item to remove.
  Throws:
    `ChangeVetoException` - if it doesn't want to remove it.

### addRelationship

    public void addRelationship(BioEntryRelationship relation)
                         throws ChangeVetoException

  Adds a relation instance to this bioentry. It must not be null.

  Specified by:
    `addRelationship` in interface `BioEntry`
  Parameters:
    `relation` - the item to add.
  Throws:
    `ChangeVetoException` - if it doesn't want to add it.

### removeRelationship

    public void removeRelationship(BioEntryRelationship relation)
                            throws ChangeVetoException

  Removes a relation instance from this bioentry. If it wasn't present, nothing will happen.

  Specified by:
    `removeRelationship` in interface `BioEntry`
  Parameters:
    `relation` - the item to remove.
  Throws:
    `ChangeVetoException` - if it doesn't want to remove it.

### setRankedCrossRefs

    public void setRankedCrossRefs(Set rankedcrossrefs)

  Description copied from interface: `RankedCrossRefable`
  Sets the ranked cross references associated with an object. Null will throw an exception but the empty set is fine.

  Specified by:
    `setRankedCrossRefs` in interface `RankedCrossRefable`
  Parameters:
    `rankedcrossrefs` - a set of RankedCrossRef objects.

### 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.

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