Package org.biojavax

Class SimpleDocRef

java.lang.Object

org.biojava.utils.AbstractChangeable

org.biojavax.SimpleDocRef

All Implemented Interfaces:

Comparable, Changeable, DocRef

public class SimpleDocRef
extends AbstractChangeable
implements DocRef

A basic DocRef implementation.

Since:

1.5

Author:

Richard Holland, Mark Schreiber, George Waldon

Field Summary

Fields inherited from interface org.biojavax.DocRef

CROSSREF, REMARK

Constructor Summary

Constructors

Modifier	Constructor	Description
protected	SimpleDocRef()
	SimpleDocRef(String authors, String location)	Creates a new document reference from the given immutable authors and location and title.
	SimpleDocRef(String authors, String location, String title)	Creates a new document reference from the given immutable authors and location and title.
	SimpleDocRef(String authors, String location, String title, String crossRefKey, String crossRefValue, Integer crossRefVersion)	Construct a doc ref with populated cross ref.
	SimpleDocRef(List<DocRefAuthor> authors, String location)	Creates a new document reference from the given immutable authors and location and title.
	SimpleDocRef(List<DocRefAuthor> authors, String location, String title)	Creates a new document reference from the given immutable authors and location and title.
	SimpleDocRef(List authors, String location, String title, String crossRefKey, String crossRefValue, Integer crossRefVersion)	Construct a doc ref with populated cross ref.

Method Summary

Modifier and Type	Method	Description
int	compareTo(Object o)	Document references are compared first by author, then by location, then by title.
boolean	equals(Object obj)	Document references are equal if they have the same author and location and title.
List<DocRefAuthor>	getAuthorList()	Returns the authors of the document reference as a set of DocRefAuthor implementation instances.
String	getAuthors()	Returns the authors of the document reference.
String	getCRC()	Returns a CRC64 checksum of this document reference, allowing for easy comparisons with other document references.
CrossRef	getCrossref()	The document reference may refer to an object in another database.
Integer	getId()	Gets the Hibernate ID.
String	getLocation()	Returns a textual description of the document reference.
String	getRemark()	If remarks have been made about this document reference, this method will return them.
String	getTitle()	Returns the title of the document reference.
int	hashCode()
void	setCrossref(CrossRef crossref)	The document reference may refer to an object in another database.
void	setId(Integer id)	Sets the Hibernate ID.
void	setRemark(String remark)	Set the remarks for this document reference using this method.
String	toString()	Form: "authors; location"

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

SimpleDocRef

public SimpleDocRef(List<DocRefAuthor> authors,
                    String location)

Creates a new document reference from the given immutable authors and location and title. Will throw exceptions if either authors or location are null, but a null title is allowable.

Parameters:

authors - The authors of the referenced document, as a set of DocRefAuthor instances.

location - The location of the document, e.g. the journal name and page range.

SimpleDocRef

public SimpleDocRef(String authors,
                    String location)

Creates a new document reference from the given immutable authors and location and title. Will throw exceptions if either authors or location are null, but a null title is allowable.

Parameters:

authors - The authors of the referenced document, as a string to be parsed with DocRefAuthor.Tools.parseAuthorString(String).

location - The location of the document, eg. the journal name and page range.

SimpleDocRef

public SimpleDocRef(String authors,
                    String location,
                    String title)

Creates a new document reference from the given immutable authors and location and title. Will throw exceptions if either authors or location are null, but a null title is allowable.

Parameters:

authors - The authors of the referenced document, as a string to be parsed with DocRefAuthor.Tools.parseAuthorString(String).

location - The location of the document, e.g. the journal name and page range.

title - The title of the document.

SimpleDocRef

public SimpleDocRef(List<DocRefAuthor> authors,
                    String location,
                    String title)

Creates a new document reference from the given immutable authors and location and title. Will throw exceptions if either authors or location are null, but a null title is allowable.

Parameters:

authors - The authors of the referenced document, as a set of DocRefAuthor instances.

location - The location of the document, e.g. the journal name and page range.

title - The title of the document.

SimpleDocRef

public SimpleDocRef(String authors,
                    String location,
                    String title,
                    String crossRefKey,
                    String crossRefValue,
                    Integer crossRefVersion)

Construct a doc ref with populated cross ref.

Parameters:

authors -

location -

title -

crossRefKey -

crossRefValue -

crossRefVersion -

SimpleDocRef

public SimpleDocRef(List authors,
                    String location,
                    String title,
                    String crossRefKey,
                    String crossRefValue,
                    Integer crossRefVersion)

Construct a doc ref with populated cross ref.

Parameters:

authors -

location -

title -

crossRefKey -

crossRefValue -

crossRefVersion -

SimpleDocRef

protected SimpleDocRef()

Method Detail

setRemark

public void setRemark(String remark)
               throws ChangeVetoException

Set the remarks for this document reference using this method. Remarks can be anything, it is derived from the equivalent field in the GenBank format.

Specified by:

setRemark in interface DocRef

Parameters:

remark - New value of property Remark.

Throws:

ChangeVetoException - in case of objections.

setCrossref

public void setCrossref(CrossRef crossref)
                 throws ChangeVetoException

The document reference may refer to an object in another database. Use this method to set that reference. Null will unset it.

Specified by:

setCrossref in interface DocRef

Parameters:

crossref - New value of property crossref.

Throws:

ChangeVetoException - in case of objections.

getAuthors

public String getAuthors()

Returns the authors of the document reference. It will usually be in the form "Jones H., Bloggs J et al" or similar - a human-readable text value. Editors will have (ed.) appended, consortiums will have (consortium) appended.

Specified by:

getAuthors in interface DocRef

Returns:

Value of property authors.

getAuthorList

public List<DocRefAuthor> getAuthorList()

Returns the authors of the document reference as a set of DocRefAuthor implementation instances. This field is immutable so should be set using the constructor of the implementing class.

Specified by:

getAuthorList in interface DocRef

Returns:

The set of authors.

getCRC

public String getCRC()

Returns a CRC64 checksum of this document reference, allowing for easy comparisons with other document references. The string to be checksummed is constructed by concatenating the authors, title, and location in that order, with no space between. If any values are null they are substituted with the text "<undef>".

Specified by:

getCRC in interface DocRef

Returns:

Value of property CRC.

See Also:

CRC64Checksum

getRemark

public String getRemark()

If remarks have been made about this document reference, this method will return them.

Specified by:

getRemark in interface DocRef

Returns:

Value of property Remark.

getCrossref

public CrossRef getCrossref()

The document reference may refer to an object in another database. If so, this method will return that reference.

Specified by:

getCrossref in interface DocRef

Returns:

Value of property crossref.

getLocation

public String getLocation()

Returns a textual description of the document reference. This field is immutable so should be set using the constructor of the implementing class.

Specified by:

getLocation in interface DocRef

Returns:

Value of property location.

getTitle

public String getTitle()

Returns the title of the document reference.

Specified by:

getTitle in interface DocRef

Returns:

Value of property title.

compareTo

public int compareTo(Object o)

Document references are compared first by author, then by location, then by title. If Author and location are equal and this title is null, and theirs isn't, then this will return -1. For symmetry if our title is not null and theirs is then we return 1. If both are null then we return 0.

Specified by:

compareTo in interface Comparable

equals

public boolean equals(Object obj)

Document references are equal if they have the same author and location and title.

Overrides:

equals in class Object

hashCode

public int hashCode()

Overrides:

hashCode in class Object

toString

public String toString()

Form: "authors; location"

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.