Hi.
Does anybody have any strong opinions about taxanomic data in BioJava? I
was going to pop in a new package org.biojava.bio.taxa with interfaces &
in-memory implementations of taxonomies. The aim is that this should
play well with the ebi taxonomy database (and by extention the taxonomy
stuff in embl & swissprot files). This will not be merged into the 1.2
release untill/unless it gets very stable very quickly.
All views greatfully accepted. If this code already exists out there
somewhere, I would be more than happy to take a copy & BioJava'ise it &
check it in.
I've attached my simple/stupid taxa interface.
Matthew
import java.util.*;
/**
* A taxa within a classification.
* <P>
* Taxa may be 'leaf' nodes specifying species, or 'internal' nodes specifying
* kingdoms and the like.
*
* @author Matthew Pocock
*/
public interface Taxa {
/**
* The common name of the Taxa.
* <P>
* This is the normal name used in common speach, such as 'human'.
*
* @return a String representing this taxa's common name
*/
public String getCommonName();
/**
* The scientific name of this species.
* <P>
* This will be the portion of the scientific classification pertaining to
* just this node within the classifictaion. It will be something like
* 'homo sapien' or 'archaeal group 2', rather than the full classification
* list.
*/
public String getScientificName();
/**
* The parent of this Taxa.
* <P>
* Taxas live within a tree data-structure, so every taxa has a single parent
* except for the root type. This has the null parent.
*
* @return the parent Taxa, or null if this is the root type.
*/
public Taxa getParent();
/**
* The children of this Taxa.
* <P>
* Taxas live within a tree data-structure, so every taxa has zero or more
* children. In the case of zero children, the empty set is returned.
* <P>
* ? read-only ? dynamicaly updated with taxa object ? copy of data ?
*
* @return the Set (possibly empty) of all child Taxa
*/
public Set getChildren();
/**
* Add a taxa as a child to this one.
* <P>
* ? should this be add on getChildren ? is child added or coppied in ?
*
* @param child the Taxa to add as a child
* @throws ChangeVetoException if for any reason the child can't be added
*/
public void addChild(Taxa child)
throws ChangeVetoException;
/**
* Remove a taxa as a child to this one.
* <P>
* ? should this be remove on getChildren ? what if child is not actualy a
* child ? what if child is equal to but not the same as a child ?
*
* @param child the Taxa to remove as a child
* @throws ChangeVetoException if for any reason the child can't be removed
*/
public void removeChild(Taxa child)
throws ChangeVetoException;
}
