org.biomoby.shared.data
Class MobyDataObject

java.lang.Object
  org.biomoby.shared.MobyData
      org.biomoby.shared.MobyPrimaryData
          org.biomoby.shared.MobyPrimaryDataSimple
              org.biomoby.shared.data.MobyDataObject

All Implemented Interfaces:

Cloneable, Comparable, MobyDataInstance

Direct Known Subclasses:

MobyDataBoolean, MobyDataComposite, MobyDataDateTime, MobyDataFloat, MobyDataInt, MobyDataObjectSAI, MobyDataObjectVector, MobyDataString

public class MobyDataObject
extends MobyPrimaryDataSimple
implements MobyDataInstance, Cloneable, Comparable

A class representing a base MOBY object (i.e. just a namespace and id) that has been instantiated. If you are looking to represent an object with members (e.g. DNASequence), look at MobyDataComposite. If you are looking to represent a MOBY primitive object, please see the appropriate subclass of this class (e.g. MobyDataInteger). This class provides methods to instantiate the object value either simply using an ID (in which case an Object tag is created automatically), or via XML input either from a DOM Element (preferred) or a string containing the XML. The toXML method will return either service call or search template formatted XML depending on the mode set. Having both modes is useful because the data instance created from a previous call can be passed to a service search template by switching the XML mode. By default the object is in MobyDataInstance.SERVICE_XML_MODE.

Author:

Paul Gordon (gordonp@ucalgary.ca)

Field Summary

Fields inherited from interface org.biomoby.shared.data.MobyDataInstance

CENTRAL_XML_MODE, SERVICE_XML_MODE

Constructor Summary

MobyDataObject(Element element)
Construct the object using a DOM fragment.

MobyDataObject(Element element, Registry registry)

MobyDataObject(MobyDataObject mobj)
Creates a base object with the same name, namespace and id as the input instance, as opposed to clone, which creates an exact copy of all the fields and the datatype.

MobyDataObject(String name)
Constructor with no instance information, just a name (which can be blank).

MobyDataObject(String name, Registry registry)

MobyDataObject(String namespace, String id)
Constructor convenient for a base object with a namespace and ID.

MobyDataObject(String namespace, String id, Registry registry)

Method Summary

void	addCrossReference(MobyDataObject mdsi)
void	addCrossReferences(Element e)
void	addCrossReferences(Element e, Registry reg)
void	addProvisionInfo(Element e)
MobyDataObject	clone() Simply calls new constructor with object's existing data type, name and value.
int	compareTo(Object o) This method lexically compares in the order of value, ID, name if passed in object is a MobyDataObject.
static MobyDataInstance	createInstanceFromDOM(Element objectTag) This method creates a MobyDataObject of the appropriate subclass for a given input XML tree (e.g. base objects like MobyDataObject and MobyDataInt, or complex objects like MobyDataDateTime or MobyDataComposite, or even a MobyDataSecondaryInstance).
static MobyDataInstance	createInstanceFromDOM(Element objectTag, Registry registry)
static MobyDataObject	createInstanceFromString(String typeName, String value) Construct a primitive data type instance from a string value.
static MobyDataObject	createInstanceFromString(String typeName, String value, Registry registry)
static MobyDataInstance	createInstanceFromXML(String mobyXML) Similar to createObjectFromDOM(), but parses the XML for you using the JAXP parser discovery mechanism.
boolean	equals(Object passedInObject) Used to see if two objects are equivalent.
Collection	getCrossReferences() Call this method if you would like to modify the cross references, such as removing items, clearing the collection, etc.
static String	getId(Element e)
static String	getName(Element e) Determine the name of the element if an enclosing tag (e.g.
Object	getObject() Gives access to the Java object instance underlying the MobyData instance.
MobyNamespace	getPrimaryNamespace()
MobyProvisionInfo	getProvisionInfo()
static String	getTextContents(Element element) Similar to DOM level 3 getTextContent, but only elements are excepted as input, and text inside children elements is not picked up.
String	getValue() A lexical (prefereably human readable) representation of the underlying object value (not including the namespace and ID).
int	getXmlMode() Report whether toXML will produce Central template or service call instance XML.
boolean	hasCrossReferences()
void	setId(String value) Used to set the data instance value based on an ID string. i.e. just an Object.
void	setName(String name) Please note that you almost never want to call this method in a client.
void	setPrimaryNamespace(MobyNamespace ns) This sets the namespace that will be used in toXML(), since in the XML representation for service execution, you can only have one namespace.
void	setProvisionInfo(MobyProvisionInfo info)
void	setXmlMode(int mode) Determined whether toXML will return a Central template value or a service call instance value.
String	toString() Convenience method to get the basic XML representation
String	toXML() Produces a full-blown XML fragment that depending on the value of getXmlMode() is either a template for use in MOBY Central services, or a Simple element for use in calling a service instance.

Methods inherited from class org.biomoby.shared.MobyPrimaryDataSimple

addNamespace, format, getDataType, getNamespaces, removeNamespace, removeNamespace, setDataType, setNamespaces

Methods inherited from class org.biomoby.shared.MobyPrimaryData

isPrimary

Methods inherited from class org.biomoby.shared.MobyData

getId, getName, getUserData, setUserData

Methods inherited from class java.lang.Object

getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface org.biomoby.shared.data.MobyDataInstance

getName, getUserData, setUserData

Constructor Detail

MobyDataObject

public MobyDataObject(Element element)
               throws MobyException

Construct the object using a DOM fragment.

Throws:

MobyException - if the element is not an Object tag, or is missing a required attribute

MobyDataObject

public MobyDataObject(Element element,
                      Registry registry)
               throws MobyException

Throws:

MobyException

MobyDataObject

public MobyDataObject(String name)

Constructor with no instance information, just a name (which can be blank). Instance information can be filled out later with setId() and setNamespace().

MobyDataObject

public MobyDataObject(String name,
                      Registry registry)

MobyDataObject

public MobyDataObject(String namespace,
                      String id)

Constructor convenient for a base object with a namespace and ID.

MobyDataObject

public MobyDataObject(String namespace,
                      String id,
                      Registry registry)

MobyDataObject

public MobyDataObject(MobyDataObject mobj)

Creates a base object with the same name, namespace and id as the input instance, as opposed to clone, which creates an exact copy of all the fields and the datatype.

Method Detail

createInstanceFromString

public static MobyDataObject createInstanceFromString(String typeName,
                                                      String value)
                                               throws MobyException

Construct a primitive data type instance from a string value. In the case of data type "Object", the value is used as the ID.

Throws:

MobyException - if the requested datatype is not a primtive, or the value could not be used for that data type (e.g an integer out of the string "Bar")

createInstanceFromString

public static MobyDataObject createInstanceFromString(String typeName,
                                                      String value,
                                                      Registry registry)
                                               throws MobyException

Throws:

MobyException

createInstanceFromDOM

public static MobyDataInstance createInstanceFromDOM(Element objectTag)
                                              throws MobyException

This method creates a MobyDataObject of the appropriate subclass for a given input XML tree (e.g. base objects like MobyDataObject and MobyDataInt, or complex objects like MobyDataDateTime or MobyDataComposite, or even a MobyDataSecondaryInstance). This method will also parse a MOBY XML Object wrapped in a Simple tag when the Simple is passed in as the main element.

Parameters:

objectTag - the W3C DOM Element node corresponding to the object's enclosing tag, or a Simple tag

Throws:

MobyException

createInstanceFromDOM

public static MobyDataInstance createInstanceFromDOM(Element objectTag,
                                                     Registry registry)
                                              throws MobyException

Throws:

MobyException

setName

public void setName(String name)

Please note that you almost never want to call this method in a client. The articleName of a MOBY Ontology object is normally fully determined by either the parameter name in the service being called (MobyContentInstance handles this), or the member field name when included as part of a composite object (MobyDataComposite handles this).

Specified by:

setName in interface MobyDataInstance

Overrides:

setName in class MobyData

getTextContents

public static String getTextContents(Element element)

Similar to DOM level 3 getTextContent, but only elements are excepted as input, and text inside children elements is not picked up. Actually calls MobyObjectDecompositionImpl.getTextContent()

getName

public static String getName(Element e)

Determine the name of the element if an enclosing tag (e.g. Simple or composite class) exists

getId

public static String getId(Element e)

createInstanceFromXML

public static MobyDataInstance createInstanceFromXML(String mobyXML)
                                              throws IllegalArgumentException

Similar to createObjectFromDOM(), but parses the XML for you using the JAXP parser discovery mechanism. NOT YET IMPLEMENTED.

Throws:

IllegalArgumentException

equals

public boolean equals(Object passedInObject)
               throws ClassCastException

Used to see if two objects are equivalent. If the passed in object is a MobyDataObject, its getObject() value will be used for the comparison. The namespace and ID are ignored, only the value is compared (such as a MobyDataInteger or Integer or BigInteger vs. a MobyDataInteger).

Overrides:

equals in class Object

Returns:

true if the values are equals according to the underlying Java object's equals() method

Throws:

ClassCastException - if and only if a child class or underlying Java object decides the comparison classes are invalid

compareTo

public int compareTo(Object o)

This method lexically compares in the order of value, ID, name if passed in object is a MobyDataObject. Otherwise it returns -1 (null fields get pushed to the end of the list). Child classes are encouraged to override this method for numerical comparison, etc. where appropriate, falling back to this method if the result is 0.

Specified by:

compareTo in interface Comparable

setXmlMode

public void setXmlMode(int mode)
                throws IllegalArgumentException

Determined whether toXML will return a Central template value or a service call instance value.

Specified by:

setXmlMode in interface MobyDataInstance

Parameters:

mode - one of MobyDataInstance.CENTRAL_XML_MODE or MobyDataInstance.SERVICE_XML_MODE

Throws:

IllegalArgumentException - if the mode is not one of the specified values

getXmlMode

public int getXmlMode()

Report whether toXML will produce Central template or service call instance XML.

Specified by:

getXmlMode in interface MobyDataInstance

Returns:

one of MobyDataInstance.CENTRAL_XML_MODE or MobyDataInstance.SERVICE_XML_MODE

getObject

public Object getObject()

Gives access to the Java object instance underlying the MobyData instance. For example, to change a MOBY String object, call ((StringBuffer) (data.getObject()).append("extra text to add to the end") In the case of a base Moby Object, there really is no underlying Java equivalent to return, so a java.lang.Object is returned for completeness's sake. possibly useful for notification events and pointer equivalency testing in derived classes such as MobyDataServiceAssocInstance?

Specified by:

getObject in interface MobyDataInstance

getValue

public String getValue()

A lexical (prefereably human readable) representation of the underlying object value (not including the namespace and ID). This value is used in sorting, and potentially for user interface elements such as tool tips and comment fields. For base objects, there is no underlying value (just a namespace and id), so the result is always a constant string "[Object]".

addCrossReferences

public void addCrossReferences(Element e)
                        throws MobyException

Throws:

MobyException

addCrossReferences

public void addCrossReferences(Element e,
                               Registry reg)
                        throws MobyException

Throws:

MobyException

addCrossReference

public void addCrossReference(MobyDataObject mdsi)
                       throws NullPointerException

Throws:

NullPointerException

getCrossReferences

public Collection getCrossReferences()

Call this method if you would like to modify the cross references, such as removing items, clearing the collection, etc. Be sure only to add MobyDataXref and MobyDataObject to the collecton or you'll have a type casting problem later! When we start requiring Java 1.5, this Collection will have a Generic template applied to it.

hasCrossReferences

public boolean hasCrossReferences()

addProvisionInfo

public void addProvisionInfo(Element e)
                      throws MobyException

Throws:

MobyException

setProvisionInfo

public void setProvisionInfo(MobyProvisionInfo info)

getProvisionInfo

public MobyProvisionInfo getProvisionInfo()

setId

public void setId(String value)

Used to set the data instance value based on an ID string. i.e. just an Object.

Overrides:

setId in class MobyData

toString

public String toString()

Convenience method to get the basic XML representation

Overrides:

toString in class MobyPrimaryDataSimple

Returns:

the raw XML representation of the object

clone

public MobyDataObject clone()

Simply calls new constructor with object's existing data type, name and value. Subclasses should override this method if more datafields need to be copied for an accurate clone of the Moby Data Instance (i.e. anything but a base object). The subclasses should ensure that they also return a MobyDataObject.

Overrides:

clone in class MobyPrimaryDataSimple

Returns:

an object of class MobyDataObject

setPrimaryNamespace

public void setPrimaryNamespace(MobyNamespace ns)

This sets the namespace that will be used in toXML(), since in the XML representation for service execution, you can only have one namespace. If this namespace is not already part of the namespaces for this object, it will be added. By default, if this method isn't called, the first namespace in the namespace array will be used, and in fact this method rearranges the array to have the desired effect.

getPrimaryNamespace

public MobyNamespace getPrimaryNamespace()

toXML

public String toXML()

Produces a full-blown XML fragment that depending on the value of getXmlMode() is either a template for use in MOBY Central services, or a Simple element for use in calling a service instance.

Specified by:

toXML in interface MobyDataInstance

Overrides:

toXML in class MobyPrimaryDataSimple

Returns:

the MOBY XML representation of the data instance