uk.ac.vamsas.objects.core
Class AlignmentSequenceAnnotation

java.lang.Object
  extended byuk.ac.vamsas.client.Vobject
      extended byuk.ac.vamsas.objects.core.RangeType
          extended byuk.ac.vamsas.objects.core.RangeAnnotation
              extended byuk.ac.vamsas.objects.core.AlignmentSequenceAnnotation
All Implemented Interfaces:
java.io.Serializable

public class AlignmentSequenceAnnotation
extends RangeAnnotation
implements java.io.Serializable

Class AlignmentSequenceAnnotation.

Version:
$Revision$ $Date$
See Also:
Serialized Form

Field Summary
 
Fields inherited from class uk.ac.vamsas.client.Vobject
__added_since_last_read, __last_hash, __stored_in_document, __updated_since_last_read, __visited, __vorba, registerable, V_parent, vorbaId
 
Constructor Summary
AlignmentSequenceAnnotation()
           
 
Method Summary
 void deleteGraph()
           
 boolean equals(java.lang.Object obj)
          Overrides the java.lang.Object.equals method.
 boolean getGraph()
          Returns the value of field 'graph'.
 Provenance getProvenance()
          Returns the value of field 'provenance'.
 boolean hasGraph()
          Method hasGraph.
 int hashCode()
          Overrides the java.lang.Object.hashCode method.
 boolean isGraph()
          Returns the value of field 'graph'.
 boolean isValid()
          Method isValid.
 void marshal(org.xml.sax.ContentHandler handler)
           
 void marshal(java.io.Writer out)
           
 void setGraph(boolean graph)
          Sets the value of field 'graph'.
 void setProvenance(Provenance provenance)
          Sets the value of field 'provenance'.
static RangeType unmarshal(java.io.Reader reader)
          Method unmarshal.
 void validate()
           
 
Methods inherited from class uk.ac.vamsas.objects.core.RangeAnnotation
addAnnotationElement, addAnnotationElement, addLink, addLink, addProperty, addProperty, addScore, addScore, enumerateAnnotationElement, enumerateLink, enumerateProperty, enumerateScore, getAnnotationElement, getAnnotationElement, getAnnotationElementAsReference, getAnnotationElementCount, getDescription, getGroup, getId, getLabel, getLink, getLink, getLinkAsReference, getLinkCount, getModifiable, getProperty, getProperty, getPropertyAsReference, getPropertyCount, getScore, getScore, getScoreAsReference, getScoreCount, getStatus, getType, removeAllAnnotationElement, removeAllLink, removeAllProperty, removeAllScore, removeAnnotationElement, removeAnnotationElementAt, removeLink, removeLinkAt, removeProperty, removePropertyAt, removeScore, removeScoreAt, setAnnotationElement, setAnnotationElement, setAnnotationElement, setAnnotationElementAsReference, setDescription, setGroup, setId, setLabel, setLink, setLink, setLink, setLinkAsReference, setModifiable, setProperty, setProperty, setProperty, setPropertyAsReference, setScore, setScore, setScore, setScoreAsReference, setStatus, setType
 
Methods inherited from class uk.ac.vamsas.objects.core.RangeType
addPos, addPos, addSeg, addSeg, enumeratePos, enumerateSeg, getChoiceValue, getPos, getPos, getPosAsReference, getPosCount, getSeg, getSeg, getSegAsReference, getSegCount, removeAllPos, removeAllSeg, removePos, removePosAt, removeSeg, removeSegAt, setPos, setPos, setPos, setPosAsReference, setSeg, setSeg, setSeg, setSegAsReference
 
Methods inherited from class uk.ac.vamsas.client.Vobject
__callHash, __ensure_instance_ids, __ensure_instance_ids, __getInstanceIdField, __getLHash, __setFinalHash, __setInitHash, doHash, finalize, get__last_hash, getV_parent, getVorbaId, is__stored_in_document, isNewInDocument, isRegisterable, isRegistered, isUpdated, merge, set__added_since_last_read, set__stored_in_document, set__updated_since_last_read, setInstanceIdField, setRegisterable, setV_parent, setVorbaId
 
Methods inherited from class java.lang.Object
clone, getClass, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

AlignmentSequenceAnnotation

public AlignmentSequenceAnnotation()
Method Detail

deleteGraph

public void deleteGraph()

equals

public boolean equals(java.lang.Object obj)
Overrides the java.lang.Object.equals method.

Overrides:
equals in class RangeAnnotation
Parameters:
obj -
Returns:
true if the objects are equal.

getGraph

public boolean getGraph()
Returns the value of field 'graph'. The field 'graph' has the following description: TODO: decide if this flag is redundant - when true it would suggest that the annotationElement values together form a graph

Returns:
the value of field 'Graph'.

getProvenance

public Provenance getProvenance()
Returns the value of field 'provenance'.

Returns:
the value of field 'Provenance'.

hasGraph

public boolean hasGraph()
Method hasGraph.

Returns:
true if at least one Graph has been added

hashCode

public int hashCode()
Overrides the java.lang.Object.hashCode method.

The following steps came from Effective Java Programming Language Guide by Joshua Bloch, Chapter 3

Overrides:
hashCode in class RangeAnnotation
Returns:
a hash code value for the object.

isGraph

public boolean isGraph()
Returns the value of field 'graph'. The field 'graph' has the following description: TODO: decide if this flag is redundant - when true it would suggest that the annotationElement values together form a graph

Returns:
the value of field 'Graph'.

isValid

public boolean isValid()
Method isValid.

Overrides:
isValid in class RangeAnnotation
Returns:
true if this object is valid according to the schema

marshal

public void marshal(java.io.Writer out)
             throws org.exolab.castor.xml.MarshalException,
                    org.exolab.castor.xml.ValidationException
Overrides:
marshal in class RangeAnnotation
Parameters:
out -
Throws:
org.exolab.castor.xml.MarshalException - if object is null or if any SAXException is thrown during marshaling
org.exolab.castor.xml.ValidationException - if this object is an invalid instance according to the schema

marshal

public void marshal(org.xml.sax.ContentHandler handler)
             throws java.io.IOException,
                    org.exolab.castor.xml.MarshalException,
                    org.exolab.castor.xml.ValidationException
Overrides:
marshal in class RangeAnnotation
Parameters:
handler -
Throws:
java.io.IOException - if an IOException occurs during marshaling
org.exolab.castor.xml.ValidationException - if this object is an invalid instance according to the schema
org.exolab.castor.xml.MarshalException - if object is null or if any SAXException is thrown during marshaling

setGraph

public void setGraph(boolean graph)
Sets the value of field 'graph'. The field 'graph' has the following description: TODO: decide if this flag is redundant - when true it would suggest that the annotationElement values together form a graph

Parameters:
graph - the value of field 'graph'.

setProvenance

public void setProvenance(Provenance provenance)
Sets the value of field 'provenance'.

Parameters:
provenance - the value of field 'provenance'.

unmarshal

public static RangeType unmarshal(java.io.Reader reader)
                           throws org.exolab.castor.xml.MarshalException,
                                  org.exolab.castor.xml.ValidationException
Method unmarshal.

Parameters:
reader -
Returns:
the unmarshaled uk.ac.vamsas.objects.core.RangeType
Throws:
org.exolab.castor.xml.MarshalException - if object is null or if any SAXException is thrown during marshaling
org.exolab.castor.xml.ValidationException - if this object is an invalid instance according to the schema

validate

public void validate()
              throws org.exolab.castor.xml.ValidationException
Overrides:
validate in class RangeAnnotation
Throws:
org.exolab.castor.xml.ValidationException - if this object is an invalid instance according to the schema