uk.ac.vamsas.objects.core
Class AlignmentSequence

java.lang.Object
  extended byuk.ac.vamsas.client.Vobject
      extended byuk.ac.vamsas.objects.core.SequenceType
          extended byuk.ac.vamsas.objects.core.AlignmentSequence
All Implemented Interfaces:
java.io.Serializable

public class AlignmentSequence
extends SequenceType
implements java.io.Serializable

Class AlignmentSequence.

Version:
$Revision: 496 $ $Date: 2007-06-28 14:51:44 +0100 (Thu, 28 Jun 2007) $
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
AlignmentSequence()
           
 
Method Summary
 void addAlignmentSequenceAnnotation(AlignmentSequenceAnnotation vAlignmentSequenceAnnotation)
           
 void addAlignmentSequenceAnnotation(int index, AlignmentSequenceAnnotation vAlignmentSequenceAnnotation)
           
 java.util.Enumeration enumerateAlignmentSequenceAnnotation()
          Method enumerateAlignmentSequenceAnnotation.
 boolean equals(java.lang.Object obj)
          Overrides the java.lang.Object.equals method.
 AlignmentSequenceAnnotation[] getAlignmentSequenceAnnotation()
          Method getAlignmentSequenceAnnotation.Returns the contents of the collection in an Array.
 AlignmentSequenceAnnotation getAlignmentSequenceAnnotation(int index)
          Method getAlignmentSequenceAnnotation.
 java.util.Vector getAlignmentSequenceAnnotationAsReference()
          Method getAlignmentSequenceAnnotationAsReference.Returns a reference to '_alignmentSequenceAnnotationList'.
 int getAlignmentSequenceAnnotationCount()
          Method getAlignmentSequenceAnnotationCount.
 java.lang.String getId()
          Returns the value of field 'id'.
 java.lang.Object getRefid()
          Returns the value of field 'refid'.
 int hashCode()
          Overrides the java.lang.Object.hashCode method.
 boolean isValid()
          Method isValid.
 void marshal(org.xml.sax.ContentHandler handler)
           
 void marshal(java.io.Writer out)
           
 boolean removeAlignmentSequenceAnnotation(AlignmentSequenceAnnotation vAlignmentSequenceAnnotation)
          Method removeAlignmentSequenceAnnotation.
 AlignmentSequenceAnnotation removeAlignmentSequenceAnnotationAt(int index)
          Method removeAlignmentSequenceAnnotationAt.
 void removeAllAlignmentSequenceAnnotation()
           
 void setAlignmentSequenceAnnotation(AlignmentSequenceAnnotation[] vAlignmentSequenceAnnotationArray)
           
 void setAlignmentSequenceAnnotation(int index, AlignmentSequenceAnnotation vAlignmentSequenceAnnotation)
           
 void setAlignmentSequenceAnnotation(java.util.Vector vAlignmentSequenceAnnotationList)
          Sets the value of '_alignmentSequenceAnnotationList' by copying the given Vector.
 void setAlignmentSequenceAnnotationAsReference(java.util.Vector alignmentSequenceAnnotationVector)
          Deprecated.  
 void setId(java.lang.String id)
          Sets the value of field 'id'.
 void setRefid(java.lang.Object refid)
          Sets the value of field 'refid'.
static SequenceType unmarshal(java.io.Reader reader)
          Method unmarshal.
 void validate()
           
 
Methods inherited from class uk.ac.vamsas.objects.core.SequenceType
addProperty, addProperty, deleteEnd, deleteStart, enumerateProperty, getDescription, getEnd, getName, getProperty, getProperty, getPropertyAsReference, getPropertyCount, getSequence, getStart, hasEnd, hasStart, removeAllProperty, removeProperty, removePropertyAt, setDescription, setEnd, setName, setProperty, setProperty, setProperty, setPropertyAsReference, setSequence, setStart
 
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

AlignmentSequence

public AlignmentSequence()
Method Detail

addAlignmentSequenceAnnotation

public void addAlignmentSequenceAnnotation(AlignmentSequenceAnnotation vAlignmentSequenceAnnotation)
                                    throws java.lang.IndexOutOfBoundsException
Parameters:
vAlignmentSequenceAnnotation -
Throws:
java.lang.IndexOutOfBoundsException - if the index given is outside the bounds of the collection

addAlignmentSequenceAnnotation

public void addAlignmentSequenceAnnotation(int index,
                                           AlignmentSequenceAnnotation vAlignmentSequenceAnnotation)
                                    throws java.lang.IndexOutOfBoundsException
Parameters:
index -
vAlignmentSequenceAnnotation -
Throws:
java.lang.IndexOutOfBoundsException - if the index given is outside the bounds of the collection

enumerateAlignmentSequenceAnnotation

public java.util.Enumeration enumerateAlignmentSequenceAnnotation()
Method enumerateAlignmentSequenceAnnotation.

Returns:
an Enumeration over all uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation element

equals

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

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

getAlignmentSequenceAnnotation

public AlignmentSequenceAnnotation getAlignmentSequenceAnnotation(int index)
                                                           throws java.lang.IndexOutOfBoundsException
Method getAlignmentSequenceAnnotation.

Parameters:
index -
Returns:
the value of the uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation at the given index
Throws:
java.lang.IndexOutOfBoundsException - if the index given is outside the bounds of the collection

getAlignmentSequenceAnnotation

public AlignmentSequenceAnnotation[] getAlignmentSequenceAnnotation()
Method getAlignmentSequenceAnnotation.Returns the contents of the collection in an Array.

Note: Just in case the collection contents are changing in another thread, we pass a 0-length Array of the correct type into the API call. This way we know that the Array returned is of exactly the correct length.

Returns:
this collection as an Array

getAlignmentSequenceAnnotationAsReference

public java.util.Vector getAlignmentSequenceAnnotationAsReference()
Method getAlignmentSequenceAnnotationAsReference.Returns a reference to '_alignmentSequenceAnnotationList'. No type checking is performed on any modifications to the Vector.

Returns:
a reference to the Vector backing this class

getAlignmentSequenceAnnotationCount

public int getAlignmentSequenceAnnotationCount()
Method getAlignmentSequenceAnnotationCount.

Returns:
the size of this collection

getId

public java.lang.String getId()
Returns the value of field 'id'. The field 'id' has the following description: Primary Key for vamsas object referencing

Returns:
the value of field 'Id'.

getRefid

public java.lang.Object getRefid()
Returns the value of field 'refid'. The field 'refid' has the following description: Dataset Sequence from which this alignment sequence is taken from

Returns:
the value of field 'Refid'.

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 SequenceType
Returns:
a hash code value for the object.

isValid

public boolean isValid()
Method isValid.

Overrides:
isValid in class SequenceType
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 SequenceType
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 SequenceType
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

removeAlignmentSequenceAnnotation

public boolean removeAlignmentSequenceAnnotation(AlignmentSequenceAnnotation vAlignmentSequenceAnnotation)
Method removeAlignmentSequenceAnnotation.

Parameters:
vAlignmentSequenceAnnotation -
Returns:
true if the object was removed from the collection.

removeAlignmentSequenceAnnotationAt

public AlignmentSequenceAnnotation removeAlignmentSequenceAnnotationAt(int index)
Method removeAlignmentSequenceAnnotationAt.

Parameters:
index -
Returns:
the element removed from the collection

removeAllAlignmentSequenceAnnotation

public void removeAllAlignmentSequenceAnnotation()

setAlignmentSequenceAnnotation

public void setAlignmentSequenceAnnotation(int index,
                                           AlignmentSequenceAnnotation vAlignmentSequenceAnnotation)
                                    throws java.lang.IndexOutOfBoundsException
Parameters:
index -
vAlignmentSequenceAnnotation -
Throws:
java.lang.IndexOutOfBoundsException - if the index given is outside the bounds of the collection

setAlignmentSequenceAnnotation

public void setAlignmentSequenceAnnotation(AlignmentSequenceAnnotation[] vAlignmentSequenceAnnotationArray)
Parameters:
vAlignmentSequenceAnnotationArray -

setAlignmentSequenceAnnotation

public void setAlignmentSequenceAnnotation(java.util.Vector vAlignmentSequenceAnnotationList)
Sets the value of '_alignmentSequenceAnnotationList' by copying the given Vector. All elements will be checked for type safety.

Parameters:
vAlignmentSequenceAnnotationList - the Vector to copy.

setAlignmentSequenceAnnotationAsReference

public void setAlignmentSequenceAnnotationAsReference(java.util.Vector alignmentSequenceAnnotationVector)
Deprecated.  

Sets the value of '_alignmentSequenceAnnotationList' by setting it to the given Vector. No type checking is performed.

Parameters:
alignmentSequenceAnnotationVector - the Vector to set.

setId

public void setId(java.lang.String id)
Sets the value of field 'id'. The field 'id' has the following description: Primary Key for vamsas object referencing

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

setRefid

public void setRefid(java.lang.Object refid)
Sets the value of field 'refid'. The field 'refid' has the following description: Dataset Sequence from which this alignment sequence is taken from

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

unmarshal

public static SequenceType 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.SequenceTyp
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 SequenceType
Throws:
org.exolab.castor.xml.ValidationException - if this object is an invalid instance according to the schema