uk.ac.vamsas.objects.core
Class SequenceType

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

public class SequenceType
extends Vobject
implements java.io.Serializable

Class SequenceType.

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
SequenceType()
           
 
Method Summary
 void addProperty(int index, Property vProperty)
           
 void addProperty(Property vProperty)
           
 void deleteEnd()
           
 void deleteStart()
           
 java.util.Enumeration enumerateProperty()
          Method enumerateProperty.
 boolean equals(java.lang.Object obj)
          Overrides the java.lang.Object.equals method.
 java.lang.String getDescription()
          Returns the value of field 'description'.
 long getEnd()
          Returns the value of field 'end'.
 java.lang.String getName()
          Returns the value of field 'name'.
 Property[] getProperty()
          Method getProperty.Returns the contents of the collection in an Array.
 Property getProperty(int index)
          Method getProperty.
 java.util.Vector getPropertyAsReference()
          Method getPropertyAsReference.Returns a reference to '_propertyList'.
 int getPropertyCount()
          Method getPropertyCount.
 java.lang.String getSequence()
          Returns the value of field 'sequence'.
 long getStart()
          Returns the value of field 'start'.
 boolean hasEnd()
          Method hasEnd.
 int hashCode()
          Overrides the java.lang.Object.hashCode method.
 boolean hasStart()
          Method hasStart.
 boolean isValid()
          Method isValid.
 void marshal(org.xml.sax.ContentHandler handler)
           
 void marshal(java.io.Writer out)
           
 void removeAllProperty()
           
 boolean removeProperty(Property vProperty)
          Method removeProperty.
 Property removePropertyAt(int index)
          Method removePropertyAt.
 void setDescription(java.lang.String description)
          Sets the value of field 'description'.
 void setEnd(long end)
          Sets the value of field 'end'.
 void setName(java.lang.String name)
          Sets the value of field 'name'.
 void setProperty(int index, Property vProperty)
           
 void setProperty(Property[] vPropertyArray)
           
 void setProperty(java.util.Vector vPropertyList)
          Sets the value of '_propertyList' by copying the given Vector.
 void setPropertyAsReference(java.util.Vector propertyVector)
          Deprecated.  
 void setSequence(java.lang.String sequence)
          Sets the value of field 'sequence'.
 void setStart(long start)
          Sets the value of field 'start'.
static SequenceType unmarshal(java.io.Reader reader)
          Method unmarshal.
 void validate()
           
 
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

SequenceType

public SequenceType()
Method Detail

addProperty

public void addProperty(Property vProperty)
                 throws java.lang.IndexOutOfBoundsException
Parameters:
vProperty -
Throws:
java.lang.IndexOutOfBoundsException - if the index given is outside the bounds of the collection

addProperty

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

deleteEnd

public void deleteEnd()

deleteStart

public void deleteStart()

enumerateProperty

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

Returns:
an Enumeration over all uk.ac.vamsas.objects.core.Property elements

equals

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

Parameters:
obj -
Returns:
true if the objects are equal.

getDescription

public java.lang.String getDescription()
Returns the value of field 'description'.

Returns:
the value of field 'Description'.

getEnd

public long getEnd()
Returns the value of field 'end'.

Returns:
the value of field 'End'.

getName

public java.lang.String getName()
Returns the value of field 'name'.

Returns:
the value of field 'Name'.

getProperty

public Property getProperty(int index)
                     throws java.lang.IndexOutOfBoundsException
Method getProperty.

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

getProperty

public Property[] getProperty()
Method getProperty.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

getPropertyAsReference

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

Returns:
a reference to the Vector backing this class

getPropertyCount

public int getPropertyCount()
Method getPropertyCount.

Returns:
the size of this collection

getSequence

public java.lang.String getSequence()
Returns the value of field 'sequence'.

Returns:
the value of field 'Sequence'.

getStart

public long getStart()
Returns the value of field 'start'.

Returns:
the value of field 'Start'.

hasEnd

public boolean hasEnd()
Method hasEnd.

Returns:
true if at least one End has been added

hasStart

public boolean hasStart()
Method hasStart.

Returns:
true if at least one Start 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 Vobject
Returns:
a hash code value for the object.

isValid

public boolean isValid()
Method isValid.

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
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
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

removeAllProperty

public void removeAllProperty()

removeProperty

public boolean removeProperty(Property vProperty)
Method removeProperty.

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

removePropertyAt

public Property removePropertyAt(int index)
Method removePropertyAt.

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

setDescription

public void setDescription(java.lang.String description)
Sets the value of field 'description'.

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

setEnd

public void setEnd(long end)
Sets the value of field 'end'.

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

setName

public void setName(java.lang.String name)
Sets the value of field 'name'.

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

setProperty

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

setProperty

public void setProperty(Property[] vPropertyArray)
Parameters:
vPropertyArray -

setProperty

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

Parameters:
vPropertyList - the Vector to copy.

setPropertyAsReference

public void setPropertyAsReference(java.util.Vector propertyVector)
Deprecated.  

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

Parameters:
propertyVector - the Vector to set.

setSequence

public void setSequence(java.lang.String sequence)
Sets the value of field 'sequence'.

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

setStart

public void setStart(long start)
Sets the value of field 'start'.

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

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