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java.lang.Objectuk.ac.vamsas.client.Vobject
uk.ac.vamsas.objects.core.SequenceType
uk.ac.vamsas.objects.core.AlignmentSequence
Class AlignmentSequence.
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 |
public AlignmentSequence()
Method Detail |
public void addAlignmentSequenceAnnotation(AlignmentSequenceAnnotation vAlignmentSequenceAnnotation) throws java.lang.IndexOutOfBoundsException
vAlignmentSequenceAnnotation
-
java.lang.IndexOutOfBoundsException
- if the index given is outside the bounds of the collectionpublic void addAlignmentSequenceAnnotation(int index, AlignmentSequenceAnnotation vAlignmentSequenceAnnotation) throws java.lang.IndexOutOfBoundsException
index
- vAlignmentSequenceAnnotation
-
java.lang.IndexOutOfBoundsException
- if the index given is outside the bounds of the collectionpublic java.util.Enumeration enumerateAlignmentSequenceAnnotation()
public boolean equals(java.lang.Object obj)
equals
in class SequenceType
obj
-
public AlignmentSequenceAnnotation getAlignmentSequenceAnnotation(int index) throws java.lang.IndexOutOfBoundsException
index
-
java.lang.IndexOutOfBoundsException
- if the index given is outside the bounds of the collectionpublic AlignmentSequenceAnnotation[] getAlignmentSequenceAnnotation()
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.
public java.util.Vector getAlignmentSequenceAnnotationAsReference()
public int getAlignmentSequenceAnnotationCount()
public java.lang.String getId()
public java.lang.Object getRefid()
public int hashCode()
The following steps came from Effective Java Programming Language Guide by Joshua Bloch, Chapter 3
hashCode
in class SequenceType
public boolean isValid()
isValid
in class SequenceType
public void marshal(java.io.Writer out) throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
marshal
in class SequenceType
out
-
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 schemapublic void marshal(org.xml.sax.ContentHandler handler) throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
marshal
in class SequenceType
handler
-
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
marshalingpublic boolean removeAlignmentSequenceAnnotation(AlignmentSequenceAnnotation vAlignmentSequenceAnnotation)
vAlignmentSequenceAnnotation
-
public AlignmentSequenceAnnotation removeAlignmentSequenceAnnotationAt(int index)
index
-
public void removeAllAlignmentSequenceAnnotation()
public void setAlignmentSequenceAnnotation(int index, AlignmentSequenceAnnotation vAlignmentSequenceAnnotation) throws java.lang.IndexOutOfBoundsException
index
- vAlignmentSequenceAnnotation
-
java.lang.IndexOutOfBoundsException
- if the index given is outside the bounds of the collectionpublic void setAlignmentSequenceAnnotation(AlignmentSequenceAnnotation[] vAlignmentSequenceAnnotationArray)
vAlignmentSequenceAnnotationArray
- public void setAlignmentSequenceAnnotation(java.util.Vector vAlignmentSequenceAnnotationList)
vAlignmentSequenceAnnotationList
- the Vector to copy.public void setAlignmentSequenceAnnotationAsReference(java.util.Vector alignmentSequenceAnnotationVector)
alignmentSequenceAnnotationVector
- the Vector to set.public void setId(java.lang.String id)
id
- the value of field 'id'.public void setRefid(java.lang.Object refid)
refid
- the value of field 'refid'.public static SequenceType unmarshal(java.io.Reader reader) throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
reader
-
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 schemapublic void validate() throws org.exolab.castor.xml.ValidationException
validate
in class SequenceType
org.exolab.castor.xml.ValidationException
- if this object is an invalid instance according to the schema
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