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java.lang.Objectuk.ac.vamsas.client.Vobject
uk.ac.vamsas.objects.core.RangeType
uk.ac.vamsas.objects.core.RangeAnnotation
uk.ac.vamsas.objects.core.AlignmentAnnotation
This is annotation over the coordinate frame defined by all the columns in the alignment.
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 | |
AlignmentAnnotation()
|
Method Summary | |
void |
addSeqrefs(int index,
java.lang.Object vSeqrefs)
|
void |
addSeqrefs(java.lang.Object vSeqrefs)
|
void |
deleteGraph()
|
java.util.Enumeration |
enumerateSeqrefs()
Method enumerateSeqrefs. |
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'. |
java.lang.Object[] |
getSeqrefs()
Method getSeqrefs.Returns the contents of the collection in an Array. |
java.lang.Object |
getSeqrefs(int index)
Method getSeqrefs. |
java.util.Vector |
getSeqrefsAsReference()
Method getSeqrefsAsReference.Returns a reference to '_seqrefs'. |
int |
getSeqrefsCount()
Method getSeqrefsCount. |
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 |
removeAllSeqrefs()
|
boolean |
removeSeqrefs(java.lang.Object vSeqrefs)
Method removeSeqrefs. |
java.lang.Object |
removeSeqrefsAt(int index)
Method removeSeqrefsAt. |
void |
setGraph(boolean graph)
Sets the value of field 'graph'. |
void |
setProvenance(Provenance provenance)
Sets the value of field 'provenance'. |
void |
setSeqrefs(int index,
java.lang.Object vSeqrefs)
|
void |
setSeqrefs(java.lang.Object[] vSeqrefsArray)
|
void |
setSeqrefs(java.util.Vector vSeqrefsList)
Sets the value of '_seqrefs' by copying the given Vector. |
void |
setSeqrefsAsReference(java.util.Vector seqrefsVector)
Deprecated. |
static RangeType |
unmarshal(java.io.Reader reader)
Method unmarshal. |
void |
validate()
|
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 |
public AlignmentAnnotation()
Method Detail |
public void addSeqrefs(java.lang.Object vSeqrefs) throws java.lang.IndexOutOfBoundsException
vSeqrefs
-
java.lang.IndexOutOfBoundsException
- if the index given is outside the bounds of the collectionpublic void addSeqrefs(int index, java.lang.Object vSeqrefs) throws java.lang.IndexOutOfBoundsException
index
- vSeqrefs
-
java.lang.IndexOutOfBoundsException
- if the index given is outside the bounds of the collectionpublic void deleteGraph()
public java.util.Enumeration enumerateSeqrefs()
public boolean equals(java.lang.Object obj)
equals
in class RangeAnnotation
obj
-
public boolean getGraph()
public Provenance getProvenance()
public java.lang.Object getSeqrefs(int index) throws java.lang.IndexOutOfBoundsException
index
-
java.lang.IndexOutOfBoundsException
- if the index given is outside the bounds of the collectionpublic java.lang.Object[] getSeqrefs()
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 getSeqrefsAsReference()
public int getSeqrefsCount()
public boolean hasGraph()
public int hashCode()
The following steps came from Effective Java Programming Language Guide by Joshua Bloch, Chapter 3
hashCode
in class RangeAnnotation
public boolean isGraph()
public boolean isValid()
isValid
in class RangeAnnotation
public void marshal(java.io.Writer out) throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
marshal
in class RangeAnnotation
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 RangeAnnotation
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 void removeAllSeqrefs()
public boolean removeSeqrefs(java.lang.Object vSeqrefs)
vSeqrefs
-
public java.lang.Object removeSeqrefsAt(int index)
index
-
public void setGraph(boolean graph)
graph
- the value of field 'graph'.public void setProvenance(Provenance provenance)
provenance
- the value of field 'provenance'.public void setSeqrefs(int index, java.lang.Object vSeqrefs) throws java.lang.IndexOutOfBoundsException
index
- vSeqrefs
-
java.lang.IndexOutOfBoundsException
- if the index given is outside the bounds of the collectionpublic void setSeqrefs(java.lang.Object[] vSeqrefsArray)
vSeqrefsArray
- public void setSeqrefs(java.util.Vector vSeqrefsList)
vSeqrefsList
- the Vector to copy.public void setSeqrefsAsReference(java.util.Vector seqrefsVector)
seqrefsVector
- the Vector to set.public static RangeType 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 RangeAnnotation
org.exolab.castor.xml.ValidationException
- if this object is an invalid instance according to the schema
|
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