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java.lang.Objectuk.ac.vamsas.client.Vobject
uk.ac.vamsas.objects.core.DataSet
Class DataSet.
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 | |
DataSet()
|
Method Summary | |
void |
addAlignment(Alignment vAlignment)
|
void |
addAlignment(int index,
Alignment vAlignment)
|
void |
addDataSetAnnotations(DataSetAnnotations vDataSetAnnotations)
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void |
addDataSetAnnotations(int index,
DataSetAnnotations vDataSetAnnotations)
|
void |
addSequence(int index,
Sequence vSequence)
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void |
addSequence(Sequence vSequence)
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void |
addSequenceMapping(int index,
SequenceMapping vSequenceMapping)
|
void |
addSequenceMapping(SequenceMapping vSequenceMapping)
|
void |
addTree(int index,
Tree vTree)
|
void |
addTree(Tree vTree)
|
java.util.Enumeration |
enumerateAlignment()
Method enumerateAlignment. |
java.util.Enumeration |
enumerateDataSetAnnotations()
Method enumerateDataSetAnnotations. |
java.util.Enumeration |
enumerateSequence()
Method enumerateSequence. |
java.util.Enumeration |
enumerateSequenceMapping()
Method enumerateSequenceMapping. |
java.util.Enumeration |
enumerateTree()
Method enumerateTree. |
boolean |
equals(java.lang.Object obj)
Overrides the java.lang.Object.equals method. |
Alignment[] |
getAlignment()
Method getAlignment.Returns the contents of the collection in an Array. |
Alignment |
getAlignment(int index)
Method getAlignment. |
java.util.Vector |
getAlignmentAsReference()
Method getAlignmentAsReference.Returns a reference to '_alignmentList'. |
int |
getAlignmentCount()
Method getAlignmentCount. |
DataSetAnnotations[] |
getDataSetAnnotations()
Method getDataSetAnnotations.Returns the contents of the collection in an Array. |
DataSetAnnotations |
getDataSetAnnotations(int index)
Method getDataSetAnnotations. |
java.util.Vector |
getDataSetAnnotationsAsReference()
Method getDataSetAnnotationsAsReference.Returns a reference to '_dataSetAnnotationsList'. |
int |
getDataSetAnnotationsCount()
Method getDataSetAnnotationsCount. |
java.lang.String |
getId()
Returns the value of field 'id'. |
Provenance |
getProvenance()
Returns the value of field 'provenance'. |
Sequence[] |
getSequence()
Method getSequence.Returns the contents of the collection in an Array. |
Sequence |
getSequence(int index)
Method getSequence. |
java.util.Vector |
getSequenceAsReference()
Method getSequenceAsReference.Returns a reference to '_sequenceList'. |
int |
getSequenceCount()
Method getSequenceCount. |
SequenceMapping[] |
getSequenceMapping()
Method getSequenceMapping.Returns the contents of the collection in an Array. |
SequenceMapping |
getSequenceMapping(int index)
Method getSequenceMapping. |
java.util.Vector |
getSequenceMappingAsReference()
Method getSequenceMappingAsReference.Returns a reference to '_sequenceMappingList'. |
int |
getSequenceMappingCount()
Method getSequenceMappingCount. |
Tree[] |
getTree()
Method getTree.Returns the contents of the collection in an Array. |
Tree |
getTree(int index)
Method getTree. |
java.util.Vector |
getTreeAsReference()
Method getTreeAsReference.Returns a reference to '_treeList'. |
int |
getTreeCount()
Method getTreeCount. |
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 |
removeAlignment(Alignment vAlignment)
Method removeAlignment. |
Alignment |
removeAlignmentAt(int index)
Method removeAlignmentAt. |
void |
removeAllAlignment()
|
void |
removeAllDataSetAnnotations()
|
void |
removeAllSequence()
|
void |
removeAllSequenceMapping()
|
void |
removeAllTree()
|
boolean |
removeDataSetAnnotations(DataSetAnnotations vDataSetAnnotations)
Method removeDataSetAnnotations. |
DataSetAnnotations |
removeDataSetAnnotationsAt(int index)
Method removeDataSetAnnotationsAt. |
boolean |
removeSequence(Sequence vSequence)
Method removeSequence. |
Sequence |
removeSequenceAt(int index)
Method removeSequenceAt. |
boolean |
removeSequenceMapping(SequenceMapping vSequenceMapping)
Method removeSequenceMapping. |
SequenceMapping |
removeSequenceMappingAt(int index)
Method removeSequenceMappingAt. |
boolean |
removeTree(Tree vTree)
Method removeTree. |
Tree |
removeTreeAt(int index)
Method removeTreeAt. |
void |
setAlignment(Alignment[] vAlignmentArray)
|
void |
setAlignment(int index,
Alignment vAlignment)
|
void |
setAlignment(java.util.Vector vAlignmentList)
Sets the value of '_alignmentList' by copying the given Vector. |
void |
setAlignmentAsReference(java.util.Vector alignmentVector)
Deprecated. |
void |
setDataSetAnnotations(DataSetAnnotations[] vDataSetAnnotationsArray)
|
void |
setDataSetAnnotations(int index,
DataSetAnnotations vDataSetAnnotations)
|
void |
setDataSetAnnotations(java.util.Vector vDataSetAnnotationsList)
Sets the value of '_dataSetAnnotationsList' by copying the given Vector. |
void |
setDataSetAnnotationsAsReference(java.util.Vector dataSetAnnotationsVector)
Deprecated. |
void |
setId(java.lang.String id)
Sets the value of field 'id'. |
void |
setProvenance(Provenance provenance)
Sets the value of field 'provenance'. |
void |
setSequence(int index,
Sequence vSequence)
|
void |
setSequence(Sequence[] vSequenceArray)
|
void |
setSequence(java.util.Vector vSequenceList)
Sets the value of '_sequenceList' by copying the given Vector. |
void |
setSequenceAsReference(java.util.Vector sequenceVector)
Deprecated. |
void |
setSequenceMapping(int index,
SequenceMapping vSequenceMapping)
|
void |
setSequenceMapping(SequenceMapping[] vSequenceMappingArray)
|
void |
setSequenceMapping(java.util.Vector vSequenceMappingList)
Sets the value of '_sequenceMappingList' by copying the given Vector. |
void |
setSequenceMappingAsReference(java.util.Vector sequenceMappingVector)
Deprecated. |
void |
setTree(int index,
Tree vTree)
|
void |
setTree(Tree[] vTreeArray)
|
void |
setTree(java.util.Vector vTreeList)
Sets the value of '_treeList' by copying the given Vector. |
void |
setTreeAsReference(java.util.Vector treeVector)
Deprecated. |
static DataSet |
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 |
public DataSet()
Method Detail |
public void addAlignment(Alignment vAlignment) throws java.lang.IndexOutOfBoundsException
vAlignment
-
java.lang.IndexOutOfBoundsException
- if the index given is outside the bounds of the collectionpublic void addAlignment(int index, Alignment vAlignment) throws java.lang.IndexOutOfBoundsException
index
- vAlignment
-
java.lang.IndexOutOfBoundsException
- if the index given is outside the bounds of the collectionpublic void addDataSetAnnotations(DataSetAnnotations vDataSetAnnotations) throws java.lang.IndexOutOfBoundsException
vDataSetAnnotations
-
java.lang.IndexOutOfBoundsException
- if the index given is outside the bounds of the collectionpublic void addDataSetAnnotations(int index, DataSetAnnotations vDataSetAnnotations) throws java.lang.IndexOutOfBoundsException
index
- vDataSetAnnotations
-
java.lang.IndexOutOfBoundsException
- if the index given is outside the bounds of the collectionpublic void addSequence(Sequence vSequence) throws java.lang.IndexOutOfBoundsException
vSequence
-
java.lang.IndexOutOfBoundsException
- if the index given is outside the bounds of the collectionpublic void addSequence(int index, Sequence vSequence) throws java.lang.IndexOutOfBoundsException
index
- vSequence
-
java.lang.IndexOutOfBoundsException
- if the index given is outside the bounds of the collectionpublic void addSequenceMapping(SequenceMapping vSequenceMapping) throws java.lang.IndexOutOfBoundsException
vSequenceMapping
-
java.lang.IndexOutOfBoundsException
- if the index given is outside the bounds of the collectionpublic void addSequenceMapping(int index, SequenceMapping vSequenceMapping) throws java.lang.IndexOutOfBoundsException
index
- vSequenceMapping
-
java.lang.IndexOutOfBoundsException
- if the index given is outside the bounds of the collectionpublic void addTree(Tree vTree) throws java.lang.IndexOutOfBoundsException
vTree
-
java.lang.IndexOutOfBoundsException
- if the index given is outside the bounds of the collectionpublic void addTree(int index, Tree vTree) throws java.lang.IndexOutOfBoundsException
index
- vTree
-
java.lang.IndexOutOfBoundsException
- if the index given is outside the bounds of the collectionpublic java.util.Enumeration enumerateAlignment()
public java.util.Enumeration enumerateDataSetAnnotations()
public java.util.Enumeration enumerateSequence()
public java.util.Enumeration enumerateSequenceMapping()
public java.util.Enumeration enumerateTree()
public boolean equals(java.lang.Object obj)
obj
-
public Alignment getAlignment(int index) throws java.lang.IndexOutOfBoundsException
index
-
java.lang.IndexOutOfBoundsException
- if the index given is outside the bounds of the collectionpublic Alignment[] getAlignment()
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 getAlignmentAsReference()
public int getAlignmentCount()
public DataSetAnnotations getDataSetAnnotations(int index) throws java.lang.IndexOutOfBoundsException
index
-
java.lang.IndexOutOfBoundsException
- if the index given is outside the bounds of the collectionpublic DataSetAnnotations[] getDataSetAnnotations()
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 getDataSetAnnotationsAsReference()
public int getDataSetAnnotationsCount()
public java.lang.String getId()
public Provenance getProvenance()
public Sequence getSequence(int index) throws java.lang.IndexOutOfBoundsException
index
-
java.lang.IndexOutOfBoundsException
- if the index given is outside the bounds of the collectionpublic Sequence[] getSequence()
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 getSequenceAsReference()
public int getSequenceCount()
public SequenceMapping getSequenceMapping(int index) throws java.lang.IndexOutOfBoundsException
index
-
java.lang.IndexOutOfBoundsException
- if the index given is outside the bounds of the collectionpublic SequenceMapping[] getSequenceMapping()
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 getSequenceMappingAsReference()
public int getSequenceMappingCount()
public Tree getTree(int index) throws java.lang.IndexOutOfBoundsException
index
-
java.lang.IndexOutOfBoundsException
- if the index given is outside the bounds of the collectionpublic Tree[] getTree()
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 getTreeAsReference()
public int getTreeCount()
public int hashCode()
The following steps came from Effective Java Programming Language Guide by Joshua Bloch, Chapter 3
hashCode
in class Vobject
public boolean isValid()
public void marshal(java.io.Writer out) throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
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
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 removeAlignment(Alignment vAlignment)
vAlignment
-
public Alignment removeAlignmentAt(int index)
index
-
public void removeAllAlignment()
public void removeAllDataSetAnnotations()
public void removeAllSequence()
public void removeAllSequenceMapping()
public void removeAllTree()
public boolean removeDataSetAnnotations(DataSetAnnotations vDataSetAnnotations)
vDataSetAnnotations
-
public DataSetAnnotations removeDataSetAnnotationsAt(int index)
index
-
public boolean removeSequence(Sequence vSequence)
vSequence
-
public Sequence removeSequenceAt(int index)
index
-
public boolean removeSequenceMapping(SequenceMapping vSequenceMapping)
vSequenceMapping
-
public SequenceMapping removeSequenceMappingAt(int index)
index
-
public boolean removeTree(Tree vTree)
vTree
-
public Tree removeTreeAt(int index)
index
-
public void setAlignment(int index, Alignment vAlignment) throws java.lang.IndexOutOfBoundsException
index
- vAlignment
-
java.lang.IndexOutOfBoundsException
- if the index given is outside the bounds of the collectionpublic void setAlignment(Alignment[] vAlignmentArray)
vAlignmentArray
- public void setAlignment(java.util.Vector vAlignmentList)
vAlignmentList
- the Vector to copy.public void setAlignmentAsReference(java.util.Vector alignmentVector)
alignmentVector
- the Vector to set.public void setDataSetAnnotations(int index, DataSetAnnotations vDataSetAnnotations) throws java.lang.IndexOutOfBoundsException
index
- vDataSetAnnotations
-
java.lang.IndexOutOfBoundsException
- if the index given is outside the bounds of the collectionpublic void setDataSetAnnotations(DataSetAnnotations[] vDataSetAnnotationsArray)
vDataSetAnnotationsArray
- public void setDataSetAnnotations(java.util.Vector vDataSetAnnotationsList)
vDataSetAnnotationsList
- the Vector to copy.public void setDataSetAnnotationsAsReference(java.util.Vector dataSetAnnotationsVector)
dataSetAnnotationsVector
- the Vector to set.public void setId(java.lang.String id)
id
- the value of field 'id'.public void setProvenance(Provenance provenance)
provenance
- the value of field 'provenance'.public void setSequence(int index, Sequence vSequence) throws java.lang.IndexOutOfBoundsException
index
- vSequence
-
java.lang.IndexOutOfBoundsException
- if the index given is outside the bounds of the collectionpublic void setSequence(Sequence[] vSequenceArray)
vSequenceArray
- public void setSequence(java.util.Vector vSequenceList)
vSequenceList
- the Vector to copy.public void setSequenceAsReference(java.util.Vector sequenceVector)
sequenceVector
- the Vector to set.public void setSequenceMapping(int index, SequenceMapping vSequenceMapping) throws java.lang.IndexOutOfBoundsException
index
- vSequenceMapping
-
java.lang.IndexOutOfBoundsException
- if the index given is outside the bounds of the collectionpublic void setSequenceMapping(SequenceMapping[] vSequenceMappingArray)
vSequenceMappingArray
- public void setSequenceMapping(java.util.Vector vSequenceMappingList)
vSequenceMappingList
- the Vector to copy.public void setSequenceMappingAsReference(java.util.Vector sequenceMappingVector)
sequenceMappingVector
- the Vector to set.public void setTree(int index, Tree vTree) throws java.lang.IndexOutOfBoundsException
index
- vTree
-
java.lang.IndexOutOfBoundsException
- if the index given is outside the bounds of the collectionpublic void setTree(Tree[] vTreeArray)
vTreeArray
- public void setTree(java.util.Vector vTreeList)
vTreeList
- the Vector to copy.public void setTreeAsReference(java.util.Vector treeVector)
treeVector
- the Vector to set.public static DataSet 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
org.exolab.castor.xml.ValidationException
- if this object is an invalid instance according to the schema
|
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