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java.lang.Objectuk.ac.vamsas.client.Vobject
uk.ac.vamsas.objects.core.Alignment
Class 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 | |
Alignment()
|
Method Summary | |
void |
addAlignmentAnnotation(AlignmentAnnotation vAlignmentAnnotation)
|
void |
addAlignmentAnnotation(int index,
AlignmentAnnotation vAlignmentAnnotation)
|
void |
addAlignmentSequence(AlignmentSequence vAlignmentSequence)
|
void |
addAlignmentSequence(int index,
AlignmentSequence vAlignmentSequence)
|
void |
addProperty(int index,
Property vProperty)
|
void |
addProperty(Property vProperty)
|
void |
addTree(int index,
Tree vTree)
|
void |
addTree(Tree vTree)
|
void |
deleteAligned()
|
java.util.Enumeration |
enumerateAlignmentAnnotation()
Method enumerateAlignmentAnnotation. |
java.util.Enumeration |
enumerateAlignmentSequence()
Method enumerateAlignmentSequence. |
java.util.Enumeration |
enumerateProperty()
Method enumerateProperty. |
java.util.Enumeration |
enumerateTree()
Method enumerateTree. |
boolean |
equals(java.lang.Object obj)
Overrides the java.lang.Object.equals method. |
boolean |
getAligned()
Returns the value of field 'aligned'. |
AlignmentAnnotation[] |
getAlignmentAnnotation()
Method getAlignmentAnnotation.Returns the contents of the collection in an Array. |
AlignmentAnnotation |
getAlignmentAnnotation(int index)
Method getAlignmentAnnotation. |
java.util.Vector |
getAlignmentAnnotationAsReference()
Method getAlignmentAnnotationAsReference.Returns a reference to '_alignmentAnnotationList'. |
int |
getAlignmentAnnotationCount()
Method getAlignmentAnnotationCount. |
AlignmentSequence[] |
getAlignmentSequence()
Method getAlignmentSequence.Returns the contents of the collection in an Array. |
AlignmentSequence |
getAlignmentSequence(int index)
Method getAlignmentSequence. |
java.util.Vector |
getAlignmentSequenceAsReference()
Method getAlignmentSequenceAsReference.Returns a reference to '_alignmentSequenceList'. |
int |
getAlignmentSequenceCount()
Method getAlignmentSequenceCount. |
java.lang.String |
getGapChar()
Returns the value of field 'gapChar'. |
java.lang.String |
getId()
Returns the value of field 'id'. |
java.lang.String |
getModifiable()
Returns the value of field 'modifiable'. |
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. |
Provenance |
getProvenance()
Returns the value of field 'provenance'. |
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. |
boolean |
hasAligned()
Method hasAligned. |
int |
hashCode()
Overrides the java.lang.Object.hashCode method. |
boolean |
isAligned()
Returns the value of field 'aligned'. |
boolean |
isValid()
Method isValid. |
void |
marshal(org.xml.sax.ContentHandler handler)
|
void |
marshal(java.io.Writer out)
|
boolean |
removeAlignmentAnnotation(AlignmentAnnotation vAlignmentAnnotation)
Method removeAlignmentAnnotation. |
AlignmentAnnotation |
removeAlignmentAnnotationAt(int index)
Method removeAlignmentAnnotationAt. |
boolean |
removeAlignmentSequence(AlignmentSequence vAlignmentSequence)
Method removeAlignmentSequence. |
AlignmentSequence |
removeAlignmentSequenceAt(int index)
Method removeAlignmentSequenceAt. |
void |
removeAllAlignmentAnnotation()
|
void |
removeAllAlignmentSequence()
|
void |
removeAllProperty()
|
void |
removeAllTree()
|
boolean |
removeProperty(Property vProperty)
Method removeProperty. |
Property |
removePropertyAt(int index)
Method removePropertyAt. |
boolean |
removeTree(Tree vTree)
Method removeTree. |
Tree |
removeTreeAt(int index)
Method removeTreeAt. |
void |
setAligned(boolean aligned)
Sets the value of field 'aligned'. |
void |
setAlignmentAnnotation(AlignmentAnnotation[] vAlignmentAnnotationArray)
|
void |
setAlignmentAnnotation(int index,
AlignmentAnnotation vAlignmentAnnotation)
|
void |
setAlignmentAnnotation(java.util.Vector vAlignmentAnnotationList)
Sets the value of '_alignmentAnnotationList' by copying the given Vector. |
void |
setAlignmentAnnotationAsReference(java.util.Vector alignmentAnnotationVector)
Deprecated. |
void |
setAlignmentSequence(AlignmentSequence[] vAlignmentSequenceArray)
|
void |
setAlignmentSequence(int index,
AlignmentSequence vAlignmentSequence)
|
void |
setAlignmentSequence(java.util.Vector vAlignmentSequenceList)
Sets the value of '_alignmentSequenceList' by copying the given Vector. |
void |
setAlignmentSequenceAsReference(java.util.Vector alignmentSequenceVector)
Deprecated. |
void |
setGapChar(java.lang.String gapChar)
Sets the value of field 'gapChar'. |
void |
setId(java.lang.String id)
Sets the value of field 'id'. |
void |
setModifiable(java.lang.String modifiable)
Sets the value of field 'modifiable'. |
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 |
setProvenance(Provenance provenance)
Sets the value of field 'provenance'. |
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 Alignment |
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 Alignment()
Method Detail |
public void addAlignmentAnnotation(AlignmentAnnotation vAlignmentAnnotation) throws java.lang.IndexOutOfBoundsException
vAlignmentAnnotation
-
java.lang.IndexOutOfBoundsException
- if the index given is outside the bounds of the collectionpublic void addAlignmentAnnotation(int index, AlignmentAnnotation vAlignmentAnnotation) throws java.lang.IndexOutOfBoundsException
index
- vAlignmentAnnotation
-
java.lang.IndexOutOfBoundsException
- if the index given is outside the bounds of the collectionpublic void addAlignmentSequence(AlignmentSequence vAlignmentSequence) throws java.lang.IndexOutOfBoundsException
vAlignmentSequence
-
java.lang.IndexOutOfBoundsException
- if the index given is outside the bounds of the collectionpublic void addAlignmentSequence(int index, AlignmentSequence vAlignmentSequence) throws java.lang.IndexOutOfBoundsException
index
- vAlignmentSequence
-
java.lang.IndexOutOfBoundsException
- if the index given is outside the bounds of the collectionpublic void addProperty(Property vProperty) throws java.lang.IndexOutOfBoundsException
vProperty
-
java.lang.IndexOutOfBoundsException
- if the index given is outside the bounds of the collectionpublic void addProperty(int index, Property vProperty) throws java.lang.IndexOutOfBoundsException
index
- vProperty
-
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 void deleteAligned()
public java.util.Enumeration enumerateAlignmentAnnotation()
public java.util.Enumeration enumerateAlignmentSequence()
public java.util.Enumeration enumerateProperty()
public java.util.Enumeration enumerateTree()
public boolean equals(java.lang.Object obj)
obj
-
public boolean getAligned()
public AlignmentAnnotation getAlignmentAnnotation(int index) throws java.lang.IndexOutOfBoundsException
index
-
java.lang.IndexOutOfBoundsException
- if the index given is outside the bounds of the collectionpublic AlignmentAnnotation[] getAlignmentAnnotation()
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 getAlignmentAnnotationAsReference()
public int getAlignmentAnnotationCount()
public AlignmentSequence getAlignmentSequence(int index) throws java.lang.IndexOutOfBoundsException
index
-
java.lang.IndexOutOfBoundsException
- if the index given is outside the bounds of the collectionpublic AlignmentSequence[] getAlignmentSequence()
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 getAlignmentSequenceAsReference()
public int getAlignmentSequenceCount()
public java.lang.String getGapChar()
public java.lang.String getId()
public java.lang.String getModifiable()
public Property getProperty(int index) throws java.lang.IndexOutOfBoundsException
index
-
java.lang.IndexOutOfBoundsException
- if the index given is outside the bounds of the collectionpublic Property[] getProperty()
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 getPropertyAsReference()
public int getPropertyCount()
public Provenance getProvenance()
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 boolean hasAligned()
public int hashCode()
The following steps came from Effective Java Programming Language Guide by Joshua Bloch, Chapter 3
hashCode
in class Vobject
public boolean isAligned()
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 removeAlignmentAnnotation(AlignmentAnnotation vAlignmentAnnotation)
vAlignmentAnnotation
-
public AlignmentAnnotation removeAlignmentAnnotationAt(int index)
index
-
public boolean removeAlignmentSequence(AlignmentSequence vAlignmentSequence)
vAlignmentSequence
-
public AlignmentSequence removeAlignmentSequenceAt(int index)
index
-
public void removeAllAlignmentAnnotation()
public void removeAllAlignmentSequence()
public void removeAllProperty()
public void removeAllTree()
public boolean removeProperty(Property vProperty)
vProperty
-
public Property removePropertyAt(int index)
index
-
public boolean removeTree(Tree vTree)
vTree
-
public Tree removeTreeAt(int index)
index
-
public void setAligned(boolean aligned)
aligned
- the value of field 'aligned'.public void setAlignmentAnnotation(int index, AlignmentAnnotation vAlignmentAnnotation) throws java.lang.IndexOutOfBoundsException
index
- vAlignmentAnnotation
-
java.lang.IndexOutOfBoundsException
- if the index given is outside the bounds of the collectionpublic void setAlignmentAnnotation(AlignmentAnnotation[] vAlignmentAnnotationArray)
vAlignmentAnnotationArray
- public void setAlignmentAnnotation(java.util.Vector vAlignmentAnnotationList)
vAlignmentAnnotationList
- the Vector to copy.public void setAlignmentAnnotationAsReference(java.util.Vector alignmentAnnotationVector)
alignmentAnnotationVector
- the Vector to set.public void setAlignmentSequence(int index, AlignmentSequence vAlignmentSequence) throws java.lang.IndexOutOfBoundsException
index
- vAlignmentSequence
-
java.lang.IndexOutOfBoundsException
- if the index given is outside the bounds of the collectionpublic void setAlignmentSequence(AlignmentSequence[] vAlignmentSequenceArray)
vAlignmentSequenceArray
- public void setAlignmentSequence(java.util.Vector vAlignmentSequenceList)
vAlignmentSequenceList
- the Vector to copy.public void setAlignmentSequenceAsReference(java.util.Vector alignmentSequenceVector)
alignmentSequenceVector
- the Vector to set.public void setGapChar(java.lang.String gapChar)
gapChar
- the value of field 'gapChar'.public void setId(java.lang.String id)
id
- the value of field 'id'.public void setModifiable(java.lang.String modifiable)
modifiable
- the value of field 'modifiable'.public void setProperty(int index, Property vProperty) throws java.lang.IndexOutOfBoundsException
index
- vProperty
-
java.lang.IndexOutOfBoundsException
- if the index given is outside the bounds of the collectionpublic void setProperty(Property[] vPropertyArray)
vPropertyArray
- public void setProperty(java.util.Vector vPropertyList)
vPropertyList
- the Vector to copy.public void setPropertyAsReference(java.util.Vector propertyVector)
propertyVector
- the Vector to set.public void setProvenance(Provenance provenance)
provenance
- the value of field 'provenance'.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 Alignment 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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