* to a specified ClientHandle's information.
*/
public class ClientDocument implements IClientDocument {
- /* (non-Javadoc)
+ IClient vorba;
+ /* (non-Javadoc)
* @see org.vamsas.client.IClientDocument#getApplicationData()
*/
public byte[] getApplicationData() {
- // TODO Auto-generated method stub
+ // Look up client byte stash using client and user handle
+
return null;
}
/* (non-Javadoc)
* @see org.vamsas.client.IClientDocument#getObject(org.vamsas.client.VorbaId)
*/
public object getObject(VorbaId id) {
- // TODO Auto-generated method stub
+ // look up id in document object
+ // retrieve object and return
return null;
}
/* (non-Javadoc)
* @see org.vamsas.client.IClientDocument#getObjects(org.vamsas.client.VorbaId[])
*/
public object[] getObjects(VorbaId[] ids) {
- // TODO Auto-generated method stub
+ // getObject in bulk
return null;
}
/* (non-Javadoc)
* @see org.vamsas.client.IClientDocument#getVamsasRoots()
*/
public object[] getVamsasRoots() {
- // TODO Auto-generated method stub
+ // extract root objects
return null;
}
/* (non-Javadoc)
-- listing properties --
-org.vamsas.objects.core.ProvenanceItem=org.vamsas.objects.core.ProvenanceIte...
-org.vamsas.objects.core.AlignmentAnnotations=org.vamsas.objects.core.AlignmentAnno...
org.vamsas.objects.core.Tree=org.vamsas.objects.core.TreeDescriptor
-org.vamsas.objects.core.Sequence=org.vamsas.objects.core.SequenceDescr...
+org.vamsas.objects.core.Provenance=org.vamsas.objects.core.ProvenanceDes...
+org.vamsas.objects.core.SequenceType=org.vamsas.objects.core.SequenceTypeD...
+org.vamsas.objects.core.ProvenanceItem=org.vamsas.objects.core.ProvenanceIte...
+org.vamsas.objects.core.TreeType=org.vamsas.objects.core.TreeTypeDescr...
org.vamsas.objects.core.AnnotationElement=org.vamsas.objects.core.AnnotationEle...
+org.vamsas.objects.core.AlignmentSequence=org.vamsas.objects.core.AlignmentSequ...
+org.vamsas.objects.core.Alignment=org.vamsas.objects.core.AlignmentDesc...
+org.vamsas.objects.core.DbRef=org.vamsas.objects.core.DbRefDescriptor
+org.vamsas.objects.core.SequenceSetAnnotations=org.vamsas.objects.core.SequenceSetAn...
+org.vamsas.objects.core.Application=org.vamsas.objects.core.ApplicationDe...
+org.vamsas.objects.core.VAMSAS=org.vamsas.objects.core.VAMSASDescriptor
+org.vamsas.objects.core.Sequence=org.vamsas.objects.core.SequenceDescr...
org.vamsas.objects.core.LockFile=org.vamsas.objects.core.LockFileDescr...
org.vamsas.objects.core.Entry=org.vamsas.objects.core.EntryDescriptor
-org.vamsas.objects.core.SequenceType=org.vamsas.objects.core.SequenceTypeD...
-org.vamsas.objects.core.VAMSAS=org.vamsas.objects.core.VAMSASDescriptor
org.vamsas.objects.core.SequenceSet=org.vamsas.objects.core.SequenceSetDe...
-org.vamsas.objects.core.DbRef=org.vamsas.objects.core.DbRefDescriptor
org.vamsas.objects.core.ApplicationData=org.vamsas.objects.core.ApplicationDa...
-org.vamsas.objects.core.Application=org.vamsas.objects.core.ApplicationDe...
-org.vamsas.objects.core.Provenance=org.vamsas.objects.core.ProvenanceDes...
-org.vamsas.objects.core.AlignmentSequence=org.vamsas.objects.core.AlignmentSequ...
-org.vamsas.objects.core.Alignment=org.vamsas.objects.core.AlignmentDesc...
-org.vamsas.objects.core.SequenceSetAnnotations=org.vamsas.objects.core.SequenceSetAn...
+org.vamsas.objects.core.AlignmentAnnotations=org.vamsas.objects.core.AlignmentAnno...
+org.vamsas.objects.core.Dendro=org.vamsas.objects.core.DendroDescriptor
/*
* This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M1</a>, using an XML
+ * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
* Schema.
* $Id$
*/
/*
* This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M1</a>, using an XML
+ * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
* Schema.
* $Id$
*/
private boolean _has_graph;
/**
+ * Field _id
+ */
+ private java.lang.String _id;
+
+ /**
* Field _annotationElementList
*/
private java.util.Vector _annotationElementList;
return false;
if (this._has_graph != temp._has_graph)
return false;
+ if (this._id != null) {
+ if (temp._id == null) return false;
+ else if (!(this._id.equals(temp._id)))
+ return false;
+ }
+ else if (temp._id != null)
+ return false;
if (this._annotationElementList != null) {
if (temp._annotationElementList == null) return false;
else if (!(this._annotationElementList.equals(temp._annotationElementList)))
} //-- boolean getGraph()
/**
+ * Returns the value of field 'id'.
+ *
+ * @return String
+ * @return the value of field 'id'.
+ */
+ public java.lang.String getId()
+ {
+ return this._id;
+ } //-- java.lang.String getId()
+
+ /**
* Returns the value of field 'label'.
*
* @return String
} //-- void setGraph(boolean)
/**
+ * Sets the value of field 'id'.
+ *
+ * @param id the value of field 'id'.
+ */
+ public void setId(java.lang.String id)
+ {
+ this._id = id;
+ } //-- void setId(java.lang.String)
+
+ /**
* Sets the value of field 'label'.
*
* @param label the value of field 'label'.
/*
* This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M1</a>, using an XML
+ * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
* Schema.
* $Id$
*/
fieldValidator.setValidator(typeValidator);
}
desc.setValidator(fieldValidator);
+ //-- _id
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute);
+ this.identity = desc;
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ AlignmentAnnotations target = (AlignmentAnnotations) object;
+ return target.getId();
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ AlignmentAnnotations target = (AlignmentAnnotations) object;
+ target.setId( (java.lang.String) value);
+ }
+ catch (java.lang.Exception ex) {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+ public java.lang.Object newInstance( java.lang.Object parent ) {
+ return new java.lang.String();
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _id
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { //-- local scope
+ }
+ desc.setValidator(fieldValidator);
//-- initialize element descriptors
//-- _annotationElementList
/*
* This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M1</a>, using an XML
+ * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
* Schema.
* $Id$
*/
/*
* This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M1</a>, using an XML
+ * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
* Schema.
* $Id$
*/
//--------------------------/
/**
- * Field _id
+ * Field _refid
*/
- private java.lang.Object _id;
+ private java.lang.Object _refid;
//----------------/
if (obj instanceof AlignmentSequence) {
AlignmentSequence temp = (AlignmentSequence)obj;
- if (this._id != null) {
- if (temp._id == null) return false;
- else if (!(this._id.equals(temp._id)))
+ if (this._refid != null) {
+ if (temp._refid == null) return false;
+ else if (!(this._refid.equals(temp._refid)))
return false;
}
- else if (temp._id != null)
+ else if (temp._refid != null)
return false;
return true;
}
} //-- boolean equals(java.lang.Object)
/**
- * Returns the value of field 'id'.
+ * Returns the value of field 'refid'.
*
* @return Object
- * @return the value of field 'id'.
+ * @return the value of field 'refid'.
*/
- public java.lang.Object getId()
+ public java.lang.Object getRefid()
{
- return this._id;
- } //-- java.lang.Object getId()
+ return this._refid;
+ } //-- java.lang.Object getRefid()
/**
* Method isValid
} //-- void marshal(org.xml.sax.ContentHandler)
/**
- * Sets the value of field 'id'.
+ * Sets the value of field 'refid'.
*
- * @param id the value of field 'id'.
+ * @param refid the value of field 'refid'.
*/
- public void setId(java.lang.Object id)
+ public void setRefid(java.lang.Object refid)
{
- this._id = id;
- } //-- void setId(java.lang.Object)
+ this._refid = refid;
+ } //-- void setRefid(java.lang.Object)
/**
* Method unmarshal
/*
* This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M1</a>, using an XML
+ * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
* Schema.
* $Id$
*/
org.exolab.castor.xml.FieldValidator fieldValidator = null;
//-- initialize attribute descriptors
- //-- _id
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Object.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute);
+ //-- _refid
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Object.class, "_refid", "refid", org.exolab.castor.xml.NodeType.Attribute);
desc.setReference(true);
handler = new org.exolab.castor.xml.XMLFieldHandler() {
public java.lang.Object getValue( java.lang.Object object )
throws IllegalStateException
{
AlignmentSequence target = (AlignmentSequence) object;
- return target.getId();
+ return target.getRefid();
}
public void setValue( java.lang.Object object, java.lang.Object value)
throws IllegalStateException, IllegalArgumentException
{
try {
AlignmentSequence target = (AlignmentSequence) object;
- target.setId( (java.lang.Object) value);
+ target.setRefid( (java.lang.Object) value);
}
catch (java.lang.Exception ex) {
throw new IllegalStateException(ex.toString());
desc.setMultivalued(false);
addFieldDescriptor(desc);
- //-- validation code for: _id
+ //-- validation code for: _refid
fieldValidator = new org.exolab.castor.xml.FieldValidator();
fieldValidator.setMinOccurs(1);
{ //-- local scope
/*
* This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M1</a>, using an XML
+ * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
* Schema.
* $Id$
*/
private boolean _has_position;
/**
+ * Field _id
+ */
+ private java.lang.String _id;
+
+ /**
* Field _displayCharacter
*/
private java.lang.String _displayCharacter;
return false;
if (this._has_position != temp._has_position)
return false;
+ if (this._id != null) {
+ if (temp._id == null) return false;
+ else if (!(this._id.equals(temp._id)))
+ return false;
+ }
+ else if (temp._id != null)
+ return false;
if (this._displayCharacter != null) {
if (temp._displayCharacter == null) return false;
else if (!(this._displayCharacter.equals(temp._displayCharacter)))
} //-- java.lang.String getDisplayCharacter()
/**
+ * Returns the value of field 'id'.
+ *
+ * @return String
+ * @return the value of field 'id'.
+ */
+ public java.lang.String getId()
+ {
+ return this._id;
+ } //-- java.lang.String getId()
+
+ /**
* Returns the value of field 'position'.
*
* @return int
} //-- void setDisplayCharacter(java.lang.String)
/**
+ * Sets the value of field 'id'.
+ *
+ * @param id the value of field 'id'.
+ */
+ public void setId(java.lang.String id)
+ {
+ this._id = id;
+ } //-- void setId(java.lang.String)
+
+ /**
* Sets the value of field 'position'.
*
* @param position the value of field 'position'.
/*
* This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M1</a>, using an XML
+ * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
* Schema.
* $Id$
*/
fieldValidator.setValidator(typeValidator);
}
desc.setValidator(fieldValidator);
+ //-- _id
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute);
+ this.identity = desc;
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ AnnotationElement target = (AnnotationElement) object;
+ return target.getId();
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ AnnotationElement target = (AnnotationElement) object;
+ target.setId( (java.lang.String) value);
+ }
+ catch (java.lang.Exception ex) {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+ public java.lang.Object newInstance( java.lang.Object parent ) {
+ return new java.lang.String();
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _id
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { //-- local scope
+ }
+ desc.setValidator(fieldValidator);
//-- initialize element descriptors
//-- _displayCharacter
/*
* This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M1</a>, using an XML
+ * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
* Schema.
* $Id$
*/
/**
* Field _version
*/
- private java.lang.Object _version;
+ private java.lang.String _version;
/**
* Field _name
*/
- private java.lang.Object _name;
+ private java.lang.String _name;
+
+ /**
+ * Field _session
+ */
+ private java.lang.String _session;
+
+ /**
+ * Field _data
+ */
+ private java.lang.String _data;
//----------------/
}
else if (temp._name != null)
return false;
+ if (this._session != null) {
+ if (temp._session == null) return false;
+ else if (!(this._session.equals(temp._session)))
+ return false;
+ }
+ else if (temp._session != null)
+ return false;
+ if (this._data != null) {
+ if (temp._data == null) return false;
+ else if (!(this._data.equals(temp._data)))
+ return false;
+ }
+ else if (temp._data != null)
+ return false;
return true;
}
return false;
} //-- boolean equals(java.lang.Object)
/**
+ * Returns the value of field 'data'.
+ *
+ * @return String
+ * @return the value of field 'data'.
+ */
+ public java.lang.String getData()
+ {
+ return this._data;
+ } //-- java.lang.String getData()
+
+ /**
* Returns the value of field 'name'.
*
- * @return Object
+ * @return String
* @return the value of field 'name'.
*/
- public java.lang.Object getName()
+ public java.lang.String getName()
{
return this._name;
- } //-- java.lang.Object getName()
+ } //-- java.lang.String getName()
+
+ /**
+ * Returns the value of field 'session'.
+ *
+ * @return String
+ * @return the value of field 'session'.
+ */
+ public java.lang.String getSession()
+ {
+ return this._session;
+ } //-- java.lang.String getSession()
/**
* Returns the value of field 'version'.
*
- * @return Object
+ * @return String
* @return the value of field 'version'.
*/
- public java.lang.Object getVersion()
+ public java.lang.String getVersion()
{
return this._version;
- } //-- java.lang.Object getVersion()
+ } //-- java.lang.String getVersion()
/**
* Method isValid
} //-- void marshal(org.xml.sax.ContentHandler)
/**
+ * Sets the value of field 'data'.
+ *
+ * @param data the value of field 'data'.
+ */
+ public void setData(java.lang.String data)
+ {
+ this._data = data;
+ } //-- void setData(java.lang.String)
+
+ /**
* Sets the value of field 'name'.
*
* @param name the value of field 'name'.
*/
- public void setName(java.lang.Object name)
+ public void setName(java.lang.String name)
{
this._name = name;
- } //-- void setName(java.lang.Object)
+ } //-- void setName(java.lang.String)
+
+ /**
+ * Sets the value of field 'session'.
+ *
+ * @param session the value of field 'session'.
+ */
+ public void setSession(java.lang.String session)
+ {
+ this._session = session;
+ } //-- void setSession(java.lang.String)
/**
* Sets the value of field 'version'.
*
* @param version the value of field 'version'.
*/
- public void setVersion(java.lang.Object version)
+ public void setVersion(java.lang.String version)
{
this._version = version;
- } //-- void setVersion(java.lang.Object)
+ } //-- void setVersion(java.lang.String)
/**
* Method unmarshal
/*
* This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M1</a>, using an XML
+ * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
* Schema.
* $Id$
*/
/*
* This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M1</a>, using an XML
+ * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
* Schema.
* $Id$
*/
/*
* This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M1</a>, using an XML
+ * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
* Schema.
* $Id$
*/
//-- initialize attribute descriptors
//-- _version
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Object.class, "_version", "version", org.exolab.castor.xml.NodeType.Attribute);
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_version", "version", org.exolab.castor.xml.NodeType.Attribute);
+ desc.setImmutable(true);
handler = new org.exolab.castor.xml.XMLFieldHandler() {
public java.lang.Object getValue( java.lang.Object object )
throws IllegalStateException
{
try {
Application target = (Application) object;
- target.setVersion( (java.lang.Object) value);
+ target.setVersion( (java.lang.String) value);
}
catch (java.lang.Exception ex) {
throw new IllegalStateException(ex.toString());
}
}
public java.lang.Object newInstance( java.lang.Object parent ) {
- return new java.lang.Object();
+ return null;
}
};
desc.setHandler(handler);
//-- validation code for: _version
fieldValidator = new org.exolab.castor.xml.FieldValidator();
{ //-- local scope
+ StringValidator typeValidator = new StringValidator();
+ typeValidator.setWhiteSpace("preserve");
+ fieldValidator.setValidator(typeValidator);
}
desc.setValidator(fieldValidator);
//-- _name
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Object.class, "_name", "name", org.exolab.castor.xml.NodeType.Attribute);
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_name", "name", org.exolab.castor.xml.NodeType.Attribute);
+ desc.setImmutable(true);
handler = new org.exolab.castor.xml.XMLFieldHandler() {
public java.lang.Object getValue( java.lang.Object object )
throws IllegalStateException
{
try {
Application target = (Application) object;
- target.setName( (java.lang.Object) value);
+ target.setName( (java.lang.String) value);
}
catch (java.lang.Exception ex) {
throw new IllegalStateException(ex.toString());
}
}
public java.lang.Object newInstance( java.lang.Object parent ) {
- return new java.lang.Object();
+ return null;
}
};
desc.setHandler(handler);
//-- validation code for: _name
fieldValidator = new org.exolab.castor.xml.FieldValidator();
{ //-- local scope
+ StringValidator typeValidator = new StringValidator();
+ typeValidator.setWhiteSpace("preserve");
+ fieldValidator.setValidator(typeValidator);
+ }
+ desc.setValidator(fieldValidator);
+ //-- _session
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_session", "session", org.exolab.castor.xml.NodeType.Attribute);
+ desc.setImmutable(true);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ Application target = (Application) object;
+ return target.getSession();
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ Application target = (Application) object;
+ target.setSession( (java.lang.String) value);
+ }
+ catch (java.lang.Exception ex) {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+ public java.lang.Object newInstance( java.lang.Object parent ) {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _session
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { //-- local scope
+ StringValidator typeValidator = new StringValidator();
+ typeValidator.setWhiteSpace("preserve");
+ fieldValidator.setValidator(typeValidator);
+ }
+ desc.setValidator(fieldValidator);
+ //-- _data
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_data", "data", org.exolab.castor.xml.NodeType.Attribute);
+ desc.setImmutable(true);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ Application target = (Application) object;
+ return target.getData();
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ Application target = (Application) object;
+ target.setData( (java.lang.String) value);
+ }
+ catch (java.lang.Exception ex) {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+ public java.lang.Object newInstance( java.lang.Object parent ) {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _data
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { //-- local scope
+ StringValidator typeValidator = new StringValidator();
+ typeValidator.setWhiteSpace("preserve");
+ fieldValidator.setValidator(typeValidator);
}
desc.setValidator(fieldValidator);
//-- initialize element descriptors
/*
* This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M1</a>, using an XML
+ * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
* Schema.
* $Id$
*/
*/
private java.lang.Object _accessionId;
+ /**
+ * Field _id
+ */
+ private java.lang.String _id;
+
//----------------/
//- Constructors -/
}
else if (temp._accessionId != null)
return false;
+ if (this._id != null) {
+ if (temp._id == null) return false;
+ else if (!(this._id.equals(temp._id)))
+ return false;
+ }
+ else if (temp._id != null)
+ return false;
return true;
}
return false;
} //-- java.lang.Object getAccessionId()
/**
+ * Returns the value of field 'id'.
+ *
+ * @return String
+ * @return the value of field 'id'.
+ */
+ public java.lang.String getId()
+ {
+ return this._id;
+ } //-- java.lang.String getId()
+
+ /**
* Returns the value of field 'source'.
*
* @return Object
} //-- void setAccessionId(java.lang.Object)
/**
+ * Sets the value of field 'id'.
+ *
+ * @param id the value of field 'id'.
+ */
+ public void setId(java.lang.String id)
+ {
+ this._id = id;
+ } //-- void setId(java.lang.String)
+
+ /**
* Sets the value of field 'source'.
*
* @param source the value of field 'source'.
/*
* This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M1</a>, using an XML
+ * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
* Schema.
* $Id$
*/
{ //-- local scope
}
desc.setValidator(fieldValidator);
+ //-- _id
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute);
+ this.identity = desc;
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ DbRef target = (DbRef) object;
+ return target.getId();
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ DbRef target = (DbRef) object;
+ target.setId( (java.lang.String) value);
+ }
+ catch (java.lang.Exception ex) {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+ public java.lang.Object newInstance( java.lang.Object parent ) {
+ return new java.lang.String();
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _id
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { //-- local scope
+ }
+ desc.setValidator(fieldValidator);
//-- initialize element descriptors
} //-- org.vamsas.objects.core.DbRefDescriptor()
--- /dev/null
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package org.vamsas.objects.core;
+
+ //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import java.io.IOException;
+import java.io.Reader;
+import java.io.Serializable;
+import java.io.Writer;
+import org.exolab.castor.xml.MarshalException;
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+import org.exolab.castor.xml.ValidationException;
+import org.xml.sax.ContentHandler;
+
+/**
+ * Class Dendro.
+ *
+ * @version $Revision$ $Date$
+ */
+public class Dendro extends TreeType
+implements java.io.Serializable
+{
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public Dendro()
+ {
+ super();
+ } //-- org.vamsas.objects.core.Dendro()
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ * Note: hashCode() has not been overriden
+ *
+ * @param obj
+ * @return boolean
+ */
+ public boolean equals(java.lang.Object obj)
+ {
+ if ( this == obj )
+ return true;
+
+ if (super.equals(obj)==false)
+ return false;
+
+ if (obj instanceof Dendro) {
+
+ Dendro temp = (Dendro)obj;
+ return true;
+ }
+ return false;
+ } //-- boolean equals(java.lang.Object)
+
+ /**
+ * Method isValid
+ *
+ *
+ *
+ * @return boolean
+ */
+ public boolean isValid()
+ {
+ try {
+ validate();
+ }
+ catch (org.exolab.castor.xml.ValidationException vex) {
+ return false;
+ }
+ return true;
+ } //-- boolean isValid()
+
+ /**
+ * Method marshal
+ *
+ *
+ *
+ * @param out
+ */
+ public void marshal(java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+ {
+
+ Marshaller.marshal(this, out);
+ } //-- void marshal(java.io.Writer)
+
+ /**
+ * Method marshal
+ *
+ *
+ *
+ * @param handler
+ */
+ public void marshal(org.xml.sax.ContentHandler handler)
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+ {
+
+ Marshaller.marshal(this, handler);
+ } //-- void marshal(org.xml.sax.ContentHandler)
+
+ /**
+ * Method unmarshal
+ *
+ *
+ *
+ * @param reader
+ * @return Dendro
+ */
+ public static org.vamsas.objects.core.Dendro unmarshal(java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+ {
+ return (org.vamsas.objects.core.Dendro) Unmarshaller.unmarshal(org.vamsas.objects.core.Dendro.class, reader);
+ } //-- org.vamsas.objects.core.Dendro unmarshal(java.io.Reader)
+
+ /**
+ * Method validate
+ *
+ */
+ public void validate()
+ throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ } //-- void validate()
+
+}
--- /dev/null
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package org.vamsas.objects.core;
+
+ //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.mapping.AccessMode;
+import org.exolab.castor.xml.TypeValidator;
+import org.exolab.castor.xml.XMLFieldDescriptor;
+import org.exolab.castor.xml.validators.*;
+
+/**
+ * Class DendroDescriptor.
+ *
+ * @version $Revision$ $Date$
+ */
+public class DendroDescriptor extends TreeTypeDescriptor {
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * Field nsPrefix
+ */
+ private java.lang.String nsPrefix;
+
+ /**
+ * Field nsURI
+ */
+ private java.lang.String nsURI;
+
+ /**
+ * Field xmlName
+ */
+ private java.lang.String xmlName;
+
+ /**
+ * Field identity
+ */
+ private org.exolab.castor.xml.XMLFieldDescriptor identity;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public DendroDescriptor()
+ {
+ super();
+ setExtendsWithoutFlatten(new TreeTypeDescriptor());
+ nsURI = "http://www.vamsas.org";
+ xmlName = "Dendro";
+ } //-- org.vamsas.objects.core.DendroDescriptor()
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ * Method getAccessMode
+ *
+ *
+ *
+ * @return AccessMode
+ */
+ public org.exolab.castor.mapping.AccessMode getAccessMode()
+ {
+ return null;
+ } //-- org.exolab.castor.mapping.AccessMode getAccessMode()
+
+ /**
+ * Method getExtends
+ *
+ *
+ *
+ * @return ClassDescriptor
+ */
+ public org.exolab.castor.mapping.ClassDescriptor getExtends()
+ {
+ return super.getExtends();
+ } //-- org.exolab.castor.mapping.ClassDescriptor getExtends()
+
+ /**
+ * Method getIdentity
+ *
+ *
+ *
+ * @return FieldDescriptor
+ */
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+ {
+ if (identity == null)
+ return super.getIdentity();
+ return identity;
+ } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity()
+
+ /**
+ * Method getJavaClass
+ *
+ *
+ *
+ * @return Class
+ */
+ public java.lang.Class getJavaClass()
+ {
+ return org.vamsas.objects.core.Dendro.class;
+ } //-- java.lang.Class getJavaClass()
+
+ /**
+ * Method getNameSpacePrefix
+ *
+ *
+ *
+ * @return String
+ */
+ public java.lang.String getNameSpacePrefix()
+ {
+ return nsPrefix;
+ } //-- java.lang.String getNameSpacePrefix()
+
+ /**
+ * Method getNameSpaceURI
+ *
+ *
+ *
+ * @return String
+ */
+ public java.lang.String getNameSpaceURI()
+ {
+ return nsURI;
+ } //-- java.lang.String getNameSpaceURI()
+
+ /**
+ * Method getValidator
+ *
+ *
+ *
+ * @return TypeValidator
+ */
+ public org.exolab.castor.xml.TypeValidator getValidator()
+ {
+ return this;
+ } //-- org.exolab.castor.xml.TypeValidator getValidator()
+
+ /**
+ * Method getXMLName
+ *
+ *
+ *
+ * @return String
+ */
+ public java.lang.String getXMLName()
+ {
+ return xmlName;
+ } //-- java.lang.String getXMLName()
+
+}
/*
* This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M1</a>, using an XML
+ * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
* Schema.
* $Id$
*/
//--------------------------/
/**
+ * Field _id
+ */
+ private java.lang.String _id;
+
+ /**
* Field _user
*/
private java.lang.String _user;
if (obj instanceof Entry) {
Entry temp = (Entry)obj;
+ if (this._id != null) {
+ if (temp._id == null) return false;
+ else if (!(this._id.equals(temp._id)))
+ return false;
+ }
+ else if (temp._id != null)
+ return false;
if (this._user != null) {
if (temp._user == null) return false;
else if (!(this._user.equals(temp._user)))
} //-- org.exolab.castor.types.Date getDate()
/**
+ * Returns the value of field 'id'.
+ *
+ * @return String
+ * @return the value of field 'id'.
+ */
+ public java.lang.String getId()
+ {
+ return this._id;
+ } //-- java.lang.String getId()
+
+ /**
* Returns the value of field 'user'.
*
* @return String
} //-- void setDate(org.exolab.castor.types.Date)
/**
+ * Sets the value of field 'id'.
+ *
+ * @param id the value of field 'id'.
+ */
+ public void setId(java.lang.String id)
+ {
+ this._id = id;
+ } //-- void setId(java.lang.String)
+
+ /**
* Sets the value of field 'user'.
*
* @param user the value of field 'user'.
/*
* This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M1</a>, using an XML
+ * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
* Schema.
* $Id$
*/
org.exolab.castor.xml.FieldValidator fieldValidator = null;
//-- initialize attribute descriptors
+ //-- _id
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute);
+ this.identity = desc;
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ Entry target = (Entry) object;
+ return target.getId();
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ Entry target = (Entry) object;
+ target.setId( (java.lang.String) value);
+ }
+ catch (java.lang.Exception ex) {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+ public java.lang.Object newInstance( java.lang.Object parent ) {
+ return new java.lang.String();
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _id
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { //-- local scope
+ }
+ desc.setValidator(fieldValidator);
//-- initialize element descriptors
//-- _user
/*
* This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M1</a>, using an XML
+ * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
* Schema.
* $Id$
*/
/*
* This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M1</a>, using an XML
+ * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
* Schema.
* $Id$
*/
/*
* This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M1</a>, using an XML
+ * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
* Schema.
* $Id$
*/
/*
* This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M1</a>, using an XML
+ * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
* Schema.
* $Id$
*/
/*
* This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M1</a>, using an XML
+ * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
* Schema.
* $Id$
*/
/*
* This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M1</a>, using an XML
+ * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
* Schema.
* $Id$
*/
/*
* This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M1</a>, using an XML
+ * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
* Schema.
* $Id$
*/
*/
private java.lang.String _dictionary;
- /**
- * Field _id
- */
- private java.lang.String _id;
-
//----------------/
//- Constructors -/
}
else if (temp._dictionary != null)
return false;
- if (this._id != null) {
- if (temp._id == null) return false;
- else if (!(this._id.equals(temp._id)))
- return false;
- }
- else if (temp._id != null)
- return false;
return true;
}
return false;
} //-- java.lang.String getDictionary()
/**
- * Returns the value of field 'id'.
- *
- * @return String
- * @return the value of field 'id'.
- */
- public java.lang.String getId()
- {
- return this._id;
- } //-- java.lang.String getId()
-
- /**
* Method isValid
*
*
} //-- void setDictionary(java.lang.String)
/**
- * Sets the value of field 'id'.
- *
- * @param id the value of field 'id'.
- */
- public void setId(java.lang.String id)
- {
- this._id = id;
- } //-- void setId(java.lang.String)
-
- /**
* Method unmarshal
*
*
/*
* This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M1</a>, using an XML
+ * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
* Schema.
* $Id$
*/
fieldValidator.setValidator(typeValidator);
}
desc.setValidator(fieldValidator);
- //-- _id
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute);
- this.identity = desc;
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Sequence target = (Sequence) object;
- return target.getId();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Sequence target = (Sequence) object;
- target.setId( (java.lang.String) value);
- }
- catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance( java.lang.Object parent ) {
- return new java.lang.String();
- }
- };
- desc.setHandler(handler);
- desc.setRequired(true);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _id
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(1);
- { //-- local scope
- }
- desc.setValidator(fieldValidator);
//-- initialize element descriptors
} //-- org.vamsas.objects.core.SequenceDescriptor()
/*
* This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M1</a>, using an XML
+ * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
* Schema.
* $Id$
*/
private boolean _has_aligned;
/**
+ * Field _id
+ */
+ private java.lang.String _id;
+
+ /**
* Field _sequenceList
*/
private java.util.Vector _sequenceList;
return false;
if (this._has_aligned != temp._has_aligned)
return false;
+ if (this._id != null) {
+ if (temp._id == null) return false;
+ else if (!(this._id.equals(temp._id)))
+ return false;
+ }
+ else if (temp._id != null)
+ return false;
if (this._sequenceList != null) {
if (temp._sequenceList == null) return false;
else if (!(this._sequenceList.equals(temp._sequenceList)))
} //-- java.lang.String getGapChar()
/**
+ * Returns the value of field 'id'.
+ *
+ * @return String
+ * @return the value of field 'id'.
+ */
+ public java.lang.String getId()
+ {
+ return this._id;
+ } //-- java.lang.String getId()
+
+ /**
* Returns the value of field 'provenance'.
*
* @return Provenance
} //-- void setGapChar(java.lang.String)
/**
+ * Sets the value of field 'id'.
+ *
+ * @param id the value of field 'id'.
+ */
+ public void setId(java.lang.String id)
+ {
+ this._id = id;
+ } //-- void setId(java.lang.String)
+
+ /**
* Sets the value of field 'provenance'.
*
* @param provenance the value of field 'provenance'.
/*
* This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M1</a>, using an XML
+ * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
* Schema.
* $Id$
*/
private java.lang.Object _seqRef;
/**
+ * Field _id
+ */
+ private java.lang.String _id;
+
+ /**
* Field _description
*/
private java.lang.String _description;
}
else if (temp._seqRef != null)
return false;
+ if (this._id != null) {
+ if (temp._id == null) return false;
+ else if (!(this._id.equals(temp._id)))
+ return false;
+ }
+ else if (temp._id != null)
+ return false;
if (this._description != null) {
if (temp._description == null) return false;
else if (!(this._description.equals(temp._description)))
} //-- java.lang.String getEnd()
/**
+ * Returns the value of field 'id'.
+ *
+ * @return String
+ * @return the value of field 'id'.
+ */
+ public java.lang.String getId()
+ {
+ return this._id;
+ } //-- java.lang.String getId()
+
+ /**
* Returns the value of field 'provenance'.
*
* @return Provenance
} //-- void setEnd(java.lang.String)
/**
+ * Sets the value of field 'id'.
+ *
+ * @param id the value of field 'id'.
+ */
+ public void setId(java.lang.String id)
+ {
+ this._id = id;
+ } //-- void setId(java.lang.String)
+
+ /**
* Sets the value of field 'provenance'.
*
* @param provenance the value of field 'provenance'.
/*
* This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M1</a>, using an XML
+ * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
* Schema.
* $Id$
*/
{ //-- local scope
}
desc.setValidator(fieldValidator);
+ //-- _id
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute);
+ this.identity = desc;
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ SequenceSetAnnotations target = (SequenceSetAnnotations) object;
+ return target.getId();
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ SequenceSetAnnotations target = (SequenceSetAnnotations) object;
+ target.setId( (java.lang.String) value);
+ }
+ catch (java.lang.Exception ex) {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+ public java.lang.Object newInstance( java.lang.Object parent ) {
+ return new java.lang.String();
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _id
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { //-- local scope
+ }
+ desc.setValidator(fieldValidator);
//-- initialize element descriptors
//-- _description
/*
* This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M1</a>, using an XML
+ * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
* Schema.
* $Id$
*/
fieldValidator.setValidator(typeValidator);
}
desc.setValidator(fieldValidator);
+ //-- _id
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute);
+ this.identity = desc;
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ SequenceSet target = (SequenceSet) object;
+ return target.getId();
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ SequenceSet target = (SequenceSet) object;
+ target.setId( (java.lang.String) value);
+ }
+ catch (java.lang.Exception ex) {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+ public java.lang.Object newInstance( java.lang.Object parent ) {
+ return new java.lang.String();
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _id
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { //-- local scope
+ }
+ desc.setValidator(fieldValidator);
//-- initialize element descriptors
//-- _sequenceList
/*
* This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M1</a>, using an XML
+ * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
* Schema.
* $Id$
*/
private boolean _has_end;
/**
+ * Field _id
+ */
+ private java.lang.String _id;
+
+ /**
* Field _sequence
*/
private java.lang.String _sequence;
return false;
if (this._has_end != temp._has_end)
return false;
+ if (this._id != null) {
+ if (temp._id == null) return false;
+ else if (!(this._id.equals(temp._id)))
+ return false;
+ }
+ else if (temp._id != null)
+ return false;
if (this._sequence != null) {
if (temp._sequence == null) return false;
else if (!(this._sequence.equals(temp._sequence)))
} //-- int getEnd()
/**
+ * Returns the value of field 'id'.
+ *
+ * @return String
+ * @return the value of field 'id'.
+ */
+ public java.lang.String getId()
+ {
+ return this._id;
+ } //-- java.lang.String getId()
+
+ /**
* Returns the value of field 'name'.
*
* @return String
} //-- void setEnd(int)
/**
+ * Sets the value of field 'id'.
+ *
+ * @param id the value of field 'id'.
+ */
+ public void setId(java.lang.String id)
+ {
+ this._id = id;
+ } //-- void setId(java.lang.String)
+
+ /**
* Sets the value of field 'name'.
*
* @param name the value of field 'name'.
/*
* This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M1</a>, using an XML
+ * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
* Schema.
* $Id$
*/
fieldValidator.setValidator(typeValidator);
}
desc.setValidator(fieldValidator);
+ //-- _id
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute);
+ this.identity = desc;
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ SequenceType target = (SequenceType) object;
+ return target.getId();
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ SequenceType target = (SequenceType) object;
+ target.setId( (java.lang.String) value);
+ }
+ catch (java.lang.Exception ex) {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+ public java.lang.Object newInstance( java.lang.Object parent ) {
+ return new java.lang.String();
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _id
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { //-- local scope
+ }
+ desc.setValidator(fieldValidator);
//-- initialize element descriptors
//-- _sequence
/*
* This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M1</a>, using an XML
+ * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
* Schema.
* $Id$
*/
*
* @version $Revision$ $Date$
*/
-public class Tree extends org.vamsas.client.object
+public class Tree extends TreeType
implements java.io.Serializable
{
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _provenance
- */
- private org.vamsas.objects.core.Provenance _provenance;
-
- /**
- * Field _newickFormat
- */
- private java.lang.String _newickFormat;
-
-
//----------------/
//- Constructors -/
//----------------/
if (obj instanceof Tree) {
Tree temp = (Tree)obj;
- if (this._provenance != null) {
- if (temp._provenance == null) return false;
- else if (!(this._provenance.equals(temp._provenance)))
- return false;
- }
- else if (temp._provenance != null)
- return false;
- if (this._newickFormat != null) {
- if (temp._newickFormat == null) return false;
- else if (!(this._newickFormat.equals(temp._newickFormat)))
- return false;
- }
- else if (temp._newickFormat != null)
- return false;
return true;
}
return false;
} //-- boolean equals(java.lang.Object)
/**
- * Returns the value of field 'newickFormat'.
- *
- * @return String
- * @return the value of field 'newickFormat'.
- */
- public java.lang.String getNewickFormat()
- {
- return this._newickFormat;
- } //-- java.lang.String getNewickFormat()
-
- /**
- * Returns the value of field 'provenance'.
- *
- * @return Provenance
- * @return the value of field 'provenance'.
- */
- public org.vamsas.objects.core.Provenance getProvenance()
- {
- return this._provenance;
- } //-- org.vamsas.objects.core.Provenance getProvenance()
-
- /**
* Method isValid
*
*
} //-- void marshal(org.xml.sax.ContentHandler)
/**
- * Sets the value of field 'newickFormat'.
- *
- * @param newickFormat the value of field 'newickFormat'.
- */
- public void setNewickFormat(java.lang.String newickFormat)
- {
- this._newickFormat = newickFormat;
- } //-- void setNewickFormat(java.lang.String)
-
- /**
- * Sets the value of field 'provenance'.
- *
- * @param provenance the value of field 'provenance'.
- */
- public void setProvenance(org.vamsas.objects.core.Provenance provenance)
- {
- this._provenance = provenance;
- } //-- void setProvenance(org.vamsas.objects.core.Provenance)
-
- /**
* Method unmarshal
*
*
/*
* This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M1</a>, using an XML
+ * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
* Schema.
* $Id$
*/
*
* @version $Revision$ $Date$
*/
-public class TreeDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
+public class TreeDescriptor extends TreeTypeDescriptor {
//--------------------------/
public TreeDescriptor()
{
super();
+ setExtendsWithoutFlatten(new TreeTypeDescriptor());
nsURI = "http://www.vamsas.org";
xmlName = "tree";
-
- //-- set grouping compositor
- setCompositorAsSequence();
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
- org.exolab.castor.mapping.FieldHandler handler = null;
- org.exolab.castor.xml.FieldValidator fieldValidator = null;
- //-- initialize attribute descriptors
-
- //-- initialize element descriptors
-
- //-- _provenance
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Provenance.class, "_provenance", "Provenance", org.exolab.castor.xml.NodeType.Element);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Tree target = (Tree) object;
- return target.getProvenance();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Tree target = (Tree) object;
- target.setProvenance( (org.vamsas.objects.core.Provenance) value);
- }
- catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance( java.lang.Object parent ) {
- return new org.vamsas.objects.core.Provenance();
- }
- };
- desc.setHandler(handler);
- desc.setNameSpaceURI("http://www.vamsas.org");
- desc.setRequired(true);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _provenance
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(1);
- { //-- local scope
- }
- desc.setValidator(fieldValidator);
- //-- _newickFormat
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_newickFormat", "newickFormat", org.exolab.castor.xml.NodeType.Element);
- desc.setImmutable(true);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Tree target = (Tree) object;
- return target.getNewickFormat();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Tree target = (Tree) object;
- target.setNewickFormat( (java.lang.String) value);
- }
- catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance( java.lang.Object parent ) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setNameSpaceURI("http://www.vamsas.org");
- desc.setRequired(true);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _newickFormat
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(1);
- { //-- local scope
- StringValidator typeValidator = new StringValidator();
- typeValidator.setWhiteSpace("preserve");
- fieldValidator.setValidator(typeValidator);
- }
- desc.setValidator(fieldValidator);
} //-- org.vamsas.objects.core.TreeDescriptor()
*/
public org.exolab.castor.mapping.ClassDescriptor getExtends()
{
- return null;
+ return super.getExtends();
} //-- org.exolab.castor.mapping.ClassDescriptor getExtends()
/**
*/
public org.exolab.castor.mapping.FieldDescriptor getIdentity()
{
+ if (identity == null)
+ return super.getIdentity();
return identity;
} //-- org.exolab.castor.mapping.FieldDescriptor getIdentity()
--- /dev/null
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package org.vamsas.objects.core;
+
+ //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import java.io.IOException;
+import java.io.Reader;
+import java.io.Serializable;
+import java.io.Writer;
+import java.util.Enumeration;
+import java.util.Vector;
+import org.exolab.castor.xml.MarshalException;
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+import org.exolab.castor.xml.ValidationException;
+import org.xml.sax.ContentHandler;
+
+/**
+ * Class TreeType.
+ *
+ * @version $Revision$ $Date$
+ */
+public class TreeType extends org.vamsas.client.object
+implements java.io.Serializable
+{
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * Field _id
+ */
+ private java.lang.String _id;
+
+ /**
+ * Field _newickFormatList
+ */
+ private java.util.Vector _newickFormatList;
+
+ /**
+ * Field _provenance
+ */
+ private org.vamsas.objects.core.Provenance _provenance;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public TreeType()
+ {
+ super();
+ _newickFormatList = new Vector();
+ } //-- org.vamsas.objects.core.TreeType()
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ * Method addNewickFormat
+ *
+ *
+ *
+ * @param vNewickFormat
+ */
+ public void addNewickFormat(java.lang.String vNewickFormat)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _newickFormatList.addElement(vNewickFormat);
+ } //-- void addNewickFormat(java.lang.String)
+
+ /**
+ * Method addNewickFormat
+ *
+ *
+ *
+ * @param index
+ * @param vNewickFormat
+ */
+ public void addNewickFormat(int index, java.lang.String vNewickFormat)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _newickFormatList.insertElementAt(vNewickFormat, index);
+ } //-- void addNewickFormat(int, java.lang.String)
+
+ /**
+ * Method enumerateNewickFormat
+ *
+ *
+ *
+ * @return Enumeration
+ */
+ public java.util.Enumeration enumerateNewickFormat()
+ {
+ return _newickFormatList.elements();
+ } //-- java.util.Enumeration enumerateNewickFormat()
+
+ /**
+ * Note: hashCode() has not been overriden
+ *
+ * @param obj
+ * @return boolean
+ */
+ public boolean equals(java.lang.Object obj)
+ {
+ if ( this == obj )
+ return true;
+
+ if (super.equals(obj)==false)
+ return false;
+
+ if (obj instanceof TreeType) {
+
+ TreeType temp = (TreeType)obj;
+ if (this._id != null) {
+ if (temp._id == null) return false;
+ else if (!(this._id.equals(temp._id)))
+ return false;
+ }
+ else if (temp._id != null)
+ return false;
+ if (this._newickFormatList != null) {
+ if (temp._newickFormatList == null) return false;
+ else if (!(this._newickFormatList.equals(temp._newickFormatList)))
+ return false;
+ }
+ else if (temp._newickFormatList != null)
+ return false;
+ if (this._provenance != null) {
+ if (temp._provenance == null) return false;
+ else if (!(this._provenance.equals(temp._provenance)))
+ return false;
+ }
+ else if (temp._provenance != null)
+ return false;
+ return true;
+ }
+ return false;
+ } //-- boolean equals(java.lang.Object)
+
+ /**
+ * Returns the value of field 'id'.
+ *
+ * @return String
+ * @return the value of field 'id'.
+ */
+ public java.lang.String getId()
+ {
+ return this._id;
+ } //-- java.lang.String getId()
+
+ /**
+ * Method getNewickFormat
+ *
+ *
+ *
+ * @param index
+ * @return String
+ */
+ public java.lang.String getNewickFormat(int index)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ //-- check bounds for index
+ if ((index < 0) || (index > _newickFormatList.size())) {
+ throw new IndexOutOfBoundsException("getNewickFormat: Index value '"+index+"' not in range [0.."+_newickFormatList.size()+ "]");
+ }
+
+ return (String)_newickFormatList.elementAt(index);
+ } //-- java.lang.String getNewickFormat(int)
+
+ /**
+ * Method getNewickFormat
+ *
+ *
+ *
+ * @return String
+ */
+ public java.lang.String[] getNewickFormat()
+ {
+ int size = _newickFormatList.size();
+ java.lang.String[] mArray = new java.lang.String[size];
+ for (int index = 0; index < size; index++) {
+ mArray[index] = (String)_newickFormatList.elementAt(index);
+ }
+ return mArray;
+ } //-- java.lang.String[] getNewickFormat()
+
+ /**
+ * Method getNewickFormatCount
+ *
+ *
+ *
+ * @return int
+ */
+ public int getNewickFormatCount()
+ {
+ return _newickFormatList.size();
+ } //-- int getNewickFormatCount()
+
+ /**
+ * Returns the value of field 'provenance'.
+ *
+ * @return Provenance
+ * @return the value of field 'provenance'.
+ */
+ public org.vamsas.objects.core.Provenance getProvenance()
+ {
+ return this._provenance;
+ } //-- org.vamsas.objects.core.Provenance getProvenance()
+
+ /**
+ * Method isValid
+ *
+ *
+ *
+ * @return boolean
+ */
+ public boolean isValid()
+ {
+ try {
+ validate();
+ }
+ catch (org.exolab.castor.xml.ValidationException vex) {
+ return false;
+ }
+ return true;
+ } //-- boolean isValid()
+
+ /**
+ * Method marshal
+ *
+ *
+ *
+ * @param out
+ */
+ public void marshal(java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+ {
+
+ Marshaller.marshal(this, out);
+ } //-- void marshal(java.io.Writer)
+
+ /**
+ * Method marshal
+ *
+ *
+ *
+ * @param handler
+ */
+ public void marshal(org.xml.sax.ContentHandler handler)
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+ {
+
+ Marshaller.marshal(this, handler);
+ } //-- void marshal(org.xml.sax.ContentHandler)
+
+ /**
+ * Method removeAllNewickFormat
+ *
+ */
+ public void removeAllNewickFormat()
+ {
+ _newickFormatList.removeAllElements();
+ } //-- void removeAllNewickFormat()
+
+ /**
+ * Method removeNewickFormat
+ *
+ *
+ *
+ * @param index
+ * @return String
+ */
+ public java.lang.String removeNewickFormat(int index)
+ {
+ java.lang.Object obj = _newickFormatList.elementAt(index);
+ _newickFormatList.removeElementAt(index);
+ return (String)obj;
+ } //-- java.lang.String removeNewickFormat(int)
+
+ /**
+ * Sets the value of field 'id'.
+ *
+ * @param id the value of field 'id'.
+ */
+ public void setId(java.lang.String id)
+ {
+ this._id = id;
+ } //-- void setId(java.lang.String)
+
+ /**
+ * Method setNewickFormat
+ *
+ *
+ *
+ * @param index
+ * @param vNewickFormat
+ */
+ public void setNewickFormat(int index, java.lang.String vNewickFormat)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ //-- check bounds for index
+ if ((index < 0) || (index > _newickFormatList.size())) {
+ throw new IndexOutOfBoundsException("setNewickFormat: Index value '"+index+"' not in range [0.."+_newickFormatList.size()+ "]");
+ }
+ _newickFormatList.setElementAt(vNewickFormat, index);
+ } //-- void setNewickFormat(int, java.lang.String)
+
+ /**
+ * Method setNewickFormat
+ *
+ *
+ *
+ * @param newickFormatArray
+ */
+ public void setNewickFormat(java.lang.String[] newickFormatArray)
+ {
+ //-- copy array
+ _newickFormatList.removeAllElements();
+ for (int i = 0; i < newickFormatArray.length; i++) {
+ _newickFormatList.addElement(newickFormatArray[i]);
+ }
+ } //-- void setNewickFormat(java.lang.String)
+
+ /**
+ * Sets the value of field 'provenance'.
+ *
+ * @param provenance the value of field 'provenance'.
+ */
+ public void setProvenance(org.vamsas.objects.core.Provenance provenance)
+ {
+ this._provenance = provenance;
+ } //-- void setProvenance(org.vamsas.objects.core.Provenance)
+
+ /**
+ * Method unmarshal
+ *
+ *
+ *
+ * @param reader
+ * @return TreeType
+ */
+ public static org.vamsas.objects.core.TreeType unmarshal(java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+ {
+ return (org.vamsas.objects.core.TreeType) Unmarshaller.unmarshal(org.vamsas.objects.core.TreeType.class, reader);
+ } //-- org.vamsas.objects.core.TreeType unmarshal(java.io.Reader)
+
+ /**
+ * Method validate
+ *
+ */
+ public void validate()
+ throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ } //-- void validate()
+
+}
--- /dev/null
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package org.vamsas.objects.core;
+
+ //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.mapping.AccessMode;
+import org.exolab.castor.xml.TypeValidator;
+import org.exolab.castor.xml.XMLFieldDescriptor;
+import org.exolab.castor.xml.validators.*;
+
+/**
+ * Class TreeTypeDescriptor.
+ *
+ * @version $Revision$ $Date$
+ */
+public class TreeTypeDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * Field nsPrefix
+ */
+ private java.lang.String nsPrefix;
+
+ /**
+ * Field nsURI
+ */
+ private java.lang.String nsURI;
+
+ /**
+ * Field xmlName
+ */
+ private java.lang.String xmlName;
+
+ /**
+ * Field identity
+ */
+ private org.exolab.castor.xml.XMLFieldDescriptor identity;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public TreeTypeDescriptor()
+ {
+ super();
+ nsURI = "http://www.vamsas.org";
+ xmlName = "TreeType";
+
+ //-- set grouping compositor
+ setCompositorAsSequence();
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+ org.exolab.castor.mapping.FieldHandler handler = null;
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;
+ //-- initialize attribute descriptors
+
+ //-- _id
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute);
+ this.identity = desc;
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ TreeType target = (TreeType) object;
+ return target.getId();
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ TreeType target = (TreeType) object;
+ target.setId( (java.lang.String) value);
+ }
+ catch (java.lang.Exception ex) {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+ public java.lang.Object newInstance( java.lang.Object parent ) {
+ return new java.lang.String();
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _id
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { //-- local scope
+ }
+ desc.setValidator(fieldValidator);
+ //-- initialize element descriptors
+
+ //-- _newickFormatList
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_newickFormatList", "newickFormat", org.exolab.castor.xml.NodeType.Element);
+ desc.setImmutable(true);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ TreeType target = (TreeType) object;
+ return target.getNewickFormat();
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ TreeType target = (TreeType) object;
+ target.addNewickFormat( (java.lang.String) value);
+ }
+ catch (java.lang.Exception ex) {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+ public java.lang.Object newInstance( java.lang.Object parent ) {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setNameSpaceURI("http://www.vamsas.org");
+ desc.setRequired(true);
+ desc.setMultivalued(true);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _newickFormatList
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(1);
+ { //-- local scope
+ StringValidator typeValidator = new StringValidator();
+ typeValidator.setWhiteSpace("preserve");
+ fieldValidator.setValidator(typeValidator);
+ }
+ desc.setValidator(fieldValidator);
+ //-- _provenance
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Provenance.class, "_provenance", "Provenance", org.exolab.castor.xml.NodeType.Element);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ TreeType target = (TreeType) object;
+ return target.getProvenance();
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ TreeType target = (TreeType) object;
+ target.setProvenance( (org.vamsas.objects.core.Provenance) value);
+ }
+ catch (java.lang.Exception ex) {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+ public java.lang.Object newInstance( java.lang.Object parent ) {
+ return new org.vamsas.objects.core.Provenance();
+ }
+ };
+ desc.setHandler(handler);
+ desc.setNameSpaceURI("http://www.vamsas.org");
+ desc.setRequired(true);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _provenance
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(1);
+ { //-- local scope
+ }
+ desc.setValidator(fieldValidator);
+ } //-- org.vamsas.objects.core.TreeTypeDescriptor()
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ * Method getAccessMode
+ *
+ *
+ *
+ * @return AccessMode
+ */
+ public org.exolab.castor.mapping.AccessMode getAccessMode()
+ {
+ return null;
+ } //-- org.exolab.castor.mapping.AccessMode getAccessMode()
+
+ /**
+ * Method getExtends
+ *
+ *
+ *
+ * @return ClassDescriptor
+ */
+ public org.exolab.castor.mapping.ClassDescriptor getExtends()
+ {
+ return null;
+ } //-- org.exolab.castor.mapping.ClassDescriptor getExtends()
+
+ /**
+ * Method getIdentity
+ *
+ *
+ *
+ * @return FieldDescriptor
+ */
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+ {
+ return identity;
+ } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity()
+
+ /**
+ * Method getJavaClass
+ *
+ *
+ *
+ * @return Class
+ */
+ public java.lang.Class getJavaClass()
+ {
+ return org.vamsas.objects.core.TreeType.class;
+ } //-- java.lang.Class getJavaClass()
+
+ /**
+ * Method getNameSpacePrefix
+ *
+ *
+ *
+ * @return String
+ */
+ public java.lang.String getNameSpacePrefix()
+ {
+ return nsPrefix;
+ } //-- java.lang.String getNameSpacePrefix()
+
+ /**
+ * Method getNameSpaceURI
+ *
+ *
+ *
+ * @return String
+ */
+ public java.lang.String getNameSpaceURI()
+ {
+ return nsURI;
+ } //-- java.lang.String getNameSpaceURI()
+
+ /**
+ * Method getValidator
+ *
+ *
+ *
+ * @return TypeValidator
+ */
+ public org.exolab.castor.xml.TypeValidator getValidator()
+ {
+ return this;
+ } //-- org.exolab.castor.xml.TypeValidator getValidator()
+
+ /**
+ * Method getXMLName
+ *
+ *
+ *
+ * @return String
+ */
+ public java.lang.String getXMLName()
+ {
+ return xmlName;
+ } //-- java.lang.String getXMLName()
+
+}
/*
* This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M1</a>, using an XML
+ * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
* Schema.
* $Id$
*/
//--------------------------/
/**
- * Field _treeList
+ * Field _id
*/
- private java.util.Vector _treeList;
+ private java.lang.String _id;
+
+ /**
+ * Field _dendroList
+ */
+ private java.util.Vector _dendroList;
/**
* Field _sequenceSetList
public VAMSAS()
{
super();
- _treeList = new Vector();
+ _dendroList = new Vector();
_sequenceSetList = new Vector();
} //-- org.vamsas.objects.core.VAMSAS()
//-----------/
/**
- * Method addSequenceSet
+ * Method addDendro
*
*
*
- * @param vSequenceSet
+ * @param vDendro
*/
- public void addSequenceSet(org.vamsas.objects.core.SequenceSet vSequenceSet)
+ public void addDendro(org.vamsas.objects.core.Dendro vDendro)
throws java.lang.IndexOutOfBoundsException
{
- _sequenceSetList.addElement(vSequenceSet);
- } //-- void addSequenceSet(org.vamsas.objects.core.SequenceSet)
+ _dendroList.addElement(vDendro);
+ } //-- void addDendro(org.vamsas.objects.core.Dendro)
/**
- * Method addSequenceSet
+ * Method addDendro
*
*
*
* @param index
- * @param vSequenceSet
+ * @param vDendro
*/
- public void addSequenceSet(int index, org.vamsas.objects.core.SequenceSet vSequenceSet)
+ public void addDendro(int index, org.vamsas.objects.core.Dendro vDendro)
throws java.lang.IndexOutOfBoundsException
{
- _sequenceSetList.insertElementAt(vSequenceSet, index);
- } //-- void addSequenceSet(int, org.vamsas.objects.core.SequenceSet)
+ _dendroList.insertElementAt(vDendro, index);
+ } //-- void addDendro(int, org.vamsas.objects.core.Dendro)
/**
- * Method addTree
+ * Method addSequenceSet
*
*
*
- * @param vTree
+ * @param vSequenceSet
*/
- public void addTree(java.lang.String vTree)
+ public void addSequenceSet(org.vamsas.objects.core.SequenceSet vSequenceSet)
throws java.lang.IndexOutOfBoundsException
{
- _treeList.addElement(vTree);
- } //-- void addTree(java.lang.String)
+ _sequenceSetList.addElement(vSequenceSet);
+ } //-- void addSequenceSet(org.vamsas.objects.core.SequenceSet)
/**
- * Method addTree
+ * Method addSequenceSet
*
*
*
* @param index
- * @param vTree
+ * @param vSequenceSet
*/
- public void addTree(int index, java.lang.String vTree)
+ public void addSequenceSet(int index, org.vamsas.objects.core.SequenceSet vSequenceSet)
throws java.lang.IndexOutOfBoundsException
{
- _treeList.insertElementAt(vTree, index);
- } //-- void addTree(int, java.lang.String)
+ _sequenceSetList.insertElementAt(vSequenceSet, index);
+ } //-- void addSequenceSet(int, org.vamsas.objects.core.SequenceSet)
/**
- * Method enumerateSequenceSet
+ * Method enumerateDendro
*
*
*
* @return Enumeration
*/
- public java.util.Enumeration enumerateSequenceSet()
+ public java.util.Enumeration enumerateDendro()
{
- return _sequenceSetList.elements();
- } //-- java.util.Enumeration enumerateSequenceSet()
+ return _dendroList.elements();
+ } //-- java.util.Enumeration enumerateDendro()
/**
- * Method enumerateTree
+ * Method enumerateSequenceSet
*
*
*
* @return Enumeration
*/
- public java.util.Enumeration enumerateTree()
+ public java.util.Enumeration enumerateSequenceSet()
{
- return _treeList.elements();
- } //-- java.util.Enumeration enumerateTree()
+ return _sequenceSetList.elements();
+ } //-- java.util.Enumeration enumerateSequenceSet()
/**
* Note: hashCode() has not been overriden
if (obj instanceof VAMSAS) {
VAMSAS temp = (VAMSAS)obj;
- if (this._treeList != null) {
- if (temp._treeList == null) return false;
- else if (!(this._treeList.equals(temp._treeList)))
+ if (this._id != null) {
+ if (temp._id == null) return false;
+ else if (!(this._id.equals(temp._id)))
return false;
}
- else if (temp._treeList != null)
+ else if (temp._id != null)
+ return false;
+ if (this._dendroList != null) {
+ if (temp._dendroList == null) return false;
+ else if (!(this._dendroList.equals(temp._dendroList)))
+ return false;
+ }
+ else if (temp._dendroList != null)
return false;
if (this._sequenceSetList != null) {
if (temp._sequenceSetList == null) return false;
} //-- boolean equals(java.lang.Object)
/**
- * Method getSequenceSet
+ * Method getDendro
*
*
*
* @param index
- * @return SequenceSet
+ * @return Dendro
*/
- public org.vamsas.objects.core.SequenceSet getSequenceSet(int index)
+ public org.vamsas.objects.core.Dendro getDendro(int index)
throws java.lang.IndexOutOfBoundsException
{
//-- check bounds for index
- if ((index < 0) || (index > _sequenceSetList.size())) {
- throw new IndexOutOfBoundsException("getSequenceSet: Index value '"+index+"' not in range [0.."+_sequenceSetList.size()+ "]");
+ if ((index < 0) || (index > _dendroList.size())) {
+ throw new IndexOutOfBoundsException("getDendro: Index value '"+index+"' not in range [0.."+_dendroList.size()+ "]");
}
- return (org.vamsas.objects.core.SequenceSet) _sequenceSetList.elementAt(index);
- } //-- org.vamsas.objects.core.SequenceSet getSequenceSet(int)
+ return (org.vamsas.objects.core.Dendro) _dendroList.elementAt(index);
+ } //-- org.vamsas.objects.core.Dendro getDendro(int)
/**
- * Method getSequenceSet
+ * Method getDendro
*
*
*
- * @return SequenceSet
+ * @return Dendro
*/
- public org.vamsas.objects.core.SequenceSet[] getSequenceSet()
+ public org.vamsas.objects.core.Dendro[] getDendro()
{
- int size = _sequenceSetList.size();
- org.vamsas.objects.core.SequenceSet[] mArray = new org.vamsas.objects.core.SequenceSet[size];
+ int size = _dendroList.size();
+ org.vamsas.objects.core.Dendro[] mArray = new org.vamsas.objects.core.Dendro[size];
for (int index = 0; index < size; index++) {
- mArray[index] = (org.vamsas.objects.core.SequenceSet) _sequenceSetList.elementAt(index);
+ mArray[index] = (org.vamsas.objects.core.Dendro) _dendroList.elementAt(index);
}
return mArray;
- } //-- org.vamsas.objects.core.SequenceSet[] getSequenceSet()
+ } //-- org.vamsas.objects.core.Dendro[] getDendro()
/**
- * Method getSequenceSetCount
+ * Method getDendroCount
*
*
*
* @return int
*/
- public int getSequenceSetCount()
+ public int getDendroCount()
{
- return _sequenceSetList.size();
- } //-- int getSequenceSetCount()
+ return _dendroList.size();
+ } //-- int getDendroCount()
/**
- * Method getTree
+ * Returns the value of field 'id'.
+ *
+ * @return String
+ * @return the value of field 'id'.
+ */
+ public java.lang.String getId()
+ {
+ return this._id;
+ } //-- java.lang.String getId()
+
+ /**
+ * Method getSequenceSet
*
*
*
* @param index
- * @return String
+ * @return SequenceSet
*/
- public java.lang.String getTree(int index)
+ public org.vamsas.objects.core.SequenceSet getSequenceSet(int index)
throws java.lang.IndexOutOfBoundsException
{
//-- check bounds for index
- if ((index < 0) || (index > _treeList.size())) {
- throw new IndexOutOfBoundsException("getTree: Index value '"+index+"' not in range [0.."+_treeList.size()+ "]");
+ if ((index < 0) || (index > _sequenceSetList.size())) {
+ throw new IndexOutOfBoundsException("getSequenceSet: Index value '"+index+"' not in range [0.."+_sequenceSetList.size()+ "]");
}
- return (String)_treeList.elementAt(index);
- } //-- java.lang.String getTree(int)
+ return (org.vamsas.objects.core.SequenceSet) _sequenceSetList.elementAt(index);
+ } //-- org.vamsas.objects.core.SequenceSet getSequenceSet(int)
/**
- * Method getTree
+ * Method getSequenceSet
*
*
*
- * @return String
+ * @return SequenceSet
*/
- public java.lang.String[] getTree()
+ public org.vamsas.objects.core.SequenceSet[] getSequenceSet()
{
- int size = _treeList.size();
- java.lang.String[] mArray = new java.lang.String[size];
+ int size = _sequenceSetList.size();
+ org.vamsas.objects.core.SequenceSet[] mArray = new org.vamsas.objects.core.SequenceSet[size];
for (int index = 0; index < size; index++) {
- mArray[index] = (String)_treeList.elementAt(index);
+ mArray[index] = (org.vamsas.objects.core.SequenceSet) _sequenceSetList.elementAt(index);
}
return mArray;
- } //-- java.lang.String[] getTree()
+ } //-- org.vamsas.objects.core.SequenceSet[] getSequenceSet()
/**
- * Method getTreeCount
+ * Method getSequenceSetCount
*
*
*
* @return int
*/
- public int getTreeCount()
+ public int getSequenceSetCount()
{
- return _treeList.size();
- } //-- int getTreeCount()
+ return _sequenceSetList.size();
+ } //-- int getSequenceSetCount()
/**
* Method isValid
} //-- void marshal(org.xml.sax.ContentHandler)
/**
+ * Method removeAllDendro
+ *
+ */
+ public void removeAllDendro()
+ {
+ _dendroList.removeAllElements();
+ } //-- void removeAllDendro()
+
+ /**
* Method removeAllSequenceSet
*
*/
} //-- void removeAllSequenceSet()
/**
- * Method removeAllTree
+ * Method removeDendro
+ *
*
+ *
+ * @param index
+ * @return Dendro
*/
- public void removeAllTree()
+ public org.vamsas.objects.core.Dendro removeDendro(int index)
{
- _treeList.removeAllElements();
- } //-- void removeAllTree()
+ java.lang.Object obj = _dendroList.elementAt(index);
+ _dendroList.removeElementAt(index);
+ return (org.vamsas.objects.core.Dendro) obj;
+ } //-- org.vamsas.objects.core.Dendro removeDendro(int)
/**
* Method removeSequenceSet
} //-- org.vamsas.objects.core.SequenceSet removeSequenceSet(int)
/**
- * Method removeTree
+ * Method setDendro
*
*
*
* @param index
- * @return String
+ * @param vDendro
+ */
+ public void setDendro(int index, org.vamsas.objects.core.Dendro vDendro)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ //-- check bounds for index
+ if ((index < 0) || (index > _dendroList.size())) {
+ throw new IndexOutOfBoundsException("setDendro: Index value '"+index+"' not in range [0.."+_dendroList.size()+ "]");
+ }
+ _dendroList.setElementAt(vDendro, index);
+ } //-- void setDendro(int, org.vamsas.objects.core.Dendro)
+
+ /**
+ * Method setDendro
+ *
+ *
+ *
+ * @param dendroArray
+ */
+ public void setDendro(org.vamsas.objects.core.Dendro[] dendroArray)
+ {
+ //-- copy array
+ _dendroList.removeAllElements();
+ for (int i = 0; i < dendroArray.length; i++) {
+ _dendroList.addElement(dendroArray[i]);
+ }
+ } //-- void setDendro(org.vamsas.objects.core.Dendro)
+
+ /**
+ * Sets the value of field 'id'.
+ *
+ * @param id the value of field 'id'.
*/
- public java.lang.String removeTree(int index)
+ public void setId(java.lang.String id)
{
- java.lang.Object obj = _treeList.elementAt(index);
- _treeList.removeElementAt(index);
- return (String)obj;
- } //-- java.lang.String removeTree(int)
+ this._id = id;
+ } //-- void setId(java.lang.String)
/**
* Method setSequenceSet
} //-- void setSequenceSet(org.vamsas.objects.core.SequenceSet)
/**
- * Method setTree
- *
- *
- *
- * @param index
- * @param vTree
- */
- public void setTree(int index, java.lang.String vTree)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _treeList.size())) {
- throw new IndexOutOfBoundsException("setTree: Index value '"+index+"' not in range [0.."+_treeList.size()+ "]");
- }
- _treeList.setElementAt(vTree, index);
- } //-- void setTree(int, java.lang.String)
-
- /**
- * Method setTree
- *
- *
- *
- * @param treeArray
- */
- public void setTree(java.lang.String[] treeArray)
- {
- //-- copy array
- _treeList.removeAllElements();
- for (int i = 0; i < treeArray.length; i++) {
- _treeList.addElement(treeArray[i]);
- }
- } //-- void setTree(java.lang.String)
-
- /**
* Method unmarshal
*
*
/*
* This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M1</a>, using an XML
+ * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
* Schema.
* $Id$
*/
org.exolab.castor.xml.FieldValidator fieldValidator = null;
//-- initialize attribute descriptors
+ //-- _id
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute);
+ this.identity = desc;
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ VAMSAS target = (VAMSAS) object;
+ return target.getId();
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ VAMSAS target = (VAMSAS) object;
+ target.setId( (java.lang.String) value);
+ }
+ catch (java.lang.Exception ex) {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+ public java.lang.Object newInstance( java.lang.Object parent ) {
+ return new java.lang.String();
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _id
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { //-- local scope
+ }
+ desc.setValidator(fieldValidator);
//-- initialize element descriptors
- //-- _treeList
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_treeList", "Tree", org.exolab.castor.xml.NodeType.Element);
- desc.setImmutable(true);
+ //-- _dendroList
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Dendro.class, "_dendroList", "Dendro", org.exolab.castor.xml.NodeType.Element);
handler = new org.exolab.castor.xml.XMLFieldHandler() {
public java.lang.Object getValue( java.lang.Object object )
throws IllegalStateException
{
VAMSAS target = (VAMSAS) object;
- return target.getTree();
+ return target.getDendro();
}
public void setValue( java.lang.Object object, java.lang.Object value)
throws IllegalStateException, IllegalArgumentException
{
try {
VAMSAS target = (VAMSAS) object;
- target.addTree( (java.lang.String) value);
+ target.addDendro( (org.vamsas.objects.core.Dendro) value);
}
catch (java.lang.Exception ex) {
throw new IllegalStateException(ex.toString());
}
}
public java.lang.Object newInstance( java.lang.Object parent ) {
- return null;
+ return new org.vamsas.objects.core.Dendro();
}
};
desc.setHandler(handler);
desc.setMultivalued(true);
addFieldDescriptor(desc);
- //-- validation code for: _treeList
+ //-- validation code for: _dendroList
fieldValidator = new org.exolab.castor.xml.FieldValidator();
fieldValidator.setMinOccurs(0);
{ //-- local scope
- StringValidator typeValidator = new StringValidator();
- typeValidator.setWhiteSpace("preserve");
- fieldValidator.setValidator(typeValidator);
}
desc.setValidator(fieldValidator);
//-- _sequenceSetList
git://source.jalview.org / vamsas.git / commitdiff