<xs:element ref="vamsas:Tree" minOccurs="0" maxOccurs="unbounded"/>
<xs:element ref="vamsas:SequenceSet" minOccurs="0" maxOccurs="unbounded"/>
</xs:sequence>
- <xs:attribute name="id" type="xs:ID"/>
+ <xs:attribute name="id" type="xs:ID" minOccurs="0" maxOccurs="1"/>
</xs:complexType>
<xs:element name="Tree">
<xs:complexType>
<xs:sequence>
- <xs:element name="newickFormat" type="xs:string" minOccurs="1" maxOccurs="unbounded"/>
+ <xs:element name="title" type="xs:string" minOccurs="0" maxOccurs="1"/>
+ <xs:element name="newick" minOccurs="1" maxOccurs="unbounded">
+ <xs:complexType>
+ <xs:simpleContent>
+ <xs:extension base="xs:string">
+ <xs:attribute name="title" type="xs:string" minOccurs="0" maxOccurs="1"/>
+ <xs:attribute name="id" type="xs:ID" minOccurs="0" maxOccurs="1"/>
+ </xs:extension>
+ </xs:simpleContent>
+ </xs:complexType>
+ </xs:element>
<xs:element ref="vamsas:Provenance" minOccurs="1" maxOccurs="1"/>
</xs:sequence>
- <xs:attribute name="id" type="xs:ID"/>
+ <xs:attribute name="id" type="xs:ID" minOccurs="0" maxOccurs="1"/>
</xs:complexType>
</xs:element>
<xs:element name="Provenance">
<xs:complexType>
- <xs:sequence maxOccurs="unbounded">
- <xs:element name="entry">
+ <xs:sequence>
+ <xs:element name="entry" minOccurs="0" maxOccurs="unbounded">
<xs:complexType>
<xs:sequence>
<xs:element name="User" type="xs:string"/>
<xs:element name="Action" type="xs:string"/>
<xs:element name="Date" type="xs:date"/>
</xs:sequence>
- <xs:attribute name="id" type="xs:ID"/>
+ <xs:attribute name="id" type="xs:ID" minOccurs="0" maxOccurs="1"/>
</xs:complexType>
</xs:element>
</xs:sequence>
</xs:complexType>
</xs:element>
+
<xs:element name="SequenceSet">
<xs:complexType>
<xs:sequence>
<xs:complexType>
<xs:complexContent>
<xs:extension base="vamsas:SequenceType">
+ <xs:sequence>
+ <xs:element name="dbRef" minOccurs="0" maxOccurs="unbounded">
+ <xs:complexType>
+ <xs:attribute name="source"/>
+ <xs:attribute name="version"/>
+ <xs:attribute name="accessionId"/>
+ <xs:attribute name="id" type="xs:ID" minOccurs="0" maxOccurs="1"/>
+ </xs:complexType>
+ </xs:element>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:ID" minOccurs="1" maxOccurs="1"/>
<xs:attribute name="dictionary" type="xs:string"/>
</xs:extension>
</xs:complexContent>
<xs:element name="description" type="xs:string" minOccurs="0"/>
<xs:element name="status" type="xs:string" minOccurs="0"/>
<xs:element ref="vamsas:annotationElement" minOccurs="0" maxOccurs="unbounded"/>
- <xs:element ref="vamsas:Provenance"/>
+ <xs:element ref="vamsas:Provenance" minOccurs="0" maxOccurs="unbounded"/>
</xs:sequence>
<xs:attribute name="type" type="xs:string" use="required"/>
<xs:attribute name="end" type="xs:string" use="required"/>
<xs:attribute name="begin" type="xs:string" use="required"/>
<xs:attribute name="seqRef" type="xs:IDREF" use="required"/>
- <xs:attribute name="id" type="xs:ID"/>
+ <xs:attribute name="id" type="xs:ID" minOccurs="0" maxOccurs="1"/>
</xs:complexType>
</xs:element>
<xs:element name="Alignment" minOccurs="0" maxOccurs="unbounded">
<xs:element ref="vamsas:Provenance"/>
</xs:sequence>
<xs:attribute name="graph" type="xs:boolean" use="required"/>
- <xs:attribute name="id" type="xs:ID"/>
+ <xs:attribute name="id" type="xs:ID" minOccurs="0" maxOccurs="1"/>
</xs:complexType>
</xs:element>
<xs:element ref="vamsas:Tree" minOccurs="0" maxOccurs="unbounded"/>
<xs:complexType>
<xs:complexContent>
<xs:extension base="vamsas:SequenceType">
+ <xs:attribute name="id" type="xs:ID" minOccurs="0" maxOccurs="1"/>
<xs:attribute name="refid" type="xs:IDREF" use="required"/>
</xs:extension>
</xs:complexContent>
</xs:element>
<xs:element ref="vamsas:Provenance"/>
</xs:sequence>
+ <xs:attribute name="id" type="xs:ID" minOccurs="0" maxOccurs="1"/>
</xs:complexType>
</xs:element>
<xs:element ref="vamsas:Tree" minOccurs="0" maxOccurs="unbounded"/>
</xs:sequence>
<xs:attribute name="gapChar" type="xs:string" use="required"/>
<xs:attribute name="aligned" type="xs:boolean" use="optional"/>
- <xs:attribute name="id" type="xs:ID"/>
+ <xs:attribute name="id" type="xs:ID" minOccurs="0" maxOccurs="1"/>
</xs:complexType>
</xs:element>
<xs:element name="annotationElement">
<xs:element name="value" type="xs:float"/>
</xs:sequence>
<xs:attribute name="position" type="xs:int" use="required"/>
- <xs:attribute name="id" type="xs:ID"/>
+ <xs:attribute name="id" type="xs:ID" minOccurs="0" maxOccurs="1"/>
</xs:complexType>
</xs:element>
<xs:complexType name="SequenceType">
<xs:sequence>
<xs:element name="sequence" type="xs:string"/>
<xs:element name="name" type="xs:string"/>
- <xs:element name="dbRef" minOccurs="0" maxOccurs="unbounded">
- <xs:complexType>
- <xs:attribute name="source"/>
- <xs:attribute name="version"/>
- <xs:attribute name="accessionId"/>
- <xs:attribute name="id" type="xs:ID"/>
- </xs:complexType>
- </xs:element>
</xs:sequence>
<xs:attribute name="start" type="xs:int" use="required"/>
<xs:attribute name="end" type="xs:int" use="required"/>
- <xs:attribute name="id" type="xs:ID"/>
</xs:complexType>
<xs:complexType name="ApplicationData">
<xs:sequence>
<xs:element name="Application">
<xs:complexType>
+ <xs:sequence>
+ <xs:element name="User">
+ <xs:complexType>
+ <xs:attribute name="fullname" type="xs:string"/>
+ <xs:attribute name="organization" type="xs:string"/>
+ <xs:attribute name="data" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ </xs:sequence>
<xs:attribute name="version" type="xs:string"/>
<xs:attribute name="name" type="xs:string"/>
- <xs:attribute name="session" type="xs:string"/>
+ <xs:attribute name="urn" type="xs:string"/>
<xs:attribute name="data" type="xs:string"/>
</xs:complexType>
</xs:element>
package org.vamsas.client;
+
+import java.io.File;
+import java.io.IOException;
+
/**
* TODO document type SimpleClientFactory
* @author jimp
*
*/
public class SimpleClientFactory implements IClientFactory {
- static SimpleClientFactory singleton = null;
-
- static private void CreateClientFactory() {
- if (singleton != null) {
-
- } else {
- // Create singleton class.
-
- }
+
+ File sessionArena;
+
+ /**
+ * default constructor - called by CreateClientFactory only.
+ *
+ */
+ public SimpleClientFactory() {
+ sessionArena = null;
}
/**
* Create a client factory that works with sessions at the given
* path.
* @param path
*/
- public SimpleClientFactory(String path) {
+ public SimpleClientFactory(String path) throws IOException {
// Check path is valid and read/writeable.
- // make housekeeping files...
+ File newarena = new File(path);
+ if (newarena.isDirectory() && newarena.canRead() && newarena.canWrite()) {
+ sessionArena = newarena;
+ } else {
+ sessionArena = null;
+ throw(new IOException("Cannot read and write to a directory called "+path));
+ }
}
/* (non-Javadoc)
* @see org.vamsas.client.IClientFactory#getIClient(org.vamsas.client.ClientHandle)
* to any object in the vamsas document
*/
protected boolean __stored_in_document=false;
+ protected long __last_hash=0;
protected VorbaId vorbaId=null;
protected IVorbaIdFactory __vorba=null;
/**
protected void set__stored_in_document(boolean __stored_in_document) {
this.__stored_in_document = __stored_in_document;
}
+ /**
+ * __last_hash is the hash value computed
+ * when the object was last checked against
+ * a IClientDocument generated by the
+ * object's parent IClient instance.
+ * @return Returns the __last_hash.
+ */
+ public long get__last_hash() {
+ return __last_hash;
+ }
}
-- 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.Newick=org.vamsas.objects.core.NewickDescriptor
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.User=org.vamsas.objects.core.UserDescriptor
+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...
//--------------------------/
/**
+ * Field _id
+ */
+ private java.lang.String _id;
+
+ /**
* Field _alignmentAnnotations
*/
private org.vamsas.objects.core.AlignmentAnnotations _alignmentAnnotations;
if (obj instanceof Alignment) {
Alignment temp = (Alignment)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._alignmentAnnotations != null) {
if (temp._alignmentAnnotations == null) return false;
else if (!(this._alignmentAnnotations.equals(temp._alignmentAnnotations)))
} //-- int getAlignmentSequenceCount()
/**
+ * 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 setAlignmentSequence(org.vamsas.objects.core.AlignmentSequence)
/**
+ * 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'.
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
+ {
+ Alignment target = (Alignment) object;
+ return target.getId();
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ Alignment target = (Alignment) 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
//-- _alignmentAnnotations
//--------------------------/
/**
+ * Field _id
+ */
+ private java.lang.String _id;
+
+ /**
* Field _refid
*/
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)))
+ return false;
+ }
+ else if (temp._id != null)
+ return false;
if (this._refid != null) {
if (temp._refid == null) return false;
else if (!(this._refid.equals(temp._refid)))
} //-- 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()
+
+ /**
* Returns the value of field 'refid'.
*
* @return Object
} //-- void marshal(org.xml.sax.ContentHandler)
/**
+ * 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 'refid'.
*
* @param refid the value of field 'refid'.
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
+ {
+ AlignmentSequence target = (AlignmentSequence) object;
+ return target.getId();
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ AlignmentSequence target = (AlignmentSequence) 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);
//-- _refid
desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Object.class, "_refid", "refid", org.exolab.castor.xml.NodeType.Attribute);
desc.setReference(true);
private java.lang.String _name;
/**
- * Field _session
+ * Field _urn
*/
- private java.lang.String _session;
+ private java.lang.String _urn;
/**
* Field _data
*/
private java.lang.String _data;
+ /**
+ * Field _user
+ */
+ private org.vamsas.objects.core.User _user;
+
//----------------/
//- Constructors -/
}
else if (temp._name != null)
return false;
- if (this._session != null) {
- if (temp._session == null) return false;
- else if (!(this._session.equals(temp._session)))
+ if (this._urn != null) {
+ if (temp._urn == null) return false;
+ else if (!(this._urn.equals(temp._urn)))
return false;
}
- else if (temp._session != null)
+ else if (temp._urn != null)
return false;
if (this._data != null) {
if (temp._data == null) return false;
}
else if (temp._data != null)
return false;
+ if (this._user != null) {
+ if (temp._user == null) return false;
+ else if (!(this._user.equals(temp._user)))
+ return false;
+ }
+ else if (temp._user != null)
+ return false;
return true;
}
return false;
} //-- java.lang.String getName()
/**
- * Returns the value of field 'session'.
+ * Returns the value of field 'urn'.
*
* @return String
- * @return the value of field 'session'.
+ * @return the value of field 'urn'.
+ */
+ public java.lang.String getUrn()
+ {
+ return this._urn;
+ } //-- java.lang.String getUrn()
+
+ /**
+ * Returns the value of field 'user'.
+ *
+ * @return User
+ * @return the value of field 'user'.
*/
- public java.lang.String getSession()
+ public org.vamsas.objects.core.User getUser()
{
- return this._session;
- } //-- java.lang.String getSession()
+ return this._user;
+ } //-- org.vamsas.objects.core.User getUser()
/**
* Returns the value of field 'version'.
} //-- void setName(java.lang.String)
/**
- * Sets the value of field 'session'.
+ * Sets the value of field 'urn'.
+ *
+ * @param urn the value of field 'urn'.
+ */
+ public void setUrn(java.lang.String urn)
+ {
+ this._urn = urn;
+ } //-- void setUrn(java.lang.String)
+
+ /**
+ * Sets the value of field 'user'.
*
- * @param session the value of field 'session'.
+ * @param user the value of field 'user'.
*/
- public void setSession(java.lang.String session)
+ public void setUser(org.vamsas.objects.core.User user)
{
- this._session = session;
- } //-- void setSession(java.lang.String)
+ this._user = user;
+ } //-- void setUser(org.vamsas.objects.core.User)
/**
* Sets the value of field 'version'.
super();
nsURI = "http://www.vamsas.org";
xmlName = "Application";
+
+ //-- 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;
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);
+ //-- _urn
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_urn", "urn", 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();
+ return target.getUrn();
}
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);
+ target.setUrn( (java.lang.String) value);
}
catch (java.lang.Exception ex) {
throw new IllegalStateException(ex.toString());
desc.setMultivalued(false);
addFieldDescriptor(desc);
- //-- validation code for: _session
+ //-- validation code for: _urn
fieldValidator = new org.exolab.castor.xml.FieldValidator();
{ //-- local scope
StringValidator typeValidator = new StringValidator();
desc.setValidator(fieldValidator);
//-- initialize element descriptors
+ //-- _user
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.User.class, "_user", "User", org.exolab.castor.xml.NodeType.Element);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ Application target = (Application) object;
+ return target.getUser();
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ Application target = (Application) object;
+ target.setUser( (org.vamsas.objects.core.User) 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.User();
+ }
+ };
+ desc.setHandler(handler);
+ desc.setNameSpaceURI("http://www.vamsas.org");
+ desc.setRequired(true);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _user
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(1);
+ { //-- local scope
+ }
+ desc.setValidator(fieldValidator);
} //-- org.vamsas.objects.core.ApplicationDescriptor()
--- /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 Newick.
+ *
+ * @version $Revision$ $Date$
+ */
+public class Newick extends org.vamsas.client.object
+implements java.io.Serializable
+{
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * internal content storage
+ */
+ private java.lang.String _content = "";
+
+ /**
+ * Field _title
+ */
+ private java.lang.String _title;
+
+ /**
+ * Field _id
+ */
+ private java.lang.String _id;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public Newick()
+ {
+ super();
+ setContent("");
+ } //-- org.vamsas.objects.core.Newick()
+
+
+ //-----------/
+ //- 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 Newick) {
+
+ Newick temp = (Newick)obj;
+ if (this._content != null) {
+ if (temp._content == null) return false;
+ else if (!(this._content.equals(temp._content)))
+ return false;
+ }
+ else if (temp._content != null)
+ return false;
+ if (this._title != null) {
+ if (temp._title == null) return false;
+ else if (!(this._title.equals(temp._title)))
+ return false;
+ }
+ else if (temp._title != 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;
+ } //-- boolean equals(java.lang.Object)
+
+ /**
+ * Returns the value of field 'content'. The field 'content'
+ * has the following description: internal content storage
+ *
+ * @return String
+ * @return the value of field 'content'.
+ */
+ public java.lang.String getContent()
+ {
+ return this._content;
+ } //-- java.lang.String getContent()
+
+ /**
+ * 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 'title'.
+ *
+ * @return String
+ * @return the value of field 'title'.
+ */
+ public java.lang.String getTitle()
+ {
+ return this._title;
+ } //-- java.lang.String getTitle()
+
+ /**
+ * 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)
+
+ /**
+ * Sets the value of field 'content'. The field 'content' has
+ * the following description: internal content storage
+ *
+ * @param content the value of field 'content'.
+ */
+ public void setContent(java.lang.String content)
+ {
+ this._content = content;
+ } //-- void setContent(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 'title'.
+ *
+ * @param title the value of field 'title'.
+ */
+ public void setTitle(java.lang.String title)
+ {
+ this._title = title;
+ } //-- void setTitle(java.lang.String)
+
+ /**
+ * Method unmarshal
+ *
+ *
+ *
+ * @param reader
+ * @return Newick
+ */
+ public static org.vamsas.objects.core.Newick unmarshal(java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+ {
+ return (org.vamsas.objects.core.Newick) Unmarshaller.unmarshal(org.vamsas.objects.core.Newick.class, reader);
+ } //-- org.vamsas.objects.core.Newick 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 NewickDescriptor.
+ *
+ * @version $Revision$ $Date$
+ */
+public class NewickDescriptor 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 NewickDescriptor()
+ {
+ super();
+ nsURI = "http://www.vamsas.org";
+ xmlName = "newick";
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+ org.exolab.castor.mapping.FieldHandler handler = null;
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;
+ //-- _content
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_content", "PCDATA", org.exolab.castor.xml.NodeType.Text);
+ desc.setImmutable(true);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ Newick target = (Newick) object;
+ return target.getContent();
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ Newick target = (Newick) object;
+ target.setContent( (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);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _content
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { //-- local scope
+ StringValidator typeValidator = new StringValidator();
+ typeValidator.setWhiteSpace("preserve");
+ fieldValidator.setValidator(typeValidator);
+ }
+ desc.setValidator(fieldValidator);
+ //-- initialize attribute descriptors
+
+ //-- _title
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_title", "title", 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
+ {
+ Newick target = (Newick) object;
+ return target.getTitle();
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ Newick target = (Newick) object;
+ target.setTitle( (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: _title
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { //-- local scope
+ StringValidator typeValidator = new StringValidator();
+ typeValidator.setWhiteSpace("preserve");
+ 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
+ {
+ Newick target = (Newick) object;
+ return target.getId();
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ Newick target = (Newick) 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.NewickDescriptor()
+
+
+ //-----------/
+ //- 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.Newick.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()
+
+}
//--------------------------/
/**
- * Field _items
+ * Field _entryList
*/
- private java.util.Vector _items;
+ private java.util.Vector _entryList;
//----------------/
public Provenance()
{
super();
- _items = new Vector();
+ _entryList = new Vector();
} //-- org.vamsas.objects.core.Provenance()
//-----------/
/**
- * Method addProvenanceItem
+ * Method addEntry
*
*
*
- * @param vProvenanceItem
+ * @param vEntry
*/
- public void addProvenanceItem(org.vamsas.objects.core.ProvenanceItem vProvenanceItem)
+ public void addEntry(org.vamsas.objects.core.Entry vEntry)
throws java.lang.IndexOutOfBoundsException
{
- _items.addElement(vProvenanceItem);
- } //-- void addProvenanceItem(org.vamsas.objects.core.ProvenanceItem)
+ _entryList.addElement(vEntry);
+ } //-- void addEntry(org.vamsas.objects.core.Entry)
/**
- * Method addProvenanceItem
+ * Method addEntry
*
*
*
* @param index
- * @param vProvenanceItem
+ * @param vEntry
*/
- public void addProvenanceItem(int index, org.vamsas.objects.core.ProvenanceItem vProvenanceItem)
+ public void addEntry(int index, org.vamsas.objects.core.Entry vEntry)
throws java.lang.IndexOutOfBoundsException
{
- _items.insertElementAt(vProvenanceItem, index);
- } //-- void addProvenanceItem(int, org.vamsas.objects.core.ProvenanceItem)
+ _entryList.insertElementAt(vEntry, index);
+ } //-- void addEntry(int, org.vamsas.objects.core.Entry)
/**
- * Method enumerateProvenanceItem
+ * Method enumerateEntry
*
*
*
* @return Enumeration
*/
- public java.util.Enumeration enumerateProvenanceItem()
+ public java.util.Enumeration enumerateEntry()
{
- return _items.elements();
- } //-- java.util.Enumeration enumerateProvenanceItem()
+ return _entryList.elements();
+ } //-- java.util.Enumeration enumerateEntry()
/**
* Note: hashCode() has not been overriden
if (obj instanceof Provenance) {
Provenance temp = (Provenance)obj;
- if (this._items != null) {
- if (temp._items == null) return false;
- else if (!(this._items.equals(temp._items)))
+ if (this._entryList != null) {
+ if (temp._entryList == null) return false;
+ else if (!(this._entryList.equals(temp._entryList)))
return false;
}
- else if (temp._items != null)
+ else if (temp._entryList != null)
return false;
return true;
}
} //-- boolean equals(java.lang.Object)
/**
- * Method getProvenanceItem
+ * Method getEntry
*
*
*
* @param index
- * @return ProvenanceItem
+ * @return Entry
*/
- public org.vamsas.objects.core.ProvenanceItem getProvenanceItem(int index)
+ public org.vamsas.objects.core.Entry getEntry(int index)
throws java.lang.IndexOutOfBoundsException
{
//-- check bounds for index
- if ((index < 0) || (index > _items.size())) {
- throw new IndexOutOfBoundsException("getProvenanceItem: Index value '"+index+"' not in range [0.."+_items.size()+ "]");
+ if ((index < 0) || (index > _entryList.size())) {
+ throw new IndexOutOfBoundsException("getEntry: Index value '"+index+"' not in range [0.."+_entryList.size()+ "]");
}
- return (org.vamsas.objects.core.ProvenanceItem) _items.elementAt(index);
- } //-- org.vamsas.objects.core.ProvenanceItem getProvenanceItem(int)
+ return (org.vamsas.objects.core.Entry) _entryList.elementAt(index);
+ } //-- org.vamsas.objects.core.Entry getEntry(int)
/**
- * Method getProvenanceItem
+ * Method getEntry
*
*
*
- * @return ProvenanceItem
+ * @return Entry
*/
- public org.vamsas.objects.core.ProvenanceItem[] getProvenanceItem()
+ public org.vamsas.objects.core.Entry[] getEntry()
{
- int size = _items.size();
- org.vamsas.objects.core.ProvenanceItem[] mArray = new org.vamsas.objects.core.ProvenanceItem[size];
+ int size = _entryList.size();
+ org.vamsas.objects.core.Entry[] mArray = new org.vamsas.objects.core.Entry[size];
for (int index = 0; index < size; index++) {
- mArray[index] = (org.vamsas.objects.core.ProvenanceItem) _items.elementAt(index);
+ mArray[index] = (org.vamsas.objects.core.Entry) _entryList.elementAt(index);
}
return mArray;
- } //-- org.vamsas.objects.core.ProvenanceItem[] getProvenanceItem()
+ } //-- org.vamsas.objects.core.Entry[] getEntry()
/**
- * Method getProvenanceItemCount
+ * Method getEntryCount
*
*
*
* @return int
*/
- public int getProvenanceItemCount()
+ public int getEntryCount()
{
- return _items.size();
- } //-- int getProvenanceItemCount()
+ return _entryList.size();
+ } //-- int getEntryCount()
/**
* Method isValid
} //-- void marshal(org.xml.sax.ContentHandler)
/**
- * Method removeAllProvenanceItem
+ * Method removeAllEntry
*
*/
- public void removeAllProvenanceItem()
+ public void removeAllEntry()
{
- _items.removeAllElements();
- } //-- void removeAllProvenanceItem()
+ _entryList.removeAllElements();
+ } //-- void removeAllEntry()
/**
- * Method removeProvenanceItem
+ * Method removeEntry
*
*
*
* @param index
- * @return ProvenanceItem
+ * @return Entry
*/
- public org.vamsas.objects.core.ProvenanceItem removeProvenanceItem(int index)
+ public org.vamsas.objects.core.Entry removeEntry(int index)
{
- java.lang.Object obj = _items.elementAt(index);
- _items.removeElementAt(index);
- return (org.vamsas.objects.core.ProvenanceItem) obj;
- } //-- org.vamsas.objects.core.ProvenanceItem removeProvenanceItem(int)
+ java.lang.Object obj = _entryList.elementAt(index);
+ _entryList.removeElementAt(index);
+ return (org.vamsas.objects.core.Entry) obj;
+ } //-- org.vamsas.objects.core.Entry removeEntry(int)
/**
- * Method setProvenanceItem
+ * Method setEntry
*
*
*
* @param index
- * @param vProvenanceItem
+ * @param vEntry
*/
- public void setProvenanceItem(int index, org.vamsas.objects.core.ProvenanceItem vProvenanceItem)
+ public void setEntry(int index, org.vamsas.objects.core.Entry vEntry)
throws java.lang.IndexOutOfBoundsException
{
//-- check bounds for index
- if ((index < 0) || (index > _items.size())) {
- throw new IndexOutOfBoundsException("setProvenanceItem: Index value '"+index+"' not in range [0.."+_items.size()+ "]");
+ if ((index < 0) || (index > _entryList.size())) {
+ throw new IndexOutOfBoundsException("setEntry: Index value '"+index+"' not in range [0.."+_entryList.size()+ "]");
}
- _items.setElementAt(vProvenanceItem, index);
- } //-- void setProvenanceItem(int, org.vamsas.objects.core.ProvenanceItem)
+ _entryList.setElementAt(vEntry, index);
+ } //-- void setEntry(int, org.vamsas.objects.core.Entry)
/**
- * Method setProvenanceItem
+ * Method setEntry
*
*
*
- * @param provenanceItemArray
+ * @param entryArray
*/
- public void setProvenanceItem(org.vamsas.objects.core.ProvenanceItem[] provenanceItemArray)
+ public void setEntry(org.vamsas.objects.core.Entry[] entryArray)
{
//-- copy array
- _items.removeAllElements();
- for (int i = 0; i < provenanceItemArray.length; i++) {
- _items.addElement(provenanceItemArray[i]);
+ _entryList.removeAllElements();
+ for (int i = 0; i < entryArray.length; i++) {
+ _entryList.addElement(entryArray[i]);
}
- } //-- void setProvenanceItem(org.vamsas.objects.core.ProvenanceItem)
+ } //-- void setEntry(org.vamsas.objects.core.Entry)
/**
* Method unmarshal
public ProvenanceDescriptor()
{
super();
+ nsURI = "http://www.vamsas.org";
xmlName = "Provenance";
+
+ //-- 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 element descriptors
- //-- _items
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.ProvenanceItem.class, "_items", (String)null, org.exolab.castor.xml.NodeType.Element);
+ //-- _entryList
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Entry.class, "_entryList", "entry", org.exolab.castor.xml.NodeType.Element);
handler = new org.exolab.castor.xml.XMLFieldHandler() {
public java.lang.Object getValue( java.lang.Object object )
throws IllegalStateException
{
Provenance target = (Provenance) object;
- return target.getProvenanceItem();
+ return target.getEntry();
}
public void setValue( java.lang.Object object, java.lang.Object value)
throws IllegalStateException, IllegalArgumentException
{
try {
Provenance target = (Provenance) object;
- target.addProvenanceItem( (org.vamsas.objects.core.ProvenanceItem) value);
+ target.addEntry( (org.vamsas.objects.core.Entry) 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.ProvenanceItem();
+ return new org.vamsas.objects.core.Entry();
}
};
desc.setHandler(handler);
- desc.setContainer(true);
- desc.setClassDescriptor(new org.vamsas.objects.core.ProvenanceItemDescriptor());
+ desc.setNameSpaceURI("http://www.vamsas.org");
desc.setMultivalued(true);
addFieldDescriptor(desc);
- //-- validation code for: _items
+ //-- validation code for: _entryList
fieldValidator = new org.exolab.castor.xml.FieldValidator();
fieldValidator.setMinOccurs(0);
{ //-- local scope
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;
//--------------------------/
/**
+ * Field _id
+ */
+ private java.lang.String _id;
+
+ /**
* Field _dictionary
*/
private java.lang.String _dictionary;
+ /**
+ * Field _dbRefList
+ */
+ private java.util.Vector _dbRefList;
+
//----------------/
//- Constructors -/
public Sequence()
{
super();
+ _dbRefList = new Vector();
} //-- org.vamsas.objects.core.Sequence()
//-----------/
/**
+ * Method addDbRef
+ *
+ *
+ *
+ * @param vDbRef
+ */
+ public void addDbRef(org.vamsas.objects.core.DbRef vDbRef)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _dbRefList.addElement(vDbRef);
+ } //-- void addDbRef(org.vamsas.objects.core.DbRef)
+
+ /**
+ * Method addDbRef
+ *
+ *
+ *
+ * @param index
+ * @param vDbRef
+ */
+ public void addDbRef(int index, org.vamsas.objects.core.DbRef vDbRef)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _dbRefList.insertElementAt(vDbRef, index);
+ } //-- void addDbRef(int, org.vamsas.objects.core.DbRef)
+
+ /**
+ * Method enumerateDbRef
+ *
+ *
+ *
+ * @return Enumeration
+ */
+ public java.util.Enumeration enumerateDbRef()
+ {
+ return _dbRefList.elements();
+ } //-- java.util.Enumeration enumerateDbRef()
+
+ /**
* Note: hashCode() has not been overriden
*
* @param obj
if (obj instanceof Sequence) {
Sequence temp = (Sequence)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._dictionary != null) {
if (temp._dictionary == null) return false;
else if (!(this._dictionary.equals(temp._dictionary)))
}
else if (temp._dictionary != null)
return false;
+ if (this._dbRefList != null) {
+ if (temp._dbRefList == null) return false;
+ else if (!(this._dbRefList.equals(temp._dbRefList)))
+ return false;
+ }
+ else if (temp._dbRefList != null)
+ return false;
return true;
}
return false;
} //-- boolean equals(java.lang.Object)
/**
+ * Method getDbRef
+ *
+ *
+ *
+ * @param index
+ * @return DbRef
+ */
+ public org.vamsas.objects.core.DbRef getDbRef(int index)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ //-- check bounds for index
+ if ((index < 0) || (index > _dbRefList.size())) {
+ throw new IndexOutOfBoundsException("getDbRef: Index value '"+index+"' not in range [0.."+_dbRefList.size()+ "]");
+ }
+
+ return (org.vamsas.objects.core.DbRef) _dbRefList.elementAt(index);
+ } //-- org.vamsas.objects.core.DbRef getDbRef(int)
+
+ /**
+ * Method getDbRef
+ *
+ *
+ *
+ * @return DbRef
+ */
+ public org.vamsas.objects.core.DbRef[] getDbRef()
+ {
+ int size = _dbRefList.size();
+ org.vamsas.objects.core.DbRef[] mArray = new org.vamsas.objects.core.DbRef[size];
+ for (int index = 0; index < size; index++) {
+ mArray[index] = (org.vamsas.objects.core.DbRef) _dbRefList.elementAt(index);
+ }
+ return mArray;
+ } //-- org.vamsas.objects.core.DbRef[] getDbRef()
+
+ /**
+ * Method getDbRefCount
+ *
+ *
+ *
+ * @return int
+ */
+ public int getDbRefCount()
+ {
+ return _dbRefList.size();
+ } //-- int getDbRefCount()
+
+ /**
* Returns the value of field 'dictionary'.
*
* @return String
} //-- 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 marshal(org.xml.sax.ContentHandler)
/**
+ * Method removeAllDbRef
+ *
+ */
+ public void removeAllDbRef()
+ {
+ _dbRefList.removeAllElements();
+ } //-- void removeAllDbRef()
+
+ /**
+ * Method removeDbRef
+ *
+ *
+ *
+ * @param index
+ * @return DbRef
+ */
+ public org.vamsas.objects.core.DbRef removeDbRef(int index)
+ {
+ java.lang.Object obj = _dbRefList.elementAt(index);
+ _dbRefList.removeElementAt(index);
+ return (org.vamsas.objects.core.DbRef) obj;
+ } //-- org.vamsas.objects.core.DbRef removeDbRef(int)
+
+ /**
+ * Method setDbRef
+ *
+ *
+ *
+ * @param index
+ * @param vDbRef
+ */
+ public void setDbRef(int index, org.vamsas.objects.core.DbRef vDbRef)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ //-- check bounds for index
+ if ((index < 0) || (index > _dbRefList.size())) {
+ throw new IndexOutOfBoundsException("setDbRef: Index value '"+index+"' not in range [0.."+_dbRefList.size()+ "]");
+ }
+ _dbRefList.setElementAt(vDbRef, index);
+ } //-- void setDbRef(int, org.vamsas.objects.core.DbRef)
+
+ /**
+ * Method setDbRef
+ *
+ *
+ *
+ * @param dbRefArray
+ */
+ public void setDbRef(org.vamsas.objects.core.DbRef[] dbRefArray)
+ {
+ //-- copy array
+ _dbRefList.removeAllElements();
+ for (int i = 0; i < dbRefArray.length; i++) {
+ _dbRefList.addElement(dbRefArray[i]);
+ }
+ } //-- void setDbRef(org.vamsas.objects.core.DbRef)
+
+ /**
* Sets the value of field 'dictionary'.
*
* @param dictionary the value of field 'dictionary'.
} //-- 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
*
*
setExtendsWithoutFlatten(new org.vamsas.objects.core.SequenceTypeDescriptor());
nsURI = "http://www.vamsas.org";
xmlName = "Sequence";
+
+ //-- 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
+ {
+ 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.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _id
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { //-- local scope
+ }
+ desc.setValidator(fieldValidator);
//-- _dictionary
desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_dictionary", "dictionary", org.exolab.castor.xml.NodeType.Attribute);
desc.setImmutable(true);
desc.setValidator(fieldValidator);
//-- initialize element descriptors
+ //-- _dbRefList
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.DbRef.class, "_dbRefList", "dbRef", org.exolab.castor.xml.NodeType.Element);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ Sequence target = (Sequence) object;
+ return target.getDbRef();
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ Sequence target = (Sequence) object;
+ target.addDbRef( (org.vamsas.objects.core.DbRef) 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.DbRef();
+ }
+ };
+ desc.setHandler(handler);
+ desc.setNameSpaceURI("http://www.vamsas.org");
+ desc.setMultivalued(true);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _dbRefList
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(0);
+ { //-- local scope
+ }
+ desc.setValidator(fieldValidator);
} //-- org.vamsas.objects.core.SequenceDescriptor()
private java.util.Vector _annotationElementList;
/**
- * Field _provenance
+ * Field _provenanceList
*/
- private org.vamsas.objects.core.Provenance _provenance;
+ private java.util.Vector _provenanceList;
//----------------/
{
super();
_annotationElementList = new Vector();
+ _provenanceList = new Vector();
} //-- org.vamsas.objects.core.SequenceSetAnnotations()
} //-- void addAnnotationElement(int, org.vamsas.objects.core.AnnotationElement)
/**
+ * Method addProvenance
+ *
+ *
+ *
+ * @param vProvenance
+ */
+ public void addProvenance(org.vamsas.objects.core.Provenance vProvenance)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _provenanceList.addElement(vProvenance);
+ } //-- void addProvenance(org.vamsas.objects.core.Provenance)
+
+ /**
+ * Method addProvenance
+ *
+ *
+ *
+ * @param index
+ * @param vProvenance
+ */
+ public void addProvenance(int index, org.vamsas.objects.core.Provenance vProvenance)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _provenanceList.insertElementAt(vProvenance, index);
+ } //-- void addProvenance(int, org.vamsas.objects.core.Provenance)
+
+ /**
* Method enumerateAnnotationElement
*
*
} //-- java.util.Enumeration enumerateAnnotationElement()
/**
+ * Method enumerateProvenance
+ *
+ *
+ *
+ * @return Enumeration
+ */
+ public java.util.Enumeration enumerateProvenance()
+ {
+ return _provenanceList.elements();
+ } //-- java.util.Enumeration enumerateProvenance()
+
+ /**
* Note: hashCode() has not been overriden
*
* @param obj
}
else if (temp._annotationElementList != null)
return false;
- if (this._provenance != null) {
- if (temp._provenance == null) return false;
- else if (!(this._provenance.equals(temp._provenance)))
+ if (this._provenanceList != null) {
+ if (temp._provenanceList == null) return false;
+ else if (!(this._provenanceList.equals(temp._provenanceList)))
return false;
}
- else if (temp._provenance != null)
+ else if (temp._provenanceList != null)
return false;
return true;
}
} //-- java.lang.String getId()
/**
- * Returns the value of field 'provenance'.
+ * Method getProvenance
+ *
+ *
+ *
+ * @param index
+ * @return Provenance
+ */
+ public org.vamsas.objects.core.Provenance getProvenance(int index)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ //-- check bounds for index
+ if ((index < 0) || (index > _provenanceList.size())) {
+ throw new IndexOutOfBoundsException("getProvenance: Index value '"+index+"' not in range [0.."+_provenanceList.size()+ "]");
+ }
+
+ return (org.vamsas.objects.core.Provenance) _provenanceList.elementAt(index);
+ } //-- org.vamsas.objects.core.Provenance getProvenance(int)
+
+ /**
+ * Method getProvenance
+ *
+ *
*
* @return Provenance
- * @return the value of field 'provenance'.
*/
- public org.vamsas.objects.core.Provenance getProvenance()
+ public org.vamsas.objects.core.Provenance[] getProvenance()
{
- return this._provenance;
- } //-- org.vamsas.objects.core.Provenance getProvenance()
+ int size = _provenanceList.size();
+ org.vamsas.objects.core.Provenance[] mArray = new org.vamsas.objects.core.Provenance[size];
+ for (int index = 0; index < size; index++) {
+ mArray[index] = (org.vamsas.objects.core.Provenance) _provenanceList.elementAt(index);
+ }
+ return mArray;
+ } //-- org.vamsas.objects.core.Provenance[] getProvenance()
+
+ /**
+ * Method getProvenanceCount
+ *
+ *
+ *
+ * @return int
+ */
+ public int getProvenanceCount()
+ {
+ return _provenanceList.size();
+ } //-- int getProvenanceCount()
/**
* Returns the value of field 'seqRef'.
} //-- void removeAllAnnotationElement()
/**
+ * Method removeAllProvenance
+ *
+ */
+ public void removeAllProvenance()
+ {
+ _provenanceList.removeAllElements();
+ } //-- void removeAllProvenance()
+
+ /**
* Method removeAnnotationElement
*
*
} //-- org.vamsas.objects.core.AnnotationElement removeAnnotationElement(int)
/**
+ * Method removeProvenance
+ *
+ *
+ *
+ * @param index
+ * @return Provenance
+ */
+ public org.vamsas.objects.core.Provenance removeProvenance(int index)
+ {
+ java.lang.Object obj = _provenanceList.elementAt(index);
+ _provenanceList.removeElementAt(index);
+ return (org.vamsas.objects.core.Provenance) obj;
+ } //-- org.vamsas.objects.core.Provenance removeProvenance(int)
+
+ /**
* Method setAnnotationElement
*
*
} //-- void setId(java.lang.String)
/**
- * Sets the value of field 'provenance'.
+ * Method setProvenance
+ *
+ *
+ *
+ * @param index
+ * @param vProvenance
+ */
+ public void setProvenance(int index, org.vamsas.objects.core.Provenance vProvenance)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ //-- check bounds for index
+ if ((index < 0) || (index > _provenanceList.size())) {
+ throw new IndexOutOfBoundsException("setProvenance: Index value '"+index+"' not in range [0.."+_provenanceList.size()+ "]");
+ }
+ _provenanceList.setElementAt(vProvenance, index);
+ } //-- void setProvenance(int, org.vamsas.objects.core.Provenance)
+
+ /**
+ * Method setProvenance
+ *
+ *
*
- * @param provenance the value of field 'provenance'.
+ * @param provenanceArray
*/
- public void setProvenance(org.vamsas.objects.core.Provenance provenance)
+ public void setProvenance(org.vamsas.objects.core.Provenance[] provenanceArray)
{
- this._provenance = provenance;
+ //-- copy array
+ _provenanceList.removeAllElements();
+ for (int i = 0; i < provenanceArray.length; i++) {
+ _provenanceList.addElement(provenanceArray[i]);
+ }
} //-- void setProvenance(org.vamsas.objects.core.Provenance)
/**
{ //-- local scope
}
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);
+ //-- _provenanceList
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Provenance.class, "_provenanceList", "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
{
try {
SequenceSetAnnotations target = (SequenceSetAnnotations) object;
- target.setProvenance( (org.vamsas.objects.core.Provenance) value);
+ target.addProvenance( (org.vamsas.objects.core.Provenance) value);
}
catch (java.lang.Exception ex) {
throw new IllegalStateException(ex.toString());
};
desc.setHandler(handler);
desc.setNameSpaceURI("http://www.vamsas.org");
- desc.setRequired(true);
- desc.setMultivalued(false);
+ desc.setMultivalued(true);
addFieldDescriptor(desc);
- //-- validation code for: _provenance
+ //-- validation code for: _provenanceList
fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(1);
+ fieldValidator.setMinOccurs(0);
{ //-- local scope
}
desc.setValidator(fieldValidator);
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;
private boolean _has_end;
/**
- * Field _id
- */
- private java.lang.String _id;
-
- /**
* Field _sequence
*/
private java.lang.String _sequence;
*/
private java.lang.String _name;
- /**
- * Field _dbRefList
- */
- private java.util.Vector _dbRefList;
-
//----------------/
//- Constructors -/
public SequenceType()
{
super();
- _dbRefList = new Vector();
} //-- org.vamsas.objects.core.SequenceType()
//-----------/
/**
- * Method addDbRef
- *
- *
- *
- * @param vDbRef
- */
- public void addDbRef(org.vamsas.objects.core.DbRef vDbRef)
- throws java.lang.IndexOutOfBoundsException
- {
- _dbRefList.addElement(vDbRef);
- } //-- void addDbRef(org.vamsas.objects.core.DbRef)
-
- /**
- * Method addDbRef
- *
- *
- *
- * @param index
- * @param vDbRef
- */
- public void addDbRef(int index, org.vamsas.objects.core.DbRef vDbRef)
- throws java.lang.IndexOutOfBoundsException
- {
- _dbRefList.insertElementAt(vDbRef, index);
- } //-- void addDbRef(int, org.vamsas.objects.core.DbRef)
-
- /**
* Method deleteEnd
*
*/
} //-- void deleteStart()
/**
- * Method enumerateDbRef
- *
- *
- *
- * @return Enumeration
- */
- public java.util.Enumeration enumerateDbRef()
- {
- return _dbRefList.elements();
- } //-- java.util.Enumeration enumerateDbRef()
-
- /**
* Note: hashCode() has not been overriden
*
* @param obj
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)))
}
else if (temp._name != null)
return false;
- if (this._dbRefList != null) {
- if (temp._dbRefList == null) return false;
- else if (!(this._dbRefList.equals(temp._dbRefList)))
- return false;
- }
- else if (temp._dbRefList != null)
- return false;
return true;
}
return false;
} //-- boolean equals(java.lang.Object)
/**
- * Method getDbRef
- *
- *
- *
- * @param index
- * @return DbRef
- */
- public org.vamsas.objects.core.DbRef getDbRef(int index)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _dbRefList.size())) {
- throw new IndexOutOfBoundsException("getDbRef: Index value '"+index+"' not in range [0.."+_dbRefList.size()+ "]");
- }
-
- return (org.vamsas.objects.core.DbRef) _dbRefList.elementAt(index);
- } //-- org.vamsas.objects.core.DbRef getDbRef(int)
-
- /**
- * Method getDbRef
- *
- *
- *
- * @return DbRef
- */
- public org.vamsas.objects.core.DbRef[] getDbRef()
- {
- int size = _dbRefList.size();
- org.vamsas.objects.core.DbRef[] mArray = new org.vamsas.objects.core.DbRef[size];
- for (int index = 0; index < size; index++) {
- mArray[index] = (org.vamsas.objects.core.DbRef) _dbRefList.elementAt(index);
- }
- return mArray;
- } //-- org.vamsas.objects.core.DbRef[] getDbRef()
-
- /**
- * Method getDbRefCount
- *
- *
- *
- * @return int
- */
- public int getDbRefCount()
- {
- return _dbRefList.size();
- } //-- int getDbRefCount()
-
- /**
* Returns the value of field 'end'.
*
* @return int
} //-- 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 marshal(org.xml.sax.ContentHandler)
/**
- * Method removeAllDbRef
- *
- */
- public void removeAllDbRef()
- {
- _dbRefList.removeAllElements();
- } //-- void removeAllDbRef()
-
- /**
- * Method removeDbRef
- *
- *
- *
- * @param index
- * @return DbRef
- */
- public org.vamsas.objects.core.DbRef removeDbRef(int index)
- {
- java.lang.Object obj = _dbRefList.elementAt(index);
- _dbRefList.removeElementAt(index);
- return (org.vamsas.objects.core.DbRef) obj;
- } //-- org.vamsas.objects.core.DbRef removeDbRef(int)
-
- /**
- * Method setDbRef
- *
- *
- *
- * @param index
- * @param vDbRef
- */
- public void setDbRef(int index, org.vamsas.objects.core.DbRef vDbRef)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _dbRefList.size())) {
- throw new IndexOutOfBoundsException("setDbRef: Index value '"+index+"' not in range [0.."+_dbRefList.size()+ "]");
- }
- _dbRefList.setElementAt(vDbRef, index);
- } //-- void setDbRef(int, org.vamsas.objects.core.DbRef)
-
- /**
- * Method setDbRef
- *
- *
- *
- * @param dbRefArray
- */
- public void setDbRef(org.vamsas.objects.core.DbRef[] dbRefArray)
- {
- //-- copy array
- _dbRefList.removeAllElements();
- for (int i = 0; i < dbRefArray.length; i++) {
- _dbRefList.addElement(dbRefArray[i]);
- }
- } //-- void setDbRef(org.vamsas.objects.core.DbRef)
-
- /**
* Sets the value of field 'end'.
*
* @param end the value of field 'end'.
} //-- 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'.
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
fieldValidator.setValidator(typeValidator);
}
desc.setValidator(fieldValidator);
- //-- _dbRefList
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.DbRef.class, "_dbRefList", "dbRef", org.exolab.castor.xml.NodeType.Element);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- SequenceType target = (SequenceType) object;
- return target.getDbRef();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- SequenceType target = (SequenceType) object;
- target.addDbRef( (org.vamsas.objects.core.DbRef) 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.DbRef();
- }
- };
- desc.setHandler(handler);
- desc.setNameSpaceURI("http://www.vamsas.org");
- desc.setMultivalued(true);
- addFieldDescriptor(desc);
-
- //-- validation code for: _dbRefList
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(0);
- { //-- local scope
- }
- desc.setValidator(fieldValidator);
} //-- org.vamsas.objects.core.SequenceTypeDescriptor()
private java.lang.String _id;
/**
- * Field _newickFormatList
+ * Field _title
*/
- private java.util.Vector _newickFormatList;
+ private java.lang.String _title;
+
+ /**
+ * Field _newickList
+ */
+ private java.util.Vector _newickList;
/**
* Field _provenance
public Tree()
{
super();
- _newickFormatList = new Vector();
+ _newickList = new Vector();
} //-- org.vamsas.objects.core.Tree()
//-----------/
/**
- * Method addNewickFormat
+ * Method addNewick
*
*
*
- * @param vNewickFormat
+ * @param vNewick
*/
- public void addNewickFormat(java.lang.String vNewickFormat)
+ public void addNewick(org.vamsas.objects.core.Newick vNewick)
throws java.lang.IndexOutOfBoundsException
{
- _newickFormatList.addElement(vNewickFormat);
- } //-- void addNewickFormat(java.lang.String)
+ _newickList.addElement(vNewick);
+ } //-- void addNewick(org.vamsas.objects.core.Newick)
/**
- * Method addNewickFormat
+ * Method addNewick
*
*
*
* @param index
- * @param vNewickFormat
+ * @param vNewick
*/
- public void addNewickFormat(int index, java.lang.String vNewickFormat)
+ public void addNewick(int index, org.vamsas.objects.core.Newick vNewick)
throws java.lang.IndexOutOfBoundsException
{
- _newickFormatList.insertElementAt(vNewickFormat, index);
- } //-- void addNewickFormat(int, java.lang.String)
+ _newickList.insertElementAt(vNewick, index);
+ } //-- void addNewick(int, org.vamsas.objects.core.Newick)
/**
- * Method enumerateNewickFormat
+ * Method enumerateNewick
*
*
*
* @return Enumeration
*/
- public java.util.Enumeration enumerateNewickFormat()
+ public java.util.Enumeration enumerateNewick()
{
- return _newickFormatList.elements();
- } //-- java.util.Enumeration enumerateNewickFormat()
+ return _newickList.elements();
+ } //-- java.util.Enumeration enumerateNewick()
/**
* Note: hashCode() has not been overriden
}
else if (temp._id != null)
return false;
- if (this._newickFormatList != null) {
- if (temp._newickFormatList == null) return false;
- else if (!(this._newickFormatList.equals(temp._newickFormatList)))
+ if (this._title != null) {
+ if (temp._title == null) return false;
+ else if (!(this._title.equals(temp._title)))
+ return false;
+ }
+ else if (temp._title != null)
+ return false;
+ if (this._newickList != null) {
+ if (temp._newickList == null) return false;
+ else if (!(this._newickList.equals(temp._newickList)))
return false;
}
- else if (temp._newickFormatList != null)
+ else if (temp._newickList != null)
return false;
if (this._provenance != null) {
if (temp._provenance == null) return false;
} //-- java.lang.String getId()
/**
- * Method getNewickFormat
+ * Method getNewick
*
*
*
* @param index
- * @return String
+ * @return Newick
*/
- public java.lang.String getNewickFormat(int index)
+ public org.vamsas.objects.core.Newick getNewick(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()+ "]");
+ if ((index < 0) || (index > _newickList.size())) {
+ throw new IndexOutOfBoundsException("getNewick: Index value '"+index+"' not in range [0.."+_newickList.size()+ "]");
}
- return (String)_newickFormatList.elementAt(index);
- } //-- java.lang.String getNewickFormat(int)
+ return (org.vamsas.objects.core.Newick) _newickList.elementAt(index);
+ } //-- org.vamsas.objects.core.Newick getNewick(int)
/**
- * Method getNewickFormat
+ * Method getNewick
*
*
*
- * @return String
+ * @return Newick
*/
- public java.lang.String[] getNewickFormat()
+ public org.vamsas.objects.core.Newick[] getNewick()
{
- int size = _newickFormatList.size();
- java.lang.String[] mArray = new java.lang.String[size];
+ int size = _newickList.size();
+ org.vamsas.objects.core.Newick[] mArray = new org.vamsas.objects.core.Newick[size];
for (int index = 0; index < size; index++) {
- mArray[index] = (String)_newickFormatList.elementAt(index);
+ mArray[index] = (org.vamsas.objects.core.Newick) _newickList.elementAt(index);
}
return mArray;
- } //-- java.lang.String[] getNewickFormat()
+ } //-- org.vamsas.objects.core.Newick[] getNewick()
/**
- * Method getNewickFormatCount
+ * Method getNewickCount
*
*
*
* @return int
*/
- public int getNewickFormatCount()
+ public int getNewickCount()
{
- return _newickFormatList.size();
- } //-- int getNewickFormatCount()
+ return _newickList.size();
+ } //-- int getNewickCount()
/**
* Returns the value of field 'provenance'.
} //-- org.vamsas.objects.core.Provenance getProvenance()
/**
+ * Returns the value of field 'title'.
+ *
+ * @return String
+ * @return the value of field 'title'.
+ */
+ public java.lang.String getTitle()
+ {
+ return this._title;
+ } //-- java.lang.String getTitle()
+
+ /**
* Method isValid
*
*
} //-- void marshal(org.xml.sax.ContentHandler)
/**
- * Method removeAllNewickFormat
+ * Method removeAllNewick
*
*/
- public void removeAllNewickFormat()
+ public void removeAllNewick()
{
- _newickFormatList.removeAllElements();
- } //-- void removeAllNewickFormat()
+ _newickList.removeAllElements();
+ } //-- void removeAllNewick()
/**
- * Method removeNewickFormat
+ * Method removeNewick
*
*
*
* @param index
- * @return String
+ * @return Newick
*/
- public java.lang.String removeNewickFormat(int index)
+ public org.vamsas.objects.core.Newick removeNewick(int index)
{
- java.lang.Object obj = _newickFormatList.elementAt(index);
- _newickFormatList.removeElementAt(index);
- return (String)obj;
- } //-- java.lang.String removeNewickFormat(int)
+ java.lang.Object obj = _newickList.elementAt(index);
+ _newickList.removeElementAt(index);
+ return (org.vamsas.objects.core.Newick) obj;
+ } //-- org.vamsas.objects.core.Newick removeNewick(int)
/**
* Sets the value of field 'id'.
} //-- void setId(java.lang.String)
/**
- * Method setNewickFormat
+ * Method setNewick
*
*
*
* @param index
- * @param vNewickFormat
+ * @param vNewick
*/
- public void setNewickFormat(int index, java.lang.String vNewickFormat)
+ public void setNewick(int index, org.vamsas.objects.core.Newick vNewick)
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()+ "]");
+ if ((index < 0) || (index > _newickList.size())) {
+ throw new IndexOutOfBoundsException("setNewick: Index value '"+index+"' not in range [0.."+_newickList.size()+ "]");
}
- _newickFormatList.setElementAt(vNewickFormat, index);
- } //-- void setNewickFormat(int, java.lang.String)
+ _newickList.setElementAt(vNewick, index);
+ } //-- void setNewick(int, org.vamsas.objects.core.Newick)
/**
- * Method setNewickFormat
+ * Method setNewick
*
*
*
- * @param newickFormatArray
+ * @param newickArray
*/
- public void setNewickFormat(java.lang.String[] newickFormatArray)
+ public void setNewick(org.vamsas.objects.core.Newick[] newickArray)
{
//-- copy array
- _newickFormatList.removeAllElements();
- for (int i = 0; i < newickFormatArray.length; i++) {
- _newickFormatList.addElement(newickFormatArray[i]);
+ _newickList.removeAllElements();
+ for (int i = 0; i < newickArray.length; i++) {
+ _newickList.addElement(newickArray[i]);
}
- } //-- void setNewickFormat(java.lang.String)
+ } //-- void setNewick(org.vamsas.objects.core.Newick)
/**
* Sets the value of field 'provenance'.
} //-- void setProvenance(org.vamsas.objects.core.Provenance)
/**
+ * Sets the value of field 'title'.
+ *
+ * @param title the value of field 'title'.
+ */
+ public void setTitle(java.lang.String title)
+ {
+ this._title = title;
+ } //-- void setTitle(java.lang.String)
+
+ /**
* Method unmarshal
*
*
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);
+ //-- _title
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_title", "title", 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();
+ return target.getTitle();
}
public void setValue( java.lang.Object object, java.lang.Object value)
throws IllegalStateException, IllegalArgumentException
{
try {
Tree target = (Tree) object;
- target.addNewickFormat( (java.lang.String) value);
+ target.setTitle( (java.lang.String) value);
}
catch (java.lang.Exception ex) {
throw new IllegalStateException(ex.toString());
};
desc.setHandler(handler);
desc.setNameSpaceURI("http://www.vamsas.org");
- desc.setRequired(true);
- desc.setMultivalued(true);
+ desc.setMultivalued(false);
addFieldDescriptor(desc);
- //-- validation code for: _newickFormatList
+ //-- validation code for: _title
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);
+ //-- _newickList
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Newick.class, "_newickList", "newick", 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.getNewick();
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ Tree target = (Tree) object;
+ target.addNewick( (org.vamsas.objects.core.Newick) 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.Newick();
+ }
+ };
+ desc.setHandler(handler);
+ desc.setNameSpaceURI("http://www.vamsas.org");
+ desc.setRequired(true);
+ desc.setMultivalued(true);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _newickList
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(1);
+ { //-- local scope
+ }
+ 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() {
--- /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 User.
+ *
+ * @version $Revision$ $Date$
+ */
+public class User extends org.vamsas.client.object
+implements java.io.Serializable
+{
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * Field _fullname
+ */
+ private java.lang.String _fullname;
+
+ /**
+ * Field _organization
+ */
+ private java.lang.String _organization;
+
+ /**
+ * Field _data
+ */
+ private java.lang.String _data;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public User()
+ {
+ super();
+ } //-- org.vamsas.objects.core.User()
+
+
+ //-----------/
+ //- 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 User) {
+
+ User temp = (User)obj;
+ if (this._fullname != null) {
+ if (temp._fullname == null) return false;
+ else if (!(this._fullname.equals(temp._fullname)))
+ return false;
+ }
+ else if (temp._fullname != null)
+ return false;
+ if (this._organization != null) {
+ if (temp._organization == null) return false;
+ else if (!(this._organization.equals(temp._organization)))
+ return false;
+ }
+ else if (temp._organization != 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 'fullname'.
+ *
+ * @return String
+ * @return the value of field 'fullname'.
+ */
+ public java.lang.String getFullname()
+ {
+ return this._fullname;
+ } //-- java.lang.String getFullname()
+
+ /**
+ * Returns the value of field 'organization'.
+ *
+ * @return String
+ * @return the value of field 'organization'.
+ */
+ public java.lang.String getOrganization()
+ {
+ return this._organization;
+ } //-- java.lang.String getOrganization()
+
+ /**
+ * 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)
+
+ /**
+ * 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 'fullname'.
+ *
+ * @param fullname the value of field 'fullname'.
+ */
+ public void setFullname(java.lang.String fullname)
+ {
+ this._fullname = fullname;
+ } //-- void setFullname(java.lang.String)
+
+ /**
+ * Sets the value of field 'organization'.
+ *
+ * @param organization the value of field 'organization'.
+ */
+ public void setOrganization(java.lang.String organization)
+ {
+ this._organization = organization;
+ } //-- void setOrganization(java.lang.String)
+
+ /**
+ * Method unmarshal
+ *
+ *
+ *
+ * @param reader
+ * @return User
+ */
+ public static org.vamsas.objects.core.User unmarshal(java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+ {
+ return (org.vamsas.objects.core.User) Unmarshaller.unmarshal(org.vamsas.objects.core.User.class, reader);
+ } //-- org.vamsas.objects.core.User 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 UserDescriptor.
+ *
+ * @version $Revision$ $Date$
+ */
+public class UserDescriptor 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 UserDescriptor()
+ {
+ super();
+ nsURI = "http://www.vamsas.org";
+ xmlName = "User";
+ 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
+
+ //-- _fullname
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_fullname", "fullname", 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
+ {
+ User target = (User) object;
+ return target.getFullname();
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ User target = (User) object;
+ target.setFullname( (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: _fullname
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { //-- local scope
+ StringValidator typeValidator = new StringValidator();
+ typeValidator.setWhiteSpace("preserve");
+ fieldValidator.setValidator(typeValidator);
+ }
+ desc.setValidator(fieldValidator);
+ //-- _organization
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_organization", "organization", 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
+ {
+ User target = (User) object;
+ return target.getOrganization();
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ User target = (User) object;
+ target.setOrganization( (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: _organization
+ 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
+ {
+ User target = (User) object;
+ return target.getData();
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ User target = (User) 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
+
+ } //-- org.vamsas.objects.core.UserDescriptor()
+
+
+ //-----------/
+ //- 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.User.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()
+
+}
git://source.jalview.org / vamsas.git / commitdiff