* to any object in the vamsas document
*/
protected boolean __stored_in_document=false;
- protected VorbaId __vorba__id=null;
+ protected VorbaId vorbaId=null;
protected IVorbaIdFactory __vorba=null;
/**
*
* @return true if object is registered
*/
public boolean isRegistered() {
- return (__vorba__id!=null);
+ return (vorbaId!=null);
}
/**
* Method to get fixed reference for
* or not associated with a properly instantiated
* VorbaIdFactory.
*/
- public String getId() {
- if (__vorba__id==null) {
+ public String getVorbaId() {
+ if (vorbaId==null) {
// Try to use the associated factory.
if (__vorba!=null)
- if ((__vorba__id = __vorba.makeVorbaId())==null)
+ if ((vorbaId = __vorba.makeVorbaId())==null)
return null; // Factory not valid.
else
return null;
}
- return __vorba__id.getId();
+ return vorbaId.getId();
}
/**
* used by the IClient implementation
* client applications current namespace.
*/
protected void setVorbaId(VorbaId newid) {
- __vorba__id = newid;
+ vorbaId = newid;
}
/**
+++ /dev/null
-/*
- * This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M1</a>, using an XML
- * Schema.
- * $Id$
- */
-
-package org.vamsas.client.objects;
-
- //---------------------------------/
- //- 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 Alignment.
- *
- * @version $Revision$ $Date$
- */
-public class Alignment extends org.vamsas.client.object
-implements java.io.Serializable
-{
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _alignmentAnnotations
- */
- private org.vamsas.client.objects.AlignmentAnnotations _alignmentAnnotations;
-
- /**
- * Field _treeList
- */
- private java.util.Vector _treeList;
-
- /**
- * Field _alignmentSequenceList
- */
- private java.util.Vector _alignmentSequenceList;
-
- /**
- * Field _provenance
- */
- private org.vamsas.client.objects.Provenance _provenance;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public Alignment()
- {
- super();
- _treeList = new Vector();
- _alignmentSequenceList = new Vector();
- } //-- org.vamsas.client.objects.Alignment()
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- * Method addAlignmentSequence
- *
- *
- *
- * @param vAlignmentSequence
- */
- public void addAlignmentSequence(org.vamsas.client.objects.AlignmentSequence vAlignmentSequence)
- throws java.lang.IndexOutOfBoundsException
- {
- _alignmentSequenceList.addElement(vAlignmentSequence);
- } //-- void addAlignmentSequence(org.vamsas.client.objects.AlignmentSequence)
-
- /**
- * Method addAlignmentSequence
- *
- *
- *
- * @param index
- * @param vAlignmentSequence
- */
- public void addAlignmentSequence(int index, org.vamsas.client.objects.AlignmentSequence vAlignmentSequence)
- throws java.lang.IndexOutOfBoundsException
- {
- _alignmentSequenceList.insertElementAt(vAlignmentSequence, index);
- } //-- void addAlignmentSequence(int, org.vamsas.client.objects.AlignmentSequence)
-
- /**
- * Method addTree
- *
- *
- *
- * @param vTree
- */
- public void addTree(org.vamsas.client.objects.Tree vTree)
- throws java.lang.IndexOutOfBoundsException
- {
- _treeList.addElement(vTree);
- } //-- void addTree(org.vamsas.client.objects.Tree)
-
- /**
- * Method addTree
- *
- *
- *
- * @param index
- * @param vTree
- */
- public void addTree(int index, org.vamsas.client.objects.Tree vTree)
- throws java.lang.IndexOutOfBoundsException
- {
- _treeList.insertElementAt(vTree, index);
- } //-- void addTree(int, org.vamsas.client.objects.Tree)
-
- /**
- * Method enumerateAlignmentSequence
- *
- *
- *
- * @return Enumeration
- */
- public java.util.Enumeration enumerateAlignmentSequence()
- {
- return _alignmentSequenceList.elements();
- } //-- java.util.Enumeration enumerateAlignmentSequence()
-
- /**
- * Method enumerateTree
- *
- *
- *
- * @return Enumeration
- */
- public java.util.Enumeration enumerateTree()
- {
- return _treeList.elements();
- } //-- java.util.Enumeration enumerateTree()
-
- /**
- * 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 Alignment) {
-
- Alignment temp = (Alignment)obj;
- if (this._alignmentAnnotations != null) {
- if (temp._alignmentAnnotations == null) return false;
- else if (!(this._alignmentAnnotations.equals(temp._alignmentAnnotations)))
- return false;
- }
- else if (temp._alignmentAnnotations != null)
- return false;
- if (this._treeList != null) {
- if (temp._treeList == null) return false;
- else if (!(this._treeList.equals(temp._treeList)))
- return false;
- }
- else if (temp._treeList != null)
- return false;
- if (this._alignmentSequenceList != null) {
- if (temp._alignmentSequenceList == null) return false;
- else if (!(this._alignmentSequenceList.equals(temp._alignmentSequenceList)))
- return false;
- }
- else if (temp._alignmentSequenceList != 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 'alignmentAnnotations'.
- *
- * @return AlignmentAnnotations
- * @return the value of field 'alignmentAnnotations'.
- */
- public org.vamsas.client.objects.AlignmentAnnotations getAlignmentAnnotations()
- {
- return this._alignmentAnnotations;
- } //-- org.vamsas.client.objects.AlignmentAnnotations getAlignmentAnnotations()
-
- /**
- * Method getAlignmentSequence
- *
- *
- *
- * @param index
- * @return AlignmentSequence
- */
- public org.vamsas.client.objects.AlignmentSequence getAlignmentSequence(int index)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _alignmentSequenceList.size())) {
- throw new IndexOutOfBoundsException("getAlignmentSequence: Index value '"+index+"' not in range [0.."+_alignmentSequenceList.size()+ "]");
- }
-
- return (org.vamsas.client.objects.AlignmentSequence) _alignmentSequenceList.elementAt(index);
- } //-- org.vamsas.client.objects.AlignmentSequence getAlignmentSequence(int)
-
- /**
- * Method getAlignmentSequence
- *
- *
- *
- * @return AlignmentSequence
- */
- public org.vamsas.client.objects.AlignmentSequence[] getAlignmentSequence()
- {
- int size = _alignmentSequenceList.size();
- org.vamsas.client.objects.AlignmentSequence[] mArray = new org.vamsas.client.objects.AlignmentSequence[size];
- for (int index = 0; index < size; index++) {
- mArray[index] = (org.vamsas.client.objects.AlignmentSequence) _alignmentSequenceList.elementAt(index);
- }
- return mArray;
- } //-- org.vamsas.client.objects.AlignmentSequence[] getAlignmentSequence()
-
- /**
- * Method getAlignmentSequenceAsReference
- *
- * Returns a reference to 'alignmentSequence'. No type checking
- * is performed on any modications to the Vector.
- *
- * @return Vector
- * @return returns a reference to the Vector.
- */
- public java.util.Vector getAlignmentSequenceAsReference()
- {
- return _alignmentSequenceList;
- } //-- java.util.Vector getAlignmentSequenceAsReference()
-
- /**
- * Method getAlignmentSequenceCount
- *
- *
- *
- * @return int
- */
- public int getAlignmentSequenceCount()
- {
- return _alignmentSequenceList.size();
- } //-- int getAlignmentSequenceCount()
-
- /**
- * Returns the value of field 'provenance'.
- *
- * @return Provenance
- * @return the value of field 'provenance'.
- */
- public org.vamsas.client.objects.Provenance getProvenance()
- {
- return this._provenance;
- } //-- org.vamsas.client.objects.Provenance getProvenance()
-
- /**
- * Method getTree
- *
- *
- *
- * @param index
- * @return Tree
- */
- public org.vamsas.client.objects.Tree getTree(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()+ "]");
- }
-
- return (org.vamsas.client.objects.Tree) _treeList.elementAt(index);
- } //-- org.vamsas.client.objects.Tree getTree(int)
-
- /**
- * Method getTree
- *
- *
- *
- * @return Tree
- */
- public org.vamsas.client.objects.Tree[] getTree()
- {
- int size = _treeList.size();
- org.vamsas.client.objects.Tree[] mArray = new org.vamsas.client.objects.Tree[size];
- for (int index = 0; index < size; index++) {
- mArray[index] = (org.vamsas.client.objects.Tree) _treeList.elementAt(index);
- }
- return mArray;
- } //-- org.vamsas.client.objects.Tree[] getTree()
-
- /**
- * Method getTreeAsReference
- *
- * Returns a reference to 'tree'. No type checking is performed
- * on any modications to the Vector.
- *
- * @return Vector
- * @return returns a reference to the Vector.
- */
- public java.util.Vector getTreeAsReference()
- {
- return _treeList;
- } //-- java.util.Vector getTreeAsReference()
-
- /**
- * Method getTreeCount
- *
- *
- *
- * @return int
- */
- public int getTreeCount()
- {
- return _treeList.size();
- } //-- int getTreeCount()
-
- /**
- * 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 removeAlignmentSequence
- *
- *
- *
- * @param index
- * @return AlignmentSequence
- */
- public org.vamsas.client.objects.AlignmentSequence removeAlignmentSequence(int index)
- {
- java.lang.Object obj = _alignmentSequenceList.elementAt(index);
- _alignmentSequenceList.removeElementAt(index);
- return (org.vamsas.client.objects.AlignmentSequence) obj;
- } //-- org.vamsas.client.objects.AlignmentSequence removeAlignmentSequence(int)
-
- /**
- * Method removeAllAlignmentSequence
- *
- */
- public void removeAllAlignmentSequence()
- {
- _alignmentSequenceList.removeAllElements();
- } //-- void removeAllAlignmentSequence()
-
- /**
- * Method removeAllTree
- *
- */
- public void removeAllTree()
- {
- _treeList.removeAllElements();
- } //-- void removeAllTree()
-
- /**
- * Method removeTree
- *
- *
- *
- * @param index
- * @return Tree
- */
- public org.vamsas.client.objects.Tree removeTree(int index)
- {
- java.lang.Object obj = _treeList.elementAt(index);
- _treeList.removeElementAt(index);
- return (org.vamsas.client.objects.Tree) obj;
- } //-- org.vamsas.client.objects.Tree removeTree(int)
-
- /**
- * Sets the value of field 'alignmentAnnotations'.
- *
- * @param alignmentAnnotations the value of field
- * 'alignmentAnnotations'.
- */
- public void setAlignmentAnnotations(org.vamsas.client.objects.AlignmentAnnotations alignmentAnnotations)
- {
- this._alignmentAnnotations = alignmentAnnotations;
- } //-- void setAlignmentAnnotations(org.vamsas.client.objects.AlignmentAnnotations)
-
- /**
- * Method setAlignmentSequence
- *
- *
- *
- * @param index
- * @param vAlignmentSequence
- */
- public void setAlignmentSequence(int index, org.vamsas.client.objects.AlignmentSequence vAlignmentSequence)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _alignmentSequenceList.size())) {
- throw new IndexOutOfBoundsException("setAlignmentSequence: Index value '"+index+"' not in range [0.."+_alignmentSequenceList.size()+ "]");
- }
- _alignmentSequenceList.setElementAt(vAlignmentSequence, index);
- } //-- void setAlignmentSequence(int, org.vamsas.client.objects.AlignmentSequence)
-
- /**
- * Method setAlignmentSequence
- *
- *
- *
- * @param alignmentSequenceArray
- */
- public void setAlignmentSequence(org.vamsas.client.objects.AlignmentSequence[] alignmentSequenceArray)
- {
- //-- copy array
- _alignmentSequenceList.removeAllElements();
- for (int i = 0; i < alignmentSequenceArray.length; i++) {
- _alignmentSequenceList.addElement(alignmentSequenceArray[i]);
- }
- } //-- void setAlignmentSequence(org.vamsas.client.objects.AlignmentSequence)
-
- /**
- * Method setAlignmentSequence
- *
- * Sets the value of 'alignmentSequence' by copying the given
- * Vector.
- *
- * @param alignmentSequenceVector the Vector to copy.
- */
- public void setAlignmentSequence(java.util.Vector alignmentSequenceVector)
- {
- //-- copy vector
- _alignmentSequenceList.removeAllElements();
- for (int i = 0; i < alignmentSequenceVector.size(); i++) {
- _alignmentSequenceList.addElement((org.vamsas.client.objects.AlignmentSequence)alignmentSequenceVector.elementAt(i));
- }
- } //-- void setAlignmentSequence(java.util.Vector)
-
- /**
- * Method setAlignmentSequenceAsReference
- *
- * Sets the value of 'alignmentSequence' by setting it to the
- * given Vector. No type checking is performed.
- *
- * @param alignmentSequenceVector the Vector to copy.
- */
- public void setAlignmentSequenceAsReference(java.util.Vector alignmentSequenceVector)
- {
- _alignmentSequenceList = alignmentSequenceVector;
- } //-- void setAlignmentSequenceAsReference(java.util.Vector)
-
- /**
- * Sets the value of field 'provenance'.
- *
- * @param provenance the value of field 'provenance'.
- */
- public void setProvenance(org.vamsas.client.objects.Provenance provenance)
- {
- this._provenance = provenance;
- } //-- void setProvenance(org.vamsas.client.objects.Provenance)
-
- /**
- * Method setTree
- *
- *
- *
- * @param index
- * @param vTree
- */
- public void setTree(int index, org.vamsas.client.objects.Tree 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, org.vamsas.client.objects.Tree)
-
- /**
- * Method setTree
- *
- *
- *
- * @param treeArray
- */
- public void setTree(org.vamsas.client.objects.Tree[] treeArray)
- {
- //-- copy array
- _treeList.removeAllElements();
- for (int i = 0; i < treeArray.length; i++) {
- _treeList.addElement(treeArray[i]);
- }
- } //-- void setTree(org.vamsas.client.objects.Tree)
-
- /**
- * Method setTree
- *
- * Sets the value of 'tree' by copying the given Vector.
- *
- * @param treeVector the Vector to copy.
- */
- public void setTree(java.util.Vector treeVector)
- {
- //-- copy vector
- _treeList.removeAllElements();
- for (int i = 0; i < treeVector.size(); i++) {
- _treeList.addElement((org.vamsas.client.objects.Tree)treeVector.elementAt(i));
- }
- } //-- void setTree(java.util.Vector)
-
- /**
- * Method setTreeAsReference
- *
- * Sets the value of 'tree' by setting it to the given Vector.
- * No type checking is performed.
- *
- * @param treeVector the Vector to copy.
- */
- public void setTreeAsReference(java.util.Vector treeVector)
- {
- _treeList = treeVector;
- } //-- void setTreeAsReference(java.util.Vector)
-
- /**
- * Method unmarshal
- *
- *
- *
- * @param reader
- * @return Alignment
- */
- public static org.vamsas.client.objects.Alignment unmarshal(java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
- {
- return (org.vamsas.client.objects.Alignment) Unmarshaller.unmarshal(org.vamsas.client.objects.Alignment.class, reader);
- } //-- org.vamsas.client.objects.Alignment 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 0.9.9M1</a>, using an XML
- * Schema.
- * $Id$
- */
-
-package org.vamsas.client.objects;
-
- //---------------------------------/
- //- 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 AlignmentAnnotations.
- *
- * @version $Revision$ $Date$
- */
-public class AlignmentAnnotations extends org.vamsas.client.object
-implements java.io.Serializable
-{
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _graph
- */
- private boolean _graph;
-
- /**
- * keeps track of state for field: _graph
- */
- private boolean _has_graph;
-
- /**
- * Field _annotationElementList
- */
- private java.util.Vector _annotationElementList;
-
- /**
- * Field _label
- */
- private java.lang.String _label;
-
- /**
- * Field _description
- */
- private java.lang.String _description;
-
- /**
- * Field _provenance
- */
- private org.vamsas.client.objects.Provenance _provenance;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public AlignmentAnnotations()
- {
- super();
- _annotationElementList = new Vector();
- } //-- org.vamsas.client.objects.AlignmentAnnotations()
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- * Method addAnnotationElement
- *
- *
- *
- * @param vAnnotationElement
- */
- public void addAnnotationElement(org.vamsas.client.objects.AnnotationElement vAnnotationElement)
- throws java.lang.IndexOutOfBoundsException
- {
- _annotationElementList.addElement(vAnnotationElement);
- } //-- void addAnnotationElement(org.vamsas.client.objects.AnnotationElement)
-
- /**
- * Method addAnnotationElement
- *
- *
- *
- * @param index
- * @param vAnnotationElement
- */
- public void addAnnotationElement(int index, org.vamsas.client.objects.AnnotationElement vAnnotationElement)
- throws java.lang.IndexOutOfBoundsException
- {
- _annotationElementList.insertElementAt(vAnnotationElement, index);
- } //-- void addAnnotationElement(int, org.vamsas.client.objects.AnnotationElement)
-
- /**
- * Method deleteGraph
- *
- */
- public void deleteGraph()
- {
- this._has_graph= false;
- } //-- void deleteGraph()
-
- /**
- * Method enumerateAnnotationElement
- *
- *
- *
- * @return Enumeration
- */
- public java.util.Enumeration enumerateAnnotationElement()
- {
- return _annotationElementList.elements();
- } //-- java.util.Enumeration enumerateAnnotationElement()
-
- /**
- * 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 AlignmentAnnotations) {
-
- AlignmentAnnotations temp = (AlignmentAnnotations)obj;
- if (this._graph != temp._graph)
- return false;
- if (this._has_graph != temp._has_graph)
- return false;
- if (this._annotationElementList != null) {
- if (temp._annotationElementList == null) return false;
- else if (!(this._annotationElementList.equals(temp._annotationElementList)))
- return false;
- }
- else if (temp._annotationElementList != null)
- return false;
- if (this._label != null) {
- if (temp._label == null) return false;
- else if (!(this._label.equals(temp._label)))
- return false;
- }
- else if (temp._label != null)
- return false;
- if (this._description != null) {
- if (temp._description == null) return false;
- else if (!(this._description.equals(temp._description)))
- return false;
- }
- else if (temp._description != 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)
-
- /**
- * Method getAnnotationElement
- *
- *
- *
- * @param index
- * @return AnnotationElement
- */
- public org.vamsas.client.objects.AnnotationElement getAnnotationElement(int index)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _annotationElementList.size())) {
- throw new IndexOutOfBoundsException("getAnnotationElement: Index value '"+index+"' not in range [0.."+_annotationElementList.size()+ "]");
- }
-
- return (org.vamsas.client.objects.AnnotationElement) _annotationElementList.elementAt(index);
- } //-- org.vamsas.client.objects.AnnotationElement getAnnotationElement(int)
-
- /**
- * Method getAnnotationElement
- *
- *
- *
- * @return AnnotationElement
- */
- public org.vamsas.client.objects.AnnotationElement[] getAnnotationElement()
- {
- int size = _annotationElementList.size();
- org.vamsas.client.objects.AnnotationElement[] mArray = new org.vamsas.client.objects.AnnotationElement[size];
- for (int index = 0; index < size; index++) {
- mArray[index] = (org.vamsas.client.objects.AnnotationElement) _annotationElementList.elementAt(index);
- }
- return mArray;
- } //-- org.vamsas.client.objects.AnnotationElement[] getAnnotationElement()
-
- /**
- * Method getAnnotationElementAsReference
- *
- * Returns a reference to 'annotationElement'. No type checking
- * is performed on any modications to the Vector.
- *
- * @return Vector
- * @return returns a reference to the Vector.
- */
- public java.util.Vector getAnnotationElementAsReference()
- {
- return _annotationElementList;
- } //-- java.util.Vector getAnnotationElementAsReference()
-
- /**
- * Method getAnnotationElementCount
- *
- *
- *
- * @return int
- */
- public int getAnnotationElementCount()
- {
- return _annotationElementList.size();
- } //-- int getAnnotationElementCount()
-
- /**
- * Returns the value of field 'description'.
- *
- * @return String
- * @return the value of field 'description'.
- */
- public java.lang.String getDescription()
- {
- return this._description;
- } //-- java.lang.String getDescription()
-
- /**
- * Returns the value of field 'graph'.
- *
- * @return boolean
- * @return the value of field 'graph'.
- */
- public boolean getGraph()
- {
- return this._graph;
- } //-- boolean getGraph()
-
- /**
- * Returns the value of field 'label'.
- *
- * @return String
- * @return the value of field 'label'.
- */
- public java.lang.String getLabel()
- {
- return this._label;
- } //-- java.lang.String getLabel()
-
- /**
- * Returns the value of field 'provenance'.
- *
- * @return Provenance
- * @return the value of field 'provenance'.
- */
- public org.vamsas.client.objects.Provenance getProvenance()
- {
- return this._provenance;
- } //-- org.vamsas.client.objects.Provenance getProvenance()
-
- /**
- * Method hasGraph
- *
- *
- *
- * @return boolean
- */
- public boolean hasGraph()
- {
- return this._has_graph;
- } //-- boolean hasGraph()
-
- /**
- * 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 removeAllAnnotationElement
- *
- */
- public void removeAllAnnotationElement()
- {
- _annotationElementList.removeAllElements();
- } //-- void removeAllAnnotationElement()
-
- /**
- * Method removeAnnotationElement
- *
- *
- *
- * @param index
- * @return AnnotationElement
- */
- public org.vamsas.client.objects.AnnotationElement removeAnnotationElement(int index)
- {
- java.lang.Object obj = _annotationElementList.elementAt(index);
- _annotationElementList.removeElementAt(index);
- return (org.vamsas.client.objects.AnnotationElement) obj;
- } //-- org.vamsas.client.objects.AnnotationElement removeAnnotationElement(int)
-
- /**
- * Method setAnnotationElement
- *
- *
- *
- * @param index
- * @param vAnnotationElement
- */
- public void setAnnotationElement(int index, org.vamsas.client.objects.AnnotationElement vAnnotationElement)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _annotationElementList.size())) {
- throw new IndexOutOfBoundsException("setAnnotationElement: Index value '"+index+"' not in range [0.."+_annotationElementList.size()+ "]");
- }
- _annotationElementList.setElementAt(vAnnotationElement, index);
- } //-- void setAnnotationElement(int, org.vamsas.client.objects.AnnotationElement)
-
- /**
- * Method setAnnotationElement
- *
- *
- *
- * @param annotationElementArray
- */
- public void setAnnotationElement(org.vamsas.client.objects.AnnotationElement[] annotationElementArray)
- {
- //-- copy array
- _annotationElementList.removeAllElements();
- for (int i = 0; i < annotationElementArray.length; i++) {
- _annotationElementList.addElement(annotationElementArray[i]);
- }
- } //-- void setAnnotationElement(org.vamsas.client.objects.AnnotationElement)
-
- /**
- * Method setAnnotationElement
- *
- * Sets the value of 'annotationElement' by copying the given
- * Vector.
- *
- * @param annotationElementVector the Vector to copy.
- */
- public void setAnnotationElement(java.util.Vector annotationElementVector)
- {
- //-- copy vector
- _annotationElementList.removeAllElements();
- for (int i = 0; i < annotationElementVector.size(); i++) {
- _annotationElementList.addElement((org.vamsas.client.objects.AnnotationElement)annotationElementVector.elementAt(i));
- }
- } //-- void setAnnotationElement(java.util.Vector)
-
- /**
- * Method setAnnotationElementAsReference
- *
- * Sets the value of 'annotationElement' by setting it to the
- * given Vector. No type checking is performed.
- *
- * @param annotationElementVector the Vector to copy.
- */
- public void setAnnotationElementAsReference(java.util.Vector annotationElementVector)
- {
- _annotationElementList = annotationElementVector;
- } //-- void setAnnotationElementAsReference(java.util.Vector)
-
- /**
- * Sets the value of field 'description'.
- *
- * @param description the value of field 'description'.
- */
- public void setDescription(java.lang.String description)
- {
- this._description = description;
- } //-- void setDescription(java.lang.String)
-
- /**
- * Sets the value of field 'graph'.
- *
- * @param graph the value of field 'graph'.
- */
- public void setGraph(boolean graph)
- {
- this._graph = graph;
- this._has_graph = true;
- } //-- void setGraph(boolean)
-
- /**
- * Sets the value of field 'label'.
- *
- * @param label the value of field 'label'.
- */
- public void setLabel(java.lang.String label)
- {
- this._label = label;
- } //-- void setLabel(java.lang.String)
-
- /**
- * Sets the value of field 'provenance'.
- *
- * @param provenance the value of field 'provenance'.
- */
- public void setProvenance(org.vamsas.client.objects.Provenance provenance)
- {
- this._provenance = provenance;
- } //-- void setProvenance(org.vamsas.client.objects.Provenance)
-
- /**
- * Method unmarshal
- *
- *
- *
- * @param reader
- * @return AlignmentAnnotations
- */
- public static org.vamsas.client.objects.AlignmentAnnotations unmarshal(java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
- {
- return (org.vamsas.client.objects.AlignmentAnnotations) Unmarshaller.unmarshal(org.vamsas.client.objects.AlignmentAnnotations.class, reader);
- } //-- org.vamsas.client.objects.AlignmentAnnotations 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 0.9.9M1</a>, using an XML
- * Schema.
- * $Id$
- */
-
-package org.vamsas.client.objects;
-
- //---------------------------------/
- //- 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 AlignmentAnnotationsDescriptor.
- *
- * @version $Revision$ $Date$
- */
-public class AlignmentAnnotationsDescriptor 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 AlignmentAnnotationsDescriptor()
- {
- super();
- nsURI = "http://www.vamsas.org";
- xmlName = "AlignmentAnnotations";
-
- //-- 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
-
- //-- _graph
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_graph", "graph", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- AlignmentAnnotations target = (AlignmentAnnotations) object;
- if(!target.hasGraph())
- return null;
- return (target.getGraph() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- AlignmentAnnotations target = (AlignmentAnnotations) object;
- // ignore null values for non optional primitives
- if (value == null) return;
-
- target.setGraph( ((java.lang.Boolean)value).booleanValue());
- }
- 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.setRequired(true);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _graph
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(1);
- { //-- local scope
- BooleanValidator typeValidator = new BooleanValidator();
- fieldValidator.setValidator(typeValidator);
- }
- desc.setValidator(fieldValidator);
- //-- initialize element descriptors
-
- //-- _annotationElementList
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.client.objects.AnnotationElement.class, "_annotationElementList", "annotationElement", org.exolab.castor.xml.NodeType.Element);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- AlignmentAnnotations target = (AlignmentAnnotations) object;
- return target.getAnnotationElement();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- AlignmentAnnotations target = (AlignmentAnnotations) object;
- target.addAnnotationElement( (org.vamsas.client.objects.AnnotationElement) value);
- }
- catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance( java.lang.Object parent ) {
- return new org.vamsas.client.objects.AnnotationElement();
- }
- };
- desc.setHandler(handler);
- desc.setNameSpaceURI("http://www.vamsas.org");
- desc.setRequired(true);
- desc.setMultivalued(true);
- addFieldDescriptor(desc);
-
- //-- validation code for: _annotationElementList
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(1);
- { //-- local scope
- }
- desc.setValidator(fieldValidator);
- //-- _label
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_label", "label", 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
- {
- AlignmentAnnotations target = (AlignmentAnnotations) object;
- return target.getLabel();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- AlignmentAnnotations target = (AlignmentAnnotations) object;
- target.setLabel( (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: _label
- 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);
- //-- _description
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_description", "description", 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
- {
- AlignmentAnnotations target = (AlignmentAnnotations) object;
- return target.getDescription();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- AlignmentAnnotations target = (AlignmentAnnotations) object;
- target.setDescription( (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: _description
- 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.client.objects.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
- {
- AlignmentAnnotations target = (AlignmentAnnotations) object;
- return target.getProvenance();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- AlignmentAnnotations target = (AlignmentAnnotations) object;
- target.setProvenance( (org.vamsas.client.objects.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.client.objects.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.client.objects.AlignmentAnnotationsDescriptor()
-
-
- //-----------/
- //- 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.client.objects.AlignmentAnnotations.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()
-
-}
+++ /dev/null
-/*
- * This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M1</a>, using an XML
- * Schema.
- * $Id$
- */
-
-package org.vamsas.client.objects;
-
- //---------------------------------/
- //- 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 AlignmentDescriptor.
- *
- * @version $Revision$ $Date$
- */
-public class AlignmentDescriptor 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 AlignmentDescriptor()
- {
- super();
- nsURI = "http://www.vamsas.org";
- xmlName = "Alignment";
-
- //-- 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
-
- //-- _alignmentAnnotations
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.client.objects.AlignmentAnnotations.class, "_alignmentAnnotations", "AlignmentAnnotations", org.exolab.castor.xml.NodeType.Element);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Alignment target = (Alignment) object;
- return target.getAlignmentAnnotations();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Alignment target = (Alignment) object;
- target.setAlignmentAnnotations( (org.vamsas.client.objects.AlignmentAnnotations) value);
- }
- catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance( java.lang.Object parent ) {
- return new org.vamsas.client.objects.AlignmentAnnotations();
- }
- };
- desc.setHandler(handler);
- desc.setNameSpaceURI("http://www.vamsas.org");
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _alignmentAnnotations
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- }
- desc.setValidator(fieldValidator);
- //-- _treeList
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.client.objects.Tree.class, "_treeList", "tree", org.exolab.castor.xml.NodeType.Element);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Alignment target = (Alignment) object;
- return target.getTree();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Alignment target = (Alignment) object;
- target.addTree( (org.vamsas.client.objects.Tree) value);
- }
- catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance( java.lang.Object parent ) {
- return new org.vamsas.client.objects.Tree();
- }
- };
- desc.setHandler(handler);
- desc.setNameSpaceURI("http://www.vamsas.org");
- desc.setMultivalued(true);
- addFieldDescriptor(desc);
-
- //-- validation code for: _treeList
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(0);
- { //-- local scope
- }
- desc.setValidator(fieldValidator);
- //-- _alignmentSequenceList
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.client.objects.AlignmentSequence.class, "_alignmentSequenceList", "alignmentSequence", org.exolab.castor.xml.NodeType.Element);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Alignment target = (Alignment) object;
- return target.getAlignmentSequence();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Alignment target = (Alignment) object;
- target.addAlignmentSequence( (org.vamsas.client.objects.AlignmentSequence) value);
- }
- catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance( java.lang.Object parent ) {
- return new org.vamsas.client.objects.AlignmentSequence();
- }
- };
- desc.setHandler(handler);
- desc.setNameSpaceURI("http://www.vamsas.org");
- desc.setRequired(true);
- desc.setMultivalued(true);
- addFieldDescriptor(desc);
-
- //-- validation code for: _alignmentSequenceList
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(2);
- { //-- local scope
- }
- desc.setValidator(fieldValidator);
- //-- _provenance
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.client.objects.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
- {
- Alignment target = (Alignment) object;
- return target.getProvenance();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Alignment target = (Alignment) object;
- target.setProvenance( (org.vamsas.client.objects.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.client.objects.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.client.objects.AlignmentDescriptor()
-
-
- //-----------/
- //- 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.client.objects.Alignment.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()
-
-}
+++ /dev/null
-/*
- * This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M1</a>, using an XML
- * Schema.
- * $Id$
- */
-
-package org.vamsas.client.objects;
-
- //---------------------------------/
- //- 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 AlignmentSequence.
- *
- * @version $Revision$ $Date$
- */
-public class AlignmentSequence extends org.vamsas.client.objects.SequenceType
-implements java.io.Serializable
-{
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _id
- */
- private java.lang.Object _id;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public AlignmentSequence()
- {
- super();
- } //-- org.vamsas.client.objects.AlignmentSequence()
-
-
- //-----------/
- //- 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 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;
- return true;
- }
- return false;
- } //-- boolean equals(java.lang.Object)
-
- /**
- * Returns the value of field 'id'.
- *
- * @return Object
- * @return the value of field 'id'.
- */
- public java.lang.Object getId()
- {
- return this._id;
- } //-- java.lang.Object getId()
-
- /**
- * 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 'id'.
- *
- * @param id the value of field 'id'.
- */
- public void setId(java.lang.Object id)
- {
- this._id = id;
- } //-- void setId(java.lang.Object)
-
- /**
- * Method unmarshal
- *
- *
- *
- * @param reader
- * @return SequenceType
- */
- public static org.vamsas.client.objects.SequenceType unmarshal(java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
- {
- return (org.vamsas.client.objects.AlignmentSequence) Unmarshaller.unmarshal(org.vamsas.client.objects.AlignmentSequence.class, reader);
- } //-- org.vamsas.client.objects.SequenceType 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 0.9.9M1</a>, using an XML
- * Schema.
- * $Id$
- */
-
-package org.vamsas.client.objects;
-
- //---------------------------------/
- //- 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 AlignmentSequenceDescriptor.
- *
- * @version $Revision$ $Date$
- */
-public class AlignmentSequenceDescriptor extends org.vamsas.client.objects.SequenceTypeDescriptor {
-
-
- //--------------------------/
- //- 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 AlignmentSequenceDescriptor()
- {
- super();
- setExtendsWithoutFlatten(new org.vamsas.client.objects.SequenceTypeDescriptor());
- nsURI = "http://www.vamsas.org";
- xmlName = "alignmentSequence";
- 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.Object.class, "_id", "id", 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();
- }
- 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);
- }
- catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance( java.lang.Object parent ) {
- return new java.lang.Object();
- }
- };
- 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.client.objects.AlignmentSequenceDescriptor()
-
-
- //-----------/
- //- 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.client.objects.AlignmentSequence.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()
-
-}
+++ /dev/null
-/*
- * This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M1</a>, using an XML
- * Schema.
- * $Id$
- */
-
-package org.vamsas.client.objects;
-
- //---------------------------------/
- //- 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 AnnotationElement.
- *
- * @version $Revision$ $Date$
- */
-public class AnnotationElement extends org.vamsas.client.object
-implements java.io.Serializable
-{
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _position
- */
- private int _position;
-
- /**
- * keeps track of state for field: _position
- */
- private boolean _has_position;
-
- /**
- * Field _displayCharacter
- */
- private java.lang.String _displayCharacter;
-
- /**
- * Field _description
- */
- private java.lang.String _description;
-
- /**
- * Field _secondaryStructure
- */
- private java.lang.String _secondaryStructure;
-
- /**
- * Field _value
- */
- private float _value;
-
- /**
- * keeps track of state for field: _value
- */
- private boolean _has_value;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public AnnotationElement()
- {
- super();
- } //-- org.vamsas.client.objects.AnnotationElement()
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- * Method deletePosition
- *
- */
- public void deletePosition()
- {
- this._has_position= false;
- } //-- void deletePosition()
-
- /**
- * Method deleteValue
- *
- */
- public void deleteValue()
- {
- this._has_value= false;
- } //-- void deleteValue()
-
- /**
- * 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 AnnotationElement) {
-
- AnnotationElement temp = (AnnotationElement)obj;
- if (this._position != temp._position)
- return false;
- if (this._has_position != temp._has_position)
- return false;
- if (this._displayCharacter != null) {
- if (temp._displayCharacter == null) return false;
- else if (!(this._displayCharacter.equals(temp._displayCharacter)))
- return false;
- }
- else if (temp._displayCharacter != null)
- return false;
- if (this._description != null) {
- if (temp._description == null) return false;
- else if (!(this._description.equals(temp._description)))
- return false;
- }
- else if (temp._description != null)
- return false;
- if (this._secondaryStructure != null) {
- if (temp._secondaryStructure == null) return false;
- else if (!(this._secondaryStructure.equals(temp._secondaryStructure)))
- return false;
- }
- else if (temp._secondaryStructure != null)
- return false;
- if (this._value != temp._value)
- return false;
- if (this._has_value != temp._has_value)
- return false;
- return true;
- }
- return false;
- } //-- boolean equals(java.lang.Object)
-
- /**
- * Returns the value of field 'description'.
- *
- * @return String
- * @return the value of field 'description'.
- */
- public java.lang.String getDescription()
- {
- return this._description;
- } //-- java.lang.String getDescription()
-
- /**
- * Returns the value of field 'displayCharacter'.
- *
- * @return String
- * @return the value of field 'displayCharacter'.
- */
- public java.lang.String getDisplayCharacter()
- {
- return this._displayCharacter;
- } //-- java.lang.String getDisplayCharacter()
-
- /**
- * Returns the value of field 'position'.
- *
- * @return int
- * @return the value of field 'position'.
- */
- public int getPosition()
- {
- return this._position;
- } //-- int getPosition()
-
- /**
- * Returns the value of field 'secondaryStructure'.
- *
- * @return String
- * @return the value of field 'secondaryStructure'.
- */
- public java.lang.String getSecondaryStructure()
- {
- return this._secondaryStructure;
- } //-- java.lang.String getSecondaryStructure()
-
- /**
- * Returns the value of field 'value'.
- *
- * @return float
- * @return the value of field 'value'.
- */
- public float getValue()
- {
- return this._value;
- } //-- float getValue()
-
- /**
- * Method hasPosition
- *
- *
- *
- * @return boolean
- */
- public boolean hasPosition()
- {
- return this._has_position;
- } //-- boolean hasPosition()
-
- /**
- * Method hasValue
- *
- *
- *
- * @return boolean
- */
- public boolean hasValue()
- {
- return this._has_value;
- } //-- boolean hasValue()
-
- /**
- * 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 'description'.
- *
- * @param description the value of field 'description'.
- */
- public void setDescription(java.lang.String description)
- {
- this._description = description;
- } //-- void setDescription(java.lang.String)
-
- /**
- * Sets the value of field 'displayCharacter'.
- *
- * @param displayCharacter the value of field 'displayCharacter'
- */
- public void setDisplayCharacter(java.lang.String displayCharacter)
- {
- this._displayCharacter = displayCharacter;
- } //-- void setDisplayCharacter(java.lang.String)
-
- /**
- * Sets the value of field 'position'.
- *
- * @param position the value of field 'position'.
- */
- public void setPosition(int position)
- {
- this._position = position;
- this._has_position = true;
- } //-- void setPosition(int)
-
- /**
- * Sets the value of field 'secondaryStructure'.
- *
- * @param secondaryStructure the value of field
- * 'secondaryStructure'.
- */
- public void setSecondaryStructure(java.lang.String secondaryStructure)
- {
- this._secondaryStructure = secondaryStructure;
- } //-- void setSecondaryStructure(java.lang.String)
-
- /**
- * Sets the value of field 'value'.
- *
- * @param value the value of field 'value'.
- */
- public void setValue(float value)
- {
- this._value = value;
- this._has_value = true;
- } //-- void setValue(float)
-
- /**
- * Method unmarshal
- *
- *
- *
- * @param reader
- * @return AnnotationElement
- */
- public static org.vamsas.client.objects.AnnotationElement unmarshal(java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
- {
- return (org.vamsas.client.objects.AnnotationElement) Unmarshaller.unmarshal(org.vamsas.client.objects.AnnotationElement.class, reader);
- } //-- org.vamsas.client.objects.AnnotationElement 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 0.9.9M1</a>, using an XML
- * Schema.
- * $Id$
- */
-
-package org.vamsas.client.objects;
-
- //---------------------------------/
- //- 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 AnnotationElementDescriptor.
- *
- * @version $Revision$ $Date$
- */
-public class AnnotationElementDescriptor 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 AnnotationElementDescriptor()
- {
- super();
- nsURI = "http://www.vamsas.org";
- xmlName = "annotationElement";
-
- //-- 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
-
- //-- _position
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_position", "position", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- AnnotationElement target = (AnnotationElement) object;
- if(!target.hasPosition())
- return null;
- return new java.lang.Integer(target.getPosition());
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- AnnotationElement target = (AnnotationElement) object;
- // ignore null values for non optional primitives
- if (value == null) return;
-
- target.setPosition( ((java.lang.Integer)value).intValue());
- }
- 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.setRequired(true);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _position
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(1);
- { //-- local scope
- IntegerValidator typeValidator= new IntegerValidator();
- fieldValidator.setValidator(typeValidator);
- }
- desc.setValidator(fieldValidator);
- //-- initialize element descriptors
-
- //-- _displayCharacter
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_displayCharacter", "displayCharacter", 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
- {
- AnnotationElement target = (AnnotationElement) object;
- return target.getDisplayCharacter();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- AnnotationElement target = (AnnotationElement) object;
- target.setDisplayCharacter( (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: _displayCharacter
- 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);
- //-- _description
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_description", "description", 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
- {
- AnnotationElement target = (AnnotationElement) object;
- return target.getDescription();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- AnnotationElement target = (AnnotationElement) object;
- target.setDescription( (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: _description
- 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);
- //-- _secondaryStructure
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_secondaryStructure", "secondaryStructure", 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
- {
- AnnotationElement target = (AnnotationElement) object;
- return target.getSecondaryStructure();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- AnnotationElement target = (AnnotationElement) object;
- target.setSecondaryStructure( (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: _secondaryStructure
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(1);
- { //-- local scope
- StringValidator typeValidator = new StringValidator();
- typeValidator.setLength(1);
- typeValidator.setWhiteSpace("preserve");
- fieldValidator.setValidator(typeValidator);
- }
- desc.setValidator(fieldValidator);
- //-- _value
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(float.class, "_value", "value", org.exolab.castor.xml.NodeType.Element);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- AnnotationElement target = (AnnotationElement) object;
- if(!target.hasValue())
- return null;
- return new java.lang.Float(target.getValue());
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- AnnotationElement target = (AnnotationElement) object;
- // ignore null values for non optional primitives
- if (value == null) return;
-
- target.setValue( ((java.lang.Float)value).floatValue());
- }
- 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: _value
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(1);
- { //-- local scope
- FloatValidator typeValidator = new FloatValidator();
- fieldValidator.setValidator(typeValidator);
- }
- desc.setValidator(fieldValidator);
- } //-- org.vamsas.client.objects.AnnotationElementDescriptor()
-
-
- //-----------/
- //- 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.client.objects.AnnotationElement.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()
-
-}
+++ /dev/null
-/*
- * This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M1</a>, using an XML
- * Schema.
- * $Id$
- */
-
-package org.vamsas.client.objects;
-
- //---------------------------------/
- //- 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 Application.
- *
- * @version $Revision$ $Date$
- */
-public class Application extends org.vamsas.client.object
-implements java.io.Serializable
-{
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _version
- */
- private java.lang.Object _version;
-
- /**
- * Field _name
- */
- private java.lang.Object _name;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public Application()
- {
- super();
- } //-- org.vamsas.client.objects.Application()
-
-
- //-----------/
- //- 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 Application) {
-
- Application temp = (Application)obj;
- if (this._version != null) {
- if (temp._version == null) return false;
- else if (!(this._version.equals(temp._version)))
- return false;
- }
- else if (temp._version != null)
- return false;
- if (this._name != null) {
- if (temp._name == null) return false;
- else if (!(this._name.equals(temp._name)))
- return false;
- }
- else if (temp._name != null)
- return false;
- return true;
- }
- return false;
- } //-- boolean equals(java.lang.Object)
-
- /**
- * Returns the value of field 'name'.
- *
- * @return Object
- * @return the value of field 'name'.
- */
- public java.lang.Object getName()
- {
- return this._name;
- } //-- java.lang.Object getName()
-
- /**
- * Returns the value of field 'version'.
- *
- * @return Object
- * @return the value of field 'version'.
- */
- public java.lang.Object getVersion()
- {
- return this._version;
- } //-- java.lang.Object getVersion()
-
- /**
- * 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 'name'.
- *
- * @param name the value of field 'name'.
- */
- public void setName(java.lang.Object name)
- {
- this._name = name;
- } //-- void setName(java.lang.Object)
-
- /**
- * Sets the value of field 'version'.
- *
- * @param version the value of field 'version'.
- */
- public void setVersion(java.lang.Object version)
- {
- this._version = version;
- } //-- void setVersion(java.lang.Object)
-
- /**
- * Method unmarshal
- *
- *
- *
- * @param reader
- * @return Application
- */
- public static org.vamsas.client.objects.Application unmarshal(java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
- {
- return (org.vamsas.client.objects.Application) Unmarshaller.unmarshal(org.vamsas.client.objects.Application.class, reader);
- } //-- org.vamsas.client.objects.Application 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 0.9.9M1</a>, using an XML
- * Schema.
- * $Id$
- */
-
-package org.vamsas.client.objects;
-
- //---------------------------------/
- //- 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 ApplicationData.
- *
- * @version $Revision$ $Date$
- */
-public class ApplicationData extends org.vamsas.client.object
-implements java.io.Serializable
-{
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _application
- */
- private org.vamsas.client.objects.Application _application;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public ApplicationData()
- {
- super();
- } //-- org.vamsas.client.objects.ApplicationData()
-
-
- //-----------/
- //- 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 ApplicationData) {
-
- ApplicationData temp = (ApplicationData)obj;
- if (this._application != null) {
- if (temp._application == null) return false;
- else if (!(this._application.equals(temp._application)))
- return false;
- }
- else if (temp._application != null)
- return false;
- return true;
- }
- return false;
- } //-- boolean equals(java.lang.Object)
-
- /**
- * Returns the value of field 'application'.
- *
- * @return Application
- * @return the value of field 'application'.
- */
- public org.vamsas.client.objects.Application getApplication()
- {
- return this._application;
- } //-- org.vamsas.client.objects.Application getApplication()
-
- /**
- * 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 'application'.
- *
- * @param application the value of field 'application'.
- */
- public void setApplication(org.vamsas.client.objects.Application application)
- {
- this._application = application;
- } //-- void setApplication(org.vamsas.client.objects.Application)
-
- /**
- * Method unmarshal
- *
- *
- *
- * @param reader
- * @return ApplicationData
- */
- public static org.vamsas.client.objects.ApplicationData unmarshal(java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
- {
- return (org.vamsas.client.objects.ApplicationData) Unmarshaller.unmarshal(org.vamsas.client.objects.ApplicationData.class, reader);
- } //-- org.vamsas.client.objects.ApplicationData 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 0.9.9M1</a>, using an XML
- * Schema.
- * $Id$
- */
-
-package org.vamsas.client.objects;
-
- //---------------------------------/
- //- 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 ApplicationDataDescriptor.
- *
- * @version $Revision$ $Date$
- */
-public class ApplicationDataDescriptor 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 ApplicationDataDescriptor()
- {
- super();
- nsURI = "http://www.vamsas.org";
- xmlName = "ApplicationData";
-
- //-- 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
-
- //-- _application
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.client.objects.Application.class, "_application", "Application", org.exolab.castor.xml.NodeType.Element);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- ApplicationData target = (ApplicationData) object;
- return target.getApplication();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- ApplicationData target = (ApplicationData) object;
- target.setApplication( (org.vamsas.client.objects.Application) value);
- }
- catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance( java.lang.Object parent ) {
- return new org.vamsas.client.objects.Application();
- }
- };
- desc.setHandler(handler);
- desc.setNameSpaceURI("http://www.vamsas.org");
- desc.setRequired(true);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _application
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(1);
- { //-- local scope
- }
- desc.setValidator(fieldValidator);
- } //-- org.vamsas.client.objects.ApplicationDataDescriptor()
-
-
- //-----------/
- //- 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.client.objects.ApplicationData.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()
-
-}
+++ /dev/null
-/*
- * This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M1</a>, using an XML
- * Schema.
- * $Id$
- */
-
-package org.vamsas.client.objects;
-
- //---------------------------------/
- //- 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 ApplicationDescriptor.
- *
- * @version $Revision$ $Date$
- */
-public class ApplicationDescriptor 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 ApplicationDescriptor()
- {
- super();
- nsURI = "http://www.vamsas.org";
- xmlName = "Application";
- 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
-
- //-- _version
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Object.class, "_version", "version", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Application target = (Application) object;
- return target.getVersion();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Application target = (Application) object;
- target.setVersion( (java.lang.Object) 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();
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _version
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- }
- desc.setValidator(fieldValidator);
- //-- _name
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Object.class, "_name", "name", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Application target = (Application) object;
- return target.getName();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Application target = (Application) object;
- target.setName( (java.lang.Object) 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();
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _name
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- }
- desc.setValidator(fieldValidator);
- //-- initialize element descriptors
-
- } //-- org.vamsas.client.objects.ApplicationDescriptor()
-
-
- //-----------/
- //- 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.client.objects.Application.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()
-
-}
+++ /dev/null
-/*
- * This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M1</a>, using an XML
- * Schema.
- * $Id$
- */
-
-package org.vamsas.client.objects;
-
- //---------------------------------/
- //- 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 DbRef.
- *
- * @version $Revision$ $Date$
- */
-public class DbRef extends org.vamsas.client.object
-implements java.io.Serializable
-{
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _source
- */
- private java.lang.Object _source;
-
- /**
- * Field _version
- */
- private java.lang.Object _version;
-
- /**
- * Field _accessionId
- */
- private java.lang.Object _accessionId;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public DbRef()
- {
- super();
- } //-- org.vamsas.client.objects.DbRef()
-
-
- //-----------/
- //- 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 DbRef) {
-
- DbRef temp = (DbRef)obj;
- if (this._source != null) {
- if (temp._source == null) return false;
- else if (!(this._source.equals(temp._source)))
- return false;
- }
- else if (temp._source != null)
- return false;
- if (this._version != null) {
- if (temp._version == null) return false;
- else if (!(this._version.equals(temp._version)))
- return false;
- }
- else if (temp._version != null)
- return false;
- if (this._accessionId != null) {
- if (temp._accessionId == null) return false;
- else if (!(this._accessionId.equals(temp._accessionId)))
- return false;
- }
- else if (temp._accessionId != null)
- return false;
- return true;
- }
- return false;
- } //-- boolean equals(java.lang.Object)
-
- /**
- * Returns the value of field 'accessionId'.
- *
- * @return Object
- * @return the value of field 'accessionId'.
- */
- public java.lang.Object getAccessionId()
- {
- return this._accessionId;
- } //-- java.lang.Object getAccessionId()
-
- /**
- * Returns the value of field 'source'.
- *
- * @return Object
- * @return the value of field 'source'.
- */
- public java.lang.Object getSource()
- {
- return this._source;
- } //-- java.lang.Object getSource()
-
- /**
- * Returns the value of field 'version'.
- *
- * @return Object
- * @return the value of field 'version'.
- */
- public java.lang.Object getVersion()
- {
- return this._version;
- } //-- java.lang.Object getVersion()
-
- /**
- * 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 'accessionId'.
- *
- * @param accessionId the value of field 'accessionId'.
- */
- public void setAccessionId(java.lang.Object accessionId)
- {
- this._accessionId = accessionId;
- } //-- void setAccessionId(java.lang.Object)
-
- /**
- * Sets the value of field 'source'.
- *
- * @param source the value of field 'source'.
- */
- public void setSource(java.lang.Object source)
- {
- this._source = source;
- } //-- void setSource(java.lang.Object)
-
- /**
- * Sets the value of field 'version'.
- *
- * @param version the value of field 'version'.
- */
- public void setVersion(java.lang.Object version)
- {
- this._version = version;
- } //-- void setVersion(java.lang.Object)
-
- /**
- * Method unmarshal
- *
- *
- *
- * @param reader
- * @return DbRef
- */
- public static org.vamsas.client.objects.DbRef unmarshal(java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
- {
- return (org.vamsas.client.objects.DbRef) Unmarshaller.unmarshal(org.vamsas.client.objects.DbRef.class, reader);
- } //-- org.vamsas.client.objects.DbRef 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 0.9.9M1</a>, using an XML
- * Schema.
- * $Id$
- */
-
-package org.vamsas.client.objects;
-
- //---------------------------------/
- //- 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 DbRefDescriptor.
- *
- * @version $Revision$ $Date$
- */
-public class DbRefDescriptor 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 DbRefDescriptor()
- {
- super();
- nsURI = "http://www.vamsas.org";
- xmlName = "dbRef";
- 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
-
- //-- _source
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Object.class, "_source", "source", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- DbRef target = (DbRef) object;
- return target.getSource();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- DbRef target = (DbRef) object;
- target.setSource( (java.lang.Object) 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();
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _source
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- }
- desc.setValidator(fieldValidator);
- //-- _version
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Object.class, "_version", "version", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- DbRef target = (DbRef) object;
- return target.getVersion();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- DbRef target = (DbRef) object;
- target.setVersion( (java.lang.Object) 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();
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _version
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- }
- desc.setValidator(fieldValidator);
- //-- _accessionId
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Object.class, "_accessionId", "accessionId", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- DbRef target = (DbRef) object;
- return target.getAccessionId();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- DbRef target = (DbRef) object;
- target.setAccessionId( (java.lang.Object) 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();
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _accessionId
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- }
- desc.setValidator(fieldValidator);
- //-- initialize element descriptors
-
- } //-- org.vamsas.client.objects.DbRefDescriptor()
-
-
- //-----------/
- //- 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.client.objects.DbRef.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()
-
-}
+++ /dev/null
-/*
- * This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M1</a>, using an XML
- * Schema.
- * $Id$
- */
-
-package org.vamsas.client.objects;
-
- //---------------------------------/
- //- 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 Entry.
- *
- * @version $Revision$ $Date$
- */
-public class Entry extends org.vamsas.client.object
-implements java.io.Serializable
-{
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _user
- */
- private java.lang.String _user;
-
- /**
- * Field _action
- */
- private java.lang.String _action;
-
- /**
- * Field _date
- */
- private org.exolab.castor.types.Date _date;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public Entry()
- {
- super();
- } //-- org.vamsas.client.objects.Entry()
-
-
- //-----------/
- //- 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 Entry) {
-
- Entry temp = (Entry)obj;
- 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;
- if (this._action != null) {
- if (temp._action == null) return false;
- else if (!(this._action.equals(temp._action)))
- return false;
- }
- else if (temp._action != null)
- return false;
- if (this._date != null) {
- if (temp._date == null) return false;
- else if (!(this._date.equals(temp._date)))
- return false;
- }
- else if (temp._date != null)
- return false;
- return true;
- }
- return false;
- } //-- boolean equals(java.lang.Object)
-
- /**
- * Returns the value of field 'action'.
- *
- * @return String
- * @return the value of field 'action'.
- */
- public java.lang.String getAction()
- {
- return this._action;
- } //-- java.lang.String getAction()
-
- /**
- * Returns the value of field 'date'.
- *
- * @return Date
- * @return the value of field 'date'.
- */
- public org.exolab.castor.types.Date getDate()
- {
- return this._date;
- } //-- org.exolab.castor.types.Date getDate()
-
- /**
- * Returns the value of field 'user'.
- *
- * @return String
- * @return the value of field 'user'.
- */
- public java.lang.String getUser()
- {
- return this._user;
- } //-- java.lang.String getUser()
-
- /**
- * 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 'action'.
- *
- * @param action the value of field 'action'.
- */
- public void setAction(java.lang.String action)
- {
- this._action = action;
- } //-- void setAction(java.lang.String)
-
- /**
- * Sets the value of field 'date'.
- *
- * @param date the value of field 'date'.
- */
- public void setDate(org.exolab.castor.types.Date date)
- {
- this._date = date;
- } //-- void setDate(org.exolab.castor.types.Date)
-
- /**
- * Sets the value of field 'user'.
- *
- * @param user the value of field 'user'.
- */
- public void setUser(java.lang.String user)
- {
- this._user = user;
- } //-- void setUser(java.lang.String)
-
- /**
- * Method unmarshal
- *
- *
- *
- * @param reader
- * @return Entry
- */
- public static org.vamsas.client.objects.Entry unmarshal(java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
- {
- return (org.vamsas.client.objects.Entry) Unmarshaller.unmarshal(org.vamsas.client.objects.Entry.class, reader);
- } //-- org.vamsas.client.objects.Entry 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 0.9.9M1</a>, using an XML
- * Schema.
- * $Id$
- */
-
-package org.vamsas.client.objects;
-
- //---------------------------------/
- //- 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 EntryDescriptor.
- *
- * @version $Revision$ $Date$
- */
-public class EntryDescriptor 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 EntryDescriptor()
- {
- super();
- nsURI = "http://www.vamsas.org";
- xmlName = "entry";
-
- //-- 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
-
- //-- _user
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_user", "User", 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
- {
- Entry target = (Entry) object;
- return target.getUser();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Entry target = (Entry) object;
- target.setUser( (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: _user
- 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);
- //-- _action
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_action", "Action", 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
- {
- Entry target = (Entry) object;
- return target.getAction();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Entry target = (Entry) object;
- target.setAction( (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: _action
- 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);
- //-- _date
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.exolab.castor.types.Date.class, "_date", "Date", org.exolab.castor.xml.NodeType.Element);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Entry target = (Entry) object;
- return target.getDate();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Entry target = (Entry) object;
- target.setDate( (org.exolab.castor.types.Date) value);
- }
- catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance( java.lang.Object parent ) {
- return new org.exolab.castor.types.Date();
- }
- };
- desc.setHandler(handler);
- desc.setNameSpaceURI("http://www.vamsas.org");
- desc.setRequired(true);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _date
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(1);
- { //-- local scope
- DateTimeValidator typeValidator = new DateTimeValidator();
- fieldValidator.setValidator(typeValidator);
- }
- desc.setValidator(fieldValidator);
- } //-- org.vamsas.client.objects.EntryDescriptor()
-
-
- //-----------/
- //- 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.client.objects.Entry.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()
-
-}
+++ /dev/null
-/*
- * This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M1</a>, using an XML
- * Schema.
- * $Id$
- */
-
-package org.vamsas.client.objects;
-
- //---------------------------------/
- //- 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 LockFile.
- *
- * @version $Revision$ $Date$
- */
-public class LockFile extends org.vamsas.client.object
-implements java.io.Serializable
-{
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * internal content storage
- */
- private java.lang.String _content = "";
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public LockFile()
- {
- super();
- setContent("");
- } //-- org.vamsas.client.objects.LockFile()
-
-
- //-----------/
- //- 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 LockFile) {
-
- LockFile temp = (LockFile)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;
- 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()
-
- /**
- * 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)
-
- /**
- * Method unmarshal
- *
- *
- *
- * @param reader
- * @return LockFile
- */
- public static org.vamsas.client.objects.LockFile unmarshal(java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
- {
- return (org.vamsas.client.objects.LockFile) Unmarshaller.unmarshal(org.vamsas.client.objects.LockFile.class, reader);
- } //-- org.vamsas.client.objects.LockFile 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 0.9.9M1</a>, using an XML
- * Schema.
- * $Id$
- */
-
-package org.vamsas.client.objects;
-
- //---------------------------------/
- //- 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 LockFileDescriptor.
- *
- * @version $Revision$ $Date$
- */
-public class LockFileDescriptor 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 LockFileDescriptor()
- {
- super();
- nsURI = "http://www.vamsas.org";
- xmlName = "LockFile";
- 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
- {
- LockFile target = (LockFile) object;
- return target.getContent();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- LockFile target = (LockFile) 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
-
- //-- initialize element descriptors
-
- } //-- org.vamsas.client.objects.LockFileDescriptor()
-
-
- //-----------/
- //- 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.client.objects.LockFile.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()
-
-}
+++ /dev/null
-/*
- * This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M1</a>, using an XML
- * Schema.
- * $Id$
- */
-
-package org.vamsas.client.objects;
-
- //---------------------------------/
- //- 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 Provenance.
- *
- * @version $Revision$ $Date$
- */
-public class Provenance extends org.vamsas.client.object
-implements java.io.Serializable
-{
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _items
- */
- private java.util.Vector _items;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public Provenance()
- {
- super();
- _items = new Vector();
- } //-- org.vamsas.client.objects.Provenance()
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- * Method addProvenanceItem
- *
- *
- *
- * @param vProvenanceItem
- */
- public void addProvenanceItem(org.vamsas.client.objects.ProvenanceItem vProvenanceItem)
- throws java.lang.IndexOutOfBoundsException
- {
- _items.addElement(vProvenanceItem);
- } //-- void addProvenanceItem(org.vamsas.client.objects.ProvenanceItem)
-
- /**
- * Method addProvenanceItem
- *
- *
- *
- * @param index
- * @param vProvenanceItem
- */
- public void addProvenanceItem(int index, org.vamsas.client.objects.ProvenanceItem vProvenanceItem)
- throws java.lang.IndexOutOfBoundsException
- {
- _items.insertElementAt(vProvenanceItem, index);
- } //-- void addProvenanceItem(int, org.vamsas.client.objects.ProvenanceItem)
-
- /**
- * Method enumerateProvenanceItem
- *
- *
- *
- * @return Enumeration
- */
- public java.util.Enumeration enumerateProvenanceItem()
- {
- return _items.elements();
- } //-- java.util.Enumeration enumerateProvenanceItem()
-
- /**
- * 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 Provenance) {
-
- Provenance temp = (Provenance)obj;
- if (this._items != null) {
- if (temp._items == null) return false;
- else if (!(this._items.equals(temp._items)))
- return false;
- }
- else if (temp._items != null)
- return false;
- return true;
- }
- return false;
- } //-- boolean equals(java.lang.Object)
-
- /**
- * Method getProvenanceItem
- *
- *
- *
- * @param index
- * @return ProvenanceItem
- */
- public org.vamsas.client.objects.ProvenanceItem getProvenanceItem(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()+ "]");
- }
-
- return (org.vamsas.client.objects.ProvenanceItem) _items.elementAt(index);
- } //-- org.vamsas.client.objects.ProvenanceItem getProvenanceItem(int)
-
- /**
- * Method getProvenanceItem
- *
- *
- *
- * @return ProvenanceItem
- */
- public org.vamsas.client.objects.ProvenanceItem[] getProvenanceItem()
- {
- int size = _items.size();
- org.vamsas.client.objects.ProvenanceItem[] mArray = new org.vamsas.client.objects.ProvenanceItem[size];
- for (int index = 0; index < size; index++) {
- mArray[index] = (org.vamsas.client.objects.ProvenanceItem) _items.elementAt(index);
- }
- return mArray;
- } //-- org.vamsas.client.objects.ProvenanceItem[] getProvenanceItem()
-
- /**
- * Method getProvenanceItemAsReference
- *
- * Returns a reference to 'provenanceItem'. No type checking is
- * performed on any modications to the Vector.
- *
- * @return Vector
- * @return returns a reference to the Vector.
- */
- public java.util.Vector getProvenanceItemAsReference()
- {
- return _items;
- } //-- java.util.Vector getProvenanceItemAsReference()
-
- /**
- * Method getProvenanceItemCount
- *
- *
- *
- * @return int
- */
- public int getProvenanceItemCount()
- {
- return _items.size();
- } //-- int getProvenanceItemCount()
-
- /**
- * 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 removeAllProvenanceItem
- *
- */
- public void removeAllProvenanceItem()
- {
- _items.removeAllElements();
- } //-- void removeAllProvenanceItem()
-
- /**
- * Method removeProvenanceItem
- *
- *
- *
- * @param index
- * @return ProvenanceItem
- */
- public org.vamsas.client.objects.ProvenanceItem removeProvenanceItem(int index)
- {
- java.lang.Object obj = _items.elementAt(index);
- _items.removeElementAt(index);
- return (org.vamsas.client.objects.ProvenanceItem) obj;
- } //-- org.vamsas.client.objects.ProvenanceItem removeProvenanceItem(int)
-
- /**
- * Method setProvenanceItem
- *
- *
- *
- * @param index
- * @param vProvenanceItem
- */
- public void setProvenanceItem(int index, org.vamsas.client.objects.ProvenanceItem vProvenanceItem)
- 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()+ "]");
- }
- _items.setElementAt(vProvenanceItem, index);
- } //-- void setProvenanceItem(int, org.vamsas.client.objects.ProvenanceItem)
-
- /**
- * Method setProvenanceItem
- *
- *
- *
- * @param provenanceItemArray
- */
- public void setProvenanceItem(org.vamsas.client.objects.ProvenanceItem[] provenanceItemArray)
- {
- //-- copy array
- _items.removeAllElements();
- for (int i = 0; i < provenanceItemArray.length; i++) {
- _items.addElement(provenanceItemArray[i]);
- }
- } //-- void setProvenanceItem(org.vamsas.client.objects.ProvenanceItem)
-
- /**
- * Method setProvenanceItem
- *
- * Sets the value of 'provenanceItem' by copying the given
- * Vector.
- *
- * @param provenanceItemVector the Vector to copy.
- */
- public void setProvenanceItem(java.util.Vector provenanceItemVector)
- {
- //-- copy vector
- _items.removeAllElements();
- for (int i = 0; i < provenanceItemVector.size(); i++) {
- _items.addElement((org.vamsas.client.objects.ProvenanceItem)provenanceItemVector.elementAt(i));
- }
- } //-- void setProvenanceItem(java.util.Vector)
-
- /**
- * Method setProvenanceItemAsReference
- *
- * Sets the value of 'provenanceItem' by setting it to the
- * given Vector. No type checking is performed.
- *
- * @param provenanceItemVector the Vector to copy.
- */
- public void setProvenanceItemAsReference(java.util.Vector provenanceItemVector)
- {
- _items = provenanceItemVector;
- } //-- void setProvenanceItemAsReference(java.util.Vector)
-
- /**
- * Method unmarshal
- *
- *
- *
- * @param reader
- * @return Provenance
- */
- public static org.vamsas.client.objects.Provenance unmarshal(java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
- {
- return (org.vamsas.client.objects.Provenance) Unmarshaller.unmarshal(org.vamsas.client.objects.Provenance.class, reader);
- } //-- org.vamsas.client.objects.Provenance 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 0.9.9M1</a>, using an XML
- * Schema.
- * $Id$
- */
-
-package org.vamsas.client.objects;
-
- //---------------------------------/
- //- 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 ProvenanceDescriptor.
- *
- * @version $Revision$ $Date$
- */
-public class ProvenanceDescriptor 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 ProvenanceDescriptor()
- {
- super();
- xmlName = "Provenance";
- 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
-
- //-- _items
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.client.objects.ProvenanceItem.class, "_items", (String)null, 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();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Provenance target = (Provenance) object;
- target.addProvenanceItem( (org.vamsas.client.objects.ProvenanceItem) value);
- }
- catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance( java.lang.Object parent ) {
- return new org.vamsas.client.objects.ProvenanceItem();
- }
- };
- desc.setHandler(handler);
- desc.setContainer(true);
- desc.setClassDescriptor(new org.vamsas.client.objects.ProvenanceItemDescriptor());
- desc.setMultivalued(true);
- addFieldDescriptor(desc);
-
- //-- validation code for: _items
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(0);
- { //-- local scope
- }
- desc.setValidator(fieldValidator);
- } //-- org.vamsas.client.objects.ProvenanceDescriptor()
-
-
- //-----------/
- //- 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.client.objects.Provenance.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()
-
-}
+++ /dev/null
-/*
- * This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M1</a>, using an XML
- * Schema.
- * $Id$
- */
-
-package org.vamsas.client.objects;
-
- //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
-
-import java.io.Serializable;
-import org.exolab.castor.xml.Marshaller;
-import org.exolab.castor.xml.Unmarshaller;
-
-/**
- * Class ProvenanceItem.
- *
- * @version $Revision$ $Date$
- */
-public class ProvenanceItem implements java.io.Serializable {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _entry
- */
- private org.vamsas.client.objects.Entry _entry;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public ProvenanceItem()
- {
- super();
- } //-- org.vamsas.client.objects.ProvenanceItem()
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- * Returns the value of field 'entry'.
- *
- * @return Entry
- * @return the value of field 'entry'.
- */
- public org.vamsas.client.objects.Entry getEntry()
- {
- return this._entry;
- } //-- org.vamsas.client.objects.Entry getEntry()
-
- /**
- * Sets the value of field 'entry'.
- *
- * @param entry the value of field 'entry'.
- */
- public void setEntry(org.vamsas.client.objects.Entry entry)
- {
- this._entry = entry;
- } //-- void setEntry(org.vamsas.client.objects.Entry)
-
-}
+++ /dev/null
-/*
- * This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M1</a>, using an XML
- * Schema.
- * $Id$
- */
-
-package org.vamsas.client.objects;
-
- //---------------------------------/
- //- 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 ProvenanceItemDescriptor.
- *
- * @version $Revision$ $Date$
- */
-public class ProvenanceItemDescriptor 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 ProvenanceItemDescriptor()
- {
- 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 attribute descriptors
-
- //-- initialize element descriptors
-
- //-- _entry
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.client.objects.Entry.class, "_entry", "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
- {
- ProvenanceItem target = (ProvenanceItem) object;
- return target.getEntry();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- ProvenanceItem target = (ProvenanceItem) object;
- target.setEntry( (org.vamsas.client.objects.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.client.objects.Entry();
- }
- };
- desc.setHandler(handler);
- desc.setNameSpaceURI("http://www.vamsas.org");
- desc.setRequired(true);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _entry
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(1);
- { //-- local scope
- }
- desc.setValidator(fieldValidator);
- } //-- org.vamsas.client.objects.ProvenanceItemDescriptor()
-
-
- //-----------/
- //- 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.client.objects.ProvenanceItem.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()
-
-}
+++ /dev/null
-/*
- * This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M1</a>, using an XML
- * Schema.
- * $Id$
- */
-
-package org.vamsas.client.objects;
-
- //---------------------------------/
- //- 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 Sequence.
- *
- * @version $Revision$ $Date$
- */
-public class Sequence extends org.vamsas.client.objects.SequenceType
-implements java.io.Serializable
-{
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _dictionary
- */
- private java.lang.String _dictionary;
-
- /**
- * Field _id
- */
- private java.lang.String _id;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public Sequence()
- {
- super();
- } //-- org.vamsas.client.objects.Sequence()
-
-
- //-----------/
- //- 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 Sequence) {
-
- Sequence temp = (Sequence)obj;
- if (this._dictionary != null) {
- if (temp._dictionary == null) return false;
- else if (!(this._dictionary.equals(temp._dictionary)))
- return false;
- }
- 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;
- } //-- boolean equals(java.lang.Object)
-
- /**
- * Returns the value of field 'dictionary'.
- *
- * @return String
- * @return the value of field 'dictionary'.
- */
- public java.lang.String getDictionary()
- {
- return this._dictionary;
- } //-- 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
- *
- *
- *
- * @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 'dictionary'.
- *
- * @param dictionary the value of field 'dictionary'.
- */
- public void setDictionary(java.lang.String dictionary)
- {
- this._dictionary = 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
- *
- *
- *
- * @param reader
- * @return SequenceType
- */
- public static org.vamsas.client.objects.SequenceType unmarshal(java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
- {
- return (org.vamsas.client.objects.Sequence) Unmarshaller.unmarshal(org.vamsas.client.objects.Sequence.class, reader);
- } //-- org.vamsas.client.objects.SequenceType 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 0.9.9M1</a>, using an XML
- * Schema.
- * $Id$
- */
-
-package org.vamsas.client.objects;
-
- //---------------------------------/
- //- 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 SequenceDescriptor.
- *
- * @version $Revision$ $Date$
- */
-public class SequenceDescriptor extends org.vamsas.client.objects.SequenceTypeDescriptor {
-
-
- //--------------------------/
- //- 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 SequenceDescriptor()
- {
- super();
- setExtendsWithoutFlatten(new org.vamsas.client.objects.SequenceTypeDescriptor());
- nsURI = "http://www.vamsas.org";
- xmlName = "Sequence";
- 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
-
- //-- _dictionary
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_dictionary", "dictionary", 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
- {
- Sequence target = (Sequence) object;
- return target.getDictionary();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Sequence target = (Sequence) object;
- target.setDictionary( (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: _dictionary
- 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
- {
- 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.client.objects.SequenceDescriptor()
-
-
- //-----------/
- //- 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.client.objects.Sequence.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()
-
-}
+++ /dev/null
-/*
- * This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M1</a>, using an XML
- * Schema.
- * $Id$
- */
-
-package org.vamsas.client.objects;
-
- //---------------------------------/
- //- 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 SequenceSet.
- *
- * @version $Revision$ $Date$
- */
-public class SequenceSet extends org.vamsas.client.object
-implements java.io.Serializable
-{
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _gapChar
- */
- private java.lang.String _gapChar;
-
- /**
- * Field _aligned
- */
- private boolean _aligned;
-
- /**
- * keeps track of state for field: _aligned
- */
- private boolean _has_aligned;
-
- /**
- * Field _sequenceList
- */
- private java.util.Vector _sequenceList;
-
- /**
- * Field _sequenceSetAnnotationsList
- */
- private java.util.Vector _sequenceSetAnnotationsList;
-
- /**
- * Field _alignmentList
- */
- private java.util.Vector _alignmentList;
-
- /**
- * Field _tree
- */
- private org.vamsas.client.objects.Tree _tree;
-
- /**
- * Field _provenance
- */
- private org.vamsas.client.objects.Provenance _provenance;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public SequenceSet()
- {
- super();
- _sequenceList = new Vector();
- _sequenceSetAnnotationsList = new Vector();
- _alignmentList = new Vector();
- } //-- org.vamsas.client.objects.SequenceSet()
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- * Method addAlignment
- *
- *
- *
- * @param vAlignment
- */
- public void addAlignment(org.vamsas.client.objects.Alignment vAlignment)
- throws java.lang.IndexOutOfBoundsException
- {
- _alignmentList.addElement(vAlignment);
- } //-- void addAlignment(org.vamsas.client.objects.Alignment)
-
- /**
- * Method addAlignment
- *
- *
- *
- * @param index
- * @param vAlignment
- */
- public void addAlignment(int index, org.vamsas.client.objects.Alignment vAlignment)
- throws java.lang.IndexOutOfBoundsException
- {
- _alignmentList.insertElementAt(vAlignment, index);
- } //-- void addAlignment(int, org.vamsas.client.objects.Alignment)
-
- /**
- * Method addSequence
- *
- *
- *
- * @param vSequence
- */
- public void addSequence(org.vamsas.client.objects.Sequence vSequence)
- throws java.lang.IndexOutOfBoundsException
- {
- _sequenceList.addElement(vSequence);
- } //-- void addSequence(org.vamsas.client.objects.Sequence)
-
- /**
- * Method addSequence
- *
- *
- *
- * @param index
- * @param vSequence
- */
- public void addSequence(int index, org.vamsas.client.objects.Sequence vSequence)
- throws java.lang.IndexOutOfBoundsException
- {
- _sequenceList.insertElementAt(vSequence, index);
- } //-- void addSequence(int, org.vamsas.client.objects.Sequence)
-
- /**
- * Method addSequenceSetAnnotations
- *
- *
- *
- * @param vSequenceSetAnnotations
- */
- public void addSequenceSetAnnotations(org.vamsas.client.objects.SequenceSetAnnotations vSequenceSetAnnotations)
- throws java.lang.IndexOutOfBoundsException
- {
- _sequenceSetAnnotationsList.addElement(vSequenceSetAnnotations);
- } //-- void addSequenceSetAnnotations(org.vamsas.client.objects.SequenceSetAnnotations)
-
- /**
- * Method addSequenceSetAnnotations
- *
- *
- *
- * @param index
- * @param vSequenceSetAnnotations
- */
- public void addSequenceSetAnnotations(int index, org.vamsas.client.objects.SequenceSetAnnotations vSequenceSetAnnotations)
- throws java.lang.IndexOutOfBoundsException
- {
- _sequenceSetAnnotationsList.insertElementAt(vSequenceSetAnnotations, index);
- } //-- void addSequenceSetAnnotations(int, org.vamsas.client.objects.SequenceSetAnnotations)
-
- /**
- * Method deleteAligned
- *
- */
- public void deleteAligned()
- {
- this._has_aligned= false;
- } //-- void deleteAligned()
-
- /**
- * Method enumerateAlignment
- *
- *
- *
- * @return Enumeration
- */
- public java.util.Enumeration enumerateAlignment()
- {
- return _alignmentList.elements();
- } //-- java.util.Enumeration enumerateAlignment()
-
- /**
- * Method enumerateSequence
- *
- *
- *
- * @return Enumeration
- */
- public java.util.Enumeration enumerateSequence()
- {
- return _sequenceList.elements();
- } //-- java.util.Enumeration enumerateSequence()
-
- /**
- * Method enumerateSequenceSetAnnotations
- *
- *
- *
- * @return Enumeration
- */
- public java.util.Enumeration enumerateSequenceSetAnnotations()
- {
- return _sequenceSetAnnotationsList.elements();
- } //-- java.util.Enumeration enumerateSequenceSetAnnotations()
-
- /**
- * 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 SequenceSet) {
-
- SequenceSet temp = (SequenceSet)obj;
- if (this._gapChar != null) {
- if (temp._gapChar == null) return false;
- else if (!(this._gapChar.equals(temp._gapChar)))
- return false;
- }
- else if (temp._gapChar != null)
- return false;
- if (this._aligned != temp._aligned)
- return false;
- if (this._has_aligned != temp._has_aligned)
- return false;
- if (this._sequenceList != null) {
- if (temp._sequenceList == null) return false;
- else if (!(this._sequenceList.equals(temp._sequenceList)))
- return false;
- }
- else if (temp._sequenceList != null)
- return false;
- if (this._sequenceSetAnnotationsList != null) {
- if (temp._sequenceSetAnnotationsList == null) return false;
- else if (!(this._sequenceSetAnnotationsList.equals(temp._sequenceSetAnnotationsList)))
- return false;
- }
- else if (temp._sequenceSetAnnotationsList != null)
- return false;
- if (this._alignmentList != null) {
- if (temp._alignmentList == null) return false;
- else if (!(this._alignmentList.equals(temp._alignmentList)))
- return false;
- }
- else if (temp._alignmentList != null)
- return false;
- if (this._tree != null) {
- if (temp._tree == null) return false;
- else if (!(this._tree.equals(temp._tree)))
- return false;
- }
- else if (temp._tree != 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 'aligned'.
- *
- * @return boolean
- * @return the value of field 'aligned'.
- */
- public boolean getAligned()
- {
- return this._aligned;
- } //-- boolean getAligned()
-
- /**
- * Method getAlignment
- *
- *
- *
- * @param index
- * @return Alignment
- */
- public org.vamsas.client.objects.Alignment getAlignment(int index)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _alignmentList.size())) {
- throw new IndexOutOfBoundsException("getAlignment: Index value '"+index+"' not in range [0.."+_alignmentList.size()+ "]");
- }
-
- return (org.vamsas.client.objects.Alignment) _alignmentList.elementAt(index);
- } //-- org.vamsas.client.objects.Alignment getAlignment(int)
-
- /**
- * Method getAlignment
- *
- *
- *
- * @return Alignment
- */
- public org.vamsas.client.objects.Alignment[] getAlignment()
- {
- int size = _alignmentList.size();
- org.vamsas.client.objects.Alignment[] mArray = new org.vamsas.client.objects.Alignment[size];
- for (int index = 0; index < size; index++) {
- mArray[index] = (org.vamsas.client.objects.Alignment) _alignmentList.elementAt(index);
- }
- return mArray;
- } //-- org.vamsas.client.objects.Alignment[] getAlignment()
-
- /**
- * Method getAlignmentAsReference
- *
- * Returns a reference to 'alignment'. No type checking is
- * performed on any modications to the Vector.
- *
- * @return Vector
- * @return returns a reference to the Vector.
- */
- public java.util.Vector getAlignmentAsReference()
- {
- return _alignmentList;
- } //-- java.util.Vector getAlignmentAsReference()
-
- /**
- * Method getAlignmentCount
- *
- *
- *
- * @return int
- */
- public int getAlignmentCount()
- {
- return _alignmentList.size();
- } //-- int getAlignmentCount()
-
- /**
- * Returns the value of field 'gapChar'.
- *
- * @return String
- * @return the value of field 'gapChar'.
- */
- public java.lang.String getGapChar()
- {
- return this._gapChar;
- } //-- java.lang.String getGapChar()
-
- /**
- * Returns the value of field 'provenance'.
- *
- * @return Provenance
- * @return the value of field 'provenance'.
- */
- public org.vamsas.client.objects.Provenance getProvenance()
- {
- return this._provenance;
- } //-- org.vamsas.client.objects.Provenance getProvenance()
-
- /**
- * Method getSequence
- *
- *
- *
- * @param index
- * @return Sequence
- */
- public org.vamsas.client.objects.Sequence getSequence(int index)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _sequenceList.size())) {
- throw new IndexOutOfBoundsException("getSequence: Index value '"+index+"' not in range [0.."+_sequenceList.size()+ "]");
- }
-
- return (org.vamsas.client.objects.Sequence) _sequenceList.elementAt(index);
- } //-- org.vamsas.client.objects.Sequence getSequence(int)
-
- /**
- * Method getSequence
- *
- *
- *
- * @return Sequence
- */
- public org.vamsas.client.objects.Sequence[] getSequence()
- {
- int size = _sequenceList.size();
- org.vamsas.client.objects.Sequence[] mArray = new org.vamsas.client.objects.Sequence[size];
- for (int index = 0; index < size; index++) {
- mArray[index] = (org.vamsas.client.objects.Sequence) _sequenceList.elementAt(index);
- }
- return mArray;
- } //-- org.vamsas.client.objects.Sequence[] getSequence()
-
- /**
- * Method getSequenceAsReference
- *
- * Returns a reference to 'sequence'. No type checking is
- * performed on any modications to the Vector.
- *
- * @return Vector
- * @return returns a reference to the Vector.
- */
- public java.util.Vector getSequenceAsReference()
- {
- return _sequenceList;
- } //-- java.util.Vector getSequenceAsReference()
-
- /**
- * Method getSequenceCount
- *
- *
- *
- * @return int
- */
- public int getSequenceCount()
- {
- return _sequenceList.size();
- } //-- int getSequenceCount()
-
- /**
- * Method getSequenceSetAnnotations
- *
- *
- *
- * @param index
- * @return SequenceSetAnnotations
- */
- public org.vamsas.client.objects.SequenceSetAnnotations getSequenceSetAnnotations(int index)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _sequenceSetAnnotationsList.size())) {
- throw new IndexOutOfBoundsException("getSequenceSetAnnotations: Index value '"+index+"' not in range [0.."+_sequenceSetAnnotationsList.size()+ "]");
- }
-
- return (org.vamsas.client.objects.SequenceSetAnnotations) _sequenceSetAnnotationsList.elementAt(index);
- } //-- org.vamsas.client.objects.SequenceSetAnnotations getSequenceSetAnnotations(int)
-
- /**
- * Method getSequenceSetAnnotations
- *
- *
- *
- * @return SequenceSetAnnotations
- */
- public org.vamsas.client.objects.SequenceSetAnnotations[] getSequenceSetAnnotations()
- {
- int size = _sequenceSetAnnotationsList.size();
- org.vamsas.client.objects.SequenceSetAnnotations[] mArray = new org.vamsas.client.objects.SequenceSetAnnotations[size];
- for (int index = 0; index < size; index++) {
- mArray[index] = (org.vamsas.client.objects.SequenceSetAnnotations) _sequenceSetAnnotationsList.elementAt(index);
- }
- return mArray;
- } //-- org.vamsas.client.objects.SequenceSetAnnotations[] getSequenceSetAnnotations()
-
- /**
- * Method getSequenceSetAnnotationsAsReference
- *
- * Returns a reference to 'sequenceSetAnnotations'. No type
- * checking is performed on any modications to the Vector.
- *
- * @return Vector
- * @return returns a reference to the Vector.
- */
- public java.util.Vector getSequenceSetAnnotationsAsReference()
- {
- return _sequenceSetAnnotationsList;
- } //-- java.util.Vector getSequenceSetAnnotationsAsReference()
-
- /**
- * Method getSequenceSetAnnotationsCount
- *
- *
- *
- * @return int
- */
- public int getSequenceSetAnnotationsCount()
- {
- return _sequenceSetAnnotationsList.size();
- } //-- int getSequenceSetAnnotationsCount()
-
- /**
- * Returns the value of field 'tree'.
- *
- * @return Tree
- * @return the value of field 'tree'.
- */
- public org.vamsas.client.objects.Tree getTree()
- {
- return this._tree;
- } //-- org.vamsas.client.objects.Tree getTree()
-
- /**
- * Method hasAligned
- *
- *
- *
- * @return boolean
- */
- public boolean hasAligned()
- {
- return this._has_aligned;
- } //-- boolean hasAligned()
-
- /**
- * 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 removeAlignment
- *
- *
- *
- * @param index
- * @return Alignment
- */
- public org.vamsas.client.objects.Alignment removeAlignment(int index)
- {
- java.lang.Object obj = _alignmentList.elementAt(index);
- _alignmentList.removeElementAt(index);
- return (org.vamsas.client.objects.Alignment) obj;
- } //-- org.vamsas.client.objects.Alignment removeAlignment(int)
-
- /**
- * Method removeAllAlignment
- *
- */
- public void removeAllAlignment()
- {
- _alignmentList.removeAllElements();
- } //-- void removeAllAlignment()
-
- /**
- * Method removeAllSequence
- *
- */
- public void removeAllSequence()
- {
- _sequenceList.removeAllElements();
- } //-- void removeAllSequence()
-
- /**
- * Method removeAllSequenceSetAnnotations
- *
- */
- public void removeAllSequenceSetAnnotations()
- {
- _sequenceSetAnnotationsList.removeAllElements();
- } //-- void removeAllSequenceSetAnnotations()
-
- /**
- * Method removeSequence
- *
- *
- *
- * @param index
- * @return Sequence
- */
- public org.vamsas.client.objects.Sequence removeSequence(int index)
- {
- java.lang.Object obj = _sequenceList.elementAt(index);
- _sequenceList.removeElementAt(index);
- return (org.vamsas.client.objects.Sequence) obj;
- } //-- org.vamsas.client.objects.Sequence removeSequence(int)
-
- /**
- * Method removeSequenceSetAnnotations
- *
- *
- *
- * @param index
- * @return SequenceSetAnnotations
- */
- public org.vamsas.client.objects.SequenceSetAnnotations removeSequenceSetAnnotations(int index)
- {
- java.lang.Object obj = _sequenceSetAnnotationsList.elementAt(index);
- _sequenceSetAnnotationsList.removeElementAt(index);
- return (org.vamsas.client.objects.SequenceSetAnnotations) obj;
- } //-- org.vamsas.client.objects.SequenceSetAnnotations removeSequenceSetAnnotations(int)
-
- /**
- * Sets the value of field 'aligned'.
- *
- * @param aligned the value of field 'aligned'.
- */
- public void setAligned(boolean aligned)
- {
- this._aligned = aligned;
- this._has_aligned = true;
- } //-- void setAligned(boolean)
-
- /**
- * Method setAlignment
- *
- *
- *
- * @param index
- * @param vAlignment
- */
- public void setAlignment(int index, org.vamsas.client.objects.Alignment vAlignment)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _alignmentList.size())) {
- throw new IndexOutOfBoundsException("setAlignment: Index value '"+index+"' not in range [0.."+_alignmentList.size()+ "]");
- }
- _alignmentList.setElementAt(vAlignment, index);
- } //-- void setAlignment(int, org.vamsas.client.objects.Alignment)
-
- /**
- * Method setAlignment
- *
- *
- *
- * @param alignmentArray
- */
- public void setAlignment(org.vamsas.client.objects.Alignment[] alignmentArray)
- {
- //-- copy array
- _alignmentList.removeAllElements();
- for (int i = 0; i < alignmentArray.length; i++) {
- _alignmentList.addElement(alignmentArray[i]);
- }
- } //-- void setAlignment(org.vamsas.client.objects.Alignment)
-
- /**
- * Method setAlignment
- *
- * Sets the value of 'alignment' by copying the given Vector.
- *
- * @param alignmentVector the Vector to copy.
- */
- public void setAlignment(java.util.Vector alignmentVector)
- {
- //-- copy vector
- _alignmentList.removeAllElements();
- for (int i = 0; i < alignmentVector.size(); i++) {
- _alignmentList.addElement((org.vamsas.client.objects.Alignment)alignmentVector.elementAt(i));
- }
- } //-- void setAlignment(java.util.Vector)
-
- /**
- * Method setAlignmentAsReference
- *
- * Sets the value of 'alignment' by setting it to the given
- * Vector. No type checking is performed.
- *
- * @param alignmentVector the Vector to copy.
- */
- public void setAlignmentAsReference(java.util.Vector alignmentVector)
- {
- _alignmentList = alignmentVector;
- } //-- void setAlignmentAsReference(java.util.Vector)
-
- /**
- * Sets the value of field 'gapChar'.
- *
- * @param gapChar the value of field 'gapChar'.
- */
- public void setGapChar(java.lang.String gapChar)
- {
- this._gapChar = gapChar;
- } //-- void setGapChar(java.lang.String)
-
- /**
- * Sets the value of field 'provenance'.
- *
- * @param provenance the value of field 'provenance'.
- */
- public void setProvenance(org.vamsas.client.objects.Provenance provenance)
- {
- this._provenance = provenance;
- } //-- void setProvenance(org.vamsas.client.objects.Provenance)
-
- /**
- * Method setSequence
- *
- *
- *
- * @param index
- * @param vSequence
- */
- public void setSequence(int index, org.vamsas.client.objects.Sequence vSequence)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _sequenceList.size())) {
- throw new IndexOutOfBoundsException("setSequence: Index value '"+index+"' not in range [0.."+_sequenceList.size()+ "]");
- }
- _sequenceList.setElementAt(vSequence, index);
- } //-- void setSequence(int, org.vamsas.client.objects.Sequence)
-
- /**
- * Method setSequence
- *
- *
- *
- * @param sequenceArray
- */
- public void setSequence(org.vamsas.client.objects.Sequence[] sequenceArray)
- {
- //-- copy array
- _sequenceList.removeAllElements();
- for (int i = 0; i < sequenceArray.length; i++) {
- _sequenceList.addElement(sequenceArray[i]);
- }
- } //-- void setSequence(org.vamsas.client.objects.Sequence)
-
- /**
- * Method setSequence
- *
- * Sets the value of 'sequence' by copying the given Vector.
- *
- * @param sequenceVector the Vector to copy.
- */
- public void setSequence(java.util.Vector sequenceVector)
- {
- //-- copy vector
- _sequenceList.removeAllElements();
- for (int i = 0; i < sequenceVector.size(); i++) {
- _sequenceList.addElement((org.vamsas.client.objects.Sequence)sequenceVector.elementAt(i));
- }
- } //-- void setSequence(java.util.Vector)
-
- /**
- * Method setSequenceAsReference
- *
- * Sets the value of 'sequence' by setting it to the given
- * Vector. No type checking is performed.
- *
- * @param sequenceVector the Vector to copy.
- */
- public void setSequenceAsReference(java.util.Vector sequenceVector)
- {
- _sequenceList = sequenceVector;
- } //-- void setSequenceAsReference(java.util.Vector)
-
- /**
- * Method setSequenceSetAnnotations
- *
- *
- *
- * @param index
- * @param vSequenceSetAnnotations
- */
- public void setSequenceSetAnnotations(int index, org.vamsas.client.objects.SequenceSetAnnotations vSequenceSetAnnotations)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _sequenceSetAnnotationsList.size())) {
- throw new IndexOutOfBoundsException("setSequenceSetAnnotations: Index value '"+index+"' not in range [0.."+_sequenceSetAnnotationsList.size()+ "]");
- }
- _sequenceSetAnnotationsList.setElementAt(vSequenceSetAnnotations, index);
- } //-- void setSequenceSetAnnotations(int, org.vamsas.client.objects.SequenceSetAnnotations)
-
- /**
- * Method setSequenceSetAnnotations
- *
- *
- *
- * @param sequenceSetAnnotationsArray
- */
- public void setSequenceSetAnnotations(org.vamsas.client.objects.SequenceSetAnnotations[] sequenceSetAnnotationsArray)
- {
- //-- copy array
- _sequenceSetAnnotationsList.removeAllElements();
- for (int i = 0; i < sequenceSetAnnotationsArray.length; i++) {
- _sequenceSetAnnotationsList.addElement(sequenceSetAnnotationsArray[i]);
- }
- } //-- void setSequenceSetAnnotations(org.vamsas.client.objects.SequenceSetAnnotations)
-
- /**
- * Method setSequenceSetAnnotations
- *
- * Sets the value of 'sequenceSetAnnotations' by copying the
- * given Vector.
- *
- * @param sequenceSetAnnotationsVector the Vector to copy.
- */
- public void setSequenceSetAnnotations(java.util.Vector sequenceSetAnnotationsVector)
- {
- //-- copy vector
- _sequenceSetAnnotationsList.removeAllElements();
- for (int i = 0; i < sequenceSetAnnotationsVector.size(); i++) {
- _sequenceSetAnnotationsList.addElement((org.vamsas.client.objects.SequenceSetAnnotations)sequenceSetAnnotationsVector.elementAt(i));
- }
- } //-- void setSequenceSetAnnotations(java.util.Vector)
-
- /**
- * Method setSequenceSetAnnotationsAsReference
- *
- * Sets the value of 'sequenceSetAnnotations' by setting it to
- * the given Vector. No type checking is performed.
- *
- * @param sequenceSetAnnotationsVector the Vector to copy.
- */
- public void setSequenceSetAnnotationsAsReference(java.util.Vector sequenceSetAnnotationsVector)
- {
- _sequenceSetAnnotationsList = sequenceSetAnnotationsVector;
- } //-- void setSequenceSetAnnotationsAsReference(java.util.Vector)
-
- /**
- * Sets the value of field 'tree'.
- *
- * @param tree the value of field 'tree'.
- */
- public void setTree(org.vamsas.client.objects.Tree tree)
- {
- this._tree = tree;
- } //-- void setTree(org.vamsas.client.objects.Tree)
-
- /**
- * Method unmarshal
- *
- *
- *
- * @param reader
- * @return SequenceSet
- */
- public static org.vamsas.client.objects.SequenceSet unmarshal(java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
- {
- return (org.vamsas.client.objects.SequenceSet) Unmarshaller.unmarshal(org.vamsas.client.objects.SequenceSet.class, reader);
- } //-- org.vamsas.client.objects.SequenceSet 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 0.9.9M1</a>, using an XML
- * Schema.
- * $Id$
- */
-
-package org.vamsas.client.objects;
-
- //---------------------------------/
- //- 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 SequenceSetAnnotations.
- *
- * @version $Revision$ $Date$
- */
-public class SequenceSetAnnotations extends org.vamsas.client.object
-implements java.io.Serializable
-{
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _type
- */
- private java.lang.String _type;
-
- /**
- * Field _end
- */
- private java.lang.String _end;
-
- /**
- * Field _begin
- */
- private java.lang.String _begin;
-
- /**
- * Field _seqRef
- */
- private java.lang.Object _seqRef;
-
- /**
- * Field _description
- */
- private java.lang.String _description;
-
- /**
- * Field _status
- */
- private java.lang.String _status;
-
- /**
- * Field _annotationElementList
- */
- private java.util.Vector _annotationElementList;
-
- /**
- * Field _provenance
- */
- private org.vamsas.client.objects.Provenance _provenance;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public SequenceSetAnnotations()
- {
- super();
- _annotationElementList = new Vector();
- } //-- org.vamsas.client.objects.SequenceSetAnnotations()
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- * Method addAnnotationElement
- *
- *
- *
- * @param vAnnotationElement
- */
- public void addAnnotationElement(org.vamsas.client.objects.AnnotationElement vAnnotationElement)
- throws java.lang.IndexOutOfBoundsException
- {
- _annotationElementList.addElement(vAnnotationElement);
- } //-- void addAnnotationElement(org.vamsas.client.objects.AnnotationElement)
-
- /**
- * Method addAnnotationElement
- *
- *
- *
- * @param index
- * @param vAnnotationElement
- */
- public void addAnnotationElement(int index, org.vamsas.client.objects.AnnotationElement vAnnotationElement)
- throws java.lang.IndexOutOfBoundsException
- {
- _annotationElementList.insertElementAt(vAnnotationElement, index);
- } //-- void addAnnotationElement(int, org.vamsas.client.objects.AnnotationElement)
-
- /**
- * Method enumerateAnnotationElement
- *
- *
- *
- * @return Enumeration
- */
- public java.util.Enumeration enumerateAnnotationElement()
- {
- return _annotationElementList.elements();
- } //-- java.util.Enumeration enumerateAnnotationElement()
-
- /**
- * 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 SequenceSetAnnotations) {
-
- SequenceSetAnnotations temp = (SequenceSetAnnotations)obj;
- if (this._type != null) {
- if (temp._type == null) return false;
- else if (!(this._type.equals(temp._type)))
- return false;
- }
- else if (temp._type != null)
- return false;
- if (this._end != null) {
- if (temp._end == null) return false;
- else if (!(this._end.equals(temp._end)))
- return false;
- }
- else if (temp._end != null)
- return false;
- if (this._begin != null) {
- if (temp._begin == null) return false;
- else if (!(this._begin.equals(temp._begin)))
- return false;
- }
- else if (temp._begin != null)
- return false;
- if (this._seqRef != null) {
- if (temp._seqRef == null) return false;
- else if (!(this._seqRef.equals(temp._seqRef)))
- return false;
- }
- else if (temp._seqRef != null)
- return false;
- if (this._description != null) {
- if (temp._description == null) return false;
- else if (!(this._description.equals(temp._description)))
- return false;
- }
- else if (temp._description != null)
- return false;
- if (this._status != null) {
- if (temp._status == null) return false;
- else if (!(this._status.equals(temp._status)))
- return false;
- }
- else if (temp._status != null)
- return false;
- if (this._annotationElementList != null) {
- if (temp._annotationElementList == null) return false;
- else if (!(this._annotationElementList.equals(temp._annotationElementList)))
- return false;
- }
- else if (temp._annotationElementList != 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)
-
- /**
- * Method getAnnotationElement
- *
- *
- *
- * @param index
- * @return AnnotationElement
- */
- public org.vamsas.client.objects.AnnotationElement getAnnotationElement(int index)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _annotationElementList.size())) {
- throw new IndexOutOfBoundsException("getAnnotationElement: Index value '"+index+"' not in range [0.."+_annotationElementList.size()+ "]");
- }
-
- return (org.vamsas.client.objects.AnnotationElement) _annotationElementList.elementAt(index);
- } //-- org.vamsas.client.objects.AnnotationElement getAnnotationElement(int)
-
- /**
- * Method getAnnotationElement
- *
- *
- *
- * @return AnnotationElement
- */
- public org.vamsas.client.objects.AnnotationElement[] getAnnotationElement()
- {
- int size = _annotationElementList.size();
- org.vamsas.client.objects.AnnotationElement[] mArray = new org.vamsas.client.objects.AnnotationElement[size];
- for (int index = 0; index < size; index++) {
- mArray[index] = (org.vamsas.client.objects.AnnotationElement) _annotationElementList.elementAt(index);
- }
- return mArray;
- } //-- org.vamsas.client.objects.AnnotationElement[] getAnnotationElement()
-
- /**
- * Method getAnnotationElementAsReference
- *
- * Returns a reference to 'annotationElement'. No type checking
- * is performed on any modications to the Vector.
- *
- * @return Vector
- * @return returns a reference to the Vector.
- */
- public java.util.Vector getAnnotationElementAsReference()
- {
- return _annotationElementList;
- } //-- java.util.Vector getAnnotationElementAsReference()
-
- /**
- * Method getAnnotationElementCount
- *
- *
- *
- * @return int
- */
- public int getAnnotationElementCount()
- {
- return _annotationElementList.size();
- } //-- int getAnnotationElementCount()
-
- /**
- * Returns the value of field 'begin'.
- *
- * @return String
- * @return the value of field 'begin'.
- */
- public java.lang.String getBegin()
- {
- return this._begin;
- } //-- java.lang.String getBegin()
-
- /**
- * Returns the value of field 'description'.
- *
- * @return String
- * @return the value of field 'description'.
- */
- public java.lang.String getDescription()
- {
- return this._description;
- } //-- java.lang.String getDescription()
-
- /**
- * Returns the value of field 'end'.
- *
- * @return String
- * @return the value of field 'end'.
- */
- public java.lang.String getEnd()
- {
- return this._end;
- } //-- java.lang.String getEnd()
-
- /**
- * Returns the value of field 'provenance'.
- *
- * @return Provenance
- * @return the value of field 'provenance'.
- */
- public org.vamsas.client.objects.Provenance getProvenance()
- {
- return this._provenance;
- } //-- org.vamsas.client.objects.Provenance getProvenance()
-
- /**
- * Returns the value of field 'seqRef'.
- *
- * @return Object
- * @return the value of field 'seqRef'.
- */
- public java.lang.Object getSeqRef()
- {
- return this._seqRef;
- } //-- java.lang.Object getSeqRef()
-
- /**
- * Returns the value of field 'status'.
- *
- * @return String
- * @return the value of field 'status'.
- */
- public java.lang.String getStatus()
- {
- return this._status;
- } //-- java.lang.String getStatus()
-
- /**
- * Returns the value of field 'type'.
- *
- * @return String
- * @return the value of field 'type'.
- */
- public java.lang.String getType()
- {
- return this._type;
- } //-- java.lang.String getType()
-
- /**
- * 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 removeAllAnnotationElement
- *
- */
- public void removeAllAnnotationElement()
- {
- _annotationElementList.removeAllElements();
- } //-- void removeAllAnnotationElement()
-
- /**
- * Method removeAnnotationElement
- *
- *
- *
- * @param index
- * @return AnnotationElement
- */
- public org.vamsas.client.objects.AnnotationElement removeAnnotationElement(int index)
- {
- java.lang.Object obj = _annotationElementList.elementAt(index);
- _annotationElementList.removeElementAt(index);
- return (org.vamsas.client.objects.AnnotationElement) obj;
- } //-- org.vamsas.client.objects.AnnotationElement removeAnnotationElement(int)
-
- /**
- * Method setAnnotationElement
- *
- *
- *
- * @param index
- * @param vAnnotationElement
- */
- public void setAnnotationElement(int index, org.vamsas.client.objects.AnnotationElement vAnnotationElement)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _annotationElementList.size())) {
- throw new IndexOutOfBoundsException("setAnnotationElement: Index value '"+index+"' not in range [0.."+_annotationElementList.size()+ "]");
- }
- _annotationElementList.setElementAt(vAnnotationElement, index);
- } //-- void setAnnotationElement(int, org.vamsas.client.objects.AnnotationElement)
-
- /**
- * Method setAnnotationElement
- *
- *
- *
- * @param annotationElementArray
- */
- public void setAnnotationElement(org.vamsas.client.objects.AnnotationElement[] annotationElementArray)
- {
- //-- copy array
- _annotationElementList.removeAllElements();
- for (int i = 0; i < annotationElementArray.length; i++) {
- _annotationElementList.addElement(annotationElementArray[i]);
- }
- } //-- void setAnnotationElement(org.vamsas.client.objects.AnnotationElement)
-
- /**
- * Method setAnnotationElement
- *
- * Sets the value of 'annotationElement' by copying the given
- * Vector.
- *
- * @param annotationElementVector the Vector to copy.
- */
- public void setAnnotationElement(java.util.Vector annotationElementVector)
- {
- //-- copy vector
- _annotationElementList.removeAllElements();
- for (int i = 0; i < annotationElementVector.size(); i++) {
- _annotationElementList.addElement((org.vamsas.client.objects.AnnotationElement)annotationElementVector.elementAt(i));
- }
- } //-- void setAnnotationElement(java.util.Vector)
-
- /**
- * Method setAnnotationElementAsReference
- *
- * Sets the value of 'annotationElement' by setting it to the
- * given Vector. No type checking is performed.
- *
- * @param annotationElementVector the Vector to copy.
- */
- public void setAnnotationElementAsReference(java.util.Vector annotationElementVector)
- {
- _annotationElementList = annotationElementVector;
- } //-- void setAnnotationElementAsReference(java.util.Vector)
-
- /**
- * Sets the value of field 'begin'.
- *
- * @param begin the value of field 'begin'.
- */
- public void setBegin(java.lang.String begin)
- {
- this._begin = begin;
- } //-- void setBegin(java.lang.String)
-
- /**
- * Sets the value of field 'description'.
- *
- * @param description the value of field 'description'.
- */
- public void setDescription(java.lang.String description)
- {
- this._description = description;
- } //-- void setDescription(java.lang.String)
-
- /**
- * Sets the value of field 'end'.
- *
- * @param end the value of field 'end'.
- */
- public void setEnd(java.lang.String end)
- {
- this._end = end;
- } //-- void setEnd(java.lang.String)
-
- /**
- * Sets the value of field 'provenance'.
- *
- * @param provenance the value of field 'provenance'.
- */
- public void setProvenance(org.vamsas.client.objects.Provenance provenance)
- {
- this._provenance = provenance;
- } //-- void setProvenance(org.vamsas.client.objects.Provenance)
-
- /**
- * Sets the value of field 'seqRef'.
- *
- * @param seqRef the value of field 'seqRef'.
- */
- public void setSeqRef(java.lang.Object seqRef)
- {
- this._seqRef = seqRef;
- } //-- void setSeqRef(java.lang.Object)
-
- /**
- * Sets the value of field 'status'.
- *
- * @param status the value of field 'status'.
- */
- public void setStatus(java.lang.String status)
- {
- this._status = status;
- } //-- void setStatus(java.lang.String)
-
- /**
- * Sets the value of field 'type'.
- *
- * @param type the value of field 'type'.
- */
- public void setType(java.lang.String type)
- {
- this._type = type;
- } //-- void setType(java.lang.String)
-
- /**
- * Method unmarshal
- *
- *
- *
- * @param reader
- * @return SequenceSetAnnotations
- */
- public static org.vamsas.client.objects.SequenceSetAnnotations unmarshal(java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
- {
- return (org.vamsas.client.objects.SequenceSetAnnotations) Unmarshaller.unmarshal(org.vamsas.client.objects.SequenceSetAnnotations.class, reader);
- } //-- org.vamsas.client.objects.SequenceSetAnnotations 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 0.9.9M1</a>, using an XML
- * Schema.
- * $Id$
- */
-
-package org.vamsas.client.objects;
-
- //---------------------------------/
- //- 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 SequenceSetAnnotationsDescriptor.
- *
- * @version $Revision$ $Date$
- */
-public class SequenceSetAnnotationsDescriptor 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 SequenceSetAnnotationsDescriptor()
- {
- super();
- nsURI = "http://www.vamsas.org";
- xmlName = "SequenceSetAnnotations";
-
- //-- 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
-
- //-- _type
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_type", "type", 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
- {
- SequenceSetAnnotations target = (SequenceSetAnnotations) object;
- return target.getType();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- SequenceSetAnnotations target = (SequenceSetAnnotations) object;
- target.setType( (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.setRequired(true);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _type
- 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);
- //-- _end
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_end", "end", 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
- {
- SequenceSetAnnotations target = (SequenceSetAnnotations) object;
- return target.getEnd();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- SequenceSetAnnotations target = (SequenceSetAnnotations) object;
- target.setEnd( (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.setRequired(true);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _end
- 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);
- //-- _begin
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_begin", "begin", 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
- {
- SequenceSetAnnotations target = (SequenceSetAnnotations) object;
- return target.getBegin();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- SequenceSetAnnotations target = (SequenceSetAnnotations) object;
- target.setBegin( (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.setRequired(true);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _begin
- 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);
- //-- _seqRef
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Object.class, "_seqRef", "seqRef", 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
- {
- SequenceSetAnnotations target = (SequenceSetAnnotations) object;
- return target.getSeqRef();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- SequenceSetAnnotations target = (SequenceSetAnnotations) object;
- target.setSeqRef( (java.lang.Object) 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();
- }
- };
- desc.setHandler(handler);
- desc.setRequired(true);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _seqRef
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(1);
- { //-- local scope
- }
- desc.setValidator(fieldValidator);
- //-- initialize element descriptors
-
- //-- _description
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_description", "description", 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
- {
- SequenceSetAnnotations target = (SequenceSetAnnotations) object;
- return target.getDescription();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- SequenceSetAnnotations target = (SequenceSetAnnotations) object;
- target.setDescription( (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.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _description
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- StringValidator typeValidator = new StringValidator();
- typeValidator.setWhiteSpace("preserve");
- fieldValidator.setValidator(typeValidator);
- }
- desc.setValidator(fieldValidator);
- //-- _status
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_status", "status", 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
- {
- SequenceSetAnnotations target = (SequenceSetAnnotations) object;
- return target.getStatus();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- SequenceSetAnnotations target = (SequenceSetAnnotations) object;
- target.setStatus( (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.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _status
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- StringValidator typeValidator = new StringValidator();
- typeValidator.setWhiteSpace("preserve");
- fieldValidator.setValidator(typeValidator);
- }
- desc.setValidator(fieldValidator);
- //-- _annotationElementList
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.client.objects.AnnotationElement.class, "_annotationElementList", "annotationElement", org.exolab.castor.xml.NodeType.Element);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- SequenceSetAnnotations target = (SequenceSetAnnotations) object;
- return target.getAnnotationElement();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- SequenceSetAnnotations target = (SequenceSetAnnotations) object;
- target.addAnnotationElement( (org.vamsas.client.objects.AnnotationElement) value);
- }
- catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance( java.lang.Object parent ) {
- return new org.vamsas.client.objects.AnnotationElement();
- }
- };
- desc.setHandler(handler);
- desc.setNameSpaceURI("http://www.vamsas.org");
- desc.setMultivalued(true);
- addFieldDescriptor(desc);
-
- //-- validation code for: _annotationElementList
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(0);
- { //-- local scope
- }
- desc.setValidator(fieldValidator);
- //-- _provenance
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.client.objects.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
- {
- SequenceSetAnnotations target = (SequenceSetAnnotations) object;
- return target.getProvenance();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- SequenceSetAnnotations target = (SequenceSetAnnotations) object;
- target.setProvenance( (org.vamsas.client.objects.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.client.objects.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.client.objects.SequenceSetAnnotationsDescriptor()
-
-
- //-----------/
- //- 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.client.objects.SequenceSetAnnotations.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()
-
-}
+++ /dev/null
-/*
- * This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M1</a>, using an XML
- * Schema.
- * $Id$
- */
-
-package org.vamsas.client.objects;
-
- //---------------------------------/
- //- 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 SequenceSetDescriptor.
- *
- * @version $Revision$ $Date$
- */
-public class SequenceSetDescriptor 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 SequenceSetDescriptor()
- {
- super();
- nsURI = "http://www.vamsas.org";
- xmlName = "SequenceSet";
-
- //-- 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
-
- //-- _gapChar
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_gapChar", "gapChar", 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
- {
- SequenceSet target = (SequenceSet) object;
- return target.getGapChar();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- SequenceSet target = (SequenceSet) object;
- target.setGapChar( (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.setRequired(true);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _gapChar
- 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);
- //-- _aligned
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_aligned", "aligned", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- SequenceSet target = (SequenceSet) object;
- if(!target.hasAligned())
- return null;
- return (target.getAligned() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- SequenceSet target = (SequenceSet) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteAligned();
- return;
- }
- target.setAligned( ((java.lang.Boolean)value).booleanValue());
- }
- 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: _aligned
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- BooleanValidator typeValidator = new BooleanValidator();
- fieldValidator.setValidator(typeValidator);
- }
- desc.setValidator(fieldValidator);
- //-- initialize element descriptors
-
- //-- _sequenceList
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.client.objects.Sequence.class, "_sequenceList", "Sequence", org.exolab.castor.xml.NodeType.Element);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- SequenceSet target = (SequenceSet) object;
- return target.getSequence();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- SequenceSet target = (SequenceSet) object;
- target.addSequence( (org.vamsas.client.objects.Sequence) value);
- }
- catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance( java.lang.Object parent ) {
- return new org.vamsas.client.objects.Sequence();
- }
- };
- desc.setHandler(handler);
- desc.setNameSpaceURI("http://www.vamsas.org");
- desc.setRequired(true);
- desc.setMultivalued(true);
- addFieldDescriptor(desc);
-
- //-- validation code for: _sequenceList
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(1);
- { //-- local scope
- }
- desc.setValidator(fieldValidator);
- //-- _sequenceSetAnnotationsList
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.client.objects.SequenceSetAnnotations.class, "_sequenceSetAnnotationsList", "SequenceSetAnnotations", org.exolab.castor.xml.NodeType.Element);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- SequenceSet target = (SequenceSet) object;
- return target.getSequenceSetAnnotations();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- SequenceSet target = (SequenceSet) object;
- target.addSequenceSetAnnotations( (org.vamsas.client.objects.SequenceSetAnnotations) value);
- }
- catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance( java.lang.Object parent ) {
- return new org.vamsas.client.objects.SequenceSetAnnotations();
- }
- };
- desc.setHandler(handler);
- desc.setNameSpaceURI("http://www.vamsas.org");
- desc.setMultivalued(true);
- addFieldDescriptor(desc);
-
- //-- validation code for: _sequenceSetAnnotationsList
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(0);
- { //-- local scope
- }
- desc.setValidator(fieldValidator);
- //-- _alignmentList
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.client.objects.Alignment.class, "_alignmentList", "Alignment", org.exolab.castor.xml.NodeType.Element);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- SequenceSet target = (SequenceSet) object;
- return target.getAlignment();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- SequenceSet target = (SequenceSet) object;
- target.addAlignment( (org.vamsas.client.objects.Alignment) value);
- }
- catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance( java.lang.Object parent ) {
- return new org.vamsas.client.objects.Alignment();
- }
- };
- desc.setHandler(handler);
- desc.setNameSpaceURI("http://www.vamsas.org");
- desc.setMultivalued(true);
- addFieldDescriptor(desc);
-
- //-- validation code for: _alignmentList
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(0);
- { //-- local scope
- }
- desc.setValidator(fieldValidator);
- //-- _tree
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.client.objects.Tree.class, "_tree", "tree", org.exolab.castor.xml.NodeType.Element);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- SequenceSet target = (SequenceSet) object;
- return target.getTree();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- SequenceSet target = (SequenceSet) object;
- target.setTree( (org.vamsas.client.objects.Tree) value);
- }
- catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance( java.lang.Object parent ) {
- return new org.vamsas.client.objects.Tree();
- }
- };
- desc.setHandler(handler);
- desc.setNameSpaceURI("http://www.vamsas.org");
- desc.setRequired(true);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _tree
- 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.client.objects.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
- {
- SequenceSet target = (SequenceSet) object;
- return target.getProvenance();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- SequenceSet target = (SequenceSet) object;
- target.setProvenance( (org.vamsas.client.objects.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.client.objects.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.client.objects.SequenceSetDescriptor()
-
-
- //-----------/
- //- 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.client.objects.SequenceSet.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()
-
-}
+++ /dev/null
-/*
- * This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M1</a>, using an XML
- * Schema.
- * $Id$
- */
-
-package org.vamsas.client.objects;
-
- //---------------------------------/
- //- 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 SequenceType.
- *
- * @version $Revision$ $Date$
- */
-public class SequenceType extends org.vamsas.client.object
-implements java.io.Serializable
-{
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _start
- */
- private int _start;
-
- /**
- * keeps track of state for field: _start
- */
- private boolean _has_start;
-
- /**
- * Field _end
- */
- private int _end;
-
- /**
- * keeps track of state for field: _end
- */
- private boolean _has_end;
-
- /**
- * Field _sequence
- */
- private java.lang.String _sequence;
-
- /**
- * Field _name
- */
- private java.lang.String _name;
-
- /**
- * Field _dbRefList
- */
- private java.util.Vector _dbRefList;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public SequenceType()
- {
- super();
- _dbRefList = new Vector();
- } //-- org.vamsas.client.objects.SequenceType()
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- * Method addDbRef
- *
- *
- *
- * @param vDbRef
- */
- public void addDbRef(org.vamsas.client.objects.DbRef vDbRef)
- throws java.lang.IndexOutOfBoundsException
- {
- _dbRefList.addElement(vDbRef);
- } //-- void addDbRef(org.vamsas.client.objects.DbRef)
-
- /**
- * Method addDbRef
- *
- *
- *
- * @param index
- * @param vDbRef
- */
- public void addDbRef(int index, org.vamsas.client.objects.DbRef vDbRef)
- throws java.lang.IndexOutOfBoundsException
- {
- _dbRefList.insertElementAt(vDbRef, index);
- } //-- void addDbRef(int, org.vamsas.client.objects.DbRef)
-
- /**
- * Method deleteEnd
- *
- */
- public void deleteEnd()
- {
- this._has_end= false;
- } //-- void deleteEnd()
-
- /**
- * Method deleteStart
- *
- */
- public void deleteStart()
- {
- this._has_start= false;
- } //-- 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 boolean
- */
- public boolean equals(java.lang.Object obj)
- {
- if ( this == obj )
- return true;
-
- if (super.equals(obj)==false)
- return false;
-
- if (obj instanceof SequenceType) {
-
- SequenceType temp = (SequenceType)obj;
- if (this._start != temp._start)
- return false;
- if (this._has_start != temp._has_start)
- return false;
- if (this._end != temp._end)
- return false;
- if (this._has_end != temp._has_end)
- return false;
- if (this._sequence != null) {
- if (temp._sequence == null) return false;
- else if (!(this._sequence.equals(temp._sequence)))
- return false;
- }
- else if (temp._sequence != null)
- return false;
- if (this._name != null) {
- if (temp._name == null) return false;
- else if (!(this._name.equals(temp._name)))
- return false;
- }
- 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.client.objects.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.client.objects.DbRef) _dbRefList.elementAt(index);
- } //-- org.vamsas.client.objects.DbRef getDbRef(int)
-
- /**
- * Method getDbRef
- *
- *
- *
- * @return DbRef
- */
- public org.vamsas.client.objects.DbRef[] getDbRef()
- {
- int size = _dbRefList.size();
- org.vamsas.client.objects.DbRef[] mArray = new org.vamsas.client.objects.DbRef[size];
- for (int index = 0; index < size; index++) {
- mArray[index] = (org.vamsas.client.objects.DbRef) _dbRefList.elementAt(index);
- }
- return mArray;
- } //-- org.vamsas.client.objects.DbRef[] getDbRef()
-
- /**
- * Method getDbRefAsReference
- *
- * Returns a reference to 'dbRef'. No type checking is
- * performed on any modications to the Vector.
- *
- * @return Vector
- * @return returns a reference to the Vector.
- */
- public java.util.Vector getDbRefAsReference()
- {
- return _dbRefList;
- } //-- java.util.Vector getDbRefAsReference()
-
- /**
- * Method getDbRefCount
- *
- *
- *
- * @return int
- */
- public int getDbRefCount()
- {
- return _dbRefList.size();
- } //-- int getDbRefCount()
-
- /**
- * Returns the value of field 'end'.
- *
- * @return int
- * @return the value of field 'end'.
- */
- public int getEnd()
- {
- return this._end;
- } //-- int getEnd()
-
- /**
- * Returns the value of field 'name'.
- *
- * @return String
- * @return the value of field 'name'.
- */
- public java.lang.String getName()
- {
- return this._name;
- } //-- java.lang.String getName()
-
- /**
- * Returns the value of field 'sequence'.
- *
- * @return String
- * @return the value of field 'sequence'.
- */
- public java.lang.String getSequence()
- {
- return this._sequence;
- } //-- java.lang.String getSequence()
-
- /**
- * Returns the value of field 'start'.
- *
- * @return int
- * @return the value of field 'start'.
- */
- public int getStart()
- {
- return this._start;
- } //-- int getStart()
-
- /**
- * Method hasEnd
- *
- *
- *
- * @return boolean
- */
- public boolean hasEnd()
- {
- return this._has_end;
- } //-- boolean hasEnd()
-
- /**
- * Method hasStart
- *
- *
- *
- * @return boolean
- */
- public boolean hasStart()
- {
- return this._has_start;
- } //-- boolean hasStart()
-
- /**
- * 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 removeAllDbRef
- *
- */
- public void removeAllDbRef()
- {
- _dbRefList.removeAllElements();
- } //-- void removeAllDbRef()
-
- /**
- * Method removeDbRef
- *
- *
- *
- * @param index
- * @return DbRef
- */
- public org.vamsas.client.objects.DbRef removeDbRef(int index)
- {
- java.lang.Object obj = _dbRefList.elementAt(index);
- _dbRefList.removeElementAt(index);
- return (org.vamsas.client.objects.DbRef) obj;
- } //-- org.vamsas.client.objects.DbRef removeDbRef(int)
-
- /**
- * Method setDbRef
- *
- *
- *
- * @param index
- * @param vDbRef
- */
- public void setDbRef(int index, org.vamsas.client.objects.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.client.objects.DbRef)
-
- /**
- * Method setDbRef
- *
- *
- *
- * @param dbRefArray
- */
- public void setDbRef(org.vamsas.client.objects.DbRef[] dbRefArray)
- {
- //-- copy array
- _dbRefList.removeAllElements();
- for (int i = 0; i < dbRefArray.length; i++) {
- _dbRefList.addElement(dbRefArray[i]);
- }
- } //-- void setDbRef(org.vamsas.client.objects.DbRef)
-
- /**
- * Method setDbRef
- *
- * Sets the value of 'dbRef' by copying the given Vector.
- *
- * @param dbRefVector the Vector to copy.
- */
- public void setDbRef(java.util.Vector dbRefVector)
- {
- //-- copy vector
- _dbRefList.removeAllElements();
- for (int i = 0; i < dbRefVector.size(); i++) {
- _dbRefList.addElement((org.vamsas.client.objects.DbRef)dbRefVector.elementAt(i));
- }
- } //-- void setDbRef(java.util.Vector)
-
- /**
- * Method setDbRefAsReference
- *
- * Sets the value of 'dbRef' by setting it to the given Vector.
- * No type checking is performed.
- *
- * @param dbRefVector the Vector to copy.
- */
- public void setDbRefAsReference(java.util.Vector dbRefVector)
- {
- _dbRefList = dbRefVector;
- } //-- void setDbRefAsReference(java.util.Vector)
-
- /**
- * Sets the value of field 'end'.
- *
- * @param end the value of field 'end'.
- */
- public void setEnd(int end)
- {
- this._end = end;
- this._has_end = true;
- } //-- void setEnd(int)
-
- /**
- * Sets the value of field 'name'.
- *
- * @param name the value of field 'name'.
- */
- public void setName(java.lang.String name)
- {
- this._name = name;
- } //-- void setName(java.lang.String)
-
- /**
- * Sets the value of field 'sequence'.
- *
- * @param sequence the value of field 'sequence'.
- */
- public void setSequence(java.lang.String sequence)
- {
- this._sequence = sequence;
- } //-- void setSequence(java.lang.String)
-
- /**
- * Sets the value of field 'start'.
- *
- * @param start the value of field 'start'.
- */
- public void setStart(int start)
- {
- this._start = start;
- this._has_start = true;
- } //-- void setStart(int)
-
- /**
- * Method unmarshal
- *
- *
- *
- * @param reader
- * @return SequenceType
- */
- public static org.vamsas.client.objects.SequenceType unmarshal(java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
- {
- return (org.vamsas.client.objects.SequenceType) Unmarshaller.unmarshal(org.vamsas.client.objects.SequenceType.class, reader);
- } //-- org.vamsas.client.objects.SequenceType 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 0.9.9M1</a>, using an XML
- * Schema.
- * $Id$
- */
-
-package org.vamsas.client.objects;
-
- //---------------------------------/
- //- 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 SequenceTypeDescriptor.
- *
- * @version $Revision$ $Date$
- */
-public class SequenceTypeDescriptor 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 SequenceTypeDescriptor()
- {
- super();
- nsURI = "http://www.vamsas.org";
- xmlName = "SequenceType";
-
- //-- 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
-
- //-- _start
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_start", "start", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- SequenceType target = (SequenceType) object;
- if(!target.hasStart())
- return null;
- return new java.lang.Integer(target.getStart());
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- SequenceType target = (SequenceType) object;
- // ignore null values for non optional primitives
- if (value == null) return;
-
- target.setStart( ((java.lang.Integer)value).intValue());
- }
- 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.setRequired(true);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _start
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(1);
- { //-- local scope
- IntegerValidator typeValidator= new IntegerValidator();
- fieldValidator.setValidator(typeValidator);
- }
- desc.setValidator(fieldValidator);
- //-- _end
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_end", "end", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- SequenceType target = (SequenceType) object;
- if(!target.hasEnd())
- return null;
- return new java.lang.Integer(target.getEnd());
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- SequenceType target = (SequenceType) object;
- // ignore null values for non optional primitives
- if (value == null) return;
-
- target.setEnd( ((java.lang.Integer)value).intValue());
- }
- 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.setRequired(true);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _end
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(1);
- { //-- local scope
- IntegerValidator typeValidator= new IntegerValidator();
- fieldValidator.setValidator(typeValidator);
- }
- desc.setValidator(fieldValidator);
- //-- initialize element descriptors
-
- //-- _sequence
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_sequence", "sequence", 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
- {
- SequenceType target = (SequenceType) object;
- return target.getSequence();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- SequenceType target = (SequenceType) object;
- target.setSequence( (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: _sequence
- 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);
- //-- _name
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_name", "name", 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
- {
- SequenceType target = (SequenceType) object;
- return target.getName();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- SequenceType target = (SequenceType) object;
- 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 null;
- }
- };
- desc.setHandler(handler);
- desc.setNameSpaceURI("http://www.vamsas.org");
- desc.setRequired(true);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _name
- 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);
- //-- _dbRefList
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.client.objects.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.client.objects.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.client.objects.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.client.objects.SequenceTypeDescriptor()
-
-
- //-----------/
- //- 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.client.objects.SequenceType.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()
-
-}
+++ /dev/null
-/*
- * This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M1</a>, using an XML
- * Schema.
- * $Id$
- */
-
-package org.vamsas.client.objects;
-
- //---------------------------------/
- //- 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 Tree.
- *
- * @version $Revision$ $Date$
- */
-public class Tree extends org.vamsas.client.object
-implements java.io.Serializable
-{
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _provenance
- */
- private org.vamsas.client.objects.Provenance _provenance;
-
- /**
- * Field _newickFormat
- */
- private java.lang.String _newickFormat;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public Tree()
- {
- super();
- } //-- org.vamsas.client.objects.Tree()
-
-
- //-----------/
- //- 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 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.client.objects.Provenance getProvenance()
- {
- return this._provenance;
- } //-- org.vamsas.client.objects.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)
-
- /**
- * 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.client.objects.Provenance provenance)
- {
- this._provenance = provenance;
- } //-- void setProvenance(org.vamsas.client.objects.Provenance)
-
- /**
- * Method unmarshal
- *
- *
- *
- * @param reader
- * @return Tree
- */
- public static org.vamsas.client.objects.Tree unmarshal(java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
- {
- return (org.vamsas.client.objects.Tree) Unmarshaller.unmarshal(org.vamsas.client.objects.Tree.class, reader);
- } //-- org.vamsas.client.objects.Tree 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 0.9.9M1</a>, using an XML
- * Schema.
- * $Id$
- */
-
-package org.vamsas.client.objects;
-
- //---------------------------------/
- //- 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 TreeDescriptor.
- *
- * @version $Revision$ $Date$
- */
-public class TreeDescriptor 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 TreeDescriptor()
- {
- super();
- 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.client.objects.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.client.objects.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.client.objects.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.client.objects.TreeDescriptor()
-
-
- //-----------/
- //- 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.client.objects.Tree.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()
-
-}
+++ /dev/null
-/*
- * This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M1</a>, using an XML
- * Schema.
- * $Id$
- */
-
-package org.vamsas.client.objects;
-
- //---------------------------------/
- //- 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 VAMSAS.
- *
- * @version $Revision$ $Date$
- */
-public class VAMSAS extends org.vamsas.client.object
-implements java.io.Serializable
-{
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _treeList
- */
- private java.util.Vector _treeList;
-
- /**
- * Field _sequenceSetList
- */
- private java.util.Vector _sequenceSetList;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public VAMSAS()
- {
- super();
- _treeList = new Vector();
- _sequenceSetList = new Vector();
- } //-- org.vamsas.client.objects.VAMSAS()
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- * Method addSequenceSet
- *
- *
- *
- * @param vSequenceSet
- */
- public void addSequenceSet(org.vamsas.client.objects.SequenceSet vSequenceSet)
- throws java.lang.IndexOutOfBoundsException
- {
- _sequenceSetList.addElement(vSequenceSet);
- } //-- void addSequenceSet(org.vamsas.client.objects.SequenceSet)
-
- /**
- * Method addSequenceSet
- *
- *
- *
- * @param index
- * @param vSequenceSet
- */
- public void addSequenceSet(int index, org.vamsas.client.objects.SequenceSet vSequenceSet)
- throws java.lang.IndexOutOfBoundsException
- {
- _sequenceSetList.insertElementAt(vSequenceSet, index);
- } //-- void addSequenceSet(int, org.vamsas.client.objects.SequenceSet)
-
- /**
- * Method addTree
- *
- *
- *
- * @param vTree
- */
- public void addTree(java.lang.String vTree)
- throws java.lang.IndexOutOfBoundsException
- {
- _treeList.addElement(vTree);
- } //-- void addTree(java.lang.String)
-
- /**
- * Method addTree
- *
- *
- *
- * @param index
- * @param vTree
- */
- public void addTree(int index, java.lang.String vTree)
- throws java.lang.IndexOutOfBoundsException
- {
- _treeList.insertElementAt(vTree, index);
- } //-- void addTree(int, java.lang.String)
-
- /**
- * Method enumerateSequenceSet
- *
- *
- *
- * @return Enumeration
- */
- public java.util.Enumeration enumerateSequenceSet()
- {
- return _sequenceSetList.elements();
- } //-- java.util.Enumeration enumerateSequenceSet()
-
- /**
- * Method enumerateTree
- *
- *
- *
- * @return Enumeration
- */
- public java.util.Enumeration enumerateTree()
- {
- return _treeList.elements();
- } //-- java.util.Enumeration enumerateTree()
-
- /**
- * 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 VAMSAS) {
-
- VAMSAS temp = (VAMSAS)obj;
- if (this._treeList != null) {
- if (temp._treeList == null) return false;
- else if (!(this._treeList.equals(temp._treeList)))
- return false;
- }
- else if (temp._treeList != null)
- return false;
- if (this._sequenceSetList != null) {
- if (temp._sequenceSetList == null) return false;
- else if (!(this._sequenceSetList.equals(temp._sequenceSetList)))
- return false;
- }
- else if (temp._sequenceSetList != null)
- return false;
- return true;
- }
- return false;
- } //-- boolean equals(java.lang.Object)
-
- /**
- * Method getSequenceSet
- *
- *
- *
- * @param index
- * @return SequenceSet
- */
- public org.vamsas.client.objects.SequenceSet getSequenceSet(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()+ "]");
- }
-
- return (org.vamsas.client.objects.SequenceSet) _sequenceSetList.elementAt(index);
- } //-- org.vamsas.client.objects.SequenceSet getSequenceSet(int)
-
- /**
- * Method getSequenceSet
- *
- *
- *
- * @return SequenceSet
- */
- public org.vamsas.client.objects.SequenceSet[] getSequenceSet()
- {
- int size = _sequenceSetList.size();
- org.vamsas.client.objects.SequenceSet[] mArray = new org.vamsas.client.objects.SequenceSet[size];
- for (int index = 0; index < size; index++) {
- mArray[index] = (org.vamsas.client.objects.SequenceSet) _sequenceSetList.elementAt(index);
- }
- return mArray;
- } //-- org.vamsas.client.objects.SequenceSet[] getSequenceSet()
-
- /**
- * Method getSequenceSetAsReference
- *
- * Returns a reference to 'sequenceSet'. No type checking is
- * performed on any modications to the Vector.
- *
- * @return Vector
- * @return returns a reference to the Vector.
- */
- public java.util.Vector getSequenceSetAsReference()
- {
- return _sequenceSetList;
- } //-- java.util.Vector getSequenceSetAsReference()
-
- /**
- * Method getSequenceSetCount
- *
- *
- *
- * @return int
- */
- public int getSequenceSetCount()
- {
- return _sequenceSetList.size();
- } //-- int getSequenceSetCount()
-
- /**
- * Method getTree
- *
- *
- *
- * @param index
- * @return String
- */
- public java.lang.String getTree(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()+ "]");
- }
-
- return (String)_treeList.elementAt(index);
- } //-- java.lang.String getTree(int)
-
- /**
- * Method getTree
- *
- *
- *
- * @return String
- */
- public java.lang.String[] getTree()
- {
- int size = _treeList.size();
- java.lang.String[] mArray = new java.lang.String[size];
- for (int index = 0; index < size; index++) {
- mArray[index] = (String)_treeList.elementAt(index);
- }
- return mArray;
- } //-- java.lang.String[] getTree()
-
- /**
- * Method getTreeAsReference
- *
- * Returns a reference to 'tree'. No type checking is performed
- * on any modications to the Vector.
- *
- * @return Vector
- * @return returns a reference to the Vector.
- */
- public java.util.Vector getTreeAsReference()
- {
- return _treeList;
- } //-- java.util.Vector getTreeAsReference()
-
- /**
- * Method getTreeCount
- *
- *
- *
- * @return int
- */
- public int getTreeCount()
- {
- return _treeList.size();
- } //-- int getTreeCount()
-
- /**
- * 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 removeAllSequenceSet
- *
- */
- public void removeAllSequenceSet()
- {
- _sequenceSetList.removeAllElements();
- } //-- void removeAllSequenceSet()
-
- /**
- * Method removeAllTree
- *
- */
- public void removeAllTree()
- {
- _treeList.removeAllElements();
- } //-- void removeAllTree()
-
- /**
- * Method removeSequenceSet
- *
- *
- *
- * @param index
- * @return SequenceSet
- */
- public org.vamsas.client.objects.SequenceSet removeSequenceSet(int index)
- {
- java.lang.Object obj = _sequenceSetList.elementAt(index);
- _sequenceSetList.removeElementAt(index);
- return (org.vamsas.client.objects.SequenceSet) obj;
- } //-- org.vamsas.client.objects.SequenceSet removeSequenceSet(int)
-
- /**
- * Method removeTree
- *
- *
- *
- * @param index
- * @return String
- */
- public java.lang.String removeTree(int index)
- {
- java.lang.Object obj = _treeList.elementAt(index);
- _treeList.removeElementAt(index);
- return (String)obj;
- } //-- java.lang.String removeTree(int)
-
- /**
- * Method setSequenceSet
- *
- *
- *
- * @param index
- * @param vSequenceSet
- */
- public void setSequenceSet(int index, org.vamsas.client.objects.SequenceSet vSequenceSet)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _sequenceSetList.size())) {
- throw new IndexOutOfBoundsException("setSequenceSet: Index value '"+index+"' not in range [0.."+_sequenceSetList.size()+ "]");
- }
- _sequenceSetList.setElementAt(vSequenceSet, index);
- } //-- void setSequenceSet(int, org.vamsas.client.objects.SequenceSet)
-
- /**
- * Method setSequenceSet
- *
- *
- *
- * @param sequenceSetArray
- */
- public void setSequenceSet(org.vamsas.client.objects.SequenceSet[] sequenceSetArray)
- {
- //-- copy array
- _sequenceSetList.removeAllElements();
- for (int i = 0; i < sequenceSetArray.length; i++) {
- _sequenceSetList.addElement(sequenceSetArray[i]);
- }
- } //-- void setSequenceSet(org.vamsas.client.objects.SequenceSet)
-
- /**
- * Method setSequenceSet
- *
- * Sets the value of 'sequenceSet' by copying the given Vector.
- *
- * @param sequenceSetVector the Vector to copy.
- */
- public void setSequenceSet(java.util.Vector sequenceSetVector)
- {
- //-- copy vector
- _sequenceSetList.removeAllElements();
- for (int i = 0; i < sequenceSetVector.size(); i++) {
- _sequenceSetList.addElement((org.vamsas.client.objects.SequenceSet)sequenceSetVector.elementAt(i));
- }
- } //-- void setSequenceSet(java.util.Vector)
-
- /**
- * Method setSequenceSetAsReference
- *
- * Sets the value of 'sequenceSet' by setting it to the given
- * Vector. No type checking is performed.
- *
- * @param sequenceSetVector the Vector to copy.
- */
- public void setSequenceSetAsReference(java.util.Vector sequenceSetVector)
- {
- _sequenceSetList = sequenceSetVector;
- } //-- void setSequenceSetAsReference(java.util.Vector)
-
- /**
- * 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 setTree
- *
- * Sets the value of 'tree' by copying the given Vector.
- *
- * @param treeVector the Vector to copy.
- */
- public void setTree(java.util.Vector treeVector)
- {
- //-- copy vector
- _treeList.removeAllElements();
- for (int i = 0; i < treeVector.size(); i++) {
- _treeList.addElement((java.lang.String)treeVector.elementAt(i));
- }
- } //-- void setTree(java.util.Vector)
-
- /**
- * Method setTreeAsReference
- *
- * Sets the value of 'tree' by setting it to the given Vector.
- * No type checking is performed.
- *
- * @param treeVector the Vector to copy.
- */
- public void setTreeAsReference(java.util.Vector treeVector)
- {
- _treeList = treeVector;
- } //-- void setTreeAsReference(java.util.Vector)
-
- /**
- * Method unmarshal
- *
- *
- *
- * @param reader
- * @return VAMSAS
- */
- public static org.vamsas.client.objects.VAMSAS unmarshal(java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
- {
- return (org.vamsas.client.objects.VAMSAS) Unmarshaller.unmarshal(org.vamsas.client.objects.VAMSAS.class, reader);
- } //-- org.vamsas.client.objects.VAMSAS 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 0.9.9M1</a>, using an XML
- * Schema.
- * $Id$
- */
-
-package org.vamsas.client.objects;
-
- //---------------------------------/
- //- 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 VAMSASDescriptor.
- *
- * @version $Revision$ $Date$
- */
-public class VAMSASDescriptor 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 VAMSASDescriptor()
- {
- super();
- nsURI = "http://www.vamsas.org";
- xmlName = "VAMSAS";
-
- //-- 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
-
- //-- _treeList
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_treeList", "Tree", 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
- {
- VAMSAS target = (VAMSAS) object;
- return target.getTree();
- }
- 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);
- }
- 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.setMultivalued(true);
- addFieldDescriptor(desc);
-
- //-- validation code for: _treeList
- 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
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.client.objects.SequenceSet.class, "_sequenceSetList", "SequenceSet", 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.getSequenceSet();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- VAMSAS target = (VAMSAS) object;
- target.addSequenceSet( (org.vamsas.client.objects.SequenceSet) value);
- }
- catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance( java.lang.Object parent ) {
- return new org.vamsas.client.objects.SequenceSet();
- }
- };
- desc.setHandler(handler);
- desc.setNameSpaceURI("http://www.vamsas.org");
- desc.setMultivalued(true);
- addFieldDescriptor(desc);
-
- //-- validation code for: _sequenceSetList
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(0);
- { //-- local scope
- }
- desc.setValidator(fieldValidator);
- } //-- org.vamsas.client.objects.VAMSASDescriptor()
-
-
- //-----------/
- //- 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.client.objects.VAMSAS.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