private boolean _has_aligned;
/**
- * Field _id
+ * Primary Key for vamsas object
+ * referencing
+ *
*/
private java.lang.String _id;
/**
- * Field _alignmentAnnotationsList
+ * objects with modifiable=false will
+ * not be modified by a vamsas client
+ * update
+ *
*/
- private java.util.Vector _alignmentAnnotationsList;
+ private boolean _modifiable = true;
+
+ /**
+ * keeps track of state for field: _modifiable
+ */
+ private boolean _has_modifiable;
+
+ /**
+ * This is annotation over the
+ * coordinate frame defined by all
+ * the columns in the alignment.
+ *
+ */
+ private java.util.Vector _alignmentAnnotationList;
/**
* Field _treeList
private java.util.Vector _alignmentSequenceList;
/**
+ * typical properties may be
+ * additional alignment score
+ * objects
+ *
+ */
+ private java.util.Vector _propertyList;
+
+ /**
* Field _provenance
*/
private org.vamsas.objects.core.Provenance _provenance;
public Alignment()
{
super();
- _alignmentAnnotationsList = new Vector();
+ _alignmentAnnotationList = new Vector();
_treeList = new Vector();
_alignmentSequenceList = new Vector();
+ _propertyList = new Vector();
} //-- org.vamsas.objects.core.Alignment()
//-----------/
/**
- * Method addAlignmentAnnotations
+ * Method addAlignmentAnnotation
*
*
*
- * @param vAlignmentAnnotations
+ * @param vAlignmentAnnotation
*/
- public void addAlignmentAnnotations(org.vamsas.objects.core.AlignmentAnnotations vAlignmentAnnotations)
+ public void addAlignmentAnnotation(org.vamsas.objects.core.AlignmentAnnotation vAlignmentAnnotation)
throws java.lang.IndexOutOfBoundsException
{
- _alignmentAnnotationsList.addElement(vAlignmentAnnotations);
- } //-- void addAlignmentAnnotations(org.vamsas.objects.core.AlignmentAnnotations)
+ _alignmentAnnotationList.addElement(vAlignmentAnnotation);
+ } //-- void addAlignmentAnnotation(org.vamsas.objects.core.AlignmentAnnotation)
/**
- * Method addAlignmentAnnotations
+ * Method addAlignmentAnnotation
*
*
*
* @param index
- * @param vAlignmentAnnotations
+ * @param vAlignmentAnnotation
*/
- public void addAlignmentAnnotations(int index, org.vamsas.objects.core.AlignmentAnnotations vAlignmentAnnotations)
+ public void addAlignmentAnnotation(int index, org.vamsas.objects.core.AlignmentAnnotation vAlignmentAnnotation)
throws java.lang.IndexOutOfBoundsException
{
- _alignmentAnnotationsList.insertElementAt(vAlignmentAnnotations, index);
- } //-- void addAlignmentAnnotations(int, org.vamsas.objects.core.AlignmentAnnotations)
+ _alignmentAnnotationList.insertElementAt(vAlignmentAnnotation, index);
+ } //-- void addAlignmentAnnotation(int, org.vamsas.objects.core.AlignmentAnnotation)
/**
* Method addAlignmentSequence
} //-- void addAlignmentSequence(int, org.vamsas.objects.core.AlignmentSequence)
/**
+ * Method addProperty
+ *
+ *
+ *
+ * @param vProperty
+ */
+ public void addProperty(org.vamsas.objects.core.Property vProperty)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _propertyList.addElement(vProperty);
+ } //-- void addProperty(org.vamsas.objects.core.Property)
+
+ /**
+ * Method addProperty
+ *
+ *
+ *
+ * @param index
+ * @param vProperty
+ */
+ public void addProperty(int index, org.vamsas.objects.core.Property vProperty)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _propertyList.insertElementAt(vProperty, index);
+ } //-- void addProperty(int, org.vamsas.objects.core.Property)
+
+ /**
* Method addTree
*
*
} //-- void deleteAligned()
/**
- * Method enumerateAlignmentAnnotations
+ * Method deleteModifiable
+ *
+ */
+ public void deleteModifiable()
+ {
+ this._has_modifiable= false;
+ } //-- void deleteModifiable()
+
+ /**
+ * Method enumerateAlignmentAnnotation
*
*
*
* @return Enumeration
*/
- public java.util.Enumeration enumerateAlignmentAnnotations()
+ public java.util.Enumeration enumerateAlignmentAnnotation()
{
- return _alignmentAnnotationsList.elements();
- } //-- java.util.Enumeration enumerateAlignmentAnnotations()
+ return _alignmentAnnotationList.elements();
+ } //-- java.util.Enumeration enumerateAlignmentAnnotation()
/**
* Method enumerateAlignmentSequence
} //-- java.util.Enumeration enumerateAlignmentSequence()
/**
+ * Method enumerateProperty
+ *
+ *
+ *
+ * @return Enumeration
+ */
+ public java.util.Enumeration enumerateProperty()
+ {
+ return _propertyList.elements();
+ } //-- java.util.Enumeration enumerateProperty()
+
+ /**
* Method enumerateTree
*
*
}
else if (temp._id != null)
return false;
- if (this._alignmentAnnotationsList != null) {
- if (temp._alignmentAnnotationsList == null) return false;
- else if (!(this._alignmentAnnotationsList.equals(temp._alignmentAnnotationsList)))
+ if (this._modifiable != temp._modifiable)
+ return false;
+ if (this._has_modifiable != temp._has_modifiable)
+ return false;
+ if (this._alignmentAnnotationList != null) {
+ if (temp._alignmentAnnotationList == null) return false;
+ else if (!(this._alignmentAnnotationList.equals(temp._alignmentAnnotationList)))
return false;
}
- else if (temp._alignmentAnnotationsList != null)
+ else if (temp._alignmentAnnotationList != null)
return false;
if (this._treeList != null) {
if (temp._treeList == null) return false;
}
else if (temp._alignmentSequenceList != null)
return false;
+ if (this._propertyList != null) {
+ if (temp._propertyList == null) return false;
+ else if (!(this._propertyList.equals(temp._propertyList)))
+ return false;
+ }
+ else if (temp._propertyList != null)
+ return false;
if (this._provenance != null) {
if (temp._provenance == null) return false;
else if (!(this._provenance.equals(temp._provenance)))
} //-- boolean getAligned()
/**
- * Method getAlignmentAnnotations
+ * Method getAlignmentAnnotation
*
*
*
* @param index
- * @return AlignmentAnnotations
+ * @return AlignmentAnnotation
*/
- public org.vamsas.objects.core.AlignmentAnnotations getAlignmentAnnotations(int index)
+ public org.vamsas.objects.core.AlignmentAnnotation getAlignmentAnnotation(int index)
throws java.lang.IndexOutOfBoundsException
{
//-- check bounds for index
- if ((index < 0) || (index > _alignmentAnnotationsList.size())) {
- throw new IndexOutOfBoundsException("getAlignmentAnnotations: Index value '"+index+"' not in range [0.."+_alignmentAnnotationsList.size()+ "]");
+ if ((index < 0) || (index > _alignmentAnnotationList.size())) {
+ throw new IndexOutOfBoundsException("getAlignmentAnnotation: Index value '"+index+"' not in range [0.."+_alignmentAnnotationList.size()+ "]");
}
- return (org.vamsas.objects.core.AlignmentAnnotations) _alignmentAnnotationsList.elementAt(index);
- } //-- org.vamsas.objects.core.AlignmentAnnotations getAlignmentAnnotations(int)
+ return (org.vamsas.objects.core.AlignmentAnnotation) _alignmentAnnotationList.elementAt(index);
+ } //-- org.vamsas.objects.core.AlignmentAnnotation getAlignmentAnnotation(int)
/**
- * Method getAlignmentAnnotations
+ * Method getAlignmentAnnotation
*
*
*
- * @return AlignmentAnnotations
+ * @return AlignmentAnnotation
*/
- public org.vamsas.objects.core.AlignmentAnnotations[] getAlignmentAnnotations()
+ public org.vamsas.objects.core.AlignmentAnnotation[] getAlignmentAnnotation()
{
- int size = _alignmentAnnotationsList.size();
- org.vamsas.objects.core.AlignmentAnnotations[] mArray = new org.vamsas.objects.core.AlignmentAnnotations[size];
+ int size = _alignmentAnnotationList.size();
+ org.vamsas.objects.core.AlignmentAnnotation[] mArray = new org.vamsas.objects.core.AlignmentAnnotation[size];
for (int index = 0; index < size; index++) {
- mArray[index] = (org.vamsas.objects.core.AlignmentAnnotations) _alignmentAnnotationsList.elementAt(index);
+ mArray[index] = (org.vamsas.objects.core.AlignmentAnnotation) _alignmentAnnotationList.elementAt(index);
}
return mArray;
- } //-- org.vamsas.objects.core.AlignmentAnnotations[] getAlignmentAnnotations()
+ } //-- org.vamsas.objects.core.AlignmentAnnotation[] getAlignmentAnnotation()
/**
- * Method getAlignmentAnnotationsCount
+ * Method getAlignmentAnnotationCount
*
*
*
* @return int
*/
- public int getAlignmentAnnotationsCount()
+ public int getAlignmentAnnotationCount()
{
- return _alignmentAnnotationsList.size();
- } //-- int getAlignmentAnnotationsCount()
+ return _alignmentAnnotationList.size();
+ } //-- int getAlignmentAnnotationCount()
/**
* Method getAlignmentSequence
} //-- java.lang.String getGapChar()
/**
- * Returns the value of field 'id'.
+ * Returns the value of field 'id'. The field 'id' has the
+ * following description: Primary Key for vamsas object
+ * referencing
+ *
*
* @return String
* @return the value of field 'id'.
} //-- java.lang.String getId()
/**
+ * Returns the value of field 'modifiable'. The field
+ * 'modifiable' has the following description: objects with
+ * modifiable=false will
+ * not be modified by a vamsas client
+ * update
+ *
+ *
+ * @return boolean
+ * @return the value of field 'modifiable'.
+ */
+ public boolean getModifiable()
+ {
+ return this._modifiable;
+ } //-- boolean getModifiable()
+
+ /**
+ * Method getProperty
+ *
+ *
+ *
+ * @param index
+ * @return Property
+ */
+ public org.vamsas.objects.core.Property getProperty(int index)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ //-- check bounds for index
+ if ((index < 0) || (index > _propertyList.size())) {
+ throw new IndexOutOfBoundsException("getProperty: Index value '"+index+"' not in range [0.."+_propertyList.size()+ "]");
+ }
+
+ return (org.vamsas.objects.core.Property) _propertyList.elementAt(index);
+ } //-- org.vamsas.objects.core.Property getProperty(int)
+
+ /**
+ * Method getProperty
+ *
+ *
+ *
+ * @return Property
+ */
+ public org.vamsas.objects.core.Property[] getProperty()
+ {
+ int size = _propertyList.size();
+ org.vamsas.objects.core.Property[] mArray = new org.vamsas.objects.core.Property[size];
+ for (int index = 0; index < size; index++) {
+ mArray[index] = (org.vamsas.objects.core.Property) _propertyList.elementAt(index);
+ }
+ return mArray;
+ } //-- org.vamsas.objects.core.Property[] getProperty()
+
+ /**
+ * Method getPropertyCount
+ *
+ *
+ *
+ * @return int
+ */
+ public int getPropertyCount()
+ {
+ return _propertyList.size();
+ } //-- int getPropertyCount()
+
+ /**
* Returns the value of field 'provenance'.
*
* @return Provenance
} //-- boolean hasAligned()
/**
+ * Method hasModifiable
+ *
+ *
+ *
+ * @return boolean
+ */
+ public boolean hasModifiable()
+ {
+ return this._has_modifiable;
+ } //-- boolean hasModifiable()
+
+ /**
* Method isValid
*
*
} //-- void marshal(org.xml.sax.ContentHandler)
/**
- * Method removeAlignmentAnnotations
+ * Method removeAlignmentAnnotation
*
*
*
* @param index
- * @return AlignmentAnnotations
+ * @return AlignmentAnnotation
*/
- public org.vamsas.objects.core.AlignmentAnnotations removeAlignmentAnnotations(int index)
+ public org.vamsas.objects.core.AlignmentAnnotation removeAlignmentAnnotation(int index)
{
- java.lang.Object obj = _alignmentAnnotationsList.elementAt(index);
- _alignmentAnnotationsList.removeElementAt(index);
- return (org.vamsas.objects.core.AlignmentAnnotations) obj;
- } //-- org.vamsas.objects.core.AlignmentAnnotations removeAlignmentAnnotations(int)
+ java.lang.Object obj = _alignmentAnnotationList.elementAt(index);
+ _alignmentAnnotationList.removeElementAt(index);
+ return (org.vamsas.objects.core.AlignmentAnnotation) obj;
+ } //-- org.vamsas.objects.core.AlignmentAnnotation removeAlignmentAnnotation(int)
/**
* Method removeAlignmentSequence
} //-- org.vamsas.objects.core.AlignmentSequence removeAlignmentSequence(int)
/**
- * Method removeAllAlignmentAnnotations
+ * Method removeAllAlignmentAnnotation
*
*/
- public void removeAllAlignmentAnnotations()
+ public void removeAllAlignmentAnnotation()
{
- _alignmentAnnotationsList.removeAllElements();
- } //-- void removeAllAlignmentAnnotations()
+ _alignmentAnnotationList.removeAllElements();
+ } //-- void removeAllAlignmentAnnotation()
/**
* Method removeAllAlignmentSequence
} //-- void removeAllAlignmentSequence()
/**
+ * Method removeAllProperty
+ *
+ */
+ public void removeAllProperty()
+ {
+ _propertyList.removeAllElements();
+ } //-- void removeAllProperty()
+
+ /**
* Method removeAllTree
*
*/
} //-- void removeAllTree()
/**
+ * Method removeProperty
+ *
+ *
+ *
+ * @param index
+ * @return Property
+ */
+ public org.vamsas.objects.core.Property removeProperty(int index)
+ {
+ java.lang.Object obj = _propertyList.elementAt(index);
+ _propertyList.removeElementAt(index);
+ return (org.vamsas.objects.core.Property) obj;
+ } //-- org.vamsas.objects.core.Property removeProperty(int)
+
+ /**
* Method removeTree
*
*
} //-- void setAligned(boolean)
/**
- * Method setAlignmentAnnotations
+ * Method setAlignmentAnnotation
*
*
*
* @param index
- * @param vAlignmentAnnotations
+ * @param vAlignmentAnnotation
*/
- public void setAlignmentAnnotations(int index, org.vamsas.objects.core.AlignmentAnnotations vAlignmentAnnotations)
+ public void setAlignmentAnnotation(int index, org.vamsas.objects.core.AlignmentAnnotation vAlignmentAnnotation)
throws java.lang.IndexOutOfBoundsException
{
//-- check bounds for index
- if ((index < 0) || (index > _alignmentAnnotationsList.size())) {
- throw new IndexOutOfBoundsException("setAlignmentAnnotations: Index value '"+index+"' not in range [0.."+_alignmentAnnotationsList.size()+ "]");
+ if ((index < 0) || (index > _alignmentAnnotationList.size())) {
+ throw new IndexOutOfBoundsException("setAlignmentAnnotation: Index value '"+index+"' not in range [0.."+_alignmentAnnotationList.size()+ "]");
}
- _alignmentAnnotationsList.setElementAt(vAlignmentAnnotations, index);
- } //-- void setAlignmentAnnotations(int, org.vamsas.objects.core.AlignmentAnnotations)
+ _alignmentAnnotationList.setElementAt(vAlignmentAnnotation, index);
+ } //-- void setAlignmentAnnotation(int, org.vamsas.objects.core.AlignmentAnnotation)
/**
- * Method setAlignmentAnnotations
+ * Method setAlignmentAnnotation
*
*
*
- * @param alignmentAnnotationsArray
+ * @param alignmentAnnotationArray
*/
- public void setAlignmentAnnotations(org.vamsas.objects.core.AlignmentAnnotations[] alignmentAnnotationsArray)
+ public void setAlignmentAnnotation(org.vamsas.objects.core.AlignmentAnnotation[] alignmentAnnotationArray)
{
//-- copy array
- _alignmentAnnotationsList.removeAllElements();
- for (int i = 0; i < alignmentAnnotationsArray.length; i++) {
- _alignmentAnnotationsList.addElement(alignmentAnnotationsArray[i]);
+ _alignmentAnnotationList.removeAllElements();
+ for (int i = 0; i < alignmentAnnotationArray.length; i++) {
+ _alignmentAnnotationList.addElement(alignmentAnnotationArray[i]);
}
- } //-- void setAlignmentAnnotations(org.vamsas.objects.core.AlignmentAnnotations)
+ } //-- void setAlignmentAnnotation(org.vamsas.objects.core.AlignmentAnnotation)
/**
* Method setAlignmentSequence
} //-- void setGapChar(java.lang.String)
/**
- * Sets the value of field 'id'.
+ * Sets the value of field 'id'. The field 'id' has the
+ * following description: Primary Key for vamsas object
+ * referencing
+ *
*
* @param id the value of field 'id'.
*/
} //-- void setId(java.lang.String)
/**
+ * Sets the value of field 'modifiable'. The field 'modifiable'
+ * has the following description: objects with modifiable=false
+ * will
+ * not be modified by a vamsas client
+ * update
+ *
+ *
+ * @param modifiable the value of field 'modifiable'.
+ */
+ public void setModifiable(boolean modifiable)
+ {
+ this._modifiable = modifiable;
+ this._has_modifiable = true;
+ } //-- void setModifiable(boolean)
+
+ /**
+ * Method setProperty
+ *
+ *
+ *
+ * @param index
+ * @param vProperty
+ */
+ public void setProperty(int index, org.vamsas.objects.core.Property vProperty)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ //-- check bounds for index
+ if ((index < 0) || (index > _propertyList.size())) {
+ throw new IndexOutOfBoundsException("setProperty: Index value '"+index+"' not in range [0.."+_propertyList.size()+ "]");
+ }
+ _propertyList.setElementAt(vProperty, index);
+ } //-- void setProperty(int, org.vamsas.objects.core.Property)
+
+ /**
+ * Method setProperty
+ *
+ *
+ *
+ * @param propertyArray
+ */
+ public void setProperty(org.vamsas.objects.core.Property[] propertyArray)
+ {
+ //-- copy array
+ _propertyList.removeAllElements();
+ for (int i = 0; i < propertyArray.length; i++) {
+ _propertyList.addElement(propertyArray[i]);
+ }
+ } //-- void setProperty(org.vamsas.objects.core.Property)
+
+ /**
* Sets the value of field 'provenance'.
*
* @param provenance the value of field 'provenance'.
--- /dev/null
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package org.vamsas.objects.core;
+
+ //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import java.io.IOException;
+import java.io.Reader;
+import java.io.Serializable;
+import java.io.Writer;
+import org.exolab.castor.xml.MarshalException;
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+import org.exolab.castor.xml.ValidationException;
+import org.xml.sax.ContentHandler;
+
+/**
+ * This is annotation over the
+ * coordinate frame defined by all
+ * the columns in the alignment.
+ *
+ *
+ * @version $Revision$ $Date$
+ */
+public class AlignmentAnnotation extends org.vamsas.objects.core.RangeAnnotation
+implements java.io.Serializable
+{
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * TODO: decide if
+ * this flag is
+ * redundant - when
+ * true it would
+ * suggest that the
+ * annotationElement
+ * values together
+ * form a graph
+ *
+ */
+ private boolean _graph;
+
+ /**
+ * keeps track of state for field: _graph
+ */
+ private boolean _has_graph;
+
+ /**
+ * Field _provenance
+ */
+ private org.vamsas.objects.core.Provenance _provenance;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public AlignmentAnnotation()
+ {
+ super();
+ } //-- org.vamsas.objects.core.AlignmentAnnotation()
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ * Method deleteGraph
+ *
+ */
+ public void deleteGraph()
+ {
+ this._has_graph= false;
+ } //-- void deleteGraph()
+
+ /**
+ * 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 AlignmentAnnotation) {
+
+ AlignmentAnnotation temp = (AlignmentAnnotation)obj;
+ if (this._graph != temp._graph)
+ return false;
+ if (this._has_graph != temp._has_graph)
+ 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 'graph'. The field 'graph' has
+ * the following description: TODO: decide if
+ * this flag is
+ * redundant - when
+ * true it would
+ * suggest that the
+ * annotationElement
+ * values together
+ * form a graph
+ *
+ *
+ * @return boolean
+ * @return the value of field 'graph'.
+ */
+ public boolean getGraph()
+ {
+ return this._graph;
+ } //-- boolean getGraph()
+
+ /**
+ * Returns the value of field 'provenance'.
+ *
+ * @return Provenance
+ * @return the value of field 'provenance'.
+ */
+ public org.vamsas.objects.core.Provenance getProvenance()
+ {
+ return this._provenance;
+ } //-- org.vamsas.objects.core.Provenance getProvenance()
+
+ /**
+ * Method 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)
+
+ /**
+ * Sets the value of field 'graph'. The field 'graph' has the
+ * following description: TODO: decide if
+ * this flag is
+ * redundant - when
+ * true it would
+ * suggest that the
+ * annotationElement
+ * values together
+ * form a 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 'provenance'.
+ *
+ * @param provenance the value of field 'provenance'.
+ */
+ public void setProvenance(org.vamsas.objects.core.Provenance provenance)
+ {
+ this._provenance = provenance;
+ } //-- void setProvenance(org.vamsas.objects.core.Provenance)
+
+ /**
+ * Method unmarshal
+ *
+ *
+ *
+ * @param reader
+ * @return RangeType
+ */
+ public static org.vamsas.objects.core.RangeType unmarshal(java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+ {
+ return (org.vamsas.objects.core.AlignmentAnnotation) Unmarshaller.unmarshal(org.vamsas.objects.core.AlignmentAnnotation.class, reader);
+ } //-- org.vamsas.objects.core.RangeType unmarshal(java.io.Reader)
+
+ /**
+ * Method validate
+ *
+ */
+ public void validate()
+ throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ } //-- void validate()
+
+}
--- /dev/null
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package org.vamsas.objects.core;
+
+ //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.mapping.AccessMode;
+import org.exolab.castor.xml.TypeValidator;
+import org.exolab.castor.xml.XMLFieldDescriptor;
+import org.exolab.castor.xml.validators.*;
+
+/**
+ * Class AlignmentAnnotationDescriptor.
+ *
+ * @version $Revision$ $Date$
+ */
+public class AlignmentAnnotationDescriptor extends org.vamsas.objects.core.RangeAnnotationDescriptor {
+
+
+ //--------------------------/
+ //- 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 AlignmentAnnotationDescriptor()
+ {
+ super();
+ setExtendsWithoutFlatten(new org.vamsas.objects.core.RangeAnnotationDescriptor());
+ nsURI = "http://www.vamsas.org";
+ xmlName = "AlignmentAnnotation";
+
+ //-- 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
+ {
+ AlignmentAnnotation target = (AlignmentAnnotation) 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 {
+ AlignmentAnnotation target = (AlignmentAnnotation) 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
+
+ //-- _provenance
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Provenance.class, "_provenance", "Provenance", org.exolab.castor.xml.NodeType.Element);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ AlignmentAnnotation target = (AlignmentAnnotation) object;
+ return target.getProvenance();
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ AlignmentAnnotation target = (AlignmentAnnotation) object;
+ target.setProvenance( (org.vamsas.objects.core.Provenance) value);
+ }
+ catch (java.lang.Exception ex) {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+ public java.lang.Object newInstance( java.lang.Object parent ) {
+ return new org.vamsas.objects.core.Provenance();
+ }
+ };
+ desc.setHandler(handler);
+ desc.setNameSpaceURI("http://www.vamsas.org");
+ desc.setRequired(true);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _provenance
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(1);
+ { //-- local scope
+ }
+ desc.setValidator(fieldValidator);
+ } //-- org.vamsas.objects.core.AlignmentAnnotationDescriptor()
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ * Method getAccessMode
+ *
+ *
+ *
+ * @return AccessMode
+ */
+ public org.exolab.castor.mapping.AccessMode getAccessMode()
+ {
+ return null;
+ } //-- org.exolab.castor.mapping.AccessMode getAccessMode()
+
+ /**
+ * Method getExtends
+ *
+ *
+ *
+ * @return ClassDescriptor
+ */
+ public org.exolab.castor.mapping.ClassDescriptor getExtends()
+ {
+ return super.getExtends();
+ } //-- org.exolab.castor.mapping.ClassDescriptor getExtends()
+
+ /**
+ * Method getIdentity
+ *
+ *
+ *
+ * @return FieldDescriptor
+ */
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+ {
+ if (identity == null)
+ return super.getIdentity();
+ return identity;
+ } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity()
+
+ /**
+ * Method getJavaClass
+ *
+ *
+ *
+ * @return Class
+ */
+ public java.lang.Class getJavaClass()
+ {
+ return org.vamsas.objects.core.AlignmentAnnotation.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()
+
+}
{ //-- local scope
}
desc.setValidator(fieldValidator);
+ //-- _modifiable
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_modifiable", "modifiable", org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ Alignment target = (Alignment) object;
+ if(!target.hasModifiable())
+ return null;
+ return (target.getModifiable() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ Alignment target = (Alignment) object;
+ // if null, use delete method for optional primitives
+ if (value == null) {
+ target.deleteModifiable();
+ return;
+ }
+ target.setModifiable( ((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: _modifiable
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { //-- local scope
+ BooleanValidator typeValidator = new BooleanValidator();
+ fieldValidator.setValidator(typeValidator);
+ }
+ desc.setValidator(fieldValidator);
//-- initialize element descriptors
- //-- _alignmentAnnotationsList
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.AlignmentAnnotations.class, "_alignmentAnnotationsList", "AlignmentAnnotations", org.exolab.castor.xml.NodeType.Element);
+ //-- _alignmentAnnotationList
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.AlignmentAnnotation.class, "_alignmentAnnotationList", "AlignmentAnnotation", 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();
+ return target.getAlignmentAnnotation();
}
public void setValue( java.lang.Object object, java.lang.Object value)
throws IllegalStateException, IllegalArgumentException
{
try {
Alignment target = (Alignment) object;
- target.addAlignmentAnnotations( (org.vamsas.objects.core.AlignmentAnnotations) value);
+ target.addAlignmentAnnotation( (org.vamsas.objects.core.AlignmentAnnotation) value);
}
catch (java.lang.Exception ex) {
throw new IllegalStateException(ex.toString());
}
}
public java.lang.Object newInstance( java.lang.Object parent ) {
- return new org.vamsas.objects.core.AlignmentAnnotations();
+ return new org.vamsas.objects.core.AlignmentAnnotation();
}
};
desc.setHandler(handler);
desc.setMultivalued(true);
addFieldDescriptor(desc);
- //-- validation code for: _alignmentAnnotationsList
+ //-- validation code for: _alignmentAnnotationList
fieldValidator = new org.exolab.castor.xml.FieldValidator();
fieldValidator.setMinOccurs(0);
{ //-- local scope
{ //-- local scope
}
desc.setValidator(fieldValidator);
+ //-- _propertyList
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Property.class, "_propertyList", "property", 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.getProperty();
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ Alignment target = (Alignment) object;
+ target.addProperty( (org.vamsas.objects.core.Property) value);
+ }
+ catch (java.lang.Exception ex) {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+ public java.lang.Object newInstance( java.lang.Object parent ) {
+ return new org.vamsas.objects.core.Property();
+ }
+ };
+ desc.setHandler(handler);
+ desc.setNameSpaceURI("http://www.vamsas.org");
+ desc.setMultivalued(true);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _propertyList
+ 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.objects.core.Provenance.class, "_provenance", "Provenance", org.exolab.castor.xml.NodeType.Element);
handler = new org.exolab.castor.xml.XMLFieldHandler() {
import java.io.Reader;
import java.io.Serializable;
import java.io.Writer;
+import java.util.Enumeration;
+import java.util.Vector;
import org.exolab.castor.xml.MarshalException;
import org.exolab.castor.xml.Marshaller;
import org.exolab.castor.xml.Unmarshaller;
//--------------------------/
/**
- * Field _id
+ * Primary Key for
+ * vamsas object
+ * referencing
+ *
*/
private java.lang.String _id;
/**
- * Field _refid
+ * Dataset Sequence
+ * from which this
+ * alignment
+ * sequence is
+ * taken from
+ *
*/
private java.lang.Object _refid;
+ /**
+ * Field _alignmentSequenceAnnotationList
+ */
+ private java.util.Vector _alignmentSequenceAnnotationList;
+
//----------------/
//- Constructors -/
public AlignmentSequence()
{
super();
+ _alignmentSequenceAnnotationList = new Vector();
} //-- org.vamsas.objects.core.AlignmentSequence()
//-----------/
/**
+ * Method addAlignmentSequenceAnnotation
+ *
+ *
+ *
+ * @param vAlignmentSequenceAnnotation
+ */
+ public void addAlignmentSequenceAnnotation(org.vamsas.objects.core.AlignmentSequenceAnnotation vAlignmentSequenceAnnotation)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _alignmentSequenceAnnotationList.addElement(vAlignmentSequenceAnnotation);
+ } //-- void addAlignmentSequenceAnnotation(org.vamsas.objects.core.AlignmentSequenceAnnotation)
+
+ /**
+ * Method addAlignmentSequenceAnnotation
+ *
+ *
+ *
+ * @param index
+ * @param vAlignmentSequenceAnnotation
+ */
+ public void addAlignmentSequenceAnnotation(int index, org.vamsas.objects.core.AlignmentSequenceAnnotation vAlignmentSequenceAnnotation)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _alignmentSequenceAnnotationList.insertElementAt(vAlignmentSequenceAnnotation, index);
+ } //-- void addAlignmentSequenceAnnotation(int, org.vamsas.objects.core.AlignmentSequenceAnnotation)
+
+ /**
+ * Method enumerateAlignmentSequenceAnnotation
+ *
+ *
+ *
+ * @return Enumeration
+ */
+ public java.util.Enumeration enumerateAlignmentSequenceAnnotation()
+ {
+ return _alignmentSequenceAnnotationList.elements();
+ } //-- java.util.Enumeration enumerateAlignmentSequenceAnnotation()
+
+ /**
* Note: hashCode() has not been overriden
*
* @param obj
}
else if (temp._refid != null)
return false;
+ if (this._alignmentSequenceAnnotationList != null) {
+ if (temp._alignmentSequenceAnnotationList == null) return false;
+ else if (!(this._alignmentSequenceAnnotationList.equals(temp._alignmentSequenceAnnotationList)))
+ return false;
+ }
+ else if (temp._alignmentSequenceAnnotationList != null)
+ return false;
return true;
}
return false;
} //-- boolean equals(java.lang.Object)
/**
- * Returns the value of field 'id'.
+ * Method getAlignmentSequenceAnnotation
+ *
+ *
+ *
+ * @param index
+ * @return AlignmentSequenceAnnotation
+ */
+ public org.vamsas.objects.core.AlignmentSequenceAnnotation getAlignmentSequenceAnnotation(int index)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ //-- check bounds for index
+ if ((index < 0) || (index > _alignmentSequenceAnnotationList.size())) {
+ throw new IndexOutOfBoundsException("getAlignmentSequenceAnnotation: Index value '"+index+"' not in range [0.."+_alignmentSequenceAnnotationList.size()+ "]");
+ }
+
+ return (org.vamsas.objects.core.AlignmentSequenceAnnotation) _alignmentSequenceAnnotationList.elementAt(index);
+ } //-- org.vamsas.objects.core.AlignmentSequenceAnnotation getAlignmentSequenceAnnotation(int)
+
+ /**
+ * Method getAlignmentSequenceAnnotation
+ *
+ *
+ *
+ * @return AlignmentSequenceAnnotation
+ */
+ public org.vamsas.objects.core.AlignmentSequenceAnnotation[] getAlignmentSequenceAnnotation()
+ {
+ int size = _alignmentSequenceAnnotationList.size();
+ org.vamsas.objects.core.AlignmentSequenceAnnotation[] mArray = new org.vamsas.objects.core.AlignmentSequenceAnnotation[size];
+ for (int index = 0; index < size; index++) {
+ mArray[index] = (org.vamsas.objects.core.AlignmentSequenceAnnotation) _alignmentSequenceAnnotationList.elementAt(index);
+ }
+ return mArray;
+ } //-- org.vamsas.objects.core.AlignmentSequenceAnnotation[] getAlignmentSequenceAnnotation()
+
+ /**
+ * Method getAlignmentSequenceAnnotationCount
+ *
+ *
+ *
+ * @return int
+ */
+ public int getAlignmentSequenceAnnotationCount()
+ {
+ return _alignmentSequenceAnnotationList.size();
+ } //-- int getAlignmentSequenceAnnotationCount()
+
+ /**
+ * Returns the value of field 'id'. The field 'id' has the
+ * following description: Primary Key for
+ * vamsas object
+ * referencing
+ *
*
* @return String
* @return the value of field 'id'.
} //-- java.lang.String getId()
/**
- * Returns the value of field 'refid'.
+ * Returns the value of field 'refid'. The field 'refid' has
+ * the following description: Dataset Sequence
+ * from which this
+ * alignment
+ * sequence is
+ * taken from
+ *
*
* @return Object
* @return the value of field 'refid'.
} //-- void marshal(org.xml.sax.ContentHandler)
/**
- * Sets the value of field 'id'.
+ * Method removeAlignmentSequenceAnnotation
+ *
+ *
+ *
+ * @param index
+ * @return AlignmentSequenceAnnotation
+ */
+ public org.vamsas.objects.core.AlignmentSequenceAnnotation removeAlignmentSequenceAnnotation(int index)
+ {
+ java.lang.Object obj = _alignmentSequenceAnnotationList.elementAt(index);
+ _alignmentSequenceAnnotationList.removeElementAt(index);
+ return (org.vamsas.objects.core.AlignmentSequenceAnnotation) obj;
+ } //-- org.vamsas.objects.core.AlignmentSequenceAnnotation removeAlignmentSequenceAnnotation(int)
+
+ /**
+ * Method removeAllAlignmentSequenceAnnotation
+ *
+ */
+ public void removeAllAlignmentSequenceAnnotation()
+ {
+ _alignmentSequenceAnnotationList.removeAllElements();
+ } //-- void removeAllAlignmentSequenceAnnotation()
+
+ /**
+ * Method setAlignmentSequenceAnnotation
+ *
+ *
+ *
+ * @param index
+ * @param vAlignmentSequenceAnnotation
+ */
+ public void setAlignmentSequenceAnnotation(int index, org.vamsas.objects.core.AlignmentSequenceAnnotation vAlignmentSequenceAnnotation)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ //-- check bounds for index
+ if ((index < 0) || (index > _alignmentSequenceAnnotationList.size())) {
+ throw new IndexOutOfBoundsException("setAlignmentSequenceAnnotation: Index value '"+index+"' not in range [0.."+_alignmentSequenceAnnotationList.size()+ "]");
+ }
+ _alignmentSequenceAnnotationList.setElementAt(vAlignmentSequenceAnnotation, index);
+ } //-- void setAlignmentSequenceAnnotation(int, org.vamsas.objects.core.AlignmentSequenceAnnotation)
+
+ /**
+ * Method setAlignmentSequenceAnnotation
+ *
+ *
+ *
+ * @param alignmentSequenceAnnotationArray
+ */
+ public void setAlignmentSequenceAnnotation(org.vamsas.objects.core.AlignmentSequenceAnnotation[] alignmentSequenceAnnotationArray)
+ {
+ //-- copy array
+ _alignmentSequenceAnnotationList.removeAllElements();
+ for (int i = 0; i < alignmentSequenceAnnotationArray.length; i++) {
+ _alignmentSequenceAnnotationList.addElement(alignmentSequenceAnnotationArray[i]);
+ }
+ } //-- void setAlignmentSequenceAnnotation(org.vamsas.objects.core.AlignmentSequenceAnnotation)
+
+ /**
+ * Sets the value of field 'id'. The field 'id' has the
+ * following description: Primary Key for
+ * vamsas object
+ * referencing
+ *
*
* @param id the value of field 'id'.
*/
} //-- void setId(java.lang.String)
/**
- * Sets the value of field 'refid'.
+ * Sets the value of field 'refid'. The field 'refid' has the
+ * following description: Dataset Sequence
+ * from which this
+ * alignment
+ * sequence is
+ * taken from
+ *
*
* @param refid the value of field 'refid'.
*/
--- /dev/null
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package org.vamsas.objects.core;
+
+ //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import java.io.IOException;
+import java.io.Reader;
+import java.io.Serializable;
+import java.io.Writer;
+import org.exolab.castor.xml.MarshalException;
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+import org.exolab.castor.xml.ValidationException;
+import org.xml.sax.ContentHandler;
+
+/**
+ * Class AlignmentSequenceAnnotation.
+ *
+ * @version $Revision$ $Date$
+ */
+public class AlignmentSequenceAnnotation extends org.vamsas.objects.core.RangeAnnotation
+implements java.io.Serializable
+{
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * TODO:
+ * decide
+ * if
+ * this
+ * flag
+ * is
+ * redundant
+ * -
+ * when
+ * true
+ * it
+ * would
+ * suggest
+ * that
+ * the
+ * annotationElement
+ * values
+ * together
+ * form
+ * a
+ * graph
+ *
+ */
+ private boolean _graph;
+
+ /**
+ * keeps track of state for field: _graph
+ */
+ private boolean _has_graph;
+
+ /**
+ * Field _provenance
+ */
+ private org.vamsas.objects.core.Provenance _provenance;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public AlignmentSequenceAnnotation()
+ {
+ super();
+ } //-- org.vamsas.objects.core.AlignmentSequenceAnnotation()
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ * Method deleteGraph
+ *
+ */
+ public void deleteGraph()
+ {
+ this._has_graph= false;
+ } //-- void deleteGraph()
+
+ /**
+ * 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 AlignmentSequenceAnnotation) {
+
+ AlignmentSequenceAnnotation temp = (AlignmentSequenceAnnotation)obj;
+ if (this._graph != temp._graph)
+ return false;
+ if (this._has_graph != temp._has_graph)
+ 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 'graph'. The field 'graph' has
+ * the following description: TODO:
+ * decide
+ * if
+ * this
+ * flag
+ * is
+ * redundant
+ * -
+ * when
+ * true
+ * it
+ * would
+ * suggest
+ * that
+ * the
+ * annotationElement
+ * values
+ * together
+ * form
+ * a
+ * graph
+ *
+ *
+ * @return boolean
+ * @return the value of field 'graph'.
+ */
+ public boolean getGraph()
+ {
+ return this._graph;
+ } //-- boolean getGraph()
+
+ /**
+ * Returns the value of field 'provenance'.
+ *
+ * @return Provenance
+ * @return the value of field 'provenance'.
+ */
+ public org.vamsas.objects.core.Provenance getProvenance()
+ {
+ return this._provenance;
+ } //-- org.vamsas.objects.core.Provenance getProvenance()
+
+ /**
+ * Method 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)
+
+ /**
+ * Sets the value of field 'graph'. The field 'graph' has the
+ * following description: TODO:
+ * decide
+ * if
+ * this
+ * flag
+ * is
+ * redundant
+ * -
+ * when
+ * true
+ * it
+ * would
+ * suggest
+ * that
+ * the
+ * annotationElement
+ * values
+ * together
+ * form
+ * a
+ * 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 'provenance'.
+ *
+ * @param provenance the value of field 'provenance'.
+ */
+ public void setProvenance(org.vamsas.objects.core.Provenance provenance)
+ {
+ this._provenance = provenance;
+ } //-- void setProvenance(org.vamsas.objects.core.Provenance)
+
+ /**
+ * Method unmarshal
+ *
+ *
+ *
+ * @param reader
+ * @return RangeType
+ */
+ public static org.vamsas.objects.core.RangeType unmarshal(java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+ {
+ return (org.vamsas.objects.core.AlignmentSequenceAnnotation) Unmarshaller.unmarshal(org.vamsas.objects.core.AlignmentSequenceAnnotation.class, reader);
+ } //-- org.vamsas.objects.core.RangeType unmarshal(java.io.Reader)
+
+ /**
+ * Method validate
+ *
+ */
+ public void validate()
+ throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ } //-- void validate()
+
+}
--- /dev/null
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package org.vamsas.objects.core;
+
+ //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.mapping.AccessMode;
+import org.exolab.castor.xml.TypeValidator;
+import org.exolab.castor.xml.XMLFieldDescriptor;
+import org.exolab.castor.xml.validators.*;
+
+/**
+ * Class AlignmentSequenceAnnotationDescriptor.
+ *
+ * @version $Revision$ $Date$
+ */
+public class AlignmentSequenceAnnotationDescriptor extends org.vamsas.objects.core.RangeAnnotationDescriptor {
+
+
+ //--------------------------/
+ //- 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 AlignmentSequenceAnnotationDescriptor()
+ {
+ super();
+ setExtendsWithoutFlatten(new org.vamsas.objects.core.RangeAnnotationDescriptor());
+ nsURI = "http://www.vamsas.org";
+ xmlName = "AlignmentSequenceAnnotation";
+
+ //-- 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
+ {
+ AlignmentSequenceAnnotation target = (AlignmentSequenceAnnotation) 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 {
+ AlignmentSequenceAnnotation target = (AlignmentSequenceAnnotation) 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
+
+ //-- _provenance
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Provenance.class, "_provenance", "Provenance", org.exolab.castor.xml.NodeType.Element);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ AlignmentSequenceAnnotation target = (AlignmentSequenceAnnotation) object;
+ return target.getProvenance();
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ AlignmentSequenceAnnotation target = (AlignmentSequenceAnnotation) object;
+ target.setProvenance( (org.vamsas.objects.core.Provenance) value);
+ }
+ catch (java.lang.Exception ex) {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+ public java.lang.Object newInstance( java.lang.Object parent ) {
+ return new org.vamsas.objects.core.Provenance();
+ }
+ };
+ desc.setHandler(handler);
+ desc.setNameSpaceURI("http://www.vamsas.org");
+ desc.setRequired(true);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _provenance
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(1);
+ { //-- local scope
+ }
+ desc.setValidator(fieldValidator);
+ } //-- org.vamsas.objects.core.AlignmentSequenceAnnotationDescriptor()
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ * Method getAccessMode
+ *
+ *
+ *
+ * @return AccessMode
+ */
+ public org.exolab.castor.mapping.AccessMode getAccessMode()
+ {
+ return null;
+ } //-- org.exolab.castor.mapping.AccessMode getAccessMode()
+
+ /**
+ * Method getExtends
+ *
+ *
+ *
+ * @return ClassDescriptor
+ */
+ public org.exolab.castor.mapping.ClassDescriptor getExtends()
+ {
+ return super.getExtends();
+ } //-- org.exolab.castor.mapping.ClassDescriptor getExtends()
+
+ /**
+ * Method getIdentity
+ *
+ *
+ *
+ * @return FieldDescriptor
+ */
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+ {
+ if (identity == null)
+ return super.getIdentity();
+ return identity;
+ } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity()
+
+ /**
+ * Method getJavaClass
+ *
+ *
+ *
+ * @return Class
+ */
+ public java.lang.Class getJavaClass()
+ {
+ return org.vamsas.objects.core.AlignmentSequenceAnnotation.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()
+
+}
setExtendsWithoutFlatten(new org.vamsas.objects.core.SequenceTypeDescriptor());
nsURI = "http://www.vamsas.org";
xmlName = "alignmentSequence";
+
+ //-- 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;
desc.setValidator(fieldValidator);
//-- initialize element descriptors
+ //-- _alignmentSequenceAnnotationList
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.AlignmentSequenceAnnotation.class, "_alignmentSequenceAnnotationList", "AlignmentSequenceAnnotation", org.exolab.castor.xml.NodeType.Element);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ AlignmentSequence target = (AlignmentSequence) object;
+ return target.getAlignmentSequenceAnnotation();
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ AlignmentSequence target = (AlignmentSequence) object;
+ target.addAlignmentSequenceAnnotation( (org.vamsas.objects.core.AlignmentSequenceAnnotation) value);
+ }
+ catch (java.lang.Exception ex) {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+ public java.lang.Object newInstance( java.lang.Object parent ) {
+ return new org.vamsas.objects.core.AlignmentSequenceAnnotation();
+ }
+ };
+ desc.setHandler(handler);
+ desc.setNameSpaceURI("http://www.vamsas.org");
+ desc.setMultivalued(true);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _alignmentSequenceAnnotationList
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(0);
+ { //-- local scope
+ }
+ desc.setValidator(fieldValidator);
} //-- org.vamsas.objects.core.AlignmentSequenceDescriptor()
import java.io.Reader;
import java.io.Serializable;
import java.io.Writer;
+import java.util.Enumeration;
+import java.util.Vector;
import org.exolab.castor.xml.MarshalException;
import org.exolab.castor.xml.Marshaller;
import org.exolab.castor.xml.Unmarshaller;
//--------------------------/
/**
- * Field _position
+ * position with respect to the coordinate frame
+ * defined by a rangeType specification
+ *
*/
private int _position;
private boolean _has_position;
/**
- * Field _id
+ * true means the annotation element appears
+ * between the specified position and the next
+ *
*/
- private java.lang.String _id;
+ private boolean _after = false;
/**
- * Field _displayCharacter
+ * keeps track of state for field: _after
*/
- private java.lang.String _displayCharacter;
+ private boolean _has_after;
/**
- * Field _description
+ * Primary Key for vamsas object referencing
+ *
*/
- private java.lang.String _description;
+ private java.lang.String _id;
/**
- * Field _secondaryStructure
+ * Free text at this position
+ *
*/
- private java.lang.String _secondaryStructure;
+ private java.lang.String _description;
/**
- * Field _value
+ * Discrete symbol - possibly graphically
+ * represented
+ *
*/
- private float _value;
+ private java.util.Vector _glyphList;
/**
- * keeps track of state for field: _value
+ * Ordered set of float values - an application
+ * may treat the values together as a vector
+ * with common support for a set of annotation
+ * elements - but this is, again, not validated
+ * so applications should deal gracefully with
+ * varying numbers of dimensions
+ *
*/
- private boolean _has_value;
+ private java.util.Vector _valueList;
//----------------/
public AnnotationElement()
{
super();
+ _glyphList = new Vector();
+ _valueList = new Vector();
} //-- org.vamsas.objects.core.AnnotationElement()
//-----------/
/**
+ * Method addGlyph
+ *
+ *
+ *
+ * @param vGlyph
+ */
+ public void addGlyph(org.vamsas.objects.core.Glyph vGlyph)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _glyphList.addElement(vGlyph);
+ } //-- void addGlyph(org.vamsas.objects.core.Glyph)
+
+ /**
+ * Method addGlyph
+ *
+ *
+ *
+ * @param index
+ * @param vGlyph
+ */
+ public void addGlyph(int index, org.vamsas.objects.core.Glyph vGlyph)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _glyphList.insertElementAt(vGlyph, index);
+ } //-- void addGlyph(int, org.vamsas.objects.core.Glyph)
+
+ /**
+ * Method addValue
+ *
+ *
+ *
+ * @param vValue
+ */
+ public void addValue(float vValue)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _valueList.addElement(new java.lang.Float(vValue));
+ } //-- void addValue(float)
+
+ /**
+ * Method addValue
+ *
+ *
+ *
+ * @param index
+ * @param vValue
+ */
+ public void addValue(int index, float vValue)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _valueList.insertElementAt(new java.lang.Float(vValue), index);
+ } //-- void addValue(int, float)
+
+ /**
+ * Method deleteAfter
+ *
+ */
+ public void deleteAfter()
+ {
+ this._has_after= false;
+ } //-- void deleteAfter()
+
+ /**
* Method deletePosition
*
*/
} //-- void deletePosition()
/**
- * Method deleteValue
+ * Method enumerateGlyph
+ *
+ *
*
+ * @return Enumeration
*/
- public void deleteValue()
+ public java.util.Enumeration enumerateGlyph()
{
- this._has_value= false;
- } //-- void deleteValue()
+ return _glyphList.elements();
+ } //-- java.util.Enumeration enumerateGlyph()
+
+ /**
+ * Method enumerateValue
+ *
+ *
+ *
+ * @return Enumeration
+ */
+ public java.util.Enumeration enumerateValue()
+ {
+ return _valueList.elements();
+ } //-- java.util.Enumeration enumerateValue()
/**
* Note: hashCode() has not been overriden
return false;
if (this._has_position != temp._has_position)
return false;
+ if (this._after != temp._after)
+ return false;
+ if (this._has_after != temp._has_after)
+ return false;
if (this._id != null) {
if (temp._id == null) return false;
else if (!(this._id.equals(temp._id)))
}
else if (temp._id != null)
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)))
}
else if (temp._description != null)
return false;
- if (this._secondaryStructure != null) {
- if (temp._secondaryStructure == null) return false;
- else if (!(this._secondaryStructure.equals(temp._secondaryStructure)))
+ if (this._glyphList != null) {
+ if (temp._glyphList == null) return false;
+ else if (!(this._glyphList.equals(temp._glyphList)))
return false;
}
- else if (temp._secondaryStructure != null)
- return false;
- if (this._value != temp._value)
+ else if (temp._glyphList != null)
return false;
- if (this._has_value != temp._has_value)
+ if (this._valueList != null) {
+ if (temp._valueList == null) return false;
+ else if (!(this._valueList.equals(temp._valueList)))
+ return false;
+ }
+ else if (temp._valueList != null)
return false;
return true;
}
} //-- boolean equals(java.lang.Object)
/**
- * Returns the value of field 'description'.
+ * Returns the value of field 'after'. The field 'after' has
+ * the following description: true means the annotation element
+ * appears
+ * between the specified position and the next
+ *
+ *
+ * @return boolean
+ * @return the value of field 'after'.
+ */
+ public boolean getAfter()
+ {
+ return this._after;
+ } //-- boolean getAfter()
+
+ /**
+ * Returns the value of field 'description'. The field
+ * 'description' has the following description: Free text at
+ * this position
+ *
*
* @return String
* @return the value of field 'description'.
} //-- java.lang.String getDescription()
/**
- * Returns the value of field 'displayCharacter'.
+ * Method getGlyph
*
- * @return String
- * @return the value of field 'displayCharacter'.
+ *
+ *
+ * @param index
+ * @return Glyph
*/
- public java.lang.String getDisplayCharacter()
+ public org.vamsas.objects.core.Glyph getGlyph(int index)
+ throws java.lang.IndexOutOfBoundsException
{
- return this._displayCharacter;
- } //-- java.lang.String getDisplayCharacter()
+ //-- check bounds for index
+ if ((index < 0) || (index > _glyphList.size())) {
+ throw new IndexOutOfBoundsException("getGlyph: Index value '"+index+"' not in range [0.."+_glyphList.size()+ "]");
+ }
+
+ return (org.vamsas.objects.core.Glyph) _glyphList.elementAt(index);
+ } //-- org.vamsas.objects.core.Glyph getGlyph(int)
/**
- * Returns the value of field 'id'.
+ * Method getGlyph
+ *
+ *
+ *
+ * @return Glyph
+ */
+ public org.vamsas.objects.core.Glyph[] getGlyph()
+ {
+ int size = _glyphList.size();
+ org.vamsas.objects.core.Glyph[] mArray = new org.vamsas.objects.core.Glyph[size];
+ for (int index = 0; index < size; index++) {
+ mArray[index] = (org.vamsas.objects.core.Glyph) _glyphList.elementAt(index);
+ }
+ return mArray;
+ } //-- org.vamsas.objects.core.Glyph[] getGlyph()
+
+ /**
+ * Method getGlyphCount
+ *
+ *
+ *
+ * @return int
+ */
+ public int getGlyphCount()
+ {
+ return _glyphList.size();
+ } //-- int getGlyphCount()
+
+ /**
+ * Returns the value of field 'id'. The field 'id' has the
+ * following description: Primary Key for vamsas object
+ * referencing
+ *
*
* @return String
* @return the value of field 'id'.
} //-- java.lang.String getId()
/**
- * Returns the value of field 'position'.
+ * Returns the value of field 'position'. The field 'position'
+ * has the following description: position with respect to the
+ * coordinate frame
+ * defined by a rangeType specification
+ *
*
* @return int
* @return the value of field 'position'.
} //-- int getPosition()
/**
- * Returns the value of field 'secondaryStructure'.
+ * Method getValue
*
- * @return String
- * @return the value of field 'secondaryStructure'.
+ *
+ *
+ * @param index
+ * @return float
*/
- public java.lang.String getSecondaryStructure()
+ public float getValue(int index)
+ throws java.lang.IndexOutOfBoundsException
{
- return this._secondaryStructure;
- } //-- java.lang.String getSecondaryStructure()
+ //-- check bounds for index
+ if ((index < 0) || (index > _valueList.size())) {
+ throw new IndexOutOfBoundsException("getValue: Index value '"+index+"' not in range [0.."+_valueList.size()+ "]");
+ }
+
+ return ((java.lang.Float)_valueList.elementAt(index)).floatValue();
+ } //-- float getValue(int)
/**
- * Returns the value of field 'value'.
+ * Method getValue
+ *
+ *
*
* @return float
- * @return the value of field 'value'.
*/
- public float getValue()
+ public float[] getValue()
{
- return this._value;
- } //-- float getValue()
+ int size = _valueList.size();
+ float[] mArray = new float[size];
+ for (int index = 0; index < size; index++) {
+ mArray[index] = ((java.lang.Float)_valueList.elementAt(index)).floatValue();
+ }
+ return mArray;
+ } //-- float[] getValue()
/**
- * Method hasPosition
+ * Method getValueCount
+ *
+ *
+ *
+ * @return int
+ */
+ public int getValueCount()
+ {
+ return _valueList.size();
+ } //-- int getValueCount()
+
+ /**
+ * Method hasAfter
*
*
*
* @return boolean
*/
- public boolean hasPosition()
+ public boolean hasAfter()
{
- return this._has_position;
- } //-- boolean hasPosition()
+ return this._has_after;
+ } //-- boolean hasAfter()
/**
- * Method hasValue
+ * Method hasPosition
*
*
*
* @return boolean
*/
- public boolean hasValue()
+ public boolean hasPosition()
{
- return this._has_value;
- } //-- boolean hasValue()
+ return this._has_position;
+ } //-- boolean hasPosition()
/**
* Method isValid
} //-- void marshal(org.xml.sax.ContentHandler)
/**
- * Sets the value of field 'description'.
+ * Method removeAllGlyph
+ *
+ */
+ public void removeAllGlyph()
+ {
+ _glyphList.removeAllElements();
+ } //-- void removeAllGlyph()
+
+ /**
+ * Method removeAllValue
+ *
+ */
+ public void removeAllValue()
+ {
+ _valueList.removeAllElements();
+ } //-- void removeAllValue()
+
+ /**
+ * Method removeGlyph
+ *
+ *
+ *
+ * @param index
+ * @return Glyph
+ */
+ public org.vamsas.objects.core.Glyph removeGlyph(int index)
+ {
+ java.lang.Object obj = _glyphList.elementAt(index);
+ _glyphList.removeElementAt(index);
+ return (org.vamsas.objects.core.Glyph) obj;
+ } //-- org.vamsas.objects.core.Glyph removeGlyph(int)
+
+ /**
+ * Method removeValue
+ *
+ *
+ *
+ * @param index
+ * @return float
+ */
+ public float removeValue(int index)
+ {
+ java.lang.Object obj = _valueList.elementAt(index);
+ _valueList.removeElementAt(index);
+ return ((java.lang.Float)obj).floatValue();
+ } //-- float removeValue(int)
+
+ /**
+ * Sets the value of field 'after'. The field 'after' has the
+ * following description: true means the annotation element
+ * appears
+ * between the specified position and the next
+ *
+ *
+ * @param after the value of field 'after'.
+ */
+ public void setAfter(boolean after)
+ {
+ this._after = after;
+ this._has_after = true;
+ } //-- void setAfter(boolean)
+
+ /**
+ * Sets the value of field 'description'. The field
+ * 'description' has the following description: Free text at
+ * this position
+ *
*
* @param description the value of field 'description'.
*/
} //-- void setDescription(java.lang.String)
/**
- * Sets the value of field 'displayCharacter'.
+ * Method setGlyph
+ *
*
- * @param displayCharacter the value of field 'displayCharacter'
+ *
+ * @param index
+ * @param vGlyph
*/
- public void setDisplayCharacter(java.lang.String displayCharacter)
+ public void setGlyph(int index, org.vamsas.objects.core.Glyph vGlyph)
+ throws java.lang.IndexOutOfBoundsException
{
- this._displayCharacter = displayCharacter;
- } //-- void setDisplayCharacter(java.lang.String)
+ //-- check bounds for index
+ if ((index < 0) || (index > _glyphList.size())) {
+ throw new IndexOutOfBoundsException("setGlyph: Index value '"+index+"' not in range [0.."+_glyphList.size()+ "]");
+ }
+ _glyphList.setElementAt(vGlyph, index);
+ } //-- void setGlyph(int, org.vamsas.objects.core.Glyph)
/**
- * Sets the value of field 'id'.
+ * Method setGlyph
+ *
+ *
+ *
+ * @param glyphArray
+ */
+ public void setGlyph(org.vamsas.objects.core.Glyph[] glyphArray)
+ {
+ //-- copy array
+ _glyphList.removeAllElements();
+ for (int i = 0; i < glyphArray.length; i++) {
+ _glyphList.addElement(glyphArray[i]);
+ }
+ } //-- void setGlyph(org.vamsas.objects.core.Glyph)
+
+ /**
+ * Sets the value of field 'id'. The field 'id' has the
+ * following description: Primary Key for vamsas object
+ * referencing
+ *
*
* @param id the value of field 'id'.
*/
} //-- void setId(java.lang.String)
/**
- * Sets the value of field 'position'.
+ * Sets the value of field 'position'. The field 'position' has
+ * the following description: position with respect to the
+ * coordinate frame
+ * defined by a rangeType specification
+ *
*
* @param position the value of field 'position'.
*/
} //-- void setPosition(int)
/**
- * Sets the value of field 'secondaryStructure'.
+ * Method setValue
+ *
+ *
*
- * @param secondaryStructure the value of field
- * 'secondaryStructure'.
+ * @param index
+ * @param vValue
*/
- public void setSecondaryStructure(java.lang.String secondaryStructure)
+ public void setValue(int index, float vValue)
+ throws java.lang.IndexOutOfBoundsException
{
- this._secondaryStructure = secondaryStructure;
- } //-- void setSecondaryStructure(java.lang.String)
+ //-- check bounds for index
+ if ((index < 0) || (index > _valueList.size())) {
+ throw new IndexOutOfBoundsException("setValue: Index value '"+index+"' not in range [0.."+_valueList.size()+ "]");
+ }
+ _valueList.setElementAt(new java.lang.Float(vValue), index);
+ } //-- void setValue(int, float)
/**
- * Sets the value of field 'value'.
+ * Method setValue
+ *
*
- * @param value the value of field 'value'.
+ *
+ * @param valueArray
*/
- public void setValue(float value)
+ public void setValue(float[] valueArray)
{
- this._value = value;
- this._has_value = true;
+ //-- copy array
+ _valueList.removeAllElements();
+ for (int i = 0; i < valueArray.length; i++) {
+ _valueList.addElement(new java.lang.Float(valueArray[i]));
+ }
} //-- void setValue(float)
/**
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;
+ //-- _after
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_after", "after", 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;
- return target.getId();
+ if(!target.hasAfter())
+ return null;
+ return (target.getAfter() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
}
public void setValue( java.lang.Object object, java.lang.Object value)
throws IllegalStateException, IllegalArgumentException
{
try {
AnnotationElement target = (AnnotationElement) object;
- target.setId( (java.lang.String) value);
+ // if null, use delete method for optional primitives
+ if (value == null) {
+ target.deleteAfter();
+ return;
+ }
+ target.setAfter( ((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 new java.lang.String();
+ return null;
}
};
desc.setHandler(handler);
desc.setMultivalued(false);
addFieldDescriptor(desc);
- //-- validation code for: _id
+ //-- validation code for: _after
fieldValidator = new org.exolab.castor.xml.FieldValidator();
{ //-- local scope
+ BooleanValidator typeValidator = new BooleanValidator();
+ 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);
+ //-- _id
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute);
+ this.identity = desc;
handler = new org.exolab.castor.xml.XMLFieldHandler() {
public java.lang.Object getValue( java.lang.Object object )
throws IllegalStateException
{
AnnotationElement target = (AnnotationElement) object;
- return target.getDisplayCharacter();
+ return target.getId();
}
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);
+ 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 null;
+ return new java.lang.String();
}
};
desc.setHandler(handler);
- desc.setNameSpaceURI("http://www.vamsas.org");
desc.setMultivalued(false);
addFieldDescriptor(desc);
- //-- validation code for: _displayCharacter
+ //-- validation code for: _id
fieldValidator = new org.exolab.castor.xml.FieldValidator();
{ //-- local scope
- StringValidator typeValidator = new StringValidator();
- typeValidator.setWhiteSpace("preserve");
- fieldValidator.setValidator(typeValidator);
}
desc.setValidator(fieldValidator);
+ //-- initialize element descriptors
+
//-- _description
desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_description", "description", org.exolab.castor.xml.NodeType.Element);
desc.setImmutable(true);
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);
+ //-- _glyphList
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Glyph.class, "_glyphList", "glyph", 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;
- return target.getSecondaryStructure();
+ return target.getGlyph();
}
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);
+ target.addGlyph( (org.vamsas.objects.core.Glyph) value);
}
catch (java.lang.Exception ex) {
throw new IllegalStateException(ex.toString());
}
}
public java.lang.Object newInstance( java.lang.Object parent ) {
- return null;
+ return new org.vamsas.objects.core.Glyph();
}
};
desc.setHandler(handler);
desc.setNameSpaceURI("http://www.vamsas.org");
- desc.setMultivalued(false);
+ desc.setMultivalued(true);
addFieldDescriptor(desc);
- //-- validation code for: _secondaryStructure
+ //-- validation code for: _glyphList
fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(0);
{ //-- 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);
+ //-- _valueList
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(float.class, "_valueList", "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());
+ return target.getValue();
}
public void setValue( java.lang.Object object, java.lang.Object value)
throws IllegalStateException, IllegalArgumentException
{
try {
AnnotationElement target = (AnnotationElement) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteValue();
- return;
- }
- target.setValue( ((java.lang.Float)value).floatValue());
+ // ignore null values for non optional primitives
+ if (value == null) return;
+
+ target.addValue( ((java.lang.Float)value).floatValue());
}
catch (java.lang.Exception ex) {
throw new IllegalStateException(ex.toString());
};
desc.setHandler(handler);
desc.setNameSpaceURI("http://www.vamsas.org");
- desc.setMultivalued(false);
+ desc.setMultivalued(true);
addFieldDescriptor(desc);
- //-- validation code for: _value
+ //-- validation code for: _valueList
fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(0);
{ //-- local scope
FloatValidator typeValidator = new FloatValidator();
fieldValidator.setValidator(typeValidator);
//--------------------------/
/**
- * Field _version
+ * Version string describing the application specific data
+ * storage version used
*/
private java.lang.String _version;
/**
- * Field _name
+ * Canonical name of application
+ *
*/
private java.lang.String _name;
/**
- * Field _urn
+ * Field _userList
*/
- private java.lang.String _urn;
+ private java.util.Vector _userList;
/**
- * Field _userList
+ * Field _common
*/
- private java.util.Vector _userList;
+ private org.vamsas.objects.core.Common _common;
+
+ /**
+ * Field _instanceList
+ */
+ private java.util.Vector _instanceList;
//----------------/
{
super();
_userList = new Vector();
+ _instanceList = new Vector();
} //-- org.vamsas.objects.core.ApplicationData()
//-----------/
/**
+ * Method addInstance
+ *
+ *
+ *
+ * @param vInstance
+ */
+ public void addInstance(org.vamsas.objects.core.Instance vInstance)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _instanceList.addElement(vInstance);
+ } //-- void addInstance(org.vamsas.objects.core.Instance)
+
+ /**
+ * Method addInstance
+ *
+ *
+ *
+ * @param index
+ * @param vInstance
+ */
+ public void addInstance(int index, org.vamsas.objects.core.Instance vInstance)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _instanceList.insertElementAt(vInstance, index);
+ } //-- void addInstance(int, org.vamsas.objects.core.Instance)
+
+ /**
* Method addUser
*
*
} //-- void addUser(int, org.vamsas.objects.core.User)
/**
+ * Method enumerateInstance
+ *
+ *
+ *
+ * @return Enumeration
+ */
+ public java.util.Enumeration enumerateInstance()
+ {
+ return _instanceList.elements();
+ } //-- java.util.Enumeration enumerateInstance()
+
+ /**
* Method enumerateUser
*
*
}
else if (temp._name != null)
return false;
- if (this._urn != null) {
- if (temp._urn == null) return false;
- else if (!(this._urn.equals(temp._urn)))
- return false;
- }
- else if (temp._urn != null)
- return false;
if (this._userList != null) {
if (temp._userList == null) return false;
else if (!(this._userList.equals(temp._userList)))
}
else if (temp._userList != null)
return false;
+ if (this._common != null) {
+ if (temp._common == null) return false;
+ else if (!(this._common.equals(temp._common)))
+ return false;
+ }
+ else if (temp._common != null)
+ return false;
+ if (this._instanceList != null) {
+ if (temp._instanceList == null) return false;
+ else if (!(this._instanceList.equals(temp._instanceList)))
+ return false;
+ }
+ else if (temp._instanceList != null)
+ return false;
return true;
}
return false;
} //-- boolean equals(java.lang.Object)
/**
- * Returns the value of field 'name'.
+ * Returns the value of field 'common'.
*
- * @return String
- * @return the value of field 'name'.
+ * @return Common
+ * @return the value of field 'common'.
*/
- public java.lang.String getName()
+ public org.vamsas.objects.core.Common getCommon()
{
- return this._name;
- } //-- java.lang.String getName()
+ return this._common;
+ } //-- org.vamsas.objects.core.Common getCommon()
/**
- * Returns the value of field 'urn'.
+ * Method getInstance
+ *
+ *
+ *
+ * @param index
+ * @return Instance
+ */
+ public org.vamsas.objects.core.Instance getInstance(int index)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ //-- check bounds for index
+ if ((index < 0) || (index > _instanceList.size())) {
+ throw new IndexOutOfBoundsException("getInstance: Index value '"+index+"' not in range [0.."+_instanceList.size()+ "]");
+ }
+
+ return (org.vamsas.objects.core.Instance) _instanceList.elementAt(index);
+ } //-- org.vamsas.objects.core.Instance getInstance(int)
+
+ /**
+ * Method getInstance
+ *
+ *
+ *
+ * @return Instance
+ */
+ public org.vamsas.objects.core.Instance[] getInstance()
+ {
+ int size = _instanceList.size();
+ org.vamsas.objects.core.Instance[] mArray = new org.vamsas.objects.core.Instance[size];
+ for (int index = 0; index < size; index++) {
+ mArray[index] = (org.vamsas.objects.core.Instance) _instanceList.elementAt(index);
+ }
+ return mArray;
+ } //-- org.vamsas.objects.core.Instance[] getInstance()
+
+ /**
+ * Method getInstanceCount
+ *
+ *
+ *
+ * @return int
+ */
+ public int getInstanceCount()
+ {
+ return _instanceList.size();
+ } //-- int getInstanceCount()
+
+ /**
+ * Returns the value of field 'name'. The field 'name' has the
+ * following description: Canonical name of application
+ *
*
* @return String
- * @return the value of field 'urn'.
+ * @return the value of field 'name'.
*/
- public java.lang.String getUrn()
+ public java.lang.String getName()
{
- return this._urn;
- } //-- java.lang.String getUrn()
+ return this._name;
+ } //-- java.lang.String getName()
/**
* Method getUser
} //-- int getUserCount()
/**
- * Returns the value of field 'version'.
+ * Returns the value of field 'version'. The field 'version'
+ * has the following description: Version string describing the
+ * application specific data storage version used
*
* @return String
* @return the value of field 'version'.
} //-- void marshal(org.xml.sax.ContentHandler)
/**
+ * Method removeAllInstance
+ *
+ */
+ public void removeAllInstance()
+ {
+ _instanceList.removeAllElements();
+ } //-- void removeAllInstance()
+
+ /**
* Method removeAllUser
*
*/
} //-- void removeAllUser()
/**
+ * Method removeInstance
+ *
+ *
+ *
+ * @param index
+ * @return Instance
+ */
+ public org.vamsas.objects.core.Instance removeInstance(int index)
+ {
+ java.lang.Object obj = _instanceList.elementAt(index);
+ _instanceList.removeElementAt(index);
+ return (org.vamsas.objects.core.Instance) obj;
+ } //-- org.vamsas.objects.core.Instance removeInstance(int)
+
+ /**
* Method removeUser
*
*
} //-- org.vamsas.objects.core.User removeUser(int)
/**
- * Sets the value of field 'name'.
+ * Sets the value of field 'common'.
*
- * @param name the value of field 'name'.
+ * @param common the value of field 'common'.
*/
- public void setName(java.lang.String name)
+ public void setCommon(org.vamsas.objects.core.Common common)
{
- this._name = name;
- } //-- void setName(java.lang.String)
+ this._common = common;
+ } //-- void setCommon(org.vamsas.objects.core.Common)
+
+ /**
+ * Method setInstance
+ *
+ *
+ *
+ * @param index
+ * @param vInstance
+ */
+ public void setInstance(int index, org.vamsas.objects.core.Instance vInstance)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ //-- check bounds for index
+ if ((index < 0) || (index > _instanceList.size())) {
+ throw new IndexOutOfBoundsException("setInstance: Index value '"+index+"' not in range [0.."+_instanceList.size()+ "]");
+ }
+ _instanceList.setElementAt(vInstance, index);
+ } //-- void setInstance(int, org.vamsas.objects.core.Instance)
/**
- * Sets the value of field 'urn'.
+ * Method setInstance
+ *
+ *
*
- * @param urn the value of field 'urn'.
+ * @param instanceArray
*/
- public void setUrn(java.lang.String urn)
+ public void setInstance(org.vamsas.objects.core.Instance[] instanceArray)
{
- this._urn = urn;
- } //-- void setUrn(java.lang.String)
+ //-- copy array
+ _instanceList.removeAllElements();
+ for (int i = 0; i < instanceArray.length; i++) {
+ _instanceList.addElement(instanceArray[i]);
+ }
+ } //-- void setInstance(org.vamsas.objects.core.Instance)
+
+ /**
+ * Sets the value of field 'name'. The field 'name' has the
+ * following description: Canonical name of application
+ *
+ *
+ * @param name the value of field 'name'.
+ */
+ public void setName(java.lang.String name)
+ {
+ this._name = name;
+ } //-- void setName(java.lang.String)
/**
* Method setUser
} //-- void setUser(org.vamsas.objects.core.User)
/**
- * Sets the value of field 'version'.
+ * Sets the value of field 'version'. The field 'version' has
+ * the following description: Version string describing the
+ * application specific data storage version used
*
* @param version the value of field 'version'.
*/
fieldValidator.setValidator(typeValidator);
}
desc.setValidator(fieldValidator);
- //-- _urn
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_urn", "urn", org.exolab.castor.xml.NodeType.Attribute);
- desc.setImmutable(true);
+ //-- initialize element descriptors
+
+ //-- _userList
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.User.class, "_userList", "User", org.exolab.castor.xml.NodeType.Element);
handler = new org.exolab.castor.xml.XMLFieldHandler() {
public java.lang.Object getValue( java.lang.Object object )
throws IllegalStateException
{
ApplicationData target = (ApplicationData) object;
- return target.getUrn();
+ return target.getUser();
}
public void setValue( java.lang.Object object, java.lang.Object value)
throws IllegalStateException, IllegalArgumentException
{
try {
ApplicationData target = (ApplicationData) object;
- target.setUrn( (java.lang.String) value);
+ target.addUser( (org.vamsas.objects.core.User) value);
}
catch (java.lang.Exception ex) {
throw new IllegalStateException(ex.toString());
}
}
public java.lang.Object newInstance( java.lang.Object parent ) {
- return null;
+ return new org.vamsas.objects.core.User();
}
};
desc.setHandler(handler);
- desc.setRequired(true);
- desc.setMultivalued(false);
+ desc.setNameSpaceURI("http://www.vamsas.org");
+ desc.setMultivalued(true);
addFieldDescriptor(desc);
- //-- validation code for: _urn
+ //-- validation code for: _userList
fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(1);
+ fieldValidator.setMinOccurs(0);
{ //-- local scope
- StringValidator typeValidator = new StringValidator();
- typeValidator.setWhiteSpace("preserve");
- fieldValidator.setValidator(typeValidator);
}
desc.setValidator(fieldValidator);
- //-- initialize element descriptors
+ //-- _common
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Common.class, "_common", "Common", 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.getCommon();
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ ApplicationData target = (ApplicationData) object;
+ target.setCommon( (org.vamsas.objects.core.Common) value);
+ }
+ catch (java.lang.Exception ex) {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+ public java.lang.Object newInstance( java.lang.Object parent ) {
+ return new org.vamsas.objects.core.Common();
+ }
+ };
+ desc.setHandler(handler);
+ desc.setNameSpaceURI("http://www.vamsas.org");
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
- //-- _userList
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.User.class, "_userList", "User", org.exolab.castor.xml.NodeType.Element);
+ //-- validation code for: _common
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { //-- local scope
+ }
+ desc.setValidator(fieldValidator);
+ //-- _instanceList
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Instance.class, "_instanceList", "Instance", 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.getUser();
+ return target.getInstance();
}
public void setValue( java.lang.Object object, java.lang.Object value)
throws IllegalStateException, IllegalArgumentException
{
try {
ApplicationData target = (ApplicationData) object;
- target.addUser( (org.vamsas.objects.core.User) value);
+ target.addInstance( (org.vamsas.objects.core.Instance) value);
}
catch (java.lang.Exception ex) {
throw new IllegalStateException(ex.toString());
}
}
public java.lang.Object newInstance( java.lang.Object parent ) {
- return new org.vamsas.objects.core.User();
+ return new org.vamsas.objects.core.Instance();
}
};
desc.setHandler(handler);
desc.setMultivalued(true);
addFieldDescriptor(desc);
- //-- validation code for: _userList
+ //-- validation code for: _instanceList
fieldValidator = new org.exolab.castor.xml.FieldValidator();
fieldValidator.setMinOccurs(0);
{ //-- local scope
--- /dev/null
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package org.vamsas.objects.core;
+
+ //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import java.io.IOException;
+import java.io.Reader;
+import java.io.Serializable;
+import java.io.Writer;
+import org.exolab.castor.xml.MarshalException;
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+import org.exolab.castor.xml.ValidationException;
+import org.xml.sax.ContentHandler;
+
+/**
+ * Class Attachment.
+ *
+ * @version $Revision$ $Date$
+ */
+public class Attachment extends org.vamsas.objects.core.AppData
+implements java.io.Serializable
+{
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * true implies data will be decompresses
+ * with Zip before presenting to
+ * application
+ *
+ */
+ private boolean _compressed = false;
+
+ /**
+ * keeps track of state for field: _compressed
+ */
+ private boolean _has_compressed;
+
+ /**
+ * Type of arbitrary data - TODO: decide
+ * format - use (extended) MIME types ?
+ *
+ */
+ private java.lang.String _type;
+
+ /**
+ * Object the arbitrary data is associated
+ * with
+ *
+ */
+ private java.lang.Object _objectref;
+
+ /**
+ * Primary Key for vamsas object
+ * referencing
+ *
+ */
+ private java.lang.String _id;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public Attachment()
+ {
+ super();
+ } //-- org.vamsas.objects.core.Attachment()
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ * Method deleteCompressed
+ *
+ */
+ public void deleteCompressed()
+ {
+ this._has_compressed= false;
+ } //-- void deleteCompressed()
+
+ /**
+ * 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 Attachment) {
+
+ Attachment temp = (Attachment)obj;
+ if (this._compressed != temp._compressed)
+ return false;
+ if (this._has_compressed != temp._has_compressed)
+ return false;
+ 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._objectref != null) {
+ if (temp._objectref == null) return false;
+ else if (!(this._objectref.equals(temp._objectref)))
+ return false;
+ }
+ else if (temp._objectref != 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 'compressed'. The field
+ * 'compressed' has the following description: true implies
+ * data will be decompresses
+ * with Zip before presenting to
+ * application
+ *
+ *
+ * @return boolean
+ * @return the value of field 'compressed'.
+ */
+ public boolean getCompressed()
+ {
+ return this._compressed;
+ } //-- boolean getCompressed()
+
+ /**
+ * Returns the value of field 'id'. The field 'id' has the
+ * following description: Primary Key for vamsas object
+ * referencing
+ *
+ *
+ * @return String
+ * @return the value of field 'id'.
+ */
+ public java.lang.String getId()
+ {
+ return this._id;
+ } //-- java.lang.String getId()
+
+ /**
+ * Returns the value of field 'objectref'. The field
+ * 'objectref' has the following description: Object the
+ * arbitrary data is associated
+ * with
+ *
+ *
+ * @return Object
+ * @return the value of field 'objectref'.
+ */
+ public java.lang.Object getObjectref()
+ {
+ return this._objectref;
+ } //-- java.lang.Object getObjectref()
+
+ /**
+ * Returns the value of field 'type'. The field 'type' has the
+ * following description: Type of arbitrary data - TODO: decide
+ * format - use (extended) MIME types ?
+ *
+ *
+ * @return String
+ * @return the value of field 'type'.
+ */
+ public java.lang.String getType()
+ {
+ return this._type;
+ } //-- java.lang.String getType()
+
+ /**
+ * Method hasCompressed
+ *
+ *
+ *
+ * @return boolean
+ */
+ public boolean hasCompressed()
+ {
+ return this._has_compressed;
+ } //-- boolean hasCompressed()
+
+ /**
+ * 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 'compressed'. The field 'compressed'
+ * has the following description: true implies data will be
+ * decompresses
+ * with Zip before presenting to
+ * application
+ *
+ *
+ * @param compressed the value of field 'compressed'.
+ */
+ public void setCompressed(boolean compressed)
+ {
+ this._compressed = compressed;
+ this._has_compressed = true;
+ } //-- void setCompressed(boolean)
+
+ /**
+ * Sets the value of field 'id'. The field 'id' has the
+ * following description: Primary Key for vamsas object
+ * referencing
+ *
+ *
+ * @param id the value of field 'id'.
+ */
+ public void setId(java.lang.String id)
+ {
+ this._id = id;
+ } //-- void setId(java.lang.String)
+
+ /**
+ * Sets the value of field 'objectref'. The field 'objectref'
+ * has the following description: Object the arbitrary data is
+ * associated
+ * with
+ *
+ *
+ * @param objectref the value of field 'objectref'.
+ */
+ public void setObjectref(java.lang.Object objectref)
+ {
+ this._objectref = objectref;
+ } //-- void setObjectref(java.lang.Object)
+
+ /**
+ * Sets the value of field 'type'. The field 'type' has the
+ * following description: Type of arbitrary data - TODO: decide
+ * format - use (extended) MIME types ?
+ *
+ *
+ * @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 AppData
+ */
+ public static org.vamsas.objects.core.AppData unmarshal(java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+ {
+ return (org.vamsas.objects.core.Attachment) Unmarshaller.unmarshal(org.vamsas.objects.core.Attachment.class, reader);
+ } //-- org.vamsas.objects.core.AppData unmarshal(java.io.Reader)
+
+ /**
+ * Method validate
+ *
+ */
+ public void validate()
+ throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ } //-- void validate()
+
+}
--- /dev/null
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package org.vamsas.objects.core;
+
+ //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.mapping.AccessMode;
+import org.exolab.castor.xml.TypeValidator;
+import org.exolab.castor.xml.XMLFieldDescriptor;
+import org.exolab.castor.xml.validators.*;
+
+/**
+ * Class AttachmentDescriptor.
+ *
+ * @version $Revision$ $Date$
+ */
+public class AttachmentDescriptor extends org.vamsas.objects.core.AppDataDescriptor {
+
+
+ //--------------------------/
+ //- 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 AttachmentDescriptor()
+ {
+ super();
+ setExtendsWithoutFlatten(new org.vamsas.objects.core.AppDataDescriptor());
+ nsURI = "http://www.vamsas.org";
+ xmlName = "Attachment";
+ 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
+
+ //-- _compressed
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_compressed", "compressed", org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ Attachment target = (Attachment) object;
+ if(!target.hasCompressed())
+ return null;
+ return (target.getCompressed() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ Attachment target = (Attachment) object;
+ // if null, use delete method for optional primitives
+ if (value == null) {
+ target.deleteCompressed();
+ return;
+ }
+ target.setCompressed( ((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: _compressed
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { //-- local scope
+ BooleanValidator typeValidator = new BooleanValidator();
+ fieldValidator.setValidator(typeValidator);
+ }
+ desc.setValidator(fieldValidator);
+ //-- _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
+ {
+ Attachment target = (Attachment) object;
+ return target.getType();
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ Attachment target = (Attachment) 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);
+ //-- _objectref
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Object.class, "_objectref", "objectref", 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
+ {
+ Attachment target = (Attachment) object;
+ return target.getObjectref();
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ Attachment target = (Attachment) object;
+ target.setObjectref( (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: _objectref
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(1);
+ { //-- local scope
+ }
+ desc.setValidator(fieldValidator);
+ //-- _id
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute);
+ this.identity = desc;
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ Attachment target = (Attachment) object;
+ return target.getId();
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ Attachment target = (Attachment) object;
+ target.setId( (java.lang.String) value);
+ }
+ catch (java.lang.Exception ex) {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+ public java.lang.Object newInstance( java.lang.Object parent ) {
+ return new java.lang.String();
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _id
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { //-- local scope
+ }
+ desc.setValidator(fieldValidator);
+ //-- initialize element descriptors
+
+ } //-- org.vamsas.objects.core.AttachmentDescriptor()
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ * Method getAccessMode
+ *
+ *
+ *
+ * @return AccessMode
+ */
+ public org.exolab.castor.mapping.AccessMode getAccessMode()
+ {
+ return null;
+ } //-- org.exolab.castor.mapping.AccessMode getAccessMode()
+
+ /**
+ * Method getExtends
+ *
+ *
+ *
+ * @return ClassDescriptor
+ */
+ public org.exolab.castor.mapping.ClassDescriptor getExtends()
+ {
+ return super.getExtends();
+ } //-- org.exolab.castor.mapping.ClassDescriptor getExtends()
+
+ /**
+ * Method getIdentity
+ *
+ *
+ *
+ * @return FieldDescriptor
+ */
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+ {
+ if (identity == null)
+ return super.getIdentity();
+ return identity;
+ } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity()
+
+ /**
+ * Method getJavaClass
+ *
+ *
+ *
+ * @return Class
+ */
+ public java.lang.Class getJavaClass()
+ {
+ return org.vamsas.objects.core.Attachment.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 0.9.9M2</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package org.vamsas.objects.core;
+
+ //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import java.io.IOException;
+import java.io.Reader;
+import java.io.Serializable;
+import java.io.Writer;
+import org.exolab.castor.xml.MarshalException;
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+import org.exolab.castor.xml.ValidationException;
+import org.xml.sax.ContentHandler;
+
+/**
+ * Class Common.
+ *
+ * @version $Revision$ $Date$
+ */
+public class Common extends org.vamsas.objects.core.AppData
+implements java.io.Serializable
+{
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public Common()
+ {
+ super();
+ } //-- org.vamsas.objects.core.Common()
+
+
+ //-----------/
+ //- 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 Common) {
+
+ Common temp = (Common)obj;
+ return true;
+ }
+ return false;
+ } //-- boolean equals(java.lang.Object)
+
+ /**
+ * Method isValid
+ *
+ *
+ *
+ * @return boolean
+ */
+ public boolean isValid()
+ {
+ try {
+ validate();
+ }
+ catch (org.exolab.castor.xml.ValidationException vex) {
+ return false;
+ }
+ return true;
+ } //-- boolean isValid()
+
+ /**
+ * Method marshal
+ *
+ *
+ *
+ * @param out
+ */
+ public void marshal(java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+ {
+
+ Marshaller.marshal(this, out);
+ } //-- void marshal(java.io.Writer)
+
+ /**
+ * Method marshal
+ *
+ *
+ *
+ * @param handler
+ */
+ public void marshal(org.xml.sax.ContentHandler handler)
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+ {
+
+ Marshaller.marshal(this, handler);
+ } //-- void marshal(org.xml.sax.ContentHandler)
+
+ /**
+ * Method unmarshal
+ *
+ *
+ *
+ * @param reader
+ * @return AppData
+ */
+ public static org.vamsas.objects.core.AppData unmarshal(java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+ {
+ return (org.vamsas.objects.core.Common) Unmarshaller.unmarshal(org.vamsas.objects.core.Common.class, reader);
+ } //-- org.vamsas.objects.core.AppData unmarshal(java.io.Reader)
+
+ /**
+ * Method validate
+ *
+ */
+ public void validate()
+ throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ } //-- void validate()
+
+}
--- /dev/null
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package org.vamsas.objects.core;
+
+ //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.mapping.AccessMode;
+import org.exolab.castor.xml.TypeValidator;
+import org.exolab.castor.xml.XMLFieldDescriptor;
+import org.exolab.castor.xml.validators.*;
+
+/**
+ * Class CommonDescriptor.
+ *
+ * @version $Revision$ $Date$
+ */
+public class CommonDescriptor extends org.vamsas.objects.core.AppDataDescriptor {
+
+
+ //--------------------------/
+ //- 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 CommonDescriptor()
+ {
+ super();
+ setExtendsWithoutFlatten(new org.vamsas.objects.core.AppDataDescriptor());
+ nsURI = "http://www.vamsas.org";
+ xmlName = "Common";
+ } //-- org.vamsas.objects.core.CommonDescriptor()
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ * Method getAccessMode
+ *
+ *
+ *
+ * @return AccessMode
+ */
+ public org.exolab.castor.mapping.AccessMode getAccessMode()
+ {
+ return null;
+ } //-- org.exolab.castor.mapping.AccessMode getAccessMode()
+
+ /**
+ * Method getExtends
+ *
+ *
+ *
+ * @return ClassDescriptor
+ */
+ public org.exolab.castor.mapping.ClassDescriptor getExtends()
+ {
+ return super.getExtends();
+ } //-- org.exolab.castor.mapping.ClassDescriptor getExtends()
+
+ /**
+ * Method getIdentity
+ *
+ *
+ *
+ * @return FieldDescriptor
+ */
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+ {
+ if (identity == null)
+ return super.getIdentity();
+ return identity;
+ } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity()
+
+ /**
+ * Method getJavaClass
+ *
+ *
+ *
+ * @return Class
+ */
+ public java.lang.Class getJavaClass()
+ {
+ return org.vamsas.objects.core.Common.class;
+ } //-- java.lang.Class getJavaClass()
+
+ /**
+ * Method getNameSpacePrefix
+ *
+ *
+ *
+ * @return String
+ */
+ public java.lang.String getNameSpacePrefix()
+ {
+ return nsPrefix;
+ } //-- java.lang.String getNameSpacePrefix()
+
+ /**
+ * Method getNameSpaceURI
+ *
+ *
+ *
+ * @return String
+ */
+ public java.lang.String getNameSpaceURI()
+ {
+ return nsURI;
+ } //-- java.lang.String getNameSpaceURI()
+
+ /**
+ * Method getValidator
+ *
+ *
+ *
+ * @return TypeValidator
+ */
+ public org.exolab.castor.xml.TypeValidator getValidator()
+ {
+ return this;
+ } //-- org.exolab.castor.xml.TypeValidator getValidator()
+
+ /**
+ * Method getXMLName
+ *
+ *
+ *
+ * @return String
+ */
+ public java.lang.String getXMLName()
+ {
+ return xmlName;
+ } //-- java.lang.String getXMLName()
+
+}
//--------------------------/
/**
- * Field _id
+ * Primary Key for vamsas object referencing
+ *
*/
private java.lang.String _id;
} //-- int getDataSetAnnotationsCount()
/**
- * Returns the value of field 'id'.
+ * Returns the value of field 'id'. The field 'id' has the
+ * following description: Primary Key for vamsas object
+ * referencing
+ *
*
* @return String
* @return the value of field 'id'.
} //-- void setDataSetAnnotations(org.vamsas.objects.core.DataSetAnnotations)
/**
- * Sets the value of field 'id'.
+ * Sets the value of field 'id'. The field 'id' has the
+ * following description: Primary Key for vamsas object
+ * referencing
+ *
*
* @param id the value of field 'id'.
*/
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;
*
* @version $Revision$ $Date$
*/
-public class DataSetAnnotations extends org.vamsas.client.Vobject
+public class DataSetAnnotations extends org.vamsas.objects.core.RangeAnnotation
implements java.io.Serializable
{
//--------------------------/
/**
- * Field _type
- */
- private java.lang.String _type;
-
- /**
- * Field _end
- */
- private int _end;
-
- /**
- * keeps track of state for field: _end
- */
- private boolean _has_end;
-
- /**
- * Field _begin
- */
- private int _begin;
-
- /**
- * keeps track of state for field: _begin
- */
- private boolean _has_begin;
-
- /**
- * Field _seqRef
+ * annotation is associated
+ * with a particular dataset
+ * sequence
+ *
*/
private java.lang.Object _seqRef;
/**
- * Field _id
- */
- private java.lang.String _id;
-
- /**
- * 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.objects.core.Provenance _provenance;
public DataSetAnnotations()
{
super();
- _annotationElementList = new Vector();
} //-- org.vamsas.objects.core.DataSetAnnotations()
//-----------/
/**
- * Method addAnnotationElement
- *
- *
- *
- * @param vAnnotationElement
- */
- public void addAnnotationElement(org.vamsas.objects.core.AnnotationElement vAnnotationElement)
- throws java.lang.IndexOutOfBoundsException
- {
- _annotationElementList.addElement(vAnnotationElement);
- } //-- void addAnnotationElement(org.vamsas.objects.core.AnnotationElement)
-
- /**
- * Method addAnnotationElement
- *
- *
- *
- * @param index
- * @param vAnnotationElement
- */
- public void addAnnotationElement(int index, org.vamsas.objects.core.AnnotationElement vAnnotationElement)
- throws java.lang.IndexOutOfBoundsException
- {
- _annotationElementList.insertElementAt(vAnnotationElement, index);
- } //-- void addAnnotationElement(int, org.vamsas.objects.core.AnnotationElement)
-
- /**
- * Method deleteBegin
- *
- */
- public void deleteBegin()
- {
- this._has_begin= false;
- } //-- void deleteBegin()
-
- /**
- * Method deleteEnd
- *
- */
- public void deleteEnd()
- {
- this._has_end= false;
- } //-- void deleteEnd()
-
- /**
- * Method enumerateAnnotationElement
- *
- *
- *
- * @return Enumeration
- */
- public java.util.Enumeration enumerateAnnotationElement()
- {
- return _annotationElementList.elements();
- } //-- java.util.Enumeration enumerateAnnotationElement()
-
- /**
* Note: hashCode() has not been overriden
*
* @param obj
if (obj instanceof DataSetAnnotations) {
DataSetAnnotations temp = (DataSetAnnotations)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 != temp._end)
- return false;
- if (this._has_end != temp._has_end)
- return false;
- if (this._begin != temp._begin)
- return false;
- if (this._has_begin != temp._has_begin)
- return false;
if (this._seqRef != null) {
if (temp._seqRef == null) return false;
else if (!(this._seqRef.equals(temp._seqRef)))
}
else if (temp._seqRef != null)
return false;
- if (this._id != null) {
- if (temp._id == null) return false;
- else if (!(this._id.equals(temp._id)))
- return false;
- }
- else if (temp._id != null)
- return false;
- if (this._description != null) {
- if (temp._description == null) return false;
- else if (!(this._description.equals(temp._description)))
- 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)))
} //-- boolean equals(java.lang.Object)
/**
- * Method getAnnotationElement
- *
- *
- *
- * @param index
- * @return AnnotationElement
- */
- public org.vamsas.objects.core.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.objects.core.AnnotationElement) _annotationElementList.elementAt(index);
- } //-- org.vamsas.objects.core.AnnotationElement getAnnotationElement(int)
-
- /**
- * Method getAnnotationElement
- *
- *
- *
- * @return AnnotationElement
- */
- public org.vamsas.objects.core.AnnotationElement[] getAnnotationElement()
- {
- int size = _annotationElementList.size();
- org.vamsas.objects.core.AnnotationElement[] mArray = new org.vamsas.objects.core.AnnotationElement[size];
- for (int index = 0; index < size; index++) {
- mArray[index] = (org.vamsas.objects.core.AnnotationElement) _annotationElementList.elementAt(index);
- }
- return mArray;
- } //-- org.vamsas.objects.core.AnnotationElement[] getAnnotationElement()
-
- /**
- * Method getAnnotationElementCount
- *
- *
- *
- * @return int
- */
- public int getAnnotationElementCount()
- {
- return _annotationElementList.size();
- } //-- int getAnnotationElementCount()
-
- /**
- * Returns the value of field 'begin'.
- *
- * @return int
- * @return the value of field 'begin'.
- */
- public int getBegin()
- {
- return this._begin;
- } //-- int 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 int
- * @return the value of field 'end'.
- */
- public int getEnd()
- {
- return this._end;
- } //-- int getEnd()
-
- /**
- * Returns the value of field 'id'.
- *
- * @return String
- * @return the value of field 'id'.
- */
- public java.lang.String getId()
- {
- return this._id;
- } //-- java.lang.String getId()
-
- /**
* Returns the value of field 'provenance'.
*
* @return Provenance
} //-- org.vamsas.objects.core.Provenance getProvenance()
/**
- * Returns the value of field 'seqRef'.
+ * Returns the value of field 'seqRef'. The field 'seqRef' has
+ * the following description: annotation is associated
+ * with a particular dataset
+ * sequence
+ *
*
* @return Object
* @return the value of field '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 hasBegin
- *
- *
- *
- * @return boolean
- */
- public boolean hasBegin()
- {
- return this._has_begin;
- } //-- boolean hasBegin()
-
- /**
- * Method hasEnd
- *
- *
- *
- * @return boolean
- */
- public boolean hasEnd()
- {
- return this._has_end;
- } //-- boolean hasEnd()
-
- /**
* Method isValid
*
*
} //-- void marshal(org.xml.sax.ContentHandler)
/**
- * Method removeAllAnnotationElement
- *
- */
- public void removeAllAnnotationElement()
- {
- _annotationElementList.removeAllElements();
- } //-- void removeAllAnnotationElement()
-
- /**
- * Method removeAnnotationElement
- *
- *
- *
- * @param index
- * @return AnnotationElement
- */
- public org.vamsas.objects.core.AnnotationElement removeAnnotationElement(int index)
- {
- java.lang.Object obj = _annotationElementList.elementAt(index);
- _annotationElementList.removeElementAt(index);
- return (org.vamsas.objects.core.AnnotationElement) obj;
- } //-- org.vamsas.objects.core.AnnotationElement removeAnnotationElement(int)
-
- /**
- * Method setAnnotationElement
- *
- *
- *
- * @param index
- * @param vAnnotationElement
- */
- public void setAnnotationElement(int index, org.vamsas.objects.core.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.objects.core.AnnotationElement)
-
- /**
- * Method setAnnotationElement
- *
- *
- *
- * @param annotationElementArray
- */
- public void setAnnotationElement(org.vamsas.objects.core.AnnotationElement[] annotationElementArray)
- {
- //-- copy array
- _annotationElementList.removeAllElements();
- for (int i = 0; i < annotationElementArray.length; i++) {
- _annotationElementList.addElement(annotationElementArray[i]);
- }
- } //-- void setAnnotationElement(org.vamsas.objects.core.AnnotationElement)
-
- /**
- * Sets the value of field 'begin'.
- *
- * @param begin the value of field 'begin'.
- */
- public void setBegin(int begin)
- {
- this._begin = begin;
- this._has_begin = true;
- } //-- void setBegin(int)
-
- /**
- * 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(int end)
- {
- this._end = end;
- this._has_end = true;
- } //-- void setEnd(int)
-
- /**
- * Sets the value of field 'id'.
- *
- * @param id the value of field 'id'.
- */
- public void setId(java.lang.String id)
- {
- this._id = id;
- } //-- void setId(java.lang.String)
-
- /**
* Sets the value of field 'provenance'.
*
* @param provenance the value of field 'provenance'.
} //-- void setProvenance(org.vamsas.objects.core.Provenance)
/**
- * Sets the value of field 'seqRef'.
+ * Sets the value of field 'seqRef'. The field 'seqRef' has the
+ * following description: annotation is associated
+ * with a particular dataset
+ * sequence
+ *
*
* @param seqRef the value of field '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 DataSetAnnotations
+ * @return RangeType
*/
- public static org.vamsas.objects.core.DataSetAnnotations unmarshal(java.io.Reader reader)
+ public static org.vamsas.objects.core.RangeType unmarshal(java.io.Reader reader)
throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
{
return (org.vamsas.objects.core.DataSetAnnotations) Unmarshaller.unmarshal(org.vamsas.objects.core.DataSetAnnotations.class, reader);
- } //-- org.vamsas.objects.core.DataSetAnnotations unmarshal(java.io.Reader)
+ } //-- org.vamsas.objects.core.RangeType unmarshal(java.io.Reader)
/**
* Method validate
*
* @version $Revision$ $Date$
*/
-public class DataSetAnnotationsDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
+public class DataSetAnnotationsDescriptor extends org.vamsas.objects.core.RangeAnnotationDescriptor {
//--------------------------/
public DataSetAnnotationsDescriptor()
{
super();
+ setExtendsWithoutFlatten(new org.vamsas.objects.core.RangeAnnotationDescriptor());
nsURI = "http://www.vamsas.org";
xmlName = "DataSetAnnotations";
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
- {
- DataSetAnnotations target = (DataSetAnnotations) object;
- return target.getType();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- DataSetAnnotations target = (DataSetAnnotations) 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.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
- {
- DataSetAnnotations target = (DataSetAnnotations) 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 {
- DataSetAnnotations target = (DataSetAnnotations) 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);
- //-- _begin
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_begin", "begin", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- DataSetAnnotations target = (DataSetAnnotations) object;
- if(!target.hasBegin())
- return null;
- return new java.lang.Integer(target.getBegin());
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- DataSetAnnotations target = (DataSetAnnotations) object;
- // ignore null values for non optional primitives
- if (value == null) return;
-
- target.setBegin( ((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: _begin
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(1);
- { //-- local scope
- IntegerValidator typeValidator = new IntegerValidator();
- 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);
{ //-- local scope
}
desc.setValidator(fieldValidator);
- //-- _id
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute);
- this.identity = desc;
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- DataSetAnnotations target = (DataSetAnnotations) object;
- return target.getId();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- DataSetAnnotations target = (DataSetAnnotations) object;
- target.setId( (java.lang.String) value);
- }
- catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance( java.lang.Object parent ) {
- return new java.lang.String();
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _id
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- }
- desc.setValidator(fieldValidator);
//-- initialize element descriptors
- //-- _description
- 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
- {
- DataSetAnnotations target = (DataSetAnnotations) object;
- return target.getDescription();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- DataSetAnnotations target = (DataSetAnnotations) 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
- {
- DataSetAnnotations target = (DataSetAnnotations) object;
- return target.getStatus();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- DataSetAnnotations target = (DataSetAnnotations) 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.objects.core.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
- {
- DataSetAnnotations target = (DataSetAnnotations) object;
- return target.getAnnotationElement();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- DataSetAnnotations target = (DataSetAnnotations) object;
- target.addAnnotationElement( (org.vamsas.objects.core.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.objects.core.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.objects.core.Provenance.class, "_provenance", "Provenance", org.exolab.castor.xml.NodeType.Element);
handler = new org.exolab.castor.xml.XMLFieldHandler() {
*/
public org.exolab.castor.mapping.ClassDescriptor getExtends()
{
- return null;
+ return super.getExtends();
} //-- org.exolab.castor.mapping.ClassDescriptor getExtends()
/**
*/
public org.exolab.castor.mapping.FieldDescriptor getIdentity()
{
+ if (identity == null)
+ return super.getIdentity();
return identity;
} //-- org.exolab.castor.mapping.FieldDescriptor getIdentity()
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.xml.sax.ContentHandler;
/**
- * Class DbRef.
+ * Store a list of database
+ * references for this
+ * sequence record - with
+ * optional mapping from
+ * database sequence to the
+ * given sequence record
+ *
*
* @version $Revision$ $Date$
*/
//--------------------------/
/**
- * Field _source
+ * TODO Database
+ * Naming
+ * Convention:
+ * either start
+ * using LSID (so
+ * change type to
+ * URI) or leave
+ * this as an
+ * uncontrolled/unspecified
+ * string ID
+ *
*/
private java.lang.String _source;
/**
- * Field _version
+ * Version must be
+ * specified -
+ *
*/
private java.lang.String _version;
/**
- * Field _accessionId
+ * TODO: make some
+ * specification of
+ * the database
+ * field from which
+ * this accessionId
+ * is taken from -
+ * should that be a
+ * special property
+ * of the dbRef
+ * object ?
+ *
*/
private java.lang.String _accessionId;
/**
- * Field _id
+ * Primary Key for
+ * vamsas object
+ * referencing
+ *
*/
private java.lang.String _id;
+ /**
+ * Field _mapList
+ */
+ private java.util.Vector _mapList;
+
+ /**
+ * Field _linkList
+ */
+ private java.util.Vector _linkList;
+
+ /**
+ * Field _propertyList
+ */
+ private java.util.Vector _propertyList;
+
//----------------/
//- Constructors -/
public DbRef()
{
super();
+ _mapList = new Vector();
+ _linkList = new Vector();
+ _propertyList = new Vector();
} //-- org.vamsas.objects.core.DbRef()
//-----------/
/**
+ * Method addLink
+ *
+ *
+ *
+ * @param vLink
+ */
+ public void addLink(org.vamsas.objects.core.Link vLink)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _linkList.addElement(vLink);
+ } //-- void addLink(org.vamsas.objects.core.Link)
+
+ /**
+ * Method addLink
+ *
+ *
+ *
+ * @param index
+ * @param vLink
+ */
+ public void addLink(int index, org.vamsas.objects.core.Link vLink)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _linkList.insertElementAt(vLink, index);
+ } //-- void addLink(int, org.vamsas.objects.core.Link)
+
+ /**
+ * Method addMap
+ *
+ *
+ *
+ * @param vMap
+ */
+ public void addMap(org.vamsas.objects.core.Map vMap)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _mapList.addElement(vMap);
+ } //-- void addMap(org.vamsas.objects.core.Map)
+
+ /**
+ * Method addMap
+ *
+ *
+ *
+ * @param index
+ * @param vMap
+ */
+ public void addMap(int index, org.vamsas.objects.core.Map vMap)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _mapList.insertElementAt(vMap, index);
+ } //-- void addMap(int, org.vamsas.objects.core.Map)
+
+ /**
+ * Method addProperty
+ *
+ *
+ *
+ * @param vProperty
+ */
+ public void addProperty(org.vamsas.objects.core.Property vProperty)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _propertyList.addElement(vProperty);
+ } //-- void addProperty(org.vamsas.objects.core.Property)
+
+ /**
+ * Method addProperty
+ *
+ *
+ *
+ * @param index
+ * @param vProperty
+ */
+ public void addProperty(int index, org.vamsas.objects.core.Property vProperty)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _propertyList.insertElementAt(vProperty, index);
+ } //-- void addProperty(int, org.vamsas.objects.core.Property)
+
+ /**
+ * Method enumerateLink
+ *
+ *
+ *
+ * @return Enumeration
+ */
+ public java.util.Enumeration enumerateLink()
+ {
+ return _linkList.elements();
+ } //-- java.util.Enumeration enumerateLink()
+
+ /**
+ * Method enumerateMap
+ *
+ *
+ *
+ * @return Enumeration
+ */
+ public java.util.Enumeration enumerateMap()
+ {
+ return _mapList.elements();
+ } //-- java.util.Enumeration enumerateMap()
+
+ /**
+ * Method enumerateProperty
+ *
+ *
+ *
+ * @return Enumeration
+ */
+ public java.util.Enumeration enumerateProperty()
+ {
+ return _propertyList.elements();
+ } //-- java.util.Enumeration enumerateProperty()
+
+ /**
* Note: hashCode() has not been overriden
*
* @param obj
}
else if (temp._id != null)
return false;
+ if (this._mapList != null) {
+ if (temp._mapList == null) return false;
+ else if (!(this._mapList.equals(temp._mapList)))
+ return false;
+ }
+ else if (temp._mapList != null)
+ return false;
+ if (this._linkList != null) {
+ if (temp._linkList == null) return false;
+ else if (!(this._linkList.equals(temp._linkList)))
+ return false;
+ }
+ else if (temp._linkList != null)
+ return false;
+ if (this._propertyList != null) {
+ if (temp._propertyList == null) return false;
+ else if (!(this._propertyList.equals(temp._propertyList)))
+ return false;
+ }
+ else if (temp._propertyList != null)
+ return false;
return true;
}
return false;
} //-- boolean equals(java.lang.Object)
/**
- * Returns the value of field 'accessionId'.
+ * Returns the value of field 'accessionId'. The field
+ * 'accessionId' has the following description: TODO: make some
+ * specification of
+ * the database
+ * field from which
+ * this accessionId
+ * is taken from -
+ * should that be a
+ * special property
+ * of the dbRef
+ * object ?
+ *
*
* @return String
* @return the value of field 'accessionId'.
} //-- java.lang.String getAccessionId()
/**
- * Returns the value of field 'id'.
+ * Returns the value of field 'id'. The field 'id' has the
+ * following description: Primary Key for
+ * vamsas object
+ * referencing
+ *
*
* @return String
* @return the value of field 'id'.
} //-- java.lang.String getId()
/**
- * Returns the value of field 'source'.
+ * Method getLink
+ *
+ *
+ *
+ * @param index
+ * @return Link
+ */
+ public org.vamsas.objects.core.Link getLink(int index)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ //-- check bounds for index
+ if ((index < 0) || (index > _linkList.size())) {
+ throw new IndexOutOfBoundsException("getLink: Index value '"+index+"' not in range [0.."+_linkList.size()+ "]");
+ }
+
+ return (org.vamsas.objects.core.Link) _linkList.elementAt(index);
+ } //-- org.vamsas.objects.core.Link getLink(int)
+
+ /**
+ * Method getLink
+ *
+ *
+ *
+ * @return Link
+ */
+ public org.vamsas.objects.core.Link[] getLink()
+ {
+ int size = _linkList.size();
+ org.vamsas.objects.core.Link[] mArray = new org.vamsas.objects.core.Link[size];
+ for (int index = 0; index < size; index++) {
+ mArray[index] = (org.vamsas.objects.core.Link) _linkList.elementAt(index);
+ }
+ return mArray;
+ } //-- org.vamsas.objects.core.Link[] getLink()
+
+ /**
+ * Method getLinkCount
+ *
+ *
+ *
+ * @return int
+ */
+ public int getLinkCount()
+ {
+ return _linkList.size();
+ } //-- int getLinkCount()
+
+ /**
+ * Method getMap
+ *
+ *
+ *
+ * @param index
+ * @return Map
+ */
+ public org.vamsas.objects.core.Map getMap(int index)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ //-- check bounds for index
+ if ((index < 0) || (index > _mapList.size())) {
+ throw new IndexOutOfBoundsException("getMap: Index value '"+index+"' not in range [0.."+_mapList.size()+ "]");
+ }
+
+ return (org.vamsas.objects.core.Map) _mapList.elementAt(index);
+ } //-- org.vamsas.objects.core.Map getMap(int)
+
+ /**
+ * Method getMap
+ *
+ *
+ *
+ * @return Map
+ */
+ public org.vamsas.objects.core.Map[] getMap()
+ {
+ int size = _mapList.size();
+ org.vamsas.objects.core.Map[] mArray = new org.vamsas.objects.core.Map[size];
+ for (int index = 0; index < size; index++) {
+ mArray[index] = (org.vamsas.objects.core.Map) _mapList.elementAt(index);
+ }
+ return mArray;
+ } //-- org.vamsas.objects.core.Map[] getMap()
+
+ /**
+ * Method getMapCount
+ *
+ *
+ *
+ * @return int
+ */
+ public int getMapCount()
+ {
+ return _mapList.size();
+ } //-- int getMapCount()
+
+ /**
+ * Method getProperty
+ *
+ *
+ *
+ * @param index
+ * @return Property
+ */
+ public org.vamsas.objects.core.Property getProperty(int index)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ //-- check bounds for index
+ if ((index < 0) || (index > _propertyList.size())) {
+ throw new IndexOutOfBoundsException("getProperty: Index value '"+index+"' not in range [0.."+_propertyList.size()+ "]");
+ }
+
+ return (org.vamsas.objects.core.Property) _propertyList.elementAt(index);
+ } //-- org.vamsas.objects.core.Property getProperty(int)
+
+ /**
+ * Method getProperty
+ *
+ *
+ *
+ * @return Property
+ */
+ public org.vamsas.objects.core.Property[] getProperty()
+ {
+ int size = _propertyList.size();
+ org.vamsas.objects.core.Property[] mArray = new org.vamsas.objects.core.Property[size];
+ for (int index = 0; index < size; index++) {
+ mArray[index] = (org.vamsas.objects.core.Property) _propertyList.elementAt(index);
+ }
+ return mArray;
+ } //-- org.vamsas.objects.core.Property[] getProperty()
+
+ /**
+ * Method getPropertyCount
+ *
+ *
+ *
+ * @return int
+ */
+ public int getPropertyCount()
+ {
+ return _propertyList.size();
+ } //-- int getPropertyCount()
+
+ /**
+ * Returns the value of field 'source'. The field 'source' has
+ * the following description: TODO Database
+ * Naming
+ * Convention:
+ * either start
+ * using LSID (so
+ * change type to
+ * URI) or leave
+ * this as an
+ * uncontrolled/unspecified
+ * string ID
+ *
*
* @return String
* @return the value of field 'source'.
} //-- java.lang.String getSource()
/**
- * Returns the value of field 'version'.
+ * Returns the value of field 'version'. The field 'version'
+ * has the following description: Version must be
+ * specified -
+ *
*
* @return String
* @return the value of field 'version'.
} //-- void marshal(org.xml.sax.ContentHandler)
/**
- * Sets the value of field 'accessionId'.
+ * Method removeAllLink
+ *
+ */
+ public void removeAllLink()
+ {
+ _linkList.removeAllElements();
+ } //-- void removeAllLink()
+
+ /**
+ * Method removeAllMap
+ *
+ */
+ public void removeAllMap()
+ {
+ _mapList.removeAllElements();
+ } //-- void removeAllMap()
+
+ /**
+ * Method removeAllProperty
+ *
+ */
+ public void removeAllProperty()
+ {
+ _propertyList.removeAllElements();
+ } //-- void removeAllProperty()
+
+ /**
+ * Method removeLink
+ *
+ *
+ *
+ * @param index
+ * @return Link
+ */
+ public org.vamsas.objects.core.Link removeLink(int index)
+ {
+ java.lang.Object obj = _linkList.elementAt(index);
+ _linkList.removeElementAt(index);
+ return (org.vamsas.objects.core.Link) obj;
+ } //-- org.vamsas.objects.core.Link removeLink(int)
+
+ /**
+ * Method removeMap
+ *
+ *
+ *
+ * @param index
+ * @return Map
+ */
+ public org.vamsas.objects.core.Map removeMap(int index)
+ {
+ java.lang.Object obj = _mapList.elementAt(index);
+ _mapList.removeElementAt(index);
+ return (org.vamsas.objects.core.Map) obj;
+ } //-- org.vamsas.objects.core.Map removeMap(int)
+
+ /**
+ * Method removeProperty
+ *
+ *
+ *
+ * @param index
+ * @return Property
+ */
+ public org.vamsas.objects.core.Property removeProperty(int index)
+ {
+ java.lang.Object obj = _propertyList.elementAt(index);
+ _propertyList.removeElementAt(index);
+ return (org.vamsas.objects.core.Property) obj;
+ } //-- org.vamsas.objects.core.Property removeProperty(int)
+
+ /**
+ * Sets the value of field 'accessionId'. The field
+ * 'accessionId' has the following description: TODO: make some
+ * specification of
+ * the database
+ * field from which
+ * this accessionId
+ * is taken from -
+ * should that be a
+ * special property
+ * of the dbRef
+ * object ?
+ *
*
* @param accessionId the value of field 'accessionId'.
*/
} //-- void setAccessionId(java.lang.String)
/**
- * Sets the value of field 'id'.
+ * Sets the value of field 'id'. The field 'id' has the
+ * following description: Primary Key for
+ * vamsas object
+ * referencing
+ *
*
* @param id the value of field 'id'.
*/
} //-- void setId(java.lang.String)
/**
- * Sets the value of field 'source'.
+ * Method setLink
+ *
+ *
+ *
+ * @param index
+ * @param vLink
+ */
+ public void setLink(int index, org.vamsas.objects.core.Link vLink)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ //-- check bounds for index
+ if ((index < 0) || (index > _linkList.size())) {
+ throw new IndexOutOfBoundsException("setLink: Index value '"+index+"' not in range [0.."+_linkList.size()+ "]");
+ }
+ _linkList.setElementAt(vLink, index);
+ } //-- void setLink(int, org.vamsas.objects.core.Link)
+
+ /**
+ * Method setLink
+ *
+ *
+ *
+ * @param linkArray
+ */
+ public void setLink(org.vamsas.objects.core.Link[] linkArray)
+ {
+ //-- copy array
+ _linkList.removeAllElements();
+ for (int i = 0; i < linkArray.length; i++) {
+ _linkList.addElement(linkArray[i]);
+ }
+ } //-- void setLink(org.vamsas.objects.core.Link)
+
+ /**
+ * Method setMap
+ *
+ *
+ *
+ * @param index
+ * @param vMap
+ */
+ public void setMap(int index, org.vamsas.objects.core.Map vMap)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ //-- check bounds for index
+ if ((index < 0) || (index > _mapList.size())) {
+ throw new IndexOutOfBoundsException("setMap: Index value '"+index+"' not in range [0.."+_mapList.size()+ "]");
+ }
+ _mapList.setElementAt(vMap, index);
+ } //-- void setMap(int, org.vamsas.objects.core.Map)
+
+ /**
+ * Method setMap
+ *
+ *
+ *
+ * @param mapArray
+ */
+ public void setMap(org.vamsas.objects.core.Map[] mapArray)
+ {
+ //-- copy array
+ _mapList.removeAllElements();
+ for (int i = 0; i < mapArray.length; i++) {
+ _mapList.addElement(mapArray[i]);
+ }
+ } //-- void setMap(org.vamsas.objects.core.Map)
+
+ /**
+ * Method setProperty
+ *
+ *
+ *
+ * @param index
+ * @param vProperty
+ */
+ public void setProperty(int index, org.vamsas.objects.core.Property vProperty)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ //-- check bounds for index
+ if ((index < 0) || (index > _propertyList.size())) {
+ throw new IndexOutOfBoundsException("setProperty: Index value '"+index+"' not in range [0.."+_propertyList.size()+ "]");
+ }
+ _propertyList.setElementAt(vProperty, index);
+ } //-- void setProperty(int, org.vamsas.objects.core.Property)
+
+ /**
+ * Method setProperty
+ *
+ *
+ *
+ * @param propertyArray
+ */
+ public void setProperty(org.vamsas.objects.core.Property[] propertyArray)
+ {
+ //-- copy array
+ _propertyList.removeAllElements();
+ for (int i = 0; i < propertyArray.length; i++) {
+ _propertyList.addElement(propertyArray[i]);
+ }
+ } //-- void setProperty(org.vamsas.objects.core.Property)
+
+ /**
+ * Sets the value of field 'source'. The field 'source' has the
+ * following description: TODO Database
+ * Naming
+ * Convention:
+ * either start
+ * using LSID (so
+ * change type to
+ * URI) or leave
+ * this as an
+ * uncontrolled/unspecified
+ * string ID
+ *
*
* @param source the value of field 'source'.
*/
} //-- void setSource(java.lang.String)
/**
- * Sets the value of field 'version'.
+ * Sets the value of field 'version'. The field 'version' has
+ * the following description: Version must be
+ * specified -
+ *
*
* @param version the value of field 'version'.
*/
super();
nsURI = "http://www.vamsas.org";
xmlName = "dbRef";
+
+ //-- 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;
}
};
desc.setHandler(handler);
+ desc.setRequired(true);
desc.setMultivalued(false);
addFieldDescriptor(desc);
//-- validation code for: _source
fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(1);
{ //-- local scope
StringValidator typeValidator = new StringValidator();
typeValidator.setWhiteSpace("preserve");
}
};
desc.setHandler(handler);
+ desc.setRequired(true);
desc.setMultivalued(false);
addFieldDescriptor(desc);
//-- validation code for: _version
fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(1);
{ //-- local scope
StringValidator typeValidator = new StringValidator();
typeValidator.setWhiteSpace("preserve");
}
};
desc.setHandler(handler);
+ desc.setRequired(true);
desc.setMultivalued(false);
addFieldDescriptor(desc);
//-- validation code for: _accessionId
fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(1);
{ //-- local scope
StringValidator typeValidator = new StringValidator();
typeValidator.setWhiteSpace("preserve");
desc.setValidator(fieldValidator);
//-- initialize element descriptors
+ //-- _mapList
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Map.class, "_mapList", "map", org.exolab.castor.xml.NodeType.Element);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ DbRef target = (DbRef) object;
+ return target.getMap();
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ DbRef target = (DbRef) object;
+ target.addMap( (org.vamsas.objects.core.Map) value);
+ }
+ catch (java.lang.Exception ex) {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+ public java.lang.Object newInstance( java.lang.Object parent ) {
+ return new org.vamsas.objects.core.Map();
+ }
+ };
+ desc.setHandler(handler);
+ desc.setNameSpaceURI("http://www.vamsas.org");
+ desc.setMultivalued(true);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _mapList
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(0);
+ { //-- local scope
+ }
+ desc.setValidator(fieldValidator);
+ //-- _linkList
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Link.class, "_linkList", "link", org.exolab.castor.xml.NodeType.Element);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ DbRef target = (DbRef) object;
+ return target.getLink();
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ DbRef target = (DbRef) object;
+ target.addLink( (org.vamsas.objects.core.Link) value);
+ }
+ catch (java.lang.Exception ex) {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+ public java.lang.Object newInstance( java.lang.Object parent ) {
+ return new org.vamsas.objects.core.Link();
+ }
+ };
+ desc.setHandler(handler);
+ desc.setNameSpaceURI("http://www.vamsas.org");
+ desc.setMultivalued(true);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _linkList
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(0);
+ { //-- local scope
+ }
+ desc.setValidator(fieldValidator);
+ //-- _propertyList
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Property.class, "_propertyList", "property", org.exolab.castor.xml.NodeType.Element);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ DbRef target = (DbRef) object;
+ return target.getProperty();
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ DbRef target = (DbRef) object;
+ target.addProperty( (org.vamsas.objects.core.Property) value);
+ }
+ catch (java.lang.Exception ex) {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+ public java.lang.Object newInstance( java.lang.Object parent ) {
+ return new org.vamsas.objects.core.Property();
+ }
+ };
+ desc.setHandler(handler);
+ desc.setNameSpaceURI("http://www.vamsas.org");
+ desc.setMultivalued(true);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _propertyList
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(0);
+ { //-- local scope
+ }
+ desc.setValidator(fieldValidator);
} //-- org.vamsas.objects.core.DbRefDescriptor()
import java.io.Reader;
import java.io.Serializable;
import java.io.Writer;
+import java.util.Enumeration;
+import java.util.Vector;
import org.exolab.castor.xml.MarshalException;
import org.exolab.castor.xml.Marshaller;
import org.exolab.castor.xml.Unmarshaller;
//--------------------------/
/**
- * Field _id
+ * Primary Key for vamsas object
+ * referencing
+ *
*/
private java.lang.String _id;
/**
- * Field _user
+ * Who
+ *
*/
private java.lang.String _user;
/**
- * Field _action
+ * With which application
+ *
+ */
+ private java.lang.String _app;
+
+ /**
+ * Did what
+ *
*/
private java.lang.String _action;
/**
- * Field _date
+ * When
+ *
*/
private org.exolab.castor.types.Date _date;
+ /**
+ * additional information
+ *
+ */
+ private java.util.Vector _propertyList;
+
+ /**
+ * parameter for the action
+ *
+ */
+ private java.util.Vector _paramList;
+
+ /**
+ * bioinformatic objects input to
+ * action
+ *
+ */
+ private java.util.Vector _inputList;
+
//----------------/
//- Constructors -/
public Entry()
{
super();
+ _propertyList = new Vector();
+ _paramList = new Vector();
+ _inputList = new Vector();
} //-- org.vamsas.objects.core.Entry()
//-----------/
/**
+ * Method addInput
+ *
+ *
+ *
+ * @param vInput
+ */
+ public void addInput(org.vamsas.objects.core.Input vInput)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _inputList.addElement(vInput);
+ } //-- void addInput(org.vamsas.objects.core.Input)
+
+ /**
+ * Method addInput
+ *
+ *
+ *
+ * @param index
+ * @param vInput
+ */
+ public void addInput(int index, org.vamsas.objects.core.Input vInput)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _inputList.insertElementAt(vInput, index);
+ } //-- void addInput(int, org.vamsas.objects.core.Input)
+
+ /**
+ * Method addParam
+ *
+ *
+ *
+ * @param vParam
+ */
+ public void addParam(org.vamsas.objects.core.Param vParam)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _paramList.addElement(vParam);
+ } //-- void addParam(org.vamsas.objects.core.Param)
+
+ /**
+ * Method addParam
+ *
+ *
+ *
+ * @param index
+ * @param vParam
+ */
+ public void addParam(int index, org.vamsas.objects.core.Param vParam)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _paramList.insertElementAt(vParam, index);
+ } //-- void addParam(int, org.vamsas.objects.core.Param)
+
+ /**
+ * Method addProperty
+ *
+ *
+ *
+ * @param vProperty
+ */
+ public void addProperty(org.vamsas.objects.core.Property vProperty)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _propertyList.addElement(vProperty);
+ } //-- void addProperty(org.vamsas.objects.core.Property)
+
+ /**
+ * Method addProperty
+ *
+ *
+ *
+ * @param index
+ * @param vProperty
+ */
+ public void addProperty(int index, org.vamsas.objects.core.Property vProperty)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _propertyList.insertElementAt(vProperty, index);
+ } //-- void addProperty(int, org.vamsas.objects.core.Property)
+
+ /**
+ * Method enumerateInput
+ *
+ *
+ *
+ * @return Enumeration
+ */
+ public java.util.Enumeration enumerateInput()
+ {
+ return _inputList.elements();
+ } //-- java.util.Enumeration enumerateInput()
+
+ /**
+ * Method enumerateParam
+ *
+ *
+ *
+ * @return Enumeration
+ */
+ public java.util.Enumeration enumerateParam()
+ {
+ return _paramList.elements();
+ } //-- java.util.Enumeration enumerateParam()
+
+ /**
+ * Method enumerateProperty
+ *
+ *
+ *
+ * @return Enumeration
+ */
+ public java.util.Enumeration enumerateProperty()
+ {
+ return _propertyList.elements();
+ } //-- java.util.Enumeration enumerateProperty()
+
+ /**
* Note: hashCode() has not been overriden
*
* @param obj
}
else if (temp._user != null)
return false;
+ if (this._app != null) {
+ if (temp._app == null) return false;
+ else if (!(this._app.equals(temp._app)))
+ return false;
+ }
+ else if (temp._app != null)
+ return false;
if (this._action != null) {
if (temp._action == null) return false;
else if (!(this._action.equals(temp._action)))
}
else if (temp._date != null)
return false;
+ if (this._propertyList != null) {
+ if (temp._propertyList == null) return false;
+ else if (!(this._propertyList.equals(temp._propertyList)))
+ return false;
+ }
+ else if (temp._propertyList != null)
+ return false;
+ if (this._paramList != null) {
+ if (temp._paramList == null) return false;
+ else if (!(this._paramList.equals(temp._paramList)))
+ return false;
+ }
+ else if (temp._paramList != null)
+ return false;
+ if (this._inputList != null) {
+ if (temp._inputList == null) return false;
+ else if (!(this._inputList.equals(temp._inputList)))
+ return false;
+ }
+ else if (temp._inputList != null)
+ return false;
return true;
}
return false;
} //-- boolean equals(java.lang.Object)
/**
- * Returns the value of field 'action'.
+ * Returns the value of field 'action'. The field 'action' has
+ * the following description: Did what
+ *
*
* @return String
* @return the value of field 'action'.
} //-- java.lang.String getAction()
/**
- * Returns the value of field 'date'.
+ * Returns the value of field 'app'. The field 'app' has the
+ * following description: With which application
+ *
+ *
+ * @return String
+ * @return the value of field 'app'.
+ */
+ public java.lang.String getApp()
+ {
+ return this._app;
+ } //-- java.lang.String getApp()
+
+ /**
+ * Returns the value of field 'date'. The field 'date' has the
+ * following description: When
+ *
*
* @return Date
* @return the value of field 'date'.
} //-- org.exolab.castor.types.Date getDate()
/**
- * Returns the value of field 'id'.
+ * Returns the value of field 'id'. The field 'id' has the
+ * following description: Primary Key for vamsas object
+ * referencing
+ *
*
* @return String
* @return the value of field 'id'.
} //-- java.lang.String getId()
/**
- * Returns the value of field 'user'.
+ * Method getInput
+ *
+ *
+ *
+ * @param index
+ * @return Input
+ */
+ public org.vamsas.objects.core.Input getInput(int index)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ //-- check bounds for index
+ if ((index < 0) || (index > _inputList.size())) {
+ throw new IndexOutOfBoundsException("getInput: Index value '"+index+"' not in range [0.."+_inputList.size()+ "]");
+ }
+
+ return (org.vamsas.objects.core.Input) _inputList.elementAt(index);
+ } //-- org.vamsas.objects.core.Input getInput(int)
+
+ /**
+ * Method getInput
+ *
+ *
+ *
+ * @return Input
+ */
+ public org.vamsas.objects.core.Input[] getInput()
+ {
+ int size = _inputList.size();
+ org.vamsas.objects.core.Input[] mArray = new org.vamsas.objects.core.Input[size];
+ for (int index = 0; index < size; index++) {
+ mArray[index] = (org.vamsas.objects.core.Input) _inputList.elementAt(index);
+ }
+ return mArray;
+ } //-- org.vamsas.objects.core.Input[] getInput()
+
+ /**
+ * Method getInputCount
+ *
+ *
+ *
+ * @return int
+ */
+ public int getInputCount()
+ {
+ return _inputList.size();
+ } //-- int getInputCount()
+
+ /**
+ * Method getParam
+ *
+ *
+ *
+ * @param index
+ * @return Param
+ */
+ public org.vamsas.objects.core.Param getParam(int index)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ //-- check bounds for index
+ if ((index < 0) || (index > _paramList.size())) {
+ throw new IndexOutOfBoundsException("getParam: Index value '"+index+"' not in range [0.."+_paramList.size()+ "]");
+ }
+
+ return (org.vamsas.objects.core.Param) _paramList.elementAt(index);
+ } //-- org.vamsas.objects.core.Param getParam(int)
+
+ /**
+ * Method getParam
+ *
+ *
+ *
+ * @return Param
+ */
+ public org.vamsas.objects.core.Param[] getParam()
+ {
+ int size = _paramList.size();
+ org.vamsas.objects.core.Param[] mArray = new org.vamsas.objects.core.Param[size];
+ for (int index = 0; index < size; index++) {
+ mArray[index] = (org.vamsas.objects.core.Param) _paramList.elementAt(index);
+ }
+ return mArray;
+ } //-- org.vamsas.objects.core.Param[] getParam()
+
+ /**
+ * Method getParamCount
+ *
+ *
+ *
+ * @return int
+ */
+ public int getParamCount()
+ {
+ return _paramList.size();
+ } //-- int getParamCount()
+
+ /**
+ * Method getProperty
+ *
+ *
+ *
+ * @param index
+ * @return Property
+ */
+ public org.vamsas.objects.core.Property getProperty(int index)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ //-- check bounds for index
+ if ((index < 0) || (index > _propertyList.size())) {
+ throw new IndexOutOfBoundsException("getProperty: Index value '"+index+"' not in range [0.."+_propertyList.size()+ "]");
+ }
+
+ return (org.vamsas.objects.core.Property) _propertyList.elementAt(index);
+ } //-- org.vamsas.objects.core.Property getProperty(int)
+
+ /**
+ * Method getProperty
+ *
+ *
+ *
+ * @return Property
+ */
+ public org.vamsas.objects.core.Property[] getProperty()
+ {
+ int size = _propertyList.size();
+ org.vamsas.objects.core.Property[] mArray = new org.vamsas.objects.core.Property[size];
+ for (int index = 0; index < size; index++) {
+ mArray[index] = (org.vamsas.objects.core.Property) _propertyList.elementAt(index);
+ }
+ return mArray;
+ } //-- org.vamsas.objects.core.Property[] getProperty()
+
+ /**
+ * Method getPropertyCount
+ *
+ *
+ *
+ * @return int
+ */
+ public int getPropertyCount()
+ {
+ return _propertyList.size();
+ } //-- int getPropertyCount()
+
+ /**
+ * Returns the value of field 'user'. The field 'user' has the
+ * following description: Who
+ *
*
* @return String
* @return the value of field 'user'.
} //-- void marshal(org.xml.sax.ContentHandler)
/**
- * Sets the value of field 'action'.
+ * Method removeAllInput
+ *
+ */
+ public void removeAllInput()
+ {
+ _inputList.removeAllElements();
+ } //-- void removeAllInput()
+
+ /**
+ * Method removeAllParam
+ *
+ */
+ public void removeAllParam()
+ {
+ _paramList.removeAllElements();
+ } //-- void removeAllParam()
+
+ /**
+ * Method removeAllProperty
+ *
+ */
+ public void removeAllProperty()
+ {
+ _propertyList.removeAllElements();
+ } //-- void removeAllProperty()
+
+ /**
+ * Method removeInput
+ *
+ *
+ *
+ * @param index
+ * @return Input
+ */
+ public org.vamsas.objects.core.Input removeInput(int index)
+ {
+ java.lang.Object obj = _inputList.elementAt(index);
+ _inputList.removeElementAt(index);
+ return (org.vamsas.objects.core.Input) obj;
+ } //-- org.vamsas.objects.core.Input removeInput(int)
+
+ /**
+ * Method removeParam
+ *
+ *
+ *
+ * @param index
+ * @return Param
+ */
+ public org.vamsas.objects.core.Param removeParam(int index)
+ {
+ java.lang.Object obj = _paramList.elementAt(index);
+ _paramList.removeElementAt(index);
+ return (org.vamsas.objects.core.Param) obj;
+ } //-- org.vamsas.objects.core.Param removeParam(int)
+
+ /**
+ * Method removeProperty
+ *
+ *
+ *
+ * @param index
+ * @return Property
+ */
+ public org.vamsas.objects.core.Property removeProperty(int index)
+ {
+ java.lang.Object obj = _propertyList.elementAt(index);
+ _propertyList.removeElementAt(index);
+ return (org.vamsas.objects.core.Property) obj;
+ } //-- org.vamsas.objects.core.Property removeProperty(int)
+
+ /**
+ * Sets the value of field 'action'. The field 'action' has the
+ * following description: Did what
+ *
*
* @param action the value of field 'action'.
*/
} //-- void setAction(java.lang.String)
/**
- * Sets the value of field 'date'.
+ * Sets the value of field 'app'. The field 'app' has the
+ * following description: With which application
+ *
+ *
+ * @param app the value of field 'app'.
+ */
+ public void setApp(java.lang.String app)
+ {
+ this._app = app;
+ } //-- void setApp(java.lang.String)
+
+ /**
+ * Sets the value of field 'date'. The field 'date' has the
+ * following description: When
+ *
*
* @param date the value of field 'date'.
*/
} //-- void setDate(org.exolab.castor.types.Date)
/**
- * Sets the value of field 'id'.
+ * Sets the value of field 'id'. The field 'id' has the
+ * following description: Primary Key for vamsas object
+ * referencing
+ *
*
* @param id the value of field 'id'.
*/
} //-- void setId(java.lang.String)
/**
- * Sets the value of field 'user'.
+ * Method setInput
+ *
+ *
+ *
+ * @param index
+ * @param vInput
+ */
+ public void setInput(int index, org.vamsas.objects.core.Input vInput)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ //-- check bounds for index
+ if ((index < 0) || (index > _inputList.size())) {
+ throw new IndexOutOfBoundsException("setInput: Index value '"+index+"' not in range [0.."+_inputList.size()+ "]");
+ }
+ _inputList.setElementAt(vInput, index);
+ } //-- void setInput(int, org.vamsas.objects.core.Input)
+
+ /**
+ * Method setInput
+ *
+ *
+ *
+ * @param inputArray
+ */
+ public void setInput(org.vamsas.objects.core.Input[] inputArray)
+ {
+ //-- copy array
+ _inputList.removeAllElements();
+ for (int i = 0; i < inputArray.length; i++) {
+ _inputList.addElement(inputArray[i]);
+ }
+ } //-- void setInput(org.vamsas.objects.core.Input)
+
+ /**
+ * Method setParam
+ *
+ *
+ *
+ * @param index
+ * @param vParam
+ */
+ public void setParam(int index, org.vamsas.objects.core.Param vParam)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ //-- check bounds for index
+ if ((index < 0) || (index > _paramList.size())) {
+ throw new IndexOutOfBoundsException("setParam: Index value '"+index+"' not in range [0.."+_paramList.size()+ "]");
+ }
+ _paramList.setElementAt(vParam, index);
+ } //-- void setParam(int, org.vamsas.objects.core.Param)
+
+ /**
+ * Method setParam
+ *
+ *
+ *
+ * @param paramArray
+ */
+ public void setParam(org.vamsas.objects.core.Param[] paramArray)
+ {
+ //-- copy array
+ _paramList.removeAllElements();
+ for (int i = 0; i < paramArray.length; i++) {
+ _paramList.addElement(paramArray[i]);
+ }
+ } //-- void setParam(org.vamsas.objects.core.Param)
+
+ /**
+ * Method setProperty
+ *
+ *
+ *
+ * @param index
+ * @param vProperty
+ */
+ public void setProperty(int index, org.vamsas.objects.core.Property vProperty)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ //-- check bounds for index
+ if ((index < 0) || (index > _propertyList.size())) {
+ throw new IndexOutOfBoundsException("setProperty: Index value '"+index+"' not in range [0.."+_propertyList.size()+ "]");
+ }
+ _propertyList.setElementAt(vProperty, index);
+ } //-- void setProperty(int, org.vamsas.objects.core.Property)
+
+ /**
+ * Method setProperty
+ *
+ *
+ *
+ * @param propertyArray
+ */
+ public void setProperty(org.vamsas.objects.core.Property[] propertyArray)
+ {
+ //-- copy array
+ _propertyList.removeAllElements();
+ for (int i = 0; i < propertyArray.length; i++) {
+ _propertyList.addElement(propertyArray[i]);
+ }
+ } //-- void setProperty(org.vamsas.objects.core.Property)
+
+ /**
+ * Sets the value of field 'user'. The field 'user' has the
+ * following description: Who
+ *
*
* @param user the value of field 'user'.
*/
fieldValidator.setValidator(typeValidator);
}
desc.setValidator(fieldValidator);
+ //-- _app
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_app", "App", 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.getApp();
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ Entry target = (Entry) object;
+ target.setApp( (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: _app
+ 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);
fieldValidator.setValidator(typeValidator);
}
desc.setValidator(fieldValidator);
+ //-- _propertyList
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Property.class, "_propertyList", "property", 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.getProperty();
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ Entry target = (Entry) object;
+ target.addProperty( (org.vamsas.objects.core.Property) value);
+ }
+ catch (java.lang.Exception ex) {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+ public java.lang.Object newInstance( java.lang.Object parent ) {
+ return new org.vamsas.objects.core.Property();
+ }
+ };
+ desc.setHandler(handler);
+ desc.setNameSpaceURI("http://www.vamsas.org");
+ desc.setMultivalued(true);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _propertyList
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(0);
+ { //-- local scope
+ }
+ desc.setValidator(fieldValidator);
+ //-- _paramList
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Param.class, "_paramList", "param", 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.getParam();
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ Entry target = (Entry) object;
+ target.addParam( (org.vamsas.objects.core.Param) value);
+ }
+ catch (java.lang.Exception ex) {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+ public java.lang.Object newInstance( java.lang.Object parent ) {
+ return new org.vamsas.objects.core.Param();
+ }
+ };
+ desc.setHandler(handler);
+ desc.setNameSpaceURI("http://www.vamsas.org");
+ desc.setMultivalued(true);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _paramList
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(0);
+ { //-- local scope
+ }
+ desc.setValidator(fieldValidator);
+ //-- _inputList
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Input.class, "_inputList", "input", 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.getInput();
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ Entry target = (Entry) object;
+ target.addInput( (org.vamsas.objects.core.Input) value);
+ }
+ catch (java.lang.Exception ex) {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+ public java.lang.Object newInstance( java.lang.Object parent ) {
+ return new org.vamsas.objects.core.Input();
+ }
+ };
+ desc.setHandler(handler);
+ desc.setNameSpaceURI("http://www.vamsas.org");
+ desc.setMultivalued(true);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _inputList
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(0);
+ { //-- local scope
+ }
+ desc.setValidator(fieldValidator);
} //-- org.vamsas.objects.core.EntryDescriptor()
--- /dev/null
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package org.vamsas.objects.core;
+
+ //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import java.io.IOException;
+import java.io.Reader;
+import java.io.Serializable;
+import java.io.Writer;
+import org.exolab.castor.xml.MarshalException;
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+import org.exolab.castor.xml.ValidationException;
+import org.xml.sax.ContentHandler;
+
+/**
+ * Discrete symbol - possibly graphically
+ * represented
+ *
+ *
+ * @version $Revision$ $Date$
+ */
+public class Glyph extends org.vamsas.client.Vobject
+implements java.io.Serializable
+{
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * internal content storage
+ */
+ private java.lang.String _content = "";
+
+ /**
+ * specifies the symbol
+ * dictionary for this glyph -
+ * eg utf8 (the default),
+ * aasecstr_3 or
+ * kd_hydrophobicity - the
+ * content is not validated so
+ * applications must ensure
+ * they gracefully deal with
+ * invalid entries here
+ *
+ */
+ private java.lang.String _dict = "utf8";
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public Glyph()
+ {
+ super();
+ setContent("");
+ setDict("utf8");
+ } //-- org.vamsas.objects.core.Glyph()
+
+
+ //-----------/
+ //- 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 Glyph) {
+
+ Glyph temp = (Glyph)obj;
+ if (this._content != null) {
+ if (temp._content == null) return false;
+ else if (!(this._content.equals(temp._content)))
+ return false;
+ }
+ else if (temp._content != null)
+ return false;
+ if (this._dict != null) {
+ if (temp._dict == null) return false;
+ else if (!(this._dict.equals(temp._dict)))
+ return false;
+ }
+ else if (temp._dict != null)
+ return false;
+ return true;
+ }
+ return false;
+ } //-- boolean equals(java.lang.Object)
+
+ /**
+ * Returns the value of field 'content'. The field 'content'
+ * has the following description: internal content storage
+ *
+ * @return String
+ * @return the value of field 'content'.
+ */
+ public java.lang.String getContent()
+ {
+ return this._content;
+ } //-- java.lang.String getContent()
+
+ /**
+ * Returns the value of field 'dict'. The field 'dict' has the
+ * following description: specifies the symbol
+ * dictionary for this glyph -
+ * eg utf8 (the default),
+ * aasecstr_3 or
+ * kd_hydrophobicity - the
+ * content is not validated so
+ * applications must ensure
+ * they gracefully deal with
+ * invalid entries here
+ *
+ *
+ * @return String
+ * @return the value of field 'dict'.
+ */
+ public java.lang.String getDict()
+ {
+ return this._dict;
+ } //-- java.lang.String getDict()
+
+ /**
+ * Method isValid
+ *
+ *
+ *
+ * @return boolean
+ */
+ public boolean isValid()
+ {
+ try {
+ validate();
+ }
+ catch (org.exolab.castor.xml.ValidationException vex) {
+ return false;
+ }
+ return true;
+ } //-- boolean isValid()
+
+ /**
+ * Method marshal
+ *
+ *
+ *
+ * @param out
+ */
+ public void marshal(java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+ {
+
+ Marshaller.marshal(this, out);
+ } //-- void marshal(java.io.Writer)
+
+ /**
+ * Method marshal
+ *
+ *
+ *
+ * @param handler
+ */
+ public void marshal(org.xml.sax.ContentHandler handler)
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+ {
+
+ Marshaller.marshal(this, handler);
+ } //-- void marshal(org.xml.sax.ContentHandler)
+
+ /**
+ * Sets the value of field 'content'. The field 'content' has
+ * the following description: internal content storage
+ *
+ * @param content the value of field 'content'.
+ */
+ public void setContent(java.lang.String content)
+ {
+ this._content = content;
+ } //-- void setContent(java.lang.String)
+
+ /**
+ * Sets the value of field 'dict'. The field 'dict' has the
+ * following description: specifies the symbol
+ * dictionary for this glyph -
+ * eg utf8 (the default),
+ * aasecstr_3 or
+ * kd_hydrophobicity - the
+ * content is not validated so
+ * applications must ensure
+ * they gracefully deal with
+ * invalid entries here
+ *
+ *
+ * @param dict the value of field 'dict'.
+ */
+ public void setDict(java.lang.String dict)
+ {
+ this._dict = dict;
+ } //-- void setDict(java.lang.String)
+
+ /**
+ * Method unmarshal
+ *
+ *
+ *
+ * @param reader
+ * @return Glyph
+ */
+ public static org.vamsas.objects.core.Glyph unmarshal(java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+ {
+ return (org.vamsas.objects.core.Glyph) Unmarshaller.unmarshal(org.vamsas.objects.core.Glyph.class, reader);
+ } //-- org.vamsas.objects.core.Glyph unmarshal(java.io.Reader)
+
+ /**
+ * Method validate
+ *
+ */
+ public void validate()
+ throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ } //-- void validate()
+
+}
--- /dev/null
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package org.vamsas.objects.core;
+
+ //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.mapping.AccessMode;
+import org.exolab.castor.xml.TypeValidator;
+import org.exolab.castor.xml.XMLFieldDescriptor;
+import org.exolab.castor.xml.validators.*;
+
+/**
+ * Class GlyphDescriptor.
+ *
+ * @version $Revision$ $Date$
+ */
+public class GlyphDescriptor 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 GlyphDescriptor()
+ {
+ super();
+ nsURI = "http://www.vamsas.org";
+ xmlName = "glyph";
+ 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
+ {
+ Glyph target = (Glyph) object;
+ return target.getContent();
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ Glyph target = (Glyph) 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
+
+ //-- _dict
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_dict", "dict", 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
+ {
+ Glyph target = (Glyph) object;
+ return target.getDict();
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ Glyph target = (Glyph) object;
+ target.setDict( (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: _dict
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { //-- local scope
+ StringValidator typeValidator = new StringValidator();
+ typeValidator.setWhiteSpace("preserve");
+ fieldValidator.setValidator(typeValidator);
+ }
+ desc.setValidator(fieldValidator);
+ //-- initialize element descriptors
+
+ } //-- org.vamsas.objects.core.GlyphDescriptor()
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ * Method getAccessMode
+ *
+ *
+ *
+ * @return AccessMode
+ */
+ public org.exolab.castor.mapping.AccessMode getAccessMode()
+ {
+ return null;
+ } //-- org.exolab.castor.mapping.AccessMode getAccessMode()
+
+ /**
+ * Method getExtends
+ *
+ *
+ *
+ * @return ClassDescriptor
+ */
+ public org.exolab.castor.mapping.ClassDescriptor getExtends()
+ {
+ return null;
+ } //-- org.exolab.castor.mapping.ClassDescriptor getExtends()
+
+ /**
+ * Method getIdentity
+ *
+ *
+ *
+ * @return FieldDescriptor
+ */
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+ {
+ return identity;
+ } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity()
+
+ /**
+ * Method getJavaClass
+ *
+ *
+ *
+ * @return Class
+ */
+ public java.lang.Class getJavaClass()
+ {
+ return org.vamsas.objects.core.Glyph.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 0.9.9M2</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package org.vamsas.objects.core;
+
+ //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import java.io.IOException;
+import java.io.Reader;
+import java.io.Serializable;
+import java.io.Writer;
+import org.exolab.castor.xml.MarshalException;
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+import org.exolab.castor.xml.ValidationException;
+import org.xml.sax.ContentHandler;
+
+/**
+ * Class Input.
+ *
+ * @version $Revision$ $Date$
+ */
+public class Input extends org.vamsas.objects.core.RangeType
+implements java.io.Serializable
+{
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * Field _name
+ */
+ private java.lang.String _name;
+
+ /**
+ * Reference Frame for rangeType
+ * specfication
+ *
+ */
+ private java.lang.Object _objRef;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public Input()
+ {
+ super();
+ } //-- org.vamsas.objects.core.Input()
+
+
+ //-----------/
+ //- 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 Input) {
+
+ Input temp = (Input)obj;
+ 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._objRef != null) {
+ if (temp._objRef == null) return false;
+ else if (!(this._objRef.equals(temp._objRef)))
+ return false;
+ }
+ else if (temp._objRef != null)
+ return false;
+ return true;
+ }
+ return false;
+ } //-- boolean equals(java.lang.Object)
+
+ /**
+ * 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 'objRef'. The field 'objRef' has
+ * the following description: Reference Frame for rangeType
+ * specfication
+ *
+ *
+ * @return Object
+ * @return the value of field 'objRef'.
+ */
+ public java.lang.Object getObjRef()
+ {
+ return this._objRef;
+ } //-- java.lang.Object getObjRef()
+
+ /**
+ * 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.String name)
+ {
+ this._name = name;
+ } //-- void setName(java.lang.String)
+
+ /**
+ * Sets the value of field 'objRef'. The field 'objRef' has the
+ * following description: Reference Frame for rangeType
+ * specfication
+ *
+ *
+ * @param objRef the value of field 'objRef'.
+ */
+ public void setObjRef(java.lang.Object objRef)
+ {
+ this._objRef = objRef;
+ } //-- void setObjRef(java.lang.Object)
+
+ /**
+ * Method unmarshal
+ *
+ *
+ *
+ * @param reader
+ * @return RangeType
+ */
+ public static org.vamsas.objects.core.RangeType unmarshal(java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+ {
+ return (org.vamsas.objects.core.Input) Unmarshaller.unmarshal(org.vamsas.objects.core.Input.class, reader);
+ } //-- org.vamsas.objects.core.RangeType unmarshal(java.io.Reader)
+
+ /**
+ * Method validate
+ *
+ */
+ public void validate()
+ throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ } //-- void validate()
+
+}
--- /dev/null
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package org.vamsas.objects.core;
+
+ //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.mapping.AccessMode;
+import org.exolab.castor.xml.TypeValidator;
+import org.exolab.castor.xml.XMLFieldDescriptor;
+import org.exolab.castor.xml.validators.*;
+
+/**
+ * Class InputDescriptor.
+ *
+ * @version $Revision$ $Date$
+ */
+public class InputDescriptor extends org.vamsas.objects.core.RangeTypeDescriptor {
+
+
+ //--------------------------/
+ //- 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 InputDescriptor()
+ {
+ super();
+ setExtendsWithoutFlatten(new org.vamsas.objects.core.RangeTypeDescriptor());
+ nsURI = "http://www.vamsas.org";
+ xmlName = "input";
+ 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
+
+ //-- _name
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_name", "name", org.exolab.castor.xml.NodeType.Attribute);
+ desc.setImmutable(true);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ Input target = (Input) object;
+ return target.getName();
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ Input target = (Input) 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.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);
+ //-- _objRef
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Object.class, "_objRef", "objRef", 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
+ {
+ Input target = (Input) object;
+ return target.getObjRef();
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ Input target = (Input) object;
+ target.setObjRef( (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: _objRef
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { //-- local scope
+ }
+ desc.setValidator(fieldValidator);
+ //-- initialize element descriptors
+
+ } //-- org.vamsas.objects.core.InputDescriptor()
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ * Method getAccessMode
+ *
+ *
+ *
+ * @return AccessMode
+ */
+ public org.exolab.castor.mapping.AccessMode getAccessMode()
+ {
+ return null;
+ } //-- org.exolab.castor.mapping.AccessMode getAccessMode()
+
+ /**
+ * Method getExtends
+ *
+ *
+ *
+ * @return ClassDescriptor
+ */
+ public org.exolab.castor.mapping.ClassDescriptor getExtends()
+ {
+ return super.getExtends();
+ } //-- org.exolab.castor.mapping.ClassDescriptor getExtends()
+
+ /**
+ * Method getIdentity
+ *
+ *
+ *
+ * @return FieldDescriptor
+ */
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+ {
+ if (identity == null)
+ return super.getIdentity();
+ return identity;
+ } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity()
+
+ /**
+ * Method getJavaClass
+ *
+ *
+ *
+ * @return Class
+ */
+ public java.lang.Class getJavaClass()
+ {
+ return org.vamsas.objects.core.Input.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 0.9.9M2</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package org.vamsas.objects.core;
+
+ //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import java.io.IOException;
+import java.io.Reader;
+import java.io.Serializable;
+import java.io.Writer;
+import org.exolab.castor.xml.MarshalException;
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+import org.exolab.castor.xml.ValidationException;
+import org.xml.sax.ContentHandler;
+
+/**
+ * Class Instance.
+ *
+ * @version $Revision$ $Date$
+ */
+public class Instance extends org.vamsas.objects.core.AppData
+implements java.io.Serializable
+{
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * Field _urn
+ */
+ private java.lang.String _urn;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public Instance()
+ {
+ super();
+ } //-- org.vamsas.objects.core.Instance()
+
+
+ //-----------/
+ //- 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 Instance) {
+
+ Instance temp = (Instance)obj;
+ if (this._urn != null) {
+ if (temp._urn == null) return false;
+ else if (!(this._urn.equals(temp._urn)))
+ return false;
+ }
+ else if (temp._urn != null)
+ return false;
+ return true;
+ }
+ return false;
+ } //-- boolean equals(java.lang.Object)
+
+ /**
+ * Returns the value of field 'urn'.
+ *
+ * @return String
+ * @return the value of field 'urn'.
+ */
+ public java.lang.String getUrn()
+ {
+ return this._urn;
+ } //-- java.lang.String getUrn()
+
+ /**
+ * 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 'urn'.
+ *
+ * @param urn the value of field 'urn'.
+ */
+ public void setUrn(java.lang.String urn)
+ {
+ this._urn = urn;
+ } //-- void setUrn(java.lang.String)
+
+ /**
+ * Method unmarshal
+ *
+ *
+ *
+ * @param reader
+ * @return AppData
+ */
+ public static org.vamsas.objects.core.AppData unmarshal(java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+ {
+ return (org.vamsas.objects.core.Instance) Unmarshaller.unmarshal(org.vamsas.objects.core.Instance.class, reader);
+ } //-- org.vamsas.objects.core.AppData unmarshal(java.io.Reader)
+
+ /**
+ * Method validate
+ *
+ */
+ public void validate()
+ throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ } //-- void validate()
+
+}
--- /dev/null
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package org.vamsas.objects.core;
+
+ //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.mapping.AccessMode;
+import org.exolab.castor.xml.TypeValidator;
+import org.exolab.castor.xml.XMLFieldDescriptor;
+import org.exolab.castor.xml.validators.*;
+
+/**
+ * Class InstanceDescriptor.
+ *
+ * @version $Revision$ $Date$
+ */
+public class InstanceDescriptor extends org.vamsas.objects.core.AppDataDescriptor {
+
+
+ //--------------------------/
+ //- 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 InstanceDescriptor()
+ {
+ super();
+ setExtendsWithoutFlatten(new org.vamsas.objects.core.AppDataDescriptor());
+ nsURI = "http://www.vamsas.org";
+ xmlName = "Instance";
+ 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
+
+ //-- _urn
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_urn", "urn", org.exolab.castor.xml.NodeType.Attribute);
+ desc.setImmutable(true);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ Instance target = (Instance) object;
+ return target.getUrn();
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ Instance target = (Instance) object;
+ target.setUrn( (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: _urn
+ 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);
+ //-- initialize element descriptors
+
+ } //-- org.vamsas.objects.core.InstanceDescriptor()
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ * Method getAccessMode
+ *
+ *
+ *
+ * @return AccessMode
+ */
+ public org.exolab.castor.mapping.AccessMode getAccessMode()
+ {
+ return null;
+ } //-- org.exolab.castor.mapping.AccessMode getAccessMode()
+
+ /**
+ * Method getExtends
+ *
+ *
+ *
+ * @return ClassDescriptor
+ */
+ public org.exolab.castor.mapping.ClassDescriptor getExtends()
+ {
+ return super.getExtends();
+ } //-- org.exolab.castor.mapping.ClassDescriptor getExtends()
+
+ /**
+ * Method getIdentity
+ *
+ *
+ *
+ * @return FieldDescriptor
+ */
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+ {
+ if (identity == null)
+ return super.getIdentity();
+ return identity;
+ } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity()
+
+ /**
+ * Method getJavaClass
+ *
+ *
+ *
+ * @return Class
+ */
+ public java.lang.Class getJavaClass()
+ {
+ return org.vamsas.objects.core.Instance.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 0.9.9M2</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package org.vamsas.objects.core;
+
+ //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import java.io.IOException;
+import java.io.Reader;
+import java.io.Serializable;
+import java.io.Writer;
+import org.exolab.castor.xml.MarshalException;
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+import org.exolab.castor.xml.ValidationException;
+import org.xml.sax.ContentHandler;
+
+/**
+ * Class Link.
+ *
+ * @version $Revision$ $Date$
+ */
+public class Link extends Uri
+implements java.io.Serializable
+{
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public Link()
+ {
+ super();
+ } //-- org.vamsas.objects.core.Link()
+
+
+ //-----------/
+ //- 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 Link) {
+
+ Link temp = (Link)obj;
+ return true;
+ }
+ return false;
+ } //-- boolean equals(java.lang.Object)
+
+ /**
+ * Method isValid
+ *
+ *
+ *
+ * @return boolean
+ */
+ public boolean isValid()
+ {
+ try {
+ validate();
+ }
+ catch (org.exolab.castor.xml.ValidationException vex) {
+ return false;
+ }
+ return true;
+ } //-- boolean isValid()
+
+ /**
+ * Method marshal
+ *
+ *
+ *
+ * @param out
+ */
+ public void marshal(java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+ {
+
+ Marshaller.marshal(this, out);
+ } //-- void marshal(java.io.Writer)
+
+ /**
+ * Method marshal
+ *
+ *
+ *
+ * @param handler
+ */
+ public void marshal(org.xml.sax.ContentHandler handler)
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+ {
+
+ Marshaller.marshal(this, handler);
+ } //-- void marshal(org.xml.sax.ContentHandler)
+
+ /**
+ * Method unmarshal
+ *
+ *
+ *
+ * @param reader
+ * @return Link
+ */
+ public static org.vamsas.objects.core.Link unmarshal(java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+ {
+ return (org.vamsas.objects.core.Link) Unmarshaller.unmarshal(org.vamsas.objects.core.Link.class, reader);
+ } //-- org.vamsas.objects.core.Link unmarshal(java.io.Reader)
+
+ /**
+ * Method validate
+ *
+ */
+ public void validate()
+ throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ } //-- void validate()
+
+}
--- /dev/null
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package org.vamsas.objects.core;
+
+ //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.mapping.AccessMode;
+import org.exolab.castor.xml.TypeValidator;
+import org.exolab.castor.xml.XMLFieldDescriptor;
+import org.exolab.castor.xml.validators.*;
+
+/**
+ * Class LinkDescriptor.
+ *
+ * @version $Revision$ $Date$
+ */
+public class LinkDescriptor extends UriDescriptor {
+
+
+ //--------------------------/
+ //- 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 LinkDescriptor()
+ {
+ super();
+ setExtendsWithoutFlatten(new UriDescriptor());
+ nsURI = "http://www.vamsas.org";
+ xmlName = "link";
+ } //-- org.vamsas.objects.core.LinkDescriptor()
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ * Method getAccessMode
+ *
+ *
+ *
+ * @return AccessMode
+ */
+ public org.exolab.castor.mapping.AccessMode getAccessMode()
+ {
+ return null;
+ } //-- org.exolab.castor.mapping.AccessMode getAccessMode()
+
+ /**
+ * Method getExtends
+ *
+ *
+ *
+ * @return ClassDescriptor
+ */
+ public org.exolab.castor.mapping.ClassDescriptor getExtends()
+ {
+ return super.getExtends();
+ } //-- org.exolab.castor.mapping.ClassDescriptor getExtends()
+
+ /**
+ * Method getIdentity
+ *
+ *
+ *
+ * @return FieldDescriptor
+ */
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+ {
+ if (identity == null)
+ return super.getIdentity();
+ return identity;
+ } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity()
+
+ /**
+ * Method getJavaClass
+ *
+ *
+ *
+ * @return Class
+ */
+ public java.lang.Class getJavaClass()
+ {
+ return org.vamsas.objects.core.Link.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 0.9.9M2</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package org.vamsas.objects.core;
+
+ //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import java.io.IOException;
+import java.io.Reader;
+import java.io.Serializable;
+import java.io.Writer;
+import org.exolab.castor.xml.MarshalException;
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+import org.exolab.castor.xml.ValidationException;
+import org.xml.sax.ContentHandler;
+
+/**
+ * Class Map.
+ *
+ * @version $Revision$ $Date$
+ */
+public class Map extends org.vamsas.client.Vobject
+implements java.io.Serializable
+{
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * Offset
+ * to
+ * first
+ * position
+ * in
+ * dataset
+ * sequence
+ * record
+ * that
+ * this
+ * database
+ * entry
+ * maps
+ * to
+ *
+ */
+ private int _from = 0;
+
+ /**
+ * keeps track of state for field: _from
+ */
+ private boolean _has_from;
+
+ /**
+ * Offset
+ * to
+ * last
+ * position
+ * in
+ * dataset
+ * sequence
+ * record
+ * that
+ * this
+ * database
+ * entry
+ * maps
+ * to
+ *
+ */
+ private int _to = 0;
+
+ /**
+ * keeps track of state for field: _to
+ */
+ private boolean _has_to;
+
+ /**
+ * Offset
+ * to first
+ * last
+ * position
+ * in
+ * database
+ * entry
+ * that
+ * first
+ * (or
+ * offset)
+ * position
+ * in
+ * sequence
+ * maps to
+ *
+ */
+ private int _start;
+
+ /**
+ * keeps track of state for field: _start
+ */
+ private boolean _has_start;
+
+ /**
+ * Offset
+ * to last
+ * position
+ * in
+ * database
+ * entry
+ * that
+ * last
+ * (offset)
+ * position
+ * in
+ * sequence
+ * maps to
+ *
+ */
+ private int _end;
+
+ /**
+ * keeps track of state for field: _end
+ */
+ private boolean _has_end;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public Map()
+ {
+ super();
+ } //-- org.vamsas.objects.core.Map()
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ * Method deleteEnd
+ *
+ */
+ public void deleteEnd()
+ {
+ this._has_end= false;
+ } //-- void deleteEnd()
+
+ /**
+ * Method deleteFrom
+ *
+ */
+ public void deleteFrom()
+ {
+ this._has_from= false;
+ } //-- void deleteFrom()
+
+ /**
+ * Method deleteStart
+ *
+ */
+ public void deleteStart()
+ {
+ this._has_start= false;
+ } //-- void deleteStart()
+
+ /**
+ * Method deleteTo
+ *
+ */
+ public void deleteTo()
+ {
+ this._has_to= false;
+ } //-- void deleteTo()
+
+ /**
+ * 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 Map) {
+
+ Map temp = (Map)obj;
+ if (this._from != temp._from)
+ return false;
+ if (this._has_from != temp._has_from)
+ return false;
+ if (this._to != temp._to)
+ return false;
+ if (this._has_to != temp._has_to)
+ return false;
+ 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;
+ return true;
+ }
+ return false;
+ } //-- boolean equals(java.lang.Object)
+
+ /**
+ * Returns the value of field 'end'. The field 'end' has the
+ * following description: Offset
+ * to last
+ * position
+ * in
+ * database
+ * entry
+ * that
+ * last
+ * (offset)
+ * position
+ * in
+ * sequence
+ * maps to
+ *
+ *
+ * @return int
+ * @return the value of field 'end'.
+ */
+ public int getEnd()
+ {
+ return this._end;
+ } //-- int getEnd()
+
+ /**
+ * Returns the value of field 'from'. The field 'from' has the
+ * following description: Offset
+ * to
+ * first
+ * position
+ * in
+ * dataset
+ * sequence
+ * record
+ * that
+ * this
+ * database
+ * entry
+ * maps
+ * to
+ *
+ *
+ * @return int
+ * @return the value of field 'from'.
+ */
+ public int getFrom()
+ {
+ return this._from;
+ } //-- int getFrom()
+
+ /**
+ * Returns the value of field 'start'. The field 'start' has
+ * the following description: Offset
+ * to first
+ * last
+ * position
+ * in
+ * database
+ * entry
+ * that
+ * first
+ * (or
+ * offset)
+ * position
+ * in
+ * sequence
+ * maps to
+ *
+ *
+ * @return int
+ * @return the value of field 'start'.
+ */
+ public int getStart()
+ {
+ return this._start;
+ } //-- int getStart()
+
+ /**
+ * Returns the value of field 'to'. The field 'to' has the
+ * following description: Offset
+ * to
+ * last
+ * position
+ * in
+ * dataset
+ * sequence
+ * record
+ * that
+ * this
+ * database
+ * entry
+ * maps
+ * to
+ *
+ *
+ * @return int
+ * @return the value of field 'to'.
+ */
+ public int getTo()
+ {
+ return this._to;
+ } //-- int getTo()
+
+ /**
+ * Method hasEnd
+ *
+ *
+ *
+ * @return boolean
+ */
+ public boolean hasEnd()
+ {
+ return this._has_end;
+ } //-- boolean hasEnd()
+
+ /**
+ * Method hasFrom
+ *
+ *
+ *
+ * @return boolean
+ */
+ public boolean hasFrom()
+ {
+ return this._has_from;
+ } //-- boolean hasFrom()
+
+ /**
+ * Method hasStart
+ *
+ *
+ *
+ * @return boolean
+ */
+ public boolean hasStart()
+ {
+ return this._has_start;
+ } //-- boolean hasStart()
+
+ /**
+ * Method hasTo
+ *
+ *
+ *
+ * @return boolean
+ */
+ public boolean hasTo()
+ {
+ return this._has_to;
+ } //-- boolean hasTo()
+
+ /**
+ * 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 'end'. The field 'end' has the
+ * following description: Offset
+ * to last
+ * position
+ * in
+ * database
+ * entry
+ * that
+ * last
+ * (offset)
+ * position
+ * in
+ * sequence
+ * maps to
+ *
+ *
+ * @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 'from'. The field 'from' has the
+ * following description: Offset
+ * to
+ * first
+ * position
+ * in
+ * dataset
+ * sequence
+ * record
+ * that
+ * this
+ * database
+ * entry
+ * maps
+ * to
+ *
+ *
+ * @param from the value of field 'from'.
+ */
+ public void setFrom(int from)
+ {
+ this._from = from;
+ this._has_from = true;
+ } //-- void setFrom(int)
+
+ /**
+ * Sets the value of field 'start'. The field 'start' has the
+ * following description: Offset
+ * to first
+ * last
+ * position
+ * in
+ * database
+ * entry
+ * that
+ * first
+ * (or
+ * offset)
+ * position
+ * in
+ * sequence
+ * maps to
+ *
+ *
+ * @param start the value of field 'start'.
+ */
+ public void setStart(int start)
+ {
+ this._start = start;
+ this._has_start = true;
+ } //-- void setStart(int)
+
+ /**
+ * Sets the value of field 'to'. The field 'to' has the
+ * following description: Offset
+ * to
+ * last
+ * position
+ * in
+ * dataset
+ * sequence
+ * record
+ * that
+ * this
+ * database
+ * entry
+ * maps
+ * to
+ *
+ *
+ * @param to the value of field 'to'.
+ */
+ public void setTo(int to)
+ {
+ this._to = to;
+ this._has_to = true;
+ } //-- void setTo(int)
+
+ /**
+ * Method unmarshal
+ *
+ *
+ *
+ * @param reader
+ * @return Map
+ */
+ public static org.vamsas.objects.core.Map unmarshal(java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+ {
+ return (org.vamsas.objects.core.Map) Unmarshaller.unmarshal(org.vamsas.objects.core.Map.class, reader);
+ } //-- org.vamsas.objects.core.Map unmarshal(java.io.Reader)
+
+ /**
+ * Method validate
+ *
+ */
+ public void validate()
+ throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ } //-- void validate()
+
+}
--- /dev/null
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package org.vamsas.objects.core;
+
+ //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.mapping.AccessMode;
+import org.exolab.castor.xml.TypeValidator;
+import org.exolab.castor.xml.XMLFieldDescriptor;
+import org.exolab.castor.xml.validators.*;
+
+/**
+ * Class MapDescriptor.
+ *
+ * @version $Revision$ $Date$
+ */
+public class MapDescriptor 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 MapDescriptor()
+ {
+ super();
+ nsURI = "http://www.vamsas.org";
+ xmlName = "map";
+ 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
+
+ //-- _from
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_from", "from", org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ Map target = (Map) object;
+ if(!target.hasFrom())
+ return null;
+ return new java.lang.Integer(target.getFrom());
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ Map target = (Map) object;
+ // if null, use delete method for optional primitives
+ if (value == null) {
+ target.deleteFrom();
+ return;
+ }
+ target.setFrom( ((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.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _from
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { //-- local scope
+ IntegerValidator typeValidator = new IntegerValidator();
+ fieldValidator.setValidator(typeValidator);
+ }
+ desc.setValidator(fieldValidator);
+ //-- _to
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_to", "to", org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ Map target = (Map) object;
+ if(!target.hasTo())
+ return null;
+ return new java.lang.Integer(target.getTo());
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ Map target = (Map) object;
+ // if null, use delete method for optional primitives
+ if (value == null) {
+ target.deleteTo();
+ return;
+ }
+ target.setTo( ((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.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _to
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { //-- local scope
+ IntegerValidator typeValidator = new IntegerValidator();
+ fieldValidator.setValidator(typeValidator);
+ }
+ desc.setValidator(fieldValidator);
+ //-- _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
+ {
+ Map target = (Map) 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 {
+ Map target = (Map) 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
+ {
+ Map target = (Map) 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 {
+ Map target = (Map) 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
+
+ } //-- org.vamsas.objects.core.MapDescriptor()
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ * Method getAccessMode
+ *
+ *
+ *
+ * @return AccessMode
+ */
+ public org.exolab.castor.mapping.AccessMode getAccessMode()
+ {
+ return null;
+ } //-- org.exolab.castor.mapping.AccessMode getAccessMode()
+
+ /**
+ * Method getExtends
+ *
+ *
+ *
+ * @return ClassDescriptor
+ */
+ public org.exolab.castor.mapping.ClassDescriptor getExtends()
+ {
+ return null;
+ } //-- org.exolab.castor.mapping.ClassDescriptor getExtends()
+
+ /**
+ * Method getIdentity
+ *
+ *
+ *
+ * @return FieldDescriptor
+ */
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+ {
+ return identity;
+ } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity()
+
+ /**
+ * Method getJavaClass
+ *
+ *
+ *
+ * @return Class
+ */
+ public java.lang.Class getJavaClass()
+ {
+ return org.vamsas.objects.core.Map.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()
+
+}
private java.lang.String _title;
/**
- * Field _id
+ * Primary Key for vamsas
+ * object referencing
+ *
*/
private java.lang.String _id;
+ /**
+ * objects with
+ * modifiable=false will not be
+ * modified by a vamsas client
+ * update
+ *
+ */
+ private boolean _modifiable = true;
+
+ /**
+ * keeps track of state for field: _modifiable
+ */
+ private boolean _has_modifiable;
+
//----------------/
//- Constructors -/
//-----------/
/**
+ * Method deleteModifiable
+ *
+ */
+ public void deleteModifiable()
+ {
+ this._has_modifiable= false;
+ } //-- void deleteModifiable()
+
+ /**
* Note: hashCode() has not been overriden
*
* @param obj
}
else if (temp._id != null)
return false;
+ if (this._modifiable != temp._modifiable)
+ return false;
+ if (this._has_modifiable != temp._has_modifiable)
+ return false;
return true;
}
return false;
} //-- java.lang.String getContent()
/**
- * Returns the value of field 'id'.
+ * Returns the value of field 'id'. The field 'id' has the
+ * following description: Primary Key for vamsas
+ * object referencing
+ *
*
* @return String
* @return the value of field 'id'.
} //-- java.lang.String getId()
/**
+ * Returns the value of field 'modifiable'. The field
+ * 'modifiable' has the following description: objects with
+ * modifiable=false will not be
+ * modified by a vamsas client
+ * update
+ *
+ *
+ * @return boolean
+ * @return the value of field 'modifiable'.
+ */
+ public boolean getModifiable()
+ {
+ return this._modifiable;
+ } //-- boolean getModifiable()
+
+ /**
* Returns the value of field 'title'.
*
* @return String
} //-- java.lang.String getTitle()
/**
+ * Method hasModifiable
+ *
+ *
+ *
+ * @return boolean
+ */
+ public boolean hasModifiable()
+ {
+ return this._has_modifiable;
+ } //-- boolean hasModifiable()
+
+ /**
* Method isValid
*
*
} //-- void setContent(java.lang.String)
/**
- * Sets the value of field 'id'.
+ * Sets the value of field 'id'. The field 'id' has the
+ * following description: Primary Key for vamsas
+ * object referencing
+ *
*
* @param id the value of field 'id'.
*/
} //-- void setId(java.lang.String)
/**
+ * Sets the value of field 'modifiable'. The field 'modifiable'
+ * has the following description: objects with
+ * modifiable=false will not be
+ * modified by a vamsas client
+ * update
+ *
+ *
+ * @param modifiable the value of field 'modifiable'.
+ */
+ public void setModifiable(boolean modifiable)
+ {
+ this._modifiable = modifiable;
+ this._has_modifiable = true;
+ } //-- void setModifiable(boolean)
+
+ /**
* Sets the value of field 'title'.
*
* @param title the value of field 'title'.
{ //-- local scope
}
desc.setValidator(fieldValidator);
+ //-- _modifiable
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_modifiable", "modifiable", org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ Newick target = (Newick) object;
+ if(!target.hasModifiable())
+ return null;
+ return (target.getModifiable() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ Newick target = (Newick) object;
+ // if null, use delete method for optional primitives
+ if (value == null) {
+ target.deleteModifiable();
+ return;
+ }
+ target.setModifiable( ((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: _modifiable
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { //-- local scope
+ BooleanValidator typeValidator = new BooleanValidator();
+ fieldValidator.setValidator(typeValidator);
+ }
+ desc.setValidator(fieldValidator);
//-- initialize element descriptors
} //-- org.vamsas.objects.core.NewickDescriptor()
--- /dev/null
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package org.vamsas.objects.core;
+
+ //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import java.io.IOException;
+import java.io.Reader;
+import java.io.Serializable;
+import java.io.Writer;
+import org.exolab.castor.xml.MarshalException;
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+import org.exolab.castor.xml.ValidationException;
+import org.xml.sax.ContentHandler;
+
+/**
+ * Class Param.
+ *
+ * @version $Revision$ $Date$
+ */
+public class Param extends org.vamsas.client.Vobject
+implements java.io.Serializable
+{
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * internal content storage
+ */
+ private java.lang.String _content = "";
+
+ /**
+ * Field _name
+ */
+ private java.lang.String _name;
+
+ /**
+ * The type specifies how the property will
+ * be parsed. Empty property strings are
+ * allowed, and can be used to prototype
+ * the input to a document. TODO: specify
+ * allowed types
+ *
+ */
+ private java.lang.String _type;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public Param()
+ {
+ super();
+ setContent("");
+ } //-- org.vamsas.objects.core.Param()
+
+
+ //-----------/
+ //- 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 Param) {
+
+ Param temp = (Param)obj;
+ if (this._content != null) {
+ if (temp._content == null) return false;
+ else if (!(this._content.equals(temp._content)))
+ return false;
+ }
+ else if (temp._content != null)
+ return false;
+ if (this._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._type != null) {
+ if (temp._type == null) return false;
+ else if (!(this._type.equals(temp._type)))
+ return false;
+ }
+ else if (temp._type != null)
+ return false;
+ return true;
+ }
+ return false;
+ } //-- boolean equals(java.lang.Object)
+
+ /**
+ * Returns the value of field 'content'. The field 'content'
+ * has the following description: internal content storage
+ *
+ * @return String
+ * @return the value of field 'content'.
+ */
+ public java.lang.String getContent()
+ {
+ return this._content;
+ } //-- java.lang.String getContent()
+
+ /**
+ * Returns the value of field '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 'type'. The field 'type' has the
+ * following description: The type specifies how the property
+ * will
+ * be parsed. Empty property strings are
+ * allowed, and can be used to prototype
+ * the input to a document. TODO: specify
+ * allowed types
+ *
+ *
+ * @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)
+
+ /**
+ * Sets the value of field 'content'. The field 'content' has
+ * the following description: internal content storage
+ *
+ * @param content the value of field 'content'.
+ */
+ public void setContent(java.lang.String content)
+ {
+ this._content = content;
+ } //-- void setContent(java.lang.String)
+
+ /**
+ * Sets the value of field '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 'type'. The field 'type' has the
+ * following description: The type specifies how the property
+ * will
+ * be parsed. Empty property strings are
+ * allowed, and can be used to prototype
+ * the input to a document. TODO: specify
+ * allowed types
+ *
+ *
+ * @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 Param
+ */
+ public static org.vamsas.objects.core.Param unmarshal(java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+ {
+ return (org.vamsas.objects.core.Param) Unmarshaller.unmarshal(org.vamsas.objects.core.Param.class, reader);
+ } //-- org.vamsas.objects.core.Param unmarshal(java.io.Reader)
+
+ /**
+ * Method validate
+ *
+ */
+ public void validate()
+ throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ } //-- void validate()
+
+}
--- /dev/null
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package org.vamsas.objects.core;
+
+ //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.mapping.AccessMode;
+import org.exolab.castor.xml.TypeValidator;
+import org.exolab.castor.xml.XMLFieldDescriptor;
+import org.exolab.castor.xml.validators.*;
+
+/**
+ * Class ParamDescriptor.
+ *
+ * @version $Revision$ $Date$
+ */
+public class ParamDescriptor 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 ParamDescriptor()
+ {
+ super();
+ nsURI = "http://www.vamsas.org";
+ xmlName = "param";
+ 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
+ {
+ Param target = (Param) object;
+ return target.getContent();
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ Param target = (Param) 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
+
+ //-- _name
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_name", "name", org.exolab.castor.xml.NodeType.Attribute);
+ desc.setImmutable(true);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ Param target = (Param) object;
+ return target.getName();
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ Param target = (Param) 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.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);
+ //-- _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
+ {
+ Param target = (Param) object;
+ return target.getType();
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ Param target = (Param) 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);
+ //-- initialize element descriptors
+
+ } //-- org.vamsas.objects.core.ParamDescriptor()
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ * Method getAccessMode
+ *
+ *
+ *
+ * @return AccessMode
+ */
+ public org.exolab.castor.mapping.AccessMode getAccessMode()
+ {
+ return null;
+ } //-- org.exolab.castor.mapping.AccessMode getAccessMode()
+
+ /**
+ * Method getExtends
+ *
+ *
+ *
+ * @return ClassDescriptor
+ */
+ public org.exolab.castor.mapping.ClassDescriptor getExtends()
+ {
+ return null;
+ } //-- org.exolab.castor.mapping.ClassDescriptor getExtends()
+
+ /**
+ * Method getIdentity
+ *
+ *
+ *
+ * @return FieldDescriptor
+ */
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+ {
+ return identity;
+ } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity()
+
+ /**
+ * Method getJavaClass
+ *
+ *
+ *
+ * @return Class
+ */
+ public java.lang.Class getJavaClass()
+ {
+ return org.vamsas.objects.core.Param.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 0.9.9M2</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package org.vamsas.objects.core;
+
+ //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import java.io.IOException;
+import java.io.Reader;
+import java.io.Serializable;
+import java.io.Writer;
+import org.exolab.castor.xml.MarshalException;
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+import org.exolab.castor.xml.ValidationException;
+import org.xml.sax.ContentHandler;
+
+/**
+ * a position within the associated object's
+ * coordinate system
+ *
+ *
+ * @version $Revision$ $Date$
+ */
+public class Pos extends org.vamsas.client.Vobject
+implements java.io.Serializable
+{
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * Field _i
+ */
+ private int _i;
+
+ /**
+ * keeps track of state for field: _i
+ */
+ private boolean _has_i;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public Pos()
+ {
+ super();
+ } //-- org.vamsas.objects.core.Pos()
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ * Method deleteI
+ *
+ */
+ public void deleteI()
+ {
+ this._has_i= false;
+ } //-- void deleteI()
+
+ /**
+ * 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 Pos) {
+
+ Pos temp = (Pos)obj;
+ if (this._i != temp._i)
+ return false;
+ if (this._has_i != temp._has_i)
+ return false;
+ return true;
+ }
+ return false;
+ } //-- boolean equals(java.lang.Object)
+
+ /**
+ * Returns the value of field 'i'.
+ *
+ * @return int
+ * @return the value of field 'i'.
+ */
+ public int getI()
+ {
+ return this._i;
+ } //-- int getI()
+
+ /**
+ * Method hasI
+ *
+ *
+ *
+ * @return boolean
+ */
+ public boolean hasI()
+ {
+ return this._has_i;
+ } //-- boolean hasI()
+
+ /**
+ * 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 'i'.
+ *
+ * @param i the value of field 'i'.
+ */
+ public void setI(int i)
+ {
+ this._i = i;
+ this._has_i = true;
+ } //-- void setI(int)
+
+ /**
+ * Method unmarshal
+ *
+ *
+ *
+ * @param reader
+ * @return Pos
+ */
+ public static org.vamsas.objects.core.Pos unmarshal(java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+ {
+ return (org.vamsas.objects.core.Pos) Unmarshaller.unmarshal(org.vamsas.objects.core.Pos.class, reader);
+ } //-- org.vamsas.objects.core.Pos unmarshal(java.io.Reader)
+
+ /**
+ * Method validate
+ *
+ */
+ public void validate()
+ throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ } //-- void validate()
+
+}
--- /dev/null
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package org.vamsas.objects.core;
+
+ //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.mapping.AccessMode;
+import org.exolab.castor.xml.TypeValidator;
+import org.exolab.castor.xml.XMLFieldDescriptor;
+import org.exolab.castor.xml.validators.*;
+
+/**
+ * Class PosDescriptor.
+ *
+ * @version $Revision$ $Date$
+ */
+public class PosDescriptor 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 PosDescriptor()
+ {
+ super();
+ nsURI = "http://www.vamsas.org";
+ xmlName = "pos";
+ 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
+
+ //-- _i
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_i", "i", org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ Pos target = (Pos) object;
+ if(!target.hasI())
+ return null;
+ return new java.lang.Integer(target.getI());
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ Pos target = (Pos) object;
+ // ignore null values for non optional primitives
+ if (value == null) return;
+
+ target.setI( ((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: _i
+ 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
+
+ } //-- org.vamsas.objects.core.PosDescriptor()
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ * Method getAccessMode
+ *
+ *
+ *
+ * @return AccessMode
+ */
+ public org.exolab.castor.mapping.AccessMode getAccessMode()
+ {
+ return null;
+ } //-- org.exolab.castor.mapping.AccessMode getAccessMode()
+
+ /**
+ * Method getExtends
+ *
+ *
+ *
+ * @return ClassDescriptor
+ */
+ public org.exolab.castor.mapping.ClassDescriptor getExtends()
+ {
+ return null;
+ } //-- org.exolab.castor.mapping.ClassDescriptor getExtends()
+
+ /**
+ * Method getIdentity
+ *
+ *
+ *
+ * @return FieldDescriptor
+ */
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+ {
+ return identity;
+ } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity()
+
+ /**
+ * Method getJavaClass
+ *
+ *
+ *
+ * @return Class
+ */
+ public java.lang.Class getJavaClass()
+ {
+ return org.vamsas.objects.core.Pos.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 0.9.9M2</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package org.vamsas.objects.core;
+
+ //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import java.io.IOException;
+import java.io.Reader;
+import java.io.Serializable;
+import java.io.Writer;
+import org.exolab.castor.xml.MarshalException;
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+import org.exolab.castor.xml.ValidationException;
+import org.xml.sax.ContentHandler;
+
+/**
+ * Class Property.
+ *
+ * @version $Revision$ $Date$
+ */
+public class Property extends org.vamsas.client.Vobject
+implements java.io.Serializable
+{
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * internal content storage
+ */
+ private java.lang.String _content = "";
+
+ /**
+ * Field _name
+ */
+ private java.lang.String _name;
+
+ /**
+ * The type specifies how the property will
+ * be parsed. Empty property strings are
+ * allowed, and can be used to prototype
+ * the input to a document. TODO: specify
+ * allowed types
+ *
+ */
+ private java.lang.String _type;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public Property()
+ {
+ super();
+ setContent("");
+ } //-- org.vamsas.objects.core.Property()
+
+
+ //-----------/
+ //- 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 Property) {
+
+ Property temp = (Property)obj;
+ if (this._content != null) {
+ if (temp._content == null) return false;
+ else if (!(this._content.equals(temp._content)))
+ return false;
+ }
+ else if (temp._content != null)
+ return false;
+ if (this._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._type != null) {
+ if (temp._type == null) return false;
+ else if (!(this._type.equals(temp._type)))
+ return false;
+ }
+ else if (temp._type != null)
+ return false;
+ return true;
+ }
+ return false;
+ } //-- boolean equals(java.lang.Object)
+
+ /**
+ * Returns the value of field 'content'. The field 'content'
+ * has the following description: internal content storage
+ *
+ * @return String
+ * @return the value of field 'content'.
+ */
+ public java.lang.String getContent()
+ {
+ return this._content;
+ } //-- java.lang.String getContent()
+
+ /**
+ * Returns the value of field '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 'type'. The field 'type' has the
+ * following description: The type specifies how the property
+ * will
+ * be parsed. Empty property strings are
+ * allowed, and can be used to prototype
+ * the input to a document. TODO: specify
+ * allowed types
+ *
+ *
+ * @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)
+
+ /**
+ * Sets the value of field 'content'. The field 'content' has
+ * the following description: internal content storage
+ *
+ * @param content the value of field 'content'.
+ */
+ public void setContent(java.lang.String content)
+ {
+ this._content = content;
+ } //-- void setContent(java.lang.String)
+
+ /**
+ * Sets the value of field '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 'type'. The field 'type' has the
+ * following description: The type specifies how the property
+ * will
+ * be parsed. Empty property strings are
+ * allowed, and can be used to prototype
+ * the input to a document. TODO: specify
+ * allowed types
+ *
+ *
+ * @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 Property
+ */
+ public static org.vamsas.objects.core.Property unmarshal(java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+ {
+ return (org.vamsas.objects.core.Property) Unmarshaller.unmarshal(org.vamsas.objects.core.Property.class, reader);
+ } //-- org.vamsas.objects.core.Property unmarshal(java.io.Reader)
+
+ /**
+ * Method validate
+ *
+ */
+ public void validate()
+ throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ } //-- void validate()
+
+}
--- /dev/null
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package org.vamsas.objects.core;
+
+ //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.mapping.AccessMode;
+import org.exolab.castor.xml.TypeValidator;
+import org.exolab.castor.xml.XMLFieldDescriptor;
+import org.exolab.castor.xml.validators.*;
+
+/**
+ * Class PropertyDescriptor.
+ *
+ * @version $Revision$ $Date$
+ */
+public class PropertyDescriptor 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 PropertyDescriptor()
+ {
+ super();
+ nsURI = "http://www.vamsas.org";
+ xmlName = "property";
+ 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
+ {
+ Property target = (Property) object;
+ return target.getContent();
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ Property target = (Property) 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
+
+ //-- _name
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_name", "name", org.exolab.castor.xml.NodeType.Attribute);
+ desc.setImmutable(true);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ Property target = (Property) object;
+ return target.getName();
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ Property target = (Property) 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.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);
+ //-- _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
+ {
+ Property target = (Property) object;
+ return target.getType();
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ Property target = (Property) 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);
+ //-- initialize element descriptors
+
+ } //-- org.vamsas.objects.core.PropertyDescriptor()
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ * Method getAccessMode
+ *
+ *
+ *
+ * @return AccessMode
+ */
+ public org.exolab.castor.mapping.AccessMode getAccessMode()
+ {
+ return null;
+ } //-- org.exolab.castor.mapping.AccessMode getAccessMode()
+
+ /**
+ * Method getExtends
+ *
+ *
+ *
+ * @return ClassDescriptor
+ */
+ public org.exolab.castor.mapping.ClassDescriptor getExtends()
+ {
+ return null;
+ } //-- org.exolab.castor.mapping.ClassDescriptor getExtends()
+
+ /**
+ * Method getIdentity
+ *
+ *
+ *
+ * @return FieldDescriptor
+ */
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+ {
+ return identity;
+ } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity()
+
+ /**
+ * Method getJavaClass
+ *
+ *
+ *
+ * @return Class
+ */
+ public java.lang.Class getJavaClass()
+ {
+ return org.vamsas.objects.core.Property.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 0.9.9M2</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package org.vamsas.objects.core;
+
+ //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import java.io.IOException;
+import java.io.Reader;
+import java.io.Serializable;
+import java.io.Writer;
+import java.util.Enumeration;
+import java.util.Vector;
+import org.exolab.castor.xml.MarshalException;
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+import org.exolab.castor.xml.ValidationException;
+import org.xml.sax.ContentHandler;
+
+/**
+ * Annotation for a rangeSpec - values can be attached for the
+ * whole specification, and to each position within the spec.
+ * following the orientation specified by the ordered set of
+ * rangeSpec (pos, seg) elements.
+ *
+ *
+ * @version $Revision$ $Date$
+ */
+public class RangeAnnotation extends org.vamsas.objects.core.RangeType
+implements java.io.Serializable
+{
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * Primary Key for vamsas object referencing
+ *
+ */
+ private java.lang.String _id;
+
+ /**
+ * objects with modifiable=false will not be
+ * modified by a vamsas client update
+ *
+ */
+ private boolean _modifiable = true;
+
+ /**
+ * keeps track of state for field: _modifiable
+ */
+ private boolean _has_modifiable;
+
+ /**
+ * Annotation with the same non-empty group
+ * name are grouped together
+ *
+ */
+ private java.lang.String _group = "";
+
+ /**
+ * A Das Feature has both a type and a Type ID.
+ * We go the route of requiring the type string
+ * to be taken from a controlled vocabulary if
+ * an application expects others to make sense
+ * of it.
+ * The type may qualified - so uniprot:CHAIN is a valid type
+ * name,
+ * and considered distinct from someotherDB:CHAIN
+ *
+ */
+ private java.lang.String _type;
+
+ /**
+ * Short, meaningful name for the annotation - if this is
+ * absent, then the type string should be used in its place.
+ *
+ */
+ private java.lang.String _label;
+
+ /**
+ * Human readable description of the annotation
+ *
+ */
+ private java.lang.String _description;
+
+ /**
+ * TODO: specify this - we have considered taking the GO
+ * evidence codes as a model for assessing a measure of quality
+ * to an annotation.
+ *
+ */
+ private java.lang.String _status;
+
+ /**
+ * Annotation Element position maps to
+ * ordered positions defined by the
+ * sequence of rangeType pos positions or
+ * concatenated seg start/end segments.
+ *
+ */
+ private java.util.Vector _annotationElementList;
+
+ /**
+ * Ordered set of optionally named float
+ * values for the whole annotation
+ *
+ */
+ private java.util.Vector _scoreList;
+
+ /**
+ * Field _urlList
+ */
+ private java.util.Vector _urlList;
+
+ /**
+ * Note:These are mutable so an application
+ * should check them each time.
+ *
+ */
+ private java.util.Vector _propertyList;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public RangeAnnotation()
+ {
+ super();
+ setGroup("");
+ _annotationElementList = new Vector();
+ _scoreList = new Vector();
+ _urlList = new Vector();
+ _propertyList = new Vector();
+ } //-- org.vamsas.objects.core.RangeAnnotation()
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ * Method addAnnotationElement
+ *
+ *
+ *
+ * @param vAnnotationElement
+ */
+ public void addAnnotationElement(org.vamsas.objects.core.AnnotationElement vAnnotationElement)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _annotationElementList.addElement(vAnnotationElement);
+ } //-- void addAnnotationElement(org.vamsas.objects.core.AnnotationElement)
+
+ /**
+ * Method addAnnotationElement
+ *
+ *
+ *
+ * @param index
+ * @param vAnnotationElement
+ */
+ public void addAnnotationElement(int index, org.vamsas.objects.core.AnnotationElement vAnnotationElement)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _annotationElementList.insertElementAt(vAnnotationElement, index);
+ } //-- void addAnnotationElement(int, org.vamsas.objects.core.AnnotationElement)
+
+ /**
+ * Method addProperty
+ *
+ *
+ *
+ * @param vProperty
+ */
+ public void addProperty(org.vamsas.objects.core.Property vProperty)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _propertyList.addElement(vProperty);
+ } //-- void addProperty(org.vamsas.objects.core.Property)
+
+ /**
+ * Method addProperty
+ *
+ *
+ *
+ * @param index
+ * @param vProperty
+ */
+ public void addProperty(int index, org.vamsas.objects.core.Property vProperty)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _propertyList.insertElementAt(vProperty, index);
+ } //-- void addProperty(int, org.vamsas.objects.core.Property)
+
+ /**
+ * Method addScore
+ *
+ *
+ *
+ * @param vScore
+ */
+ public void addScore(org.vamsas.objects.core.Score vScore)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _scoreList.addElement(vScore);
+ } //-- void addScore(org.vamsas.objects.core.Score)
+
+ /**
+ * Method addScore
+ *
+ *
+ *
+ * @param index
+ * @param vScore
+ */
+ public void addScore(int index, org.vamsas.objects.core.Score vScore)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _scoreList.insertElementAt(vScore, index);
+ } //-- void addScore(int, org.vamsas.objects.core.Score)
+
+ /**
+ * Method addUrl
+ *
+ *
+ *
+ * @param vUrl
+ */
+ public void addUrl(org.vamsas.objects.core.Url vUrl)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _urlList.addElement(vUrl);
+ } //-- void addUrl(org.vamsas.objects.core.Url)
+
+ /**
+ * Method addUrl
+ *
+ *
+ *
+ * @param index
+ * @param vUrl
+ */
+ public void addUrl(int index, org.vamsas.objects.core.Url vUrl)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _urlList.insertElementAt(vUrl, index);
+ } //-- void addUrl(int, org.vamsas.objects.core.Url)
+
+ /**
+ * Method deleteModifiable
+ *
+ */
+ public void deleteModifiable()
+ {
+ this._has_modifiable= false;
+ } //-- void deleteModifiable()
+
+ /**
+ * Method enumerateAnnotationElement
+ *
+ *
+ *
+ * @return Enumeration
+ */
+ public java.util.Enumeration enumerateAnnotationElement()
+ {
+ return _annotationElementList.elements();
+ } //-- java.util.Enumeration enumerateAnnotationElement()
+
+ /**
+ * Method enumerateProperty
+ *
+ *
+ *
+ * @return Enumeration
+ */
+ public java.util.Enumeration enumerateProperty()
+ {
+ return _propertyList.elements();
+ } //-- java.util.Enumeration enumerateProperty()
+
+ /**
+ * Method enumerateScore
+ *
+ *
+ *
+ * @return Enumeration
+ */
+ public java.util.Enumeration enumerateScore()
+ {
+ return _scoreList.elements();
+ } //-- java.util.Enumeration enumerateScore()
+
+ /**
+ * Method enumerateUrl
+ *
+ *
+ *
+ * @return Enumeration
+ */
+ public java.util.Enumeration enumerateUrl()
+ {
+ return _urlList.elements();
+ } //-- java.util.Enumeration enumerateUrl()
+
+ /**
+ * 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 RangeAnnotation) {
+
+ RangeAnnotation temp = (RangeAnnotation)obj;
+ if (this._id != null) {
+ if (temp._id == null) return false;
+ else if (!(this._id.equals(temp._id)))
+ return false;
+ }
+ else if (temp._id != null)
+ return false;
+ if (this._modifiable != temp._modifiable)
+ return false;
+ if (this._has_modifiable != temp._has_modifiable)
+ return false;
+ if (this._group != null) {
+ if (temp._group == null) return false;
+ else if (!(this._group.equals(temp._group)))
+ return false;
+ }
+ else if (temp._group != null)
+ return false;
+ 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._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._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._scoreList != null) {
+ if (temp._scoreList == null) return false;
+ else if (!(this._scoreList.equals(temp._scoreList)))
+ return false;
+ }
+ else if (temp._scoreList != null)
+ return false;
+ if (this._urlList != null) {
+ if (temp._urlList == null) return false;
+ else if (!(this._urlList.equals(temp._urlList)))
+ return false;
+ }
+ else if (temp._urlList != null)
+ return false;
+ if (this._propertyList != null) {
+ if (temp._propertyList == null) return false;
+ else if (!(this._propertyList.equals(temp._propertyList)))
+ return false;
+ }
+ else if (temp._propertyList != null)
+ return false;
+ return true;
+ }
+ return false;
+ } //-- boolean equals(java.lang.Object)
+
+ /**
+ * Method getAnnotationElement
+ *
+ *
+ *
+ * @param index
+ * @return AnnotationElement
+ */
+ public org.vamsas.objects.core.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.objects.core.AnnotationElement) _annotationElementList.elementAt(index);
+ } //-- org.vamsas.objects.core.AnnotationElement getAnnotationElement(int)
+
+ /**
+ * Method getAnnotationElement
+ *
+ *
+ *
+ * @return AnnotationElement
+ */
+ public org.vamsas.objects.core.AnnotationElement[] getAnnotationElement()
+ {
+ int size = _annotationElementList.size();
+ org.vamsas.objects.core.AnnotationElement[] mArray = new org.vamsas.objects.core.AnnotationElement[size];
+ for (int index = 0; index < size; index++) {
+ mArray[index] = (org.vamsas.objects.core.AnnotationElement) _annotationElementList.elementAt(index);
+ }
+ return mArray;
+ } //-- org.vamsas.objects.core.AnnotationElement[] getAnnotationElement()
+
+ /**
+ * Method getAnnotationElementCount
+ *
+ *
+ *
+ * @return int
+ */
+ public int getAnnotationElementCount()
+ {
+ return _annotationElementList.size();
+ } //-- int getAnnotationElementCount()
+
+ /**
+ * Returns the value of field 'description'. The field
+ * 'description' has the following description: Human readable
+ * description of the annotation
+ *
+ *
+ * @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 'group'. The field 'group' has
+ * the following description: Annotation with the same
+ * non-empty group
+ * name are grouped together
+ *
+ *
+ * @return String
+ * @return the value of field 'group'.
+ */
+ public java.lang.String getGroup()
+ {
+ return this._group;
+ } //-- java.lang.String getGroup()
+
+ /**
+ * Returns the value of field 'id'. The field 'id' has the
+ * following description: Primary Key for vamsas object
+ * referencing
+ *
+ *
+ * @return String
+ * @return the value of field 'id'.
+ */
+ public java.lang.String getId()
+ {
+ return this._id;
+ } //-- java.lang.String getId()
+
+ /**
+ * Returns the value of field 'label'. The field 'label' has
+ * the following description: Short, meaningful name for the
+ * annotation - if this is absent, then the type string should
+ * be used in its place.
+ *
+ *
+ * @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 'modifiable'. The field
+ * 'modifiable' has the following description: objects with
+ * modifiable=false will not be
+ * modified by a vamsas client update
+ *
+ *
+ * @return boolean
+ * @return the value of field 'modifiable'.
+ */
+ public boolean getModifiable()
+ {
+ return this._modifiable;
+ } //-- boolean getModifiable()
+
+ /**
+ * Method getProperty
+ *
+ *
+ *
+ * @param index
+ * @return Property
+ */
+ public org.vamsas.objects.core.Property getProperty(int index)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ //-- check bounds for index
+ if ((index < 0) || (index > _propertyList.size())) {
+ throw new IndexOutOfBoundsException("getProperty: Index value '"+index+"' not in range [0.."+_propertyList.size()+ "]");
+ }
+
+ return (org.vamsas.objects.core.Property) _propertyList.elementAt(index);
+ } //-- org.vamsas.objects.core.Property getProperty(int)
+
+ /**
+ * Method getProperty
+ *
+ *
+ *
+ * @return Property
+ */
+ public org.vamsas.objects.core.Property[] getProperty()
+ {
+ int size = _propertyList.size();
+ org.vamsas.objects.core.Property[] mArray = new org.vamsas.objects.core.Property[size];
+ for (int index = 0; index < size; index++) {
+ mArray[index] = (org.vamsas.objects.core.Property) _propertyList.elementAt(index);
+ }
+ return mArray;
+ } //-- org.vamsas.objects.core.Property[] getProperty()
+
+ /**
+ * Method getPropertyCount
+ *
+ *
+ *
+ * @return int
+ */
+ public int getPropertyCount()
+ {
+ return _propertyList.size();
+ } //-- int getPropertyCount()
+
+ /**
+ * Method getScore
+ *
+ *
+ *
+ * @param index
+ * @return Score
+ */
+ public org.vamsas.objects.core.Score getScore(int index)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ //-- check bounds for index
+ if ((index < 0) || (index > _scoreList.size())) {
+ throw new IndexOutOfBoundsException("getScore: Index value '"+index+"' not in range [0.."+_scoreList.size()+ "]");
+ }
+
+ return (org.vamsas.objects.core.Score) _scoreList.elementAt(index);
+ } //-- org.vamsas.objects.core.Score getScore(int)
+
+ /**
+ * Method getScore
+ *
+ *
+ *
+ * @return Score
+ */
+ public org.vamsas.objects.core.Score[] getScore()
+ {
+ int size = _scoreList.size();
+ org.vamsas.objects.core.Score[] mArray = new org.vamsas.objects.core.Score[size];
+ for (int index = 0; index < size; index++) {
+ mArray[index] = (org.vamsas.objects.core.Score) _scoreList.elementAt(index);
+ }
+ return mArray;
+ } //-- org.vamsas.objects.core.Score[] getScore()
+
+ /**
+ * Method getScoreCount
+ *
+ *
+ *
+ * @return int
+ */
+ public int getScoreCount()
+ {
+ return _scoreList.size();
+ } //-- int getScoreCount()
+
+ /**
+ * Returns the value of field 'status'. The field 'status' has
+ * the following description: TODO: specify this - we have
+ * considered taking the GO evidence codes as a model for
+ * assessing a measure of quality to an annotation.
+ *
+ *
+ * @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'. The field 'type' has the
+ * following description: A Das Feature has both a type and a
+ * Type ID.
+ * We go the route of requiring the type string
+ * to be taken from a controlled vocabulary if
+ * an application expects others to make sense
+ * of it.
+ * The type may qualified - so uniprot:CHAIN is a valid type
+ * name,
+ * and considered distinct from someotherDB:CHAIN
+ *
+ *
+ * @return String
+ * @return the value of field 'type'.
+ */
+ public java.lang.String getType()
+ {
+ return this._type;
+ } //-- java.lang.String getType()
+
+ /**
+ * Method getUrl
+ *
+ *
+ *
+ * @param index
+ * @return Url
+ */
+ public org.vamsas.objects.core.Url getUrl(int index)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ //-- check bounds for index
+ if ((index < 0) || (index > _urlList.size())) {
+ throw new IndexOutOfBoundsException("getUrl: Index value '"+index+"' not in range [0.."+_urlList.size()+ "]");
+ }
+
+ return (org.vamsas.objects.core.Url) _urlList.elementAt(index);
+ } //-- org.vamsas.objects.core.Url getUrl(int)
+
+ /**
+ * Method getUrl
+ *
+ *
+ *
+ * @return Url
+ */
+ public org.vamsas.objects.core.Url[] getUrl()
+ {
+ int size = _urlList.size();
+ org.vamsas.objects.core.Url[] mArray = new org.vamsas.objects.core.Url[size];
+ for (int index = 0; index < size; index++) {
+ mArray[index] = (org.vamsas.objects.core.Url) _urlList.elementAt(index);
+ }
+ return mArray;
+ } //-- org.vamsas.objects.core.Url[] getUrl()
+
+ /**
+ * Method getUrlCount
+ *
+ *
+ *
+ * @return int
+ */
+ public int getUrlCount()
+ {
+ return _urlList.size();
+ } //-- int getUrlCount()
+
+ /**
+ * Method hasModifiable
+ *
+ *
+ *
+ * @return boolean
+ */
+ public boolean hasModifiable()
+ {
+ return this._has_modifiable;
+ } //-- boolean hasModifiable()
+
+ /**
+ * 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 removeAllProperty
+ *
+ */
+ public void removeAllProperty()
+ {
+ _propertyList.removeAllElements();
+ } //-- void removeAllProperty()
+
+ /**
+ * Method removeAllScore
+ *
+ */
+ public void removeAllScore()
+ {
+ _scoreList.removeAllElements();
+ } //-- void removeAllScore()
+
+ /**
+ * Method removeAllUrl
+ *
+ */
+ public void removeAllUrl()
+ {
+ _urlList.removeAllElements();
+ } //-- void removeAllUrl()
+
+ /**
+ * Method removeAnnotationElement
+ *
+ *
+ *
+ * @param index
+ * @return AnnotationElement
+ */
+ public org.vamsas.objects.core.AnnotationElement removeAnnotationElement(int index)
+ {
+ java.lang.Object obj = _annotationElementList.elementAt(index);
+ _annotationElementList.removeElementAt(index);
+ return (org.vamsas.objects.core.AnnotationElement) obj;
+ } //-- org.vamsas.objects.core.AnnotationElement removeAnnotationElement(int)
+
+ /**
+ * Method removeProperty
+ *
+ *
+ *
+ * @param index
+ * @return Property
+ */
+ public org.vamsas.objects.core.Property removeProperty(int index)
+ {
+ java.lang.Object obj = _propertyList.elementAt(index);
+ _propertyList.removeElementAt(index);
+ return (org.vamsas.objects.core.Property) obj;
+ } //-- org.vamsas.objects.core.Property removeProperty(int)
+
+ /**
+ * Method removeScore
+ *
+ *
+ *
+ * @param index
+ * @return Score
+ */
+ public org.vamsas.objects.core.Score removeScore(int index)
+ {
+ java.lang.Object obj = _scoreList.elementAt(index);
+ _scoreList.removeElementAt(index);
+ return (org.vamsas.objects.core.Score) obj;
+ } //-- org.vamsas.objects.core.Score removeScore(int)
+
+ /**
+ * Method removeUrl
+ *
+ *
+ *
+ * @param index
+ * @return Url
+ */
+ public org.vamsas.objects.core.Url removeUrl(int index)
+ {
+ java.lang.Object obj = _urlList.elementAt(index);
+ _urlList.removeElementAt(index);
+ return (org.vamsas.objects.core.Url) obj;
+ } //-- org.vamsas.objects.core.Url removeUrl(int)
+
+ /**
+ * Method setAnnotationElement
+ *
+ *
+ *
+ * @param index
+ * @param vAnnotationElement
+ */
+ public void setAnnotationElement(int index, org.vamsas.objects.core.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.objects.core.AnnotationElement)
+
+ /**
+ * Method setAnnotationElement
+ *
+ *
+ *
+ * @param annotationElementArray
+ */
+ public void setAnnotationElement(org.vamsas.objects.core.AnnotationElement[] annotationElementArray)
+ {
+ //-- copy array
+ _annotationElementList.removeAllElements();
+ for (int i = 0; i < annotationElementArray.length; i++) {
+ _annotationElementList.addElement(annotationElementArray[i]);
+ }
+ } //-- void setAnnotationElement(org.vamsas.objects.core.AnnotationElement)
+
+ /**
+ * Sets the value of field 'description'. The field
+ * 'description' has the following description: Human readable
+ * description of the annotation
+ *
+ *
+ * @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 'group'. The field 'group' has the
+ * following description: Annotation with the same non-empty
+ * group
+ * name are grouped together
+ *
+ *
+ * @param group the value of field 'group'.
+ */
+ public void setGroup(java.lang.String group)
+ {
+ this._group = group;
+ } //-- void setGroup(java.lang.String)
+
+ /**
+ * Sets the value of field 'id'. The field 'id' has the
+ * following description: Primary Key for vamsas object
+ * referencing
+ *
+ *
+ * @param id the value of field 'id'.
+ */
+ public void setId(java.lang.String id)
+ {
+ this._id = id;
+ } //-- void setId(java.lang.String)
+
+ /**
+ * Sets the value of field 'label'. The field 'label' has the
+ * following description: Short, meaningful name for the
+ * annotation - if this is absent, then the type string should
+ * be used in its place.
+ *
+ *
+ * @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 'modifiable'. The field 'modifiable'
+ * has the following description: objects with modifiable=false
+ * will not be
+ * modified by a vamsas client update
+ *
+ *
+ * @param modifiable the value of field 'modifiable'.
+ */
+ public void setModifiable(boolean modifiable)
+ {
+ this._modifiable = modifiable;
+ this._has_modifiable = true;
+ } //-- void setModifiable(boolean)
+
+ /**
+ * Method setProperty
+ *
+ *
+ *
+ * @param index
+ * @param vProperty
+ */
+ public void setProperty(int index, org.vamsas.objects.core.Property vProperty)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ //-- check bounds for index
+ if ((index < 0) || (index > _propertyList.size())) {
+ throw new IndexOutOfBoundsException("setProperty: Index value '"+index+"' not in range [0.."+_propertyList.size()+ "]");
+ }
+ _propertyList.setElementAt(vProperty, index);
+ } //-- void setProperty(int, org.vamsas.objects.core.Property)
+
+ /**
+ * Method setProperty
+ *
+ *
+ *
+ * @param propertyArray
+ */
+ public void setProperty(org.vamsas.objects.core.Property[] propertyArray)
+ {
+ //-- copy array
+ _propertyList.removeAllElements();
+ for (int i = 0; i < propertyArray.length; i++) {
+ _propertyList.addElement(propertyArray[i]);
+ }
+ } //-- void setProperty(org.vamsas.objects.core.Property)
+
+ /**
+ * Method setScore
+ *
+ *
+ *
+ * @param index
+ * @param vScore
+ */
+ public void setScore(int index, org.vamsas.objects.core.Score vScore)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ //-- check bounds for index
+ if ((index < 0) || (index > _scoreList.size())) {
+ throw new IndexOutOfBoundsException("setScore: Index value '"+index+"' not in range [0.."+_scoreList.size()+ "]");
+ }
+ _scoreList.setElementAt(vScore, index);
+ } //-- void setScore(int, org.vamsas.objects.core.Score)
+
+ /**
+ * Method setScore
+ *
+ *
+ *
+ * @param scoreArray
+ */
+ public void setScore(org.vamsas.objects.core.Score[] scoreArray)
+ {
+ //-- copy array
+ _scoreList.removeAllElements();
+ for (int i = 0; i < scoreArray.length; i++) {
+ _scoreList.addElement(scoreArray[i]);
+ }
+ } //-- void setScore(org.vamsas.objects.core.Score)
+
+ /**
+ * Sets the value of field 'status'. The field 'status' has the
+ * following description: TODO: specify this - we have
+ * considered taking the GO evidence codes as a model for
+ * assessing a measure of quality to an annotation.
+ *
+ *
+ * @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'. The field 'type' has the
+ * following description: A Das Feature has both a type and a
+ * Type ID.
+ * We go the route of requiring the type string
+ * to be taken from a controlled vocabulary if
+ * an application expects others to make sense
+ * of it.
+ * The type may qualified - so uniprot:CHAIN is a valid type
+ * name,
+ * and considered distinct from someotherDB:CHAIN
+ *
+ *
+ * @param type the value of field 'type'.
+ */
+ public void setType(java.lang.String type)
+ {
+ this._type = type;
+ } //-- void setType(java.lang.String)
+
+ /**
+ * Method setUrl
+ *
+ *
+ *
+ * @param index
+ * @param vUrl
+ */
+ public void setUrl(int index, org.vamsas.objects.core.Url vUrl)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ //-- check bounds for index
+ if ((index < 0) || (index > _urlList.size())) {
+ throw new IndexOutOfBoundsException("setUrl: Index value '"+index+"' not in range [0.."+_urlList.size()+ "]");
+ }
+ _urlList.setElementAt(vUrl, index);
+ } //-- void setUrl(int, org.vamsas.objects.core.Url)
+
+ /**
+ * Method setUrl
+ *
+ *
+ *
+ * @param urlArray
+ */
+ public void setUrl(org.vamsas.objects.core.Url[] urlArray)
+ {
+ //-- copy array
+ _urlList.removeAllElements();
+ for (int i = 0; i < urlArray.length; i++) {
+ _urlList.addElement(urlArray[i]);
+ }
+ } //-- void setUrl(org.vamsas.objects.core.Url)
+
+ /**
+ * Method unmarshal
+ *
+ *
+ *
+ * @param reader
+ * @return RangeType
+ */
+ public static org.vamsas.objects.core.RangeType unmarshal(java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+ {
+ return (org.vamsas.objects.core.RangeAnnotation) Unmarshaller.unmarshal(org.vamsas.objects.core.RangeAnnotation.class, reader);
+ } //-- org.vamsas.objects.core.RangeType unmarshal(java.io.Reader)
+
+ /**
+ * Method validate
+ *
+ */
+ public void validate()
+ throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ } //-- void validate()
+
+}
--- /dev/null
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package org.vamsas.objects.core;
+
+ //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.mapping.AccessMode;
+import org.exolab.castor.xml.TypeValidator;
+import org.exolab.castor.xml.XMLFieldDescriptor;
+import org.exolab.castor.xml.validators.*;
+
+/**
+ * Class RangeAnnotationDescriptor.
+ *
+ * @version $Revision$ $Date$
+ */
+public class RangeAnnotationDescriptor extends org.vamsas.objects.core.RangeTypeDescriptor {
+
+
+ //--------------------------/
+ //- 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 RangeAnnotationDescriptor()
+ {
+ super();
+ setExtendsWithoutFlatten(new org.vamsas.objects.core.RangeTypeDescriptor());
+ nsURI = "http://www.vamsas.org";
+ xmlName = "rangeAnnotation";
+
+ //-- set grouping compositor
+ setCompositorAsSequence();
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+ org.exolab.castor.mapping.FieldHandler handler = null;
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;
+ //-- initialize attribute descriptors
+
+ //-- _id
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute);
+ this.identity = desc;
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ RangeAnnotation target = (RangeAnnotation) object;
+ return target.getId();
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ RangeAnnotation target = (RangeAnnotation) object;
+ target.setId( (java.lang.String) value);
+ }
+ catch (java.lang.Exception ex) {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+ public java.lang.Object newInstance( java.lang.Object parent ) {
+ return new java.lang.String();
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _id
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { //-- local scope
+ }
+ desc.setValidator(fieldValidator);
+ //-- _modifiable
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_modifiable", "modifiable", org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ RangeAnnotation target = (RangeAnnotation) object;
+ if(!target.hasModifiable())
+ return null;
+ return (target.getModifiable() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ RangeAnnotation target = (RangeAnnotation) object;
+ // if null, use delete method for optional primitives
+ if (value == null) {
+ target.deleteModifiable();
+ return;
+ }
+ target.setModifiable( ((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: _modifiable
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { //-- local scope
+ BooleanValidator typeValidator = new BooleanValidator();
+ fieldValidator.setValidator(typeValidator);
+ }
+ desc.setValidator(fieldValidator);
+ //-- _group
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_group", "group", 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
+ {
+ RangeAnnotation target = (RangeAnnotation) object;
+ return target.getGroup();
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ RangeAnnotation target = (RangeAnnotation) object;
+ target.setGroup( (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: _group
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { //-- local scope
+ StringValidator typeValidator = new StringValidator();
+ typeValidator.setWhiteSpace("preserve");
+ fieldValidator.setValidator(typeValidator);
+ }
+ desc.setValidator(fieldValidator);
+ //-- _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
+ {
+ RangeAnnotation target = (RangeAnnotation) object;
+ return target.getType();
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ RangeAnnotation target = (RangeAnnotation) 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);
+ //-- initialize element descriptors
+
+ //-- _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
+ {
+ RangeAnnotation target = (RangeAnnotation) object;
+ return target.getLabel();
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ RangeAnnotation target = (RangeAnnotation) 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.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _label
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { //-- 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
+ {
+ RangeAnnotation target = (RangeAnnotation) object;
+ return target.getDescription();
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ RangeAnnotation target = (RangeAnnotation) 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
+ {
+ RangeAnnotation target = (RangeAnnotation) object;
+ return target.getStatus();
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ RangeAnnotation target = (RangeAnnotation) 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.objects.core.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
+ {
+ RangeAnnotation target = (RangeAnnotation) object;
+ return target.getAnnotationElement();
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ RangeAnnotation target = (RangeAnnotation) object;
+ target.addAnnotationElement( (org.vamsas.objects.core.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.objects.core.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);
+ //-- _scoreList
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Score.class, "_scoreList", "score", org.exolab.castor.xml.NodeType.Element);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ RangeAnnotation target = (RangeAnnotation) object;
+ return target.getScore();
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ RangeAnnotation target = (RangeAnnotation) object;
+ target.addScore( (org.vamsas.objects.core.Score) value);
+ }
+ catch (java.lang.Exception ex) {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+ public java.lang.Object newInstance( java.lang.Object parent ) {
+ return new org.vamsas.objects.core.Score();
+ }
+ };
+ desc.setHandler(handler);
+ desc.setNameSpaceURI("http://www.vamsas.org");
+ desc.setMultivalued(true);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _scoreList
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(0);
+ { //-- local scope
+ }
+ desc.setValidator(fieldValidator);
+ //-- _urlList
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Url.class, "_urlList", "url", org.exolab.castor.xml.NodeType.Element);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ RangeAnnotation target = (RangeAnnotation) object;
+ return target.getUrl();
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ RangeAnnotation target = (RangeAnnotation) object;
+ target.addUrl( (org.vamsas.objects.core.Url) value);
+ }
+ catch (java.lang.Exception ex) {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+ public java.lang.Object newInstance( java.lang.Object parent ) {
+ return new org.vamsas.objects.core.Url();
+ }
+ };
+ desc.setHandler(handler);
+ desc.setNameSpaceURI("http://www.vamsas.org");
+ desc.setMultivalued(true);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _urlList
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(0);
+ { //-- local scope
+ }
+ desc.setValidator(fieldValidator);
+ //-- _propertyList
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Property.class, "_propertyList", "property", org.exolab.castor.xml.NodeType.Element);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ RangeAnnotation target = (RangeAnnotation) object;
+ return target.getProperty();
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ RangeAnnotation target = (RangeAnnotation) object;
+ target.addProperty( (org.vamsas.objects.core.Property) value);
+ }
+ catch (java.lang.Exception ex) {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+ public java.lang.Object newInstance( java.lang.Object parent ) {
+ return new org.vamsas.objects.core.Property();
+ }
+ };
+ desc.setHandler(handler);
+ desc.setNameSpaceURI("http://www.vamsas.org");
+ desc.setMultivalued(true);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _propertyList
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(0);
+ { //-- local scope
+ }
+ desc.setValidator(fieldValidator);
+ } //-- org.vamsas.objects.core.RangeAnnotationDescriptor()
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ * Method getAccessMode
+ *
+ *
+ *
+ * @return AccessMode
+ */
+ public org.exolab.castor.mapping.AccessMode getAccessMode()
+ {
+ return null;
+ } //-- org.exolab.castor.mapping.AccessMode getAccessMode()
+
+ /**
+ * Method getExtends
+ *
+ *
+ *
+ * @return ClassDescriptor
+ */
+ public org.exolab.castor.mapping.ClassDescriptor getExtends()
+ {
+ return super.getExtends();
+ } //-- org.exolab.castor.mapping.ClassDescriptor getExtends()
+
+ /**
+ * Method getIdentity
+ *
+ *
+ *
+ * @return FieldDescriptor
+ */
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+ {
+ if (identity == null)
+ return super.getIdentity();
+ return identity;
+ } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity()
+
+ /**
+ * Method getJavaClass
+ *
+ *
+ *
+ * @return Class
+ */
+ public java.lang.Class getJavaClass()
+ {
+ return org.vamsas.objects.core.RangeAnnotation.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 0.9.9M2</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package org.vamsas.objects.core;
+
+ //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+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.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+import org.exolab.castor.xml.ValidationException;
+
+/**
+ * Specify an ordered set of positions and/or regions on the
+ * principle
+ * dimension of some associated vamsas object
+ *
+ * Keeping to jaxb-1.0 specification for the moment - this
+ * choice should become a substitution group when we use
+ * jaxb-2.0 capable bindings
+ *
+ *
+ * @version $Revision$ $Date$
+ */
+public abstract class RangeType extends org.vamsas.client.Vobject
+implements java.io.Serializable
+{
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * Internal choice value storage
+ */
+ private java.lang.Object _choiceValue;
+
+ /**
+ * a position within the associated object's
+ * coordinate system
+ *
+ */
+ private java.util.Vector _posList;
+
+ /**
+ * a region from start to end, with flag for
+ * inclusivity of terminii
+ *
+ */
+ private java.util.Vector _segList;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public RangeType()
+ {
+ super();
+ _posList = new Vector();
+ _segList = new Vector();
+ } //-- org.vamsas.objects.core.RangeType()
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ * Method addPos
+ *
+ *
+ *
+ * @param vPos
+ */
+ public void addPos(org.vamsas.objects.core.Pos vPos)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _posList.addElement(vPos);
+ } //-- void addPos(org.vamsas.objects.core.Pos)
+
+ /**
+ * Method addPos
+ *
+ *
+ *
+ * @param index
+ * @param vPos
+ */
+ public void addPos(int index, org.vamsas.objects.core.Pos vPos)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _posList.insertElementAt(vPos, index);
+ } //-- void addPos(int, org.vamsas.objects.core.Pos)
+
+ /**
+ * Method addSeg
+ *
+ *
+ *
+ * @param vSeg
+ */
+ public void addSeg(org.vamsas.objects.core.Seg vSeg)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _segList.addElement(vSeg);
+ } //-- void addSeg(org.vamsas.objects.core.Seg)
+
+ /**
+ * Method addSeg
+ *
+ *
+ *
+ * @param index
+ * @param vSeg
+ */
+ public void addSeg(int index, org.vamsas.objects.core.Seg vSeg)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _segList.insertElementAt(vSeg, index);
+ } //-- void addSeg(int, org.vamsas.objects.core.Seg)
+
+ /**
+ * Method enumeratePos
+ *
+ *
+ *
+ * @return Enumeration
+ */
+ public java.util.Enumeration enumeratePos()
+ {
+ return _posList.elements();
+ } //-- java.util.Enumeration enumeratePos()
+
+ /**
+ * Method enumerateSeg
+ *
+ *
+ *
+ * @return Enumeration
+ */
+ public java.util.Enumeration enumerateSeg()
+ {
+ return _segList.elements();
+ } //-- java.util.Enumeration enumerateSeg()
+
+ /**
+ * 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 RangeType) {
+
+ RangeType temp = (RangeType)obj;
+ if (this._choiceValue != null) {
+ if (temp._choiceValue == null) return false;
+ else if (!(this._choiceValue.equals(temp._choiceValue)))
+ return false;
+ }
+ else if (temp._choiceValue != null)
+ return false;
+ if (this._posList != null) {
+ if (temp._posList == null) return false;
+ else if (!(this._posList.equals(temp._posList)))
+ return false;
+ }
+ else if (temp._posList != null)
+ return false;
+ if (this._segList != null) {
+ if (temp._segList == null) return false;
+ else if (!(this._segList.equals(temp._segList)))
+ return false;
+ }
+ else if (temp._segList != null)
+ return false;
+ return true;
+ }
+ return false;
+ } //-- boolean equals(java.lang.Object)
+
+ /**
+ * Returns the value of field 'choiceValue'. The field
+ * 'choiceValue' has the following description: Internal choice
+ * value storage
+ *
+ * @return Object
+ * @return the value of field 'choiceValue'.
+ */
+ public java.lang.Object getChoiceValue()
+ {
+ return this._choiceValue;
+ } //-- java.lang.Object getChoiceValue()
+
+ /**
+ * Method getPos
+ *
+ *
+ *
+ * @param index
+ * @return Pos
+ */
+ public org.vamsas.objects.core.Pos getPos(int index)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ //-- check bounds for index
+ if ((index < 0) || (index > _posList.size())) {
+ throw new IndexOutOfBoundsException("getPos: Index value '"+index+"' not in range [0.."+_posList.size()+ "]");
+ }
+
+ return (org.vamsas.objects.core.Pos) _posList.elementAt(index);
+ } //-- org.vamsas.objects.core.Pos getPos(int)
+
+ /**
+ * Method getPos
+ *
+ *
+ *
+ * @return Pos
+ */
+ public org.vamsas.objects.core.Pos[] getPos()
+ {
+ int size = _posList.size();
+ org.vamsas.objects.core.Pos[] mArray = new org.vamsas.objects.core.Pos[size];
+ for (int index = 0; index < size; index++) {
+ mArray[index] = (org.vamsas.objects.core.Pos) _posList.elementAt(index);
+ }
+ return mArray;
+ } //-- org.vamsas.objects.core.Pos[] getPos()
+
+ /**
+ * Method getPosCount
+ *
+ *
+ *
+ * @return int
+ */
+ public int getPosCount()
+ {
+ return _posList.size();
+ } //-- int getPosCount()
+
+ /**
+ * Method getSeg
+ *
+ *
+ *
+ * @param index
+ * @return Seg
+ */
+ public org.vamsas.objects.core.Seg getSeg(int index)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ //-- check bounds for index
+ if ((index < 0) || (index > _segList.size())) {
+ throw new IndexOutOfBoundsException("getSeg: Index value '"+index+"' not in range [0.."+_segList.size()+ "]");
+ }
+
+ return (org.vamsas.objects.core.Seg) _segList.elementAt(index);
+ } //-- org.vamsas.objects.core.Seg getSeg(int)
+
+ /**
+ * Method getSeg
+ *
+ *
+ *
+ * @return Seg
+ */
+ public org.vamsas.objects.core.Seg[] getSeg()
+ {
+ int size = _segList.size();
+ org.vamsas.objects.core.Seg[] mArray = new org.vamsas.objects.core.Seg[size];
+ for (int index = 0; index < size; index++) {
+ mArray[index] = (org.vamsas.objects.core.Seg) _segList.elementAt(index);
+ }
+ return mArray;
+ } //-- org.vamsas.objects.core.Seg[] getSeg()
+
+ /**
+ * Method getSegCount
+ *
+ *
+ *
+ * @return int
+ */
+ public int getSegCount()
+ {
+ return _segList.size();
+ } //-- int getSegCount()
+
+ /**
+ * Method isValid
+ *
+ *
+ *
+ * @return boolean
+ */
+ public boolean isValid()
+ {
+ try {
+ validate();
+ }
+ catch (org.exolab.castor.xml.ValidationException vex) {
+ return false;
+ }
+ return true;
+ } //-- boolean isValid()
+
+ /**
+ * Method removeAllPos
+ *
+ */
+ public void removeAllPos()
+ {
+ _posList.removeAllElements();
+ } //-- void removeAllPos()
+
+ /**
+ * Method removeAllSeg
+ *
+ */
+ public void removeAllSeg()
+ {
+ _segList.removeAllElements();
+ } //-- void removeAllSeg()
+
+ /**
+ * Method removePos
+ *
+ *
+ *
+ * @param index
+ * @return Pos
+ */
+ public org.vamsas.objects.core.Pos removePos(int index)
+ {
+ java.lang.Object obj = _posList.elementAt(index);
+ _posList.removeElementAt(index);
+ return (org.vamsas.objects.core.Pos) obj;
+ } //-- org.vamsas.objects.core.Pos removePos(int)
+
+ /**
+ * Method removeSeg
+ *
+ *
+ *
+ * @param index
+ * @return Seg
+ */
+ public org.vamsas.objects.core.Seg removeSeg(int index)
+ {
+ java.lang.Object obj = _segList.elementAt(index);
+ _segList.removeElementAt(index);
+ return (org.vamsas.objects.core.Seg) obj;
+ } //-- org.vamsas.objects.core.Seg removeSeg(int)
+
+ /**
+ * Method setPos
+ *
+ *
+ *
+ * @param index
+ * @param vPos
+ */
+ public void setPos(int index, org.vamsas.objects.core.Pos vPos)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ //-- check bounds for index
+ if ((index < 0) || (index > _posList.size())) {
+ throw new IndexOutOfBoundsException("setPos: Index value '"+index+"' not in range [0.."+_posList.size()+ "]");
+ }
+ _posList.setElementAt(vPos, index);
+ } //-- void setPos(int, org.vamsas.objects.core.Pos)
+
+ /**
+ * Method setPos
+ *
+ *
+ *
+ * @param posArray
+ */
+ public void setPos(org.vamsas.objects.core.Pos[] posArray)
+ {
+ //-- copy array
+ _posList.removeAllElements();
+ for (int i = 0; i < posArray.length; i++) {
+ _posList.addElement(posArray[i]);
+ }
+ } //-- void setPos(org.vamsas.objects.core.Pos)
+
+ /**
+ * Method setSeg
+ *
+ *
+ *
+ * @param index
+ * @param vSeg
+ */
+ public void setSeg(int index, org.vamsas.objects.core.Seg vSeg)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ //-- check bounds for index
+ if ((index < 0) || (index > _segList.size())) {
+ throw new IndexOutOfBoundsException("setSeg: Index value '"+index+"' not in range [0.."+_segList.size()+ "]");
+ }
+ _segList.setElementAt(vSeg, index);
+ } //-- void setSeg(int, org.vamsas.objects.core.Seg)
+
+ /**
+ * Method setSeg
+ *
+ *
+ *
+ * @param segArray
+ */
+ public void setSeg(org.vamsas.objects.core.Seg[] segArray)
+ {
+ //-- copy array
+ _segList.removeAllElements();
+ for (int i = 0; i < segArray.length; i++) {
+ _segList.addElement(segArray[i]);
+ }
+ } //-- void setSeg(org.vamsas.objects.core.Seg)
+
+ /**
+ * Method validate
+ *
+ */
+ public void validate()
+ throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ } //-- void validate()
+
+}
--- /dev/null
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package org.vamsas.objects.core;
+
+ //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.mapping.AccessMode;
+import org.exolab.castor.xml.TypeValidator;
+import org.exolab.castor.xml.XMLFieldDescriptor;
+import org.exolab.castor.xml.validators.*;
+
+/**
+ * Class RangeTypeDescriptor.
+ *
+ * @version $Revision$ $Date$
+ */
+public class RangeTypeDescriptor 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 RangeTypeDescriptor()
+ {
+ super();
+ nsURI = "http://www.vamsas.org";
+ xmlName = "rangeType";
+
+ //-- set grouping compositor
+ setCompositorAsChoice();
+ 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
+
+ //-- _posList
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Pos.class, "_posList", "pos", org.exolab.castor.xml.NodeType.Element);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ RangeType target = (RangeType) object;
+ return target.getPos();
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ RangeType target = (RangeType) object;
+ target.addPos( (org.vamsas.objects.core.Pos) value);
+ }
+ catch (java.lang.Exception ex) {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+ public java.lang.Object newInstance( java.lang.Object parent ) {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setNameSpaceURI("http://www.vamsas.org");
+ desc.setRequired(true);
+ desc.setMultivalued(true);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _posList
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(1);
+ { //-- local scope
+ }
+ desc.setValidator(fieldValidator);
+ //-- _segList
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Seg.class, "_segList", "seg", org.exolab.castor.xml.NodeType.Element);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ RangeType target = (RangeType) object;
+ return target.getSeg();
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ RangeType target = (RangeType) object;
+ target.addSeg( (org.vamsas.objects.core.Seg) value);
+ }
+ catch (java.lang.Exception ex) {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+ public java.lang.Object newInstance( java.lang.Object parent ) {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setNameSpaceURI("http://www.vamsas.org");
+ desc.setRequired(true);
+ desc.setMultivalued(true);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _segList
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(1);
+ { //-- local scope
+ }
+ desc.setValidator(fieldValidator);
+ } //-- org.vamsas.objects.core.RangeTypeDescriptor()
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ * Method getAccessMode
+ *
+ *
+ *
+ * @return AccessMode
+ */
+ public org.exolab.castor.mapping.AccessMode getAccessMode()
+ {
+ return null;
+ } //-- org.exolab.castor.mapping.AccessMode getAccessMode()
+
+ /**
+ * Method getExtends
+ *
+ *
+ *
+ * @return ClassDescriptor
+ */
+ public org.exolab.castor.mapping.ClassDescriptor getExtends()
+ {
+ return null;
+ } //-- org.exolab.castor.mapping.ClassDescriptor getExtends()
+
+ /**
+ * Method getIdentity
+ *
+ *
+ *
+ * @return FieldDescriptor
+ */
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+ {
+ return identity;
+ } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity()
+
+ /**
+ * Method getJavaClass
+ *
+ *
+ *
+ * @return Class
+ */
+ public java.lang.Class getJavaClass()
+ {
+ return org.vamsas.objects.core.RangeType.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 0.9.9M2</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package org.vamsas.objects.core;
+
+ //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import java.io.IOException;
+import java.io.Reader;
+import java.io.Serializable;
+import java.io.Writer;
+import org.exolab.castor.xml.MarshalException;
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+import org.exolab.castor.xml.ValidationException;
+import org.xml.sax.ContentHandler;
+
+/**
+ * Ordered set of optionally named float
+ * values for the whole annotation
+ *
+ *
+ * @version $Revision$ $Date$
+ */
+public class Score extends org.vamsas.client.Vobject
+implements java.io.Serializable
+{
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * internal content storage
+ */
+ private float _content;
+
+ /**
+ * keeps track of state for field: _content
+ */
+ private boolean _has_content;
+
+ /**
+ * Field _name
+ */
+ private java.lang.String _name = "score";
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public Score()
+ {
+ super();
+ setName("score");
+ } //-- org.vamsas.objects.core.Score()
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ * Method deleteContent
+ *
+ */
+ public void deleteContent()
+ {
+ this._has_content= false;
+ } //-- void deleteContent()
+
+ /**
+ * 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 Score) {
+
+ Score temp = (Score)obj;
+ if (this._content != temp._content)
+ return false;
+ if (this._has_content != temp._has_content)
+ 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 'content'. The field 'content'
+ * has the following description: internal content storage
+ *
+ * @return float
+ * @return the value of field 'content'.
+ */
+ public float getContent()
+ {
+ return this._content;
+ } //-- float getContent()
+
+ /**
+ * 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()
+
+ /**
+ * Method hasContent
+ *
+ *
+ *
+ * @return boolean
+ */
+ public boolean hasContent()
+ {
+ return this._has_content;
+ } //-- boolean hasContent()
+
+ /**
+ * 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(float content)
+ {
+ this._content = content;
+ this._has_content = true;
+ } //-- void setContent(float)
+
+ /**
+ * 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)
+
+ /**
+ * Method unmarshal
+ *
+ *
+ *
+ * @param reader
+ * @return Score
+ */
+ public static org.vamsas.objects.core.Score unmarshal(java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+ {
+ return (org.vamsas.objects.core.Score) Unmarshaller.unmarshal(org.vamsas.objects.core.Score.class, reader);
+ } //-- org.vamsas.objects.core.Score unmarshal(java.io.Reader)
+
+ /**
+ * Method validate
+ *
+ */
+ public void validate()
+ throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ } //-- void validate()
+
+}
--- /dev/null
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package org.vamsas.objects.core;
+
+ //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.mapping.AccessMode;
+import org.exolab.castor.xml.TypeValidator;
+import org.exolab.castor.xml.XMLFieldDescriptor;
+import org.exolab.castor.xml.validators.*;
+
+/**
+ * Class ScoreDescriptor.
+ *
+ * @version $Revision$ $Date$
+ */
+public class ScoreDescriptor 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 ScoreDescriptor()
+ {
+ super();
+ nsURI = "http://www.vamsas.org";
+ xmlName = "score";
+ 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(float.class, "_content", "PCDATA", org.exolab.castor.xml.NodeType.Text);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ Score target = (Score) object;
+ if(!target.hasContent())
+ return null;
+ return new java.lang.Float(target.getContent());
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ Score target = (Score) object;
+ // if null, use delete method for optional primitives
+ if (value == null) {
+ target.deleteContent();
+ return;
+ }
+ target.setContent( ((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);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _content
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { //-- local scope
+ FloatValidator typeValidator = new FloatValidator();
+ fieldValidator.setValidator(typeValidator);
+ }
+ desc.setValidator(fieldValidator);
+ //-- initialize attribute descriptors
+
+ //-- _name
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_name", "name", org.exolab.castor.xml.NodeType.Attribute);
+ desc.setImmutable(true);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ Score target = (Score) object;
+ return target.getName();
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ Score target = (Score) 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.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _name
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { //-- local scope
+ StringValidator typeValidator = new StringValidator();
+ typeValidator.setWhiteSpace("preserve");
+ fieldValidator.setValidator(typeValidator);
+ }
+ desc.setValidator(fieldValidator);
+ //-- initialize element descriptors
+
+ } //-- org.vamsas.objects.core.ScoreDescriptor()
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ * Method getAccessMode
+ *
+ *
+ *
+ * @return AccessMode
+ */
+ public org.exolab.castor.mapping.AccessMode getAccessMode()
+ {
+ return null;
+ } //-- org.exolab.castor.mapping.AccessMode getAccessMode()
+
+ /**
+ * Method getExtends
+ *
+ *
+ *
+ * @return ClassDescriptor
+ */
+ public org.exolab.castor.mapping.ClassDescriptor getExtends()
+ {
+ return null;
+ } //-- org.exolab.castor.mapping.ClassDescriptor getExtends()
+
+ /**
+ * Method getIdentity
+ *
+ *
+ *
+ * @return FieldDescriptor
+ */
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+ {
+ return identity;
+ } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity()
+
+ /**
+ * Method getJavaClass
+ *
+ *
+ *
+ * @return Class
+ */
+ public java.lang.Class getJavaClass()
+ {
+ return org.vamsas.objects.core.Score.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 0.9.9M2</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package org.vamsas.objects.core;
+
+ //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import java.io.IOException;
+import java.io.Reader;
+import java.io.Serializable;
+import java.io.Writer;
+import org.exolab.castor.xml.MarshalException;
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+import org.exolab.castor.xml.ValidationException;
+import org.xml.sax.ContentHandler;
+
+/**
+ * a region from start to end, with flag for
+ * inclusivity of terminii
+ *
+ *
+ * @version $Revision$ $Date$
+ */
+public class Seg extends org.vamsas.client.Vobject
+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;
+
+ /**
+ * when false, a consecutive range like
+ * 'start=1, end=2' means the region lying
+ * after position 1 and before position 2
+ *
+ */
+ private boolean _inclusive;
+
+ /**
+ * keeps track of state for field: _inclusive
+ */
+ private boolean _has_inclusive;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public Seg()
+ {
+ super();
+ } //-- org.vamsas.objects.core.Seg()
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ * Method deleteEnd
+ *
+ */
+ public void deleteEnd()
+ {
+ this._has_end= false;
+ } //-- void deleteEnd()
+
+ /**
+ * Method deleteInclusive
+ *
+ */
+ public void deleteInclusive()
+ {
+ this._has_inclusive= false;
+ } //-- void deleteInclusive()
+
+ /**
+ * Method deleteStart
+ *
+ */
+ public void deleteStart()
+ {
+ this._has_start= false;
+ } //-- void deleteStart()
+
+ /**
+ * 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 Seg) {
+
+ Seg temp = (Seg)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._inclusive != temp._inclusive)
+ return false;
+ if (this._has_inclusive != temp._has_inclusive)
+ return false;
+ return true;
+ }
+ return false;
+ } //-- boolean equals(java.lang.Object)
+
+ /**
+ * 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 'inclusive'. The field
+ * 'inclusive' has the following description: when false, a
+ * consecutive range like
+ * 'start=1, end=2' means the region lying
+ * after position 1 and before position 2
+ *
+ *
+ * @return boolean
+ * @return the value of field 'inclusive'.
+ */
+ public boolean getInclusive()
+ {
+ return this._inclusive;
+ } //-- boolean getInclusive()
+
+ /**
+ * 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 hasInclusive
+ *
+ *
+ *
+ * @return boolean
+ */
+ public boolean hasInclusive()
+ {
+ return this._has_inclusive;
+ } //-- boolean hasInclusive()
+
+ /**
+ * 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)
+
+ /**
+ * 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 'inclusive'. The field 'inclusive'
+ * has the following description: when false, a consecutive
+ * range like
+ * 'start=1, end=2' means the region lying
+ * after position 1 and before position 2
+ *
+ *
+ * @param inclusive the value of field 'inclusive'.
+ */
+ public void setInclusive(boolean inclusive)
+ {
+ this._inclusive = inclusive;
+ this._has_inclusive = true;
+ } //-- void setInclusive(boolean)
+
+ /**
+ * 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 Seg
+ */
+ public static org.vamsas.objects.core.Seg unmarshal(java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+ {
+ return (org.vamsas.objects.core.Seg) Unmarshaller.unmarshal(org.vamsas.objects.core.Seg.class, reader);
+ } //-- org.vamsas.objects.core.Seg unmarshal(java.io.Reader)
+
+ /**
+ * Method validate
+ *
+ */
+ public void validate()
+ throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ } //-- void validate()
+
+}
--- /dev/null
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package org.vamsas.objects.core;
+
+ //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.mapping.AccessMode;
+import org.exolab.castor.xml.TypeValidator;
+import org.exolab.castor.xml.XMLFieldDescriptor;
+import org.exolab.castor.xml.validators.*;
+
+/**
+ * Class SegDescriptor.
+ *
+ * @version $Revision$ $Date$
+ */
+public class SegDescriptor 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 SegDescriptor()
+ {
+ super();
+ nsURI = "http://www.vamsas.org";
+ xmlName = "seg";
+ 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
+ {
+ Seg target = (Seg) 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 {
+ Seg target = (Seg) 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
+ {
+ Seg target = (Seg) 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 {
+ Seg target = (Seg) 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);
+ //-- _inclusive
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_inclusive", "inclusive", org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ Seg target = (Seg) object;
+ if(!target.hasInclusive())
+ return null;
+ return (target.getInclusive() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ Seg target = (Seg) object;
+ // ignore null values for non optional primitives
+ if (value == null) return;
+
+ target.setInclusive( ((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: _inclusive
+ 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
+
+ } //-- org.vamsas.objects.core.SegDescriptor()
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ * Method getAccessMode
+ *
+ *
+ *
+ * @return AccessMode
+ */
+ public org.exolab.castor.mapping.AccessMode getAccessMode()
+ {
+ return null;
+ } //-- org.exolab.castor.mapping.AccessMode getAccessMode()
+
+ /**
+ * Method getExtends
+ *
+ *
+ *
+ * @return ClassDescriptor
+ */
+ public org.exolab.castor.mapping.ClassDescriptor getExtends()
+ {
+ return null;
+ } //-- org.exolab.castor.mapping.ClassDescriptor getExtends()
+
+ /**
+ * Method getIdentity
+ *
+ *
+ *
+ * @return FieldDescriptor
+ */
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+ {
+ return identity;
+ } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity()
+
+ /**
+ * Method getJavaClass
+ *
+ *
+ *
+ * @return Class
+ */
+ public java.lang.Class getJavaClass()
+ {
+ return org.vamsas.objects.core.Seg.class;
+ } //-- java.lang.Class getJavaClass()
+
+ /**
+ * Method getNameSpacePrefix
+ *
+ *
+ *
+ * @return String
+ */
+ public java.lang.String getNameSpacePrefix()
+ {
+ return nsPrefix;
+ } //-- java.lang.String getNameSpacePrefix()
+
+ /**
+ * Method getNameSpaceURI
+ *
+ *
+ *
+ * @return String
+ */
+ public java.lang.String getNameSpaceURI()
+ {
+ return nsURI;
+ } //-- java.lang.String getNameSpaceURI()
+
+ /**
+ * Method getValidator
+ *
+ *
+ *
+ * @return TypeValidator
+ */
+ public org.exolab.castor.xml.TypeValidator getValidator()
+ {
+ return this;
+ } //-- org.exolab.castor.xml.TypeValidator getValidator()
+
+ /**
+ * Method getXMLName
+ *
+ *
+ *
+ * @return String
+ */
+ public java.lang.String getXMLName()
+ {
+ return xmlName;
+ } //-- java.lang.String getXMLName()
+
+}
//--------------------------/
/**
- * Field _id
+ * Primary Key for vamsas
+ * object referencing
+ *
*/
private java.lang.String _id;
/**
- * Field _dictionary
+ * symbol class for sequence
+ *
*/
private java.lang.String _dictionary;
/**
- * Field _dbRefList
+ * Store a list of database
+ * references for this
+ * sequence record - with
+ * optional mapping from
+ * database sequence to the
+ * given sequence record
+ *
*/
private java.util.Vector _dbRefList;
} //-- int getDbRefCount()
/**
- * Returns the value of field 'dictionary'.
+ * Returns the value of field 'dictionary'. The field
+ * 'dictionary' has the following description: symbol class for
+ * sequence
+ *
*
* @return String
* @return the value of field 'dictionary'.
} //-- java.lang.String getDictionary()
/**
- * Returns the value of field 'id'.
+ * Returns the value of field 'id'. The field 'id' has the
+ * following description: Primary Key for vamsas
+ * object referencing
+ *
*
* @return String
* @return the value of field 'id'.
} //-- void setDbRef(org.vamsas.objects.core.DbRef)
/**
- * Sets the value of field 'dictionary'.
+ * Sets the value of field 'dictionary'. The field 'dictionary'
+ * has the following description: symbol class for sequence
+ *
*
* @param dictionary the value of field 'dictionary'.
*/
} //-- void setDictionary(java.lang.String)
/**
- * Sets the value of field 'id'.
+ * Sets the value of field 'id'. The field 'id' has the
+ * following description: Primary Key for vamsas
+ * object referencing
+ *
*
* @param id the value of field 'id'.
*/
}
};
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);
}
};
desc.setHandler(handler);
+ desc.setRequired(true);
desc.setMultivalued(false);
addFieldDescriptor(desc);
//-- validation code for: _dictionary
fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(1);
{ //-- local scope
StringValidator typeValidator = new StringValidator();
typeValidator.setWhiteSpace("preserve");
import java.io.Reader;
import java.io.Serializable;
import java.io.Writer;
+import java.util.Enumeration;
+import java.util.Vector;
import org.exolab.castor.xml.MarshalException;
import org.exolab.castor.xml.Marshaller;
import org.exolab.castor.xml.Unmarshaller;
*/
private java.lang.String _name;
+ /**
+ * Field _description
+ */
+ private java.lang.String _description;
+
+ /**
+ * additional typed properties
+ *
+ */
+ private java.util.Vector _propertyList;
+
//----------------/
//- Constructors -/
public SequenceType()
{
super();
+ _propertyList = new Vector();
} //-- org.vamsas.objects.core.SequenceType()
//-----------/
/**
+ * Method addProperty
+ *
+ *
+ *
+ * @param vProperty
+ */
+ public void addProperty(org.vamsas.objects.core.Property vProperty)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _propertyList.addElement(vProperty);
+ } //-- void addProperty(org.vamsas.objects.core.Property)
+
+ /**
+ * Method addProperty
+ *
+ *
+ *
+ * @param index
+ * @param vProperty
+ */
+ public void addProperty(int index, org.vamsas.objects.core.Property vProperty)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _propertyList.insertElementAt(vProperty, index);
+ } //-- void addProperty(int, org.vamsas.objects.core.Property)
+
+ /**
* Method deleteEnd
*
*/
} //-- void deleteStart()
/**
+ * Method enumerateProperty
+ *
+ *
+ *
+ * @return Enumeration
+ */
+ public java.util.Enumeration enumerateProperty()
+ {
+ return _propertyList.elements();
+ } //-- java.util.Enumeration enumerateProperty()
+
+ /**
* Note: hashCode() has not been overriden
*
* @param obj
}
else if (temp._name != 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._propertyList != null) {
+ if (temp._propertyList == null) return false;
+ else if (!(this._propertyList.equals(temp._propertyList)))
+ return false;
+ }
+ else if (temp._propertyList != null)
+ 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 'end'.
*
* @return int
} //-- java.lang.String getName()
/**
+ * Method getProperty
+ *
+ *
+ *
+ * @param index
+ * @return Property
+ */
+ public org.vamsas.objects.core.Property getProperty(int index)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ //-- check bounds for index
+ if ((index < 0) || (index > _propertyList.size())) {
+ throw new IndexOutOfBoundsException("getProperty: Index value '"+index+"' not in range [0.."+_propertyList.size()+ "]");
+ }
+
+ return (org.vamsas.objects.core.Property) _propertyList.elementAt(index);
+ } //-- org.vamsas.objects.core.Property getProperty(int)
+
+ /**
+ * Method getProperty
+ *
+ *
+ *
+ * @return Property
+ */
+ public org.vamsas.objects.core.Property[] getProperty()
+ {
+ int size = _propertyList.size();
+ org.vamsas.objects.core.Property[] mArray = new org.vamsas.objects.core.Property[size];
+ for (int index = 0; index < size; index++) {
+ mArray[index] = (org.vamsas.objects.core.Property) _propertyList.elementAt(index);
+ }
+ return mArray;
+ } //-- org.vamsas.objects.core.Property[] getProperty()
+
+ /**
+ * Method getPropertyCount
+ *
+ *
+ *
+ * @return int
+ */
+ public int getPropertyCount()
+ {
+ return _propertyList.size();
+ } //-- int getPropertyCount()
+
+ /**
* Returns the value of field 'sequence'.
*
* @return String
} //-- void marshal(org.xml.sax.ContentHandler)
/**
+ * Method removeAllProperty
+ *
+ */
+ public void removeAllProperty()
+ {
+ _propertyList.removeAllElements();
+ } //-- void removeAllProperty()
+
+ /**
+ * Method removeProperty
+ *
+ *
+ *
+ * @param index
+ * @return Property
+ */
+ public org.vamsas.objects.core.Property removeProperty(int index)
+ {
+ java.lang.Object obj = _propertyList.elementAt(index);
+ _propertyList.removeElementAt(index);
+ return (org.vamsas.objects.core.Property) obj;
+ } //-- org.vamsas.objects.core.Property removeProperty(int)
+
+ /**
+ * 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'.
} //-- void setName(java.lang.String)
/**
+ * Method setProperty
+ *
+ *
+ *
+ * @param index
+ * @param vProperty
+ */
+ public void setProperty(int index, org.vamsas.objects.core.Property vProperty)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ //-- check bounds for index
+ if ((index < 0) || (index > _propertyList.size())) {
+ throw new IndexOutOfBoundsException("setProperty: Index value '"+index+"' not in range [0.."+_propertyList.size()+ "]");
+ }
+ _propertyList.setElementAt(vProperty, index);
+ } //-- void setProperty(int, org.vamsas.objects.core.Property)
+
+ /**
+ * Method setProperty
+ *
+ *
+ *
+ * @param propertyArray
+ */
+ public void setProperty(org.vamsas.objects.core.Property[] propertyArray)
+ {
+ //-- copy array
+ _propertyList.removeAllElements();
+ for (int i = 0; i < propertyArray.length; i++) {
+ _propertyList.addElement(propertyArray[i]);
+ }
+ } //-- void setProperty(org.vamsas.objects.core.Property)
+
+ /**
* Sets the value of field 'sequence'.
*
* @param sequence the value of field 'sequence'.
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
+ {
+ SequenceType target = (SequenceType) object;
+ return target.getDescription();
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ SequenceType target = (SequenceType) 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);
+ //-- _propertyList
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Property.class, "_propertyList", "property", 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.getProperty();
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ SequenceType target = (SequenceType) object;
+ target.addProperty( (org.vamsas.objects.core.Property) value);
+ }
+ catch (java.lang.Exception ex) {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+ public java.lang.Object newInstance( java.lang.Object parent ) {
+ return new org.vamsas.objects.core.Property();
+ }
+ };
+ desc.setHandler(handler);
+ desc.setNameSpaceURI("http://www.vamsas.org");
+ desc.setMultivalued(true);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _propertyList
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(0);
+ { //-- local scope
+ }
+ desc.setValidator(fieldValidator);
} //-- org.vamsas.objects.core.SequenceTypeDescriptor()
//--------------------------/
/**
- * Field _id
+ * Primary Key for vamsas object referencing
+ *
*/
private java.lang.String _id;
/**
+ * objects with modifiable=false will not be
+ * modified by a vamsas client update
+ *
+ */
+ private boolean _modifiable = true;
+
+ /**
+ * keeps track of state for field: _modifiable
+ */
+ private boolean _has_modifiable;
+
+ /**
* Field _title
*/
private java.lang.String _title;
private java.util.Vector _newickList;
/**
+ * Field _propertyList
+ */
+ private java.util.Vector _propertyList;
+
+ /**
* Field _provenance
*/
private org.vamsas.objects.core.Provenance _provenance;
{
super();
_newickList = new Vector();
+ _propertyList = new Vector();
} //-- org.vamsas.objects.core.Tree()
} //-- void addNewick(int, org.vamsas.objects.core.Newick)
/**
+ * Method addProperty
+ *
+ *
+ *
+ * @param vProperty
+ */
+ public void addProperty(org.vamsas.objects.core.Property vProperty)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _propertyList.addElement(vProperty);
+ } //-- void addProperty(org.vamsas.objects.core.Property)
+
+ /**
+ * Method addProperty
+ *
+ *
+ *
+ * @param index
+ * @param vProperty
+ */
+ public void addProperty(int index, org.vamsas.objects.core.Property vProperty)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _propertyList.insertElementAt(vProperty, index);
+ } //-- void addProperty(int, org.vamsas.objects.core.Property)
+
+ /**
+ * Method deleteModifiable
+ *
+ */
+ public void deleteModifiable()
+ {
+ this._has_modifiable= false;
+ } //-- void deleteModifiable()
+
+ /**
* Method enumerateNewick
*
*
} //-- java.util.Enumeration enumerateNewick()
/**
+ * Method enumerateProperty
+ *
+ *
+ *
+ * @return Enumeration
+ */
+ public java.util.Enumeration enumerateProperty()
+ {
+ return _propertyList.elements();
+ } //-- java.util.Enumeration enumerateProperty()
+
+ /**
* Note: hashCode() has not been overriden
*
* @param obj
}
else if (temp._id != null)
return false;
+ if (this._modifiable != temp._modifiable)
+ return false;
+ if (this._has_modifiable != temp._has_modifiable)
+ return false;
if (this._title != null) {
if (temp._title == null) return false;
else if (!(this._title.equals(temp._title)))
}
else if (temp._newickList != null)
return false;
+ if (this._propertyList != null) {
+ if (temp._propertyList == null) return false;
+ else if (!(this._propertyList.equals(temp._propertyList)))
+ return false;
+ }
+ else if (temp._propertyList != null)
+ return false;
if (this._provenance != null) {
if (temp._provenance == null) return false;
else if (!(this._provenance.equals(temp._provenance)))
} //-- boolean equals(java.lang.Object)
/**
- * Returns the value of field 'id'.
+ * Returns the value of field 'id'. The field 'id' has the
+ * following description: Primary Key for vamsas object
+ * referencing
+ *
*
* @return String
* @return the value of field 'id'.
} //-- java.lang.String getId()
/**
+ * Returns the value of field 'modifiable'. The field
+ * 'modifiable' has the following description: objects with
+ * modifiable=false will not be
+ * modified by a vamsas client update
+ *
+ *
+ * @return boolean
+ * @return the value of field 'modifiable'.
+ */
+ public boolean getModifiable()
+ {
+ return this._modifiable;
+ } //-- boolean getModifiable()
+
+ /**
* Method getNewick
*
*
} //-- int getNewickCount()
/**
+ * Method getProperty
+ *
+ *
+ *
+ * @param index
+ * @return Property
+ */
+ public org.vamsas.objects.core.Property getProperty(int index)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ //-- check bounds for index
+ if ((index < 0) || (index > _propertyList.size())) {
+ throw new IndexOutOfBoundsException("getProperty: Index value '"+index+"' not in range [0.."+_propertyList.size()+ "]");
+ }
+
+ return (org.vamsas.objects.core.Property) _propertyList.elementAt(index);
+ } //-- org.vamsas.objects.core.Property getProperty(int)
+
+ /**
+ * Method getProperty
+ *
+ *
+ *
+ * @return Property
+ */
+ public org.vamsas.objects.core.Property[] getProperty()
+ {
+ int size = _propertyList.size();
+ org.vamsas.objects.core.Property[] mArray = new org.vamsas.objects.core.Property[size];
+ for (int index = 0; index < size; index++) {
+ mArray[index] = (org.vamsas.objects.core.Property) _propertyList.elementAt(index);
+ }
+ return mArray;
+ } //-- org.vamsas.objects.core.Property[] getProperty()
+
+ /**
+ * Method getPropertyCount
+ *
+ *
+ *
+ * @return int
+ */
+ public int getPropertyCount()
+ {
+ return _propertyList.size();
+ } //-- int getPropertyCount()
+
+ /**
* Returns the value of field 'provenance'.
*
* @return Provenance
} //-- java.lang.String getTitle()
/**
+ * Method hasModifiable
+ *
+ *
+ *
+ * @return boolean
+ */
+ public boolean hasModifiable()
+ {
+ return this._has_modifiable;
+ } //-- boolean hasModifiable()
+
+ /**
* Method isValid
*
*
} //-- void removeAllNewick()
/**
+ * Method removeAllProperty
+ *
+ */
+ public void removeAllProperty()
+ {
+ _propertyList.removeAllElements();
+ } //-- void removeAllProperty()
+
+ /**
* Method removeNewick
*
*
} //-- org.vamsas.objects.core.Newick removeNewick(int)
/**
- * Sets the value of field 'id'.
+ * Method removeProperty
+ *
+ *
+ *
+ * @param index
+ * @return Property
+ */
+ public org.vamsas.objects.core.Property removeProperty(int index)
+ {
+ java.lang.Object obj = _propertyList.elementAt(index);
+ _propertyList.removeElementAt(index);
+ return (org.vamsas.objects.core.Property) obj;
+ } //-- org.vamsas.objects.core.Property removeProperty(int)
+
+ /**
+ * Sets the value of field 'id'. The field 'id' has the
+ * following description: Primary Key for vamsas object
+ * referencing
+ *
*
* @param id the value of field 'id'.
*/
} //-- void setId(java.lang.String)
/**
+ * Sets the value of field 'modifiable'. The field 'modifiable'
+ * has the following description: objects with modifiable=false
+ * will not be
+ * modified by a vamsas client update
+ *
+ *
+ * @param modifiable the value of field 'modifiable'.
+ */
+ public void setModifiable(boolean modifiable)
+ {
+ this._modifiable = modifiable;
+ this._has_modifiable = true;
+ } //-- void setModifiable(boolean)
+
+ /**
* Method setNewick
*
*
} //-- void setNewick(org.vamsas.objects.core.Newick)
/**
+ * Method setProperty
+ *
+ *
+ *
+ * @param index
+ * @param vProperty
+ */
+ public void setProperty(int index, org.vamsas.objects.core.Property vProperty)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ //-- check bounds for index
+ if ((index < 0) || (index > _propertyList.size())) {
+ throw new IndexOutOfBoundsException("setProperty: Index value '"+index+"' not in range [0.."+_propertyList.size()+ "]");
+ }
+ _propertyList.setElementAt(vProperty, index);
+ } //-- void setProperty(int, org.vamsas.objects.core.Property)
+
+ /**
+ * Method setProperty
+ *
+ *
+ *
+ * @param propertyArray
+ */
+ public void setProperty(org.vamsas.objects.core.Property[] propertyArray)
+ {
+ //-- copy array
+ _propertyList.removeAllElements();
+ for (int i = 0; i < propertyArray.length; i++) {
+ _propertyList.addElement(propertyArray[i]);
+ }
+ } //-- void setProperty(org.vamsas.objects.core.Property)
+
+ /**
* Sets the value of field 'provenance'.
*
* @param provenance the value of field 'provenance'.
{ //-- local scope
}
desc.setValidator(fieldValidator);
+ //-- _modifiable
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_modifiable", "modifiable", org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ Tree target = (Tree) object;
+ if(!target.hasModifiable())
+ return null;
+ return (target.getModifiable() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ Tree target = (Tree) object;
+ // if null, use delete method for optional primitives
+ if (value == null) {
+ target.deleteModifiable();
+ return;
+ }
+ target.setModifiable( ((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: _modifiable
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { //-- local scope
+ BooleanValidator typeValidator = new BooleanValidator();
+ fieldValidator.setValidator(typeValidator);
+ }
+ desc.setValidator(fieldValidator);
//-- initialize element descriptors
//-- _title
{ //-- local scope
}
desc.setValidator(fieldValidator);
+ //-- _propertyList
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Property.class, "_propertyList", "property", 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.getProperty();
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ Tree target = (Tree) object;
+ target.addProperty( (org.vamsas.objects.core.Property) value);
+ }
+ catch (java.lang.Exception ex) {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+ public java.lang.Object newInstance( java.lang.Object parent ) {
+ return new org.vamsas.objects.core.Property();
+ }
+ };
+ desc.setHandler(handler);
+ desc.setNameSpaceURI("http://www.vamsas.org");
+ desc.setMultivalued(true);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _propertyList
+ 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.objects.core.Provenance.class, "_provenance", "Provenance", org.exolab.castor.xml.NodeType.Element);
handler = new org.exolab.castor.xml.XMLFieldHandler() {
--- /dev/null
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package org.vamsas.objects.core;
+
+ //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import java.io.IOException;
+import java.io.Reader;
+import java.io.Serializable;
+import java.io.Writer;
+import org.exolab.castor.xml.MarshalException;
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+import org.exolab.castor.xml.ValidationException;
+import org.xml.sax.ContentHandler;
+
+/**
+ * Primitive labelled URI object
+ *
+ *
+ * @version $Revision$ $Date$
+ */
+public class Uri extends org.vamsas.client.Vobject
+implements java.io.Serializable
+{
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * internal content storage
+ */
+ private java.lang.String _content = "";
+
+ /**
+ * The URI
+ */
+ private java.lang.String _href;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public Uri()
+ {
+ super();
+ setContent("");
+ } //-- org.vamsas.objects.core.Uri()
+
+
+ //-----------/
+ //- 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 Uri) {
+
+ Uri temp = (Uri)obj;
+ if (this._content != null) {
+ if (temp._content == null) return false;
+ else if (!(this._content.equals(temp._content)))
+ return false;
+ }
+ else if (temp._content != null)
+ return false;
+ if (this._href != null) {
+ if (temp._href == null) return false;
+ else if (!(this._href.equals(temp._href)))
+ return false;
+ }
+ else if (temp._href != null)
+ return false;
+ return true;
+ }
+ return false;
+ } //-- boolean equals(java.lang.Object)
+
+ /**
+ * Returns the value of field 'content'. The field 'content'
+ * has the following description: internal content storage
+ *
+ * @return String
+ * @return the value of field 'content'.
+ */
+ public java.lang.String getContent()
+ {
+ return this._content;
+ } //-- java.lang.String getContent()
+
+ /**
+ * Returns the value of field 'href'. The field 'href' has the
+ * following description: The URI
+ *
+ * @return String
+ * @return the value of field 'href'.
+ */
+ public java.lang.String getHref()
+ {
+ return this._href;
+ } //-- java.lang.String getHref()
+
+ /**
+ * Method isValid
+ *
+ *
+ *
+ * @return boolean
+ */
+ public boolean isValid()
+ {
+ try {
+ validate();
+ }
+ catch (org.exolab.castor.xml.ValidationException vex) {
+ return false;
+ }
+ return true;
+ } //-- boolean isValid()
+
+ /**
+ * Method marshal
+ *
+ *
+ *
+ * @param out
+ */
+ public void marshal(java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+ {
+
+ Marshaller.marshal(this, out);
+ } //-- void marshal(java.io.Writer)
+
+ /**
+ * Method marshal
+ *
+ *
+ *
+ * @param handler
+ */
+ public void marshal(org.xml.sax.ContentHandler handler)
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+ {
+
+ Marshaller.marshal(this, handler);
+ } //-- void marshal(org.xml.sax.ContentHandler)
+
+ /**
+ * Sets the value of field 'content'. The field 'content' has
+ * the following description: internal content storage
+ *
+ * @param content the value of field 'content'.
+ */
+ public void setContent(java.lang.String content)
+ {
+ this._content = content;
+ } //-- void setContent(java.lang.String)
+
+ /**
+ * Sets the value of field 'href'. The field 'href' has the
+ * following description: The URI
+ *
+ * @param href the value of field 'href'.
+ */
+ public void setHref(java.lang.String href)
+ {
+ this._href = href;
+ } //-- void setHref(java.lang.String)
+
+ /**
+ * Method unmarshal
+ *
+ *
+ *
+ * @param reader
+ * @return Uri
+ */
+ public static org.vamsas.objects.core.Uri unmarshal(java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+ {
+ return (org.vamsas.objects.core.Uri) Unmarshaller.unmarshal(org.vamsas.objects.core.Uri.class, reader);
+ } //-- org.vamsas.objects.core.Uri unmarshal(java.io.Reader)
+
+ /**
+ * Method validate
+ *
+ */
+ public void validate()
+ throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ } //-- void validate()
+
+}
--- /dev/null
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package org.vamsas.objects.core;
+
+ //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.mapping.AccessMode;
+import org.exolab.castor.xml.TypeValidator;
+import org.exolab.castor.xml.XMLFieldDescriptor;
+import org.exolab.castor.xml.validators.*;
+
+/**
+ * Class UriDescriptor.
+ *
+ * @version $Revision$ $Date$
+ */
+public class UriDescriptor 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 UriDescriptor()
+ {
+ super();
+ nsURI = "http://www.vamsas.org";
+ xmlName = "uri";
+ 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
+ {
+ Uri target = (Uri) object;
+ return target.getContent();
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ Uri target = (Uri) 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
+
+ //-- _href
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_href", "href", org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ Uri target = (Uri) object;
+ return target.getHref();
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ Uri target = (Uri) object;
+ target.setHref( (java.lang.String) value);
+ }
+ catch (java.lang.Exception ex) {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+ public java.lang.Object newInstance( java.lang.Object parent ) {
+ return new java.lang.String();
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _href
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { //-- local scope
+ }
+ desc.setValidator(fieldValidator);
+ //-- initialize element descriptors
+
+ } //-- org.vamsas.objects.core.UriDescriptor()
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ * Method getAccessMode
+ *
+ *
+ *
+ * @return AccessMode
+ */
+ public org.exolab.castor.mapping.AccessMode getAccessMode()
+ {
+ return null;
+ } //-- org.exolab.castor.mapping.AccessMode getAccessMode()
+
+ /**
+ * Method getExtends
+ *
+ *
+ *
+ * @return ClassDescriptor
+ */
+ public org.exolab.castor.mapping.ClassDescriptor getExtends()
+ {
+ return null;
+ } //-- org.exolab.castor.mapping.ClassDescriptor getExtends()
+
+ /**
+ * Method getIdentity
+ *
+ *
+ *
+ * @return FieldDescriptor
+ */
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+ {
+ return identity;
+ } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity()
+
+ /**
+ * Method getJavaClass
+ *
+ *
+ *
+ * @return Class
+ */
+ public java.lang.Class getJavaClass()
+ {
+ return org.vamsas.objects.core.Uri.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 0.9.9M2</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package org.vamsas.objects.core;
+
+ //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import java.io.IOException;
+import java.io.Reader;
+import java.io.Serializable;
+import java.io.Writer;
+import org.exolab.castor.xml.MarshalException;
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+import org.exolab.castor.xml.ValidationException;
+import org.xml.sax.ContentHandler;
+
+/**
+ * Class Url.
+ *
+ * @version $Revision$ $Date$
+ */
+public class Url extends Uri
+implements java.io.Serializable
+{
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public Url()
+ {
+ super();
+ } //-- org.vamsas.objects.core.Url()
+
+
+ //-----------/
+ //- 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 Url) {
+
+ Url temp = (Url)obj;
+ return true;
+ }
+ return false;
+ } //-- boolean equals(java.lang.Object)
+
+ /**
+ * Method isValid
+ *
+ *
+ *
+ * @return boolean
+ */
+ public boolean isValid()
+ {
+ try {
+ validate();
+ }
+ catch (org.exolab.castor.xml.ValidationException vex) {
+ return false;
+ }
+ return true;
+ } //-- boolean isValid()
+
+ /**
+ * Method marshal
+ *
+ *
+ *
+ * @param out
+ */
+ public void marshal(java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+ {
+
+ Marshaller.marshal(this, out);
+ } //-- void marshal(java.io.Writer)
+
+ /**
+ * Method marshal
+ *
+ *
+ *
+ * @param handler
+ */
+ public void marshal(org.xml.sax.ContentHandler handler)
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+ {
+
+ Marshaller.marshal(this, handler);
+ } //-- void marshal(org.xml.sax.ContentHandler)
+
+ /**
+ * Method unmarshal
+ *
+ *
+ *
+ * @param reader
+ * @return Url
+ */
+ public static org.vamsas.objects.core.Url unmarshal(java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+ {
+ return (org.vamsas.objects.core.Url) Unmarshaller.unmarshal(org.vamsas.objects.core.Url.class, reader);
+ } //-- org.vamsas.objects.core.Url unmarshal(java.io.Reader)
+
+ /**
+ * Method validate
+ *
+ */
+ public void validate()
+ throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ } //-- void validate()
+
+}
--- /dev/null
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package org.vamsas.objects.core;
+
+ //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.mapping.AccessMode;
+import org.exolab.castor.xml.TypeValidator;
+import org.exolab.castor.xml.XMLFieldDescriptor;
+import org.exolab.castor.xml.validators.*;
+
+/**
+ * Class UrlDescriptor.
+ *
+ * @version $Revision$ $Date$
+ */
+public class UrlDescriptor extends UriDescriptor {
+
+
+ //--------------------------/
+ //- 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 UrlDescriptor()
+ {
+ super();
+ setExtendsWithoutFlatten(new UriDescriptor());
+ nsURI = "http://www.vamsas.org";
+ xmlName = "url";
+ } //-- org.vamsas.objects.core.UrlDescriptor()
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ * Method getAccessMode
+ *
+ *
+ *
+ * @return AccessMode
+ */
+ public org.exolab.castor.mapping.AccessMode getAccessMode()
+ {
+ return null;
+ } //-- org.exolab.castor.mapping.AccessMode getAccessMode()
+
+ /**
+ * Method getExtends
+ *
+ *
+ *
+ * @return ClassDescriptor
+ */
+ public org.exolab.castor.mapping.ClassDescriptor getExtends()
+ {
+ return super.getExtends();
+ } //-- org.exolab.castor.mapping.ClassDescriptor getExtends()
+
+ /**
+ * Method getIdentity
+ *
+ *
+ *
+ * @return FieldDescriptor
+ */
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+ {
+ if (identity == null)
+ return super.getIdentity();
+ return identity;
+ } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity()
+
+ /**
+ * Method getJavaClass
+ *
+ *
+ *
+ * @return Class
+ */
+ public java.lang.Class getJavaClass()
+ {
+ return org.vamsas.objects.core.Url.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()
+
+}
import org.xml.sax.ContentHandler;
/**
- * Class VAMSAS.
+ * contains unassociated trees and a number of analysis
+ * sets
+ *
*
* @version $Revision$ $Date$
*/
//--------------------------/
/**
- * Field _id
+ * Primary Key for vamsas object referencing
+ *
*/
private java.lang.String _id;
/**
+ * objects with modifiable=false will not be
+ * modified by a vamsas client update
+ *
+ */
+ private boolean _modifiable = true;
+
+ /**
+ * keeps track of state for field: _modifiable
+ */
+ private boolean _has_modifiable;
+
+ /**
* Field _treeList
*/
private java.util.Vector _treeList;
} //-- void addTree(int, org.vamsas.objects.core.Tree)
/**
+ * Method deleteModifiable
+ *
+ */
+ public void deleteModifiable()
+ {
+ this._has_modifiable= false;
+ } //-- void deleteModifiable()
+
+ /**
* Method enumerateDataSet
*
*
}
else if (temp._id != null)
return false;
+ if (this._modifiable != temp._modifiable)
+ return false;
+ if (this._has_modifiable != temp._has_modifiable)
+ return false;
if (this._treeList != null) {
if (temp._treeList == null) return false;
else if (!(this._treeList.equals(temp._treeList)))
} //-- int getDataSetCount()
/**
- * Returns the value of field 'id'.
+ * Returns the value of field 'id'. The field 'id' has the
+ * following description: Primary Key for vamsas object
+ * referencing
+ *
*
* @return String
* @return the value of field 'id'.
} //-- java.lang.String getId()
/**
+ * Returns the value of field 'modifiable'. The field
+ * 'modifiable' has the following description: objects with
+ * modifiable=false will not be
+ * modified by a vamsas client update
+ *
+ *
+ * @return boolean
+ * @return the value of field 'modifiable'.
+ */
+ public boolean getModifiable()
+ {
+ return this._modifiable;
+ } //-- boolean getModifiable()
+
+ /**
* Method getTree
*
*
} //-- int getTreeCount()
/**
+ * Method hasModifiable
+ *
+ *
+ *
+ * @return boolean
+ */
+ public boolean hasModifiable()
+ {
+ return this._has_modifiable;
+ } //-- boolean hasModifiable()
+
+ /**
* Method isValid
*
*
} //-- void setDataSet(org.vamsas.objects.core.DataSet)
/**
- * Sets the value of field 'id'.
+ * Sets the value of field 'id'. The field 'id' has the
+ * following description: Primary Key for vamsas object
+ * referencing
+ *
*
* @param id the value of field 'id'.
*/
} //-- void setId(java.lang.String)
/**
+ * Sets the value of field 'modifiable'. The field 'modifiable'
+ * has the following description: objects with modifiable=false
+ * will not be
+ * modified by a vamsas client update
+ *
+ *
+ * @param modifiable the value of field 'modifiable'.
+ */
+ public void setModifiable(boolean modifiable)
+ {
+ this._modifiable = modifiable;
+ this._has_modifiable = true;
+ } //-- void setModifiable(boolean)
+
+ /**
* Method setTree
*
*
{ //-- local scope
}
desc.setValidator(fieldValidator);
+ //-- _modifiable
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_modifiable", "modifiable", org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ VAMSAS target = (VAMSAS) object;
+ if(!target.hasModifiable())
+ return null;
+ return (target.getModifiable() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ VAMSAS target = (VAMSAS) object;
+ // if null, use delete method for optional primitives
+ if (value == null) {
+ target.deleteModifiable();
+ return;
+ }
+ target.setModifiable( ((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: _modifiable
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { //-- local scope
+ BooleanValidator typeValidator = new BooleanValidator();
+ fieldValidator.setValidator(typeValidator);
+ }
+ desc.setValidator(fieldValidator);
//-- initialize element descriptors
//-- _treeList
private Provenance _provenance;
/**
- * Field _VAMSASList
+ * contains unassociated trees and a number of analysis
+ * sets
+ *
*/
private java.util.Vector _VAMSASList;
*/
private java.util.Vector _applicationDataList;
+ /**
+ * Field _attachmentList
+ */
+ private java.util.Vector _attachmentList;
+
//----------------/
//- Constructors -/
super();
_VAMSASList = new Vector();
_applicationDataList = new Vector();
+ _attachmentList = new Vector();
} //-- org.vamsas.objects.core.VamsasDocument()
} //-- void addApplicationData(int, ApplicationData)
/**
+ * Method addAttachment
+ *
+ *
+ *
+ * @param vAttachment
+ */
+ public void addAttachment(Attachment vAttachment)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _attachmentList.addElement(vAttachment);
+ } //-- void addAttachment(Attachment)
+
+ /**
+ * Method addAttachment
+ *
+ *
+ *
+ * @param index
+ * @param vAttachment
+ */
+ public void addAttachment(int index, Attachment vAttachment)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _attachmentList.insertElementAt(vAttachment, index);
+ } //-- void addAttachment(int, Attachment)
+
+ /**
* Method addVAMSAS
*
*
} //-- java.util.Enumeration enumerateApplicationData()
/**
+ * Method enumerateAttachment
+ *
+ *
+ *
+ * @return Enumeration
+ */
+ public java.util.Enumeration enumerateAttachment()
+ {
+ return _attachmentList.elements();
+ } //-- java.util.Enumeration enumerateAttachment()
+
+ /**
* Method enumerateVAMSAS
*
*
}
else if (temp._applicationDataList != null)
return false;
+ if (this._attachmentList != null) {
+ if (temp._attachmentList == null) return false;
+ else if (!(this._attachmentList.equals(temp._attachmentList)))
+ return false;
+ }
+ else if (temp._attachmentList != null)
+ return false;
return true;
}
return false;
} //-- int getApplicationDataCount()
/**
+ * Method getAttachment
+ *
+ *
+ *
+ * @param index
+ * @return Attachment
+ */
+ public Attachment getAttachment(int index)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ //-- check bounds for index
+ if ((index < 0) || (index > _attachmentList.size())) {
+ throw new IndexOutOfBoundsException("getAttachment: Index value '"+index+"' not in range [0.."+_attachmentList.size()+ "]");
+ }
+
+ return (Attachment) _attachmentList.elementAt(index);
+ } //-- Attachment getAttachment(int)
+
+ /**
+ * Method getAttachment
+ *
+ *
+ *
+ * @return Attachment
+ */
+ public Attachment[] getAttachment()
+ {
+ int size = _attachmentList.size();
+ Attachment[] mArray = new Attachment[size];
+ for (int index = 0; index < size; index++) {
+ mArray[index] = (Attachment) _attachmentList.elementAt(index);
+ }
+ return mArray;
+ } //-- Attachment[] getAttachment()
+
+ /**
+ * Method getAttachmentCount
+ *
+ *
+ *
+ * @return int
+ */
+ public int getAttachmentCount()
+ {
+ return _attachmentList.size();
+ } //-- int getAttachmentCount()
+
+ /**
* Returns the value of field 'lockFile'.
*
* @return LockFile
} //-- void removeAllApplicationData()
/**
+ * Method removeAllAttachment
+ *
+ */
+ public void removeAllAttachment()
+ {
+ _attachmentList.removeAllElements();
+ } //-- void removeAllAttachment()
+
+ /**
* Method removeAllVAMSAS
*
*/
} //-- ApplicationData removeApplicationData(int)
/**
+ * Method removeAttachment
+ *
+ *
+ *
+ * @param index
+ * @return Attachment
+ */
+ public Attachment removeAttachment(int index)
+ {
+ java.lang.Object obj = _attachmentList.elementAt(index);
+ _attachmentList.removeElementAt(index);
+ return (Attachment) obj;
+ } //-- Attachment removeAttachment(int)
+
+ /**
* Method removeVAMSAS
*
*
} //-- void setApplicationData(ApplicationData)
/**
+ * Method setAttachment
+ *
+ *
+ *
+ * @param index
+ * @param vAttachment
+ */
+ public void setAttachment(int index, Attachment vAttachment)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ //-- check bounds for index
+ if ((index < 0) || (index > _attachmentList.size())) {
+ throw new IndexOutOfBoundsException("setAttachment: Index value '"+index+"' not in range [0.."+_attachmentList.size()+ "]");
+ }
+ _attachmentList.setElementAt(vAttachment, index);
+ } //-- void setAttachment(int, Attachment)
+
+ /**
+ * Method setAttachment
+ *
+ *
+ *
+ * @param attachmentArray
+ */
+ public void setAttachment(Attachment[] attachmentArray)
+ {
+ //-- copy array
+ _attachmentList.removeAllElements();
+ for (int i = 0; i < attachmentArray.length; i++) {
+ _attachmentList.addElement(attachmentArray[i]);
+ }
+ } //-- void setAttachment(Attachment)
+
+ /**
* Sets the value of field 'lockFile'.
*
* @param lockFile the value of field 'lockFile'.
{ //-- local scope
}
desc.setValidator(fieldValidator);
+ //-- _attachmentList
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(Attachment.class, "_attachmentList", "Attachment", org.exolab.castor.xml.NodeType.Element);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ VamsasDocument target = (VamsasDocument) object;
+ return target.getAttachment();
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ VamsasDocument target = (VamsasDocument) object;
+ target.addAttachment( (Attachment) value);
+ }
+ catch (java.lang.Exception ex) {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+ public java.lang.Object newInstance( java.lang.Object parent ) {
+ return new Attachment();
+ }
+ };
+ desc.setHandler(handler);
+ desc.setNameSpaceURI("http://www.vamsas.org");
+ desc.setMultivalued(true);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _attachmentList
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(0);
+ { //-- local scope
+ }
+ desc.setValidator(fieldValidator);
} //-- org.vamsas.objects.core.VamsasDocumentDescriptor()
git://source.jalview.org / vamsas.git / commitdiff