/* * This class was automatically generated with * Castor 0.9.9M2, using an XML * Schema. * $Id$ */ package org.vamsas.objects.core; //---------------------------------/ //- Imported classes and packages -/ //---------------------------------/ import java.io.IOException; import java.io.Reader; import java.io.Serializable; import java.io.Writer; import java.util.Enumeration; import java.util.Vector; import org.exolab.castor.xml.MarshalException; import org.exolab.castor.xml.Marshaller; import org.exolab.castor.xml.Unmarshaller; import org.exolab.castor.xml.ValidationException; import org.xml.sax.ContentHandler; /** * Class AlignmentAnnotations. * * @version $Revision$ $Date$ */ public class AlignmentAnnotations extends org.vamsas.client.Vobject implements java.io.Serializable { //--------------------------/ //- Class/Member Variables -/ //--------------------------/ /** * Field _graph */ private boolean _graph; /** * keeps track of state for field: _graph */ private boolean _has_graph; /** * Field _id */ private java.lang.String _id; /** * Field _annotationElementList */ private java.util.Vector _annotationElementList; /** * Field _label */ private java.lang.String _label; /** * Field _description */ private java.lang.String _description; /** * Field _provenance */ private org.vamsas.objects.core.Provenance _provenance; //----------------/ //- Constructors -/ //----------------/ public AlignmentAnnotations() { super(); _annotationElementList = new Vector(); } //-- org.vamsas.objects.core.AlignmentAnnotations() //-----------/ //- 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 deleteGraph * */ public void deleteGraph() { this._has_graph= false; } //-- void deleteGraph() /** * Method enumerateAnnotationElement * * * * @return Enumeration */ public java.util.Enumeration enumerateAnnotationElement() { return _annotationElementList.elements(); } //-- java.util.Enumeration enumerateAnnotationElement() /** * Note: hashCode() has not been overriden * * @param obj * @return boolean */ public boolean equals(java.lang.Object obj) { if ( this == obj ) return true; if (super.equals(obj)==false) return false; if (obj instanceof AlignmentAnnotations) { AlignmentAnnotations temp = (AlignmentAnnotations)obj; if (this._graph != temp._graph) return false; if (this._has_graph != temp._has_graph) return false; if (this._id != null) { if (temp._id == null) return false; else if (!(this._id.equals(temp._id))) return false; } else if (temp._id != null) return false; if (this._annotationElementList != null) { if (temp._annotationElementList == null) return false; else if (!(this._annotationElementList.equals(temp._annotationElementList))) return false; } else if (temp._annotationElementList != null) return false; if (this._label != null) { if (temp._label == null) return false; else if (!(this._label.equals(temp._label))) return false; } else if (temp._label != null) return false; if (this._description != null) { if (temp._description == null) return false; else if (!(this._description.equals(temp._description))) return false; } else if (temp._description != null) return false; if (this._provenance != null) { if (temp._provenance == null) return false; else if (!(this._provenance.equals(temp._provenance))) return false; } else if (temp._provenance != null) return false; return true; } return false; } //-- boolean equals(java.lang.Object) /** * Method getAnnotationElement * * * * @param index * @return AnnotationElement */ public org.vamsas.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'. * * @return String * @return the value of field 'description'. */ public java.lang.String getDescription() { return this._description; } //-- java.lang.String getDescription() /** * Returns the value of field 'graph'. * * @return boolean * @return the value of field 'graph'. */ public boolean getGraph() { return this._graph; } //-- boolean getGraph() /** * Returns the value of field 'id'. * * @return String * @return the value of field 'id'. */ public java.lang.String getId() { return this._id; } //-- java.lang.String getId() /** * Returns the value of field 'label'. * * @return String * @return the value of field 'label'. */ public java.lang.String getLabel() { return this._label; } //-- java.lang.String getLabel() /** * Returns the value of field 'provenance'. * * @return Provenance * @return the value of field 'provenance'. */ public org.vamsas.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) /** * 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 'description'. * * @param description the value of field 'description'. */ public void setDescription(java.lang.String description) { this._description = description; } //-- void setDescription(java.lang.String) /** * Sets the value of field 'graph'. * * @param graph the value of field 'graph'. */ public void setGraph(boolean graph) { this._graph = graph; this._has_graph = true; } //-- void setGraph(boolean) /** * Sets the value of field 'id'. * * @param id the value of field 'id'. */ public void setId(java.lang.String id) { this._id = id; } //-- void setId(java.lang.String) /** * Sets the value of field 'label'. * * @param label the value of field 'label'. */ public void setLabel(java.lang.String label) { this._label = label; } //-- void setLabel(java.lang.String) /** * Sets the value of field 'provenance'. * * @param provenance the value of field 'provenance'. */ public void setProvenance(org.vamsas.objects.core.Provenance provenance) { this._provenance = provenance; } //-- void setProvenance(org.vamsas.objects.core.Provenance) /** * Method unmarshal * * * * @param reader * @return AlignmentAnnotations */ public static org.vamsas.objects.core.AlignmentAnnotations unmarshal(java.io.Reader reader) throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { return (org.vamsas.objects.core.AlignmentAnnotations) Unmarshaller.unmarshal(org.vamsas.objects.core.AlignmentAnnotations.class, reader); } //-- org.vamsas.objects.core.AlignmentAnnotations unmarshal(java.io.Reader) /** * Method validate * */ public void validate() throws org.exolab.castor.xml.ValidationException { org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); validator.validate(this); } //-- void validate() }