Note: Just in case the collection contents are - * changing in another thread, we pass a 0-length Array of the - * correct type into the API call. This way we know - * that the Array returned is of exactly the correct length. - * - * @return this collection as an Array - */ - public uk.ac.vamsas.objects.core.Link[] getLink( - ) { - uk.ac.vamsas.objects.core.Link[] array = new uk.ac.vamsas.objects.core.Link[0]; - return (uk.ac.vamsas.objects.core.Link[]) this._linkList.toArray(array); - } - - /** - * Method getLinkAsReference.Returns a reference to - * '_linkList'. No type checking is performed on any - * modifications to the Vector. - * - * @return a reference to the Vector backing this class - */ - public java.util.Vector getLinkAsReference( - ) { - return this._linkList; - } - - /** - * Method getLinkCount. - * - * @return the size of this collection - */ - public int getLinkCount( - ) { - return this._linkList.size(); - } - - /** - * Method getMap. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - * @return the value of the uk.ac.vamsas.objects.core.Map at - * the given index - */ - public uk.ac.vamsas.objects.core.Map getMap( - final int index) - throws java.lang.IndexOutOfBoundsException { - // check bounds for index - if (index < 0 || index >= this._mapList.size()) { - throw new IndexOutOfBoundsException("getMap: Index value '" + index + "' not in range [0.." + (this._mapList.size() - 1) + "]"); - } - - return (uk.ac.vamsas.objects.core.Map) _mapList.get(index); - } - - /** - * Method getMap.Returns the contents of the collection in an - * Array.
Note: Just in case the collection contents are - * changing in another thread, we pass a 0-length Array of the - * correct type into the API call. This way we know - * that the Array returned is of exactly the correct length. - * - * @return this collection as an Array - */ - public uk.ac.vamsas.objects.core.Map[] getMap( - ) { - uk.ac.vamsas.objects.core.Map[] array = new uk.ac.vamsas.objects.core.Map[0]; - return (uk.ac.vamsas.objects.core.Map[]) this._mapList.toArray(array); - } - - /** - * Method getMapAsReference.Returns a reference to '_mapList'. - * No type checking is performed on any modifications to the - * Vector. - * - * @return a reference to the Vector backing this class - */ - public java.util.Vector getMapAsReference( - ) { - return this._mapList; - } - - /** - * Method getMapCount. - * - * @return the size of this collection - */ - public int getMapCount( - ) { - return this._mapList.size(); - } - - /** - * Method getProperty. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - * @return the value of the uk.ac.vamsas.objects.core.Property - * at the given index - */ - public uk.ac.vamsas.objects.core.Property getProperty( - final int index) - throws java.lang.IndexOutOfBoundsException { - // check bounds for index - if (index < 0 || index >= this._propertyList.size()) { - throw new IndexOutOfBoundsException("getProperty: Index value '" + index + "' not in range [0.." + (this._propertyList.size() - 1) + "]"); - } - - return (uk.ac.vamsas.objects.core.Property) _propertyList.get(index); - } - - /** - * Method getProperty.Returns the contents of the collection in - * an Array.
Note: Just in case the collection contents - * are changing in another thread, we pass a 0-length Array of - * the correct type into the API call. This way we know - * that the Array returned is of exactly the correct length. - * - * @return this collection as an Array - */ - public uk.ac.vamsas.objects.core.Property[] getProperty( - ) { - uk.ac.vamsas.objects.core.Property[] array = new uk.ac.vamsas.objects.core.Property[0]; - return (uk.ac.vamsas.objects.core.Property[]) this._propertyList.toArray(array); - } - - /** - * Method getPropertyAsReference.Returns a reference to - * '_propertyList'. No type checking is performed on any - * modifications to the Vector. - * - * @return a reference to the Vector backing this class - */ - public java.util.Vector getPropertyAsReference( - ) { - return this._propertyList; - } - - /** - * Method getPropertyCount. - * - * @return the size of this collection - */ - public int getPropertyCount( - ) { - return this._propertyList.size(); - } - - /** - * 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 the value of field 'Source'. - */ - public java.lang.String getSource( - ) { - return this._source; - } - - /** - * Returns the value of field 'version'. The field 'version' - * has the following description: Version must be specified - - * - * - * @return the value of field 'Version'. - */ - public java.lang.String getVersion( - ) { - return this._version; - } - - /** - * Overrides the java.lang.Object.hashCode method. - *
- * The following steps came from Effective Java Programming - * Language Guide by Joshua Bloch, Chapter 3 - * - * @return a hash code value for the object. - */ - public int hashCode( - ) { - int result = super.hashCode(); - - long tmp; - if (_source != null) { - result = 37 * result + _source.hashCode(); - } - if (_version != null) { - result = 37 * result + _version.hashCode(); - } - if (_accessionId != null) { - result = 37 * result + _accessionId.hashCode(); - } - if (_id != null) { - result = 37 * result + _id.hashCode(); - } - if (_mapList != null) { - result = 37 * result + _mapList.hashCode(); + if (this._id != null) { + if (temp._id == null) + return false; + if (this._id != temp._id) { + thcycle = org.castor.util.CycleBreaker.startingToCycle(this._id); + tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._id); + if (thcycle != tmcycle) { + if (!thcycle) { + org.castor.util.CycleBreaker.releaseCycleHandle(this._id); + } + ; + if (!tmcycle) { + org.castor.util.CycleBreaker.releaseCycleHandle(temp._id); + } + ; + return false; + } + if (!thcycle) { + if (!this._id.equals(temp._id)) { + org.castor.util.CycleBreaker.releaseCycleHandle(this._id); + org.castor.util.CycleBreaker.releaseCycleHandle(temp._id); + return false; + } + org.castor.util.CycleBreaker.releaseCycleHandle(this._id); + org.castor.util.CycleBreaker.releaseCycleHandle(temp._id); + } } - if (_linkList != null) { - result = 37 * result + _linkList.hashCode(); + } else if (temp._id != null) + return false; + if (this._mapList != null) { + if (temp._mapList == null) + return false; + if (this._mapList != temp._mapList) { + thcycle = org.castor.util.CycleBreaker.startingToCycle(this._mapList); + tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._mapList); + if (thcycle != tmcycle) { + if (!thcycle) { + org.castor.util.CycleBreaker.releaseCycleHandle(this._mapList); + } + ; + if (!tmcycle) { + org.castor.util.CycleBreaker.releaseCycleHandle(temp._mapList); + } + ; + return false; + } + if (!thcycle) { + if (!this._mapList.equals(temp._mapList)) { + org.castor.util.CycleBreaker.releaseCycleHandle(this._mapList); + org.castor.util.CycleBreaker.releaseCycleHandle(temp._mapList); + return false; + } + org.castor.util.CycleBreaker.releaseCycleHandle(this._mapList); + org.castor.util.CycleBreaker.releaseCycleHandle(temp._mapList); + } } - if (_propertyList != null) { - result = 37 * result + _propertyList.hashCode(); + } else if (temp._mapList != null) + return false; + if (this._linkList != null) { + if (temp._linkList == null) + return false; + if (this._linkList != temp._linkList) { + thcycle = org.castor.util.CycleBreaker + .startingToCycle(this._linkList); + tmcycle = org.castor.util.CycleBreaker + .startingToCycle(temp._linkList); + if (thcycle != tmcycle) { + if (!thcycle) { + org.castor.util.CycleBreaker.releaseCycleHandle(this._linkList); + } + ; + if (!tmcycle) { + org.castor.util.CycleBreaker.releaseCycleHandle(temp._linkList); + } + ; + return false; + } + if (!thcycle) { + if (!this._linkList.equals(temp._linkList)) { + org.castor.util.CycleBreaker.releaseCycleHandle(this._linkList); + org.castor.util.CycleBreaker.releaseCycleHandle(temp._linkList); + return false; + } + org.castor.util.CycleBreaker.releaseCycleHandle(this._linkList); + org.castor.util.CycleBreaker.releaseCycleHandle(temp._linkList); + } } - - return result; - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid( - ) { - try { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) { + } else if (temp._linkList != null) + return false; + if (this._propertyList != null) { + if (temp._propertyList == null) + return false; + if (this._propertyList != temp._propertyList) { + thcycle = org.castor.util.CycleBreaker + .startingToCycle(this._propertyList); + tmcycle = org.castor.util.CycleBreaker + .startingToCycle(temp._propertyList); + if (thcycle != tmcycle) { + if (!thcycle) { + org.castor.util.CycleBreaker + .releaseCycleHandle(this._propertyList); + } + ; + if (!tmcycle) { + org.castor.util.CycleBreaker + .releaseCycleHandle(temp._propertyList); + } + ; return false; + } + if (!thcycle) { + if (!this._propertyList.equals(temp._propertyList)) { + org.castor.util.CycleBreaker + .releaseCycleHandle(this._propertyList); + org.castor.util.CycleBreaker + .releaseCycleHandle(temp._propertyList); + return false; + } + org.castor.util.CycleBreaker.releaseCycleHandle(this._propertyList); + org.castor.util.CycleBreaker.releaseCycleHandle(temp._propertyList); + } } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - */ - public void marshal( - final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException if an IOException occurs during - * marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - */ - public void marshal( - final org.xml.sax.ContentHandler handler) - throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - Marshaller.marshal(this, handler); - } - - /** - */ - public void removeAllLink( - ) { - this._linkList.clear(); - } - - /** - */ - public void removeAllMap( - ) { - this._mapList.clear(); - } - - /** - */ - public void removeAllProperty( - ) { - this._propertyList.clear(); + } else if (temp._propertyList != null) + return false; + return true; } - - /** - * Method removeLink. - * - * @param vLink - * @return true if the object was removed from the collection. - */ - public boolean removeLink( - final uk.ac.vamsas.objects.core.Link vLink) { - boolean removed = _linkList.remove(vLink); - return removed; + return false; + } + + /** + * 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 the value of field 'AccessionId'. + */ + public java.lang.String getAccessionId() { + return this._accessionId; + } + + /** + * Returns the value of field 'id'. The field 'id' has the following + * description: Primary Key for vamsas object referencing + * + * @return the value of field 'Id'. + */ + public java.lang.String getId() { + return this._id; + } + + /** + * Method getLink. + * + * @param index + * @throws java.lang.IndexOutOfBoundsException + * if the index given is outside the bounds of the collection + * @return the value of the uk.ac.vamsas.objects.core.Link at the given index + */ + public uk.ac.vamsas.objects.core.Link getLink(final int index) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._linkList.size()) { + throw new IndexOutOfBoundsException("getLink: Index value '" + index + + "' not in range [0.." + (this._linkList.size() - 1) + "]"); } - /** - * Method removeLinkAt. - * - * @param index - * @return the element removed from the collection - */ - public uk.ac.vamsas.objects.core.Link removeLinkAt( - final int index) { - java.lang.Object obj = this._linkList.remove(index); - return (uk.ac.vamsas.objects.core.Link) obj; + return (uk.ac.vamsas.objects.core.Link) _linkList.get(index); + } + + /** + * Method getLink.Returns the contents of the collection in an Array. + *
+ * Note: Just in case the collection contents are changing in another thread, + * we pass a 0-length Array of the correct type into the API call. This way we + * know that the Array returned is of exactly the correct length. + * + * @return this collection as an Array + */ + public uk.ac.vamsas.objects.core.Link[] getLink() { + uk.ac.vamsas.objects.core.Link[] array = new uk.ac.vamsas.objects.core.Link[0]; + return (uk.ac.vamsas.objects.core.Link[]) this._linkList.toArray(array); + } + + /** + * Method getLinkAsReference.Returns a reference to '_linkList'. No type + * checking is performed on any modifications to the Vector. + * + * @return a reference to the Vector backing this class + */ + public java.util.Vector getLinkAsReference() { + return this._linkList; + } + + /** + * Method getLinkCount. + * + * @return the size of this collection + */ + public int getLinkCount() { + return this._linkList.size(); + } + + /** + * Method getMap. + * + * @param index + * @throws java.lang.IndexOutOfBoundsException + * if the index given is outside the bounds of the collection + * @return the value of the uk.ac.vamsas.objects.core.Map at the given index + */ + public uk.ac.vamsas.objects.core.Map getMap(final int index) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._mapList.size()) { + throw new IndexOutOfBoundsException("getMap: Index value '" + index + + "' not in range [0.." + (this._mapList.size() - 1) + "]"); } - /** - * Method removeMap. - * - * @param vMap - * @return true if the object was removed from the collection. - */ - public boolean removeMap( - final uk.ac.vamsas.objects.core.Map vMap) { - boolean removed = _mapList.remove(vMap); - return removed; + return (uk.ac.vamsas.objects.core.Map) _mapList.get(index); + } + + /** + * Method getMap.Returns the contents of the collection in an Array. + *
+ * Note: Just in case the collection contents are changing in another thread, + * we pass a 0-length Array of the correct type into the API call. This way we + * know that the Array returned is of exactly the correct length. + * + * @return this collection as an Array + */ + public uk.ac.vamsas.objects.core.Map[] getMap() { + uk.ac.vamsas.objects.core.Map[] array = new uk.ac.vamsas.objects.core.Map[0]; + return (uk.ac.vamsas.objects.core.Map[]) this._mapList.toArray(array); + } + + /** + * Method getMapAsReference.Returns a reference to '_mapList'. No type + * checking is performed on any modifications to the Vector. + * + * @return a reference to the Vector backing this class + */ + public java.util.Vector getMapAsReference() { + return this._mapList; + } + + /** + * Method getMapCount. + * + * @return the size of this collection + */ + public int getMapCount() { + return this._mapList.size(); + } + + /** + * Method getProperty. + * + * @param index + * @throws java.lang.IndexOutOfBoundsException + * if the index given is outside the bounds of the collection + * @return the value of the uk.ac.vamsas.objects.core.Property at the given + * index + */ + public uk.ac.vamsas.objects.core.Property getProperty(final int index) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._propertyList.size()) { + throw new IndexOutOfBoundsException("getProperty: Index value '" + index + + "' not in range [0.." + (this._propertyList.size() - 1) + "]"); } - /** - * Method removeMapAt. - * - * @param index - * @return the element removed from the collection - */ - public uk.ac.vamsas.objects.core.Map removeMapAt( - final int index) { - java.lang.Object obj = this._mapList.remove(index); - return (uk.ac.vamsas.objects.core.Map) obj; + return (uk.ac.vamsas.objects.core.Property) _propertyList.get(index); + } + + /** + * Method getProperty.Returns the contents of the collection in an Array. + *
+ * Note: Just in case the collection contents are changing in another thread, + * we pass a 0-length Array of the correct type into the API call. This way we + * know that the Array returned is of exactly the correct length. + * + * @return this collection as an Array + */ + public uk.ac.vamsas.objects.core.Property[] getProperty() { + uk.ac.vamsas.objects.core.Property[] array = new uk.ac.vamsas.objects.core.Property[0]; + return (uk.ac.vamsas.objects.core.Property[]) this._propertyList + .toArray(array); + } + + /** + * Method getPropertyAsReference.Returns a reference to '_propertyList'. No + * type checking is performed on any modifications to the Vector. + * + * @return a reference to the Vector backing this class + */ + public java.util.Vector getPropertyAsReference() { + return this._propertyList; + } + + /** + * Method getPropertyCount. + * + * @return the size of this collection + */ + public int getPropertyCount() { + return this._propertyList.size(); + } + + /** + * 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 the value of field 'Source'. + */ + public java.lang.String getSource() { + return this._source; + } + + /** + * Returns the value of field 'version'. The field 'version' has the following + * description: Version must be specified - + * + * + * @return the value of field 'Version'. + */ + public java.lang.String getVersion() { + return this._version; + } + + /** + * Overrides the java.lang.Object.hashCode method. + *
+ * The following steps came from Effective Java Programming Language + * Guide by Joshua Bloch, Chapter 3 + * + * @return a hash code value for the object. + */ + public int hashCode() { + int result = super.hashCode(); + + long tmp; + if (_source != null + && !org.castor.util.CycleBreaker.startingToCycle(_source)) { + result = 37 * result + _source.hashCode(); + org.castor.util.CycleBreaker.releaseCycleHandle(_source); } - - /** - * Method removeProperty. - * - * @param vProperty - * @return true if the object was removed from the collection. - */ - public boolean removeProperty( - final uk.ac.vamsas.objects.core.Property vProperty) { - boolean removed = _propertyList.remove(vProperty); - return removed; + if (_version != null + && !org.castor.util.CycleBreaker.startingToCycle(_version)) { + result = 37 * result + _version.hashCode(); + org.castor.util.CycleBreaker.releaseCycleHandle(_version); } - - /** - * Method removePropertyAt. - * - * @param index - * @return the element removed from the collection - */ - public uk.ac.vamsas.objects.core.Property removePropertyAt( - final int index) { - java.lang.Object obj = this._propertyList.remove(index); - return (uk.ac.vamsas.objects.core.Property) obj; + if (_accessionId != null + && !org.castor.util.CycleBreaker.startingToCycle(_accessionId)) { + result = 37 * result + _accessionId.hashCode(); + org.castor.util.CycleBreaker.releaseCycleHandle(_accessionId); } - - /** - * 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'. - */ - public void setAccessionId( - final java.lang.String accessionId) { - this._accessionId = accessionId; + if (_id != null && !org.castor.util.CycleBreaker.startingToCycle(_id)) { + result = 37 * result + _id.hashCode(); + org.castor.util.CycleBreaker.releaseCycleHandle(_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'. - */ - public void setId( - final java.lang.String id) { - this._id = id; + if (_mapList != null + && !org.castor.util.CycleBreaker.startingToCycle(_mapList)) { + result = 37 * result + _mapList.hashCode(); + org.castor.util.CycleBreaker.releaseCycleHandle(_mapList); } - - /** - * - * - * @param index - * @param vLink - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void setLink( - final int index, - final uk.ac.vamsas.objects.core.Link vLink) - throws java.lang.IndexOutOfBoundsException { - // check bounds for index - if (index < 0 || index >= this._linkList.size()) { - throw new IndexOutOfBoundsException("setLink: Index value '" + index + "' not in range [0.." + (this._linkList.size() - 1) + "]"); - } - - this._linkList.set(index, vLink); + if (_linkList != null + && !org.castor.util.CycleBreaker.startingToCycle(_linkList)) { + result = 37 * result + _linkList.hashCode(); + org.castor.util.CycleBreaker.releaseCycleHandle(_linkList); } - - /** - * - * - * @param vLinkArray - */ - public void setLink( - final uk.ac.vamsas.objects.core.Link[] vLinkArray) { - //-- copy array - _linkList.clear(); - - for (int i = 0; i < vLinkArray.length; i++) { - this._linkList.add(vLinkArray[i]); - } + if (_propertyList != null + && !org.castor.util.CycleBreaker.startingToCycle(_propertyList)) { + result = 37 * result + _propertyList.hashCode(); + org.castor.util.CycleBreaker.releaseCycleHandle(_propertyList); } - /** - * Sets the value of '_linkList' by copying the given Vector. - * All elements will be checked for type safety. - * - * @param vLinkList the Vector to copy. - */ - public void setLink( - final java.util.Vector vLinkList) { - // copy vector - this._linkList.clear(); - - this._linkList.addAll(vLinkList); + return result; + } + + /** + * Method isValid. + * + * @return true if this object is valid according to the schema + */ + public boolean isValid() { + try { + validate(); + } catch (org.exolab.castor.xml.ValidationException vex) { + return false; } - - /** - * Sets the value of '_linkList' by setting it to the given - * Vector. No type checking is performed. - * @deprecated - * - * @param linkVector the Vector to set. - */ - public void setLinkAsReference( - final java.util.Vector linkVector) { - this._linkList = linkVector; + return true; + } + + /** + * + * + * @param out + * @throws org.exolab.castor.xml.MarshalException + * if object is null or if any SAXException is thrown during + * marshaling + * @throws org.exolab.castor.xml.ValidationException + * if this object is an invalid instance according to the schema + */ + public void marshal(final java.io.Writer out) + throws org.exolab.castor.xml.MarshalException, + org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, out); + } + + /** + * + * + * @param handler + * @throws java.io.IOException + * if an IOException occurs during marshaling + * @throws org.exolab.castor.xml.ValidationException + * if this object is an invalid instance according to the schema + * @throws org.exolab.castor.xml.MarshalException + * if object is null or if any SAXException is thrown during + * marshaling + */ + public void marshal(final org.xml.sax.ContentHandler handler) + throws java.io.IOException, org.exolab.castor.xml.MarshalException, + org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, handler); + } + + /** + */ + public void removeAllLink() { + this._linkList.clear(); + } + + /** + */ + public void removeAllMap() { + this._mapList.clear(); + } + + /** + */ + public void removeAllProperty() { + this._propertyList.clear(); + } + + /** + * Method removeLink. + * + * @param vLink + * @return true if the object was removed from the collection. + */ + public boolean removeLink(final uk.ac.vamsas.objects.core.Link vLink) { + boolean removed = _linkList.remove(vLink); + return removed; + } + + /** + * Method removeLinkAt. + * + * @param index + * @return the element removed from the collection + */ + public uk.ac.vamsas.objects.core.Link removeLinkAt(final int index) { + java.lang.Object obj = this._linkList.remove(index); + return (uk.ac.vamsas.objects.core.Link) obj; + } + + /** + * Method removeMap. + * + * @param vMap + * @return true if the object was removed from the collection. + */ + public boolean removeMap(final uk.ac.vamsas.objects.core.Map vMap) { + boolean removed = _mapList.remove(vMap); + return removed; + } + + /** + * Method removeMapAt. + * + * @param index + * @return the element removed from the collection + */ + public uk.ac.vamsas.objects.core.Map removeMapAt(final int index) { + java.lang.Object obj = this._mapList.remove(index); + return (uk.ac.vamsas.objects.core.Map) obj; + } + + /** + * Method removeProperty. + * + * @param vProperty + * @return true if the object was removed from the collection. + */ + public boolean removeProperty( + final uk.ac.vamsas.objects.core.Property vProperty) { + boolean removed = _propertyList.remove(vProperty); + return removed; + } + + /** + * Method removePropertyAt. + * + * @param index + * @return the element removed from the collection + */ + public uk.ac.vamsas.objects.core.Property removePropertyAt(final int index) { + java.lang.Object obj = this._propertyList.remove(index); + return (uk.ac.vamsas.objects.core.Property) obj; + } + + /** + * 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'. + */ + public void setAccessionId(final java.lang.String accessionId) { + this._accessionId = accessionId; + } + + /** + * 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(final java.lang.String id) { + this._id = id; + } + + /** + * + * + * @param index + * @param vLink + * @throws java.lang.IndexOutOfBoundsException + * if the index given is outside the bounds of the collection + */ + public void setLink(final int index, + final uk.ac.vamsas.objects.core.Link vLink) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._linkList.size()) { + throw new IndexOutOfBoundsException("setLink: Index value '" + index + + "' not in range [0.." + (this._linkList.size() - 1) + "]"); } - /** - * - * - * @param index - * @param vMap - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void setMap( - final int index, - final uk.ac.vamsas.objects.core.Map vMap) - throws java.lang.IndexOutOfBoundsException { - // check bounds for index - if (index < 0 || index >= this._mapList.size()) { - throw new IndexOutOfBoundsException("setMap: Index value '" + index + "' not in range [0.." + (this._mapList.size() - 1) + "]"); - } - - this._mapList.set(index, vMap); - } + this._linkList.set(index, vLink); + } - /** - * - * - * @param vMapArray - */ - public void setMap( - final uk.ac.vamsas.objects.core.Map[] vMapArray) { - //-- copy array - _mapList.clear(); - - for (int i = 0; i < vMapArray.length; i++) { - this._mapList.add(vMapArray[i]); - } - } + /** + * + * + * @param vLinkArray + */ + public void setLink(final uk.ac.vamsas.objects.core.Link[] vLinkArray) { + // -- copy array + _linkList.clear(); - /** - * Sets the value of '_mapList' by copying the given Vector. - * All elements will be checked for type safety. - * - * @param vMapList the Vector to copy. - */ - public void setMap( - final java.util.Vector vMapList) { - // copy vector - this._mapList.clear(); - - this._mapList.addAll(vMapList); + for (int i = 0; i < vLinkArray.length; i++) { + this._linkList.add(vLinkArray[i]); } - - /** - * Sets the value of '_mapList' by setting it to the given - * Vector. No type checking is performed. - * @deprecated - * - * @param mapVector the Vector to set. - */ - public void setMapAsReference( - final java.util.Vector mapVector) { - this._mapList = mapVector; + } + + /** + * Sets the value of '_linkList' by copying the given Vector. All elements + * will be checked for type safety. + * + * @param vLinkList + * the Vector to copy. + */ + public void setLink(final java.util.Vector vLinkList) { + // copy vector + this._linkList.clear(); + + this._linkList.addAll(vLinkList); + } + + /** + * Sets the value of '_linkList' by setting it to the given Vector. No type + * checking is performed. + * + * @deprecated + * + * @param linkVector + * the Vector to set. + */ + public void setLinkAsReference(final java.util.Vector linkVector) { + this._linkList = linkVector; + } + + /** + * + * + * @param index + * @param vMap + * @throws java.lang.IndexOutOfBoundsException + * if the index given is outside the bounds of the collection + */ + public void setMap(final int index, final uk.ac.vamsas.objects.core.Map vMap) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._mapList.size()) { + throw new IndexOutOfBoundsException("setMap: Index value '" + index + + "' not in range [0.." + (this._mapList.size() - 1) + "]"); } - /** - * - * - * @param index - * @param vProperty - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void setProperty( - final int index, - final uk.ac.vamsas.objects.core.Property vProperty) - throws java.lang.IndexOutOfBoundsException { - // check bounds for index - if (index < 0 || index >= this._propertyList.size()) { - throw new IndexOutOfBoundsException("setProperty: Index value '" + index + "' not in range [0.." + (this._propertyList.size() - 1) + "]"); - } - - this._propertyList.set(index, vProperty); - } + this._mapList.set(index, vMap); + } - /** - * - * - * @param vPropertyArray - */ - public void setProperty( - final uk.ac.vamsas.objects.core.Property[] vPropertyArray) { - //-- copy array - _propertyList.clear(); - - for (int i = 0; i < vPropertyArray.length; i++) { - this._propertyList.add(vPropertyArray[i]); - } - } + /** + * + * + * @param vMapArray + */ + public void setMap(final uk.ac.vamsas.objects.core.Map[] vMapArray) { + // -- copy array + _mapList.clear(); - /** - * Sets the value of '_propertyList' by copying the given - * Vector. All elements will be checked for type safety. - * - * @param vPropertyList the Vector to copy. - */ - public void setProperty( - final java.util.Vector vPropertyList) { - // copy vector - this._propertyList.clear(); - - this._propertyList.addAll(vPropertyList); + for (int i = 0; i < vMapArray.length; i++) { + this._mapList.add(vMapArray[i]); } - - /** - * Sets the value of '_propertyList' by setting it to the given - * Vector. No type checking is performed. - * @deprecated - * - * @param propertyVector the Vector to set. - */ - public void setPropertyAsReference( - final java.util.Vector propertyVector) { - this._propertyList = propertyVector; - } - - /** - * 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'. - */ - public void setSource( - final java.lang.String source) { - this._source = source; - } - - /** - * Sets the value of field 'version'. The field 'version' has - * the following description: Version must be specified - - * - * - * @param version the value of field 'version'. - */ - public void setVersion( - final java.lang.String version) { - this._version = version; - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - * @return the unmarshaled uk.ac.vamsas.objects.core.DbRef - */ - public static uk.ac.vamsas.objects.core.DbRef unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - return (uk.ac.vamsas.objects.core.DbRef) Unmarshaller.unmarshal(uk.ac.vamsas.objects.core.DbRef.class, reader); + } + + /** + * Sets the value of '_mapList' by copying the given Vector. All elements will + * be checked for type safety. + * + * @param vMapList + * the Vector to copy. + */ + public void setMap(final java.util.Vector vMapList) { + // copy vector + this._mapList.clear(); + + this._mapList.addAll(vMapList); + } + + /** + * Sets the value of '_mapList' by setting it to the given Vector. No type + * checking is performed. + * + * @deprecated + * + * @param mapVector + * the Vector to set. + */ + public void setMapAsReference(final java.util.Vector mapVector) { + this._mapList = mapVector; + } + + /** + * + * + * @param index + * @param vProperty + * @throws java.lang.IndexOutOfBoundsException + * if the index given is outside the bounds of the collection + */ + public void setProperty(final int index, + final uk.ac.vamsas.objects.core.Property vProperty) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._propertyList.size()) { + throw new IndexOutOfBoundsException("setProperty: Index value '" + index + + "' not in range [0.." + (this._propertyList.size() - 1) + "]"); } - /** - * - * - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - */ - public void validate( - ) - throws org.exolab.castor.xml.ValidationException { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); + this._propertyList.set(index, vProperty); + } + + /** + * + * + * @param vPropertyArray + */ + public void setProperty( + final uk.ac.vamsas.objects.core.Property[] vPropertyArray) { + // -- copy array + _propertyList.clear(); + + for (int i = 0; i < vPropertyArray.length; i++) { + this._propertyList.add(vPropertyArray[i]); } + } + + /** + * Sets the value of '_propertyList' by copying the given Vector. All elements + * will be checked for type safety. + * + * @param vPropertyList + * the Vector to copy. + */ + public void setProperty(final java.util.Vector vPropertyList) { + // copy vector + this._propertyList.clear(); + + this._propertyList.addAll(vPropertyList); + } + + /** + * Sets the value of '_propertyList' by setting it to the given Vector. No + * type checking is performed. + * + * @deprecated + * + * @param propertyVector + * the Vector to set. + */ + public void setPropertyAsReference(final java.util.Vector propertyVector) { + this._propertyList = propertyVector; + } + + /** + * 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'. + */ + public void setSource(final java.lang.String source) { + this._source = source; + } + + /** + * Sets the value of field 'version'. The field 'version' has the following + * description: Version must be specified - + * + * + * @param version + * the value of field 'version'. + */ + public void setVersion(final java.lang.String version) { + this._version = version; + } + + /** + * Method unmarshal. + * + * @param reader + * @throws org.exolab.castor.xml.MarshalException + * if object is null or if any SAXException is thrown during + * marshaling + * @throws org.exolab.castor.xml.ValidationException + * if this object is an invalid instance according to the schema + * @return the unmarshaled uk.ac.vamsas.objects.core.DbRef + */ + public static uk.ac.vamsas.objects.core.DbRef unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, + org.exolab.castor.xml.ValidationException { + return (uk.ac.vamsas.objects.core.DbRef) Unmarshaller.unmarshal( + uk.ac.vamsas.objects.core.DbRef.class, reader); + } + + /** + * + * + * @throws org.exolab.castor.xml.ValidationException + * if this object is an invalid instance according to the schema + */ + public void validate() throws org.exolab.castor.xml.ValidationException { + org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); + validator.validate(this); + } }