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 Link + * @return this collection as an Array */ - public uk.ac.vamsas.objects.core.Link[] getLink() - { - int size = _linkList.size(); - uk.ac.vamsas.objects.core.Link[] mArray = new uk.ac.vamsas.objects.core.Link[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (uk.ac.vamsas.objects.core.Link) _linkList.elementAt(index); - } - return mArray; - } //-- uk.ac.vamsas.objects.core.Link[] getLink() + 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 getLinkCount - * + * Method getLinkAsReference.Returns a reference to + * '_linkList'. No type checking is performed on any + * modifications to the Vector. * - * - * @return int + * @return a reference to the Vector backing this class */ - public int getLinkCount() - { - return _linkList.size(); - } //-- int getLinkCount() + public java.util.Vector getLinkAsReference( + ) { + return this._linkList; + } /** - * Method getMap - * - * - * - * @param index - * @return Map - */ - public uk.ac.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 (uk.ac.vamsas.objects.core.Map) _mapList.elementAt(index); - } //-- uk.ac.vamsas.objects.core.Map getMap(int) - - /** - * Method getMap - * - * + * Method getLinkCount. * - * @return Map + * @return the size of this collection */ - public uk.ac.vamsas.objects.core.Map[] getMap() - { - int size = _mapList.size(); - uk.ac.vamsas.objects.core.Map[] mArray = new uk.ac.vamsas.objects.core.Map[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (uk.ac.vamsas.objects.core.Map) _mapList.elementAt(index); - } - return mArray; - } //-- uk.ac.vamsas.objects.core.Map[] getMap() + public int getLinkCount( + ) { + return this._linkList.size(); + } /** - * Method getMapCount - * - * + * Returns the value of field 'map'. The field 'map' has the + * following description: the local mapType maps from the + * parent + * sequence coordinate frame to the reference + * frame defined by the dbRef element. + * The mapped mapType is the mapped range defined + * on the dbRef element's reference frame. + * Conventionally, the unit attribute defaults to 1, or + * will be inferred from the local sequence's + * dictionary type and any dictionary type associated + * with the database being mapped to. + * However, it may be used to avoid ambiguity. + * * - * @return int + * @return the value of field 'Map'. */ - public int getMapCount() - { - return _mapList.size(); - } //-- int getMapCount() + public uk.ac.vamsas.objects.core.Map getMap( + ) { + return this._map; + } /** - * Method getProperty - * - * + * Method getProperty. * * @param index - * @return Property - */ - public uk.ac.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()+ "]"); + * @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.elementAt(index); - } //-- uk.ac.vamsas.objects.core.Property getProperty(int) + return (uk.ac.vamsas.objects.core.Property) _propertyList.get(index); + } /** - * Method getProperty - * - * + * 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 Property + * @return this collection as an Array */ - public uk.ac.vamsas.objects.core.Property[] getProperty() - { - int size = _propertyList.size(); - uk.ac.vamsas.objects.core.Property[] mArray = new uk.ac.vamsas.objects.core.Property[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (uk.ac.vamsas.objects.core.Property) _propertyList.elementAt(index); - } - return mArray; - } //-- uk.ac.vamsas.objects.core.Property[] getProperty() + 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 getPropertyCount - * + * 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 int + * @return the size of this collection */ - public int getPropertyCount() - { - return _propertyList.size(); - } //-- int getPropertyCount() + public int getPropertyCount( + ) { + return this._propertyList.size(); + } /** * Returns the value of field 'source'. The field 'source' has @@ -482,144 +529,185 @@ implements java.io.Serializable * uncontrolled/unspecified string ID * * - * @return String - * @return the value of field 'source'. + * @return the value of field 'Source'. */ - public java.lang.String getSource() - { + public java.lang.String getSource( + ) { return this._source; - } //-- java.lang.String getSource() + } /** * 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'. + * @return the value of field 'Version'. */ - public java.lang.String getVersion() - { + public java.lang.String getVersion( + ) { return this._version; - } //-- java.lang.String getVersion() + } /** - * Method isValid - * + * 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); + } + if (_version != null + && !org.castor.util.CycleBreaker.startingToCycle(_version)) { + result = 37 * result + _version.hashCode(); + org.castor.util.CycleBreaker.releaseCycleHandle(_version); + } + if (_accessionId != null + && !org.castor.util.CycleBreaker.startingToCycle(_accessionId)) { + result = 37 * result + _accessionId.hashCode(); + org.castor.util.CycleBreaker.releaseCycleHandle(_accessionId); + } + if (_id != null + && !org.castor.util.CycleBreaker.startingToCycle(_id)) { + result = 37 * result + _id.hashCode(); + org.castor.util.CycleBreaker.releaseCycleHandle(_id); + } + if (_map != null + && !org.castor.util.CycleBreaker.startingToCycle(_map)) { + result = 37 * result + _map.hashCode(); + org.castor.util.CycleBreaker.releaseCycleHandle(_map); + } + if (_linkList != null + && !org.castor.util.CycleBreaker.startingToCycle(_linkList)) { + result = 37 * result + _linkList.hashCode(); + org.castor.util.CycleBreaker.releaseCycleHandle(_linkList); + } + if (_propertyList != null + && !org.castor.util.CycleBreaker.startingToCycle(_propertyList)) { + result = 37 * result + _propertyList.hashCode(); + org.castor.util.CycleBreaker.releaseCycleHandle(_propertyList); + } + + return result; + } + + /** + * Method isValid. * - * @return boolean + * @return true if this object is valid according to the schema */ - public boolean isValid() - { + public boolean isValid( + ) { try { validate(); - } - catch (org.exolab.castor.xml.ValidationException vex) { + } 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 - { - + * @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); - } //-- 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 - { - + * @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); - } //-- void marshal(org.xml.sax.ContentHandler) + } /** - * Method removeAllLink - * */ - public void removeAllLink() - { - _linkList.removeAllElements(); - } //-- void removeAllLink() + public void removeAllLink( + ) { + this._linkList.clear(); + } /** - * Method removeAllMap - * */ - public void removeAllMap() - { - _mapList.removeAllElements(); - } //-- void removeAllMap() + public void removeAllProperty( + ) { + this._propertyList.clear(); + } /** - * Method removeAllProperty + * Method removeLink. * + * @param vLink + * @return true if the object was removed from the collection. */ - public void removeAllProperty() - { - _propertyList.removeAllElements(); - } //-- void removeAllProperty() + public boolean removeLink( + final uk.ac.vamsas.objects.core.Link vLink) { + boolean removed = _linkList.remove(vLink); + return removed; + } /** - * Method removeLink - * - * + * Method removeLinkAt. * * @param index - * @return Link + * @return the element removed from the collection */ - public uk.ac.vamsas.objects.core.Link removeLink(int index) - { - java.lang.Object obj = _linkList.elementAt(index); - _linkList.removeElementAt(index); + 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; - } //-- uk.ac.vamsas.objects.core.Link removeLink(int) + } /** - * Method removeMap + * Method removeProperty. * - * - * - * @param index - * @return Map + * @param vProperty + * @return true if the object was removed from the collection. */ - public uk.ac.vamsas.objects.core.Map removeMap(int index) - { - java.lang.Object obj = _mapList.elementAt(index); - _mapList.removeElementAt(index); - return (uk.ac.vamsas.objects.core.Map) obj; - } //-- uk.ac.vamsas.objects.core.Map removeMap(int) + public boolean removeProperty( + final uk.ac.vamsas.objects.core.Property vProperty) { + boolean removed = _propertyList.remove(vProperty); + return removed; + } /** - * Method removeProperty - * - * + * Method removePropertyAt. * * @param index - * @return Property + * @return the element removed from the collection */ - public uk.ac.vamsas.objects.core.Property removeProperty(int index) - { - java.lang.Object obj = _propertyList.elementAt(index); - _propertyList.removeElementAt(index); + 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; - } //-- uk.ac.vamsas.objects.core.Property removeProperty(int) + } /** * Sets the value of field 'accessionId'. The field @@ -632,10 +720,10 @@ implements java.io.Serializable * * @param accessionId the value of field 'accessionId'. */ - public void setAccessionId(java.lang.String accessionId) - { + public void setAccessionId( + final java.lang.String accessionId) { this._accessionId = accessionId; - } //-- void setAccessionId(java.lang.String) + } /** * Sets the value of field 'id'. The field 'id' has the @@ -644,112 +732,154 @@ implements java.io.Serializable * * @param id the value of field 'id'. */ - public void setId(java.lang.String id) - { + public void setId( + final java.lang.String id) { this._id = id; - } //-- void setId(java.lang.String) + } /** - * Method setLink - * * * * @param index * @param vLink - */ - public void setLink(int index, uk.ac.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()+ "]"); + * @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) + "]"); } - _linkList.setElementAt(vLink, index); - } //-- void setLink(int, uk.ac.vamsas.objects.core.Link) + + this._linkList.set(index, vLink); + } /** - * Method setLink * * - * - * @param linkArray + * @param vLinkArray */ - public void setLink(uk.ac.vamsas.objects.core.Link[] linkArray) - { + public void setLink( + final uk.ac.vamsas.objects.core.Link[] vLinkArray) { //-- copy array - _linkList.removeAllElements(); - for (int i = 0; i < linkArray.length; i++) { - _linkList.addElement(linkArray[i]); + _linkList.clear(); + + for (int i = 0; i < vLinkArray.length; i++) { + this._linkList.add(vLinkArray[i]); } - } //-- void setLink(uk.ac.vamsas.objects.core.Link) + } /** - * Method setMap + * 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; + } + + /** + * Sets the value of field 'map'. The field 'map' has the + * following description: the local mapType maps from the + * parent + * sequence coordinate frame to the reference + * frame defined by the dbRef element. + * The mapped mapType is the mapped range defined + * on the dbRef element's reference frame. + * Conventionally, the unit attribute defaults to 1, or + * will be inferred from the local sequence's + * dictionary type and any dictionary type associated + * with the database being mapped to. + * However, it may be used to avoid ambiguity. + * + * + * @param map the value of field 'map'. + */ + public void setMap( + final uk.ac.vamsas.objects.core.Map map) { + this._map = map; + } + + /** * * * @param index - * @param vMap - */ - public void setMap(int index, uk.ac.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()+ "]"); + * @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) + "]"); } - _mapList.setElementAt(vMap, index); - } //-- void setMap(int, uk.ac.vamsas.objects.core.Map) + + this._propertyList.set(index, vProperty); + } /** - * Method setMap - * * * - * @param mapArray + * @param vPropertyArray */ - public void setMap(uk.ac.vamsas.objects.core.Map[] mapArray) - { + public void setProperty( + final uk.ac.vamsas.objects.core.Property[] vPropertyArray) { //-- copy array - _mapList.removeAllElements(); - for (int i = 0; i < mapArray.length; i++) { - _mapList.addElement(mapArray[i]); + _propertyList.clear(); + + for (int i = 0; i < vPropertyArray.length; i++) { + this._propertyList.add(vPropertyArray[i]); } - } //-- void setMap(uk.ac.vamsas.objects.core.Map) + } /** - * Method setProperty + * Sets the value of '_propertyList' by copying the given + * Vector. All elements will be checked for type safety. * - * - * - * @param index - * @param vProperty + * @param vPropertyList the Vector to copy. */ - public void setProperty(int index, uk.ac.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, uk.ac.vamsas.objects.core.Property) + public void setProperty( + final java.util.Vector vPropertyList) { + // copy vector + this._propertyList.clear(); + + this._propertyList.addAll(vPropertyList); + } /** - * Method setProperty - * + * Sets the value of '_propertyList' by setting it to the given + * Vector. No type checking is performed. + * @deprecated * - * - * @param propertyArray + * @param propertyVector the Vector to set. */ - public void setProperty(uk.ac.vamsas.objects.core.Property[] propertyArray) - { - //-- copy array - _propertyList.removeAllElements(); - for (int i = 0; i < propertyArray.length; i++) { - _propertyList.addElement(propertyArray[i]); - } - } //-- void setProperty(uk.ac.vamsas.objects.core.Property) + public void setPropertyAsReference( + final java.util.Vector propertyVector) { + this._propertyList = propertyVector; + } /** * Sets the value of field 'source'. The field 'source' has the @@ -761,10 +891,10 @@ implements java.io.Serializable * * @param source the value of field 'source'. */ - public void setSource(java.lang.String source) - { + public void setSource( + final java.lang.String source) { this._source = source; - } //-- void setSource(java.lang.String) + } /** * Sets the value of field 'version'. The field 'version' has @@ -773,34 +903,38 @@ implements java.io.Serializable * * @param version the value of field 'version'. */ - public void setVersion(java.lang.String version) - { + public void setVersion( + final java.lang.String version) { this._version = version; - } //-- void setVersion(java.lang.String) + } /** - * Method unmarshal - * - * + * Method unmarshal. * * @param reader - * @return DbRef - */ - public static uk.ac.vamsas.objects.core.DbRef unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { + * @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); - } //-- uk.ac.vamsas.objects.core.DbRef unmarshal(java.io.Reader) + } /** - * Method validate * + * + * @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 - { + 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() + } }