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 Newick + * @return this collection as an Array */ - public uk.ac.vamsas.objects.core.Newick[] getNewick() - { - int size = _newickList.size(); - uk.ac.vamsas.objects.core.Newick[] mArray = new uk.ac.vamsas.objects.core.Newick[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (uk.ac.vamsas.objects.core.Newick) _newickList.elementAt(index); - } - return mArray; - } //-- uk.ac.vamsas.objects.core.Newick[] getNewick() + public uk.ac.vamsas.objects.core.Newick[] getNewick( + ) { + uk.ac.vamsas.objects.core.Newick[] array = new uk.ac.vamsas.objects.core.Newick[0]; + return (uk.ac.vamsas.objects.core.Newick[]) this._newickList.toArray(array); + } /** - * Method getNewickCount - * + * Method getNewickAsReference.Returns a reference to + * '_newickList'. No type checking is performed on any + * modifications to the Vector. * - * - * @return int + * @return a reference to the Vector backing this class */ - public int getNewickCount() - { - return _newickList.size(); - } //-- int getNewickCount() + public java.util.Vector getNewickAsReference( + ) { + return this._newickList; + } /** - * Method getProperty - * + * Method getNewickCount. * + * @return the size of this collection + */ + public int getNewickCount( + ) { + return this._newickList.size(); + } + + /** + * 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 'provenance'. * - * @return Provenance - * @return the value of field 'provenance'. + * @return the value of field 'Provenance'. */ - public uk.ac.vamsas.objects.core.Provenance getProvenance() - { + public uk.ac.vamsas.objects.core.Provenance getProvenance( + ) { return this._provenance; - } //-- uk.ac.vamsas.objects.core.Provenance getProvenance() + } /** * Returns the value of field 'title'. * - * @return String - * @return the value of field 'title'. + * @return the value of field 'Title'. */ - public java.lang.String getTitle() - { + public java.lang.String getTitle( + ) { return this._title; - } //-- java.lang.String getTitle() + } + + /** + * Method getTreenode. + * + * @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.Treenode + * at the given index + */ + public uk.ac.vamsas.objects.core.Treenode getTreenode( + final int index) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._treenodeList.size()) { + throw new IndexOutOfBoundsException("getTreenode: Index value '" + index + "' not in range [0.." + (this._treenodeList.size() - 1) + "]"); + } + + return (uk.ac.vamsas.objects.core.Treenode) _treenodeList.get(index); + } /** - * Method isValid + * Method getTreenode.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.Treenode[] getTreenode( + ) { + uk.ac.vamsas.objects.core.Treenode[] array = new uk.ac.vamsas.objects.core.Treenode[0]; + return (uk.ac.vamsas.objects.core.Treenode[]) this._treenodeList.toArray(array); + } + + /** + * Method getTreenodeAsReference.Returns a reference to + * '_treenodeList'. No type checking is performed on any + * modifications to the Vector. + * + * @return a reference to the Vector backing this class + */ + public java.util.Vector getTreenodeAsReference( + ) { + return this._treenodeList; + } + + /** + * Method getTreenodeCount. + * + * @return the size of this collection + */ + public int getTreenodeCount( + ) { + return this._treenodeList.size(); + } + + /** + * 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 (_id != null + && !org.castor.util.CycleBreaker.startingToCycle(_id)) { + result = 37 * result + _id.hashCode(); + org.castor.util.CycleBreaker.releaseCycleHandle(_id); + } + if (_modifiable != null + && !org.castor.util.CycleBreaker.startingToCycle(_modifiable)) { + result = 37 * result + _modifiable.hashCode(); + org.castor.util.CycleBreaker.releaseCycleHandle(_modifiable); + } + if (_title != null + && !org.castor.util.CycleBreaker.startingToCycle(_title)) { + result = 37 * result + _title.hashCode(); + org.castor.util.CycleBreaker.releaseCycleHandle(_title); + } + if (_newickList != null + && !org.castor.util.CycleBreaker.startingToCycle(_newickList)) { + result = 37 * result + _newickList.hashCode(); + org.castor.util.CycleBreaker.releaseCycleHandle(_newickList); + } + if (_treenodeList != null + && !org.castor.util.CycleBreaker.startingToCycle(_treenodeList)) { + result = 37 * result + _treenodeList.hashCode(); + org.castor.util.CycleBreaker.releaseCycleHandle(_treenodeList); + } + if (_propertyList != null + && !org.castor.util.CycleBreaker.startingToCycle(_propertyList)) { + result = 37 * result + _propertyList.hashCode(); + org.castor.util.CycleBreaker.releaseCycleHandle(_propertyList); + } + if (_provenance != null + && !org.castor.util.CycleBreaker.startingToCycle(_provenance)) { + result = 37 * result + _provenance.hashCode(); + org.castor.util.CycleBreaker.releaseCycleHandle(_provenance); + } + + 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 + * @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(java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - + 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 + * @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(org.xml.sax.ContentHandler handler) - throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - + 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 removeAllNewick - * */ - public void removeAllNewick() - { - _newickList.removeAllElements(); - } //-- void removeAllNewick() + public void removeAllNewick( + ) { + this._newickList.clear(); + } /** - * Method removeAllProperty - * */ - public void removeAllProperty() - { - _propertyList.removeAllElements(); - } //-- void removeAllProperty() + public void removeAllProperty( + ) { + this._propertyList.clear(); + } /** - * Method removeNewick - * + */ + public void removeAllTreenode( + ) { + this._treenodeList.clear(); + } + + /** + * Method removeNewick. * + * @param vNewick + * @return true if the object was removed from the collection. + */ + public boolean removeNewick( + final uk.ac.vamsas.objects.core.Newick vNewick) { + boolean removed = _newickList.remove(vNewick); + return removed; + } + + /** + * Method removeNewickAt. * * @param index - * @return Newick + * @return the element removed from the collection */ - public uk.ac.vamsas.objects.core.Newick removeNewick(int index) - { - java.lang.Object obj = _newickList.elementAt(index); - _newickList.removeElementAt(index); + public uk.ac.vamsas.objects.core.Newick removeNewickAt( + final int index) { + java.lang.Object obj = this._newickList.remove(index); return (uk.ac.vamsas.objects.core.Newick) obj; - } //-- uk.ac.vamsas.objects.core.Newick removeNewick(int) + } /** - * Method removeProperty - * + * 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 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) + } + + /** + * Method removeTreenode. + * + * @param vTreenode + * @return true if the object was removed from the collection. + */ + public boolean removeTreenode( + final uk.ac.vamsas.objects.core.Treenode vTreenode) { + boolean removed = _treenodeList.remove(vTreenode); + return removed; + } + + /** + * Method removeTreenodeAt. + * + * @param index + * @return the element removed from the collection + */ + public uk.ac.vamsas.objects.core.Treenode removeTreenodeAt( + final int index) { + java.lang.Object obj = this._treenodeList.remove(index); + return (uk.ac.vamsas.objects.core.Treenode) obj; + } /** * Sets the value of field 'id'. The field 'id' has the @@ -469,132 +788,251 @@ 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) + } /** * Sets the value of field 'modifiable'. * * @param modifiable the value of field 'modifiable'. */ - public void setModifiable(java.lang.String modifiable) - { + public void setModifiable( + final java.lang.String modifiable) { this._modifiable = modifiable; - } //-- void setModifiable(java.lang.String) + } /** - * Method setNewick - * * * * @param index * @param vNewick + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection */ - public void setNewick(int index, uk.ac.vamsas.objects.core.Newick vNewick) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _newickList.size())) { - throw new IndexOutOfBoundsException("setNewick: Index value '"+index+"' not in range [0.."+_newickList.size()+ "]"); + public void setNewick( + final int index, + final uk.ac.vamsas.objects.core.Newick vNewick) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._newickList.size()) { + throw new IndexOutOfBoundsException("setNewick: Index value '" + index + "' not in range [0.." + (this._newickList.size() - 1) + "]"); } - _newickList.setElementAt(vNewick, index); - } //-- void setNewick(int, uk.ac.vamsas.objects.core.Newick) + + this._newickList.set(index, vNewick); + } /** - * Method setNewick - * * * - * @param newickArray + * @param vNewickArray */ - public void setNewick(uk.ac.vamsas.objects.core.Newick[] newickArray) - { + public void setNewick( + final uk.ac.vamsas.objects.core.Newick[] vNewickArray) { //-- copy array - _newickList.removeAllElements(); - for (int i = 0; i < newickArray.length; i++) { - _newickList.addElement(newickArray[i]); + _newickList.clear(); + + for (int i = 0; i < vNewickArray.length; i++) { + this._newickList.add(vNewickArray[i]); } - } //-- void setNewick(uk.ac.vamsas.objects.core.Newick) + } /** - * Method setProperty + * Sets the value of '_newickList' by copying the given Vector. + * All elements will be checked for type safety. * + * @param vNewickList the Vector to copy. + */ + public void setNewick( + final java.util.Vector vNewickList) { + // copy vector + this._newickList.clear(); + + this._newickList.addAll(vNewickList); + } + + /** + * Sets the value of '_newickList' by setting it to the given + * Vector. No type checking is performed. + * @deprecated + * + * @param newickVector the Vector to set. + */ + public void setNewickAsReference( + final java.util.Vector newickVector) { + this._newickList = newickVector; + } + + /** * * * @param index * @param vProperty + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection */ - 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()+ "]"); + 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) + "]"); } - _propertyList.setElementAt(vProperty, index); - } //-- void setProperty(int, uk.ac.vamsas.objects.core.Property) + + this._propertyList.set(index, vProperty); + } /** - * Method setProperty - * * * - * @param propertyArray + * @param vPropertyArray */ - public void setProperty(uk.ac.vamsas.objects.core.Property[] propertyArray) - { + public void setProperty( + final uk.ac.vamsas.objects.core.Property[] vPropertyArray) { //-- copy array - _propertyList.removeAllElements(); - for (int i = 0; i < propertyArray.length; i++) { - _propertyList.addElement(propertyArray[i]); + _propertyList.clear(); + + for (int i = 0; i < vPropertyArray.length; i++) { + this._propertyList.add(vPropertyArray[i]); } - } //-- void setProperty(uk.ac.vamsas.objects.core.Property) + } + + /** + * 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 'provenance'. * * @param provenance the value of field 'provenance'. */ - public void setProvenance(uk.ac.vamsas.objects.core.Provenance provenance) - { + public void setProvenance( + final uk.ac.vamsas.objects.core.Provenance provenance) { this._provenance = provenance; - } //-- void setProvenance(uk.ac.vamsas.objects.core.Provenance) + } /** * Sets the value of field 'title'. * * @param title the value of field 'title'. */ - public void setTitle(java.lang.String title) - { + public void setTitle( + final java.lang.String title) { this._title = title; - } //-- void setTitle(java.lang.String) + } + + /** + * + * + * @param index + * @param vTreenode + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void setTreenode( + final int index, + final uk.ac.vamsas.objects.core.Treenode vTreenode) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._treenodeList.size()) { + throw new IndexOutOfBoundsException("setTreenode: Index value '" + index + "' not in range [0.." + (this._treenodeList.size() - 1) + "]"); + } + + this._treenodeList.set(index, vTreenode); + } + + /** + * + * + * @param vTreenodeArray + */ + public void setTreenode( + final uk.ac.vamsas.objects.core.Treenode[] vTreenodeArray) { + //-- copy array + _treenodeList.clear(); + + for (int i = 0; i < vTreenodeArray.length; i++) { + this._treenodeList.add(vTreenodeArray[i]); + } + } /** - * Method unmarshal + * Sets the value of '_treenodeList' by copying the given + * Vector. All elements will be checked for type safety. * + * @param vTreenodeList the Vector to copy. + */ + public void setTreenode( + final java.util.Vector vTreenodeList) { + // copy vector + this._treenodeList.clear(); + + this._treenodeList.addAll(vTreenodeList); + } + + /** + * Sets the value of '_treenodeList' by setting it to the given + * Vector. No type checking is performed. + * @deprecated * + * @param treenodeVector the Vector to set. + */ + public void setTreenodeAsReference( + final java.util.Vector treenodeVector) { + this._treenodeList = treenodeVector; + } + + /** + * Method unmarshal. * * @param reader - * @return Tree + * @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.Tree */ - public static uk.ac.vamsas.objects.core.Tree unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { + public static uk.ac.vamsas.objects.core.Tree unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { return (uk.ac.vamsas.objects.core.Tree) Unmarshaller.unmarshal(uk.ac.vamsas.objects.core.Tree.class, reader); - } //-- uk.ac.vamsas.objects.core.Tree 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() + } }