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 java.lang.Object[] getSeqrefs( - ) { - java.lang.Object[] array = new java.lang.Object[0]; - return (java.lang.Object[]) this._seqrefs.toArray(array); - } - - /** - * Method getSeqrefsAsReference.Returns a reference to - * '_seqrefs'. No type checking is performed on any - * modifications to the Vector. - * - * @return a reference to the Vector backing this class - */ - public java.util.Vector getSeqrefsAsReference( - ) { - return this._seqrefs; - } - - /** - * Method getSeqrefsCount. - * - * @return the size of this collection - */ - public int getSeqrefsCount( - ) { - return this._seqrefs.size(); - } - - /** - * Method hasGraph. - * - * @return true if at least one Graph has been added - */ - public boolean hasGraph( - ) { - return this._has_graph; - } - - /** - * 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; - result = 37 * result + (_graph?0:1); - if (_seqrefs != null - && !org.castor.util.CycleBreaker.startingToCycle(_seqrefs)) { - result = 37 * result + _seqrefs.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_seqrefs); - } - if (_provenance != null - && !org.castor.util.CycleBreaker.startingToCycle(_provenance)) { - result = 37 * result + _provenance.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_provenance); - } - - return result; - } - - /** - * 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 the value of field 'Graph'. - */ - public boolean isGraph( - ) { - return this._graph; - } - - /** - * 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) { + if (this._provenance != null) { + if (temp._provenance == null) + return false; + if (this._provenance != temp._provenance) { + thcycle = org.castor.util.CycleBreaker + .startingToCycle(this._provenance); + tmcycle = org.castor.util.CycleBreaker + .startingToCycle(temp._provenance); + if (thcycle != tmcycle) { + if (!thcycle) { + org.castor.util.CycleBreaker.releaseCycleHandle(this._provenance); + } + ; + if (!tmcycle) { + org.castor.util.CycleBreaker.releaseCycleHandle(temp._provenance); + } + ; return false; + } + if (!thcycle) { + if (!this._provenance.equals(temp._provenance)) { + org.castor.util.CycleBreaker.releaseCycleHandle(this._provenance); + org.castor.util.CycleBreaker.releaseCycleHandle(temp._provenance); + return false; + } + org.castor.util.CycleBreaker.releaseCycleHandle(this._provenance); + org.castor.util.CycleBreaker.releaseCycleHandle(temp._provenance); + } } - 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 removeAllSeqrefs( - ) { - this._seqrefs.clear(); - } - - /** - * Method removeSeqrefs. - * - * @param vSeqrefs - * @return true if the object was removed from the collection. - */ - public boolean removeSeqrefs( - final java.lang.Object vSeqrefs) { - boolean removed = _seqrefs.remove(vSeqrefs); - return removed; - } - - /** - * Method removeSeqrefsAt. - * - * @param index - * @return the element removed from the collection - */ - public java.lang.Object removeSeqrefsAt( - final int index) { - java.lang.Object obj = this._seqrefs.remove(index); - return obj; + } else if (temp._provenance != null) + return false; + return true; } - - /** - * 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( - final boolean graph) { - this._graph = graph; - this._has_graph = true; + return false; + } + + /** + * 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 the value of field 'Graph'. + */ + public boolean getGraph() { + return this._graph; + } + + /** + * Returns the value of field 'provenance'. + * + * @return the value of field 'Provenance'. + */ + public uk.ac.vamsas.objects.core.Provenance getProvenance() { + return this._provenance; + } + + /** + * Method getSeqrefs. + * + * @param index + * @throws java.lang.IndexOutOfBoundsException + * if the index given is outside the bounds of the collection + * @return the value of the java.lang.Object at the given index + */ + public java.lang.Object getSeqrefs(final int index) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._seqrefs.size()) { + throw new IndexOutOfBoundsException("getSeqrefs: Index value '" + index + + "' not in range [0.." + (this._seqrefs.size() - 1) + "]"); } - /** - * Sets the value of field 'provenance'. - * - * @param provenance the value of field 'provenance'. - */ - public void setProvenance( - final uk.ac.vamsas.objects.core.Provenance provenance) { - this._provenance = provenance; + return _seqrefs.get(index); + } + + /** + * Method getSeqrefs.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 java.lang.Object[] getSeqrefs() { + java.lang.Object[] array = new java.lang.Object[0]; + return (java.lang.Object[]) this._seqrefs.toArray(array); + } + + /** + * Method getSeqrefsAsReference.Returns a reference to '_seqrefs'. No type + * checking is performed on any modifications to the Vector. + * + * @return a reference to the Vector backing this class + */ + public java.util.Vector getSeqrefsAsReference() { + return this._seqrefs; + } + + /** + * Method getSeqrefsCount. + * + * @return the size of this collection + */ + public int getSeqrefsCount() { + return this._seqrefs.size(); + } + + /** + * Method hasGraph. + * + * @return true if at least one Graph has been added + */ + public boolean hasGraph() { + return this._has_graph; + } + + /** + * 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; + result = 37 * result + (_graph ? 0 : 1); + if (_seqrefs != null + && !org.castor.util.CycleBreaker.startingToCycle(_seqrefs)) { + result = 37 * result + _seqrefs.hashCode(); + org.castor.util.CycleBreaker.releaseCycleHandle(_seqrefs); } - - /** - * - * - * @param index - * @param vSeqrefs - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void setSeqrefs( - final int index, - final java.lang.Object vSeqrefs) - throws java.lang.IndexOutOfBoundsException { - // check bounds for index - if (index < 0 || index >= this._seqrefs.size()) { - throw new IndexOutOfBoundsException("setSeqrefs: Index value '" + index + "' not in range [0.." + (this._seqrefs.size() - 1) + "]"); - } - - this._seqrefs.set(index, vSeqrefs); + if (_provenance != null + && !org.castor.util.CycleBreaker.startingToCycle(_provenance)) { + result = 37 * result + _provenance.hashCode(); + org.castor.util.CycleBreaker.releaseCycleHandle(_provenance); } - /** - * - * - * @param vSeqrefsArray - */ - public void setSeqrefs( - final java.lang.Object[] vSeqrefsArray) { - //-- copy array - _seqrefs.clear(); - - for (int i = 0; i < vSeqrefsArray.length; i++) { - this._seqrefs.add(vSeqrefsArray[i]); - } + return result; + } + + /** + * 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 the value of field 'Graph'. + */ + public boolean isGraph() { + return this._graph; + } + + /** + * 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 '_seqrefs' by copying the given Vector. - * All elements will be checked for type safety. - * - * @param vSeqrefsList the Vector to copy. - */ - public void setSeqrefs( - final java.util.Vector vSeqrefsList) { - // copy vector - this._seqrefs.clear(); - - this._seqrefs.addAll(vSeqrefsList); + 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 removeAllSeqrefs() { + this._seqrefs.clear(); + } + + /** + * Method removeSeqrefs. + * + * @param vSeqrefs + * @return true if the object was removed from the collection. + */ + public boolean removeSeqrefs(final java.lang.Object vSeqrefs) { + boolean removed = _seqrefs.remove(vSeqrefs); + return removed; + } + + /** + * Method removeSeqrefsAt. + * + * @param index + * @return the element removed from the collection + */ + public java.lang.Object removeSeqrefsAt(final int index) { + java.lang.Object obj = this._seqrefs.remove(index); + return obj; + } + + /** + * 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(final boolean graph) { + this._graph = graph; + this._has_graph = true; + } + + /** + * Sets the value of field 'provenance'. + * + * @param provenance + * the value of field 'provenance'. + */ + public void setProvenance( + final uk.ac.vamsas.objects.core.Provenance provenance) { + this._provenance = provenance; + } + + /** + * + * + * @param index + * @param vSeqrefs + * @throws java.lang.IndexOutOfBoundsException + * if the index given is outside the bounds of the collection + */ + public void setSeqrefs(final int index, final java.lang.Object vSeqrefs) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._seqrefs.size()) { + throw new IndexOutOfBoundsException("setSeqrefs: Index value '" + index + + "' not in range [0.." + (this._seqrefs.size() - 1) + "]"); } - /** - * Sets the value of '_seqrefs' by setting it to the given - * Vector. No type checking is performed. - * @deprecated - * - * @param seqrefsVector the Vector to set. - */ - public void setSeqrefsAsReference( - final java.util.Vector seqrefsVector) { - this._seqrefs = seqrefsVector; - } + this._seqrefs.set(index, vSeqrefs); + } - /** - * 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.RangeType - */ - public static uk.ac.vamsas.objects.core.RangeType unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - return (uk.ac.vamsas.objects.core.RangeType) Unmarshaller.unmarshal(uk.ac.vamsas.objects.core.AlignmentAnnotation.class, reader); - } + /** + * + * + * @param vSeqrefsArray + */ + public void setSeqrefs(final java.lang.Object[] vSeqrefsArray) { + // -- copy array + _seqrefs.clear(); - /** - * - * - * @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); + for (int i = 0; i < vSeqrefsArray.length; i++) { + this._seqrefs.add(vSeqrefsArray[i]); } + } + + /** + * Sets the value of '_seqrefs' by copying the given Vector. All elements will + * be checked for type safety. + * + * @param vSeqrefsList + * the Vector to copy. + */ + public void setSeqrefs(final java.util.Vector vSeqrefsList) { + // copy vector + this._seqrefs.clear(); + + this._seqrefs.addAll(vSeqrefsList); + } + + /** + * Sets the value of '_seqrefs' by setting it to the given Vector. No type + * checking is performed. + * + * @deprecated + * + * @param seqrefsVector + * the Vector to set. + */ + public void setSeqrefsAsReference(final java.util.Vector seqrefsVector) { + this._seqrefs = seqrefsVector; + } + + /** + * 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.RangeType + */ + public static uk.ac.vamsas.objects.core.RangeType unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, + org.exolab.castor.xml.ValidationException { + return (uk.ac.vamsas.objects.core.RangeType) Unmarshaller.unmarshal( + uk.ac.vamsas.objects.core.AlignmentAnnotation.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); + } }