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 boolean + * @return true if at least one Graph has been added */ - public boolean hasGraph() - { + public boolean hasGraph( + ) { return this._has_graph; - } //-- boolean hasGraph() + } /** - * 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; + 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 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) + } + + /** + */ + 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 @@ -205,45 +406,110 @@ implements java.io.Serializable * * @param graph the value of field 'graph'. */ - public void setGraph(boolean graph) - { + public void setGraph( + final boolean graph) { this._graph = graph; this._has_graph = true; - } //-- void setGraph(boolean) + } /** * 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) + } /** - * Method unmarshal * * + * @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); + } + + /** + * + * + * @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]); + } + } + + /** + * 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 - * @return RangeType + * @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(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - return (uk.ac.vamsas.objects.core.AlignmentAnnotation) Unmarshaller.unmarshal(uk.ac.vamsas.objects.core.AlignmentAnnotation.class, reader); - } //-- uk.ac.vamsas.objects.core.RangeType unmarshal(java.io.Reader) + 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); + } /** - * 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() + } }