- }
-
- /**
- * Method getAlignmentSequenceAnnotation.
- *
- * @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.AlignmentSequenceAnnotation at the
- * given index
- */
- public uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation getAlignmentSequenceAnnotation(
- final int index)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._alignmentSequenceAnnotationList.size()) {
- throw new IndexOutOfBoundsException("getAlignmentSequenceAnnotation: Index value '" + index + "' not in range [0.." + (this._alignmentSequenceAnnotationList.size() - 1) + "]");
- }
-
- return (uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation) _alignmentSequenceAnnotationList.get(index);
- }
-
- /**
- * Method getAlignmentSequenceAnnotation.Returns the contents
- * of the collection in an Array. <p>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 <i>know</i> that the Array returned is of
- * exactly the correct length.
- *
- * @return this collection as an Array
- */
- public uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation[] getAlignmentSequenceAnnotation(
- ) {
- uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation[] array = new uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation[0];
- return (uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation[]) this._alignmentSequenceAnnotationList.toArray(array);
- }
-
- /**
- * Method getAlignmentSequenceAnnotationAsReference.Returns a
- * reference to '_alignmentSequenceAnnotationList'. No type
- * checking is performed on any modifications to the Vector.
- *
- * @return a reference to the Vector backing this class
- */
- public java.util.Vector getAlignmentSequenceAnnotationAsReference(
- ) {
- return this._alignmentSequenceAnnotationList;
- }
-
- /**
- * Method getAlignmentSequenceAnnotationCount.
- *
- * @return the size of this collection
- */
- public int getAlignmentSequenceAnnotationCount(
- ) {
- return this._alignmentSequenceAnnotationList.size();
- }
-
- /**
- * 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;
- }
-
- /**
- * Returns the value of field 'refid'. The field 'refid' has
- * the following description: Dataset Sequence from which
- * this alignment sequence is taken from
- *
- *
- * @return the value of field 'Refid'.
- */
- public java.lang.Object getRefid(
- ) {
- return this._refid;
- }
-
- /**
- * Overrides the java.lang.Object.hashCode method.
- * <p>
- * The following steps came from <b>Effective Java Programming
- * Language Guide</b> 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 (_refid != null
- && !org.castor.util.CycleBreaker.startingToCycle(_refid)) {
- result = 37 * result + _refid.hashCode();
- org.castor.util.CycleBreaker.releaseCycleHandle(_refid);
- }
- if (_alignmentSequenceAnnotationList != null
- && !org.castor.util.CycleBreaker.startingToCycle(_alignmentSequenceAnnotationList)) {
- result = 37 * result + _alignmentSequenceAnnotationList.hashCode();
- org.castor.util.CycleBreaker.releaseCycleHandle(_alignmentSequenceAnnotationList);
- }
-
- 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) {