+ * Sets the value of field 'aligned'.
+ *
+ * @param aligned the value of field 'aligned'.
+ */
+ public void setAligned(boolean aligned)
+ {
+ this._aligned = aligned;
+ this._has_aligned = true;
+ } //-- void setAligned(boolean)
+
+ /**
+ * Method setAlignmentAnnotations
+ *
+ *
+ *
+ * @param index
+ * @param vAlignmentAnnotations
+ */
+ public void setAlignmentAnnotations(int index, org.vamsas.objects.core.AlignmentAnnotations vAlignmentAnnotations)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ //-- check bounds for index
+ if ((index < 0) || (index > _alignmentAnnotationsList.size())) {
+ throw new IndexOutOfBoundsException("setAlignmentAnnotations: Index value '"+index+"' not in range [0.."+_alignmentAnnotationsList.size()+ "]");
+ }
+ _alignmentAnnotationsList.setElementAt(vAlignmentAnnotations, index);
+ } //-- void setAlignmentAnnotations(int, org.vamsas.objects.core.AlignmentAnnotations)
+
+ /**
+ * Method setAlignmentAnnotations
+ *