2 * This file is part of the Vamsas Client version 0.1.
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3 * Copyright 2009 by Jim Procter, Iain Milne, Pierre Marguerite,
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4 * Andrew Waterhouse and Dominik Lindner.
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6 * Earlier versions have also been incorporated into Jalview version 2.4
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7 * since 2008, and TOPALi version 2 since 2007.
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9 * The Vamsas Client is free software: you can redistribute it and/or modify
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10 * it under the terms of the GNU Lesser General Public License as published by
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11 * the Free Software Foundation, either version 3 of the License, or
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12 * (at your option) any later version.
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14 * The Vamsas Client is distributed in the hope that it will be useful,
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15 * but WITHOUT ANY WARRANTY; without even the implied warranty of
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16 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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17 * GNU Lesser General Public License for more details.
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19 * You should have received a copy of the GNU Lesser General Public License
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20 * along with the Vamsas Client. If not, see <http://www.gnu.org/licenses/>.
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22 package uk.ac.vamsas.objects.core.descriptors;
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24 //---------------------------------/
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25 //- Imported classes and packages -/
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26 //---------------------------------/
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28 import uk.ac.vamsas.objects.core.AlignmentAnnotation;
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31 * Class AlignmentAnnotationDescriptor.
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33 * @version $Revision$ $Date$
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35 public class AlignmentAnnotationDescriptor extends
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36 uk.ac.vamsas.objects.core.descriptors.RangeAnnotationDescriptor {
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38 // --------------------------/
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39 // - Class/Member Variables -/
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40 // --------------------------/
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43 * Field _elementDefinition.
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45 private boolean _elementDefinition;
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50 private java.lang.String _nsPrefix;
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55 private java.lang.String _nsURI;
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60 private java.lang.String _xmlName;
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62 // ----------------/
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63 // - Constructors -/
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64 // ----------------/
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66 public AlignmentAnnotationDescriptor() {
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68 setExtendsWithoutFlatten(new uk.ac.vamsas.objects.core.descriptors.RangeAnnotationDescriptor());
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69 _nsURI = "http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes";
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70 _xmlName = "AlignmentAnnotation";
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71 _elementDefinition = true;
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73 // -- set grouping compositor
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74 setCompositorAsSequence();
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75 org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
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76 org.exolab.castor.mapping.FieldHandler handler = null;
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77 org.exolab.castor.xml.FieldValidator fieldValidator = null;
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78 // -- initialize attribute descriptors
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81 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
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82 java.lang.Boolean.TYPE, "_graph", "graph",
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83 org.exolab.castor.xml.NodeType.Attribute);
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84 handler = new org.exolab.castor.xml.XMLFieldHandler() {
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85 public java.lang.Object getValue(java.lang.Object object)
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86 throws IllegalStateException {
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87 AlignmentAnnotation target = (AlignmentAnnotation) object;
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88 if (!target.hasGraph()) {
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91 return (target.getGraph() ? java.lang.Boolean.TRUE
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92 : java.lang.Boolean.FALSE);
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95 public void setValue(java.lang.Object object, java.lang.Object value)
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96 throws IllegalStateException, IllegalArgumentException {
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98 AlignmentAnnotation target = (AlignmentAnnotation) object;
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99 // ignore null values for non optional primitives
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100 if (value == null) {
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104 target.setGraph(((java.lang.Boolean) value).booleanValue());
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105 } catch (java.lang.Exception ex) {
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106 throw new IllegalStateException(ex.toString());
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110 public java.lang.Object newInstance(java.lang.Object parent) {
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114 desc.setHandler(handler);
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115 desc.setRequired(true);
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116 desc.setMultivalued(false);
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117 addFieldDescriptor(desc);
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119 // -- validation code for: _graph
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120 fieldValidator = new org.exolab.castor.xml.FieldValidator();
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121 fieldValidator.setMinOccurs(1);
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122 { // -- local scope
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123 org.exolab.castor.xml.validators.BooleanValidator typeValidator;
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124 typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
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125 fieldValidator.setValidator(typeValidator);
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127 desc.setValidator(fieldValidator);
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129 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
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130 java.lang.Object.class, "_seqrefs", "seqrefs",
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131 org.exolab.castor.xml.NodeType.Attribute);
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132 desc.setReference(true);
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133 handler = new org.exolab.castor.xml.XMLFieldHandler() {
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134 public java.lang.Object getValue(java.lang.Object object)
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135 throws IllegalStateException {
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136 AlignmentAnnotation target = (AlignmentAnnotation) object;
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137 return target.getSeqrefs();
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140 public void setValue(java.lang.Object object, java.lang.Object value)
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141 throws IllegalStateException, IllegalArgumentException {
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143 AlignmentAnnotation target = (AlignmentAnnotation) object;
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144 target.addSeqrefs((java.lang.Object) value);
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145 } catch (java.lang.Exception ex) {
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146 throw new IllegalStateException(ex.toString());
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150 public void resetValue(Object object) throws IllegalStateException,
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151 IllegalArgumentException {
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153 AlignmentAnnotation target = (AlignmentAnnotation) object;
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154 target.removeAllSeqrefs();
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155 } catch (java.lang.Exception ex) {
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156 throw new IllegalStateException(ex.toString());
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160 public java.lang.Object newInstance(java.lang.Object parent) {
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161 return new java.lang.Object();
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164 desc.setMultivalued(true);
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165 desc.setHandler(handler);
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166 desc.setMultivalued(true);
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167 addFieldDescriptor(desc);
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169 // -- validation code for: _seqrefs
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170 fieldValidator = new org.exolab.castor.xml.FieldValidator();
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171 fieldValidator.setMinOccurs(0);
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172 { // -- local scope
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173 org.exolab.castor.xml.validators.IdRefsValidator typeValidator = new org.exolab.castor.xml.validators.IdRefsValidator();
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174 fieldValidator.setValidator(typeValidator);
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175 desc.setValidator(fieldValidator);
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177 desc.setValidator(fieldValidator);
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178 // -- initialize element descriptors
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181 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
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182 uk.ac.vamsas.objects.core.Provenance.class, "_provenance",
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183 "Provenance", org.exolab.castor.xml.NodeType.Element);
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184 handler = new org.exolab.castor.xml.XMLFieldHandler() {
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185 public java.lang.Object getValue(java.lang.Object object)
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186 throws IllegalStateException {
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187 AlignmentAnnotation target = (AlignmentAnnotation) object;
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188 return target.getProvenance();
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191 public void setValue(java.lang.Object object, java.lang.Object value)
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192 throws IllegalStateException, IllegalArgumentException {
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194 AlignmentAnnotation target = (AlignmentAnnotation) object;
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195 target.setProvenance((uk.ac.vamsas.objects.core.Provenance) value);
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196 } catch (java.lang.Exception ex) {
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197 throw new IllegalStateException(ex.toString());
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201 public java.lang.Object newInstance(java.lang.Object parent) {
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202 return new uk.ac.vamsas.objects.core.Provenance();
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205 desc.setHandler(handler);
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206 desc.setNameSpaceURI("http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes");
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207 desc.setRequired(true);
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208 desc.setMultivalued(false);
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209 addFieldDescriptor(desc);
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211 // -- validation code for: _provenance
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212 fieldValidator = new org.exolab.castor.xml.FieldValidator();
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213 fieldValidator.setMinOccurs(1);
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214 { // -- local scope
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216 desc.setValidator(fieldValidator);
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224 * Method getAccessMode.
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226 * @return the access mode specified for this class.
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228 public org.exolab.castor.mapping.AccessMode getAccessMode() {
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233 * Method getIdentity.
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235 * @return the identity field, null if this class has no identity.
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237 public org.exolab.castor.mapping.FieldDescriptor getIdentity() {
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238 return super.getIdentity();
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242 * Method getJavaClass.
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244 * @return the Java class represented by this descriptor.
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246 public java.lang.Class getJavaClass() {
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247 return uk.ac.vamsas.objects.core.AlignmentAnnotation.class;
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251 * Method getNameSpacePrefix.
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253 * @return the namespace prefix to use when marshaling as XML.
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255 public java.lang.String getNameSpacePrefix() {
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260 * Method getNameSpaceURI.
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262 * @return the namespace URI used when marshaling and unmarshaling as XML.
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264 public java.lang.String getNameSpaceURI() {
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269 * Method getValidator.
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271 * @return a specific validator for the class described by this
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274 public org.exolab.castor.xml.TypeValidator getValidator() {
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279 * Method getXMLName.
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281 * @return the XML Name for the Class being described.
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283 public java.lang.String getXMLName() {
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288 * Method isElementDefinition.
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290 * @return true if XML schema definition of this Class is that of a global
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291 * element or element with anonymous type definition.
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293 public boolean isElementDefinition() {
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294 return _elementDefinition;
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