2 * This file is part of the Vamsas Client version 0.2.
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3 * Copyright 2010 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.Alignment;
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31 * Class AlignmentDescriptor.
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33 * @version $Revision$ $Date$
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35 public class AlignmentDescriptor extends
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36 org.exolab.castor.xml.util.XMLClassDescriptorImpl {
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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 AlignmentDescriptor() {
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68 _nsURI = "http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes";
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69 _xmlName = "Alignment";
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70 _elementDefinition = true;
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72 // -- set grouping compositor
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73 setCompositorAsSequence();
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74 org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
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75 org.exolab.castor.mapping.FieldHandler handler = null;
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76 org.exolab.castor.xml.FieldValidator fieldValidator = null;
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77 // -- initialize attribute descriptors
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80 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
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81 java.lang.String.class, "_gapChar", "gapChar",
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82 org.exolab.castor.xml.NodeType.Attribute);
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83 desc.setImmutable(true);
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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 Alignment target = (Alignment) object;
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88 return target.getGapChar();
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91 public void setValue(java.lang.Object object, java.lang.Object value)
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92 throws IllegalStateException, IllegalArgumentException {
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94 Alignment target = (Alignment) object;
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95 target.setGapChar((java.lang.String) value);
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96 } catch (java.lang.Exception ex) {
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97 throw new IllegalStateException(ex.toString());
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101 public java.lang.Object newInstance(java.lang.Object parent) {
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105 desc.setHandler(handler);
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106 desc.setRequired(true);
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107 desc.setMultivalued(false);
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108 addFieldDescriptor(desc);
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110 // -- validation code for: _gapChar
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111 fieldValidator = new org.exolab.castor.xml.FieldValidator();
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112 fieldValidator.setMinOccurs(1);
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113 { // -- local scope
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114 org.exolab.castor.xml.validators.StringValidator typeValidator;
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115 typeValidator = new org.exolab.castor.xml.validators.StringValidator();
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116 fieldValidator.setValidator(typeValidator);
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117 typeValidator.setWhiteSpace("preserve");
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119 desc.setValidator(fieldValidator);
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121 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
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122 java.lang.Boolean.TYPE, "_aligned", "aligned",
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123 org.exolab.castor.xml.NodeType.Attribute);
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124 handler = new org.exolab.castor.xml.XMLFieldHandler() {
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125 public java.lang.Object getValue(java.lang.Object object)
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126 throws IllegalStateException {
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127 Alignment target = (Alignment) object;
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128 if (!target.hasAligned()) {
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131 return (target.getAligned() ? java.lang.Boolean.TRUE
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132 : java.lang.Boolean.FALSE);
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135 public void setValue(java.lang.Object object, java.lang.Object value)
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136 throws IllegalStateException, IllegalArgumentException {
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138 Alignment target = (Alignment) object;
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139 // if null, use delete method for optional primitives
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140 if (value == null) {
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141 target.deleteAligned();
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144 target.setAligned(((java.lang.Boolean) value).booleanValue());
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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 java.lang.Object newInstance(java.lang.Object parent) {
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154 desc.setHandler(handler);
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155 desc.setMultivalued(false);
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156 addFieldDescriptor(desc);
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158 // -- validation code for: _aligned
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159 fieldValidator = new org.exolab.castor.xml.FieldValidator();
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160 { // -- local scope
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161 org.exolab.castor.xml.validators.BooleanValidator typeValidator;
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162 typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
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163 fieldValidator.setValidator(typeValidator);
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165 desc.setValidator(fieldValidator);
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167 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
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168 java.lang.String.class, "_id", "id",
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169 org.exolab.castor.xml.NodeType.Attribute);
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170 super.setIdentity(desc);
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171 handler = new org.exolab.castor.xml.XMLFieldHandler() {
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172 public java.lang.Object getValue(java.lang.Object object)
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173 throws IllegalStateException {
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174 Alignment target = (Alignment) object;
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175 return target.getId();
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178 public void setValue(java.lang.Object object, java.lang.Object value)
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179 throws IllegalStateException, IllegalArgumentException {
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181 Alignment target = (Alignment) object;
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182 target.setId((java.lang.String) value);
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183 } catch (java.lang.Exception ex) {
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184 throw new IllegalStateException(ex.toString());
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188 public java.lang.Object newInstance(java.lang.Object parent) {
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189 return new java.lang.String();
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192 desc.setHandler(handler);
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193 desc.setMultivalued(false);
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194 addFieldDescriptor(desc);
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196 // -- validation code for: _id
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197 fieldValidator = new org.exolab.castor.xml.FieldValidator();
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198 { // -- local scope
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199 org.exolab.castor.xml.validators.IdValidator typeValidator;
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200 typeValidator = new org.exolab.castor.xml.validators.IdValidator();
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201 fieldValidator.setValidator(typeValidator);
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203 desc.setValidator(fieldValidator);
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205 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
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206 java.lang.String.class, "_modifiable", "modifiable",
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207 org.exolab.castor.xml.NodeType.Attribute);
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208 desc.setImmutable(true);
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209 handler = new org.exolab.castor.xml.XMLFieldHandler() {
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210 public java.lang.Object getValue(java.lang.Object object)
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211 throws IllegalStateException {
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212 Alignment target = (Alignment) object;
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213 return target.getModifiable();
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216 public void setValue(java.lang.Object object, java.lang.Object value)
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217 throws IllegalStateException, IllegalArgumentException {
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219 Alignment target = (Alignment) object;
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220 target.setModifiable((java.lang.String) value);
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221 } catch (java.lang.Exception ex) {
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222 throw new IllegalStateException(ex.toString());
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226 public java.lang.Object newInstance(java.lang.Object parent) {
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230 desc.setHandler(handler);
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231 desc.setMultivalued(false);
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232 addFieldDescriptor(desc);
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234 // -- validation code for: _modifiable
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235 fieldValidator = new org.exolab.castor.xml.FieldValidator();
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236 { // -- local scope
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237 org.exolab.castor.xml.validators.StringValidator typeValidator;
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238 typeValidator = new org.exolab.castor.xml.validators.StringValidator();
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239 fieldValidator.setValidator(typeValidator);
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240 typeValidator.setWhiteSpace("preserve");
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242 desc.setValidator(fieldValidator);
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243 // -- initialize element descriptors
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245 // -- _alignmentAnnotationList
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246 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
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247 uk.ac.vamsas.objects.core.AlignmentAnnotation.class,
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248 "_alignmentAnnotationList", "AlignmentAnnotation",
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249 org.exolab.castor.xml.NodeType.Element);
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250 handler = new org.exolab.castor.xml.XMLFieldHandler() {
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251 public java.lang.Object getValue(java.lang.Object object)
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252 throws IllegalStateException {
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253 Alignment target = (Alignment) object;
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254 return target.getAlignmentAnnotation();
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257 public void setValue(java.lang.Object object, java.lang.Object value)
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258 throws IllegalStateException, IllegalArgumentException {
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260 Alignment target = (Alignment) object;
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262 .addAlignmentAnnotation((uk.ac.vamsas.objects.core.AlignmentAnnotation) value);
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263 } catch (java.lang.Exception ex) {
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264 throw new IllegalStateException(ex.toString());
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268 public void resetValue(Object object) throws IllegalStateException,
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269 IllegalArgumentException {
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271 Alignment target = (Alignment) object;
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272 target.removeAllAlignmentAnnotation();
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273 } catch (java.lang.Exception ex) {
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274 throw new IllegalStateException(ex.toString());
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278 public java.lang.Object newInstance(java.lang.Object parent) {
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279 return new uk.ac.vamsas.objects.core.AlignmentAnnotation();
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282 desc.setHandler(handler);
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283 desc.setNameSpaceURI("http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes");
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284 desc.setMultivalued(true);
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285 addFieldDescriptor(desc);
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287 // -- validation code for: _alignmentAnnotationList
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288 fieldValidator = new org.exolab.castor.xml.FieldValidator();
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289 fieldValidator.setMinOccurs(0);
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290 { // -- local scope
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292 desc.setValidator(fieldValidator);
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294 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
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295 uk.ac.vamsas.objects.core.Tree.class, "_treeList", "Tree",
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296 org.exolab.castor.xml.NodeType.Element);
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297 handler = new org.exolab.castor.xml.XMLFieldHandler() {
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298 public java.lang.Object getValue(java.lang.Object object)
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299 throws IllegalStateException {
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300 Alignment target = (Alignment) object;
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301 return target.getTree();
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304 public void setValue(java.lang.Object object, java.lang.Object value)
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305 throws IllegalStateException, IllegalArgumentException {
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307 Alignment target = (Alignment) object;
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308 target.addTree((uk.ac.vamsas.objects.core.Tree) value);
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309 } catch (java.lang.Exception ex) {
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310 throw new IllegalStateException(ex.toString());
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314 public void resetValue(Object object) throws IllegalStateException,
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315 IllegalArgumentException {
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317 Alignment target = (Alignment) object;
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318 target.removeAllTree();
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319 } catch (java.lang.Exception ex) {
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320 throw new IllegalStateException(ex.toString());
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324 public java.lang.Object newInstance(java.lang.Object parent) {
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325 return new uk.ac.vamsas.objects.core.Tree();
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328 desc.setHandler(handler);
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329 desc.setNameSpaceURI("http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes");
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330 desc.setMultivalued(true);
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331 addFieldDescriptor(desc);
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333 // -- validation code for: _treeList
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334 fieldValidator = new org.exolab.castor.xml.FieldValidator();
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335 fieldValidator.setMinOccurs(0);
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336 { // -- local scope
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338 desc.setValidator(fieldValidator);
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339 // -- _alignmentSequenceList
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340 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
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341 uk.ac.vamsas.objects.core.AlignmentSequence.class,
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342 "_alignmentSequenceList", "alignmentSequence",
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343 org.exolab.castor.xml.NodeType.Element);
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344 handler = new org.exolab.castor.xml.XMLFieldHandler() {
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345 public java.lang.Object getValue(java.lang.Object object)
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346 throws IllegalStateException {
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347 Alignment target = (Alignment) object;
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348 return target.getAlignmentSequence();
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351 public void setValue(java.lang.Object object, java.lang.Object value)
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352 throws IllegalStateException, IllegalArgumentException {
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354 Alignment target = (Alignment) object;
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356 .addAlignmentSequence((uk.ac.vamsas.objects.core.AlignmentSequence) value);
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357 } catch (java.lang.Exception ex) {
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358 throw new IllegalStateException(ex.toString());
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362 public void resetValue(Object object) throws IllegalStateException,
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363 IllegalArgumentException {
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365 Alignment target = (Alignment) object;
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366 target.removeAllAlignmentSequence();
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367 } catch (java.lang.Exception ex) {
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368 throw new IllegalStateException(ex.toString());
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372 public java.lang.Object newInstance(java.lang.Object parent) {
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373 return new uk.ac.vamsas.objects.core.AlignmentSequence();
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376 desc.setHandler(handler);
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377 desc.setNameSpaceURI("http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes");
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378 desc.setRequired(true);
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379 desc.setMultivalued(true);
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380 addFieldDescriptor(desc);
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382 // -- validation code for: _alignmentSequenceList
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383 fieldValidator = new org.exolab.castor.xml.FieldValidator();
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384 fieldValidator.setMinOccurs(1);
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385 { // -- local scope
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387 desc.setValidator(fieldValidator);
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388 // -- _propertyList
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389 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
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390 uk.ac.vamsas.objects.core.Property.class, "_propertyList", "property",
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391 org.exolab.castor.xml.NodeType.Element);
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392 handler = new org.exolab.castor.xml.XMLFieldHandler() {
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393 public java.lang.Object getValue(java.lang.Object object)
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394 throws IllegalStateException {
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395 Alignment target = (Alignment) object;
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396 return target.getProperty();
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399 public void setValue(java.lang.Object object, java.lang.Object value)
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400 throws IllegalStateException, IllegalArgumentException {
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402 Alignment target = (Alignment) object;
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403 target.addProperty((uk.ac.vamsas.objects.core.Property) value);
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404 } catch (java.lang.Exception ex) {
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405 throw new IllegalStateException(ex.toString());
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409 public void resetValue(Object object) throws IllegalStateException,
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410 IllegalArgumentException {
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412 Alignment target = (Alignment) object;
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413 target.removeAllProperty();
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414 } catch (java.lang.Exception ex) {
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415 throw new IllegalStateException(ex.toString());
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419 public java.lang.Object newInstance(java.lang.Object parent) {
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420 return new uk.ac.vamsas.objects.core.Property();
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423 desc.setHandler(handler);
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424 desc.setNameSpaceURI("http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes");
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425 desc.setMultivalued(true);
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426 addFieldDescriptor(desc);
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428 // -- validation code for: _propertyList
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429 fieldValidator = new org.exolab.castor.xml.FieldValidator();
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430 fieldValidator.setMinOccurs(0);
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431 { // -- local scope
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433 desc.setValidator(fieldValidator);
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435 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
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436 uk.ac.vamsas.objects.core.Provenance.class, "_provenance",
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437 "Provenance", org.exolab.castor.xml.NodeType.Element);
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438 handler = new org.exolab.castor.xml.XMLFieldHandler() {
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439 public java.lang.Object getValue(java.lang.Object object)
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440 throws IllegalStateException {
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441 Alignment target = (Alignment) object;
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442 return target.getProvenance();
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445 public void setValue(java.lang.Object object, java.lang.Object value)
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446 throws IllegalStateException, IllegalArgumentException {
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448 Alignment target = (Alignment) object;
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449 target.setProvenance((uk.ac.vamsas.objects.core.Provenance) value);
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450 } catch (java.lang.Exception ex) {
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451 throw new IllegalStateException(ex.toString());
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455 public java.lang.Object newInstance(java.lang.Object parent) {
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456 return new uk.ac.vamsas.objects.core.Provenance();
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459 desc.setHandler(handler);
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460 desc.setNameSpaceURI("http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes");
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461 desc.setRequired(true);
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462 desc.setMultivalued(false);
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463 addFieldDescriptor(desc);
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465 // -- validation code for: _provenance
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466 fieldValidator = new org.exolab.castor.xml.FieldValidator();
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467 fieldValidator.setMinOccurs(1);
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468 { // -- local scope
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470 desc.setValidator(fieldValidator);
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478 * Method getAccessMode.
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480 * @return the access mode specified for this class.
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482 public org.exolab.castor.mapping.AccessMode getAccessMode() {
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487 * Method getIdentity.
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489 * @return the identity field, null if this class has no identity.
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491 public org.exolab.castor.mapping.FieldDescriptor getIdentity() {
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492 return super.getIdentity();
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496 * Method getJavaClass.
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498 * @return the Java class represented by this descriptor.
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500 public java.lang.Class getJavaClass() {
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501 return uk.ac.vamsas.objects.core.Alignment.class;
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505 * Method getNameSpacePrefix.
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507 * @return the namespace prefix to use when marshaling as XML.
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509 public java.lang.String getNameSpacePrefix() {
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514 * Method getNameSpaceURI.
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516 * @return the namespace URI used when marshaling and unmarshaling as XML.
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518 public java.lang.String getNameSpaceURI() {
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523 * Method getValidator.
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525 * @return a specific validator for the class described by this
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528 public org.exolab.castor.xml.TypeValidator getValidator() {
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533 * Method getXMLName.
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535 * @return the XML Name for the Class being described.
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537 public java.lang.String getXMLName() {
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542 * Method isElementDefinition.
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544 * @return true if XML schema definition of this Class is that of a global
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545 * element or element with anonymous type definition.
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547 public boolean isElementDefinition() {
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548 return _elementDefinition;
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