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.RangeAnnotation;
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31 * Class RangeAnnotationDescriptor.
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33 * @version $Revision$ $Date$
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35 public class RangeAnnotationDescriptor extends
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36 uk.ac.vamsas.objects.core.descriptors.RangeTypeDescriptor {
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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 RangeAnnotationDescriptor() {
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68 setExtendsWithoutFlatten(new uk.ac.vamsas.objects.core.descriptors.RangeTypeDescriptor());
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69 _nsURI = "http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes";
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70 _xmlName = "rangeAnnotation";
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71 _elementDefinition = false;
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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.String.class, "_id", "id",
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83 org.exolab.castor.xml.NodeType.Attribute);
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84 super.setIdentity(desc);
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85 handler = new org.exolab.castor.xml.XMLFieldHandler() {
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86 public java.lang.Object getValue(java.lang.Object object)
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87 throws IllegalStateException {
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88 RangeAnnotation target = (RangeAnnotation) object;
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89 return target.getId();
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92 public void setValue(java.lang.Object object, java.lang.Object value)
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93 throws IllegalStateException, IllegalArgumentException {
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95 RangeAnnotation target = (RangeAnnotation) object;
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96 target.setId((java.lang.String) value);
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97 } catch (java.lang.Exception ex) {
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98 throw new IllegalStateException(ex.toString());
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102 public java.lang.Object newInstance(java.lang.Object parent) {
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103 return new java.lang.String();
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106 desc.setHandler(handler);
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107 desc.setMultivalued(false);
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108 addFieldDescriptor(desc);
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110 // -- validation code for: _id
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111 fieldValidator = new org.exolab.castor.xml.FieldValidator();
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112 { // -- local scope
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113 org.exolab.castor.xml.validators.IdValidator typeValidator;
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114 typeValidator = new org.exolab.castor.xml.validators.IdValidator();
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115 fieldValidator.setValidator(typeValidator);
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117 desc.setValidator(fieldValidator);
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119 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
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120 java.lang.String.class, "_modifiable", "modifiable",
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121 org.exolab.castor.xml.NodeType.Attribute);
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122 desc.setImmutable(true);
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123 handler = new org.exolab.castor.xml.XMLFieldHandler() {
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124 public java.lang.Object getValue(java.lang.Object object)
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125 throws IllegalStateException {
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126 RangeAnnotation target = (RangeAnnotation) object;
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127 return target.getModifiable();
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130 public void setValue(java.lang.Object object, java.lang.Object value)
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131 throws IllegalStateException, IllegalArgumentException {
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133 RangeAnnotation target = (RangeAnnotation) object;
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134 target.setModifiable((java.lang.String) value);
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135 } catch (java.lang.Exception ex) {
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136 throw new IllegalStateException(ex.toString());
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140 public java.lang.Object newInstance(java.lang.Object parent) {
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144 desc.setHandler(handler);
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145 desc.setMultivalued(false);
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146 addFieldDescriptor(desc);
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148 // -- validation code for: _modifiable
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149 fieldValidator = new org.exolab.castor.xml.FieldValidator();
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150 { // -- local scope
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151 org.exolab.castor.xml.validators.StringValidator typeValidator;
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152 typeValidator = new org.exolab.castor.xml.validators.StringValidator();
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153 fieldValidator.setValidator(typeValidator);
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154 typeValidator.setWhiteSpace("preserve");
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156 desc.setValidator(fieldValidator);
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158 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
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159 java.lang.String.class, "_group", "group",
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160 org.exolab.castor.xml.NodeType.Attribute);
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161 desc.setImmutable(true);
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162 handler = new org.exolab.castor.xml.XMLFieldHandler() {
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163 public java.lang.Object getValue(java.lang.Object object)
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164 throws IllegalStateException {
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165 RangeAnnotation target = (RangeAnnotation) object;
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166 return target.getGroup();
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169 public void setValue(java.lang.Object object, java.lang.Object value)
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170 throws IllegalStateException, IllegalArgumentException {
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172 RangeAnnotation target = (RangeAnnotation) object;
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173 target.setGroup((java.lang.String) value);
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174 } catch (java.lang.Exception ex) {
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175 throw new IllegalStateException(ex.toString());
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179 public java.lang.Object newInstance(java.lang.Object parent) {
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183 desc.setHandler(handler);
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184 desc.setMultivalued(false);
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185 addFieldDescriptor(desc);
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187 // -- validation code for: _group
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188 fieldValidator = new org.exolab.castor.xml.FieldValidator();
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189 { // -- local scope
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190 org.exolab.castor.xml.validators.StringValidator typeValidator;
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191 typeValidator = new org.exolab.castor.xml.validators.StringValidator();
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192 fieldValidator.setValidator(typeValidator);
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193 typeValidator.setWhiteSpace("preserve");
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195 desc.setValidator(fieldValidator);
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197 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
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198 java.lang.String.class, "_type", "type",
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199 org.exolab.castor.xml.NodeType.Attribute);
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200 desc.setImmutable(true);
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201 handler = new org.exolab.castor.xml.XMLFieldHandler() {
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202 public java.lang.Object getValue(java.lang.Object object)
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203 throws IllegalStateException {
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204 RangeAnnotation target = (RangeAnnotation) object;
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205 return target.getType();
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208 public void setValue(java.lang.Object object, java.lang.Object value)
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209 throws IllegalStateException, IllegalArgumentException {
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211 RangeAnnotation target = (RangeAnnotation) object;
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212 target.setType((java.lang.String) value);
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213 } catch (java.lang.Exception ex) {
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214 throw new IllegalStateException(ex.toString());
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218 public java.lang.Object newInstance(java.lang.Object parent) {
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222 desc.setHandler(handler);
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223 desc.setRequired(true);
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224 desc.setMultivalued(false);
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225 addFieldDescriptor(desc);
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227 // -- validation code for: _type
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228 fieldValidator = new org.exolab.castor.xml.FieldValidator();
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229 fieldValidator.setMinOccurs(1);
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230 { // -- local scope
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231 org.exolab.castor.xml.validators.StringValidator typeValidator;
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232 typeValidator = new org.exolab.castor.xml.validators.StringValidator();
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233 fieldValidator.setValidator(typeValidator);
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234 typeValidator.setWhiteSpace("preserve");
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236 desc.setValidator(fieldValidator);
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237 // -- initialize element descriptors
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240 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
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241 java.lang.String.class, "_label", "label",
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242 org.exolab.castor.xml.NodeType.Element);
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243 desc.setImmutable(true);
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244 handler = new org.exolab.castor.xml.XMLFieldHandler() {
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245 public java.lang.Object getValue(java.lang.Object object)
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246 throws IllegalStateException {
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247 RangeAnnotation target = (RangeAnnotation) object;
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248 return target.getLabel();
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251 public void setValue(java.lang.Object object, java.lang.Object value)
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252 throws IllegalStateException, IllegalArgumentException {
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254 RangeAnnotation target = (RangeAnnotation) object;
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255 target.setLabel((java.lang.String) value);
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256 } catch (java.lang.Exception ex) {
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257 throw new IllegalStateException(ex.toString());
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261 public java.lang.Object newInstance(java.lang.Object parent) {
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265 desc.setHandler(handler);
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266 desc.setNameSpaceURI("http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes");
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267 desc.setMultivalued(false);
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268 addFieldDescriptor(desc);
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270 // -- validation code for: _label
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271 fieldValidator = new org.exolab.castor.xml.FieldValidator();
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272 { // -- local scope
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273 org.exolab.castor.xml.validators.StringValidator typeValidator;
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274 typeValidator = new org.exolab.castor.xml.validators.StringValidator();
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275 fieldValidator.setValidator(typeValidator);
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276 typeValidator.setWhiteSpace("preserve");
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278 desc.setValidator(fieldValidator);
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280 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
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281 java.lang.String.class, "_description", "description",
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282 org.exolab.castor.xml.NodeType.Element);
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283 desc.setImmutable(true);
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284 handler = new org.exolab.castor.xml.XMLFieldHandler() {
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285 public java.lang.Object getValue(java.lang.Object object)
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286 throws IllegalStateException {
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287 RangeAnnotation target = (RangeAnnotation) object;
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288 return target.getDescription();
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291 public void setValue(java.lang.Object object, java.lang.Object value)
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292 throws IllegalStateException, IllegalArgumentException {
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294 RangeAnnotation target = (RangeAnnotation) object;
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295 target.setDescription((java.lang.String) value);
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296 } catch (java.lang.Exception ex) {
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297 throw new IllegalStateException(ex.toString());
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301 public java.lang.Object newInstance(java.lang.Object parent) {
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305 desc.setHandler(handler);
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306 desc.setNameSpaceURI("http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes");
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307 desc.setMultivalued(false);
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308 addFieldDescriptor(desc);
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310 // -- validation code for: _description
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311 fieldValidator = new org.exolab.castor.xml.FieldValidator();
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312 { // -- local scope
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313 org.exolab.castor.xml.validators.StringValidator typeValidator;
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314 typeValidator = new org.exolab.castor.xml.validators.StringValidator();
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315 fieldValidator.setValidator(typeValidator);
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316 typeValidator.setWhiteSpace("preserve");
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318 desc.setValidator(fieldValidator);
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320 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
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321 java.lang.String.class, "_status", "status",
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322 org.exolab.castor.xml.NodeType.Element);
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323 desc.setImmutable(true);
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324 handler = new org.exolab.castor.xml.XMLFieldHandler() {
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325 public java.lang.Object getValue(java.lang.Object object)
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326 throws IllegalStateException {
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327 RangeAnnotation target = (RangeAnnotation) object;
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328 return target.getStatus();
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331 public void setValue(java.lang.Object object, java.lang.Object value)
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332 throws IllegalStateException, IllegalArgumentException {
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334 RangeAnnotation target = (RangeAnnotation) object;
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335 target.setStatus((java.lang.String) value);
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336 } catch (java.lang.Exception ex) {
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337 throw new IllegalStateException(ex.toString());
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341 public java.lang.Object newInstance(java.lang.Object parent) {
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345 desc.setHandler(handler);
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346 desc.setNameSpaceURI("http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes");
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347 desc.setMultivalued(false);
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348 addFieldDescriptor(desc);
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350 // -- validation code for: _status
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351 fieldValidator = new org.exolab.castor.xml.FieldValidator();
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352 { // -- local scope
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353 org.exolab.castor.xml.validators.StringValidator typeValidator;
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354 typeValidator = new org.exolab.castor.xml.validators.StringValidator();
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355 fieldValidator.setValidator(typeValidator);
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356 typeValidator.setWhiteSpace("preserve");
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358 desc.setValidator(fieldValidator);
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359 // -- _annotationElementList
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360 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
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361 uk.ac.vamsas.objects.core.AnnotationElement.class,
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362 "_annotationElementList", "annotationElement",
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363 org.exolab.castor.xml.NodeType.Element);
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364 handler = new org.exolab.castor.xml.XMLFieldHandler() {
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365 public java.lang.Object getValue(java.lang.Object object)
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366 throws IllegalStateException {
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367 RangeAnnotation target = (RangeAnnotation) object;
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368 return target.getAnnotationElement();
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371 public void setValue(java.lang.Object object, java.lang.Object value)
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372 throws IllegalStateException, IllegalArgumentException {
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374 RangeAnnotation target = (RangeAnnotation) object;
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376 .addAnnotationElement((uk.ac.vamsas.objects.core.AnnotationElement) value);
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377 } catch (java.lang.Exception ex) {
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378 throw new IllegalStateException(ex.toString());
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382 public void resetValue(Object object) throws IllegalStateException,
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383 IllegalArgumentException {
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385 RangeAnnotation target = (RangeAnnotation) object;
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386 target.removeAllAnnotationElement();
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387 } catch (java.lang.Exception ex) {
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388 throw new IllegalStateException(ex.toString());
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392 public java.lang.Object newInstance(java.lang.Object parent) {
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393 return new uk.ac.vamsas.objects.core.AnnotationElement();
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396 desc.setHandler(handler);
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397 desc.setNameSpaceURI("http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes");
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398 desc.setMultivalued(true);
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399 addFieldDescriptor(desc);
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401 // -- validation code for: _annotationElementList
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402 fieldValidator = new org.exolab.castor.xml.FieldValidator();
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403 fieldValidator.setMinOccurs(0);
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404 { // -- local scope
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406 desc.setValidator(fieldValidator);
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408 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
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409 uk.ac.vamsas.objects.core.Score.class, "_scoreList", "score",
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410 org.exolab.castor.xml.NodeType.Element);
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411 handler = new org.exolab.castor.xml.XMLFieldHandler() {
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412 public java.lang.Object getValue(java.lang.Object object)
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413 throws IllegalStateException {
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414 RangeAnnotation target = (RangeAnnotation) object;
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415 return target.getScore();
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418 public void setValue(java.lang.Object object, java.lang.Object value)
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419 throws IllegalStateException, IllegalArgumentException {
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421 RangeAnnotation target = (RangeAnnotation) object;
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422 target.addScore((uk.ac.vamsas.objects.core.Score) value);
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423 } catch (java.lang.Exception ex) {
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424 throw new IllegalStateException(ex.toString());
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428 public void resetValue(Object object) throws IllegalStateException,
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429 IllegalArgumentException {
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431 RangeAnnotation target = (RangeAnnotation) object;
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432 target.removeAllScore();
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433 } catch (java.lang.Exception ex) {
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434 throw new IllegalStateException(ex.toString());
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438 public java.lang.Object newInstance(java.lang.Object parent) {
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439 return new uk.ac.vamsas.objects.core.Score();
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442 desc.setHandler(handler);
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443 desc.setNameSpaceURI("http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes");
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444 desc.setMultivalued(true);
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445 addFieldDescriptor(desc);
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447 // -- validation code for: _scoreList
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448 fieldValidator = new org.exolab.castor.xml.FieldValidator();
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449 fieldValidator.setMinOccurs(0);
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450 { // -- local scope
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452 desc.setValidator(fieldValidator);
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454 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
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455 uk.ac.vamsas.objects.core.Link.class, "_linkList", "link",
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456 org.exolab.castor.xml.NodeType.Element);
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457 handler = new org.exolab.castor.xml.XMLFieldHandler() {
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458 public java.lang.Object getValue(java.lang.Object object)
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459 throws IllegalStateException {
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460 RangeAnnotation target = (RangeAnnotation) object;
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461 return target.getLink();
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464 public void setValue(java.lang.Object object, java.lang.Object value)
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465 throws IllegalStateException, IllegalArgumentException {
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467 RangeAnnotation target = (RangeAnnotation) object;
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468 target.addLink((uk.ac.vamsas.objects.core.Link) value);
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469 } catch (java.lang.Exception ex) {
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470 throw new IllegalStateException(ex.toString());
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474 public void resetValue(Object object) throws IllegalStateException,
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475 IllegalArgumentException {
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477 RangeAnnotation target = (RangeAnnotation) object;
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478 target.removeAllLink();
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479 } catch (java.lang.Exception ex) {
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480 throw new IllegalStateException(ex.toString());
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484 public java.lang.Object newInstance(java.lang.Object parent) {
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485 return new uk.ac.vamsas.objects.core.Link();
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488 desc.setHandler(handler);
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489 desc.setNameSpaceURI("http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes");
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490 desc.setMultivalued(true);
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491 addFieldDescriptor(desc);
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493 // -- validation code for: _linkList
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494 fieldValidator = new org.exolab.castor.xml.FieldValidator();
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495 fieldValidator.setMinOccurs(0);
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496 { // -- local scope
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498 desc.setValidator(fieldValidator);
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499 // -- _propertyList
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500 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
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501 uk.ac.vamsas.objects.core.Property.class, "_propertyList", "property",
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502 org.exolab.castor.xml.NodeType.Element);
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503 handler = new org.exolab.castor.xml.XMLFieldHandler() {
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504 public java.lang.Object getValue(java.lang.Object object)
\r
505 throws IllegalStateException {
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506 RangeAnnotation target = (RangeAnnotation) object;
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507 return target.getProperty();
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510 public void setValue(java.lang.Object object, java.lang.Object value)
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511 throws IllegalStateException, IllegalArgumentException {
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513 RangeAnnotation target = (RangeAnnotation) object;
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514 target.addProperty((uk.ac.vamsas.objects.core.Property) value);
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515 } catch (java.lang.Exception ex) {
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516 throw new IllegalStateException(ex.toString());
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520 public void resetValue(Object object) throws IllegalStateException,
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521 IllegalArgumentException {
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523 RangeAnnotation target = (RangeAnnotation) object;
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524 target.removeAllProperty();
\r
525 } catch (java.lang.Exception ex) {
\r
526 throw new IllegalStateException(ex.toString());
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530 public java.lang.Object newInstance(java.lang.Object parent) {
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531 return new uk.ac.vamsas.objects.core.Property();
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534 desc.setHandler(handler);
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535 desc.setNameSpaceURI("http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes");
\r
536 desc.setMultivalued(true);
\r
537 addFieldDescriptor(desc);
\r
539 // -- validation code for: _propertyList
\r
540 fieldValidator = new org.exolab.castor.xml.FieldValidator();
\r
541 fieldValidator.setMinOccurs(0);
\r
542 { // -- local scope
\r
544 desc.setValidator(fieldValidator);
\r
552 * Method getAccessMode.
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554 * @return the access mode specified for this class.
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556 public org.exolab.castor.mapping.AccessMode getAccessMode() {
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561 * Method getIdentity.
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563 * @return the identity field, null if this class has no identity.
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565 public org.exolab.castor.mapping.FieldDescriptor getIdentity() {
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566 return super.getIdentity();
\r
570 * Method getJavaClass.
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572 * @return the Java class represented by this descriptor.
\r
574 public java.lang.Class getJavaClass() {
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575 return uk.ac.vamsas.objects.core.RangeAnnotation.class;
\r
579 * Method getNameSpacePrefix.
\r
581 * @return the namespace prefix to use when marshaling as XML.
\r
583 public java.lang.String getNameSpacePrefix() {
\r
588 * Method getNameSpaceURI.
\r
590 * @return the namespace URI used when marshaling and unmarshaling as XML.
\r
592 public java.lang.String getNameSpaceURI() {
\r
597 * Method getValidator.
\r
599 * @return a specific validator for the class described by this
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602 public org.exolab.castor.xml.TypeValidator getValidator() {
\r
607 * Method getXMLName.
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609 * @return the XML Name for the Class being described.
\r
611 public java.lang.String getXMLName() {
\r
616 * Method isElementDefinition.
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618 * @return true if XML schema definition of this Class is that of a global
\r
619 * element or element with anonymous type definition.
\r
621 public boolean isElementDefinition() {
\r
622 return _elementDefinition;
\r