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.DataSet;
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31 * Class DataSetDescriptor.
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33 * @version $Revision$ $Date$
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35 public class DataSetDescriptor 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 DataSetDescriptor() {
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68 _nsURI = "http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes";
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69 _xmlName = "DataSet";
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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, "_id", "id",
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82 org.exolab.castor.xml.NodeType.Attribute);
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83 super.setIdentity(desc);
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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 DataSet target = (DataSet) object;
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88 return target.getId();
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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 DataSet target = (DataSet) object;
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95 target.setId((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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102 return new java.lang.String();
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105 desc.setHandler(handler);
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106 desc.setMultivalued(false);
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107 addFieldDescriptor(desc);
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109 // -- validation code for: _id
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110 fieldValidator = new org.exolab.castor.xml.FieldValidator();
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111 { // -- local scope
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112 org.exolab.castor.xml.validators.IdValidator typeValidator;
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113 typeValidator = new org.exolab.castor.xml.validators.IdValidator();
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114 fieldValidator.setValidator(typeValidator);
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116 desc.setValidator(fieldValidator);
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117 // -- initialize element descriptors
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119 // -- _sequenceList
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120 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
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121 uk.ac.vamsas.objects.core.Sequence.class, "_sequenceList", "Sequence",
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122 org.exolab.castor.xml.NodeType.Element);
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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 DataSet target = (DataSet) object;
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127 return target.getSequence();
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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 DataSet target = (DataSet) object;
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134 target.addSequence((uk.ac.vamsas.objects.core.Sequence) 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 void resetValue(Object object) throws IllegalStateException,
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141 IllegalArgumentException {
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143 DataSet target = (DataSet) object;
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144 target.removeAllSequence();
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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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151 return new uk.ac.vamsas.objects.core.Sequence();
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154 desc.setHandler(handler);
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155 desc.setNameSpaceURI("http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes");
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156 desc.setRequired(true);
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157 desc.setMultivalued(true);
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158 addFieldDescriptor(desc);
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160 // -- validation code for: _sequenceList
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161 fieldValidator = new org.exolab.castor.xml.FieldValidator();
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162 fieldValidator.setMinOccurs(1);
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163 { // -- local scope
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165 desc.setValidator(fieldValidator);
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166 // -- _sequenceMappingList
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167 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
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168 uk.ac.vamsas.objects.core.SequenceMapping.class,
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169 "_sequenceMappingList", "sequenceMapping",
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170 org.exolab.castor.xml.NodeType.Element);
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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 DataSet target = (DataSet) object;
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175 return target.getSequenceMapping();
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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 DataSet target = (DataSet) object;
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183 .addSequenceMapping((uk.ac.vamsas.objects.core.SequenceMapping) value);
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184 } catch (java.lang.Exception ex) {
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185 throw new IllegalStateException(ex.toString());
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189 public void resetValue(Object object) throws IllegalStateException,
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190 IllegalArgumentException {
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192 DataSet target = (DataSet) object;
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193 target.removeAllSequenceMapping();
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194 } catch (java.lang.Exception ex) {
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195 throw new IllegalStateException(ex.toString());
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199 public java.lang.Object newInstance(java.lang.Object parent) {
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200 return new uk.ac.vamsas.objects.core.SequenceMapping();
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203 desc.setHandler(handler);
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204 desc.setNameSpaceURI("http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes");
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205 desc.setMultivalued(true);
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206 addFieldDescriptor(desc);
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208 // -- validation code for: _sequenceMappingList
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209 fieldValidator = new org.exolab.castor.xml.FieldValidator();
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210 fieldValidator.setMinOccurs(0);
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211 { // -- local scope
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213 desc.setValidator(fieldValidator);
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214 // -- _dataSetAnnotationsList
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215 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
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216 uk.ac.vamsas.objects.core.DataSetAnnotations.class,
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217 "_dataSetAnnotationsList", "DataSetAnnotations",
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218 org.exolab.castor.xml.NodeType.Element);
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219 handler = new org.exolab.castor.xml.XMLFieldHandler() {
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220 public java.lang.Object getValue(java.lang.Object object)
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221 throws IllegalStateException {
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222 DataSet target = (DataSet) object;
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223 return target.getDataSetAnnotations();
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226 public void setValue(java.lang.Object object, java.lang.Object value)
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227 throws IllegalStateException, IllegalArgumentException {
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229 DataSet target = (DataSet) object;
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231 .addDataSetAnnotations((uk.ac.vamsas.objects.core.DataSetAnnotations) value);
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232 } catch (java.lang.Exception ex) {
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233 throw new IllegalStateException(ex.toString());
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237 public void resetValue(Object object) throws IllegalStateException,
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238 IllegalArgumentException {
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240 DataSet target = (DataSet) object;
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241 target.removeAllDataSetAnnotations();
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242 } catch (java.lang.Exception ex) {
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243 throw new IllegalStateException(ex.toString());
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247 public java.lang.Object newInstance(java.lang.Object parent) {
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248 return new uk.ac.vamsas.objects.core.DataSetAnnotations();
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251 desc.setHandler(handler);
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252 desc.setNameSpaceURI("http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes");
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253 desc.setMultivalued(true);
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254 addFieldDescriptor(desc);
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256 // -- validation code for: _dataSetAnnotationsList
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257 fieldValidator = new org.exolab.castor.xml.FieldValidator();
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258 fieldValidator.setMinOccurs(0);
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259 { // -- local scope
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261 desc.setValidator(fieldValidator);
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262 // -- _alignmentList
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263 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
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264 uk.ac.vamsas.objects.core.Alignment.class, "_alignmentList",
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265 "Alignment", org.exolab.castor.xml.NodeType.Element);
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266 handler = new org.exolab.castor.xml.XMLFieldHandler() {
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267 public java.lang.Object getValue(java.lang.Object object)
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268 throws IllegalStateException {
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269 DataSet target = (DataSet) object;
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270 return target.getAlignment();
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273 public void setValue(java.lang.Object object, java.lang.Object value)
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274 throws IllegalStateException, IllegalArgumentException {
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276 DataSet target = (DataSet) object;
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277 target.addAlignment((uk.ac.vamsas.objects.core.Alignment) value);
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278 } catch (java.lang.Exception ex) {
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279 throw new IllegalStateException(ex.toString());
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283 public void resetValue(Object object) throws IllegalStateException,
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284 IllegalArgumentException {
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286 DataSet target = (DataSet) object;
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287 target.removeAllAlignment();
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288 } catch (java.lang.Exception ex) {
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289 throw new IllegalStateException(ex.toString());
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293 public java.lang.Object newInstance(java.lang.Object parent) {
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294 return new uk.ac.vamsas.objects.core.Alignment();
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297 desc.setHandler(handler);
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298 desc.setNameSpaceURI("http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes");
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299 desc.setMultivalued(true);
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300 addFieldDescriptor(desc);
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302 // -- validation code for: _alignmentList
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303 fieldValidator = new org.exolab.castor.xml.FieldValidator();
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304 fieldValidator.setMinOccurs(0);
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305 { // -- local scope
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307 desc.setValidator(fieldValidator);
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309 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
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310 uk.ac.vamsas.objects.core.Tree.class, "_treeList", "Tree",
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311 org.exolab.castor.xml.NodeType.Element);
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312 handler = new org.exolab.castor.xml.XMLFieldHandler() {
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313 public java.lang.Object getValue(java.lang.Object object)
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314 throws IllegalStateException {
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315 DataSet target = (DataSet) object;
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316 return target.getTree();
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319 public void setValue(java.lang.Object object, java.lang.Object value)
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320 throws IllegalStateException, IllegalArgumentException {
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322 DataSet target = (DataSet) object;
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323 target.addTree((uk.ac.vamsas.objects.core.Tree) value);
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324 } catch (java.lang.Exception ex) {
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325 throw new IllegalStateException(ex.toString());
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329 public void resetValue(Object object) throws IllegalStateException,
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330 IllegalArgumentException {
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332 DataSet target = (DataSet) object;
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333 target.removeAllTree();
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334 } catch (java.lang.Exception ex) {
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335 throw new IllegalStateException(ex.toString());
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339 public java.lang.Object newInstance(java.lang.Object parent) {
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340 return new uk.ac.vamsas.objects.core.Tree();
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343 desc.setHandler(handler);
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344 desc.setNameSpaceURI("http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes");
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345 desc.setMultivalued(true);
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346 addFieldDescriptor(desc);
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348 // -- validation code for: _treeList
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349 fieldValidator = new org.exolab.castor.xml.FieldValidator();
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350 fieldValidator.setMinOccurs(0);
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351 { // -- local scope
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353 desc.setValidator(fieldValidator);
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355 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
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356 uk.ac.vamsas.objects.core.Provenance.class, "_provenance",
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357 "Provenance", org.exolab.castor.xml.NodeType.Element);
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358 handler = new org.exolab.castor.xml.XMLFieldHandler() {
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359 public java.lang.Object getValue(java.lang.Object object)
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360 throws IllegalStateException {
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361 DataSet target = (DataSet) object;
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362 return target.getProvenance();
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365 public void setValue(java.lang.Object object, java.lang.Object value)
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366 throws IllegalStateException, IllegalArgumentException {
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368 DataSet target = (DataSet) object;
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369 target.setProvenance((uk.ac.vamsas.objects.core.Provenance) value);
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370 } catch (java.lang.Exception ex) {
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371 throw new IllegalStateException(ex.toString());
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375 public java.lang.Object newInstance(java.lang.Object parent) {
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376 return new uk.ac.vamsas.objects.core.Provenance();
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379 desc.setHandler(handler);
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380 desc.setNameSpaceURI("http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes");
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381 desc.setRequired(true);
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382 desc.setMultivalued(false);
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383 addFieldDescriptor(desc);
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385 // -- validation code for: _provenance
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386 fieldValidator = new org.exolab.castor.xml.FieldValidator();
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387 fieldValidator.setMinOccurs(1);
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388 { // -- local scope
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390 desc.setValidator(fieldValidator);
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398 * Method getAccessMode.
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400 * @return the access mode specified for this class.
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402 public org.exolab.castor.mapping.AccessMode getAccessMode() {
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407 * Method getIdentity.
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409 * @return the identity field, null if this class has no identity.
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411 public org.exolab.castor.mapping.FieldDescriptor getIdentity() {
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412 return super.getIdentity();
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416 * Method getJavaClass.
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418 * @return the Java class represented by this descriptor.
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420 public java.lang.Class getJavaClass() {
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421 return uk.ac.vamsas.objects.core.DataSet.class;
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425 * Method getNameSpacePrefix.
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427 * @return the namespace prefix to use when marshaling as XML.
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429 public java.lang.String getNameSpacePrefix() {
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434 * Method getNameSpaceURI.
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436 * @return the namespace URI used when marshaling and unmarshaling as XML.
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438 public java.lang.String getNameSpaceURI() {
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443 * Method getValidator.
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445 * @return a specific validator for the class described by this
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448 public org.exolab.castor.xml.TypeValidator getValidator() {
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453 * Method getXMLName.
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455 * @return the XML Name for the Class being described.
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457 public java.lang.String getXMLName() {
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462 * Method isElementDefinition.
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464 * @return true if XML schema definition of this Class is that of a global
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465 * element or element with anonymous type definition.
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467 public boolean isElementDefinition() {
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468 return _elementDefinition;
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