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.Tree;
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31 * Class TreeDescriptor.
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33 * @version $Revision$ $Date$
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35 public class TreeDescriptor 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 TreeDescriptor() {
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68 _nsURI = "http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes";
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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 Tree target = (Tree) 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 Tree target = (Tree) 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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118 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
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119 java.lang.String.class, "_modifiable", "modifiable",
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120 org.exolab.castor.xml.NodeType.Attribute);
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121 desc.setImmutable(true);
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122 handler = new org.exolab.castor.xml.XMLFieldHandler() {
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123 public java.lang.Object getValue(java.lang.Object object)
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124 throws IllegalStateException {
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125 Tree target = (Tree) object;
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126 return target.getModifiable();
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129 public void setValue(java.lang.Object object, java.lang.Object value)
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130 throws IllegalStateException, IllegalArgumentException {
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132 Tree target = (Tree) object;
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133 target.setModifiable((java.lang.String) value);
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134 } catch (java.lang.Exception ex) {
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135 throw new IllegalStateException(ex.toString());
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139 public java.lang.Object newInstance(java.lang.Object parent) {
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143 desc.setHandler(handler);
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144 desc.setMultivalued(false);
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145 addFieldDescriptor(desc);
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147 // -- validation code for: _modifiable
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148 fieldValidator = new org.exolab.castor.xml.FieldValidator();
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149 { // -- local scope
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150 org.exolab.castor.xml.validators.StringValidator typeValidator;
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151 typeValidator = new org.exolab.castor.xml.validators.StringValidator();
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152 fieldValidator.setValidator(typeValidator);
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153 typeValidator.setWhiteSpace("preserve");
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155 desc.setValidator(fieldValidator);
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156 // -- initialize element descriptors
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159 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
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160 java.lang.String.class, "_title", "title",
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161 org.exolab.castor.xml.NodeType.Element);
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162 desc.setImmutable(true);
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163 handler = new org.exolab.castor.xml.XMLFieldHandler() {
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164 public java.lang.Object getValue(java.lang.Object object)
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165 throws IllegalStateException {
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166 Tree target = (Tree) object;
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167 return target.getTitle();
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170 public void setValue(java.lang.Object object, java.lang.Object value)
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171 throws IllegalStateException, IllegalArgumentException {
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173 Tree target = (Tree) object;
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174 target.setTitle((java.lang.String) value);
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175 } catch (java.lang.Exception ex) {
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176 throw new IllegalStateException(ex.toString());
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180 public java.lang.Object newInstance(java.lang.Object parent) {
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184 desc.setHandler(handler);
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185 desc.setNameSpaceURI("http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes");
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186 desc.setMultivalued(false);
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187 addFieldDescriptor(desc);
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189 // -- validation code for: _title
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190 fieldValidator = new org.exolab.castor.xml.FieldValidator();
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191 { // -- local scope
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192 org.exolab.castor.xml.validators.StringValidator typeValidator;
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193 typeValidator = new org.exolab.castor.xml.validators.StringValidator();
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194 fieldValidator.setValidator(typeValidator);
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195 typeValidator.setWhiteSpace("preserve");
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197 desc.setValidator(fieldValidator);
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199 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
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200 uk.ac.vamsas.objects.core.Newick.class, "_newickList", "newick",
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201 org.exolab.castor.xml.NodeType.Element);
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202 handler = new org.exolab.castor.xml.XMLFieldHandler() {
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203 public java.lang.Object getValue(java.lang.Object object)
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204 throws IllegalStateException {
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205 Tree target = (Tree) object;
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206 return target.getNewick();
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209 public void setValue(java.lang.Object object, java.lang.Object value)
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210 throws IllegalStateException, IllegalArgumentException {
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212 Tree target = (Tree) object;
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213 target.addNewick((uk.ac.vamsas.objects.core.Newick) value);
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214 } catch (java.lang.Exception ex) {
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215 throw new IllegalStateException(ex.toString());
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219 public void resetValue(Object object) throws IllegalStateException,
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220 IllegalArgumentException {
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222 Tree target = (Tree) object;
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223 target.removeAllNewick();
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224 } catch (java.lang.Exception ex) {
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225 throw new IllegalStateException(ex.toString());
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229 public java.lang.Object newInstance(java.lang.Object parent) {
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230 return new uk.ac.vamsas.objects.core.Newick();
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233 desc.setHandler(handler);
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234 desc.setNameSpaceURI("http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes");
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235 desc.setRequired(true);
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236 desc.setMultivalued(true);
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237 addFieldDescriptor(desc);
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239 // -- validation code for: _newickList
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240 fieldValidator = new org.exolab.castor.xml.FieldValidator();
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241 fieldValidator.setMinOccurs(1);
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242 { // -- local scope
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244 desc.setValidator(fieldValidator);
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245 // -- _treenodeList
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246 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
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247 uk.ac.vamsas.objects.core.Treenode.class, "_treenodeList", "treenode",
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248 org.exolab.castor.xml.NodeType.Element);
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249 handler = new org.exolab.castor.xml.XMLFieldHandler() {
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250 public java.lang.Object getValue(java.lang.Object object)
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251 throws IllegalStateException {
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252 Tree target = (Tree) object;
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253 return target.getTreenode();
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256 public void setValue(java.lang.Object object, java.lang.Object value)
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257 throws IllegalStateException, IllegalArgumentException {
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259 Tree target = (Tree) object;
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260 target.addTreenode((uk.ac.vamsas.objects.core.Treenode) value);
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261 } catch (java.lang.Exception ex) {
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262 throw new IllegalStateException(ex.toString());
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266 public void resetValue(Object object) throws IllegalStateException,
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267 IllegalArgumentException {
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269 Tree target = (Tree) object;
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270 target.removeAllTreenode();
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271 } catch (java.lang.Exception ex) {
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272 throw new IllegalStateException(ex.toString());
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276 public java.lang.Object newInstance(java.lang.Object parent) {
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277 return new uk.ac.vamsas.objects.core.Treenode();
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280 desc.setHandler(handler);
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281 desc.setNameSpaceURI("http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes");
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282 desc.setMultivalued(true);
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283 addFieldDescriptor(desc);
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285 // -- validation code for: _treenodeList
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286 fieldValidator = new org.exolab.castor.xml.FieldValidator();
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287 fieldValidator.setMinOccurs(0);
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288 { // -- local scope
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290 desc.setValidator(fieldValidator);
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291 // -- _propertyList
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292 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
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293 uk.ac.vamsas.objects.core.Property.class, "_propertyList", "property",
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294 org.exolab.castor.xml.NodeType.Element);
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295 handler = new org.exolab.castor.xml.XMLFieldHandler() {
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296 public java.lang.Object getValue(java.lang.Object object)
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297 throws IllegalStateException {
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298 Tree target = (Tree) object;
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299 return target.getProperty();
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302 public void setValue(java.lang.Object object, java.lang.Object value)
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303 throws IllegalStateException, IllegalArgumentException {
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305 Tree target = (Tree) object;
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306 target.addProperty((uk.ac.vamsas.objects.core.Property) value);
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307 } catch (java.lang.Exception ex) {
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308 throw new IllegalStateException(ex.toString());
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312 public void resetValue(Object object) throws IllegalStateException,
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313 IllegalArgumentException {
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315 Tree target = (Tree) object;
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316 target.removeAllProperty();
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317 } catch (java.lang.Exception ex) {
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318 throw new IllegalStateException(ex.toString());
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322 public java.lang.Object newInstance(java.lang.Object parent) {
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323 return new uk.ac.vamsas.objects.core.Property();
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326 desc.setHandler(handler);
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327 desc.setNameSpaceURI("http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes");
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328 desc.setMultivalued(true);
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329 addFieldDescriptor(desc);
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331 // -- validation code for: _propertyList
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332 fieldValidator = new org.exolab.castor.xml.FieldValidator();
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333 fieldValidator.setMinOccurs(0);
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334 { // -- local scope
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336 desc.setValidator(fieldValidator);
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338 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
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339 uk.ac.vamsas.objects.core.Provenance.class, "_provenance",
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340 "Provenance", org.exolab.castor.xml.NodeType.Element);
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341 handler = new org.exolab.castor.xml.XMLFieldHandler() {
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342 public java.lang.Object getValue(java.lang.Object object)
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343 throws IllegalStateException {
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344 Tree target = (Tree) object;
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345 return target.getProvenance();
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348 public void setValue(java.lang.Object object, java.lang.Object value)
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349 throws IllegalStateException, IllegalArgumentException {
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351 Tree target = (Tree) object;
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352 target.setProvenance((uk.ac.vamsas.objects.core.Provenance) value);
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353 } catch (java.lang.Exception ex) {
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354 throw new IllegalStateException(ex.toString());
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358 public java.lang.Object newInstance(java.lang.Object parent) {
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359 return new uk.ac.vamsas.objects.core.Provenance();
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362 desc.setHandler(handler);
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363 desc.setNameSpaceURI("http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes");
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364 desc.setRequired(true);
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365 desc.setMultivalued(false);
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366 addFieldDescriptor(desc);
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368 // -- validation code for: _provenance
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369 fieldValidator = new org.exolab.castor.xml.FieldValidator();
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370 fieldValidator.setMinOccurs(1);
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371 { // -- local scope
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373 desc.setValidator(fieldValidator);
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381 * Method getAccessMode.
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383 * @return the access mode specified for this class.
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385 public org.exolab.castor.mapping.AccessMode getAccessMode() {
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390 * Method getIdentity.
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392 * @return the identity field, null if this class has no identity.
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394 public org.exolab.castor.mapping.FieldDescriptor getIdentity() {
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395 return super.getIdentity();
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399 * Method getJavaClass.
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401 * @return the Java class represented by this descriptor.
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403 public java.lang.Class getJavaClass() {
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404 return uk.ac.vamsas.objects.core.Tree.class;
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408 * Method getNameSpacePrefix.
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410 * @return the namespace prefix to use when marshaling as XML.
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412 public java.lang.String getNameSpacePrefix() {
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417 * Method getNameSpaceURI.
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419 * @return the namespace URI used when marshaling and unmarshaling as XML.
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421 public java.lang.String getNameSpaceURI() {
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426 * Method getValidator.
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428 * @return a specific validator for the class described by this
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431 public org.exolab.castor.xml.TypeValidator getValidator() {
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436 * Method getXMLName.
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438 * @return the XML Name for the Class being described.
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440 public java.lang.String getXMLName() {
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445 * Method isElementDefinition.
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447 * @return true if XML schema definition of this Class is that of a global
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448 * element or element with anonymous type definition.
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450 public boolean isElementDefinition() {
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451 return _elementDefinition;
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