2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1)
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3 * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
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5 * This program is free software; you can redistribute it and/or
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6 * modify it under the terms of the GNU General Public License
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7 * as published by the Free Software Foundation; either version 2
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8 * of the License, or (at your option) any later version.
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10 * This program is distributed in the hope that it will be useful,
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11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
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12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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13 * GNU General Public License for more details.
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15 * You should have received a copy of the GNU General Public License
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16 * along with this program; if not, write to the Free Software
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17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
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19 package jalview.schemabinding.version2.descriptors;
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21 //---------------------------------/
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22 //- Imported classes and packages -/
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23 //---------------------------------/
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25 import jalview.schemabinding.version2.Feature;
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28 * Class FeatureDescriptor.
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30 * @version $Revision$ $Date$
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32 public class FeatureDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
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35 //--------------------------/
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36 //- Class/Member Variables -/
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37 //--------------------------/
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40 * Field _elementDefinition.
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42 private boolean _elementDefinition;
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47 private java.lang.String _nsPrefix;
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52 private java.lang.String _nsURI;
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57 private java.lang.String _xmlName;
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64 public FeatureDescriptor() {
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66 _nsURI = "www.jalview.org";
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67 _xmlName = "feature";
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68 _elementDefinition = false;
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70 //-- set grouping compositor
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71 setCompositorAsSequence();
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72 org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
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73 org.exolab.castor.mapping.FieldHandler handler = null;
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74 org.exolab.castor.xml.FieldValidator fieldValidator = null;
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75 //-- initialize attribute descriptors
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78 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_begin", "begin", org.exolab.castor.xml.NodeType.Attribute);
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79 handler = new org.exolab.castor.xml.XMLFieldHandler() {
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80 public java.lang.Object getValue( java.lang.Object object )
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81 throws IllegalStateException
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83 Feature target = (Feature) object;
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84 if (!target.hasBegin()) { return null; }
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85 return new java.lang.Integer(target.getBegin());
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87 public void setValue( java.lang.Object object, java.lang.Object value)
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88 throws IllegalStateException, IllegalArgumentException
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91 Feature target = (Feature) object;
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92 // ignore null values for non optional primitives
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93 if (value == null) { return; }
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95 target.setBegin( ((java.lang.Integer) value).intValue());
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96 } catch (java.lang.Exception ex) {
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97 throw new IllegalStateException(ex.toString());
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100 public java.lang.Object newInstance(java.lang.Object parent) {
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104 desc.setHandler(handler);
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105 desc.setRequired(true);
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106 desc.setMultivalued(false);
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107 addFieldDescriptor(desc);
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109 //-- validation code for: _begin
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110 fieldValidator = new org.exolab.castor.xml.FieldValidator();
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111 fieldValidator.setMinOccurs(1);
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113 org.exolab.castor.xml.validators.IntValidator typeValidator;
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114 typeValidator = new org.exolab.castor.xml.validators.IntValidator();
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115 fieldValidator.setValidator(typeValidator);
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116 typeValidator.setMinInclusive(-2147483648);
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117 typeValidator.setMaxInclusive(2147483647);
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119 desc.setValidator(fieldValidator);
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121 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_end", "end", org.exolab.castor.xml.NodeType.Attribute);
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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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126 Feature target = (Feature) object;
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127 if (!target.hasEnd()) { return null; }
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128 return new java.lang.Integer(target.getEnd());
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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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134 Feature target = (Feature) object;
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135 // ignore null values for non optional primitives
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136 if (value == null) { return; }
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138 target.setEnd( ((java.lang.Integer) value).intValue());
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139 } catch (java.lang.Exception ex) {
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140 throw new IllegalStateException(ex.toString());
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143 public java.lang.Object newInstance(java.lang.Object parent) {
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147 desc.setHandler(handler);
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148 desc.setRequired(true);
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149 desc.setMultivalued(false);
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150 addFieldDescriptor(desc);
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152 //-- validation code for: _end
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153 fieldValidator = new org.exolab.castor.xml.FieldValidator();
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154 fieldValidator.setMinOccurs(1);
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156 org.exolab.castor.xml.validators.IntValidator typeValidator;
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157 typeValidator = new org.exolab.castor.xml.validators.IntValidator();
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158 fieldValidator.setValidator(typeValidator);
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159 typeValidator.setMinInclusive(-2147483648);
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160 typeValidator.setMaxInclusive(2147483647);
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162 desc.setValidator(fieldValidator);
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164 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_type", "type", org.exolab.castor.xml.NodeType.Attribute);
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165 desc.setImmutable(true);
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166 handler = new org.exolab.castor.xml.XMLFieldHandler() {
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167 public java.lang.Object getValue( java.lang.Object object )
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168 throws IllegalStateException
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170 Feature target = (Feature) object;
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171 return target.getType();
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173 public void setValue( java.lang.Object object, java.lang.Object value)
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174 throws IllegalStateException, IllegalArgumentException
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177 Feature target = (Feature) object;
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178 target.setType( (java.lang.String) value);
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179 } catch (java.lang.Exception ex) {
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180 throw new IllegalStateException(ex.toString());
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183 public java.lang.Object newInstance(java.lang.Object parent) {
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187 desc.setHandler(handler);
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188 desc.setRequired(true);
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189 desc.setMultivalued(false);
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190 addFieldDescriptor(desc);
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192 //-- validation code for: _type
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193 fieldValidator = new org.exolab.castor.xml.FieldValidator();
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194 fieldValidator.setMinOccurs(1);
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196 org.exolab.castor.xml.validators.StringValidator typeValidator;
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197 typeValidator = new org.exolab.castor.xml.validators.StringValidator();
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198 fieldValidator.setValidator(typeValidator);
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199 typeValidator.setWhiteSpace("preserve");
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201 desc.setValidator(fieldValidator);
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203 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_description", "description", org.exolab.castor.xml.NodeType.Attribute);
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204 desc.setImmutable(true);
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205 handler = new org.exolab.castor.xml.XMLFieldHandler() {
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206 public java.lang.Object getValue( java.lang.Object object )
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207 throws IllegalStateException
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209 Feature target = (Feature) object;
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210 return target.getDescription();
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212 public void setValue( java.lang.Object object, java.lang.Object value)
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213 throws IllegalStateException, IllegalArgumentException
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216 Feature target = (Feature) object;
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217 target.setDescription( (java.lang.String) value);
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218 } catch (java.lang.Exception ex) {
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219 throw new IllegalStateException(ex.toString());
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222 public java.lang.Object newInstance(java.lang.Object parent) {
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226 desc.setHandler(handler);
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227 desc.setMultivalued(false);
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228 addFieldDescriptor(desc);
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230 //-- validation code for: _description
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231 fieldValidator = new org.exolab.castor.xml.FieldValidator();
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233 org.exolab.castor.xml.validators.StringValidator typeValidator;
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234 typeValidator = new org.exolab.castor.xml.validators.StringValidator();
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235 fieldValidator.setValidator(typeValidator);
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236 typeValidator.setWhiteSpace("preserve");
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238 desc.setValidator(fieldValidator);
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240 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_status", "status", org.exolab.castor.xml.NodeType.Attribute);
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241 desc.setImmutable(true);
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242 handler = new org.exolab.castor.xml.XMLFieldHandler() {
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243 public java.lang.Object getValue( java.lang.Object object )
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244 throws IllegalStateException
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246 Feature target = (Feature) object;
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247 return target.getStatus();
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249 public void setValue( java.lang.Object object, java.lang.Object value)
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250 throws IllegalStateException, IllegalArgumentException
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253 Feature target = (Feature) object;
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254 target.setStatus( (java.lang.String) value);
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255 } catch (java.lang.Exception ex) {
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256 throw new IllegalStateException(ex.toString());
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259 public java.lang.Object newInstance(java.lang.Object parent) {
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263 desc.setHandler(handler);
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264 desc.setMultivalued(false);
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265 addFieldDescriptor(desc);
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267 //-- validation code for: _status
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268 fieldValidator = new org.exolab.castor.xml.FieldValidator();
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270 org.exolab.castor.xml.validators.StringValidator typeValidator;
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271 typeValidator = new org.exolab.castor.xml.validators.StringValidator();
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272 fieldValidator.setValidator(typeValidator);
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273 typeValidator.setWhiteSpace("preserve");
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275 desc.setValidator(fieldValidator);
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277 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_featureGroup", "featureGroup", org.exolab.castor.xml.NodeType.Attribute);
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278 desc.setImmutable(true);
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279 handler = new org.exolab.castor.xml.XMLFieldHandler() {
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280 public java.lang.Object getValue( java.lang.Object object )
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281 throws IllegalStateException
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283 Feature target = (Feature) object;
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284 return target.getFeatureGroup();
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286 public void setValue( java.lang.Object object, java.lang.Object value)
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287 throws IllegalStateException, IllegalArgumentException
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290 Feature target = (Feature) object;
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291 target.setFeatureGroup( (java.lang.String) value);
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292 } catch (java.lang.Exception ex) {
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293 throw new IllegalStateException(ex.toString());
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296 public java.lang.Object newInstance(java.lang.Object parent) {
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300 desc.setHandler(handler);
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301 desc.setMultivalued(false);
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302 addFieldDescriptor(desc);
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304 //-- validation code for: _featureGroup
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305 fieldValidator = new org.exolab.castor.xml.FieldValidator();
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307 org.exolab.castor.xml.validators.StringValidator typeValidator;
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308 typeValidator = new org.exolab.castor.xml.validators.StringValidator();
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309 fieldValidator.setValidator(typeValidator);
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310 typeValidator.setWhiteSpace("preserve");
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312 desc.setValidator(fieldValidator);
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314 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Float.TYPE, "_score", "score", org.exolab.castor.xml.NodeType.Attribute);
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315 handler = new org.exolab.castor.xml.XMLFieldHandler() {
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316 public java.lang.Object getValue( java.lang.Object object )
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317 throws IllegalStateException
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319 Feature target = (Feature) object;
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320 if (!target.hasScore()) { return null; }
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321 return new java.lang.Float(target.getScore());
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323 public void setValue( java.lang.Object object, java.lang.Object value)
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324 throws IllegalStateException, IllegalArgumentException
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327 Feature target = (Feature) object;
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328 // if null, use delete method for optional primitives
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329 if (value == null) {
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330 target.deleteScore();
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333 target.setScore( ((java.lang.Float) value).floatValue());
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334 } catch (java.lang.Exception ex) {
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335 throw new IllegalStateException(ex.toString());
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338 public java.lang.Object newInstance(java.lang.Object parent) {
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342 desc.setHandler(handler);
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343 desc.setMultivalued(false);
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344 addFieldDescriptor(desc);
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346 //-- validation code for: _score
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347 fieldValidator = new org.exolab.castor.xml.FieldValidator();
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349 org.exolab.castor.xml.validators.FloatValidator typeValidator;
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350 typeValidator = new org.exolab.castor.xml.validators.FloatValidator();
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351 fieldValidator.setValidator(typeValidator);
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352 typeValidator.setMinInclusive((float) -3.4028235E38);
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353 typeValidator.setMaxInclusive((float) 3.4028235E38);
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355 desc.setValidator(fieldValidator);
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356 //-- initialize element descriptors
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358 //-- _otherDataList
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359 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.OtherData.class, "_otherDataList", "otherData", org.exolab.castor.xml.NodeType.Element);
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360 handler = new org.exolab.castor.xml.XMLFieldHandler() {
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361 public java.lang.Object getValue( java.lang.Object object )
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362 throws IllegalStateException
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364 Feature target = (Feature) object;
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365 return target.getOtherData();
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367 public void setValue( java.lang.Object object, java.lang.Object value)
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368 throws IllegalStateException, IllegalArgumentException
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371 Feature target = (Feature) object;
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372 target.addOtherData( (jalview.schemabinding.version2.OtherData) value);
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373 } catch (java.lang.Exception ex) {
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374 throw new IllegalStateException(ex.toString());
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377 public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {
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379 Feature target = (Feature) object;
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380 target.removeAllOtherData();
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381 } catch (java.lang.Exception ex) {
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382 throw new IllegalStateException(ex.toString());
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385 public java.lang.Object newInstance(java.lang.Object parent) {
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386 return new jalview.schemabinding.version2.OtherData();
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389 desc.setHandler(handler);
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390 desc.setNameSpaceURI("www.jalview.org");
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391 desc.setMultivalued(true);
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392 addFieldDescriptor(desc);
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394 //-- validation code for: _otherDataList
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395 fieldValidator = new org.exolab.castor.xml.FieldValidator();
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396 fieldValidator.setMinOccurs(0);
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399 desc.setValidator(fieldValidator);
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408 * Method getAccessMode.
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410 * @return the access mode specified for this class.
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412 public org.exolab.castor.mapping.AccessMode getAccessMode(
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418 * Method getIdentity.
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420 * @return the identity field, null if this class has no
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423 public org.exolab.castor.mapping.FieldDescriptor getIdentity(
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425 return super.getIdentity();
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429 * Method getJavaClass.
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431 * @return the Java class represented by this descriptor.
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433 public java.lang.Class getJavaClass(
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435 return jalview.schemabinding.version2.Feature.class;
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439 * Method getNameSpacePrefix.
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441 * @return the namespace prefix to use when marshaling as XML.
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443 public java.lang.String getNameSpacePrefix(
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449 * Method getNameSpaceURI.
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451 * @return the namespace URI used when marshaling and
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452 * unmarshaling as XML.
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454 public java.lang.String getNameSpaceURI(
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460 * Method getValidator.
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462 * @return a specific validator for the class described by this
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465 public org.exolab.castor.xml.TypeValidator getValidator(
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471 * Method getXMLName.
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473 * @return the XML Name for the Class being described.
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475 public java.lang.String getXMLName(
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481 * Method isElementDefinition.
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483 * @return true if XML schema definition of this Class is that
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485 * element or element with anonymous type definition.
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487 public boolean isElementDefinition(
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489 return _elementDefinition;
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