2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
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3 * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
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5 * This file is part of Jalview.
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7 * Jalview is free software: you can redistribute it and/or
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8 * modify it under the terms of the GNU General Public License
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9 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
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11 * Jalview is distributed in the hope that it will be useful, but
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12 * WITHOUT ANY WARRANTY; without even the implied warranty
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13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
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14 * PURPOSE. See the GNU General Public License for more details.
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16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
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18 package jalview.schemabinding.version2.descriptors;
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20 //---------------------------------/
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21 //- Imported classes and packages -/
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22 //---------------------------------/
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24 import jalview.schemabinding.version2.JSeq;
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27 * Class JSeqDescriptor.
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29 * @version $Revision$ $Date$
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31 public class JSeqDescriptor extends
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32 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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59 // ----------------/
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60 // - Constructors -/
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61 // ----------------/
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63 public JSeqDescriptor()
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66 _nsURI = "www.jalview.org";
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68 _elementDefinition = true;
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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(
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79 java.lang.Integer.TYPE, "_colour", "colour",
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80 org.exolab.castor.xml.NodeType.Attribute);
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81 handler = new org.exolab.castor.xml.XMLFieldHandler()
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83 public java.lang.Object getValue(java.lang.Object object)
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84 throws IllegalStateException
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86 JSeq target = (JSeq) object;
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87 if (!target.hasColour())
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91 return new java.lang.Integer(target.getColour());
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94 public void setValue(java.lang.Object object, java.lang.Object value)
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95 throws IllegalStateException, IllegalArgumentException
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99 JSeq target = (JSeq) object;
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100 // if null, use delete method for optional primitives
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103 target.deleteColour();
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106 target.setColour(((java.lang.Integer) value).intValue());
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107 } catch (java.lang.Exception ex)
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109 throw new IllegalStateException(ex.toString());
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113 public java.lang.Object newInstance(java.lang.Object parent)
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118 desc.setHandler(handler);
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119 desc.setMultivalued(false);
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120 addFieldDescriptor(desc);
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122 // -- validation code for: _colour
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123 fieldValidator = new org.exolab.castor.xml.FieldValidator();
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124 { // -- local scope
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125 org.exolab.castor.xml.validators.IntValidator typeValidator;
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126 typeValidator = new org.exolab.castor.xml.validators.IntValidator();
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127 fieldValidator.setValidator(typeValidator);
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128 typeValidator.setMinInclusive(-2147483648);
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129 typeValidator.setMaxInclusive(2147483647);
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131 desc.setValidator(fieldValidator);
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133 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
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134 java.lang.Integer.TYPE, "_start", "start",
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135 org.exolab.castor.xml.NodeType.Attribute);
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136 handler = new org.exolab.castor.xml.XMLFieldHandler()
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138 public java.lang.Object getValue(java.lang.Object object)
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139 throws IllegalStateException
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141 JSeq target = (JSeq) object;
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142 if (!target.hasStart())
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146 return new java.lang.Integer(target.getStart());
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149 public void setValue(java.lang.Object object, java.lang.Object value)
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150 throws IllegalStateException, IllegalArgumentException
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154 JSeq target = (JSeq) object;
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155 // ignore null values for non optional primitives
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161 target.setStart(((java.lang.Integer) value).intValue());
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162 } catch (java.lang.Exception ex)
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164 throw new IllegalStateException(ex.toString());
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168 public java.lang.Object newInstance(java.lang.Object parent)
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173 desc.setHandler(handler);
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174 desc.setRequired(true);
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175 desc.setMultivalued(false);
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176 addFieldDescriptor(desc);
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178 // -- validation code for: _start
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179 fieldValidator = new org.exolab.castor.xml.FieldValidator();
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180 fieldValidator.setMinOccurs(1);
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181 { // -- local scope
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182 org.exolab.castor.xml.validators.IntValidator typeValidator;
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183 typeValidator = new org.exolab.castor.xml.validators.IntValidator();
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184 fieldValidator.setValidator(typeValidator);
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185 typeValidator.setMinInclusive(-2147483648);
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186 typeValidator.setMaxInclusive(2147483647);
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188 desc.setValidator(fieldValidator);
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190 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
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191 java.lang.Integer.TYPE, "_end", "end",
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192 org.exolab.castor.xml.NodeType.Attribute);
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193 handler = new org.exolab.castor.xml.XMLFieldHandler()
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195 public java.lang.Object getValue(java.lang.Object object)
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196 throws IllegalStateException
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198 JSeq target = (JSeq) object;
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199 if (!target.hasEnd())
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203 return new java.lang.Integer(target.getEnd());
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206 public void setValue(java.lang.Object object, java.lang.Object value)
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207 throws IllegalStateException, IllegalArgumentException
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211 JSeq target = (JSeq) object;
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212 // ignore null values for non optional primitives
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218 target.setEnd(((java.lang.Integer) value).intValue());
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219 } catch (java.lang.Exception ex)
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221 throw new IllegalStateException(ex.toString());
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225 public java.lang.Object newInstance(java.lang.Object parent)
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230 desc.setHandler(handler);
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231 desc.setRequired(true);
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232 desc.setMultivalued(false);
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233 addFieldDescriptor(desc);
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235 // -- validation code for: _end
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236 fieldValidator = new org.exolab.castor.xml.FieldValidator();
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237 fieldValidator.setMinOccurs(1);
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238 { // -- local scope
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239 org.exolab.castor.xml.validators.IntValidator typeValidator;
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240 typeValidator = new org.exolab.castor.xml.validators.IntValidator();
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241 fieldValidator.setValidator(typeValidator);
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242 typeValidator.setMinInclusive(-2147483648);
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243 typeValidator.setMaxInclusive(2147483647);
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245 desc.setValidator(fieldValidator);
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247 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
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248 java.lang.String.class, "_id", "id",
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249 org.exolab.castor.xml.NodeType.Attribute);
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250 desc.setImmutable(true);
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251 handler = new org.exolab.castor.xml.XMLFieldHandler()
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253 public java.lang.Object getValue(java.lang.Object object)
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254 throws IllegalStateException
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256 JSeq target = (JSeq) object;
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257 return target.getId();
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260 public void setValue(java.lang.Object object, java.lang.Object value)
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261 throws IllegalStateException, IllegalArgumentException
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265 JSeq target = (JSeq) object;
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266 target.setId((java.lang.String) value);
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267 } catch (java.lang.Exception ex)
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269 throw new IllegalStateException(ex.toString());
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273 public java.lang.Object newInstance(java.lang.Object parent)
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278 desc.setHandler(handler);
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279 desc.setRequired(true);
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280 desc.setMultivalued(false);
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281 addFieldDescriptor(desc);
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283 // -- validation code for: _id
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284 fieldValidator = new org.exolab.castor.xml.FieldValidator();
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285 fieldValidator.setMinOccurs(1);
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286 { // -- local scope
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287 org.exolab.castor.xml.validators.StringValidator typeValidator;
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288 typeValidator = new org.exolab.castor.xml.validators.StringValidator();
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289 fieldValidator.setValidator(typeValidator);
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290 typeValidator.setWhiteSpace("preserve");
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292 desc.setValidator(fieldValidator);
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294 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
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295 java.lang.Boolean.TYPE, "_hidden", "hidden",
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296 org.exolab.castor.xml.NodeType.Attribute);
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297 handler = new org.exolab.castor.xml.XMLFieldHandler()
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299 public java.lang.Object getValue(java.lang.Object object)
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300 throws IllegalStateException
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302 JSeq target = (JSeq) object;
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303 if (!target.hasHidden())
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307 return (target.getHidden() ? java.lang.Boolean.TRUE
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308 : java.lang.Boolean.FALSE);
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311 public void setValue(java.lang.Object object, java.lang.Object value)
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312 throws IllegalStateException, IllegalArgumentException
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316 JSeq target = (JSeq) object;
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317 // if null, use delete method for optional primitives
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320 target.deleteHidden();
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323 target.setHidden(((java.lang.Boolean) value).booleanValue());
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324 } catch (java.lang.Exception ex)
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326 throw new IllegalStateException(ex.toString());
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330 public java.lang.Object newInstance(java.lang.Object parent)
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335 desc.setHandler(handler);
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336 desc.setMultivalued(false);
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337 addFieldDescriptor(desc);
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339 // -- validation code for: _hidden
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340 fieldValidator = new org.exolab.castor.xml.FieldValidator();
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341 { // -- local scope
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342 org.exolab.castor.xml.validators.BooleanValidator typeValidator;
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343 typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
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344 fieldValidator.setValidator(typeValidator);
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346 desc.setValidator(fieldValidator);
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347 // -- initialize element descriptors
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349 // -- _featuresList
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350 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
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351 jalview.schemabinding.version2.Features.class, "_featuresList",
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352 "features", org.exolab.castor.xml.NodeType.Element);
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353 handler = new org.exolab.castor.xml.XMLFieldHandler()
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355 public java.lang.Object getValue(java.lang.Object object)
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356 throws IllegalStateException
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358 JSeq target = (JSeq) object;
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359 return target.getFeatures();
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362 public void setValue(java.lang.Object object, java.lang.Object value)
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363 throws IllegalStateException, IllegalArgumentException
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367 JSeq target = (JSeq) object;
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369 .addFeatures((jalview.schemabinding.version2.Features) value);
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370 } catch (java.lang.Exception ex)
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372 throw new IllegalStateException(ex.toString());
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376 public void resetValue(Object object) throws IllegalStateException,
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377 IllegalArgumentException
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381 JSeq target = (JSeq) object;
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382 target.removeAllFeatures();
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383 } catch (java.lang.Exception ex)
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385 throw new IllegalStateException(ex.toString());
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389 public java.lang.Object newInstance(java.lang.Object parent)
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391 return new jalview.schemabinding.version2.Features();
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394 desc.setHandler(handler);
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395 desc.setNameSpaceURI("www.jalview.org");
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396 desc.setMultivalued(true);
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397 addFieldDescriptor(desc);
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399 // -- validation code for: _featuresList
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400 fieldValidator = new org.exolab.castor.xml.FieldValidator();
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401 fieldValidator.setMinOccurs(0);
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402 { // -- local scope
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404 desc.setValidator(fieldValidator);
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406 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
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407 jalview.schemabinding.version2.Pdbids.class, "_pdbidsList",
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408 "pdbids", org.exolab.castor.xml.NodeType.Element);
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409 handler = new org.exolab.castor.xml.XMLFieldHandler()
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411 public java.lang.Object getValue(java.lang.Object object)
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412 throws IllegalStateException
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414 JSeq target = (JSeq) object;
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415 return target.getPdbids();
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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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423 JSeq target = (JSeq) object;
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424 target.addPdbids((jalview.schemabinding.version2.Pdbids) value);
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425 } catch (java.lang.Exception ex)
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427 throw new IllegalStateException(ex.toString());
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431 public void resetValue(Object object) throws IllegalStateException,
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432 IllegalArgumentException
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436 JSeq target = (JSeq) object;
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437 target.removeAllPdbids();
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438 } catch (java.lang.Exception ex)
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440 throw new IllegalStateException(ex.toString());
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444 public java.lang.Object newInstance(java.lang.Object parent)
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446 return new jalview.schemabinding.version2.Pdbids();
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449 desc.setHandler(handler);
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450 desc.setNameSpaceURI("www.jalview.org");
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451 desc.setMultivalued(true);
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452 addFieldDescriptor(desc);
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454 // -- validation code for: _pdbidsList
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455 fieldValidator = new org.exolab.castor.xml.FieldValidator();
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456 fieldValidator.setMinOccurs(0);
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457 { // -- local scope
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459 desc.setValidator(fieldValidator);
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460 // -- _hiddenSequencesList
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461 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
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462 java.lang.Integer.TYPE, "_hiddenSequencesList",
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463 "hiddenSequences", org.exolab.castor.xml.NodeType.Element);
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464 handler = new org.exolab.castor.xml.XMLFieldHandler()
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466 public java.lang.Object getValue(java.lang.Object object)
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467 throws IllegalStateException
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469 JSeq target = (JSeq) object;
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470 return target.getHiddenSequences();
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473 public void setValue(java.lang.Object object, java.lang.Object value)
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474 throws IllegalStateException, IllegalArgumentException
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478 JSeq target = (JSeq) object;
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479 // ignore null values for non optional primitives
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485 target.addHiddenSequences(((java.lang.Integer) value).intValue());
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486 } catch (java.lang.Exception ex)
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488 throw new IllegalStateException(ex.toString());
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492 public void resetValue(Object object) throws IllegalStateException,
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493 IllegalArgumentException
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497 JSeq target = (JSeq) object;
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498 target.removeAllHiddenSequences();
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499 } catch (java.lang.Exception ex)
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501 throw new IllegalStateException(ex.toString());
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505 public java.lang.Object newInstance(java.lang.Object parent)
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510 desc.setHandler(handler);
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511 desc.setNameSpaceURI("www.jalview.org");
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512 desc.setMultivalued(true);
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513 addFieldDescriptor(desc);
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515 // -- validation code for: _hiddenSequencesList
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516 fieldValidator = new org.exolab.castor.xml.FieldValidator();
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517 fieldValidator.setMinOccurs(0);
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518 { // -- local scope
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519 org.exolab.castor.xml.validators.IntValidator typeValidator;
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520 typeValidator = new org.exolab.castor.xml.validators.IntValidator();
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521 fieldValidator.setValidator(typeValidator);
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522 typeValidator.setMinInclusive(-2147483648);
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523 typeValidator.setMaxInclusive(2147483647);
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525 desc.setValidator(fieldValidator);
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533 * Method getAccessMode.
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535 * @return the access mode specified for this class.
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537 public org.exolab.castor.mapping.AccessMode getAccessMode()
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543 * Method getIdentity.
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545 * @return the identity field, null if this class has no identity.
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547 public org.exolab.castor.mapping.FieldDescriptor getIdentity()
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549 return super.getIdentity();
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553 * Method getJavaClass.
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555 * @return the Java class represented by this descriptor.
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557 public java.lang.Class getJavaClass()
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559 return jalview.schemabinding.version2.JSeq.class;
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563 * Method getNameSpacePrefix.
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565 * @return the namespace prefix to use when marshaling as XML.
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567 public java.lang.String getNameSpacePrefix()
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573 * Method getNameSpaceURI.
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575 * @return the namespace URI used when marshaling and unmarshaling as XML.
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577 public java.lang.String getNameSpaceURI()
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583 * Method getValidator.
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585 * @return a specific validator for the class described by this
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588 public org.exolab.castor.xml.TypeValidator getValidator()
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594 * Method getXMLName.
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596 * @return the XML Name for the Class being described.
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598 public java.lang.String getXMLName()
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604 * Method isElementDefinition.
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606 * @return true if XML schema definition of this Class is that of a global
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607 * element or element with anonymous type definition.
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609 public boolean isElementDefinition()
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611 return _elementDefinition;
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