2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
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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.SequenceSet;
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27 * Class SequenceSetDescriptor.
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29 * @version $Revision$ $Date$
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31 public class SequenceSetDescriptor 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 SequenceSetDescriptor()
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66 _nsURI = "www.vamsas.ac.uk/jalview/version2";
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67 _xmlName = "SequenceSet";
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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.String.class, "_gapChar", "gapChar",
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80 org.exolab.castor.xml.NodeType.Attribute);
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81 desc.setImmutable(true);
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82 handler = new org.exolab.castor.xml.XMLFieldHandler()
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84 public java.lang.Object getValue(java.lang.Object object)
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85 throws IllegalStateException
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87 SequenceSet target = (SequenceSet) object;
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88 return target.getGapChar();
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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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96 SequenceSet target = (SequenceSet) object;
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97 target.setGapChar((java.lang.String) value);
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98 } catch (java.lang.Exception ex)
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100 throw new IllegalStateException(ex.toString());
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104 public java.lang.Object newInstance(java.lang.Object parent)
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109 desc.setHandler(handler);
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110 desc.setRequired(true);
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111 desc.setMultivalued(false);
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112 addFieldDescriptor(desc);
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114 // -- validation code for: _gapChar
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115 fieldValidator = new org.exolab.castor.xml.FieldValidator();
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116 fieldValidator.setMinOccurs(1);
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117 { // -- local scope
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118 org.exolab.castor.xml.validators.StringValidator typeValidator;
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119 typeValidator = new org.exolab.castor.xml.validators.StringValidator();
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120 fieldValidator.setValidator(typeValidator);
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121 typeValidator.setWhiteSpace("preserve");
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123 desc.setValidator(fieldValidator);
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125 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
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126 java.lang.String.class, "_datasetId", "datasetId",
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127 org.exolab.castor.xml.NodeType.Attribute);
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128 desc.setImmutable(true);
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129 handler = new org.exolab.castor.xml.XMLFieldHandler()
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131 public java.lang.Object getValue(java.lang.Object object)
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132 throws IllegalStateException
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134 SequenceSet target = (SequenceSet) object;
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135 return target.getDatasetId();
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138 public void setValue(java.lang.Object object, java.lang.Object value)
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139 throws IllegalStateException, IllegalArgumentException
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143 SequenceSet target = (SequenceSet) object;
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144 target.setDatasetId((java.lang.String) value);
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145 } catch (java.lang.Exception ex)
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147 throw new IllegalStateException(ex.toString());
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151 public java.lang.Object newInstance(java.lang.Object parent)
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156 desc.setHandler(handler);
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157 desc.setMultivalued(false);
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158 addFieldDescriptor(desc);
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160 // -- validation code for: _datasetId
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161 fieldValidator = new org.exolab.castor.xml.FieldValidator();
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162 { // -- local scope
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163 org.exolab.castor.xml.validators.StringValidator typeValidator;
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164 typeValidator = new org.exolab.castor.xml.validators.StringValidator();
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165 fieldValidator.setValidator(typeValidator);
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166 typeValidator.setWhiteSpace("preserve");
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168 desc.setValidator(fieldValidator);
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169 // -- initialize element descriptors
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171 // -- _sequenceList
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172 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
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173 jalview.schemabinding.version2.Sequence.class, "_sequenceList",
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174 "Sequence", org.exolab.castor.xml.NodeType.Element);
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175 handler = new org.exolab.castor.xml.XMLFieldHandler()
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177 public java.lang.Object getValue(java.lang.Object object)
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178 throws IllegalStateException
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180 SequenceSet target = (SequenceSet) object;
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181 return target.getSequence();
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184 public void setValue(java.lang.Object object, java.lang.Object value)
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185 throws IllegalStateException, IllegalArgumentException
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189 SequenceSet target = (SequenceSet) object;
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191 .addSequence((jalview.schemabinding.version2.Sequence) value);
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192 } catch (java.lang.Exception ex)
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194 throw new IllegalStateException(ex.toString());
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198 public void resetValue(Object object) throws IllegalStateException,
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199 IllegalArgumentException
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203 SequenceSet target = (SequenceSet) object;
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204 target.removeAllSequence();
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205 } catch (java.lang.Exception ex)
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207 throw new IllegalStateException(ex.toString());
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211 public java.lang.Object newInstance(java.lang.Object parent)
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213 return new jalview.schemabinding.version2.Sequence();
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216 desc.setHandler(handler);
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217 desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
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218 desc.setMultivalued(true);
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219 addFieldDescriptor(desc);
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221 // -- validation code for: _sequenceList
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222 fieldValidator = new org.exolab.castor.xml.FieldValidator();
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223 fieldValidator.setMinOccurs(0);
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224 { // -- local scope
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226 desc.setValidator(fieldValidator);
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227 // -- _annotationList
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228 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
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229 jalview.schemabinding.version2.Annotation.class,
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230 "_annotationList", "Annotation",
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231 org.exolab.castor.xml.NodeType.Element);
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232 handler = new org.exolab.castor.xml.XMLFieldHandler()
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234 public java.lang.Object getValue(java.lang.Object object)
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235 throws IllegalStateException
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237 SequenceSet target = (SequenceSet) object;
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238 return target.getAnnotation();
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241 public void setValue(java.lang.Object object, java.lang.Object value)
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242 throws IllegalStateException, IllegalArgumentException
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246 SequenceSet target = (SequenceSet) object;
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248 .addAnnotation((jalview.schemabinding.version2.Annotation) value);
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249 } catch (java.lang.Exception ex)
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251 throw new IllegalStateException(ex.toString());
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255 public void resetValue(Object object) throws IllegalStateException,
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256 IllegalArgumentException
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260 SequenceSet target = (SequenceSet) object;
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261 target.removeAllAnnotation();
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262 } catch (java.lang.Exception ex)
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264 throw new IllegalStateException(ex.toString());
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268 public java.lang.Object newInstance(java.lang.Object parent)
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270 return new jalview.schemabinding.version2.Annotation();
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273 desc.setHandler(handler);
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274 desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
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275 desc.setMultivalued(true);
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276 addFieldDescriptor(desc);
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278 // -- validation code for: _annotationList
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279 fieldValidator = new org.exolab.castor.xml.FieldValidator();
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280 fieldValidator.setMinOccurs(0);
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281 { // -- local scope
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283 desc.setValidator(fieldValidator);
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284 // -- _sequenceSetPropertiesList
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285 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
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286 jalview.schemabinding.version2.SequenceSetProperties.class,
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287 "_sequenceSetPropertiesList", "sequenceSetProperties",
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288 org.exolab.castor.xml.NodeType.Element);
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289 handler = new org.exolab.castor.xml.XMLFieldHandler()
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291 public java.lang.Object getValue(java.lang.Object object)
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292 throws IllegalStateException
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294 SequenceSet target = (SequenceSet) object;
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295 return target.getSequenceSetProperties();
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298 public void setValue(java.lang.Object object, java.lang.Object value)
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299 throws IllegalStateException, IllegalArgumentException
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303 SequenceSet target = (SequenceSet) object;
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305 .addSequenceSetProperties((jalview.schemabinding.version2.SequenceSetProperties) value);
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306 } 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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317 SequenceSet target = (SequenceSet) object;
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318 target.removeAllSequenceSetProperties();
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319 } catch (java.lang.Exception ex)
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321 throw new IllegalStateException(ex.toString());
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325 public java.lang.Object newInstance(java.lang.Object parent)
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327 return new jalview.schemabinding.version2.SequenceSetProperties();
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330 desc.setHandler(handler);
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331 desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
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332 desc.setMultivalued(true);
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333 addFieldDescriptor(desc);
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335 // -- validation code for: _sequenceSetPropertiesList
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336 fieldValidator = new org.exolab.castor.xml.FieldValidator();
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337 fieldValidator.setMinOccurs(0);
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338 { // -- local scope
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340 desc.setValidator(fieldValidator);
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341 // -- _alcodonFrameList
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342 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
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343 jalview.schemabinding.version2.AlcodonFrame.class,
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344 "_alcodonFrameList", "AlcodonFrame",
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345 org.exolab.castor.xml.NodeType.Element);
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346 handler = new org.exolab.castor.xml.XMLFieldHandler()
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348 public java.lang.Object getValue(java.lang.Object object)
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349 throws IllegalStateException
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351 SequenceSet target = (SequenceSet) object;
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352 return target.getAlcodonFrame();
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355 public void setValue(java.lang.Object object, java.lang.Object value)
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356 throws IllegalStateException, IllegalArgumentException
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360 SequenceSet target = (SequenceSet) object;
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362 .addAlcodonFrame((jalview.schemabinding.version2.AlcodonFrame) value);
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363 } catch (java.lang.Exception ex)
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365 throw new IllegalStateException(ex.toString());
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369 public void resetValue(Object object) throws IllegalStateException,
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370 IllegalArgumentException
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374 SequenceSet target = (SequenceSet) object;
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375 target.removeAllAlcodonFrame();
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376 } catch (java.lang.Exception ex)
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378 throw new IllegalStateException(ex.toString());
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382 public java.lang.Object newInstance(java.lang.Object parent)
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384 return new jalview.schemabinding.version2.AlcodonFrame();
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387 desc.setHandler(handler);
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388 desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
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389 desc.setMultivalued(true);
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390 addFieldDescriptor(desc);
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392 // -- validation code for: _alcodonFrameList
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393 fieldValidator = new org.exolab.castor.xml.FieldValidator();
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394 fieldValidator.setMinOccurs(0);
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395 { // -- local scope
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397 desc.setValidator(fieldValidator);
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405 * Method getAccessMode.
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407 * @return the access mode specified for this class.
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409 public org.exolab.castor.mapping.AccessMode getAccessMode()
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415 * Method getIdentity.
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417 * @return the identity field, null if this class has no identity.
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419 public org.exolab.castor.mapping.FieldDescriptor getIdentity()
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421 return super.getIdentity();
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425 * Method getJavaClass.
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427 * @return the Java class represented by this descriptor.
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429 public java.lang.Class getJavaClass()
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431 return jalview.schemabinding.version2.SequenceSet.class;
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435 * Method getNameSpacePrefix.
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437 * @return the namespace prefix to use when marshaling as XML.
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439 public java.lang.String getNameSpacePrefix()
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445 * Method getNameSpaceURI.
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447 * @return the namespace URI used when marshaling and unmarshaling as XML.
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449 public java.lang.String getNameSpaceURI()
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455 * Method getValidator.
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457 * @return a specific validator for the class described by this
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460 public org.exolab.castor.xml.TypeValidator getValidator()
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466 * Method getXMLName.
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468 * @return the XML Name for the Class being described.
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470 public java.lang.String getXMLName()
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476 * Method isElementDefinition.
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478 * @return true if XML schema definition of this Class is that of a global
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479 * element or element with anonymous type definition.
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481 public boolean isElementDefinition()
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483 return _elementDefinition;
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