2 * Jalview - A Sequence Alignment Editor and Viewer (Development 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.SequenceSet;
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28 * Class SequenceSetDescriptor.
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30 * @version $Revision$ $Date$
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32 public class SequenceSetDescriptor 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 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(java.lang.String.class, "_gapChar", "gapChar", org.exolab.castor.xml.NodeType.Attribute);
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79 desc.setImmutable(true);
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80 handler = new org.exolab.castor.xml.XMLFieldHandler() {
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81 public java.lang.Object getValue( java.lang.Object object )
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82 throws IllegalStateException
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84 SequenceSet target = (SequenceSet) object;
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85 return target.getGapChar();
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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 SequenceSet target = (SequenceSet) object;
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92 target.setGapChar( (java.lang.String) value);
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93 } catch (java.lang.Exception ex) {
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94 throw new IllegalStateException(ex.toString());
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97 public java.lang.Object newInstance(java.lang.Object parent) {
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101 desc.setHandler(handler);
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102 desc.setRequired(true);
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103 desc.setMultivalued(false);
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104 addFieldDescriptor(desc);
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106 //-- validation code for: _gapChar
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107 fieldValidator = new org.exolab.castor.xml.FieldValidator();
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108 fieldValidator.setMinOccurs(1);
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110 org.exolab.castor.xml.validators.StringValidator typeValidator;
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111 typeValidator = new org.exolab.castor.xml.validators.StringValidator();
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112 fieldValidator.setValidator(typeValidator);
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113 typeValidator.setWhiteSpace("preserve");
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115 desc.setValidator(fieldValidator);
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117 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_datasetId", "datasetId", org.exolab.castor.xml.NodeType.Attribute);
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118 desc.setImmutable(true);
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119 handler = new org.exolab.castor.xml.XMLFieldHandler() {
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120 public java.lang.Object getValue( java.lang.Object object )
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121 throws IllegalStateException
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123 SequenceSet target = (SequenceSet) object;
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124 return target.getDatasetId();
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126 public void setValue( java.lang.Object object, java.lang.Object value)
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127 throws IllegalStateException, IllegalArgumentException
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130 SequenceSet target = (SequenceSet) object;
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131 target.setDatasetId( (java.lang.String) value);
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132 } catch (java.lang.Exception ex) {
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133 throw new IllegalStateException(ex.toString());
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136 public java.lang.Object newInstance(java.lang.Object parent) {
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140 desc.setHandler(handler);
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141 desc.setMultivalued(false);
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142 addFieldDescriptor(desc);
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144 //-- validation code for: _datasetId
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145 fieldValidator = new org.exolab.castor.xml.FieldValidator();
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147 org.exolab.castor.xml.validators.StringValidator typeValidator;
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148 typeValidator = new org.exolab.castor.xml.validators.StringValidator();
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149 fieldValidator.setValidator(typeValidator);
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150 typeValidator.setWhiteSpace("preserve");
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152 desc.setValidator(fieldValidator);
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153 //-- initialize element descriptors
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156 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Sequence.class, "_sequenceList", "Sequence", org.exolab.castor.xml.NodeType.Element);
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157 handler = new org.exolab.castor.xml.XMLFieldHandler() {
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158 public java.lang.Object getValue( java.lang.Object object )
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159 throws IllegalStateException
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161 SequenceSet target = (SequenceSet) object;
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162 return target.getSequence();
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164 public void setValue( java.lang.Object object, java.lang.Object value)
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165 throws IllegalStateException, IllegalArgumentException
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168 SequenceSet target = (SequenceSet) object;
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169 target.addSequence( (jalview.schemabinding.version2.Sequence) value);
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170 } catch (java.lang.Exception ex) {
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171 throw new IllegalStateException(ex.toString());
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174 public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {
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176 SequenceSet target = (SequenceSet) object;
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177 target.removeAllSequence();
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178 } catch (java.lang.Exception ex) {
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179 throw new IllegalStateException(ex.toString());
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182 public java.lang.Object newInstance(java.lang.Object parent) {
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183 return new jalview.schemabinding.version2.Sequence();
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186 desc.setHandler(handler);
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187 desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
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188 desc.setMultivalued(true);
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189 addFieldDescriptor(desc);
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191 //-- validation code for: _sequenceList
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192 fieldValidator = new org.exolab.castor.xml.FieldValidator();
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193 fieldValidator.setMinOccurs(0);
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196 desc.setValidator(fieldValidator);
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197 //-- _annotationList
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198 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Annotation.class, "_annotationList", "Annotation", org.exolab.castor.xml.NodeType.Element);
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199 handler = new org.exolab.castor.xml.XMLFieldHandler() {
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200 public java.lang.Object getValue( java.lang.Object object )
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201 throws IllegalStateException
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203 SequenceSet target = (SequenceSet) object;
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204 return target.getAnnotation();
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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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210 SequenceSet target = (SequenceSet) object;
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211 target.addAnnotation( (jalview.schemabinding.version2.Annotation) value);
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212 } catch (java.lang.Exception ex) {
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213 throw new IllegalStateException(ex.toString());
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216 public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {
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218 SequenceSet target = (SequenceSet) object;
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219 target.removeAllAnnotation();
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220 } catch (java.lang.Exception ex) {
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221 throw new IllegalStateException(ex.toString());
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224 public java.lang.Object newInstance(java.lang.Object parent) {
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225 return new jalview.schemabinding.version2.Annotation();
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228 desc.setHandler(handler);
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229 desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
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230 desc.setMultivalued(true);
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231 addFieldDescriptor(desc);
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233 //-- validation code for: _annotationList
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234 fieldValidator = new org.exolab.castor.xml.FieldValidator();
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235 fieldValidator.setMinOccurs(0);
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238 desc.setValidator(fieldValidator);
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239 //-- _sequenceSetPropertiesList
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240 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.SequenceSetProperties.class, "_sequenceSetPropertiesList", "sequenceSetProperties", org.exolab.castor.xml.NodeType.Element);
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241 handler = new org.exolab.castor.xml.XMLFieldHandler() {
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242 public java.lang.Object getValue( java.lang.Object object )
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243 throws IllegalStateException
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245 SequenceSet target = (SequenceSet) object;
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246 return target.getSequenceSetProperties();
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248 public void setValue( java.lang.Object object, java.lang.Object value)
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249 throws IllegalStateException, IllegalArgumentException
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252 SequenceSet target = (SequenceSet) object;
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253 target.addSequenceSetProperties( (jalview.schemabinding.version2.SequenceSetProperties) value);
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254 } catch (java.lang.Exception ex) {
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255 throw new IllegalStateException(ex.toString());
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258 public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {
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260 SequenceSet target = (SequenceSet) object;
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261 target.removeAllSequenceSetProperties();
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262 } catch (java.lang.Exception ex) {
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263 throw new IllegalStateException(ex.toString());
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266 public java.lang.Object newInstance(java.lang.Object parent) {
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267 return new jalview.schemabinding.version2.SequenceSetProperties();
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270 desc.setHandler(handler);
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271 desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
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272 desc.setMultivalued(true);
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273 addFieldDescriptor(desc);
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275 //-- validation code for: _sequenceSetPropertiesList
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276 fieldValidator = new org.exolab.castor.xml.FieldValidator();
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277 fieldValidator.setMinOccurs(0);
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280 desc.setValidator(fieldValidator);
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281 //-- _alcodonFrameList
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282 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.AlcodonFrame.class, "_alcodonFrameList", "AlcodonFrame", org.exolab.castor.xml.NodeType.Element);
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283 handler = new org.exolab.castor.xml.XMLFieldHandler() {
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284 public java.lang.Object getValue( java.lang.Object object )
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285 throws IllegalStateException
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287 SequenceSet target = (SequenceSet) object;
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288 return target.getAlcodonFrame();
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290 public void setValue( java.lang.Object object, java.lang.Object value)
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291 throws IllegalStateException, IllegalArgumentException
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294 SequenceSet target = (SequenceSet) object;
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295 target.addAlcodonFrame( (jalview.schemabinding.version2.AlcodonFrame) value);
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296 } catch (java.lang.Exception ex) {
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297 throw new IllegalStateException(ex.toString());
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300 public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {
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302 SequenceSet target = (SequenceSet) object;
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303 target.removeAllAlcodonFrame();
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304 } catch (java.lang.Exception ex) {
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305 throw new IllegalStateException(ex.toString());
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308 public java.lang.Object newInstance(java.lang.Object parent) {
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309 return new jalview.schemabinding.version2.AlcodonFrame();
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312 desc.setHandler(handler);
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313 desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
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314 desc.setMultivalued(true);
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315 addFieldDescriptor(desc);
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317 //-- validation code for: _alcodonFrameList
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318 fieldValidator = new org.exolab.castor.xml.FieldValidator();
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319 fieldValidator.setMinOccurs(0);
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322 desc.setValidator(fieldValidator);
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331 * Method getAccessMode.
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333 * @return the access mode specified for this class.
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335 public org.exolab.castor.mapping.AccessMode getAccessMode(
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341 * Method getIdentity.
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343 * @return the identity field, null if this class has no
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346 public org.exolab.castor.mapping.FieldDescriptor getIdentity(
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348 return super.getIdentity();
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352 * Method getJavaClass.
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354 * @return the Java class represented by this descriptor.
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356 public java.lang.Class getJavaClass(
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358 return jalview.schemabinding.version2.SequenceSet.class;
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362 * Method getNameSpacePrefix.
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364 * @return the namespace prefix to use when marshaling as XML.
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366 public java.lang.String getNameSpacePrefix(
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372 * Method getNameSpaceURI.
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374 * @return the namespace URI used when marshaling and
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375 * unmarshaling as XML.
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377 public java.lang.String getNameSpaceURI(
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383 * Method getValidator.
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385 * @return a specific validator for the class described by this
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388 public org.exolab.castor.xml.TypeValidator getValidator(
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394 * Method getXMLName.
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396 * @return the XML Name for the Class being described.
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398 public java.lang.String getXMLName(
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404 * Method isElementDefinition.
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406 * @return true if XML schema definition of this Class is that
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408 * element or element with anonymous type definition.
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410 public boolean isElementDefinition(
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412 return _elementDefinition;
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