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.JSeq;
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28 * Class JSeqDescriptor.
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30 * @version $Revision$ $Date$
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32 public class JSeqDescriptor 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 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(java.lang.Integer.TYPE, "_colour", "colour", 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 JSeq target = (JSeq) object;
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84 if (!target.hasColour()) { return null; }
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85 return new java.lang.Integer(target.getColour());
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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 JSeq target = (JSeq) object;
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92 // if null, use delete method for optional primitives
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93 if (value == null) {
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94 target.deleteColour();
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97 target.setColour( ((java.lang.Integer) value).intValue());
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98 } catch (java.lang.Exception ex) {
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99 throw new IllegalStateException(ex.toString());
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102 public java.lang.Object newInstance(java.lang.Object parent) {
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106 desc.setHandler(handler);
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107 desc.setMultivalued(false);
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108 addFieldDescriptor(desc);
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110 //-- validation code for: _colour
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111 fieldValidator = new org.exolab.castor.xml.FieldValidator();
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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, "_start", "start", 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 JSeq target = (JSeq) object;
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127 if (!target.hasStart()) { return null; }
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128 return new java.lang.Integer(target.getStart());
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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 JSeq target = (JSeq) 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.setStart( ((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: _start
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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.Integer.TYPE, "_end", "end", org.exolab.castor.xml.NodeType.Attribute);
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165 handler = new org.exolab.castor.xml.XMLFieldHandler() {
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166 public java.lang.Object getValue( java.lang.Object object )
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167 throws IllegalStateException
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169 JSeq target = (JSeq) object;
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170 if (!target.hasEnd()) { return null; }
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171 return new java.lang.Integer(target.getEnd());
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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 JSeq target = (JSeq) object;
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178 // ignore null values for non optional primitives
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179 if (value == null) { return; }
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181 target.setEnd( ((java.lang.Integer) value).intValue());
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182 } catch (java.lang.Exception ex) {
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183 throw new IllegalStateException(ex.toString());
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186 public java.lang.Object newInstance(java.lang.Object parent) {
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190 desc.setHandler(handler);
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191 desc.setRequired(true);
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192 desc.setMultivalued(false);
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193 addFieldDescriptor(desc);
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195 //-- validation code for: _end
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196 fieldValidator = new org.exolab.castor.xml.FieldValidator();
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197 fieldValidator.setMinOccurs(1);
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199 org.exolab.castor.xml.validators.IntValidator typeValidator;
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200 typeValidator = new org.exolab.castor.xml.validators.IntValidator();
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201 fieldValidator.setValidator(typeValidator);
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202 typeValidator.setMinInclusive(-2147483648);
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203 typeValidator.setMaxInclusive(2147483647);
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205 desc.setValidator(fieldValidator);
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207 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute);
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208 desc.setImmutable(true);
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209 handler = new org.exolab.castor.xml.XMLFieldHandler() {
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210 public java.lang.Object getValue( java.lang.Object object )
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211 throws IllegalStateException
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213 JSeq target = (JSeq) object;
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214 return target.getId();
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216 public void setValue( java.lang.Object object, java.lang.Object value)
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217 throws IllegalStateException, IllegalArgumentException
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220 JSeq target = (JSeq) object;
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221 target.setId( (java.lang.String) value);
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222 } catch (java.lang.Exception ex) {
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223 throw new IllegalStateException(ex.toString());
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226 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: _id
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236 fieldValidator = new org.exolab.castor.xml.FieldValidator();
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237 fieldValidator.setMinOccurs(1);
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239 org.exolab.castor.xml.validators.StringValidator typeValidator;
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240 typeValidator = new org.exolab.castor.xml.validators.StringValidator();
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241 fieldValidator.setValidator(typeValidator);
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242 typeValidator.setWhiteSpace("preserve");
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244 desc.setValidator(fieldValidator);
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246 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_hidden", "hidden", org.exolab.castor.xml.NodeType.Attribute);
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247 handler = new org.exolab.castor.xml.XMLFieldHandler() {
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248 public java.lang.Object getValue( java.lang.Object object )
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249 throws IllegalStateException
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251 JSeq target = (JSeq) object;
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252 if (!target.hasHidden()) { return null; }
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253 return (target.getHidden() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
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255 public void setValue( java.lang.Object object, java.lang.Object value)
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256 throws IllegalStateException, IllegalArgumentException
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259 JSeq target = (JSeq) object;
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260 // if null, use delete method for optional primitives
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261 if (value == null) {
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262 target.deleteHidden();
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265 target.setHidden( ((java.lang.Boolean) value).booleanValue());
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266 } catch (java.lang.Exception ex) {
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267 throw new IllegalStateException(ex.toString());
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270 public java.lang.Object newInstance(java.lang.Object parent) {
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274 desc.setHandler(handler);
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275 desc.setMultivalued(false);
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276 addFieldDescriptor(desc);
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278 //-- validation code for: _hidden
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279 fieldValidator = new org.exolab.castor.xml.FieldValidator();
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281 org.exolab.castor.xml.validators.BooleanValidator typeValidator;
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282 typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
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283 fieldValidator.setValidator(typeValidator);
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285 desc.setValidator(fieldValidator);
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286 //-- initialize element descriptors
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289 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Features.class, "_featuresList", "features", org.exolab.castor.xml.NodeType.Element);
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290 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 JSeq target = (JSeq) object;
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295 return target.getFeatures();
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297 public void setValue( java.lang.Object object, java.lang.Object value)
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298 throws IllegalStateException, IllegalArgumentException
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301 JSeq target = (JSeq) object;
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302 target.addFeatures( (jalview.schemabinding.version2.Features) value);
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303 } catch (java.lang.Exception ex) {
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304 throw new IllegalStateException(ex.toString());
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307 public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {
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309 JSeq target = (JSeq) object;
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310 target.removeAllFeatures();
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311 } catch (java.lang.Exception ex) {
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312 throw new IllegalStateException(ex.toString());
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315 public java.lang.Object newInstance(java.lang.Object parent) {
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316 return new jalview.schemabinding.version2.Features();
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319 desc.setHandler(handler);
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320 desc.setNameSpaceURI("www.jalview.org");
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321 desc.setMultivalued(true);
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322 addFieldDescriptor(desc);
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324 //-- validation code for: _featuresList
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325 fieldValidator = new org.exolab.castor.xml.FieldValidator();
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326 fieldValidator.setMinOccurs(0);
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329 desc.setValidator(fieldValidator);
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331 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Pdbids.class, "_pdbidsList", "pdbids", org.exolab.castor.xml.NodeType.Element);
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332 handler = new org.exolab.castor.xml.XMLFieldHandler() {
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333 public java.lang.Object getValue( java.lang.Object object )
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334 throws IllegalStateException
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336 JSeq target = (JSeq) object;
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337 return target.getPdbids();
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339 public void setValue( java.lang.Object object, java.lang.Object value)
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340 throws IllegalStateException, IllegalArgumentException
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343 JSeq target = (JSeq) object;
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344 target.addPdbids( (jalview.schemabinding.version2.Pdbids) value);
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345 } catch (java.lang.Exception ex) {
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346 throw new IllegalStateException(ex.toString());
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349 public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {
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351 JSeq target = (JSeq) object;
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352 target.removeAllPdbids();
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353 } catch (java.lang.Exception ex) {
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354 throw new IllegalStateException(ex.toString());
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357 public java.lang.Object newInstance(java.lang.Object parent) {
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358 return new jalview.schemabinding.version2.Pdbids();
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361 desc.setHandler(handler);
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362 desc.setNameSpaceURI("www.jalview.org");
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363 desc.setMultivalued(true);
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364 addFieldDescriptor(desc);
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366 //-- validation code for: _pdbidsList
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367 fieldValidator = new org.exolab.castor.xml.FieldValidator();
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368 fieldValidator.setMinOccurs(0);
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371 desc.setValidator(fieldValidator);
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372 //-- _hiddenSequencesList
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373 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_hiddenSequencesList", "hiddenSequences", org.exolab.castor.xml.NodeType.Element);
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374 handler = new org.exolab.castor.xml.XMLFieldHandler() {
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375 public java.lang.Object getValue( java.lang.Object object )
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376 throws IllegalStateException
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378 JSeq target = (JSeq) object;
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379 return target.getHiddenSequences();
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381 public void setValue( java.lang.Object object, java.lang.Object value)
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382 throws IllegalStateException, IllegalArgumentException
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385 JSeq target = (JSeq) object;
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386 // ignore null values for non optional primitives
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387 if (value == null) { return; }
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389 target.addHiddenSequences( ((java.lang.Integer) value).intValue());
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390 } catch (java.lang.Exception ex) {
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391 throw new IllegalStateException(ex.toString());
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394 public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {
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396 JSeq target = (JSeq) object;
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397 target.removeAllHiddenSequences();
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398 } catch (java.lang.Exception ex) {
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399 throw new IllegalStateException(ex.toString());
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402 public java.lang.Object newInstance(java.lang.Object parent) {
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406 desc.setHandler(handler);
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407 desc.setNameSpaceURI("www.jalview.org");
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408 desc.setMultivalued(true);
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409 addFieldDescriptor(desc);
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411 //-- validation code for: _hiddenSequencesList
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412 fieldValidator = new org.exolab.castor.xml.FieldValidator();
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413 fieldValidator.setMinOccurs(0);
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415 org.exolab.castor.xml.validators.IntValidator typeValidator;
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416 typeValidator = new org.exolab.castor.xml.validators.IntValidator();
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417 fieldValidator.setValidator(typeValidator);
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418 typeValidator.setMinInclusive(-2147483648);
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419 typeValidator.setMaxInclusive(2147483647);
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421 desc.setValidator(fieldValidator);
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430 * Method getAccessMode.
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432 * @return the access mode specified for this class.
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434 public org.exolab.castor.mapping.AccessMode getAccessMode(
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440 * Method getIdentity.
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442 * @return the identity field, null if this class has no
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445 public org.exolab.castor.mapping.FieldDescriptor getIdentity(
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447 return super.getIdentity();
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451 * Method getJavaClass.
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453 * @return the Java class represented by this descriptor.
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455 public java.lang.Class getJavaClass(
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457 return jalview.schemabinding.version2.JSeq.class;
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461 * Method getNameSpacePrefix.
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463 * @return the namespace prefix to use when marshaling as XML.
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465 public java.lang.String getNameSpacePrefix(
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471 * Method getNameSpaceURI.
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473 * @return the namespace URI used when marshaling and
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474 * unmarshaling as XML.
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476 public java.lang.String getNameSpaceURI(
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482 * Method getValidator.
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484 * @return a specific validator for the class described by this
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487 public org.exolab.castor.xml.TypeValidator getValidator(
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493 * Method getXMLName.
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495 * @return the XML Name for the Class being described.
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497 public java.lang.String getXMLName(
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503 * Method isElementDefinition.
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505 * @return true if XML schema definition of this Class is that
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507 * element or element with anonymous type definition.
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509 public boolean isElementDefinition(
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511 return _elementDefinition;
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