2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
3 * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
11 * Jalview is distributed in the hope that it will be useful, but
12 * WITHOUT ANY WARRANTY; without even the implied warranty
13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
14 * PURPOSE. See the GNU General Public License for more details.
16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
18 package jalview.schemabinding.version2.descriptors;
20 //---------------------------------/
21 //- Imported classes and packages -/
22 //---------------------------------/
24 import jalview.schemabinding.version2.Annotation;
27 * Class AnnotationDescriptor.
29 * @version $Revision$ $Date$
31 public class AnnotationDescriptor extends
32 org.exolab.castor.xml.util.XMLClassDescriptorImpl
35 // --------------------------/
36 // - Class/Member Variables -/
37 // --------------------------/
40 * Field _elementDefinition.
42 private boolean _elementDefinition;
47 private java.lang.String _nsPrefix;
52 private java.lang.String _nsURI;
57 private java.lang.String _xmlName;
63 public AnnotationDescriptor()
66 _nsURI = "www.vamsas.ac.uk/jalview/version2";
67 _xmlName = "Annotation";
68 _elementDefinition = true;
70 // -- set grouping compositor
71 setCompositorAsSequence();
72 org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
73 org.exolab.castor.mapping.FieldHandler handler = null;
74 org.exolab.castor.xml.FieldValidator fieldValidator = null;
75 // -- initialize attribute descriptors
78 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
79 java.lang.Boolean.TYPE, "_graph", "graph",
80 org.exolab.castor.xml.NodeType.Attribute);
81 handler = new org.exolab.castor.xml.XMLFieldHandler()
83 public java.lang.Object getValue(java.lang.Object object)
84 throws IllegalStateException
86 Annotation target = (Annotation) object;
87 if (!target.hasGraph())
91 return (target.getGraph() ? java.lang.Boolean.TRUE
92 : java.lang.Boolean.FALSE);
95 public void setValue(java.lang.Object object, java.lang.Object value)
96 throws IllegalStateException, IllegalArgumentException
100 Annotation target = (Annotation) object;
101 // ignore null values for non optional primitives
107 target.setGraph(((java.lang.Boolean) value).booleanValue());
108 } catch (java.lang.Exception ex)
110 throw new IllegalStateException(ex.toString());
114 public java.lang.Object newInstance(java.lang.Object parent)
119 desc.setHandler(handler);
120 desc.setRequired(true);
121 desc.setMultivalued(false);
122 addFieldDescriptor(desc);
124 // -- validation code for: _graph
125 fieldValidator = new org.exolab.castor.xml.FieldValidator();
126 fieldValidator.setMinOccurs(1);
128 org.exolab.castor.xml.validators.BooleanValidator typeValidator;
129 typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
130 fieldValidator.setValidator(typeValidator);
132 desc.setValidator(fieldValidator);
134 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
135 java.lang.Integer.TYPE, "_graphType", "graphType",
136 org.exolab.castor.xml.NodeType.Attribute);
137 handler = new org.exolab.castor.xml.XMLFieldHandler()
139 public java.lang.Object getValue(java.lang.Object object)
140 throws IllegalStateException
142 Annotation target = (Annotation) object;
143 if (!target.hasGraphType())
147 return new java.lang.Integer(target.getGraphType());
150 public void setValue(java.lang.Object object, java.lang.Object value)
151 throws IllegalStateException, IllegalArgumentException
155 Annotation target = (Annotation) object;
156 // if null, use delete method for optional primitives
159 target.deleteGraphType();
162 target.setGraphType(((java.lang.Integer) value).intValue());
163 } catch (java.lang.Exception ex)
165 throw new IllegalStateException(ex.toString());
169 public java.lang.Object newInstance(java.lang.Object parent)
174 desc.setHandler(handler);
175 desc.setMultivalued(false);
176 addFieldDescriptor(desc);
178 // -- validation code for: _graphType
179 fieldValidator = new org.exolab.castor.xml.FieldValidator();
181 org.exolab.castor.xml.validators.IntValidator typeValidator;
182 typeValidator = new org.exolab.castor.xml.validators.IntValidator();
183 fieldValidator.setValidator(typeValidator);
184 typeValidator.setMinInclusive(-2147483648);
185 typeValidator.setMaxInclusive(2147483647);
187 desc.setValidator(fieldValidator);
189 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
190 java.lang.String.class, "_sequenceRef", "sequenceRef",
191 org.exolab.castor.xml.NodeType.Attribute);
192 desc.setImmutable(true);
193 handler = new org.exolab.castor.xml.XMLFieldHandler()
195 public java.lang.Object getValue(java.lang.Object object)
196 throws IllegalStateException
198 Annotation target = (Annotation) object;
199 return target.getSequenceRef();
202 public void setValue(java.lang.Object object, java.lang.Object value)
203 throws IllegalStateException, IllegalArgumentException
207 Annotation target = (Annotation) object;
208 target.setSequenceRef((java.lang.String) value);
209 } catch (java.lang.Exception ex)
211 throw new IllegalStateException(ex.toString());
215 public java.lang.Object newInstance(java.lang.Object parent)
220 desc.setHandler(handler);
221 desc.setMultivalued(false);
222 addFieldDescriptor(desc);
224 // -- validation code for: _sequenceRef
225 fieldValidator = new org.exolab.castor.xml.FieldValidator();
227 org.exolab.castor.xml.validators.StringValidator typeValidator;
228 typeValidator = new org.exolab.castor.xml.validators.StringValidator();
229 fieldValidator.setValidator(typeValidator);
230 typeValidator.setWhiteSpace("preserve");
232 desc.setValidator(fieldValidator);
234 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
235 java.lang.String.class, "_groupRef", "groupRef",
236 org.exolab.castor.xml.NodeType.Attribute);
237 desc.setImmutable(true);
238 handler = new org.exolab.castor.xml.XMLFieldHandler()
240 public java.lang.Object getValue(java.lang.Object object)
241 throws IllegalStateException
243 Annotation target = (Annotation) object;
244 return target.getGroupRef();
247 public void setValue(java.lang.Object object, java.lang.Object value)
248 throws IllegalStateException, IllegalArgumentException
252 Annotation target = (Annotation) object;
253 target.setGroupRef((java.lang.String) value);
254 } catch (java.lang.Exception ex)
256 throw new IllegalStateException(ex.toString());
260 public java.lang.Object newInstance(java.lang.Object parent)
265 desc.setHandler(handler);
266 desc.setMultivalued(false);
267 addFieldDescriptor(desc);
269 // -- validation code for: _groupRef
270 fieldValidator = new org.exolab.castor.xml.FieldValidator();
272 org.exolab.castor.xml.validators.StringValidator typeValidator;
273 typeValidator = new org.exolab.castor.xml.validators.StringValidator();
274 fieldValidator.setValidator(typeValidator);
275 typeValidator.setWhiteSpace("preserve");
277 desc.setValidator(fieldValidator);
279 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
280 java.lang.Integer.TYPE, "_graphColour", "graphColour",
281 org.exolab.castor.xml.NodeType.Attribute);
282 handler = new org.exolab.castor.xml.XMLFieldHandler()
284 public java.lang.Object getValue(java.lang.Object object)
285 throws IllegalStateException
287 Annotation target = (Annotation) object;
288 if (!target.hasGraphColour())
292 return new java.lang.Integer(target.getGraphColour());
295 public void setValue(java.lang.Object object, java.lang.Object value)
296 throws IllegalStateException, IllegalArgumentException
300 Annotation target = (Annotation) object;
301 // if null, use delete method for optional primitives
304 target.deleteGraphColour();
307 target.setGraphColour(((java.lang.Integer) value).intValue());
308 } catch (java.lang.Exception ex)
310 throw new IllegalStateException(ex.toString());
314 public java.lang.Object newInstance(java.lang.Object parent)
319 desc.setHandler(handler);
320 desc.setMultivalued(false);
321 addFieldDescriptor(desc);
323 // -- validation code for: _graphColour
324 fieldValidator = new org.exolab.castor.xml.FieldValidator();
326 org.exolab.castor.xml.validators.IntValidator typeValidator;
327 typeValidator = new org.exolab.castor.xml.validators.IntValidator();
328 fieldValidator.setValidator(typeValidator);
329 typeValidator.setMinInclusive(-2147483648);
330 typeValidator.setMaxInclusive(2147483647);
332 desc.setValidator(fieldValidator);
334 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
335 java.lang.Integer.TYPE, "_graphGroup", "graphGroup",
336 org.exolab.castor.xml.NodeType.Attribute);
337 handler = new org.exolab.castor.xml.XMLFieldHandler()
339 public java.lang.Object getValue(java.lang.Object object)
340 throws IllegalStateException
342 Annotation target = (Annotation) object;
343 if (!target.hasGraphGroup())
347 return new java.lang.Integer(target.getGraphGroup());
350 public void setValue(java.lang.Object object, java.lang.Object value)
351 throws IllegalStateException, IllegalArgumentException
355 Annotation target = (Annotation) object;
356 // if null, use delete method for optional primitives
359 target.deleteGraphGroup();
362 target.setGraphGroup(((java.lang.Integer) value).intValue());
363 } catch (java.lang.Exception ex)
365 throw new IllegalStateException(ex.toString());
369 public java.lang.Object newInstance(java.lang.Object parent)
374 desc.setHandler(handler);
375 desc.setMultivalued(false);
376 addFieldDescriptor(desc);
378 // -- validation code for: _graphGroup
379 fieldValidator = new org.exolab.castor.xml.FieldValidator();
381 org.exolab.castor.xml.validators.IntValidator typeValidator;
382 typeValidator = new org.exolab.castor.xml.validators.IntValidator();
383 fieldValidator.setValidator(typeValidator);
384 typeValidator.setMinInclusive(-2147483648);
385 typeValidator.setMaxInclusive(2147483647);
387 desc.setValidator(fieldValidator);
389 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
390 java.lang.Integer.TYPE, "_graphHeight", "graphHeight",
391 org.exolab.castor.xml.NodeType.Attribute);
392 handler = new org.exolab.castor.xml.XMLFieldHandler()
394 public java.lang.Object getValue(java.lang.Object object)
395 throws IllegalStateException
397 Annotation target = (Annotation) object;
398 if (!target.hasGraphHeight())
402 return new java.lang.Integer(target.getGraphHeight());
405 public void setValue(java.lang.Object object, java.lang.Object value)
406 throws IllegalStateException, IllegalArgumentException
410 Annotation target = (Annotation) object;
411 // if null, use delete method for optional primitives
414 target.deleteGraphHeight();
417 target.setGraphHeight(((java.lang.Integer) value).intValue());
418 } catch (java.lang.Exception ex)
420 throw new IllegalStateException(ex.toString());
424 public java.lang.Object newInstance(java.lang.Object parent)
429 desc.setHandler(handler);
430 desc.setMultivalued(false);
431 addFieldDescriptor(desc);
433 // -- validation code for: _graphHeight
434 fieldValidator = new org.exolab.castor.xml.FieldValidator();
436 org.exolab.castor.xml.validators.IntValidator typeValidator;
437 typeValidator = new org.exolab.castor.xml.validators.IntValidator();
438 fieldValidator.setValidator(typeValidator);
439 typeValidator.setMinInclusive(-2147483648);
440 typeValidator.setMaxInclusive(2147483647);
442 desc.setValidator(fieldValidator);
444 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
445 java.lang.String.class, "_id", "id",
446 org.exolab.castor.xml.NodeType.Attribute);
447 desc.setImmutable(true);
448 handler = new org.exolab.castor.xml.XMLFieldHandler()
450 public java.lang.Object getValue(java.lang.Object object)
451 throws IllegalStateException
453 Annotation target = (Annotation) object;
454 return target.getId();
457 public void setValue(java.lang.Object object, java.lang.Object value)
458 throws IllegalStateException, IllegalArgumentException
462 Annotation target = (Annotation) object;
463 target.setId((java.lang.String) value);
464 } catch (java.lang.Exception ex)
466 throw new IllegalStateException(ex.toString());
470 public java.lang.Object newInstance(java.lang.Object parent)
475 desc.setHandler(handler);
476 desc.setMultivalued(false);
477 addFieldDescriptor(desc);
479 // -- validation code for: _id
480 fieldValidator = new org.exolab.castor.xml.FieldValidator();
482 org.exolab.castor.xml.validators.StringValidator typeValidator;
483 typeValidator = new org.exolab.castor.xml.validators.StringValidator();
484 fieldValidator.setValidator(typeValidator);
485 typeValidator.setWhiteSpace("preserve");
487 desc.setValidator(fieldValidator);
489 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
490 java.lang.Boolean.TYPE, "_scoreOnly", "scoreOnly",
491 org.exolab.castor.xml.NodeType.Attribute);
492 handler = new org.exolab.castor.xml.XMLFieldHandler()
494 public java.lang.Object getValue(java.lang.Object object)
495 throws IllegalStateException
497 Annotation target = (Annotation) object;
498 if (!target.hasScoreOnly())
502 return (target.getScoreOnly() ? java.lang.Boolean.TRUE
503 : java.lang.Boolean.FALSE);
506 public void setValue(java.lang.Object object, java.lang.Object value)
507 throws IllegalStateException, IllegalArgumentException
511 Annotation target = (Annotation) object;
512 // if null, use delete method for optional primitives
515 target.deleteScoreOnly();
518 target.setScoreOnly(((java.lang.Boolean) value).booleanValue());
519 } catch (java.lang.Exception ex)
521 throw new IllegalStateException(ex.toString());
525 public java.lang.Object newInstance(java.lang.Object parent)
530 desc.setHandler(handler);
531 desc.setMultivalued(false);
532 addFieldDescriptor(desc);
534 // -- validation code for: _scoreOnly
535 fieldValidator = new org.exolab.castor.xml.FieldValidator();
537 org.exolab.castor.xml.validators.BooleanValidator typeValidator;
538 typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
539 fieldValidator.setValidator(typeValidator);
541 desc.setValidator(fieldValidator);
543 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
544 java.lang.Double.TYPE, "_score", "score",
545 org.exolab.castor.xml.NodeType.Attribute);
546 handler = new org.exolab.castor.xml.XMLFieldHandler()
548 public java.lang.Object getValue(java.lang.Object object)
549 throws IllegalStateException
551 Annotation target = (Annotation) object;
552 if (!target.hasScore())
556 return new java.lang.Double(target.getScore());
559 public void setValue(java.lang.Object object, java.lang.Object value)
560 throws IllegalStateException, IllegalArgumentException
564 Annotation target = (Annotation) object;
565 // if null, use delete method for optional primitives
568 target.deleteScore();
571 target.setScore(((java.lang.Double) value).doubleValue());
572 } catch (java.lang.Exception ex)
574 throw new IllegalStateException(ex.toString());
578 public java.lang.Object newInstance(java.lang.Object parent)
583 desc.setHandler(handler);
584 desc.setMultivalued(false);
585 addFieldDescriptor(desc);
587 // -- validation code for: _score
588 fieldValidator = new org.exolab.castor.xml.FieldValidator();
590 org.exolab.castor.xml.validators.DoubleValidator typeValidator;
591 typeValidator = new org.exolab.castor.xml.validators.DoubleValidator();
592 fieldValidator.setValidator(typeValidator);
593 typeValidator.setMinInclusive(-1.7976931348623157E308);
594 typeValidator.setMaxInclusive(1.7976931348623157E308);
596 desc.setValidator(fieldValidator);
598 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
599 java.lang.Boolean.TYPE, "_visible", "visible",
600 org.exolab.castor.xml.NodeType.Attribute);
601 handler = new org.exolab.castor.xml.XMLFieldHandler()
603 public java.lang.Object getValue(java.lang.Object object)
604 throws IllegalStateException
606 Annotation target = (Annotation) object;
607 if (!target.hasVisible())
611 return (target.getVisible() ? java.lang.Boolean.TRUE
612 : java.lang.Boolean.FALSE);
615 public void setValue(java.lang.Object object, java.lang.Object value)
616 throws IllegalStateException, IllegalArgumentException
620 Annotation target = (Annotation) object;
621 // if null, use delete method for optional primitives
624 target.deleteVisible();
627 target.setVisible(((java.lang.Boolean) value).booleanValue());
628 } catch (java.lang.Exception ex)
630 throw new IllegalStateException(ex.toString());
634 public java.lang.Object newInstance(java.lang.Object parent)
639 desc.setHandler(handler);
640 desc.setMultivalued(false);
641 addFieldDescriptor(desc);
643 // -- validation code for: _visible
644 fieldValidator = new org.exolab.castor.xml.FieldValidator();
646 org.exolab.castor.xml.validators.BooleanValidator typeValidator;
647 typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
648 fieldValidator.setValidator(typeValidator);
650 desc.setValidator(fieldValidator);
651 // -- _centreColLabels
652 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
653 java.lang.Boolean.TYPE, "_centreColLabels", "centreColLabels",
654 org.exolab.castor.xml.NodeType.Attribute);
655 handler = new org.exolab.castor.xml.XMLFieldHandler()
657 public java.lang.Object getValue(java.lang.Object object)
658 throws IllegalStateException
660 Annotation target = (Annotation) object;
661 if (!target.hasCentreColLabels())
665 return (target.getCentreColLabels() ? java.lang.Boolean.TRUE
666 : java.lang.Boolean.FALSE);
669 public void setValue(java.lang.Object object, java.lang.Object value)
670 throws IllegalStateException, IllegalArgumentException
674 Annotation target = (Annotation) object;
675 // if null, use delete method for optional primitives
678 target.deleteCentreColLabels();
681 target.setCentreColLabels(((java.lang.Boolean) value)
683 } catch (java.lang.Exception ex)
685 throw new IllegalStateException(ex.toString());
689 public java.lang.Object newInstance(java.lang.Object parent)
694 desc.setHandler(handler);
695 desc.setMultivalued(false);
696 addFieldDescriptor(desc);
698 // -- validation code for: _centreColLabels
699 fieldValidator = new org.exolab.castor.xml.FieldValidator();
701 org.exolab.castor.xml.validators.BooleanValidator typeValidator;
702 typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
703 fieldValidator.setValidator(typeValidator);
705 desc.setValidator(fieldValidator);
706 // -- _scaleColLabels
707 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
708 java.lang.Boolean.TYPE, "_scaleColLabels", "scaleColLabels",
709 org.exolab.castor.xml.NodeType.Attribute);
710 handler = new org.exolab.castor.xml.XMLFieldHandler()
712 public java.lang.Object getValue(java.lang.Object object)
713 throws IllegalStateException
715 Annotation target = (Annotation) object;
716 if (!target.hasScaleColLabels())
720 return (target.getScaleColLabels() ? java.lang.Boolean.TRUE
721 : java.lang.Boolean.FALSE);
724 public void setValue(java.lang.Object object, java.lang.Object value)
725 throws IllegalStateException, IllegalArgumentException
729 Annotation target = (Annotation) object;
730 // if null, use delete method for optional primitives
733 target.deleteScaleColLabels();
736 target.setScaleColLabels(((java.lang.Boolean) value)
738 } catch (java.lang.Exception ex)
740 throw new IllegalStateException(ex.toString());
744 public java.lang.Object newInstance(java.lang.Object parent)
749 desc.setHandler(handler);
750 desc.setMultivalued(false);
751 addFieldDescriptor(desc);
753 // -- validation code for: _scaleColLabels
754 fieldValidator = new org.exolab.castor.xml.FieldValidator();
756 org.exolab.castor.xml.validators.BooleanValidator typeValidator;
757 typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
758 fieldValidator.setValidator(typeValidator);
760 desc.setValidator(fieldValidator);
761 // -- _showAllColLabels
762 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
763 java.lang.Boolean.TYPE, "_showAllColLabels",
764 "showAllColLabels", org.exolab.castor.xml.NodeType.Attribute);
765 handler = new org.exolab.castor.xml.XMLFieldHandler()
767 public java.lang.Object getValue(java.lang.Object object)
768 throws IllegalStateException
770 Annotation target = (Annotation) object;
771 if (!target.hasShowAllColLabels())
775 return (target.getShowAllColLabels() ? java.lang.Boolean.TRUE
776 : java.lang.Boolean.FALSE);
779 public void setValue(java.lang.Object object, java.lang.Object value)
780 throws IllegalStateException, IllegalArgumentException
784 Annotation target = (Annotation) object;
785 // if null, use delete method for optional primitives
788 target.deleteShowAllColLabels();
791 target.setShowAllColLabels(((java.lang.Boolean) value)
793 } catch (java.lang.Exception ex)
795 throw new IllegalStateException(ex.toString());
799 public java.lang.Object newInstance(java.lang.Object parent)
804 desc.setHandler(handler);
805 desc.setMultivalued(false);
806 addFieldDescriptor(desc);
808 // -- validation code for: _showAllColLabels
809 fieldValidator = new org.exolab.castor.xml.FieldValidator();
811 org.exolab.castor.xml.validators.BooleanValidator typeValidator;
812 typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
813 fieldValidator.setValidator(typeValidator);
815 desc.setValidator(fieldValidator);
816 // -- _autoCalculated
817 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
818 java.lang.Boolean.TYPE, "_autoCalculated", "autoCalculated",
819 org.exolab.castor.xml.NodeType.Attribute);
820 handler = new org.exolab.castor.xml.XMLFieldHandler()
822 public java.lang.Object getValue(java.lang.Object object)
823 throws IllegalStateException
825 Annotation target = (Annotation) object;
826 if (!target.hasAutoCalculated())
830 return (target.getAutoCalculated() ? java.lang.Boolean.TRUE
831 : java.lang.Boolean.FALSE);
834 public void setValue(java.lang.Object object, java.lang.Object value)
835 throws IllegalStateException, IllegalArgumentException
839 Annotation target = (Annotation) object;
840 // if null, use delete method for optional primitives
843 target.deleteAutoCalculated();
846 target.setAutoCalculated(((java.lang.Boolean) value)
848 } catch (java.lang.Exception ex)
850 throw new IllegalStateException(ex.toString());
854 public java.lang.Object newInstance(java.lang.Object parent)
859 desc.setHandler(handler);
860 desc.setMultivalued(false);
861 addFieldDescriptor(desc);
863 // -- validation code for: _autoCalculated
864 fieldValidator = new org.exolab.castor.xml.FieldValidator();
866 org.exolab.castor.xml.validators.BooleanValidator typeValidator;
867 typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
868 fieldValidator.setValidator(typeValidator);
870 desc.setValidator(fieldValidator);
871 // -- _belowAlignment
872 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
873 java.lang.Boolean.TYPE, "_belowAlignment", "belowAlignment",
874 org.exolab.castor.xml.NodeType.Attribute);
875 handler = new org.exolab.castor.xml.XMLFieldHandler()
877 public java.lang.Object getValue(java.lang.Object object)
878 throws IllegalStateException
880 Annotation target = (Annotation) object;
881 if (!target.hasBelowAlignment())
885 return (target.getBelowAlignment() ? java.lang.Boolean.TRUE
886 : java.lang.Boolean.FALSE);
889 public void setValue(java.lang.Object object, java.lang.Object value)
890 throws IllegalStateException, IllegalArgumentException
894 Annotation target = (Annotation) object;
895 // if null, use delete method for optional primitives
898 target.deleteBelowAlignment();
901 target.setBelowAlignment(((java.lang.Boolean) value)
903 } catch (java.lang.Exception ex)
905 throw new IllegalStateException(ex.toString());
909 public java.lang.Object newInstance(java.lang.Object parent)
914 desc.setHandler(handler);
915 desc.setMultivalued(false);
916 addFieldDescriptor(desc);
918 // -- validation code for: _belowAlignment
919 fieldValidator = new org.exolab.castor.xml.FieldValidator();
921 org.exolab.castor.xml.validators.BooleanValidator typeValidator;
922 typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
923 fieldValidator.setValidator(typeValidator);
925 desc.setValidator(fieldValidator);
927 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
928 java.lang.String.class, "_calcId", "calcId",
929 org.exolab.castor.xml.NodeType.Attribute);
930 desc.setImmutable(true);
931 handler = new org.exolab.castor.xml.XMLFieldHandler()
933 public java.lang.Object getValue(java.lang.Object object)
934 throws IllegalStateException
936 Annotation target = (Annotation) object;
937 return target.getCalcId();
940 public void setValue(java.lang.Object object, java.lang.Object value)
941 throws IllegalStateException, IllegalArgumentException
945 Annotation target = (Annotation) object;
946 target.setCalcId((java.lang.String) value);
947 } catch (java.lang.Exception ex)
949 throw new IllegalStateException(ex.toString());
953 public java.lang.Object newInstance(java.lang.Object parent)
958 desc.setHandler(handler);
959 desc.setMultivalued(false);
960 addFieldDescriptor(desc);
962 // -- validation code for: _calcId
963 fieldValidator = new org.exolab.castor.xml.FieldValidator();
965 org.exolab.castor.xml.validators.StringValidator typeValidator;
966 typeValidator = new org.exolab.castor.xml.validators.StringValidator();
967 fieldValidator.setValidator(typeValidator);
968 typeValidator.setWhiteSpace("preserve");
970 desc.setValidator(fieldValidator);
971 // -- initialize element descriptors
973 // -- _annotationElementList
974 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
975 jalview.schemabinding.version2.AnnotationElement.class,
976 "_annotationElementList", "annotationElement",
977 org.exolab.castor.xml.NodeType.Element);
978 handler = new org.exolab.castor.xml.XMLFieldHandler()
980 public java.lang.Object getValue(java.lang.Object object)
981 throws IllegalStateException
983 Annotation target = (Annotation) object;
984 return target.getAnnotationElement();
987 public void setValue(java.lang.Object object, java.lang.Object value)
988 throws IllegalStateException, IllegalArgumentException
992 Annotation target = (Annotation) object;
993 target.addAnnotationElement((jalview.schemabinding.version2.AnnotationElement) value);
994 } catch (java.lang.Exception ex)
996 throw new IllegalStateException(ex.toString());
1000 public void resetValue(Object object) throws IllegalStateException,
1001 IllegalArgumentException
1005 Annotation target = (Annotation) object;
1006 target.removeAllAnnotationElement();
1007 } catch (java.lang.Exception ex)
1009 throw new IllegalStateException(ex.toString());
1013 public java.lang.Object newInstance(java.lang.Object parent)
1015 return new jalview.schemabinding.version2.AnnotationElement();
1018 desc.setHandler(handler);
1019 desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
1020 desc.setMultivalued(true);
1021 addFieldDescriptor(desc);
1023 // -- validation code for: _annotationElementList
1024 fieldValidator = new org.exolab.castor.xml.FieldValidator();
1025 fieldValidator.setMinOccurs(0);
1028 desc.setValidator(fieldValidator);
1030 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
1031 java.lang.String.class, "_label", "label",
1032 org.exolab.castor.xml.NodeType.Element);
1033 desc.setImmutable(true);
1034 handler = new org.exolab.castor.xml.XMLFieldHandler()
1036 public java.lang.Object getValue(java.lang.Object object)
1037 throws IllegalStateException
1039 Annotation target = (Annotation) object;
1040 return target.getLabel();
1043 public void setValue(java.lang.Object object, java.lang.Object value)
1044 throws IllegalStateException, IllegalArgumentException
1048 Annotation target = (Annotation) object;
1049 target.setLabel((java.lang.String) value);
1050 } catch (java.lang.Exception ex)
1052 throw new IllegalStateException(ex.toString());
1056 public java.lang.Object newInstance(java.lang.Object parent)
1061 desc.setHandler(handler);
1062 desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
1063 desc.setRequired(true);
1064 desc.setMultivalued(false);
1065 addFieldDescriptor(desc);
1067 // -- validation code for: _label
1068 fieldValidator = new org.exolab.castor.xml.FieldValidator();
1069 fieldValidator.setMinOccurs(1);
1071 org.exolab.castor.xml.validators.StringValidator typeValidator;
1072 typeValidator = new org.exolab.castor.xml.validators.StringValidator();
1073 fieldValidator.setValidator(typeValidator);
1074 typeValidator.setWhiteSpace("preserve");
1076 desc.setValidator(fieldValidator);
1078 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
1079 java.lang.String.class, "_description", "description",
1080 org.exolab.castor.xml.NodeType.Element);
1081 desc.setImmutable(true);
1082 handler = new org.exolab.castor.xml.XMLFieldHandler()
1084 public java.lang.Object getValue(java.lang.Object object)
1085 throws IllegalStateException
1087 Annotation target = (Annotation) object;
1088 return target.getDescription();
1091 public void setValue(java.lang.Object object, java.lang.Object value)
1092 throws IllegalStateException, IllegalArgumentException
1096 Annotation target = (Annotation) object;
1097 target.setDescription((java.lang.String) value);
1098 } catch (java.lang.Exception ex)
1100 throw new IllegalStateException(ex.toString());
1104 public java.lang.Object newInstance(java.lang.Object parent)
1109 desc.setHandler(handler);
1110 desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
1111 desc.setMultivalued(false);
1112 addFieldDescriptor(desc);
1114 // -- validation code for: _description
1115 fieldValidator = new org.exolab.castor.xml.FieldValidator();
1117 org.exolab.castor.xml.validators.StringValidator typeValidator;
1118 typeValidator = new org.exolab.castor.xml.validators.StringValidator();
1119 fieldValidator.setValidator(typeValidator);
1120 typeValidator.setWhiteSpace("preserve");
1122 desc.setValidator(fieldValidator);
1123 // -- _thresholdLine
1124 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
1125 jalview.schemabinding.version2.ThresholdLine.class,
1126 "_thresholdLine", "thresholdLine",
1127 org.exolab.castor.xml.NodeType.Element);
1128 handler = new org.exolab.castor.xml.XMLFieldHandler()
1130 public java.lang.Object getValue(java.lang.Object object)
1131 throws IllegalStateException
1133 Annotation target = (Annotation) object;
1134 return target.getThresholdLine();
1137 public void setValue(java.lang.Object object, java.lang.Object value)
1138 throws IllegalStateException, IllegalArgumentException
1142 Annotation target = (Annotation) object;
1143 target.setThresholdLine((jalview.schemabinding.version2.ThresholdLine) value);
1144 } catch (java.lang.Exception ex)
1146 throw new IllegalStateException(ex.toString());
1150 public java.lang.Object newInstance(java.lang.Object parent)
1152 return new jalview.schemabinding.version2.ThresholdLine();
1155 desc.setHandler(handler);
1156 desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
1157 desc.setMultivalued(false);
1158 addFieldDescriptor(desc);
1160 // -- validation code for: _thresholdLine
1161 fieldValidator = new org.exolab.castor.xml.FieldValidator();
1164 desc.setValidator(fieldValidator);
1172 * Method getAccessMode.
1174 * @return the access mode specified for this class.
1176 public org.exolab.castor.mapping.AccessMode getAccessMode()
1182 * Method getIdentity.
1184 * @return the identity field, null if this class has no identity.
1186 public org.exolab.castor.mapping.FieldDescriptor getIdentity()
1188 return super.getIdentity();
1192 * Method getJavaClass.
1194 * @return the Java class represented by this descriptor.
1196 public java.lang.Class getJavaClass()
1198 return jalview.schemabinding.version2.Annotation.class;
1202 * Method getNameSpacePrefix.
1204 * @return the namespace prefix to use when marshaling as XML.
1206 public java.lang.String getNameSpacePrefix()
1212 * Method getNameSpaceURI.
1214 * @return the namespace URI used when marshaling and unmarshaling as XML.
1216 public java.lang.String getNameSpaceURI()
1222 * Method getValidator.
1224 * @return a specific validator for the class described by this
1227 public org.exolab.castor.xml.TypeValidator getValidator()
1233 * Method getXMLName.
1235 * @return the XML Name for the Class being described.
1237 public java.lang.String getXMLName()
1243 * Method isElementDefinition.
1245 * @return true if XML schema definition of this Class is that of a global
1246 * element or element with anonymous type definition.
1248 public boolean isElementDefinition()
1250 return _elementDefinition;