2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
3 * Copyright (C) 2014 The Jalview Authors
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
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 package jalview.schemabinding.version2.descriptors;
23 //---------------------------------/
24 //- Imported classes and packages -/
25 //---------------------------------/
27 import jalview.schemabinding.version2.Annotation;
30 * Class AnnotationDescriptor.
32 * @version $Revision$ $Date$
34 public class AnnotationDescriptor extends
35 org.exolab.castor.xml.util.XMLClassDescriptorImpl
38 // --------------------------/
39 // - Class/Member Variables -/
40 // --------------------------/
43 * Field _elementDefinition.
45 private boolean _elementDefinition;
50 private java.lang.String _nsPrefix;
55 private java.lang.String _nsURI;
60 private java.lang.String _xmlName;
66 public AnnotationDescriptor()
69 _nsURI = "www.vamsas.ac.uk/jalview/version2";
70 _xmlName = "Annotation";
71 _elementDefinition = true;
73 // -- set grouping compositor
74 setCompositorAsSequence();
75 org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
76 org.exolab.castor.mapping.FieldHandler handler = null;
77 org.exolab.castor.xml.FieldValidator fieldValidator = null;
78 // -- initialize attribute descriptors
81 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
82 java.lang.Boolean.TYPE, "_graph", "graph",
83 org.exolab.castor.xml.NodeType.Attribute);
84 handler = new org.exolab.castor.xml.XMLFieldHandler()
86 public java.lang.Object getValue(java.lang.Object object)
87 throws IllegalStateException
89 Annotation target = (Annotation) object;
90 if (!target.hasGraph())
94 return (target.getGraph() ? java.lang.Boolean.TRUE
95 : java.lang.Boolean.FALSE);
98 public void setValue(java.lang.Object object, java.lang.Object value)
99 throws IllegalStateException, IllegalArgumentException
103 Annotation target = (Annotation) object;
104 // ignore null values for non optional primitives
110 target.setGraph(((java.lang.Boolean) value).booleanValue());
111 } catch (java.lang.Exception ex)
113 throw new IllegalStateException(ex.toString());
117 public java.lang.Object newInstance(java.lang.Object parent)
122 desc.setHandler(handler);
123 desc.setRequired(true);
124 desc.setMultivalued(false);
125 addFieldDescriptor(desc);
127 // -- validation code for: _graph
128 fieldValidator = new org.exolab.castor.xml.FieldValidator();
129 fieldValidator.setMinOccurs(1);
131 org.exolab.castor.xml.validators.BooleanValidator typeValidator;
132 typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
133 fieldValidator.setValidator(typeValidator);
135 desc.setValidator(fieldValidator);
137 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
138 java.lang.Integer.TYPE, "_graphType", "graphType",
139 org.exolab.castor.xml.NodeType.Attribute);
140 handler = new org.exolab.castor.xml.XMLFieldHandler()
142 public java.lang.Object getValue(java.lang.Object object)
143 throws IllegalStateException
145 Annotation target = (Annotation) object;
146 if (!target.hasGraphType())
150 return new java.lang.Integer(target.getGraphType());
153 public void setValue(java.lang.Object object, java.lang.Object value)
154 throws IllegalStateException, IllegalArgumentException
158 Annotation target = (Annotation) object;
159 // if null, use delete method for optional primitives
162 target.deleteGraphType();
165 target.setGraphType(((java.lang.Integer) value).intValue());
166 } catch (java.lang.Exception ex)
168 throw new IllegalStateException(ex.toString());
172 public java.lang.Object newInstance(java.lang.Object parent)
177 desc.setHandler(handler);
178 desc.setMultivalued(false);
179 addFieldDescriptor(desc);
181 // -- validation code for: _graphType
182 fieldValidator = new org.exolab.castor.xml.FieldValidator();
184 org.exolab.castor.xml.validators.IntValidator typeValidator;
185 typeValidator = new org.exolab.castor.xml.validators.IntValidator();
186 fieldValidator.setValidator(typeValidator);
187 typeValidator.setMinInclusive(-2147483648);
188 typeValidator.setMaxInclusive(2147483647);
190 desc.setValidator(fieldValidator);
192 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
193 java.lang.String.class, "_sequenceRef", "sequenceRef",
194 org.exolab.castor.xml.NodeType.Attribute);
195 desc.setImmutable(true);
196 handler = new org.exolab.castor.xml.XMLFieldHandler()
198 public java.lang.Object getValue(java.lang.Object object)
199 throws IllegalStateException
201 Annotation target = (Annotation) object;
202 return target.getSequenceRef();
205 public void setValue(java.lang.Object object, java.lang.Object value)
206 throws IllegalStateException, IllegalArgumentException
210 Annotation target = (Annotation) object;
211 target.setSequenceRef((java.lang.String) value);
212 } catch (java.lang.Exception ex)
214 throw new IllegalStateException(ex.toString());
218 public java.lang.Object newInstance(java.lang.Object parent)
223 desc.setHandler(handler);
224 desc.setMultivalued(false);
225 addFieldDescriptor(desc);
227 // -- validation code for: _sequenceRef
228 fieldValidator = new org.exolab.castor.xml.FieldValidator();
230 org.exolab.castor.xml.validators.StringValidator typeValidator;
231 typeValidator = new org.exolab.castor.xml.validators.StringValidator();
232 fieldValidator.setValidator(typeValidator);
233 typeValidator.setWhiteSpace("preserve");
235 desc.setValidator(fieldValidator);
237 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
238 java.lang.String.class, "_groupRef", "groupRef",
239 org.exolab.castor.xml.NodeType.Attribute);
240 desc.setImmutable(true);
241 handler = new org.exolab.castor.xml.XMLFieldHandler()
243 public java.lang.Object getValue(java.lang.Object object)
244 throws IllegalStateException
246 Annotation target = (Annotation) object;
247 return target.getGroupRef();
250 public void setValue(java.lang.Object object, java.lang.Object value)
251 throws IllegalStateException, IllegalArgumentException
255 Annotation target = (Annotation) object;
256 target.setGroupRef((java.lang.String) value);
257 } catch (java.lang.Exception ex)
259 throw new IllegalStateException(ex.toString());
263 public java.lang.Object newInstance(java.lang.Object parent)
268 desc.setHandler(handler);
269 desc.setMultivalued(false);
270 addFieldDescriptor(desc);
272 // -- validation code for: _groupRef
273 fieldValidator = new org.exolab.castor.xml.FieldValidator();
275 org.exolab.castor.xml.validators.StringValidator typeValidator;
276 typeValidator = new org.exolab.castor.xml.validators.StringValidator();
277 fieldValidator.setValidator(typeValidator);
278 typeValidator.setWhiteSpace("preserve");
280 desc.setValidator(fieldValidator);
282 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
283 java.lang.Integer.TYPE, "_graphColour", "graphColour",
284 org.exolab.castor.xml.NodeType.Attribute);
285 handler = new org.exolab.castor.xml.XMLFieldHandler()
287 public java.lang.Object getValue(java.lang.Object object)
288 throws IllegalStateException
290 Annotation target = (Annotation) object;
291 if (!target.hasGraphColour())
295 return new java.lang.Integer(target.getGraphColour());
298 public void setValue(java.lang.Object object, java.lang.Object value)
299 throws IllegalStateException, IllegalArgumentException
303 Annotation target = (Annotation) object;
304 // if null, use delete method for optional primitives
307 target.deleteGraphColour();
310 target.setGraphColour(((java.lang.Integer) value).intValue());
311 } catch (java.lang.Exception ex)
313 throw new IllegalStateException(ex.toString());
317 public java.lang.Object newInstance(java.lang.Object parent)
322 desc.setHandler(handler);
323 desc.setMultivalued(false);
324 addFieldDescriptor(desc);
326 // -- validation code for: _graphColour
327 fieldValidator = new org.exolab.castor.xml.FieldValidator();
329 org.exolab.castor.xml.validators.IntValidator typeValidator;
330 typeValidator = new org.exolab.castor.xml.validators.IntValidator();
331 fieldValidator.setValidator(typeValidator);
332 typeValidator.setMinInclusive(-2147483648);
333 typeValidator.setMaxInclusive(2147483647);
335 desc.setValidator(fieldValidator);
337 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
338 java.lang.Integer.TYPE, "_graphGroup", "graphGroup",
339 org.exolab.castor.xml.NodeType.Attribute);
340 handler = new org.exolab.castor.xml.XMLFieldHandler()
342 public java.lang.Object getValue(java.lang.Object object)
343 throws IllegalStateException
345 Annotation target = (Annotation) object;
346 if (!target.hasGraphGroup())
350 return new java.lang.Integer(target.getGraphGroup());
353 public void setValue(java.lang.Object object, java.lang.Object value)
354 throws IllegalStateException, IllegalArgumentException
358 Annotation target = (Annotation) object;
359 // if null, use delete method for optional primitives
362 target.deleteGraphGroup();
365 target.setGraphGroup(((java.lang.Integer) value).intValue());
366 } catch (java.lang.Exception ex)
368 throw new IllegalStateException(ex.toString());
372 public java.lang.Object newInstance(java.lang.Object parent)
377 desc.setHandler(handler);
378 desc.setMultivalued(false);
379 addFieldDescriptor(desc);
381 // -- validation code for: _graphGroup
382 fieldValidator = new org.exolab.castor.xml.FieldValidator();
384 org.exolab.castor.xml.validators.IntValidator typeValidator;
385 typeValidator = new org.exolab.castor.xml.validators.IntValidator();
386 fieldValidator.setValidator(typeValidator);
387 typeValidator.setMinInclusive(-2147483648);
388 typeValidator.setMaxInclusive(2147483647);
390 desc.setValidator(fieldValidator);
392 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
393 java.lang.Integer.TYPE, "_graphHeight", "graphHeight",
394 org.exolab.castor.xml.NodeType.Attribute);
395 handler = new org.exolab.castor.xml.XMLFieldHandler()
397 public java.lang.Object getValue(java.lang.Object object)
398 throws IllegalStateException
400 Annotation target = (Annotation) object;
401 if (!target.hasGraphHeight())
405 return new java.lang.Integer(target.getGraphHeight());
408 public void setValue(java.lang.Object object, java.lang.Object value)
409 throws IllegalStateException, IllegalArgumentException
413 Annotation target = (Annotation) object;
414 // if null, use delete method for optional primitives
417 target.deleteGraphHeight();
420 target.setGraphHeight(((java.lang.Integer) value).intValue());
421 } catch (java.lang.Exception ex)
423 throw new IllegalStateException(ex.toString());
427 public java.lang.Object newInstance(java.lang.Object parent)
432 desc.setHandler(handler);
433 desc.setMultivalued(false);
434 addFieldDescriptor(desc);
436 // -- validation code for: _graphHeight
437 fieldValidator = new org.exolab.castor.xml.FieldValidator();
439 org.exolab.castor.xml.validators.IntValidator typeValidator;
440 typeValidator = new org.exolab.castor.xml.validators.IntValidator();
441 fieldValidator.setValidator(typeValidator);
442 typeValidator.setMinInclusive(-2147483648);
443 typeValidator.setMaxInclusive(2147483647);
445 desc.setValidator(fieldValidator);
447 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
448 java.lang.String.class, "_id", "id",
449 org.exolab.castor.xml.NodeType.Attribute);
450 desc.setImmutable(true);
451 handler = new org.exolab.castor.xml.XMLFieldHandler()
453 public java.lang.Object getValue(java.lang.Object object)
454 throws IllegalStateException
456 Annotation target = (Annotation) object;
457 return target.getId();
460 public void setValue(java.lang.Object object, java.lang.Object value)
461 throws IllegalStateException, IllegalArgumentException
465 Annotation target = (Annotation) object;
466 target.setId((java.lang.String) value);
467 } catch (java.lang.Exception ex)
469 throw new IllegalStateException(ex.toString());
473 public java.lang.Object newInstance(java.lang.Object parent)
478 desc.setHandler(handler);
479 desc.setMultivalued(false);
480 addFieldDescriptor(desc);
482 // -- validation code for: _id
483 fieldValidator = new org.exolab.castor.xml.FieldValidator();
485 org.exolab.castor.xml.validators.StringValidator typeValidator;
486 typeValidator = new org.exolab.castor.xml.validators.StringValidator();
487 fieldValidator.setValidator(typeValidator);
488 typeValidator.setWhiteSpace("preserve");
490 desc.setValidator(fieldValidator);
492 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
493 java.lang.Boolean.TYPE, "_scoreOnly", "scoreOnly",
494 org.exolab.castor.xml.NodeType.Attribute);
495 handler = new org.exolab.castor.xml.XMLFieldHandler()
497 public java.lang.Object getValue(java.lang.Object object)
498 throws IllegalStateException
500 Annotation target = (Annotation) object;
501 if (!target.hasScoreOnly())
505 return (target.getScoreOnly() ? java.lang.Boolean.TRUE
506 : java.lang.Boolean.FALSE);
509 public void setValue(java.lang.Object object, java.lang.Object value)
510 throws IllegalStateException, IllegalArgumentException
514 Annotation target = (Annotation) object;
515 // if null, use delete method for optional primitives
518 target.deleteScoreOnly();
521 target.setScoreOnly(((java.lang.Boolean) value).booleanValue());
522 } catch (java.lang.Exception ex)
524 throw new IllegalStateException(ex.toString());
528 public java.lang.Object newInstance(java.lang.Object parent)
533 desc.setHandler(handler);
534 desc.setMultivalued(false);
535 addFieldDescriptor(desc);
537 // -- validation code for: _scoreOnly
538 fieldValidator = new org.exolab.castor.xml.FieldValidator();
540 org.exolab.castor.xml.validators.BooleanValidator typeValidator;
541 typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
542 fieldValidator.setValidator(typeValidator);
544 desc.setValidator(fieldValidator);
546 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
547 java.lang.Double.TYPE, "_score", "score",
548 org.exolab.castor.xml.NodeType.Attribute);
549 handler = new org.exolab.castor.xml.XMLFieldHandler()
551 public java.lang.Object getValue(java.lang.Object object)
552 throws IllegalStateException
554 Annotation target = (Annotation) object;
555 if (!target.hasScore())
559 return new java.lang.Double(target.getScore());
562 public void setValue(java.lang.Object object, java.lang.Object value)
563 throws IllegalStateException, IllegalArgumentException
567 Annotation target = (Annotation) object;
568 // if null, use delete method for optional primitives
571 target.deleteScore();
574 target.setScore(((java.lang.Double) value).doubleValue());
575 } catch (java.lang.Exception ex)
577 throw new IllegalStateException(ex.toString());
581 public java.lang.Object newInstance(java.lang.Object parent)
586 desc.setHandler(handler);
587 desc.setMultivalued(false);
588 addFieldDescriptor(desc);
590 // -- validation code for: _score
591 fieldValidator = new org.exolab.castor.xml.FieldValidator();
593 org.exolab.castor.xml.validators.DoubleValidator typeValidator;
594 typeValidator = new org.exolab.castor.xml.validators.DoubleValidator();
595 fieldValidator.setValidator(typeValidator);
596 typeValidator.setMinInclusive(-1.7976931348623157E308);
597 typeValidator.setMaxInclusive(1.7976931348623157E308);
599 desc.setValidator(fieldValidator);
601 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
602 java.lang.Boolean.TYPE, "_visible", "visible",
603 org.exolab.castor.xml.NodeType.Attribute);
604 handler = new org.exolab.castor.xml.XMLFieldHandler()
606 public java.lang.Object getValue(java.lang.Object object)
607 throws IllegalStateException
609 Annotation target = (Annotation) object;
610 if (!target.hasVisible())
614 return (target.getVisible() ? java.lang.Boolean.TRUE
615 : java.lang.Boolean.FALSE);
618 public void setValue(java.lang.Object object, java.lang.Object value)
619 throws IllegalStateException, IllegalArgumentException
623 Annotation target = (Annotation) object;
624 // if null, use delete method for optional primitives
627 target.deleteVisible();
630 target.setVisible(((java.lang.Boolean) value).booleanValue());
631 } catch (java.lang.Exception ex)
633 throw new IllegalStateException(ex.toString());
637 public java.lang.Object newInstance(java.lang.Object parent)
642 desc.setHandler(handler);
643 desc.setMultivalued(false);
644 addFieldDescriptor(desc);
646 // -- validation code for: _visible
647 fieldValidator = new org.exolab.castor.xml.FieldValidator();
649 org.exolab.castor.xml.validators.BooleanValidator typeValidator;
650 typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
651 fieldValidator.setValidator(typeValidator);
653 desc.setValidator(fieldValidator);
654 // -- _centreColLabels
655 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
656 java.lang.Boolean.TYPE, "_centreColLabels", "centreColLabels",
657 org.exolab.castor.xml.NodeType.Attribute);
658 handler = new org.exolab.castor.xml.XMLFieldHandler()
660 public java.lang.Object getValue(java.lang.Object object)
661 throws IllegalStateException
663 Annotation target = (Annotation) object;
664 if (!target.hasCentreColLabels())
668 return (target.getCentreColLabels() ? java.lang.Boolean.TRUE
669 : java.lang.Boolean.FALSE);
672 public void setValue(java.lang.Object object, java.lang.Object value)
673 throws IllegalStateException, IllegalArgumentException
677 Annotation target = (Annotation) object;
678 // if null, use delete method for optional primitives
681 target.deleteCentreColLabels();
684 target.setCentreColLabels(((java.lang.Boolean) value)
686 } catch (java.lang.Exception ex)
688 throw new IllegalStateException(ex.toString());
692 public java.lang.Object newInstance(java.lang.Object parent)
697 desc.setHandler(handler);
698 desc.setMultivalued(false);
699 addFieldDescriptor(desc);
701 // -- validation code for: _centreColLabels
702 fieldValidator = new org.exolab.castor.xml.FieldValidator();
704 org.exolab.castor.xml.validators.BooleanValidator typeValidator;
705 typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
706 fieldValidator.setValidator(typeValidator);
708 desc.setValidator(fieldValidator);
709 // -- _scaleColLabels
710 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
711 java.lang.Boolean.TYPE, "_scaleColLabels", "scaleColLabels",
712 org.exolab.castor.xml.NodeType.Attribute);
713 handler = new org.exolab.castor.xml.XMLFieldHandler()
715 public java.lang.Object getValue(java.lang.Object object)
716 throws IllegalStateException
718 Annotation target = (Annotation) object;
719 if (!target.hasScaleColLabels())
723 return (target.getScaleColLabels() ? java.lang.Boolean.TRUE
724 : java.lang.Boolean.FALSE);
727 public void setValue(java.lang.Object object, java.lang.Object value)
728 throws IllegalStateException, IllegalArgumentException
732 Annotation target = (Annotation) object;
733 // if null, use delete method for optional primitives
736 target.deleteScaleColLabels();
739 target.setScaleColLabels(((java.lang.Boolean) value)
741 } catch (java.lang.Exception ex)
743 throw new IllegalStateException(ex.toString());
747 public java.lang.Object newInstance(java.lang.Object parent)
752 desc.setHandler(handler);
753 desc.setMultivalued(false);
754 addFieldDescriptor(desc);
756 // -- validation code for: _scaleColLabels
757 fieldValidator = new org.exolab.castor.xml.FieldValidator();
759 org.exolab.castor.xml.validators.BooleanValidator typeValidator;
760 typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
761 fieldValidator.setValidator(typeValidator);
763 desc.setValidator(fieldValidator);
764 // -- _showAllColLabels
765 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
766 java.lang.Boolean.TYPE, "_showAllColLabels",
767 "showAllColLabels", org.exolab.castor.xml.NodeType.Attribute);
768 handler = new org.exolab.castor.xml.XMLFieldHandler()
770 public java.lang.Object getValue(java.lang.Object object)
771 throws IllegalStateException
773 Annotation target = (Annotation) object;
774 if (!target.hasShowAllColLabels())
778 return (target.getShowAllColLabels() ? java.lang.Boolean.TRUE
779 : java.lang.Boolean.FALSE);
782 public void setValue(java.lang.Object object, java.lang.Object value)
783 throws IllegalStateException, IllegalArgumentException
787 Annotation target = (Annotation) object;
788 // if null, use delete method for optional primitives
791 target.deleteShowAllColLabels();
794 target.setShowAllColLabels(((java.lang.Boolean) value)
796 } catch (java.lang.Exception ex)
798 throw new IllegalStateException(ex.toString());
802 public java.lang.Object newInstance(java.lang.Object parent)
807 desc.setHandler(handler);
808 desc.setMultivalued(false);
809 addFieldDescriptor(desc);
811 // -- validation code for: _showAllColLabels
812 fieldValidator = new org.exolab.castor.xml.FieldValidator();
814 org.exolab.castor.xml.validators.BooleanValidator typeValidator;
815 typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
816 fieldValidator.setValidator(typeValidator);
818 desc.setValidator(fieldValidator);
819 // -- _autoCalculated
820 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
821 java.lang.Boolean.TYPE, "_autoCalculated", "autoCalculated",
822 org.exolab.castor.xml.NodeType.Attribute);
823 handler = new org.exolab.castor.xml.XMLFieldHandler()
825 public java.lang.Object getValue(java.lang.Object object)
826 throws IllegalStateException
828 Annotation target = (Annotation) object;
829 if (!target.hasAutoCalculated())
833 return (target.getAutoCalculated() ? java.lang.Boolean.TRUE
834 : java.lang.Boolean.FALSE);
837 public void setValue(java.lang.Object object, java.lang.Object value)
838 throws IllegalStateException, IllegalArgumentException
842 Annotation target = (Annotation) object;
843 // if null, use delete method for optional primitives
846 target.deleteAutoCalculated();
849 target.setAutoCalculated(((java.lang.Boolean) value)
851 } catch (java.lang.Exception ex)
853 throw new IllegalStateException(ex.toString());
857 public java.lang.Object newInstance(java.lang.Object parent)
862 desc.setHandler(handler);
863 desc.setMultivalued(false);
864 addFieldDescriptor(desc);
866 // -- validation code for: _autoCalculated
867 fieldValidator = new org.exolab.castor.xml.FieldValidator();
869 org.exolab.castor.xml.validators.BooleanValidator typeValidator;
870 typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
871 fieldValidator.setValidator(typeValidator);
873 desc.setValidator(fieldValidator);
874 // -- _belowAlignment
875 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
876 java.lang.Boolean.TYPE, "_belowAlignment", "belowAlignment",
877 org.exolab.castor.xml.NodeType.Attribute);
878 handler = new org.exolab.castor.xml.XMLFieldHandler()
880 public java.lang.Object getValue(java.lang.Object object)
881 throws IllegalStateException
883 Annotation target = (Annotation) object;
884 if (!target.hasBelowAlignment())
888 return (target.getBelowAlignment() ? java.lang.Boolean.TRUE
889 : java.lang.Boolean.FALSE);
892 public void setValue(java.lang.Object object, java.lang.Object value)
893 throws IllegalStateException, IllegalArgumentException
897 Annotation target = (Annotation) object;
898 // if null, use delete method for optional primitives
901 target.deleteBelowAlignment();
904 target.setBelowAlignment(((java.lang.Boolean) value)
906 } catch (java.lang.Exception ex)
908 throw new IllegalStateException(ex.toString());
912 public java.lang.Object newInstance(java.lang.Object parent)
917 desc.setHandler(handler);
918 desc.setMultivalued(false);
919 addFieldDescriptor(desc);
921 // -- validation code for: _belowAlignment
922 fieldValidator = new org.exolab.castor.xml.FieldValidator();
924 org.exolab.castor.xml.validators.BooleanValidator typeValidator;
925 typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
926 fieldValidator.setValidator(typeValidator);
928 desc.setValidator(fieldValidator);
930 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
931 java.lang.String.class, "_calcId", "calcId",
932 org.exolab.castor.xml.NodeType.Attribute);
933 desc.setImmutable(true);
934 handler = new org.exolab.castor.xml.XMLFieldHandler()
936 public java.lang.Object getValue(java.lang.Object object)
937 throws IllegalStateException
939 Annotation target = (Annotation) object;
940 return target.getCalcId();
943 public void setValue(java.lang.Object object, java.lang.Object value)
944 throws IllegalStateException, IllegalArgumentException
948 Annotation target = (Annotation) object;
949 target.setCalcId((java.lang.String) value);
950 } catch (java.lang.Exception ex)
952 throw new IllegalStateException(ex.toString());
956 public java.lang.Object newInstance(java.lang.Object parent)
961 desc.setHandler(handler);
962 desc.setMultivalued(false);
963 addFieldDescriptor(desc);
965 // -- validation code for: _calcId
966 fieldValidator = new org.exolab.castor.xml.FieldValidator();
968 org.exolab.castor.xml.validators.StringValidator typeValidator;
969 typeValidator = new org.exolab.castor.xml.validators.StringValidator();
970 fieldValidator.setValidator(typeValidator);
971 typeValidator.setWhiteSpace("preserve");
973 desc.setValidator(fieldValidator);
974 // -- initialize element descriptors
976 // -- _annotationElementList
977 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
978 jalview.schemabinding.version2.AnnotationElement.class,
979 "_annotationElementList", "annotationElement",
980 org.exolab.castor.xml.NodeType.Element);
981 handler = new org.exolab.castor.xml.XMLFieldHandler()
983 public java.lang.Object getValue(java.lang.Object object)
984 throws IllegalStateException
986 Annotation target = (Annotation) object;
987 return target.getAnnotationElement();
990 public void setValue(java.lang.Object object, java.lang.Object value)
991 throws IllegalStateException, IllegalArgumentException
995 Annotation target = (Annotation) object;
996 target.addAnnotationElement((jalview.schemabinding.version2.AnnotationElement) value);
997 } catch (java.lang.Exception ex)
999 throw new IllegalStateException(ex.toString());
1003 public void resetValue(Object object) throws IllegalStateException,
1004 IllegalArgumentException
1008 Annotation target = (Annotation) object;
1009 target.removeAllAnnotationElement();
1010 } catch (java.lang.Exception ex)
1012 throw new IllegalStateException(ex.toString());
1016 public java.lang.Object newInstance(java.lang.Object parent)
1018 return new jalview.schemabinding.version2.AnnotationElement();
1021 desc.setHandler(handler);
1022 desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
1023 desc.setMultivalued(true);
1024 addFieldDescriptor(desc);
1026 // -- validation code for: _annotationElementList
1027 fieldValidator = new org.exolab.castor.xml.FieldValidator();
1028 fieldValidator.setMinOccurs(0);
1031 desc.setValidator(fieldValidator);
1033 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
1034 java.lang.String.class, "_label", "label",
1035 org.exolab.castor.xml.NodeType.Element);
1036 desc.setImmutable(true);
1037 handler = new org.exolab.castor.xml.XMLFieldHandler()
1039 public java.lang.Object getValue(java.lang.Object object)
1040 throws IllegalStateException
1042 Annotation target = (Annotation) object;
1043 return target.getLabel();
1046 public void setValue(java.lang.Object object, java.lang.Object value)
1047 throws IllegalStateException, IllegalArgumentException
1051 Annotation target = (Annotation) object;
1052 target.setLabel((java.lang.String) value);
1053 } catch (java.lang.Exception ex)
1055 throw new IllegalStateException(ex.toString());
1059 public java.lang.Object newInstance(java.lang.Object parent)
1064 desc.setHandler(handler);
1065 desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
1066 desc.setRequired(true);
1067 desc.setMultivalued(false);
1068 addFieldDescriptor(desc);
1070 // -- validation code for: _label
1071 fieldValidator = new org.exolab.castor.xml.FieldValidator();
1072 fieldValidator.setMinOccurs(1);
1074 org.exolab.castor.xml.validators.StringValidator typeValidator;
1075 typeValidator = new org.exolab.castor.xml.validators.StringValidator();
1076 fieldValidator.setValidator(typeValidator);
1077 typeValidator.setWhiteSpace("preserve");
1079 desc.setValidator(fieldValidator);
1081 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
1082 java.lang.String.class, "_description", "description",
1083 org.exolab.castor.xml.NodeType.Element);
1084 desc.setImmutable(true);
1085 handler = new org.exolab.castor.xml.XMLFieldHandler()
1087 public java.lang.Object getValue(java.lang.Object object)
1088 throws IllegalStateException
1090 Annotation target = (Annotation) object;
1091 return target.getDescription();
1094 public void setValue(java.lang.Object object, java.lang.Object value)
1095 throws IllegalStateException, IllegalArgumentException
1099 Annotation target = (Annotation) object;
1100 target.setDescription((java.lang.String) value);
1101 } catch (java.lang.Exception ex)
1103 throw new IllegalStateException(ex.toString());
1107 public java.lang.Object newInstance(java.lang.Object parent)
1112 desc.setHandler(handler);
1113 desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
1114 desc.setMultivalued(false);
1115 addFieldDescriptor(desc);
1117 // -- validation code for: _description
1118 fieldValidator = new org.exolab.castor.xml.FieldValidator();
1120 org.exolab.castor.xml.validators.StringValidator typeValidator;
1121 typeValidator = new org.exolab.castor.xml.validators.StringValidator();
1122 fieldValidator.setValidator(typeValidator);
1123 typeValidator.setWhiteSpace("preserve");
1125 desc.setValidator(fieldValidator);
1126 // -- _thresholdLine
1127 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
1128 jalview.schemabinding.version2.ThresholdLine.class,
1129 "_thresholdLine", "thresholdLine",
1130 org.exolab.castor.xml.NodeType.Element);
1131 handler = new org.exolab.castor.xml.XMLFieldHandler()
1133 public java.lang.Object getValue(java.lang.Object object)
1134 throws IllegalStateException
1136 Annotation target = (Annotation) object;
1137 return target.getThresholdLine();
1140 public void setValue(java.lang.Object object, java.lang.Object value)
1141 throws IllegalStateException, IllegalArgumentException
1145 Annotation target = (Annotation) object;
1146 target.setThresholdLine((jalview.schemabinding.version2.ThresholdLine) value);
1147 } catch (java.lang.Exception ex)
1149 throw new IllegalStateException(ex.toString());
1153 public java.lang.Object newInstance(java.lang.Object parent)
1155 return new jalview.schemabinding.version2.ThresholdLine();
1158 desc.setHandler(handler);
1159 desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
1160 desc.setMultivalued(false);
1161 addFieldDescriptor(desc);
1163 // -- validation code for: _thresholdLine
1164 fieldValidator = new org.exolab.castor.xml.FieldValidator();
1167 desc.setValidator(fieldValidator);
1175 * Method getAccessMode.
1177 * @return the access mode specified for this class.
1179 public org.exolab.castor.mapping.AccessMode getAccessMode()
1185 * Method getIdentity.
1187 * @return the identity field, null if this class has no identity.
1189 public org.exolab.castor.mapping.FieldDescriptor getIdentity()
1191 return super.getIdentity();
1195 * Method getJavaClass.
1197 * @return the Java class represented by this descriptor.
1199 public java.lang.Class getJavaClass()
1201 return jalview.schemabinding.version2.Annotation.class;
1205 * Method getNameSpacePrefix.
1207 * @return the namespace prefix to use when marshaling as XML.
1209 public java.lang.String getNameSpacePrefix()
1215 * Method getNameSpaceURI.
1217 * @return the namespace URI used when marshaling and unmarshaling as XML.
1219 public java.lang.String getNameSpaceURI()
1225 * Method getValidator.
1227 * @return a specific validator for the class described by this
1230 public org.exolab.castor.xml.TypeValidator getValidator()
1236 * Method getXMLName.
1238 * @return the XML Name for the Class being described.
1240 public java.lang.String getXMLName()
1246 * Method isElementDefinition.
1248 * @return true if XML schema definition of this Class is that of a global
1249 * element or element with anonymous type definition.
1251 public boolean isElementDefinition()
1253 return _elementDefinition;