2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
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 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/>.
17 * The Jalview Authors are detailed in the 'AUTHORS' file.
19 package jalview.schemabinding.version2.descriptors;
21 //---------------------------------/
22 //- Imported classes and packages -/
23 //---------------------------------/
25 import jalview.schemabinding.version2.Annotation;
28 * Class AnnotationDescriptor.
30 * @version $Revision$ $Date$
32 public class AnnotationDescriptor extends
33 org.exolab.castor.xml.util.XMLClassDescriptorImpl
36 // --------------------------/
37 // - Class/Member Variables -/
38 // --------------------------/
41 * Field _elementDefinition.
43 private boolean _elementDefinition;
48 private java.lang.String _nsPrefix;
53 private java.lang.String _nsURI;
58 private java.lang.String _xmlName;
64 public AnnotationDescriptor()
67 _nsURI = "www.vamsas.ac.uk/jalview/version2";
68 _xmlName = "Annotation";
69 _elementDefinition = true;
71 // -- set grouping compositor
72 setCompositorAsSequence();
73 org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
74 org.exolab.castor.mapping.FieldHandler handler = null;
75 org.exolab.castor.xml.FieldValidator fieldValidator = null;
76 // -- initialize attribute descriptors
79 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
80 java.lang.Boolean.TYPE, "_graph", "graph",
81 org.exolab.castor.xml.NodeType.Attribute);
82 handler = new org.exolab.castor.xml.XMLFieldHandler()
84 public java.lang.Object getValue(java.lang.Object object)
85 throws IllegalStateException
87 Annotation target = (Annotation) object;
88 if (!target.hasGraph())
92 return (target.getGraph() ? java.lang.Boolean.TRUE
93 : java.lang.Boolean.FALSE);
96 public void setValue(java.lang.Object object, java.lang.Object value)
97 throws IllegalStateException, IllegalArgumentException
101 Annotation target = (Annotation) object;
102 // ignore null values for non optional primitives
108 target.setGraph(((java.lang.Boolean) value).booleanValue());
109 } catch (java.lang.Exception ex)
111 throw new IllegalStateException(ex.toString());
115 public java.lang.Object newInstance(java.lang.Object parent)
120 desc.setHandler(handler);
121 desc.setRequired(true);
122 desc.setMultivalued(false);
123 addFieldDescriptor(desc);
125 // -- validation code for: _graph
126 fieldValidator = new org.exolab.castor.xml.FieldValidator();
127 fieldValidator.setMinOccurs(1);
129 org.exolab.castor.xml.validators.BooleanValidator typeValidator;
130 typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
131 fieldValidator.setValidator(typeValidator);
133 desc.setValidator(fieldValidator);
135 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
136 java.lang.Integer.TYPE, "_graphType", "graphType",
137 org.exolab.castor.xml.NodeType.Attribute);
138 handler = new org.exolab.castor.xml.XMLFieldHandler()
140 public java.lang.Object getValue(java.lang.Object object)
141 throws IllegalStateException
143 Annotation target = (Annotation) object;
144 if (!target.hasGraphType())
148 return new java.lang.Integer(target.getGraphType());
151 public void setValue(java.lang.Object object, java.lang.Object value)
152 throws IllegalStateException, IllegalArgumentException
156 Annotation target = (Annotation) object;
157 // if null, use delete method for optional primitives
160 target.deleteGraphType();
163 target.setGraphType(((java.lang.Integer) value).intValue());
164 } catch (java.lang.Exception ex)
166 throw new IllegalStateException(ex.toString());
170 public java.lang.Object newInstance(java.lang.Object parent)
175 desc.setHandler(handler);
176 desc.setMultivalued(false);
177 addFieldDescriptor(desc);
179 // -- validation code for: _graphType
180 fieldValidator = new org.exolab.castor.xml.FieldValidator();
182 org.exolab.castor.xml.validators.IntValidator typeValidator;
183 typeValidator = new org.exolab.castor.xml.validators.IntValidator();
184 fieldValidator.setValidator(typeValidator);
185 typeValidator.setMinInclusive(-2147483648);
186 typeValidator.setMaxInclusive(2147483647);
188 desc.setValidator(fieldValidator);
190 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
191 java.lang.String.class, "_sequenceRef", "sequenceRef",
192 org.exolab.castor.xml.NodeType.Attribute);
193 desc.setImmutable(true);
194 handler = new org.exolab.castor.xml.XMLFieldHandler()
196 public java.lang.Object getValue(java.lang.Object object)
197 throws IllegalStateException
199 Annotation target = (Annotation) object;
200 return target.getSequenceRef();
203 public void setValue(java.lang.Object object, java.lang.Object value)
204 throws IllegalStateException, IllegalArgumentException
208 Annotation target = (Annotation) object;
209 target.setSequenceRef((java.lang.String) value);
210 } catch (java.lang.Exception ex)
212 throw new IllegalStateException(ex.toString());
216 public java.lang.Object newInstance(java.lang.Object parent)
221 desc.setHandler(handler);
222 desc.setMultivalued(false);
223 addFieldDescriptor(desc);
225 // -- validation code for: _sequenceRef
226 fieldValidator = new org.exolab.castor.xml.FieldValidator();
228 org.exolab.castor.xml.validators.StringValidator typeValidator;
229 typeValidator = new org.exolab.castor.xml.validators.StringValidator();
230 fieldValidator.setValidator(typeValidator);
231 typeValidator.setWhiteSpace("preserve");
233 desc.setValidator(fieldValidator);
235 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
236 java.lang.String.class, "_groupRef", "groupRef",
237 org.exolab.castor.xml.NodeType.Attribute);
238 desc.setImmutable(true);
239 handler = new org.exolab.castor.xml.XMLFieldHandler()
241 public java.lang.Object getValue(java.lang.Object object)
242 throws IllegalStateException
244 Annotation target = (Annotation) object;
245 return target.getGroupRef();
248 public void setValue(java.lang.Object object, java.lang.Object value)
249 throws IllegalStateException, IllegalArgumentException
253 Annotation target = (Annotation) object;
254 target.setGroupRef((java.lang.String) value);
255 } catch (java.lang.Exception ex)
257 throw new IllegalStateException(ex.toString());
261 public java.lang.Object newInstance(java.lang.Object parent)
266 desc.setHandler(handler);
267 desc.setMultivalued(false);
268 addFieldDescriptor(desc);
270 // -- validation code for: _groupRef
271 fieldValidator = new org.exolab.castor.xml.FieldValidator();
273 org.exolab.castor.xml.validators.StringValidator typeValidator;
274 typeValidator = new org.exolab.castor.xml.validators.StringValidator();
275 fieldValidator.setValidator(typeValidator);
276 typeValidator.setWhiteSpace("preserve");
278 desc.setValidator(fieldValidator);
280 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
281 java.lang.Integer.TYPE, "_graphColour", "graphColour",
282 org.exolab.castor.xml.NodeType.Attribute);
283 handler = new org.exolab.castor.xml.XMLFieldHandler()
285 public java.lang.Object getValue(java.lang.Object object)
286 throws IllegalStateException
288 Annotation target = (Annotation) object;
289 if (!target.hasGraphColour())
293 return new java.lang.Integer(target.getGraphColour());
296 public void setValue(java.lang.Object object, java.lang.Object value)
297 throws IllegalStateException, IllegalArgumentException
301 Annotation target = (Annotation) object;
302 // if null, use delete method for optional primitives
305 target.deleteGraphColour();
308 target.setGraphColour(((java.lang.Integer) value).intValue());
309 } catch (java.lang.Exception ex)
311 throw new IllegalStateException(ex.toString());
315 public java.lang.Object newInstance(java.lang.Object parent)
320 desc.setHandler(handler);
321 desc.setMultivalued(false);
322 addFieldDescriptor(desc);
324 // -- validation code for: _graphColour
325 fieldValidator = new org.exolab.castor.xml.FieldValidator();
327 org.exolab.castor.xml.validators.IntValidator typeValidator;
328 typeValidator = new org.exolab.castor.xml.validators.IntValidator();
329 fieldValidator.setValidator(typeValidator);
330 typeValidator.setMinInclusive(-2147483648);
331 typeValidator.setMaxInclusive(2147483647);
333 desc.setValidator(fieldValidator);
335 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
336 java.lang.Integer.TYPE, "_graphGroup", "graphGroup",
337 org.exolab.castor.xml.NodeType.Attribute);
338 handler = new org.exolab.castor.xml.XMLFieldHandler()
340 public java.lang.Object getValue(java.lang.Object object)
341 throws IllegalStateException
343 Annotation target = (Annotation) object;
344 if (!target.hasGraphGroup())
348 return new java.lang.Integer(target.getGraphGroup());
351 public void setValue(java.lang.Object object, java.lang.Object value)
352 throws IllegalStateException, IllegalArgumentException
356 Annotation target = (Annotation) object;
357 // if null, use delete method for optional primitives
360 target.deleteGraphGroup();
363 target.setGraphGroup(((java.lang.Integer) value).intValue());
364 } catch (java.lang.Exception ex)
366 throw new IllegalStateException(ex.toString());
370 public java.lang.Object newInstance(java.lang.Object parent)
375 desc.setHandler(handler);
376 desc.setMultivalued(false);
377 addFieldDescriptor(desc);
379 // -- validation code for: _graphGroup
380 fieldValidator = new org.exolab.castor.xml.FieldValidator();
382 org.exolab.castor.xml.validators.IntValidator typeValidator;
383 typeValidator = new org.exolab.castor.xml.validators.IntValidator();
384 fieldValidator.setValidator(typeValidator);
385 typeValidator.setMinInclusive(-2147483648);
386 typeValidator.setMaxInclusive(2147483647);
388 desc.setValidator(fieldValidator);
390 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
391 java.lang.Integer.TYPE, "_graphHeight", "graphHeight",
392 org.exolab.castor.xml.NodeType.Attribute);
393 handler = new org.exolab.castor.xml.XMLFieldHandler()
395 public java.lang.Object getValue(java.lang.Object object)
396 throws IllegalStateException
398 Annotation target = (Annotation) object;
399 if (!target.hasGraphHeight())
403 return new java.lang.Integer(target.getGraphHeight());
406 public void setValue(java.lang.Object object, java.lang.Object value)
407 throws IllegalStateException, IllegalArgumentException
411 Annotation target = (Annotation) object;
412 // if null, use delete method for optional primitives
415 target.deleteGraphHeight();
418 target.setGraphHeight(((java.lang.Integer) value).intValue());
419 } catch (java.lang.Exception ex)
421 throw new IllegalStateException(ex.toString());
425 public java.lang.Object newInstance(java.lang.Object parent)
430 desc.setHandler(handler);
431 desc.setMultivalued(false);
432 addFieldDescriptor(desc);
434 // -- validation code for: _graphHeight
435 fieldValidator = new org.exolab.castor.xml.FieldValidator();
437 org.exolab.castor.xml.validators.IntValidator typeValidator;
438 typeValidator = new org.exolab.castor.xml.validators.IntValidator();
439 fieldValidator.setValidator(typeValidator);
440 typeValidator.setMinInclusive(-2147483648);
441 typeValidator.setMaxInclusive(2147483647);
443 desc.setValidator(fieldValidator);
445 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
446 java.lang.String.class, "_id", "id",
447 org.exolab.castor.xml.NodeType.Attribute);
448 desc.setImmutable(true);
449 handler = new org.exolab.castor.xml.XMLFieldHandler()
451 public java.lang.Object getValue(java.lang.Object object)
452 throws IllegalStateException
454 Annotation target = (Annotation) object;
455 return target.getId();
458 public void setValue(java.lang.Object object, java.lang.Object value)
459 throws IllegalStateException, IllegalArgumentException
463 Annotation target = (Annotation) object;
464 target.setId((java.lang.String) value);
465 } catch (java.lang.Exception ex)
467 throw new IllegalStateException(ex.toString());
471 public java.lang.Object newInstance(java.lang.Object parent)
476 desc.setHandler(handler);
477 desc.setMultivalued(false);
478 addFieldDescriptor(desc);
480 // -- validation code for: _id
481 fieldValidator = new org.exolab.castor.xml.FieldValidator();
483 org.exolab.castor.xml.validators.StringValidator typeValidator;
484 typeValidator = new org.exolab.castor.xml.validators.StringValidator();
485 fieldValidator.setValidator(typeValidator);
486 typeValidator.setWhiteSpace("preserve");
488 desc.setValidator(fieldValidator);
490 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
491 java.lang.Boolean.TYPE, "_scoreOnly", "scoreOnly",
492 org.exolab.castor.xml.NodeType.Attribute);
493 handler = new org.exolab.castor.xml.XMLFieldHandler()
495 public java.lang.Object getValue(java.lang.Object object)
496 throws IllegalStateException
498 Annotation target = (Annotation) object;
499 if (!target.hasScoreOnly())
503 return (target.getScoreOnly() ? java.lang.Boolean.TRUE
504 : java.lang.Boolean.FALSE);
507 public void setValue(java.lang.Object object, java.lang.Object value)
508 throws IllegalStateException, IllegalArgumentException
512 Annotation target = (Annotation) object;
513 // if null, use delete method for optional primitives
516 target.deleteScoreOnly();
519 target.setScoreOnly(((java.lang.Boolean) value).booleanValue());
520 } catch (java.lang.Exception ex)
522 throw new IllegalStateException(ex.toString());
526 public java.lang.Object newInstance(java.lang.Object parent)
531 desc.setHandler(handler);
532 desc.setMultivalued(false);
533 addFieldDescriptor(desc);
535 // -- validation code for: _scoreOnly
536 fieldValidator = new org.exolab.castor.xml.FieldValidator();
538 org.exolab.castor.xml.validators.BooleanValidator typeValidator;
539 typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
540 fieldValidator.setValidator(typeValidator);
542 desc.setValidator(fieldValidator);
544 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
545 java.lang.Double.TYPE, "_score", "score",
546 org.exolab.castor.xml.NodeType.Attribute);
547 handler = new org.exolab.castor.xml.XMLFieldHandler()
549 public java.lang.Object getValue(java.lang.Object object)
550 throws IllegalStateException
552 Annotation target = (Annotation) object;
553 if (!target.hasScore())
557 return new java.lang.Double(target.getScore());
560 public void setValue(java.lang.Object object, java.lang.Object value)
561 throws IllegalStateException, IllegalArgumentException
565 Annotation target = (Annotation) object;
566 // if null, use delete method for optional primitives
569 target.deleteScore();
572 target.setScore(((java.lang.Double) value).doubleValue());
573 } catch (java.lang.Exception ex)
575 throw new IllegalStateException(ex.toString());
579 public java.lang.Object newInstance(java.lang.Object parent)
584 desc.setHandler(handler);
585 desc.setMultivalued(false);
586 addFieldDescriptor(desc);
588 // -- validation code for: _score
589 fieldValidator = new org.exolab.castor.xml.FieldValidator();
591 org.exolab.castor.xml.validators.DoubleValidator typeValidator;
592 typeValidator = new org.exolab.castor.xml.validators.DoubleValidator();
593 fieldValidator.setValidator(typeValidator);
594 typeValidator.setMinInclusive(-1.7976931348623157E308);
595 typeValidator.setMaxInclusive(1.7976931348623157E308);
597 desc.setValidator(fieldValidator);
599 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
600 java.lang.Boolean.TYPE, "_visible", "visible",
601 org.exolab.castor.xml.NodeType.Attribute);
602 handler = new org.exolab.castor.xml.XMLFieldHandler()
604 public java.lang.Object getValue(java.lang.Object object)
605 throws IllegalStateException
607 Annotation target = (Annotation) object;
608 if (!target.hasVisible())
612 return (target.getVisible() ? java.lang.Boolean.TRUE
613 : java.lang.Boolean.FALSE);
616 public void setValue(java.lang.Object object, java.lang.Object value)
617 throws IllegalStateException, IllegalArgumentException
621 Annotation target = (Annotation) object;
622 // if null, use delete method for optional primitives
625 target.deleteVisible();
628 target.setVisible(((java.lang.Boolean) value).booleanValue());
629 } catch (java.lang.Exception ex)
631 throw new IllegalStateException(ex.toString());
635 public java.lang.Object newInstance(java.lang.Object parent)
640 desc.setHandler(handler);
641 desc.setMultivalued(false);
642 addFieldDescriptor(desc);
644 // -- validation code for: _visible
645 fieldValidator = new org.exolab.castor.xml.FieldValidator();
647 org.exolab.castor.xml.validators.BooleanValidator typeValidator;
648 typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
649 fieldValidator.setValidator(typeValidator);
651 desc.setValidator(fieldValidator);
652 // -- _centreColLabels
653 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
654 java.lang.Boolean.TYPE, "_centreColLabels", "centreColLabels",
655 org.exolab.castor.xml.NodeType.Attribute);
656 handler = new org.exolab.castor.xml.XMLFieldHandler()
658 public java.lang.Object getValue(java.lang.Object object)
659 throws IllegalStateException
661 Annotation target = (Annotation) object;
662 if (!target.hasCentreColLabels())
666 return (target.getCentreColLabels() ? java.lang.Boolean.TRUE
667 : java.lang.Boolean.FALSE);
670 public void setValue(java.lang.Object object, java.lang.Object value)
671 throws IllegalStateException, IllegalArgumentException
675 Annotation target = (Annotation) object;
676 // if null, use delete method for optional primitives
679 target.deleteCentreColLabels();
682 target.setCentreColLabels(((java.lang.Boolean) value)
684 } catch (java.lang.Exception ex)
686 throw new IllegalStateException(ex.toString());
690 public java.lang.Object newInstance(java.lang.Object parent)
695 desc.setHandler(handler);
696 desc.setMultivalued(false);
697 addFieldDescriptor(desc);
699 // -- validation code for: _centreColLabels
700 fieldValidator = new org.exolab.castor.xml.FieldValidator();
702 org.exolab.castor.xml.validators.BooleanValidator typeValidator;
703 typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
704 fieldValidator.setValidator(typeValidator);
706 desc.setValidator(fieldValidator);
707 // -- _scaleColLabels
708 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
709 java.lang.Boolean.TYPE, "_scaleColLabels", "scaleColLabels",
710 org.exolab.castor.xml.NodeType.Attribute);
711 handler = new org.exolab.castor.xml.XMLFieldHandler()
713 public java.lang.Object getValue(java.lang.Object object)
714 throws IllegalStateException
716 Annotation target = (Annotation) object;
717 if (!target.hasScaleColLabels())
721 return (target.getScaleColLabels() ? java.lang.Boolean.TRUE
722 : java.lang.Boolean.FALSE);
725 public void setValue(java.lang.Object object, java.lang.Object value)
726 throws IllegalStateException, IllegalArgumentException
730 Annotation target = (Annotation) object;
731 // if null, use delete method for optional primitives
734 target.deleteScaleColLabels();
737 target.setScaleColLabels(((java.lang.Boolean) value)
739 } catch (java.lang.Exception ex)
741 throw new IllegalStateException(ex.toString());
745 public java.lang.Object newInstance(java.lang.Object parent)
750 desc.setHandler(handler);
751 desc.setMultivalued(false);
752 addFieldDescriptor(desc);
754 // -- validation code for: _scaleColLabels
755 fieldValidator = new org.exolab.castor.xml.FieldValidator();
757 org.exolab.castor.xml.validators.BooleanValidator typeValidator;
758 typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
759 fieldValidator.setValidator(typeValidator);
761 desc.setValidator(fieldValidator);
762 // -- _showAllColLabels
763 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
764 java.lang.Boolean.TYPE, "_showAllColLabels",
765 "showAllColLabels", org.exolab.castor.xml.NodeType.Attribute);
766 handler = new org.exolab.castor.xml.XMLFieldHandler()
768 public java.lang.Object getValue(java.lang.Object object)
769 throws IllegalStateException
771 Annotation target = (Annotation) object;
772 if (!target.hasShowAllColLabels())
776 return (target.getShowAllColLabels() ? java.lang.Boolean.TRUE
777 : java.lang.Boolean.FALSE);
780 public void setValue(java.lang.Object object, java.lang.Object value)
781 throws IllegalStateException, IllegalArgumentException
785 Annotation target = (Annotation) object;
786 // if null, use delete method for optional primitives
789 target.deleteShowAllColLabels();
792 target.setShowAllColLabels(((java.lang.Boolean) value)
794 } catch (java.lang.Exception ex)
796 throw new IllegalStateException(ex.toString());
800 public java.lang.Object newInstance(java.lang.Object parent)
805 desc.setHandler(handler);
806 desc.setMultivalued(false);
807 addFieldDescriptor(desc);
809 // -- validation code for: _showAllColLabels
810 fieldValidator = new org.exolab.castor.xml.FieldValidator();
812 org.exolab.castor.xml.validators.BooleanValidator typeValidator;
813 typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
814 fieldValidator.setValidator(typeValidator);
816 desc.setValidator(fieldValidator);
817 // -- _autoCalculated
818 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
819 java.lang.Boolean.TYPE, "_autoCalculated", "autoCalculated",
820 org.exolab.castor.xml.NodeType.Attribute);
821 handler = new org.exolab.castor.xml.XMLFieldHandler()
823 public java.lang.Object getValue(java.lang.Object object)
824 throws IllegalStateException
826 Annotation target = (Annotation) object;
827 if (!target.hasAutoCalculated())
831 return (target.getAutoCalculated() ? java.lang.Boolean.TRUE
832 : java.lang.Boolean.FALSE);
835 public void setValue(java.lang.Object object, java.lang.Object value)
836 throws IllegalStateException, IllegalArgumentException
840 Annotation target = (Annotation) object;
841 // if null, use delete method for optional primitives
844 target.deleteAutoCalculated();
847 target.setAutoCalculated(((java.lang.Boolean) value)
849 } catch (java.lang.Exception ex)
851 throw new IllegalStateException(ex.toString());
855 public java.lang.Object newInstance(java.lang.Object parent)
860 desc.setHandler(handler);
861 desc.setMultivalued(false);
862 addFieldDescriptor(desc);
864 // -- validation code for: _autoCalculated
865 fieldValidator = new org.exolab.castor.xml.FieldValidator();
867 org.exolab.castor.xml.validators.BooleanValidator typeValidator;
868 typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
869 fieldValidator.setValidator(typeValidator);
871 desc.setValidator(fieldValidator);
872 // -- _belowAlignment
873 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
874 java.lang.Boolean.TYPE, "_belowAlignment", "belowAlignment",
875 org.exolab.castor.xml.NodeType.Attribute);
876 handler = new org.exolab.castor.xml.XMLFieldHandler()
878 public java.lang.Object getValue(java.lang.Object object)
879 throws IllegalStateException
881 Annotation target = (Annotation) object;
882 if (!target.hasBelowAlignment())
886 return (target.getBelowAlignment() ? java.lang.Boolean.TRUE
887 : java.lang.Boolean.FALSE);
890 public void setValue(java.lang.Object object, java.lang.Object value)
891 throws IllegalStateException, IllegalArgumentException
895 Annotation target = (Annotation) object;
896 // if null, use delete method for optional primitives
899 target.deleteBelowAlignment();
902 target.setBelowAlignment(((java.lang.Boolean) value)
904 } catch (java.lang.Exception ex)
906 throw new IllegalStateException(ex.toString());
910 public java.lang.Object newInstance(java.lang.Object parent)
915 desc.setHandler(handler);
916 desc.setMultivalued(false);
917 addFieldDescriptor(desc);
919 // -- validation code for: _belowAlignment
920 fieldValidator = new org.exolab.castor.xml.FieldValidator();
922 org.exolab.castor.xml.validators.BooleanValidator typeValidator;
923 typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
924 fieldValidator.setValidator(typeValidator);
926 desc.setValidator(fieldValidator);
928 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
929 java.lang.String.class, "_calcId", "calcId",
930 org.exolab.castor.xml.NodeType.Attribute);
931 desc.setImmutable(true);
932 handler = new org.exolab.castor.xml.XMLFieldHandler()
934 public java.lang.Object getValue(java.lang.Object object)
935 throws IllegalStateException
937 Annotation target = (Annotation) object;
938 return target.getCalcId();
941 public void setValue(java.lang.Object object, java.lang.Object value)
942 throws IllegalStateException, IllegalArgumentException
946 Annotation target = (Annotation) object;
947 target.setCalcId((java.lang.String) value);
948 } catch (java.lang.Exception ex)
950 throw new IllegalStateException(ex.toString());
954 public java.lang.Object newInstance(java.lang.Object parent)
959 desc.setHandler(handler);
960 desc.setMultivalued(false);
961 addFieldDescriptor(desc);
963 // -- validation code for: _calcId
964 fieldValidator = new org.exolab.castor.xml.FieldValidator();
966 org.exolab.castor.xml.validators.StringValidator typeValidator;
967 typeValidator = new org.exolab.castor.xml.validators.StringValidator();
968 fieldValidator.setValidator(typeValidator);
969 typeValidator.setWhiteSpace("preserve");
971 desc.setValidator(fieldValidator);
972 // -- initialize element descriptors
974 // -- _annotationElementList
975 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
976 jalview.schemabinding.version2.AnnotationElement.class,
977 "_annotationElementList", "annotationElement",
978 org.exolab.castor.xml.NodeType.Element);
979 handler = new org.exolab.castor.xml.XMLFieldHandler()
981 public java.lang.Object getValue(java.lang.Object object)
982 throws IllegalStateException
984 Annotation target = (Annotation) object;
985 return target.getAnnotationElement();
988 public void setValue(java.lang.Object object, java.lang.Object value)
989 throws IllegalStateException, IllegalArgumentException
993 Annotation target = (Annotation) object;
994 target.addAnnotationElement((jalview.schemabinding.version2.AnnotationElement) value);
995 } catch (java.lang.Exception ex)
997 throw new IllegalStateException(ex.toString());
1001 public void resetValue(Object object) throws IllegalStateException,
1002 IllegalArgumentException
1006 Annotation target = (Annotation) object;
1007 target.removeAllAnnotationElement();
1008 } catch (java.lang.Exception ex)
1010 throw new IllegalStateException(ex.toString());
1014 public java.lang.Object newInstance(java.lang.Object parent)
1016 return new jalview.schemabinding.version2.AnnotationElement();
1019 desc.setHandler(handler);
1020 desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
1021 desc.setMultivalued(true);
1022 addFieldDescriptor(desc);
1024 // -- validation code for: _annotationElementList
1025 fieldValidator = new org.exolab.castor.xml.FieldValidator();
1026 fieldValidator.setMinOccurs(0);
1029 desc.setValidator(fieldValidator);
1031 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
1032 java.lang.String.class, "_label", "label",
1033 org.exolab.castor.xml.NodeType.Element);
1034 desc.setImmutable(true);
1035 handler = new org.exolab.castor.xml.XMLFieldHandler()
1037 public java.lang.Object getValue(java.lang.Object object)
1038 throws IllegalStateException
1040 Annotation target = (Annotation) object;
1041 return target.getLabel();
1044 public void setValue(java.lang.Object object, java.lang.Object value)
1045 throws IllegalStateException, IllegalArgumentException
1049 Annotation target = (Annotation) object;
1050 target.setLabel((java.lang.String) value);
1051 } catch (java.lang.Exception ex)
1053 throw new IllegalStateException(ex.toString());
1057 public java.lang.Object newInstance(java.lang.Object parent)
1062 desc.setHandler(handler);
1063 desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
1064 desc.setRequired(true);
1065 desc.setMultivalued(false);
1066 addFieldDescriptor(desc);
1068 // -- validation code for: _label
1069 fieldValidator = new org.exolab.castor.xml.FieldValidator();
1070 fieldValidator.setMinOccurs(1);
1072 org.exolab.castor.xml.validators.StringValidator typeValidator;
1073 typeValidator = new org.exolab.castor.xml.validators.StringValidator();
1074 fieldValidator.setValidator(typeValidator);
1075 typeValidator.setWhiteSpace("preserve");
1077 desc.setValidator(fieldValidator);
1079 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
1080 java.lang.String.class, "_description", "description",
1081 org.exolab.castor.xml.NodeType.Element);
1082 desc.setImmutable(true);
1083 handler = new org.exolab.castor.xml.XMLFieldHandler()
1085 public java.lang.Object getValue(java.lang.Object object)
1086 throws IllegalStateException
1088 Annotation target = (Annotation) object;
1089 return target.getDescription();
1092 public void setValue(java.lang.Object object, java.lang.Object value)
1093 throws IllegalStateException, IllegalArgumentException
1097 Annotation target = (Annotation) object;
1098 target.setDescription((java.lang.String) value);
1099 } catch (java.lang.Exception ex)
1101 throw new IllegalStateException(ex.toString());
1105 public java.lang.Object newInstance(java.lang.Object parent)
1110 desc.setHandler(handler);
1111 desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
1112 desc.setMultivalued(false);
1113 addFieldDescriptor(desc);
1115 // -- validation code for: _description
1116 fieldValidator = new org.exolab.castor.xml.FieldValidator();
1118 org.exolab.castor.xml.validators.StringValidator typeValidator;
1119 typeValidator = new org.exolab.castor.xml.validators.StringValidator();
1120 fieldValidator.setValidator(typeValidator);
1121 typeValidator.setWhiteSpace("preserve");
1123 desc.setValidator(fieldValidator);
1124 // -- _thresholdLine
1125 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
1126 jalview.schemabinding.version2.ThresholdLine.class,
1127 "_thresholdLine", "thresholdLine",
1128 org.exolab.castor.xml.NodeType.Element);
1129 handler = new org.exolab.castor.xml.XMLFieldHandler()
1131 public java.lang.Object getValue(java.lang.Object object)
1132 throws IllegalStateException
1134 Annotation target = (Annotation) object;
1135 return target.getThresholdLine();
1138 public void setValue(java.lang.Object object, java.lang.Object value)
1139 throws IllegalStateException, IllegalArgumentException
1143 Annotation target = (Annotation) object;
1144 target.setThresholdLine((jalview.schemabinding.version2.ThresholdLine) value);
1145 } catch (java.lang.Exception ex)
1147 throw new IllegalStateException(ex.toString());
1151 public java.lang.Object newInstance(java.lang.Object parent)
1153 return new jalview.schemabinding.version2.ThresholdLine();
1156 desc.setHandler(handler);
1157 desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
1158 desc.setMultivalued(false);
1159 addFieldDescriptor(desc);
1161 // -- validation code for: _thresholdLine
1162 fieldValidator = new org.exolab.castor.xml.FieldValidator();
1165 desc.setValidator(fieldValidator);
1173 * Method getAccessMode.
1175 * @return the access mode specified for this class.
1177 public org.exolab.castor.mapping.AccessMode getAccessMode()
1183 * Method getIdentity.
1185 * @return the identity field, null if this class has no identity.
1187 public org.exolab.castor.mapping.FieldDescriptor getIdentity()
1189 return super.getIdentity();
1193 * Method getJavaClass.
1195 * @return the Java class represented by this descriptor.
1197 public java.lang.Class getJavaClass()
1199 return jalview.schemabinding.version2.Annotation.class;
1203 * Method getNameSpacePrefix.
1205 * @return the namespace prefix to use when marshaling as XML.
1207 public java.lang.String getNameSpacePrefix()
1213 * Method getNameSpaceURI.
1215 * @return the namespace URI used when marshaling and unmarshaling as XML.
1217 public java.lang.String getNameSpaceURI()
1223 * Method getValidator.
1225 * @return a specific validator for the class described by this
1228 public org.exolab.castor.xml.TypeValidator getValidator()
1234 * Method getXMLName.
1236 * @return the XML Name for the Class being described.
1238 public java.lang.String getXMLName()
1244 * Method isElementDefinition.
1246 * @return true if XML schema definition of this Class is that of a global
1247 * element or element with anonymous type definition.
1249 public boolean isElementDefinition()
1251 return _elementDefinition;