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jalviewX

  1. Project Clover database Wed Oct 31 2018 15:13:58 GMT
  2. Package jalview.schemabinding.version2.descriptors

File JSeqDescriptor.java

 

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19% of files have more coverage

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26
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43
1
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547
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0.29
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1.63

Classes

Class Line # Actions
JSeqDescriptor 21 242 70 77
0.752411675.2%
 

Contributing tests

This file is covered by 14 tests. .

Source view

1    /*
2    * This class was automatically generated with
3    * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
4    * Schema.
5    * $Id$
6    */
7   
8    package jalview.schemabinding.version2.descriptors;
9   
10    //---------------------------------/
11    //- Imported classes and packages -/
12    //---------------------------------/
13   
14    import jalview.schemabinding.version2.JSeq;
15   
16    /**
17    * Class JSeqDescriptor.
18    *
19    * @version $Revision$ $Date$
20    */
 
21    public class JSeqDescriptor extends
22    org.exolab.castor.xml.util.XMLClassDescriptorImpl
23    {
24   
25    // --------------------------/
26    // - Class/Member Variables -/
27    // --------------------------/
28   
29    /**
30    * Field _elementDefinition.
31    */
32    private boolean _elementDefinition;
33   
34    /**
35    * Field _nsPrefix.
36    */
37    private java.lang.String _nsPrefix;
38   
39    /**
40    * Field _nsURI.
41    */
42    private java.lang.String _nsURI;
43   
44    /**
45    * Field _xmlName.
46    */
47    private java.lang.String _xmlName;
48   
49    // ----------------/
50    // - Constructors -/
51    // ----------------/
52   
 
53  2195 toggle public JSeqDescriptor()
54    {
55  2195 super();
56  2195 _nsURI = "www.jalview.org";
57  2195 _xmlName = "JSeq";
58  2195 _elementDefinition = true;
59   
60    // -- set grouping compositor
61  2195 setCompositorAsSequence();
62  2195 org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
63  2195 org.exolab.castor.mapping.FieldHandler handler = null;
64  2195 org.exolab.castor.xml.FieldValidator fieldValidator = null;
65    // -- initialize attribute descriptors
66   
67    // -- _colour
68  2195 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
69    java.lang.Integer.TYPE, "_colour", "colour",
70    org.exolab.castor.xml.NodeType.Attribute);
71  2195 handler = new org.exolab.castor.xml.XMLFieldHandler()
72    {
 
73  930 toggle public java.lang.Object getValue(java.lang.Object object)
74    throws IllegalStateException
75    {
76  930 JSeq target = (JSeq) object;
77  930 if (!target.hasColour())
78    {
79  0 return null;
80    }
81  930 return new java.lang.Integer(target.getColour());
82    }
83   
 
84  1265 toggle public void setValue(java.lang.Object object, java.lang.Object value)
85    throws IllegalStateException, IllegalArgumentException
86    {
87  1265 try
88    {
89  1265 JSeq target = (JSeq) object;
90    // if null, use delete method for optional primitives
91  1265 if (value == null)
92    {
93  0 target.deleteColour();
94  0 return;
95    }
96  1265 target.setColour(((java.lang.Integer) value).intValue());
97    } catch (java.lang.Exception ex)
98    {
99  0 throw new IllegalStateException(ex.toString());
100    }
101    }
102   
 
103  0 toggle public java.lang.Object newInstance(java.lang.Object parent)
104    {
105  0 return null;
106    }
107    };
108  2195 desc.setHandler(handler);
109  2195 desc.setMultivalued(false);
110  2195 addFieldDescriptor(desc);
111   
112    // -- validation code for: _colour
113  2195 fieldValidator = new org.exolab.castor.xml.FieldValidator();
114    { // -- local scope
115  2195 org.exolab.castor.xml.validators.IntValidator typeValidator;
116  2195 typeValidator = new org.exolab.castor.xml.validators.IntValidator();
117  2195 fieldValidator.setValidator(typeValidator);
118  2195 typeValidator.setMinInclusive(-2147483648);
119  2195 typeValidator.setMaxInclusive(2147483647);
120    }
121  2195 desc.setValidator(fieldValidator);
122    // -- _start
123  2195 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
124    java.lang.Integer.TYPE, "_start", "start",
125    org.exolab.castor.xml.NodeType.Attribute);
126  2195 handler = new org.exolab.castor.xml.XMLFieldHandler()
127    {
 
128  930 toggle public java.lang.Object getValue(java.lang.Object object)
129    throws IllegalStateException
130    {
131  930 JSeq target = (JSeq) object;
132  930 if (!target.hasStart())
133    {
134  0 return null;
135    }
136  930 return new java.lang.Integer(target.getStart());
137    }
138   
 
139  1265 toggle public void setValue(java.lang.Object object, java.lang.Object value)
140    throws IllegalStateException, IllegalArgumentException
141    {
142  1265 try
143    {
144  1265 JSeq target = (JSeq) object;
145    // ignore null values for non optional primitives
146  1265 if (value == null)
147    {
148  0 return;
149    }
150   
151  1265 target.setStart(((java.lang.Integer) value).intValue());
152    } catch (java.lang.Exception ex)
153    {
154  0 throw new IllegalStateException(ex.toString());
155    }
156    }
157   
 
158  0 toggle public java.lang.Object newInstance(java.lang.Object parent)
159    {
160  0 return null;
161    }
162    };
163  2195 desc.setHandler(handler);
164  2195 desc.setRequired(true);
165  2195 desc.setMultivalued(false);
166  2195 addFieldDescriptor(desc);
167   
168    // -- validation code for: _start
169  2195 fieldValidator = new org.exolab.castor.xml.FieldValidator();
170  2195 fieldValidator.setMinOccurs(1);
171    { // -- local scope
172  2195 org.exolab.castor.xml.validators.IntValidator typeValidator;
173  2195 typeValidator = new org.exolab.castor.xml.validators.IntValidator();
174  2195 fieldValidator.setValidator(typeValidator);
175  2195 typeValidator.setMinInclusive(-2147483648);
176  2195 typeValidator.setMaxInclusive(2147483647);
177    }
178  2195 desc.setValidator(fieldValidator);
179    // -- _end
180  2195 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
181    java.lang.Integer.TYPE, "_end", "end",
182    org.exolab.castor.xml.NodeType.Attribute);
183  2195 handler = new org.exolab.castor.xml.XMLFieldHandler()
184    {
 
185  930 toggle public java.lang.Object getValue(java.lang.Object object)
186    throws IllegalStateException
187    {
188  930 JSeq target = (JSeq) object;
189  930 if (!target.hasEnd())
190    {
191  0 return null;
192    }
193  930 return new java.lang.Integer(target.getEnd());
194    }
195   
 
196  1265 toggle public void setValue(java.lang.Object object, java.lang.Object value)
197    throws IllegalStateException, IllegalArgumentException
198    {
199  1265 try
200    {
201  1265 JSeq target = (JSeq) object;
202    // ignore null values for non optional primitives
203  1265 if (value == null)
204    {
205  0 return;
206    }
207   
208  1265 target.setEnd(((java.lang.Integer) value).intValue());
209    } catch (java.lang.Exception ex)
210    {
211  0 throw new IllegalStateException(ex.toString());
212    }
213    }
214   
 
215  0 toggle public java.lang.Object newInstance(java.lang.Object parent)
216    {
217  0 return null;
218    }
219    };
220  2195 desc.setHandler(handler);
221  2195 desc.setRequired(true);
222  2195 desc.setMultivalued(false);
223  2195 addFieldDescriptor(desc);
224   
225    // -- validation code for: _end
226  2195 fieldValidator = new org.exolab.castor.xml.FieldValidator();
227  2195 fieldValidator.setMinOccurs(1);
228    { // -- local scope
229  2195 org.exolab.castor.xml.validators.IntValidator typeValidator;
230  2195 typeValidator = new org.exolab.castor.xml.validators.IntValidator();
231  2195 fieldValidator.setValidator(typeValidator);
232  2195 typeValidator.setMinInclusive(-2147483648);
233  2195 typeValidator.setMaxInclusive(2147483647);
234    }
235  2195 desc.setValidator(fieldValidator);
236    // -- _id
237  2195 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
238    java.lang.String.class, "_id", "id",
239    org.exolab.castor.xml.NodeType.Attribute);
240  2195 desc.setImmutable(true);
241  2195 handler = new org.exolab.castor.xml.XMLFieldHandler()
242    {
 
243  930 toggle public java.lang.Object getValue(java.lang.Object object)
244    throws IllegalStateException
245    {
246  930 JSeq target = (JSeq) object;
247  930 return target.getId();
248    }
249   
 
250  1265 toggle public void setValue(java.lang.Object object, java.lang.Object value)
251    throws IllegalStateException, IllegalArgumentException
252    {
253  1265 try
254    {
255  1265 JSeq target = (JSeq) object;
256  1265 target.setId((java.lang.String) value);
257    } catch (java.lang.Exception ex)
258    {
259  0 throw new IllegalStateException(ex.toString());
260    }
261    }
262   
 
263  0 toggle public java.lang.Object newInstance(java.lang.Object parent)
264    {
265  0 return null;
266    }
267    };
268  2195 desc.setHandler(handler);
269  2195 desc.setRequired(true);
270  2195 desc.setMultivalued(false);
271  2195 addFieldDescriptor(desc);
272   
273    // -- validation code for: _id
274  2195 fieldValidator = new org.exolab.castor.xml.FieldValidator();
275  2195 fieldValidator.setMinOccurs(1);
276    { // -- local scope
277  2195 org.exolab.castor.xml.validators.StringValidator typeValidator;
278  2195 typeValidator = new org.exolab.castor.xml.validators.StringValidator();
279  2195 fieldValidator.setValidator(typeValidator);
280  2195 typeValidator.setWhiteSpace("preserve");
281    }
282  2195 desc.setValidator(fieldValidator);
283    // -- _hidden
284  2195 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
285    java.lang.Boolean.TYPE, "_hidden", "hidden",
286    org.exolab.castor.xml.NodeType.Attribute);
287  2195 handler = new org.exolab.castor.xml.XMLFieldHandler()
288    {
 
289  930 toggle public java.lang.Object getValue(java.lang.Object object)
290    throws IllegalStateException
291    {
292  930 JSeq target = (JSeq) object;
293  930 if (!target.hasHidden())
294    {
295  550 return null;
296    }
297  380 return (target.getHidden() ? java.lang.Boolean.TRUE
298    : java.lang.Boolean.FALSE);
299    }
300   
 
301  990 toggle public void setValue(java.lang.Object object, java.lang.Object value)
302    throws IllegalStateException, IllegalArgumentException
303    {
304  990 try
305    {
306  990 JSeq target = (JSeq) object;
307    // if null, use delete method for optional primitives
308  990 if (value == null)
309    {
310  0 target.deleteHidden();
311  0 return;
312    }
313  990 target.setHidden(((java.lang.Boolean) value).booleanValue());
314    } catch (java.lang.Exception ex)
315    {
316  0 throw new IllegalStateException(ex.toString());
317    }
318    }
319   
 
320  0 toggle public java.lang.Object newInstance(java.lang.Object parent)
321    {
322  0 return null;
323    }
324    };
325  2195 desc.setHandler(handler);
326  2195 desc.setMultivalued(false);
327  2195 addFieldDescriptor(desc);
328   
329    // -- validation code for: _hidden
330  2195 fieldValidator = new org.exolab.castor.xml.FieldValidator();
331    { // -- local scope
332  2195 org.exolab.castor.xml.validators.BooleanValidator typeValidator;
333  2195 typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
334  2195 fieldValidator.setValidator(typeValidator);
335    }
336  2195 desc.setValidator(fieldValidator);
337    // -- _viewreference
338  2195 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
339    java.lang.Boolean.TYPE, "_viewreference", "viewreference",
340    org.exolab.castor.xml.NodeType.Attribute);
341  2195 handler = new org.exolab.castor.xml.XMLFieldHandler()
342    {
 
343  930 toggle public java.lang.Object getValue(java.lang.Object object)
344    throws IllegalStateException
345    {
346  930 JSeq target = (JSeq) object;
347  930 if (!target.hasViewreference())
348    {
349  770 return null;
350    }
351  160 return (target.getViewreference() ? java.lang.Boolean.TRUE
352    : java.lang.Boolean.FALSE);
353    }
354   
 
355  80 toggle public void setValue(java.lang.Object object, java.lang.Object value)
356    throws IllegalStateException, IllegalArgumentException
357    {
358  80 try
359    {
360  80 JSeq target = (JSeq) object;
361    // if null, use delete method for optional primitives
362  80 if (value == null)
363    {
364  0 target.deleteViewreference();
365  0 return;
366    }
367  80 target.setViewreference(((java.lang.Boolean) value)
368    .booleanValue());
369    } catch (java.lang.Exception ex)
370    {
371  0 throw new IllegalStateException(ex.toString());
372    }
373    }
374   
 
375  0 toggle public java.lang.Object newInstance(java.lang.Object parent)
376    {
377  0 return null;
378    }
379    };
380  2195 desc.setHandler(handler);
381  2195 desc.setMultivalued(false);
382  2195 addFieldDescriptor(desc);
383   
384    // -- validation code for: _viewreference
385  2195 fieldValidator = new org.exolab.castor.xml.FieldValidator();
386    { // -- local scope
387  2195 org.exolab.castor.xml.validators.BooleanValidator typeValidator;
388  2195 typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
389  2195 fieldValidator.setValidator(typeValidator);
390    }
391  2195 desc.setValidator(fieldValidator);
392    // -- initialize element descriptors
393   
394    // -- _featuresList
395  2195 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
396    jalview.schemabinding.version2.Features.class, "_featuresList",
397    "features", org.exolab.castor.xml.NodeType.Element);
398  2195 handler = new org.exolab.castor.xml.XMLFieldHandler()
399    {
 
400  930 toggle public java.lang.Object getValue(java.lang.Object object)
401    throws IllegalStateException
402    {
403  930 JSeq target = (JSeq) object;
404  930 return target.getFeatures();
405    }
406   
 
407  33538 toggle public void setValue(java.lang.Object object, java.lang.Object value)
408    throws IllegalStateException, IllegalArgumentException
409    {
410  33538 try
411    {
412  33538 JSeq target = (JSeq) object;
413  33538 target.addFeatures((jalview.schemabinding.version2.Features) value);
414    } catch (java.lang.Exception ex)
415    {
416  0 throw new IllegalStateException(ex.toString());
417    }
418    }
419   
 
420  0 toggle public void resetValue(Object object) throws IllegalStateException,
421    IllegalArgumentException
422    {
423  0 try
424    {
425  0 JSeq target = (JSeq) object;
426  0 target.removeAllFeatures();
427    } catch (java.lang.Exception ex)
428    {
429  0 throw new IllegalStateException(ex.toString());
430    }
431    }
432   
 
433  33538 toggle public java.lang.Object newInstance(java.lang.Object parent)
434    {
435  33538 return new jalview.schemabinding.version2.Features();
436    }
437    };
438  2195 desc.setHandler(handler);
439  2195 desc.setNameSpaceURI("www.jalview.org");
440  2195 desc.setMultivalued(true);
441  2195 addFieldDescriptor(desc);
442   
443    // -- validation code for: _featuresList
444  2195 fieldValidator = new org.exolab.castor.xml.FieldValidator();
445  2195 fieldValidator.setMinOccurs(0);
446    { // -- local scope
447    }
448  2195 desc.setValidator(fieldValidator);
449    // -- _pdbidsList
450  2195 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
451    jalview.schemabinding.version2.Pdbids.class, "_pdbidsList",
452    "pdbids", org.exolab.castor.xml.NodeType.Element);
453  2195 handler = new org.exolab.castor.xml.XMLFieldHandler()
454    {
 
455  930 toggle public java.lang.Object getValue(java.lang.Object object)
456    throws IllegalStateException
457    {
458  930 JSeq target = (JSeq) object;
459  930 return target.getPdbids();
460    }
461   
 
462  200 toggle public void setValue(java.lang.Object object, java.lang.Object value)
463    throws IllegalStateException, IllegalArgumentException
464    {
465  200 try
466    {
467  200 JSeq target = (JSeq) object;
468  200 target.addPdbids((jalview.schemabinding.version2.Pdbids) value);
469    } catch (java.lang.Exception ex)
470    {
471  0 throw new IllegalStateException(ex.toString());
472    }
473    }
474   
 
475  0 toggle public void resetValue(Object object) throws IllegalStateException,
476    IllegalArgumentException
477    {
478  0 try
479    {
480  0 JSeq target = (JSeq) object;
481  0 target.removeAllPdbids();
482    } catch (java.lang.Exception ex)
483    {
484  0 throw new IllegalStateException(ex.toString());
485    }
486    }
487   
 
488  200 toggle public java.lang.Object newInstance(java.lang.Object parent)
489    {
490  200 return new jalview.schemabinding.version2.Pdbids();
491    }
492    };
493  2195 desc.setHandler(handler);
494  2195 desc.setNameSpaceURI("www.jalview.org");
495  2195 desc.setMultivalued(true);
496  2195 addFieldDescriptor(desc);
497   
498    // -- validation code for: _pdbidsList
499  2195 fieldValidator = new org.exolab.castor.xml.FieldValidator();
500  2195 fieldValidator.setMinOccurs(0);
501    { // -- local scope
502    }
503  2195 desc.setValidator(fieldValidator);
504    // -- _hiddenSequencesList
505  2195 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
506    java.lang.Integer.TYPE, "_hiddenSequencesList",
507    "hiddenSequences", org.exolab.castor.xml.NodeType.Element);
508  2195 handler = new org.exolab.castor.xml.XMLFieldHandler()
509    {
 
510  930 toggle public java.lang.Object getValue(java.lang.Object object)
511    throws IllegalStateException
512    {
513  930 JSeq target = (JSeq) object;
514  930 return target.getHiddenSequences();
515    }
516   
 
517  2 toggle public void setValue(java.lang.Object object, java.lang.Object value)
518    throws IllegalStateException, IllegalArgumentException
519    {
520  2 try
521    {
522  2 JSeq target = (JSeq) object;
523    // ignore null values for non optional primitives
524  2 if (value == null)
525    {
526  0 return;
527    }
528   
529  2 target.addHiddenSequences(((java.lang.Integer) value).intValue());
530    } catch (java.lang.Exception ex)
531    {
532  0 throw new IllegalStateException(ex.toString());
533    }
534    }
535   
 
536  0 toggle public void resetValue(Object object) throws IllegalStateException,
537    IllegalArgumentException
538    {
539  0 try
540    {
541  0 JSeq target = (JSeq) object;
542  0 target.removeAllHiddenSequences();
543    } catch (java.lang.Exception ex)
544    {
545  0 throw new IllegalStateException(ex.toString());
546    }
547    }
548   
 
549  0 toggle public java.lang.Object newInstance(java.lang.Object parent)
550    {
551  0 return null;
552    }
553    };
554  2195 desc.setHandler(handler);
555  2195 desc.setNameSpaceURI("www.jalview.org");
556  2195 desc.setMultivalued(true);
557  2195 addFieldDescriptor(desc);
558   
559    // -- validation code for: _hiddenSequencesList
560  2195 fieldValidator = new org.exolab.castor.xml.FieldValidator();
561  2195 fieldValidator.setMinOccurs(0);
562    { // -- local scope
563  2195 org.exolab.castor.xml.validators.IntValidator typeValidator;
564  2195 typeValidator = new org.exolab.castor.xml.validators.IntValidator();
565  2195 fieldValidator.setValidator(typeValidator);
566  2195 typeValidator.setMinInclusive(-2147483648);
567  2195 typeValidator.setMaxInclusive(2147483647);
568    }
569  2195 desc.setValidator(fieldValidator);
570    // -- _rnaViewerList
571  2195 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
572    jalview.schemabinding.version2.RnaViewer.class,
573    "_rnaViewerList", "rnaViewer",
574    org.exolab.castor.xml.NodeType.Element);
575  2195 handler = new org.exolab.castor.xml.XMLFieldHandler()
576    {
 
577  930 toggle public java.lang.Object getValue(java.lang.Object object)
578    throws IllegalStateException
579    {
580  930 JSeq target = (JSeq) object;
581  930 return target.getRnaViewer();
582    }
583   
 
584  0 toggle public void setValue(java.lang.Object object, java.lang.Object value)
585    throws IllegalStateException, IllegalArgumentException
586    {
587  0 try
588    {
589  0 JSeq target = (JSeq) object;
590  0 target.addRnaViewer((jalview.schemabinding.version2.RnaViewer) value);
591    } catch (java.lang.Exception ex)
592    {
593  0 throw new IllegalStateException(ex.toString());
594    }
595    }
596   
 
597  0 toggle public void resetValue(Object object) throws IllegalStateException,
598    IllegalArgumentException
599    {
600  0 try
601    {
602  0 JSeq target = (JSeq) object;
603  0 target.removeAllRnaViewer();
604    } catch (java.lang.Exception ex)
605    {
606  0 throw new IllegalStateException(ex.toString());
607    }
608    }
609   
 
610  0 toggle public java.lang.Object newInstance(java.lang.Object parent)
611    {
612  0 return new jalview.schemabinding.version2.RnaViewer();
613    }
614    };
615  2195 desc.setHandler(handler);
616  2195 desc.setNameSpaceURI("www.jalview.org");
617  2195 desc.setMultivalued(true);
618  2195 addFieldDescriptor(desc);
619   
620    // -- validation code for: _rnaViewerList
621  2195 fieldValidator = new org.exolab.castor.xml.FieldValidator();
622  2195 fieldValidator.setMinOccurs(0);
623    { // -- local scope
624    }
625  2195 desc.setValidator(fieldValidator);
626    }
627   
628    // -----------/
629    // - Methods -/
630    // -----------/
631   
632    /**
633    * Method getAccessMode.
634    *
635    * @return the access mode specified for this class.
636    */
 
637  0 toggle public org.exolab.castor.mapping.AccessMode getAccessMode()
638    {
639  0 return null;
640    }
641   
642    /**
643    * Method getIdentity.
644    *
645    * @return the identity field, null if this class has no identity.
646    */
 
647  6595 toggle public org.exolab.castor.mapping.FieldDescriptor getIdentity()
648    {
649  6595 return super.getIdentity();
650    }
651   
652    /**
653    * Method getJavaClass.
654    *
655    * @return the Java class represented by this descriptor.
656    */
 
657  1730 toggle public java.lang.Class getJavaClass()
658    {
659  1730 return jalview.schemabinding.version2.JSeq.class;
660    }
661   
662    /**
663    * Method getNameSpacePrefix.
664    *
665    * @return the namespace prefix to use when marshaling as XML.
666    */
 
667  465 toggle public java.lang.String getNameSpacePrefix()
668    {
669  465 return _nsPrefix;
670    }
671   
672    /**
673    * Method getNameSpaceURI.
674    *
675    * @return the namespace URI used when marshaling and unmarshaling as XML.
676    */
 
677  0 toggle public java.lang.String getNameSpaceURI()
678    {
679  0 return _nsURI;
680    }
681   
682    /**
683    * Method getValidator.
684    *
685    * @return a specific validator for the class described by this
686    * ClassDescriptor.
687    */
 
688  465 toggle public org.exolab.castor.xml.TypeValidator getValidator()
689    {
690  465 return this;
691    }
692   
693    /**
694    * Method getXMLName.
695    *
696    * @return the XML Name for the Class being described.
697    */
 
698  4390 toggle public java.lang.String getXMLName()
699    {
700  4390 return _xmlName;
701    }
702   
703    /**
704    * Method isElementDefinition.
705    *
706    * @return true if XML schema definition of this Class is that of a global
707    * element or element with anonymous type definition.
708    */
 
709  0 toggle public boolean isElementDefinition()
710    {
711  0 return _elementDefinition;
712    }
713   
714    }