2 * This class was automatically generated with
\r
3 * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
\r
8 package uk.ac.vamsas.objects.core;
\r
10 //---------------------------------/
\r
11 //- Imported classes and packages -/
\r
12 //---------------------------------/
\r
14 import java.io.IOException;
\r
15 import java.io.Reader;
\r
16 import java.io.Serializable;
\r
17 import java.io.Writer;
\r
18 import java.util.Enumeration;
\r
19 import java.util.Vector;
\r
20 import org.exolab.castor.xml.MarshalException;
\r
21 import org.exolab.castor.xml.Marshaller;
\r
22 import org.exolab.castor.xml.Unmarshaller;
\r
23 import org.exolab.castor.xml.ValidationException;
\r
24 import org.xml.sax.ContentHandler;
\r
27 * Annotation for a rangeSpec - values can be attached for the
\r
29 * specification, and to each position within the spec. following
\r
31 * specified by the ordered set of rangeSpec (pos, seg) elements.
\r
33 * @version $Revision$ $Date$
\r
35 public class RangeAnnotation extends uk.ac.vamsas.objects.core.RangeType
\r
36 implements java.io.Serializable
\r
40 //--------------------------/
\r
41 //- Class/Member Variables -/
\r
42 //--------------------------/
\r
45 * Primary Key for vamsas object referencing
\r
48 private java.lang.String _id;
\r
53 private java.lang.String _modifiable;
\r
56 * Annotation with the same non-empty group name are grouped
\r
59 private java.lang.String _group = "";
\r
62 * A Das Feature has both a type and a Type ID. We go the
\r
63 * route of requiring the type string to be taken from a
\r
65 * vocabulary if an application expects others to make sense
\r
67 * type may qualified - so uniprot:CHAIN is a valid type name,
\r
69 * considered distinct from someotherDB:CHAIN
\r
71 private java.lang.String _type;
\r
74 * Short, meaningful name for the annotation - if this
\r
75 * is absent, then the type string should be used in its
\r
79 private java.lang.String _label;
\r
82 * Human readable description of the annotation
\r
85 private java.lang.String _description;
\r
88 * TODO: specify this - we have considered taking the GO
\r
89 * evidence codes as a model for assessing a measure of
\r
93 private java.lang.String _status;
\r
96 * Annotation Element position maps to ordered positions
\r
97 * defined by the sequence of rangeType pos positions or
\r
99 * seg start/end segments.
\r
101 private java.util.Vector _annotationElementList;
\r
104 * Ordered set of optionally named float values for the
\r
105 * whole annotation
\r
107 private java.util.Vector _scoreList;
\r
112 private java.util.Vector _linkList;
\r
115 * Note:These are mutable so an application should check
\r
118 private java.util.Vector _propertyList;
\r
121 //----------------/
\r
122 //- Constructors -/
\r
123 //----------------/
\r
125 public RangeAnnotation()
\r
129 _annotationElementList = new Vector();
\r
130 _scoreList = new Vector();
\r
131 _linkList = new Vector();
\r
132 _propertyList = new Vector();
\r
133 } //-- uk.ac.vamsas.objects.core.RangeAnnotation()
\r
141 * Method addAnnotationElement
\r
145 * @param vAnnotationElement
\r
147 public void addAnnotationElement(uk.ac.vamsas.objects.core.AnnotationElement vAnnotationElement)
\r
148 throws java.lang.IndexOutOfBoundsException
\r
150 _annotationElementList.addElement(vAnnotationElement);
\r
151 } //-- void addAnnotationElement(uk.ac.vamsas.objects.core.AnnotationElement)
\r
154 * Method addAnnotationElement
\r
159 * @param vAnnotationElement
\r
161 public void addAnnotationElement(int index, uk.ac.vamsas.objects.core.AnnotationElement vAnnotationElement)
\r
162 throws java.lang.IndexOutOfBoundsException
\r
164 _annotationElementList.insertElementAt(vAnnotationElement, index);
\r
165 } //-- void addAnnotationElement(int, uk.ac.vamsas.objects.core.AnnotationElement)
\r
174 public void addLink(uk.ac.vamsas.objects.core.Link vLink)
\r
175 throws java.lang.IndexOutOfBoundsException
\r
177 _linkList.addElement(vLink);
\r
178 } //-- void addLink(uk.ac.vamsas.objects.core.Link)
\r
188 public void addLink(int index, uk.ac.vamsas.objects.core.Link vLink)
\r
189 throws java.lang.IndexOutOfBoundsException
\r
191 _linkList.insertElementAt(vLink, index);
\r
192 } //-- void addLink(int, uk.ac.vamsas.objects.core.Link)
\r
195 * Method addProperty
\r
201 public void addProperty(uk.ac.vamsas.objects.core.Property vProperty)
\r
202 throws java.lang.IndexOutOfBoundsException
\r
204 _propertyList.addElement(vProperty);
\r
205 } //-- void addProperty(uk.ac.vamsas.objects.core.Property)
\r
208 * Method addProperty
\r
215 public void addProperty(int index, uk.ac.vamsas.objects.core.Property vProperty)
\r
216 throws java.lang.IndexOutOfBoundsException
\r
218 _propertyList.insertElementAt(vProperty, index);
\r
219 } //-- void addProperty(int, uk.ac.vamsas.objects.core.Property)
\r
228 public void addScore(uk.ac.vamsas.objects.core.Score vScore)
\r
229 throws java.lang.IndexOutOfBoundsException
\r
231 _scoreList.addElement(vScore);
\r
232 } //-- void addScore(uk.ac.vamsas.objects.core.Score)
\r
242 public void addScore(int index, uk.ac.vamsas.objects.core.Score vScore)
\r
243 throws java.lang.IndexOutOfBoundsException
\r
245 _scoreList.insertElementAt(vScore, index);
\r
246 } //-- void addScore(int, uk.ac.vamsas.objects.core.Score)
\r
249 * Method enumerateAnnotationElement
\r
253 * @return Enumeration
\r
255 public java.util.Enumeration enumerateAnnotationElement()
\r
257 return _annotationElementList.elements();
\r
258 } //-- java.util.Enumeration enumerateAnnotationElement()
\r
261 * Method enumerateLink
\r
265 * @return Enumeration
\r
267 public java.util.Enumeration enumerateLink()
\r
269 return _linkList.elements();
\r
270 } //-- java.util.Enumeration enumerateLink()
\r
273 * Method enumerateProperty
\r
277 * @return Enumeration
\r
279 public java.util.Enumeration enumerateProperty()
\r
281 return _propertyList.elements();
\r
282 } //-- java.util.Enumeration enumerateProperty()
\r
285 * Method enumerateScore
\r
289 * @return Enumeration
\r
291 public java.util.Enumeration enumerateScore()
\r
293 return _scoreList.elements();
\r
294 } //-- java.util.Enumeration enumerateScore()
\r
297 * Note: hashCode() has not been overriden
\r
302 public boolean equals(java.lang.Object obj)
\r
307 if (super.equals(obj)==false)
\r
310 if (obj instanceof RangeAnnotation) {
\r
312 RangeAnnotation temp = (RangeAnnotation)obj;
\r
313 if (this._id != null) {
\r
314 if (temp._id == null) return false;
\r
315 else if (!(this._id.equals(temp._id)))
\r
318 else if (temp._id != null)
\r
320 if (this._modifiable != null) {
\r
321 if (temp._modifiable == null) return false;
\r
322 else if (!(this._modifiable.equals(temp._modifiable)))
\r
325 else if (temp._modifiable != null)
\r
327 if (this._group != null) {
\r
328 if (temp._group == null) return false;
\r
329 else if (!(this._group.equals(temp._group)))
\r
332 else if (temp._group != null)
\r
334 if (this._type != null) {
\r
335 if (temp._type == null) return false;
\r
336 else if (!(this._type.equals(temp._type)))
\r
339 else if (temp._type != null)
\r
341 if (this._label != null) {
\r
342 if (temp._label == null) return false;
\r
343 else if (!(this._label.equals(temp._label)))
\r
346 else if (temp._label != null)
\r
348 if (this._description != null) {
\r
349 if (temp._description == null) return false;
\r
350 else if (!(this._description.equals(temp._description)))
\r
353 else if (temp._description != null)
\r
355 if (this._status != null) {
\r
356 if (temp._status == null) return false;
\r
357 else if (!(this._status.equals(temp._status)))
\r
360 else if (temp._status != null)
\r
362 if (this._annotationElementList != null) {
\r
363 if (temp._annotationElementList == null) return false;
\r
364 else if (!(this._annotationElementList.equals(temp._annotationElementList)))
\r
367 else if (temp._annotationElementList != null)
\r
369 if (this._scoreList != null) {
\r
370 if (temp._scoreList == null) return false;
\r
371 else if (!(this._scoreList.equals(temp._scoreList)))
\r
374 else if (temp._scoreList != null)
\r
376 if (this._linkList != null) {
\r
377 if (temp._linkList == null) return false;
\r
378 else if (!(this._linkList.equals(temp._linkList)))
\r
381 else if (temp._linkList != null)
\r
383 if (this._propertyList != null) {
\r
384 if (temp._propertyList == null) return false;
\r
385 else if (!(this._propertyList.equals(temp._propertyList)))
\r
388 else if (temp._propertyList != null)
\r
393 } //-- boolean equals(java.lang.Object)
\r
396 * Method getAnnotationElement
\r
401 * @return AnnotationElement
\r
403 public uk.ac.vamsas.objects.core.AnnotationElement getAnnotationElement(int index)
\r
404 throws java.lang.IndexOutOfBoundsException
\r
406 //-- check bounds for index
\r
407 if ((index < 0) || (index > _annotationElementList.size())) {
\r
408 throw new IndexOutOfBoundsException("getAnnotationElement: Index value '"+index+"' not in range [0.."+_annotationElementList.size()+ "]");
\r
411 return (uk.ac.vamsas.objects.core.AnnotationElement) _annotationElementList.elementAt(index);
\r
412 } //-- uk.ac.vamsas.objects.core.AnnotationElement getAnnotationElement(int)
\r
415 * Method getAnnotationElement
\r
419 * @return AnnotationElement
\r
421 public uk.ac.vamsas.objects.core.AnnotationElement[] getAnnotationElement()
\r
423 int size = _annotationElementList.size();
\r
424 uk.ac.vamsas.objects.core.AnnotationElement[] mArray = new uk.ac.vamsas.objects.core.AnnotationElement[size];
\r
425 for (int index = 0; index < size; index++) {
\r
426 mArray[index] = (uk.ac.vamsas.objects.core.AnnotationElement) _annotationElementList.elementAt(index);
\r
429 } //-- uk.ac.vamsas.objects.core.AnnotationElement[] getAnnotationElement()
\r
432 * Method getAnnotationElementCount
\r
438 public int getAnnotationElementCount()
\r
440 return _annotationElementList.size();
\r
441 } //-- int getAnnotationElementCount()
\r
444 * Returns the value of field 'description'. The field
\r
445 * 'description' has the following description: Human readable
\r
446 * description of the annotation
\r
450 * @return the value of field 'description'.
\r
452 public java.lang.String getDescription()
\r
454 return this._description;
\r
455 } //-- java.lang.String getDescription()
\r
458 * Returns the value of field 'group'. The field 'group' has
\r
459 * the following description: Annotation with the same
\r
460 * non-empty group name are grouped
\r
464 * @return the value of field 'group'.
\r
466 public java.lang.String getGroup()
\r
468 return this._group;
\r
469 } //-- java.lang.String getGroup()
\r
472 * Returns the value of field 'id'. The field 'id' has the
\r
473 * following description: Primary Key for vamsas object
\r
478 * @return the value of field 'id'.
\r
480 public java.lang.String getId()
\r
483 } //-- java.lang.String getId()
\r
486 * Returns the value of field 'label'. The field 'label' has
\r
487 * the following description: Short, meaningful name for the
\r
488 * annotation - if this
\r
489 * is absent, then the type string should be used in its
\r
494 * @return the value of field 'label'.
\r
496 public java.lang.String getLabel()
\r
498 return this._label;
\r
499 } //-- java.lang.String getLabel()
\r
509 public uk.ac.vamsas.objects.core.Link getLink(int index)
\r
510 throws java.lang.IndexOutOfBoundsException
\r
512 //-- check bounds for index
\r
513 if ((index < 0) || (index > _linkList.size())) {
\r
514 throw new IndexOutOfBoundsException("getLink: Index value '"+index+"' not in range [0.."+_linkList.size()+ "]");
\r
517 return (uk.ac.vamsas.objects.core.Link) _linkList.elementAt(index);
\r
518 } //-- uk.ac.vamsas.objects.core.Link getLink(int)
\r
527 public uk.ac.vamsas.objects.core.Link[] getLink()
\r
529 int size = _linkList.size();
\r
530 uk.ac.vamsas.objects.core.Link[] mArray = new uk.ac.vamsas.objects.core.Link[size];
\r
531 for (int index = 0; index < size; index++) {
\r
532 mArray[index] = (uk.ac.vamsas.objects.core.Link) _linkList.elementAt(index);
\r
535 } //-- uk.ac.vamsas.objects.core.Link[] getLink()
\r
538 * Method getLinkCount
\r
544 public int getLinkCount()
\r
546 return _linkList.size();
\r
547 } //-- int getLinkCount()
\r
550 * Returns the value of field 'modifiable'.
\r
553 * @return the value of field 'modifiable'.
\r
555 public java.lang.String getModifiable()
\r
557 return this._modifiable;
\r
558 } //-- java.lang.String getModifiable()
\r
561 * Method getProperty
\r
568 public uk.ac.vamsas.objects.core.Property getProperty(int index)
\r
569 throws java.lang.IndexOutOfBoundsException
\r
571 //-- check bounds for index
\r
572 if ((index < 0) || (index > _propertyList.size())) {
\r
573 throw new IndexOutOfBoundsException("getProperty: Index value '"+index+"' not in range [0.."+_propertyList.size()+ "]");
\r
576 return (uk.ac.vamsas.objects.core.Property) _propertyList.elementAt(index);
\r
577 } //-- uk.ac.vamsas.objects.core.Property getProperty(int)
\r
580 * Method getProperty
\r
586 public uk.ac.vamsas.objects.core.Property[] getProperty()
\r
588 int size = _propertyList.size();
\r
589 uk.ac.vamsas.objects.core.Property[] mArray = new uk.ac.vamsas.objects.core.Property[size];
\r
590 for (int index = 0; index < size; index++) {
\r
591 mArray[index] = (uk.ac.vamsas.objects.core.Property) _propertyList.elementAt(index);
\r
594 } //-- uk.ac.vamsas.objects.core.Property[] getProperty()
\r
597 * Method getPropertyCount
\r
603 public int getPropertyCount()
\r
605 return _propertyList.size();
\r
606 } //-- int getPropertyCount()
\r
616 public uk.ac.vamsas.objects.core.Score getScore(int index)
\r
617 throws java.lang.IndexOutOfBoundsException
\r
619 //-- check bounds for index
\r
620 if ((index < 0) || (index > _scoreList.size())) {
\r
621 throw new IndexOutOfBoundsException("getScore: Index value '"+index+"' not in range [0.."+_scoreList.size()+ "]");
\r
624 return (uk.ac.vamsas.objects.core.Score) _scoreList.elementAt(index);
\r
625 } //-- uk.ac.vamsas.objects.core.Score getScore(int)
\r
634 public uk.ac.vamsas.objects.core.Score[] getScore()
\r
636 int size = _scoreList.size();
\r
637 uk.ac.vamsas.objects.core.Score[] mArray = new uk.ac.vamsas.objects.core.Score[size];
\r
638 for (int index = 0; index < size; index++) {
\r
639 mArray[index] = (uk.ac.vamsas.objects.core.Score) _scoreList.elementAt(index);
\r
642 } //-- uk.ac.vamsas.objects.core.Score[] getScore()
\r
645 * Method getScoreCount
\r
651 public int getScoreCount()
\r
653 return _scoreList.size();
\r
654 } //-- int getScoreCount()
\r
657 * Returns the value of field 'status'. The field 'status' has
\r
658 * the following description: TODO: specify this - we have
\r
659 * considered taking the GO
\r
660 * evidence codes as a model for assessing a measure of
\r
665 * @return the value of field 'status'.
\r
667 public java.lang.String getStatus()
\r
669 return this._status;
\r
670 } //-- java.lang.String getStatus()
\r
673 * Returns the value of field 'type'. The field 'type' has the
\r
674 * following description: A Das Feature has both a type and a
\r
675 * Type ID. We go the
\r
676 * route of requiring the type string to be taken from a
\r
678 * vocabulary if an application expects others to make sense
\r
680 * type may qualified - so uniprot:CHAIN is a valid type name,
\r
682 * considered distinct from someotherDB:CHAIN
\r
685 * @return the value of field 'type'.
\r
687 public java.lang.String getType()
\r
690 } //-- java.lang.String getType()
\r
699 public boolean isValid()
\r
704 catch (org.exolab.castor.xml.ValidationException vex) {
\r
708 } //-- boolean isValid()
\r
717 public void marshal(java.io.Writer out)
\r
718 throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
\r
721 Marshaller.marshal(this, out);
\r
722 } //-- void marshal(java.io.Writer)
\r
731 public void marshal(org.xml.sax.ContentHandler handler)
\r
732 throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
\r
735 Marshaller.marshal(this, handler);
\r
736 } //-- void marshal(org.xml.sax.ContentHandler)
\r
739 * Method removeAllAnnotationElement
\r
742 public void removeAllAnnotationElement()
\r
744 _annotationElementList.removeAllElements();
\r
745 } //-- void removeAllAnnotationElement()
\r
748 * Method removeAllLink
\r
751 public void removeAllLink()
\r
753 _linkList.removeAllElements();
\r
754 } //-- void removeAllLink()
\r
757 * Method removeAllProperty
\r
760 public void removeAllProperty()
\r
762 _propertyList.removeAllElements();
\r
763 } //-- void removeAllProperty()
\r
766 * Method removeAllScore
\r
769 public void removeAllScore()
\r
771 _scoreList.removeAllElements();
\r
772 } //-- void removeAllScore()
\r
775 * Method removeAnnotationElement
\r
780 * @return AnnotationElement
\r
782 public uk.ac.vamsas.objects.core.AnnotationElement removeAnnotationElement(int index)
\r
784 java.lang.Object obj = _annotationElementList.elementAt(index);
\r
785 _annotationElementList.removeElementAt(index);
\r
786 return (uk.ac.vamsas.objects.core.AnnotationElement) obj;
\r
787 } //-- uk.ac.vamsas.objects.core.AnnotationElement removeAnnotationElement(int)
\r
790 * Method removeLink
\r
797 public uk.ac.vamsas.objects.core.Link removeLink(int index)
\r
799 java.lang.Object obj = _linkList.elementAt(index);
\r
800 _linkList.removeElementAt(index);
\r
801 return (uk.ac.vamsas.objects.core.Link) obj;
\r
802 } //-- uk.ac.vamsas.objects.core.Link removeLink(int)
\r
805 * Method removeProperty
\r
812 public uk.ac.vamsas.objects.core.Property removeProperty(int index)
\r
814 java.lang.Object obj = _propertyList.elementAt(index);
\r
815 _propertyList.removeElementAt(index);
\r
816 return (uk.ac.vamsas.objects.core.Property) obj;
\r
817 } //-- uk.ac.vamsas.objects.core.Property removeProperty(int)
\r
820 * Method removeScore
\r
827 public uk.ac.vamsas.objects.core.Score removeScore(int index)
\r
829 java.lang.Object obj = _scoreList.elementAt(index);
\r
830 _scoreList.removeElementAt(index);
\r
831 return (uk.ac.vamsas.objects.core.Score) obj;
\r
832 } //-- uk.ac.vamsas.objects.core.Score removeScore(int)
\r
835 * Method setAnnotationElement
\r
840 * @param vAnnotationElement
\r
842 public void setAnnotationElement(int index, uk.ac.vamsas.objects.core.AnnotationElement vAnnotationElement)
\r
843 throws java.lang.IndexOutOfBoundsException
\r
845 //-- check bounds for index
\r
846 if ((index < 0) || (index > _annotationElementList.size())) {
\r
847 throw new IndexOutOfBoundsException("setAnnotationElement: Index value '"+index+"' not in range [0.."+_annotationElementList.size()+ "]");
\r
849 _annotationElementList.setElementAt(vAnnotationElement, index);
\r
850 } //-- void setAnnotationElement(int, uk.ac.vamsas.objects.core.AnnotationElement)
\r
853 * Method setAnnotationElement
\r
857 * @param annotationElementArray
\r
859 public void setAnnotationElement(uk.ac.vamsas.objects.core.AnnotationElement[] annotationElementArray)
\r
862 _annotationElementList.removeAllElements();
\r
863 for (int i = 0; i < annotationElementArray.length; i++) {
\r
864 _annotationElementList.addElement(annotationElementArray[i]);
\r
866 } //-- void setAnnotationElement(uk.ac.vamsas.objects.core.AnnotationElement)
\r
869 * Sets the value of field 'description'. The field
\r
870 * 'description' has the following description: Human readable
\r
871 * description of the annotation
\r
874 * @param description the value of field 'description'.
\r
876 public void setDescription(java.lang.String description)
\r
878 this._description = description;
\r
879 } //-- void setDescription(java.lang.String)
\r
882 * Sets the value of field 'group'. The field 'group' has the
\r
883 * following description: Annotation with the same non-empty
\r
884 * group name are grouped
\r
887 * @param group the value of field 'group'.
\r
889 public void setGroup(java.lang.String group)
\r
891 this._group = group;
\r
892 } //-- void setGroup(java.lang.String)
\r
895 * Sets the value of field 'id'. The field 'id' has the
\r
896 * following description: Primary Key for vamsas object
\r
900 * @param id the value of field 'id'.
\r
902 public void setId(java.lang.String id)
\r
905 } //-- void setId(java.lang.String)
\r
908 * Sets the value of field 'label'. The field 'label' has the
\r
909 * following description: Short, meaningful name for the
\r
910 * annotation - if this
\r
911 * is absent, then the type string should be used in its
\r
915 * @param label the value of field 'label'.
\r
917 public void setLabel(java.lang.String label)
\r
919 this._label = label;
\r
920 } //-- void setLabel(java.lang.String)
\r
930 public void setLink(int index, uk.ac.vamsas.objects.core.Link vLink)
\r
931 throws java.lang.IndexOutOfBoundsException
\r
933 //-- check bounds for index
\r
934 if ((index < 0) || (index > _linkList.size())) {
\r
935 throw new IndexOutOfBoundsException("setLink: Index value '"+index+"' not in range [0.."+_linkList.size()+ "]");
\r
937 _linkList.setElementAt(vLink, index);
\r
938 } //-- void setLink(int, uk.ac.vamsas.objects.core.Link)
\r
947 public void setLink(uk.ac.vamsas.objects.core.Link[] linkArray)
\r
950 _linkList.removeAllElements();
\r
951 for (int i = 0; i < linkArray.length; i++) {
\r
952 _linkList.addElement(linkArray[i]);
\r
954 } //-- void setLink(uk.ac.vamsas.objects.core.Link)
\r
957 * Sets the value of field 'modifiable'.
\r
959 * @param modifiable the value of field 'modifiable'.
\r
961 public void setModifiable(java.lang.String modifiable)
\r
963 this._modifiable = modifiable;
\r
964 } //-- void setModifiable(java.lang.String)
\r
967 * Method setProperty
\r
974 public void setProperty(int index, uk.ac.vamsas.objects.core.Property vProperty)
\r
975 throws java.lang.IndexOutOfBoundsException
\r
977 //-- check bounds for index
\r
978 if ((index < 0) || (index > _propertyList.size())) {
\r
979 throw new IndexOutOfBoundsException("setProperty: Index value '"+index+"' not in range [0.."+_propertyList.size()+ "]");
\r
981 _propertyList.setElementAt(vProperty, index);
\r
982 } //-- void setProperty(int, uk.ac.vamsas.objects.core.Property)
\r
985 * Method setProperty
\r
989 * @param propertyArray
\r
991 public void setProperty(uk.ac.vamsas.objects.core.Property[] propertyArray)
\r
994 _propertyList.removeAllElements();
\r
995 for (int i = 0; i < propertyArray.length; i++) {
\r
996 _propertyList.addElement(propertyArray[i]);
\r
998 } //-- void setProperty(uk.ac.vamsas.objects.core.Property)
\r
1008 public void setScore(int index, uk.ac.vamsas.objects.core.Score vScore)
\r
1009 throws java.lang.IndexOutOfBoundsException
\r
1011 //-- check bounds for index
\r
1012 if ((index < 0) || (index > _scoreList.size())) {
\r
1013 throw new IndexOutOfBoundsException("setScore: Index value '"+index+"' not in range [0.."+_scoreList.size()+ "]");
\r
1015 _scoreList.setElementAt(vScore, index);
\r
1016 } //-- void setScore(int, uk.ac.vamsas.objects.core.Score)
\r
1023 * @param scoreArray
\r
1025 public void setScore(uk.ac.vamsas.objects.core.Score[] scoreArray)
\r
1028 _scoreList.removeAllElements();
\r
1029 for (int i = 0; i < scoreArray.length; i++) {
\r
1030 _scoreList.addElement(scoreArray[i]);
\r
1032 } //-- void setScore(uk.ac.vamsas.objects.core.Score)
\r
1035 * Sets the value of field 'status'. The field 'status' has the
\r
1036 * following description: TODO: specify this - we have
\r
1037 * considered taking the GO
\r
1038 * evidence codes as a model for assessing a measure of
\r
1042 * @param status the value of field 'status'.
\r
1044 public void setStatus(java.lang.String status)
\r
1046 this._status = status;
\r
1047 } //-- void setStatus(java.lang.String)
\r
1050 * Sets the value of field 'type'. The field 'type' has the
\r
1051 * following description: A Das Feature has both a type and a
\r
1052 * Type ID. We go the
\r
1053 * route of requiring the type string to be taken from a
\r
1055 * vocabulary if an application expects others to make sense
\r
1057 * type may qualified - so uniprot:CHAIN is a valid type name,
\r
1059 * considered distinct from someotherDB:CHAIN
\r
1061 * @param type the value of field 'type'.
\r
1063 public void setType(java.lang.String type)
\r
1065 this._type = type;
\r
1066 } //-- void setType(java.lang.String)
\r
1069 * Method unmarshal
\r
1074 * @return RangeType
\r
1076 public static uk.ac.vamsas.objects.core.RangeType unmarshal(java.io.Reader reader)
\r
1077 throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
\r
1079 return (uk.ac.vamsas.objects.core.RangeAnnotation) Unmarshaller.unmarshal(uk.ac.vamsas.objects.core.RangeAnnotation.class, reader);
\r
1080 } //-- uk.ac.vamsas.objects.core.RangeType unmarshal(java.io.Reader)
\r
1086 public void validate()
\r
1087 throws org.exolab.castor.xml.ValidationException
\r
1089 org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
\r
1090 validator.validate(this);
\r
1091 } //-- void validate()
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