2 * This class was automatically generated with
3 * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
8 package jalview.schemabinding.version2;
10 //---------------------------------/
11 //- Imported classes and packages -/
12 //---------------------------------/
14 import org.exolab.castor.xml.Marshaller;
15 import org.exolab.castor.xml.Unmarshaller;
20 * @version $Revision$ $Date$
22 public class Annotation implements java.io.Serializable {
25 //--------------------------/
26 //- Class/Member Variables -/
27 //--------------------------/
32 private boolean _graph;
35 * keeps track of state for field: _graph
37 private boolean _has_graph;
42 private int _graphType;
45 * keeps track of state for field: _graphType
47 private boolean _has_graphType;
52 private java.lang.String _sequenceRef;
57 private java.lang.String _groupRef;
62 private int _graphColour;
65 * keeps track of state for field: _graphColour
67 private boolean _has_graphColour;
72 private int _graphGroup;
75 * keeps track of state for field: _graphGroup
77 private boolean _has_graphGroup;
80 * height in pixels for the graph if this is a graph-type
83 private int _graphHeight;
86 * keeps track of state for field: _graphHeight
88 private boolean _has_graphHeight;
93 private java.lang.String _id;
98 private boolean _scoreOnly = false;
101 * keeps track of state for field: _scoreOnly
103 private boolean _has_scoreOnly;
108 private double _score;
111 * keeps track of state for field: _score
113 private boolean _has_score;
118 private boolean _visible;
121 * keeps track of state for field: _visible
123 private boolean _has_visible;
126 * Field _centreColLabels.
128 private boolean _centreColLabels;
131 * keeps track of state for field: _centreColLabels
133 private boolean _has_centreColLabels;
136 * Field _scaleColLabels.
138 private boolean _scaleColLabels;
141 * keeps track of state for field: _scaleColLabels
143 private boolean _has_scaleColLabels;
146 * Field _showAllColLabels.
148 private boolean _showAllColLabels;
151 * keeps track of state for field: _showAllColLabels
153 private boolean _has_showAllColLabels;
156 * is an autocalculated annotation row
158 private boolean _autoCalculated = false;
161 * keeps track of state for field: _autoCalculated
163 private boolean _has_autoCalculated;
166 * is to be shown below the alignment - introduced in Jalview
167 * 2.8 for visualizing T-COFFEE alignment scores
169 private boolean _belowAlignment = true;
172 * keeps track of state for field: _belowAlignment
174 private boolean _has_belowAlignment;
177 * Optional string identifier used to group sets of annotation
178 * produced by a particular calculation. Values are opaque
179 * strings but have semantic meaning to Jalview's renderer,
180 * data importer and calculation system.
182 private java.lang.String _calcId;
185 * Field _annotationElementList.
187 private java.util.Vector _annotationElementList;
192 private java.lang.String _label;
195 * Field _description.
197 private java.lang.String _description;
200 * Field _thresholdLine.
202 private jalview.schemabinding.version2.ThresholdLine _thresholdLine;
205 * Field _propertyList.
207 private java.util.Vector _propertyList;
214 public Annotation() {
216 this._annotationElementList = new java.util.Vector();
217 this._propertyList = new java.util.Vector();
228 * @param vAnnotationElement
229 * @throws java.lang.IndexOutOfBoundsException if the index
230 * given is outside the bounds of the collection
232 public void addAnnotationElement(
233 final jalview.schemabinding.version2.AnnotationElement vAnnotationElement)
234 throws java.lang.IndexOutOfBoundsException {
235 this._annotationElementList.addElement(vAnnotationElement);
242 * @param vAnnotationElement
243 * @throws java.lang.IndexOutOfBoundsException if the index
244 * given is outside the bounds of the collection
246 public void addAnnotationElement(
248 final jalview.schemabinding.version2.AnnotationElement vAnnotationElement)
249 throws java.lang.IndexOutOfBoundsException {
250 this._annotationElementList.add(index, vAnnotationElement);
257 * @throws java.lang.IndexOutOfBoundsException if the index
258 * given is outside the bounds of the collection
260 public void addProperty(
261 final jalview.schemabinding.version2.Property vProperty)
262 throws java.lang.IndexOutOfBoundsException {
263 this._propertyList.addElement(vProperty);
271 * @throws java.lang.IndexOutOfBoundsException if the index
272 * given is outside the bounds of the collection
274 public void addProperty(
276 final jalview.schemabinding.version2.Property vProperty)
277 throws java.lang.IndexOutOfBoundsException {
278 this._propertyList.add(index, vProperty);
283 public void deleteAutoCalculated(
285 this._has_autoCalculated= false;
290 public void deleteBelowAlignment(
292 this._has_belowAlignment= false;
297 public void deleteCentreColLabels(
299 this._has_centreColLabels= false;
304 public void deleteGraph(
306 this._has_graph= false;
311 public void deleteGraphColour(
313 this._has_graphColour= false;
318 public void deleteGraphGroup(
320 this._has_graphGroup= false;
325 public void deleteGraphHeight(
327 this._has_graphHeight= false;
332 public void deleteGraphType(
334 this._has_graphType= false;
339 public void deleteScaleColLabels(
341 this._has_scaleColLabels= false;
346 public void deleteScore(
348 this._has_score= false;
353 public void deleteScoreOnly(
355 this._has_scoreOnly= false;
360 public void deleteShowAllColLabels(
362 this._has_showAllColLabels= false;
367 public void deleteVisible(
369 this._has_visible= false;
373 * Method enumerateAnnotationElement.
375 * @return an Enumeration over all
376 * jalview.schemabinding.version2.AnnotationElement elements
378 public java.util.Enumeration enumerateAnnotationElement(
380 return this._annotationElementList.elements();
384 * Method enumerateProperty.
386 * @return an Enumeration over all
387 * jalview.schemabinding.version2.Property elements
389 public java.util.Enumeration enumerateProperty(
391 return this._propertyList.elements();
395 * Method getAnnotationElement.
398 * @throws java.lang.IndexOutOfBoundsException if the index
399 * given is outside the bounds of the collection
400 * @return the value of the
401 * jalview.schemabinding.version2.AnnotationElement at the
404 public jalview.schemabinding.version2.AnnotationElement getAnnotationElement(
406 throws java.lang.IndexOutOfBoundsException {
407 // check bounds for index
408 if (index < 0 || index >= this._annotationElementList.size()) {
409 throw new IndexOutOfBoundsException("getAnnotationElement: Index value '" + index + "' not in range [0.." + (this._annotationElementList.size() - 1) + "]");
412 return (jalview.schemabinding.version2.AnnotationElement) _annotationElementList.get(index);
416 * Method getAnnotationElement.Returns the contents of the
417 * collection in an Array. <p>Note: Just in case the
418 * collection contents are changing in another thread, we pass
419 * a 0-length Array of the correct type into the API call.
420 * This way we <i>know</i> that the Array returned is of
421 * exactly the correct length.
423 * @return this collection as an Array
425 public jalview.schemabinding.version2.AnnotationElement[] getAnnotationElement(
427 jalview.schemabinding.version2.AnnotationElement[] array = new jalview.schemabinding.version2.AnnotationElement[0];
428 return (jalview.schemabinding.version2.AnnotationElement[]) this._annotationElementList.toArray(array);
432 * Method getAnnotationElementCount.
434 * @return the size of this collection
436 public int getAnnotationElementCount(
438 return this._annotationElementList.size();
442 * Returns the value of field 'autoCalculated'. The field
443 * 'autoCalculated' has the following description: is an
444 * autocalculated annotation row
446 * @return the value of field 'AutoCalculated'.
448 public boolean getAutoCalculated(
450 return this._autoCalculated;
454 * Returns the value of field 'belowAlignment'. The field
455 * 'belowAlignment' has the following description: is to be
456 * shown below the alignment - introduced in Jalview 2.8 for
457 * visualizing T-COFFEE alignment scores
459 * @return the value of field 'BelowAlignment'.
461 public boolean getBelowAlignment(
463 return this._belowAlignment;
467 * Returns the value of field 'calcId'. The field 'calcId' has
468 * the following description: Optional string identifier used
469 * to group sets of annotation produced by a particular
470 * calculation. Values are opaque strings but have semantic
471 * meaning to Jalview's renderer, data importer and calculation
474 * @return the value of field 'CalcId'.
476 public java.lang.String getCalcId(
482 * Returns the value of field 'centreColLabels'.
484 * @return the value of field 'CentreColLabels'.
486 public boolean getCentreColLabels(
488 return this._centreColLabels;
492 * Returns the value of field 'description'.
494 * @return the value of field 'Description'.
496 public java.lang.String getDescription(
498 return this._description;
502 * Returns the value of field 'graph'.
504 * @return the value of field 'Graph'.
506 public boolean getGraph(
512 * Returns the value of field 'graphColour'.
514 * @return the value of field 'GraphColour'.
516 public int getGraphColour(
518 return this._graphColour;
522 * Returns the value of field 'graphGroup'.
524 * @return the value of field 'GraphGroup'.
526 public int getGraphGroup(
528 return this._graphGroup;
532 * Returns the value of field 'graphHeight'. The field
533 * 'graphHeight' has the following description: height in
534 * pixels for the graph if this is a graph-type annotation.
536 * @return the value of field 'GraphHeight'.
538 public int getGraphHeight(
540 return this._graphHeight;
544 * Returns the value of field 'graphType'.
546 * @return the value of field 'GraphType'.
548 public int getGraphType(
550 return this._graphType;
554 * Returns the value of field 'groupRef'.
556 * @return the value of field 'GroupRef'.
558 public java.lang.String getGroupRef(
560 return this._groupRef;
564 * Returns the value of field 'id'.
566 * @return the value of field 'Id'.
568 public java.lang.String getId(
574 * Returns the value of field 'label'.
576 * @return the value of field 'Label'.
578 public java.lang.String getLabel(
584 * Method getProperty.
587 * @throws java.lang.IndexOutOfBoundsException if the index
588 * given is outside the bounds of the collection
589 * @return the value of the
590 * jalview.schemabinding.version2.Property at the given index
592 public jalview.schemabinding.version2.Property getProperty(
594 throws java.lang.IndexOutOfBoundsException {
595 // check bounds for index
596 if (index < 0 || index >= this._propertyList.size()) {
597 throw new IndexOutOfBoundsException("getProperty: Index value '" + index + "' not in range [0.." + (this._propertyList.size() - 1) + "]");
600 return (jalview.schemabinding.version2.Property) _propertyList.get(index);
604 * Method getProperty.Returns the contents of the collection in
605 * an Array. <p>Note: Just in case the collection contents
606 * are changing in another thread, we pass a 0-length Array of
607 * the correct type into the API call. This way we <i>know</i>
608 * that the Array returned is of exactly the correct length.
610 * @return this collection as an Array
612 public jalview.schemabinding.version2.Property[] getProperty(
614 jalview.schemabinding.version2.Property[] array = new jalview.schemabinding.version2.Property[0];
615 return (jalview.schemabinding.version2.Property[]) this._propertyList.toArray(array);
619 * Method getPropertyCount.
621 * @return the size of this collection
623 public int getPropertyCount(
625 return this._propertyList.size();
629 * Returns the value of field 'scaleColLabels'.
631 * @return the value of field 'ScaleColLabels'.
633 public boolean getScaleColLabels(
635 return this._scaleColLabels;
639 * Returns the value of field 'score'.
641 * @return the value of field 'Score'.
643 public double getScore(
649 * Returns the value of field 'scoreOnly'.
651 * @return the value of field 'ScoreOnly'.
653 public boolean getScoreOnly(
655 return this._scoreOnly;
659 * Returns the value of field 'sequenceRef'.
661 * @return the value of field 'SequenceRef'.
663 public java.lang.String getSequenceRef(
665 return this._sequenceRef;
669 * Returns the value of field 'showAllColLabels'.
671 * @return the value of field 'ShowAllColLabels'.
673 public boolean getShowAllColLabels(
675 return this._showAllColLabels;
679 * Returns the value of field 'thresholdLine'.
681 * @return the value of field 'ThresholdLine'.
683 public jalview.schemabinding.version2.ThresholdLine getThresholdLine(
685 return this._thresholdLine;
689 * Returns the value of field 'visible'.
691 * @return the value of field 'Visible'.
693 public boolean getVisible(
695 return this._visible;
699 * Method hasAutoCalculated.
701 * @return true if at least one AutoCalculated has been added
703 public boolean hasAutoCalculated(
705 return this._has_autoCalculated;
709 * Method hasBelowAlignment.
711 * @return true if at least one BelowAlignment has been added
713 public boolean hasBelowAlignment(
715 return this._has_belowAlignment;
719 * Method hasCentreColLabels.
721 * @return true if at least one CentreColLabels has been added
723 public boolean hasCentreColLabels(
725 return this._has_centreColLabels;
731 * @return true if at least one Graph has been added
733 public boolean hasGraph(
735 return this._has_graph;
739 * Method hasGraphColour.
741 * @return true if at least one GraphColour has been added
743 public boolean hasGraphColour(
745 return this._has_graphColour;
749 * Method hasGraphGroup.
751 * @return true if at least one GraphGroup has been added
753 public boolean hasGraphGroup(
755 return this._has_graphGroup;
759 * Method hasGraphHeight.
761 * @return true if at least one GraphHeight has been added
763 public boolean hasGraphHeight(
765 return this._has_graphHeight;
769 * Method hasGraphType.
771 * @return true if at least one GraphType has been added
773 public boolean hasGraphType(
775 return this._has_graphType;
779 * Method hasScaleColLabels.
781 * @return true if at least one ScaleColLabels has been added
783 public boolean hasScaleColLabels(
785 return this._has_scaleColLabels;
791 * @return true if at least one Score has been added
793 public boolean hasScore(
795 return this._has_score;
799 * Method hasScoreOnly.
801 * @return true if at least one ScoreOnly has been added
803 public boolean hasScoreOnly(
805 return this._has_scoreOnly;
809 * Method hasShowAllColLabels.
811 * @return true if at least one ShowAllColLabels has been added
813 public boolean hasShowAllColLabels(
815 return this._has_showAllColLabels;
821 * @return true if at least one Visible has been added
823 public boolean hasVisible(
825 return this._has_visible;
829 * Returns the value of field 'autoCalculated'. The field
830 * 'autoCalculated' has the following description: is an
831 * autocalculated annotation row
833 * @return the value of field 'AutoCalculated'.
835 public boolean isAutoCalculated(
837 return this._autoCalculated;
841 * Returns the value of field 'belowAlignment'. The field
842 * 'belowAlignment' has the following description: is to be
843 * shown below the alignment - introduced in Jalview 2.8 for
844 * visualizing T-COFFEE alignment scores
846 * @return the value of field 'BelowAlignment'.
848 public boolean isBelowAlignment(
850 return this._belowAlignment;
854 * Returns the value of field 'centreColLabels'.
856 * @return the value of field 'CentreColLabels'.
858 public boolean isCentreColLabels(
860 return this._centreColLabels;
864 * Returns the value of field 'graph'.
866 * @return the value of field 'Graph'.
868 public boolean isGraph(
874 * Returns the value of field 'scaleColLabels'.
876 * @return the value of field 'ScaleColLabels'.
878 public boolean isScaleColLabels(
880 return this._scaleColLabels;
884 * Returns the value of field 'scoreOnly'.
886 * @return the value of field 'ScoreOnly'.
888 public boolean isScoreOnly(
890 return this._scoreOnly;
894 * Returns the value of field 'showAllColLabels'.
896 * @return the value of field 'ShowAllColLabels'.
898 public boolean isShowAllColLabels(
900 return this._showAllColLabels;
906 * @return true if this object is valid according to the schema
908 public boolean isValid(
912 } catch (org.exolab.castor.xml.ValidationException vex) {
919 * Returns the value of field 'visible'.
921 * @return the value of field 'Visible'.
923 public boolean isVisible(
925 return this._visible;
932 * @throws org.exolab.castor.xml.MarshalException if object is
933 * null or if any SAXException is thrown during marshaling
934 * @throws org.exolab.castor.xml.ValidationException if this
935 * object is an invalid instance according to the schema
938 final java.io.Writer out)
939 throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
940 Marshaller.marshal(this, out);
947 * @throws java.io.IOException if an IOException occurs during
949 * @throws org.exolab.castor.xml.ValidationException if this
950 * object is an invalid instance according to the schema
951 * @throws org.exolab.castor.xml.MarshalException if object is
952 * null or if any SAXException is thrown during marshaling
955 final org.xml.sax.ContentHandler handler)
956 throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
957 Marshaller.marshal(this, handler);
962 public void removeAllAnnotationElement(
964 this._annotationElementList.clear();
969 public void removeAllProperty(
971 this._propertyList.clear();
975 * Method removeAnnotationElement.
977 * @param vAnnotationElement
978 * @return true if the object was removed from the collection.
980 public boolean removeAnnotationElement(
981 final jalview.schemabinding.version2.AnnotationElement vAnnotationElement) {
982 boolean removed = _annotationElementList.remove(vAnnotationElement);
987 * Method removeAnnotationElementAt.
990 * @return the element removed from the collection
992 public jalview.schemabinding.version2.AnnotationElement removeAnnotationElementAt(
994 java.lang.Object obj = this._annotationElementList.remove(index);
995 return (jalview.schemabinding.version2.AnnotationElement) obj;
999 * Method removeProperty.
1002 * @return true if the object was removed from the collection.
1004 public boolean removeProperty(
1005 final jalview.schemabinding.version2.Property vProperty) {
1006 boolean removed = _propertyList.remove(vProperty);
1011 * Method removePropertyAt.
1014 * @return the element removed from the collection
1016 public jalview.schemabinding.version2.Property removePropertyAt(
1018 java.lang.Object obj = this._propertyList.remove(index);
1019 return (jalview.schemabinding.version2.Property) obj;
1026 * @param vAnnotationElement
1027 * @throws java.lang.IndexOutOfBoundsException if the index
1028 * given is outside the bounds of the collection
1030 public void setAnnotationElement(
1032 final jalview.schemabinding.version2.AnnotationElement vAnnotationElement)
1033 throws java.lang.IndexOutOfBoundsException {
1034 // check bounds for index
1035 if (index < 0 || index >= this._annotationElementList.size()) {
1036 throw new IndexOutOfBoundsException("setAnnotationElement: Index value '" + index + "' not in range [0.." + (this._annotationElementList.size() - 1) + "]");
1039 this._annotationElementList.set(index, vAnnotationElement);
1045 * @param vAnnotationElementArray
1047 public void setAnnotationElement(
1048 final jalview.schemabinding.version2.AnnotationElement[] vAnnotationElementArray) {
1050 _annotationElementList.clear();
1052 for (int i = 0; i < vAnnotationElementArray.length; i++) {
1053 this._annotationElementList.add(vAnnotationElementArray[i]);
1058 * Sets the value of field 'autoCalculated'. The field
1059 * 'autoCalculated' has the following description: is an
1060 * autocalculated annotation row
1062 * @param autoCalculated the value of field 'autoCalculated'.
1064 public void setAutoCalculated(
1065 final boolean autoCalculated) {
1066 this._autoCalculated = autoCalculated;
1067 this._has_autoCalculated = true;
1071 * Sets the value of field 'belowAlignment'. The field
1072 * 'belowAlignment' has the following description: is to be
1073 * shown below the alignment - introduced in Jalview 2.8 for
1074 * visualizing T-COFFEE alignment scores
1076 * @param belowAlignment the value of field 'belowAlignment'.
1078 public void setBelowAlignment(
1079 final boolean belowAlignment) {
1080 this._belowAlignment = belowAlignment;
1081 this._has_belowAlignment = true;
1085 * Sets the value of field 'calcId'. The field 'calcId' has the
1086 * following description: Optional string identifier used to
1087 * group sets of annotation produced by a particular
1088 * calculation. Values are opaque strings but have semantic
1089 * meaning to Jalview's renderer, data importer and calculation
1092 * @param calcId the value of field 'calcId'.
1094 public void setCalcId(
1095 final java.lang.String calcId) {
1096 this._calcId = calcId;
1100 * Sets the value of field 'centreColLabels'.
1102 * @param centreColLabels the value of field 'centreColLabels'.
1104 public void setCentreColLabels(
1105 final boolean centreColLabels) {
1106 this._centreColLabels = centreColLabels;
1107 this._has_centreColLabels = true;
1111 * Sets the value of field 'description'.
1113 * @param description the value of field 'description'.
1115 public void setDescription(
1116 final java.lang.String description) {
1117 this._description = description;
1121 * Sets the value of field 'graph'.
1123 * @param graph the value of field 'graph'.
1125 public void setGraph(
1126 final boolean graph) {
1127 this._graph = graph;
1128 this._has_graph = true;
1132 * Sets the value of field 'graphColour'.
1134 * @param graphColour the value of field 'graphColour'.
1136 public void setGraphColour(
1137 final int graphColour) {
1138 this._graphColour = graphColour;
1139 this._has_graphColour = true;
1143 * Sets the value of field 'graphGroup'.
1145 * @param graphGroup the value of field 'graphGroup'.
1147 public void setGraphGroup(
1148 final int graphGroup) {
1149 this._graphGroup = graphGroup;
1150 this._has_graphGroup = true;
1154 * Sets the value of field 'graphHeight'. The field
1155 * 'graphHeight' has the following description: height in
1156 * pixels for the graph if this is a graph-type annotation.
1158 * @param graphHeight the value of field 'graphHeight'.
1160 public void setGraphHeight(
1161 final int graphHeight) {
1162 this._graphHeight = graphHeight;
1163 this._has_graphHeight = true;
1167 * Sets the value of field 'graphType'.
1169 * @param graphType the value of field 'graphType'.
1171 public void setGraphType(
1172 final int graphType) {
1173 this._graphType = graphType;
1174 this._has_graphType = true;
1178 * Sets the value of field 'groupRef'.
1180 * @param groupRef the value of field 'groupRef'.
1182 public void setGroupRef(
1183 final java.lang.String groupRef) {
1184 this._groupRef = groupRef;
1188 * Sets the value of field 'id'.
1190 * @param id the value of field 'id'.
1193 final java.lang.String id) {
1198 * Sets the value of field 'label'.
1200 * @param label the value of field 'label'.
1202 public void setLabel(
1203 final java.lang.String label) {
1204 this._label = label;
1212 * @throws java.lang.IndexOutOfBoundsException if the index
1213 * given is outside the bounds of the collection
1215 public void setProperty(
1217 final jalview.schemabinding.version2.Property vProperty)
1218 throws java.lang.IndexOutOfBoundsException {
1219 // check bounds for index
1220 if (index < 0 || index >= this._propertyList.size()) {
1221 throw new IndexOutOfBoundsException("setProperty: Index value '" + index + "' not in range [0.." + (this._propertyList.size() - 1) + "]");
1224 this._propertyList.set(index, vProperty);
1230 * @param vPropertyArray
1232 public void setProperty(
1233 final jalview.schemabinding.version2.Property[] vPropertyArray) {
1235 _propertyList.clear();
1237 for (int i = 0; i < vPropertyArray.length; i++) {
1238 this._propertyList.add(vPropertyArray[i]);
1243 * Sets the value of field 'scaleColLabels'.
1245 * @param scaleColLabels the value of field 'scaleColLabels'.
1247 public void setScaleColLabels(
1248 final boolean scaleColLabels) {
1249 this._scaleColLabels = scaleColLabels;
1250 this._has_scaleColLabels = true;
1254 * Sets the value of field 'score'.
1256 * @param score the value of field 'score'.
1258 public void setScore(
1259 final double score) {
1260 this._score = score;
1261 this._has_score = true;
1265 * Sets the value of field 'scoreOnly'.
1267 * @param scoreOnly the value of field 'scoreOnly'.
1269 public void setScoreOnly(
1270 final boolean scoreOnly) {
1271 this._scoreOnly = scoreOnly;
1272 this._has_scoreOnly = true;
1276 * Sets the value of field 'sequenceRef'.
1278 * @param sequenceRef the value of field 'sequenceRef'.
1280 public void setSequenceRef(
1281 final java.lang.String sequenceRef) {
1282 this._sequenceRef = sequenceRef;
1286 * Sets the value of field 'showAllColLabels'.
1288 * @param showAllColLabels the value of field 'showAllColLabels'
1290 public void setShowAllColLabels(
1291 final boolean showAllColLabels) {
1292 this._showAllColLabels = showAllColLabels;
1293 this._has_showAllColLabels = true;
1297 * Sets the value of field 'thresholdLine'.
1299 * @param thresholdLine the value of field 'thresholdLine'.
1301 public void setThresholdLine(
1302 final jalview.schemabinding.version2.ThresholdLine thresholdLine) {
1303 this._thresholdLine = thresholdLine;
1307 * Sets the value of field 'visible'.
1309 * @param visible the value of field 'visible'.
1311 public void setVisible(
1312 final boolean visible) {
1313 this._visible = visible;
1314 this._has_visible = true;
1321 * @throws org.exolab.castor.xml.MarshalException if object is
1322 * null or if any SAXException is thrown during marshaling
1323 * @throws org.exolab.castor.xml.ValidationException if this
1324 * object is an invalid instance according to the schema
1325 * @return the unmarshaled
1326 * jalview.schemabinding.version2.Annotation
1328 public static jalview.schemabinding.version2.Annotation unmarshal(
1329 final java.io.Reader reader)
1330 throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
1331 return (jalview.schemabinding.version2.Annotation) Unmarshaller.unmarshal(jalview.schemabinding.version2.Annotation.class, reader);
1337 * @throws org.exolab.castor.xml.ValidationException if this
1338 * object is an invalid instance according to the schema
1340 public void validate(
1342 throws org.exolab.castor.xml.ValidationException {
1343 org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
1344 validator.validate(this);