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 Viewport implements java.io.Serializable {
25 //--------------------------/
26 //- Class/Member Variables -/
27 //--------------------------/
30 * Field _conservationSelected.
32 private boolean _conservationSelected;
35 * keeps track of state for field: _conservationSelected
37 private boolean _has_conservationSelected;
42 private boolean _pidSelected;
45 * keeps track of state for field: _pidSelected
47 private boolean _has_pidSelected;
52 private java.lang.String _bgColour;
55 * Field _consThreshold.
57 private int _consThreshold;
60 * keeps track of state for field: _consThreshold
62 private boolean _has_consThreshold;
65 * Field _pidThreshold.
67 private int _pidThreshold;
70 * keeps track of state for field: _pidThreshold
72 private boolean _has_pidThreshold;
77 private java.lang.String _title;
82 private boolean _showFullId;
85 * keeps track of state for field: _showFullId
87 private boolean _has_showFullId;
90 * Field _rightAlignIds.
92 private boolean _rightAlignIds;
95 * keeps track of state for field: _rightAlignIds
97 private boolean _has_rightAlignIds;
102 private boolean _showText;
105 * keeps track of state for field: _showText
107 private boolean _has_showText;
110 * Field _showColourText.
112 private boolean _showColourText;
115 * keeps track of state for field: _showColourText
117 private boolean _has_showColourText;
120 * Field _showUnconserved.
122 private boolean _showUnconserved = false;
125 * keeps track of state for field: _showUnconserved
127 private boolean _has_showUnconserved;
132 private boolean _showBoxes;
135 * keeps track of state for field: _showBoxes
137 private boolean _has_showBoxes;
140 * Field _wrapAlignment.
142 private boolean _wrapAlignment;
145 * keeps track of state for field: _wrapAlignment
147 private boolean _has_wrapAlignment;
152 private boolean _renderGaps;
155 * keeps track of state for field: _renderGaps
157 private boolean _has_renderGaps;
160 * Field _showSequenceFeatures.
162 private boolean _showSequenceFeatures;
165 * keeps track of state for field: _showSequenceFeatures
167 private boolean _has_showSequenceFeatures;
170 * Field _showNPfeatureTooltip.
172 private boolean _showNPfeatureTooltip;
175 * keeps track of state for field: _showNPfeatureTooltip
177 private boolean _has_showNPfeatureTooltip;
180 * Field _showDbRefTooltip.
182 private boolean _showDbRefTooltip;
185 * keeps track of state for field: _showDbRefTooltip
187 private boolean _has_showDbRefTooltip;
190 * Field _followHighlight.
192 private boolean _followHighlight = true;
195 * keeps track of state for field: _followHighlight
197 private boolean _has_followHighlight;
200 * Field _followSelection.
202 private boolean _followSelection = true;
205 * keeps track of state for field: _followSelection
207 private boolean _has_followSelection;
210 * Field _showAnnotation.
212 private boolean _showAnnotation;
215 * keeps track of state for field: _showAnnotation
217 private boolean _has_showAnnotation;
220 * Field _centreColumnLabels.
222 private boolean _centreColumnLabels = false;
225 * keeps track of state for field: _centreColumnLabels
227 private boolean _has_centreColumnLabels;
230 * Field _showGroupConservation.
232 private boolean _showGroupConservation = false;
235 * keeps track of state for field: _showGroupConservation
237 private boolean _has_showGroupConservation;
240 * Field _showGroupConsensus.
242 private boolean _showGroupConsensus = false;
245 * keeps track of state for field: _showGroupConsensus
247 private boolean _has_showGroupConsensus;
250 * Field _showConsensusHistogram.
252 private boolean _showConsensusHistogram = true;
255 * keeps track of state for field: _showConsensusHistogram
257 private boolean _has_showConsensusHistogram;
260 * Field _showSequenceLogo.
262 private boolean _showSequenceLogo = false;
265 * keeps track of state for field: _showSequenceLogo
267 private boolean _has_showSequenceLogo;
270 * Field _normaliseSequenceLogo.
272 private boolean _normaliseSequenceLogo = false;
275 * keeps track of state for field: _normaliseSequenceLogo
277 private boolean _has_normaliseSequenceLogo;
280 * Field _ignoreGapsinConsensus.
282 private boolean _ignoreGapsinConsensus = true;
285 * keeps track of state for field: _ignoreGapsinConsensus
287 private boolean _has_ignoreGapsinConsensus;
292 private int _startRes;
295 * keeps track of state for field: _startRes
297 private boolean _has_startRes;
302 private int _startSeq;
305 * keeps track of state for field: _startSeq
307 private boolean _has_startSeq;
312 private java.lang.String _fontName;
317 private int _fontSize;
320 * keeps track of state for field: _fontSize
322 private boolean _has_fontSize;
327 private int _fontStyle;
330 * keeps track of state for field: _fontStyle
332 private boolean _has_fontStyle;
337 private java.lang.String _viewName;
340 * Field _sequenceSetId.
342 private java.lang.String _sequenceSetId;
345 * Field _gatheredViews.
347 private boolean _gatheredViews;
350 * keeps track of state for field: _gatheredViews
352 private boolean _has_gatheredViews;
357 private int _textCol1;
360 * keeps track of state for field: _textCol1
362 private boolean _has_textCol1;
367 private int _textCol2;
370 * keeps track of state for field: _textCol2
372 private boolean _has_textCol2;
375 * Field _textColThreshold.
377 private int _textColThreshold;
380 * keeps track of state for field: _textColThreshold
382 private boolean _has_textColThreshold;
385 * unique id used by jalview to
391 private java.lang.String _id;
394 * The viewport id of this viewport's
395 * (cdna/protein) coding complement, if any
398 private java.lang.String _complementId;
406 * keeps track of state for field: _width
408 private boolean _has_width;
416 * keeps track of state for field: _height
418 private boolean _has_height;
426 * keeps track of state for field: _xpos
428 private boolean _has_xpos;
436 * keeps track of state for field: _ypos
438 private boolean _has_ypos;
441 * Field _annotationColours.
443 private jalview.schemabinding.version2.AnnotationColours _annotationColours;
446 * Field _hiddenColumnsList.
448 private java.util.Vector _hiddenColumnsList;
451 * Field _calcIdParamList.
453 private java.util.Vector _calcIdParamList;
462 this._hiddenColumnsList = new java.util.Vector();
463 this._calcIdParamList = new java.util.Vector();
474 * @param vCalcIdParam
475 * @throws java.lang.IndexOutOfBoundsException if the index
476 * given is outside the bounds of the collection
478 public void addCalcIdParam(
479 final jalview.schemabinding.version2.CalcIdParam vCalcIdParam)
480 throws java.lang.IndexOutOfBoundsException {
481 this._calcIdParamList.addElement(vCalcIdParam);
488 * @param vCalcIdParam
489 * @throws java.lang.IndexOutOfBoundsException if the index
490 * given is outside the bounds of the collection
492 public void addCalcIdParam(
494 final jalview.schemabinding.version2.CalcIdParam vCalcIdParam)
495 throws java.lang.IndexOutOfBoundsException {
496 this._calcIdParamList.add(index, vCalcIdParam);
502 * @param vHiddenColumns
503 * @throws java.lang.IndexOutOfBoundsException if the index
504 * given is outside the bounds of the collection
506 public void addHiddenColumns(
507 final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)
508 throws java.lang.IndexOutOfBoundsException {
509 this._hiddenColumnsList.addElement(vHiddenColumns);
516 * @param vHiddenColumns
517 * @throws java.lang.IndexOutOfBoundsException if the index
518 * given is outside the bounds of the collection
520 public void addHiddenColumns(
522 final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)
523 throws java.lang.IndexOutOfBoundsException {
524 this._hiddenColumnsList.add(index, vHiddenColumns);
529 public void deleteCentreColumnLabels(
531 this._has_centreColumnLabels= false;
536 public void deleteConsThreshold(
538 this._has_consThreshold= false;
543 public void deleteConservationSelected(
545 this._has_conservationSelected= false;
550 public void deleteFollowHighlight(
552 this._has_followHighlight= false;
557 public void deleteFollowSelection(
559 this._has_followSelection= false;
564 public void deleteFontSize(
566 this._has_fontSize= false;
571 public void deleteFontStyle(
573 this._has_fontStyle= false;
578 public void deleteGatheredViews(
580 this._has_gatheredViews= false;
585 public void deleteHeight(
587 this._has_height= false;
592 public void deleteIgnoreGapsinConsensus(
594 this._has_ignoreGapsinConsensus= false;
599 public void deleteNormaliseSequenceLogo(
601 this._has_normaliseSequenceLogo= false;
606 public void deletePidSelected(
608 this._has_pidSelected= false;
613 public void deletePidThreshold(
615 this._has_pidThreshold= false;
620 public void deleteRenderGaps(
622 this._has_renderGaps= false;
627 public void deleteRightAlignIds(
629 this._has_rightAlignIds= false;
634 public void deleteShowAnnotation(
636 this._has_showAnnotation= false;
641 public void deleteShowBoxes(
643 this._has_showBoxes= false;
648 public void deleteShowColourText(
650 this._has_showColourText= false;
655 public void deleteShowConsensusHistogram(
657 this._has_showConsensusHistogram= false;
662 public void deleteShowDbRefTooltip(
664 this._has_showDbRefTooltip= false;
669 public void deleteShowFullId(
671 this._has_showFullId= false;
676 public void deleteShowGroupConsensus(
678 this._has_showGroupConsensus= false;
683 public void deleteShowGroupConservation(
685 this._has_showGroupConservation= false;
690 public void deleteShowNPfeatureTooltip(
692 this._has_showNPfeatureTooltip= false;
697 public void deleteShowSequenceFeatures(
699 this._has_showSequenceFeatures= false;
704 public void deleteShowSequenceLogo(
706 this._has_showSequenceLogo= false;
711 public void deleteShowText(
713 this._has_showText= false;
718 public void deleteShowUnconserved(
720 this._has_showUnconserved= false;
725 public void deleteStartRes(
727 this._has_startRes= false;
732 public void deleteStartSeq(
734 this._has_startSeq= false;
739 public void deleteTextCol1(
741 this._has_textCol1= false;
746 public void deleteTextCol2(
748 this._has_textCol2= false;
753 public void deleteTextColThreshold(
755 this._has_textColThreshold= false;
760 public void deleteWidth(
762 this._has_width= false;
767 public void deleteWrapAlignment(
769 this._has_wrapAlignment= false;
774 public void deleteXpos(
776 this._has_xpos= false;
781 public void deleteYpos(
783 this._has_ypos= false;
787 * Method enumerateCalcIdParam.
789 * @return an Enumeration over all
790 * jalview.schemabinding.version2.CalcIdParam elements
792 public java.util.Enumeration enumerateCalcIdParam(
794 return this._calcIdParamList.elements();
798 * Method enumerateHiddenColumns.
800 * @return an Enumeration over all
801 * jalview.schemabinding.version2.HiddenColumns elements
803 public java.util.Enumeration enumerateHiddenColumns(
805 return this._hiddenColumnsList.elements();
809 * Returns the value of field 'annotationColours'.
811 * @return the value of field 'AnnotationColours'.
813 public jalview.schemabinding.version2.AnnotationColours getAnnotationColours(
815 return this._annotationColours;
819 * Returns the value of field 'bgColour'.
821 * @return the value of field 'BgColour'.
823 public java.lang.String getBgColour(
825 return this._bgColour;
829 * Method getCalcIdParam.
832 * @throws java.lang.IndexOutOfBoundsException if the index
833 * given is outside the bounds of the collection
834 * @return the value of the
835 * jalview.schemabinding.version2.CalcIdParam at the given index
837 public jalview.schemabinding.version2.CalcIdParam getCalcIdParam(
839 throws java.lang.IndexOutOfBoundsException {
840 // check bounds for index
841 if (index < 0 || index >= this._calcIdParamList.size()) {
842 throw new IndexOutOfBoundsException("getCalcIdParam: Index value '" + index + "' not in range [0.." + (this._calcIdParamList.size() - 1) + "]");
845 return (jalview.schemabinding.version2.CalcIdParam) _calcIdParamList.get(index);
849 * Method getCalcIdParam.Returns the contents of the collection
850 * in an Array. <p>Note: Just in case the collection contents
851 * are changing in another thread, we pass a 0-length Array of
852 * the correct type into the API call. This way we <i>know</i>
853 * that the Array returned is of exactly the correct length.
855 * @return this collection as an Array
857 public jalview.schemabinding.version2.CalcIdParam[] getCalcIdParam(
859 jalview.schemabinding.version2.CalcIdParam[] array = new jalview.schemabinding.version2.CalcIdParam[0];
860 return (jalview.schemabinding.version2.CalcIdParam[]) this._calcIdParamList.toArray(array);
864 * Method getCalcIdParamCount.
866 * @return the size of this collection
868 public int getCalcIdParamCount(
870 return this._calcIdParamList.size();
874 * Returns the value of field 'centreColumnLabels'.
876 * @return the value of field 'CentreColumnLabels'.
878 public boolean getCentreColumnLabels(
880 return this._centreColumnLabels;
884 * Returns the value of field 'complementId'. The field
885 * 'complementId' has the following description: The viewport
886 * id of this viewport's
887 * (cdna/protein) coding complement, if any
890 * @return the value of field 'ComplementId'.
892 public java.lang.String getComplementId(
894 return this._complementId;
898 * Returns the value of field 'consThreshold'.
900 * @return the value of field 'ConsThreshold'.
902 public int getConsThreshold(
904 return this._consThreshold;
908 * Returns the value of field 'conservationSelected'.
910 * @return the value of field 'ConservationSelected'.
912 public boolean getConservationSelected(
914 return this._conservationSelected;
918 * Returns the value of field 'followHighlight'.
920 * @return the value of field 'FollowHighlight'.
922 public boolean getFollowHighlight(
924 return this._followHighlight;
928 * Returns the value of field 'followSelection'.
930 * @return the value of field 'FollowSelection'.
932 public boolean getFollowSelection(
934 return this._followSelection;
938 * Returns the value of field 'fontName'.
940 * @return the value of field 'FontName'.
942 public java.lang.String getFontName(
944 return this._fontName;
948 * Returns the value of field 'fontSize'.
950 * @return the value of field 'FontSize'.
952 public int getFontSize(
954 return this._fontSize;
958 * Returns the value of field 'fontStyle'.
960 * @return the value of field 'FontStyle'.
962 public int getFontStyle(
964 return this._fontStyle;
968 * Returns the value of field 'gatheredViews'.
970 * @return the value of field 'GatheredViews'.
972 public boolean getGatheredViews(
974 return this._gatheredViews;
978 * Returns the value of field 'height'.
980 * @return the value of field 'Height'.
982 public int getHeight(
988 * Method getHiddenColumns.
991 * @throws java.lang.IndexOutOfBoundsException if the index
992 * given is outside the bounds of the collection
993 * @return the value of the
994 * jalview.schemabinding.version2.HiddenColumns at the given
997 public jalview.schemabinding.version2.HiddenColumns getHiddenColumns(
999 throws java.lang.IndexOutOfBoundsException {
1000 // check bounds for index
1001 if (index < 0 || index >= this._hiddenColumnsList.size()) {
1002 throw new IndexOutOfBoundsException("getHiddenColumns: Index value '" + index + "' not in range [0.." + (this._hiddenColumnsList.size() - 1) + "]");
1005 return (jalview.schemabinding.version2.HiddenColumns) _hiddenColumnsList.get(index);
1009 * Method getHiddenColumns.Returns the contents of the
1010 * collection in an Array. <p>Note: Just in case the
1011 * collection contents are changing in another thread, we pass
1012 * a 0-length Array of the correct type into the API call.
1013 * This way we <i>know</i> that the Array returned is of
1014 * exactly the correct length.
1016 * @return this collection as an Array
1018 public jalview.schemabinding.version2.HiddenColumns[] getHiddenColumns(
1020 jalview.schemabinding.version2.HiddenColumns[] array = new jalview.schemabinding.version2.HiddenColumns[0];
1021 return (jalview.schemabinding.version2.HiddenColumns[]) this._hiddenColumnsList.toArray(array);
1025 * Method getHiddenColumnsCount.
1027 * @return the size of this collection
1029 public int getHiddenColumnsCount(
1031 return this._hiddenColumnsList.size();
1035 * Returns the value of field 'id'. The field 'id' has the
1036 * following description: unique id used by jalview to
1038 * between stored and
1039 * instantiated views
1042 * @return the value of field 'Id'.
1044 public java.lang.String getId(
1050 * Returns the value of field 'ignoreGapsinConsensus'.
1052 * @return the value of field 'IgnoreGapsinConsensus'.
1054 public boolean getIgnoreGapsinConsensus(
1056 return this._ignoreGapsinConsensus;
1060 * Returns the value of field 'normaliseSequenceLogo'.
1062 * @return the value of field 'NormaliseSequenceLogo'.
1064 public boolean getNormaliseSequenceLogo(
1066 return this._normaliseSequenceLogo;
1070 * Returns the value of field 'pidSelected'.
1072 * @return the value of field 'PidSelected'.
1074 public boolean getPidSelected(
1076 return this._pidSelected;
1080 * Returns the value of field 'pidThreshold'.
1082 * @return the value of field 'PidThreshold'.
1084 public int getPidThreshold(
1086 return this._pidThreshold;
1090 * Returns the value of field 'renderGaps'.
1092 * @return the value of field 'RenderGaps'.
1094 public boolean getRenderGaps(
1096 return this._renderGaps;
1100 * Returns the value of field 'rightAlignIds'.
1102 * @return the value of field 'RightAlignIds'.
1104 public boolean getRightAlignIds(
1106 return this._rightAlignIds;
1110 * Returns the value of field 'sequenceSetId'.
1112 * @return the value of field 'SequenceSetId'.
1114 public java.lang.String getSequenceSetId(
1116 return this._sequenceSetId;
1120 * Returns the value of field 'showAnnotation'.
1122 * @return the value of field 'ShowAnnotation'.
1124 public boolean getShowAnnotation(
1126 return this._showAnnotation;
1130 * Returns the value of field 'showBoxes'.
1132 * @return the value of field 'ShowBoxes'.
1134 public boolean getShowBoxes(
1136 return this._showBoxes;
1140 * Returns the value of field 'showColourText'.
1142 * @return the value of field 'ShowColourText'.
1144 public boolean getShowColourText(
1146 return this._showColourText;
1150 * Returns the value of field 'showConsensusHistogram'.
1152 * @return the value of field 'ShowConsensusHistogram'.
1154 public boolean getShowConsensusHistogram(
1156 return this._showConsensusHistogram;
1160 * Returns the value of field 'showDbRefTooltip'.
1162 * @return the value of field 'ShowDbRefTooltip'.
1164 public boolean getShowDbRefTooltip(
1166 return this._showDbRefTooltip;
1170 * Returns the value of field 'showFullId'.
1172 * @return the value of field 'ShowFullId'.
1174 public boolean getShowFullId(
1176 return this._showFullId;
1180 * Returns the value of field 'showGroupConsensus'.
1182 * @return the value of field 'ShowGroupConsensus'.
1184 public boolean getShowGroupConsensus(
1186 return this._showGroupConsensus;
1190 * Returns the value of field 'showGroupConservation'.
1192 * @return the value of field 'ShowGroupConservation'.
1194 public boolean getShowGroupConservation(
1196 return this._showGroupConservation;
1200 * Returns the value of field 'showNPfeatureTooltip'.
1202 * @return the value of field 'ShowNPfeatureTooltip'.
1204 public boolean getShowNPfeatureTooltip(
1206 return this._showNPfeatureTooltip;
1210 * Returns the value of field 'showSequenceFeatures'.
1212 * @return the value of field 'ShowSequenceFeatures'.
1214 public boolean getShowSequenceFeatures(
1216 return this._showSequenceFeatures;
1220 * Returns the value of field 'showSequenceLogo'.
1222 * @return the value of field 'ShowSequenceLogo'.
1224 public boolean getShowSequenceLogo(
1226 return this._showSequenceLogo;
1230 * Returns the value of field 'showText'.
1232 * @return the value of field 'ShowText'.
1234 public boolean getShowText(
1236 return this._showText;
1240 * Returns the value of field 'showUnconserved'.
1242 * @return the value of field 'ShowUnconserved'.
1244 public boolean getShowUnconserved(
1246 return this._showUnconserved;
1250 * Returns the value of field 'startRes'.
1252 * @return the value of field 'StartRes'.
1254 public int getStartRes(
1256 return this._startRes;
1260 * Returns the value of field 'startSeq'.
1262 * @return the value of field 'StartSeq'.
1264 public int getStartSeq(
1266 return this._startSeq;
1270 * Returns the value of field 'textCol1'.
1272 * @return the value of field 'TextCol1'.
1274 public int getTextCol1(
1276 return this._textCol1;
1280 * Returns the value of field 'textCol2'.
1282 * @return the value of field 'TextCol2'.
1284 public int getTextCol2(
1286 return this._textCol2;
1290 * Returns the value of field 'textColThreshold'.
1292 * @return the value of field 'TextColThreshold'.
1294 public int getTextColThreshold(
1296 return this._textColThreshold;
1300 * Returns the value of field 'title'.
1302 * @return the value of field 'Title'.
1304 public java.lang.String getTitle(
1310 * Returns the value of field 'viewName'.
1312 * @return the value of field 'ViewName'.
1314 public java.lang.String getViewName(
1316 return this._viewName;
1320 * Returns the value of field 'width'.
1322 * @return the value of field 'Width'.
1324 public int getWidth(
1330 * Returns the value of field 'wrapAlignment'.
1332 * @return the value of field 'WrapAlignment'.
1334 public boolean getWrapAlignment(
1336 return this._wrapAlignment;
1340 * Returns the value of field 'xpos'.
1342 * @return the value of field 'Xpos'.
1350 * Returns the value of field 'ypos'.
1352 * @return the value of field 'Ypos'.
1360 * Method hasCentreColumnLabels.
1362 * @return true if at least one CentreColumnLabels has been adde
1364 public boolean hasCentreColumnLabels(
1366 return this._has_centreColumnLabels;
1370 * Method hasConsThreshold.
1372 * @return true if at least one ConsThreshold has been added
1374 public boolean hasConsThreshold(
1376 return this._has_consThreshold;
1380 * Method hasConservationSelected.
1382 * @return true if at least one ConservationSelected has been
1385 public boolean hasConservationSelected(
1387 return this._has_conservationSelected;
1391 * Method hasFollowHighlight.
1393 * @return true if at least one FollowHighlight has been added
1395 public boolean hasFollowHighlight(
1397 return this._has_followHighlight;
1401 * Method hasFollowSelection.
1403 * @return true if at least one FollowSelection has been added
1405 public boolean hasFollowSelection(
1407 return this._has_followSelection;
1411 * Method hasFontSize.
1413 * @return true if at least one FontSize has been added
1415 public boolean hasFontSize(
1417 return this._has_fontSize;
1421 * Method hasFontStyle.
1423 * @return true if at least one FontStyle has been added
1425 public boolean hasFontStyle(
1427 return this._has_fontStyle;
1431 * Method hasGatheredViews.
1433 * @return true if at least one GatheredViews has been added
1435 public boolean hasGatheredViews(
1437 return this._has_gatheredViews;
1443 * @return true if at least one Height has been added
1445 public boolean hasHeight(
1447 return this._has_height;
1451 * Method hasIgnoreGapsinConsensus.
1453 * @return true if at least one IgnoreGapsinConsensus has been
1456 public boolean hasIgnoreGapsinConsensus(
1458 return this._has_ignoreGapsinConsensus;
1462 * Method hasNormaliseSequenceLogo.
1464 * @return true if at least one NormaliseSequenceLogo has been
1467 public boolean hasNormaliseSequenceLogo(
1469 return this._has_normaliseSequenceLogo;
1473 * Method hasPidSelected.
1475 * @return true if at least one PidSelected has been added
1477 public boolean hasPidSelected(
1479 return this._has_pidSelected;
1483 * Method hasPidThreshold.
1485 * @return true if at least one PidThreshold has been added
1487 public boolean hasPidThreshold(
1489 return this._has_pidThreshold;
1493 * Method hasRenderGaps.
1495 * @return true if at least one RenderGaps has been added
1497 public boolean hasRenderGaps(
1499 return this._has_renderGaps;
1503 * Method hasRightAlignIds.
1505 * @return true if at least one RightAlignIds has been added
1507 public boolean hasRightAlignIds(
1509 return this._has_rightAlignIds;
1513 * Method hasShowAnnotation.
1515 * @return true if at least one ShowAnnotation has been added
1517 public boolean hasShowAnnotation(
1519 return this._has_showAnnotation;
1523 * Method hasShowBoxes.
1525 * @return true if at least one ShowBoxes has been added
1527 public boolean hasShowBoxes(
1529 return this._has_showBoxes;
1533 * Method hasShowColourText.
1535 * @return true if at least one ShowColourText has been added
1537 public boolean hasShowColourText(
1539 return this._has_showColourText;
1543 * Method hasShowConsensusHistogram.
1545 * @return true if at least one ShowConsensusHistogram has been
1548 public boolean hasShowConsensusHistogram(
1550 return this._has_showConsensusHistogram;
1554 * Method hasShowDbRefTooltip.
1556 * @return true if at least one ShowDbRefTooltip has been added
1558 public boolean hasShowDbRefTooltip(
1560 return this._has_showDbRefTooltip;
1564 * Method hasShowFullId.
1566 * @return true if at least one ShowFullId has been added
1568 public boolean hasShowFullId(
1570 return this._has_showFullId;
1574 * Method hasShowGroupConsensus.
1576 * @return true if at least one ShowGroupConsensus has been adde
1578 public boolean hasShowGroupConsensus(
1580 return this._has_showGroupConsensus;
1584 * Method hasShowGroupConservation.
1586 * @return true if at least one ShowGroupConservation has been
1589 public boolean hasShowGroupConservation(
1591 return this._has_showGroupConservation;
1595 * Method hasShowNPfeatureTooltip.
1597 * @return true if at least one ShowNPfeatureTooltip has been
1600 public boolean hasShowNPfeatureTooltip(
1602 return this._has_showNPfeatureTooltip;
1606 * Method hasShowSequenceFeatures.
1608 * @return true if at least one ShowSequenceFeatures has been
1611 public boolean hasShowSequenceFeatures(
1613 return this._has_showSequenceFeatures;
1617 * Method hasShowSequenceLogo.
1619 * @return true if at least one ShowSequenceLogo has been added
1621 public boolean hasShowSequenceLogo(
1623 return this._has_showSequenceLogo;
1627 * Method hasShowText.
1629 * @return true if at least one ShowText has been added
1631 public boolean hasShowText(
1633 return this._has_showText;
1637 * Method hasShowUnconserved.
1639 * @return true if at least one ShowUnconserved has been added
1641 public boolean hasShowUnconserved(
1643 return this._has_showUnconserved;
1647 * Method hasStartRes.
1649 * @return true if at least one StartRes has been added
1651 public boolean hasStartRes(
1653 return this._has_startRes;
1657 * Method hasStartSeq.
1659 * @return true if at least one StartSeq has been added
1661 public boolean hasStartSeq(
1663 return this._has_startSeq;
1667 * Method hasTextCol1.
1669 * @return true if at least one TextCol1 has been added
1671 public boolean hasTextCol1(
1673 return this._has_textCol1;
1677 * Method hasTextCol2.
1679 * @return true if at least one TextCol2 has been added
1681 public boolean hasTextCol2(
1683 return this._has_textCol2;
1687 * Method hasTextColThreshold.
1689 * @return true if at least one TextColThreshold has been added
1691 public boolean hasTextColThreshold(
1693 return this._has_textColThreshold;
1699 * @return true if at least one Width has been added
1701 public boolean hasWidth(
1703 return this._has_width;
1707 * Method hasWrapAlignment.
1709 * @return true if at least one WrapAlignment has been added
1711 public boolean hasWrapAlignment(
1713 return this._has_wrapAlignment;
1719 * @return true if at least one Xpos has been added
1721 public boolean hasXpos(
1723 return this._has_xpos;
1729 * @return true if at least one Ypos has been added
1731 public boolean hasYpos(
1733 return this._has_ypos;
1737 * Returns the value of field 'centreColumnLabels'.
1739 * @return the value of field 'CentreColumnLabels'.
1741 public boolean isCentreColumnLabels(
1743 return this._centreColumnLabels;
1747 * Returns the value of field 'conservationSelected'.
1749 * @return the value of field 'ConservationSelected'.
1751 public boolean isConservationSelected(
1753 return this._conservationSelected;
1757 * Returns the value of field 'followHighlight'.
1759 * @return the value of field 'FollowHighlight'.
1761 public boolean isFollowHighlight(
1763 return this._followHighlight;
1767 * Returns the value of field 'followSelection'.
1769 * @return the value of field 'FollowSelection'.
1771 public boolean isFollowSelection(
1773 return this._followSelection;
1777 * Returns the value of field 'gatheredViews'.
1779 * @return the value of field 'GatheredViews'.
1781 public boolean isGatheredViews(
1783 return this._gatheredViews;
1787 * Returns the value of field 'ignoreGapsinConsensus'.
1789 * @return the value of field 'IgnoreGapsinConsensus'.
1791 public boolean isIgnoreGapsinConsensus(
1793 return this._ignoreGapsinConsensus;
1797 * Returns the value of field 'normaliseSequenceLogo'.
1799 * @return the value of field 'NormaliseSequenceLogo'.
1801 public boolean isNormaliseSequenceLogo(
1803 return this._normaliseSequenceLogo;
1807 * Returns the value of field 'pidSelected'.
1809 * @return the value of field 'PidSelected'.
1811 public boolean isPidSelected(
1813 return this._pidSelected;
1817 * Returns the value of field 'renderGaps'.
1819 * @return the value of field 'RenderGaps'.
1821 public boolean isRenderGaps(
1823 return this._renderGaps;
1827 * Returns the value of field 'rightAlignIds'.
1829 * @return the value of field 'RightAlignIds'.
1831 public boolean isRightAlignIds(
1833 return this._rightAlignIds;
1837 * Returns the value of field 'showAnnotation'.
1839 * @return the value of field 'ShowAnnotation'.
1841 public boolean isShowAnnotation(
1843 return this._showAnnotation;
1847 * Returns the value of field 'showBoxes'.
1849 * @return the value of field 'ShowBoxes'.
1851 public boolean isShowBoxes(
1853 return this._showBoxes;
1857 * Returns the value of field 'showColourText'.
1859 * @return the value of field 'ShowColourText'.
1861 public boolean isShowColourText(
1863 return this._showColourText;
1867 * Returns the value of field 'showConsensusHistogram'.
1869 * @return the value of field 'ShowConsensusHistogram'.
1871 public boolean isShowConsensusHistogram(
1873 return this._showConsensusHistogram;
1877 * Returns the value of field 'showDbRefTooltip'.
1879 * @return the value of field 'ShowDbRefTooltip'.
1881 public boolean isShowDbRefTooltip(
1883 return this._showDbRefTooltip;
1887 * Returns the value of field 'showFullId'.
1889 * @return the value of field 'ShowFullId'.
1891 public boolean isShowFullId(
1893 return this._showFullId;
1897 * Returns the value of field 'showGroupConsensus'.
1899 * @return the value of field 'ShowGroupConsensus'.
1901 public boolean isShowGroupConsensus(
1903 return this._showGroupConsensus;
1907 * Returns the value of field 'showGroupConservation'.
1909 * @return the value of field 'ShowGroupConservation'.
1911 public boolean isShowGroupConservation(
1913 return this._showGroupConservation;
1917 * Returns the value of field 'showNPfeatureTooltip'.
1919 * @return the value of field 'ShowNPfeatureTooltip'.
1921 public boolean isShowNPfeatureTooltip(
1923 return this._showNPfeatureTooltip;
1927 * Returns the value of field 'showSequenceFeatures'.
1929 * @return the value of field 'ShowSequenceFeatures'.
1931 public boolean isShowSequenceFeatures(
1933 return this._showSequenceFeatures;
1937 * Returns the value of field 'showSequenceLogo'.
1939 * @return the value of field 'ShowSequenceLogo'.
1941 public boolean isShowSequenceLogo(
1943 return this._showSequenceLogo;
1947 * Returns the value of field 'showText'.
1949 * @return the value of field 'ShowText'.
1951 public boolean isShowText(
1953 return this._showText;
1957 * Returns the value of field 'showUnconserved'.
1959 * @return the value of field 'ShowUnconserved'.
1961 public boolean isShowUnconserved(
1963 return this._showUnconserved;
1969 * @return true if this object is valid according to the schema
1971 public boolean isValid(
1975 } catch (org.exolab.castor.xml.ValidationException vex) {
1982 * Returns the value of field 'wrapAlignment'.
1984 * @return the value of field 'WrapAlignment'.
1986 public boolean isWrapAlignment(
1988 return this._wrapAlignment;
1995 * @throws org.exolab.castor.xml.MarshalException if object is
1996 * null or if any SAXException is thrown during marshaling
1997 * @throws org.exolab.castor.xml.ValidationException if this
1998 * object is an invalid instance according to the schema
2000 public void marshal(
2001 final java.io.Writer out)
2002 throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
2003 Marshaller.marshal(this, out);
2010 * @throws java.io.IOException if an IOException occurs during
2012 * @throws org.exolab.castor.xml.ValidationException if this
2013 * object is an invalid instance according to the schema
2014 * @throws org.exolab.castor.xml.MarshalException if object is
2015 * null or if any SAXException is thrown during marshaling
2017 public void marshal(
2018 final org.xml.sax.ContentHandler handler)
2019 throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
2020 Marshaller.marshal(this, handler);
2025 public void removeAllCalcIdParam(
2027 this._calcIdParamList.clear();
2032 public void removeAllHiddenColumns(
2034 this._hiddenColumnsList.clear();
2038 * Method removeCalcIdParam.
2040 * @param vCalcIdParam
2041 * @return true if the object was removed from the collection.
2043 public boolean removeCalcIdParam(
2044 final jalview.schemabinding.version2.CalcIdParam vCalcIdParam) {
2045 boolean removed = _calcIdParamList.remove(vCalcIdParam);
2050 * Method removeCalcIdParamAt.
2053 * @return the element removed from the collection
2055 public jalview.schemabinding.version2.CalcIdParam removeCalcIdParamAt(
2057 java.lang.Object obj = this._calcIdParamList.remove(index);
2058 return (jalview.schemabinding.version2.CalcIdParam) obj;
2062 * Method removeHiddenColumns.
2064 * @param vHiddenColumns
2065 * @return true if the object was removed from the collection.
2067 public boolean removeHiddenColumns(
2068 final jalview.schemabinding.version2.HiddenColumns vHiddenColumns) {
2069 boolean removed = _hiddenColumnsList.remove(vHiddenColumns);
2074 * Method removeHiddenColumnsAt.
2077 * @return the element removed from the collection
2079 public jalview.schemabinding.version2.HiddenColumns removeHiddenColumnsAt(
2081 java.lang.Object obj = this._hiddenColumnsList.remove(index);
2082 return (jalview.schemabinding.version2.HiddenColumns) obj;
2086 * Sets the value of field 'annotationColours'.
2088 * @param annotationColours the value of field
2089 * 'annotationColours'.
2091 public void setAnnotationColours(
2092 final jalview.schemabinding.version2.AnnotationColours annotationColours) {
2093 this._annotationColours = annotationColours;
2097 * Sets the value of field 'bgColour'.
2099 * @param bgColour the value of field 'bgColour'.
2101 public void setBgColour(
2102 final java.lang.String bgColour) {
2103 this._bgColour = bgColour;
2110 * @param vCalcIdParam
2111 * @throws java.lang.IndexOutOfBoundsException if the index
2112 * given is outside the bounds of the collection
2114 public void setCalcIdParam(
2116 final jalview.schemabinding.version2.CalcIdParam vCalcIdParam)
2117 throws java.lang.IndexOutOfBoundsException {
2118 // check bounds for index
2119 if (index < 0 || index >= this._calcIdParamList.size()) {
2120 throw new IndexOutOfBoundsException("setCalcIdParam: Index value '" + index + "' not in range [0.." + (this._calcIdParamList.size() - 1) + "]");
2123 this._calcIdParamList.set(index, vCalcIdParam);
2129 * @param vCalcIdParamArray
2131 public void setCalcIdParam(
2132 final jalview.schemabinding.version2.CalcIdParam[] vCalcIdParamArray) {
2134 _calcIdParamList.clear();
2136 for (int i = 0; i < vCalcIdParamArray.length; i++) {
2137 this._calcIdParamList.add(vCalcIdParamArray[i]);
2142 * Sets the value of field 'centreColumnLabels'.
2144 * @param centreColumnLabels the value of field
2145 * 'centreColumnLabels'.
2147 public void setCentreColumnLabels(
2148 final boolean centreColumnLabels) {
2149 this._centreColumnLabels = centreColumnLabels;
2150 this._has_centreColumnLabels = true;
2154 * Sets the value of field 'complementId'. The field
2155 * 'complementId' has the following description: The viewport
2156 * id of this viewport's
2157 * (cdna/protein) coding complement, if any
2160 * @param complementId the value of field 'complementId'.
2162 public void setComplementId(
2163 final java.lang.String complementId) {
2164 this._complementId = complementId;
2168 * Sets the value of field 'consThreshold'.
2170 * @param consThreshold the value of field 'consThreshold'.
2172 public void setConsThreshold(
2173 final int consThreshold) {
2174 this._consThreshold = consThreshold;
2175 this._has_consThreshold = true;
2179 * Sets the value of field 'conservationSelected'.
2181 * @param conservationSelected the value of field
2182 * 'conservationSelected'.
2184 public void setConservationSelected(
2185 final boolean conservationSelected) {
2186 this._conservationSelected = conservationSelected;
2187 this._has_conservationSelected = true;
2191 * Sets the value of field 'followHighlight'.
2193 * @param followHighlight the value of field 'followHighlight'.
2195 public void setFollowHighlight(
2196 final boolean followHighlight) {
2197 this._followHighlight = followHighlight;
2198 this._has_followHighlight = true;
2202 * Sets the value of field 'followSelection'.
2204 * @param followSelection the value of field 'followSelection'.
2206 public void setFollowSelection(
2207 final boolean followSelection) {
2208 this._followSelection = followSelection;
2209 this._has_followSelection = true;
2213 * Sets the value of field 'fontName'.
2215 * @param fontName the value of field 'fontName'.
2217 public void setFontName(
2218 final java.lang.String fontName) {
2219 this._fontName = fontName;
2223 * Sets the value of field 'fontSize'.
2225 * @param fontSize the value of field 'fontSize'.
2227 public void setFontSize(
2228 final int fontSize) {
2229 this._fontSize = fontSize;
2230 this._has_fontSize = true;
2234 * Sets the value of field 'fontStyle'.
2236 * @param fontStyle the value of field 'fontStyle'.
2238 public void setFontStyle(
2239 final int fontStyle) {
2240 this._fontStyle = fontStyle;
2241 this._has_fontStyle = true;
2245 * Sets the value of field 'gatheredViews'.
2247 * @param gatheredViews the value of field 'gatheredViews'.
2249 public void setGatheredViews(
2250 final boolean gatheredViews) {
2251 this._gatheredViews = gatheredViews;
2252 this._has_gatheredViews = true;
2256 * Sets the value of field 'height'.
2258 * @param height the value of field 'height'.
2260 public void setHeight(
2262 this._height = height;
2263 this._has_height = true;
2270 * @param vHiddenColumns
2271 * @throws java.lang.IndexOutOfBoundsException if the index
2272 * given is outside the bounds of the collection
2274 public void setHiddenColumns(
2276 final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)
2277 throws java.lang.IndexOutOfBoundsException {
2278 // check bounds for index
2279 if (index < 0 || index >= this._hiddenColumnsList.size()) {
2280 throw new IndexOutOfBoundsException("setHiddenColumns: Index value '" + index + "' not in range [0.." + (this._hiddenColumnsList.size() - 1) + "]");
2283 this._hiddenColumnsList.set(index, vHiddenColumns);
2289 * @param vHiddenColumnsArray
2291 public void setHiddenColumns(
2292 final jalview.schemabinding.version2.HiddenColumns[] vHiddenColumnsArray) {
2294 _hiddenColumnsList.clear();
2296 for (int i = 0; i < vHiddenColumnsArray.length; i++) {
2297 this._hiddenColumnsList.add(vHiddenColumnsArray[i]);
2302 * Sets the value of field 'id'. The field 'id' has the
2303 * following description: unique id used by jalview to
2305 * between stored and
2306 * instantiated views
2309 * @param id the value of field 'id'.
2312 final java.lang.String id) {
2317 * Sets the value of field 'ignoreGapsinConsensus'.
2319 * @param ignoreGapsinConsensus the value of field
2320 * 'ignoreGapsinConsensus'.
2322 public void setIgnoreGapsinConsensus(
2323 final boolean ignoreGapsinConsensus) {
2324 this._ignoreGapsinConsensus = ignoreGapsinConsensus;
2325 this._has_ignoreGapsinConsensus = true;
2329 * Sets the value of field 'normaliseSequenceLogo'.
2331 * @param normaliseSequenceLogo the value of field
2332 * 'normaliseSequenceLogo'.
2334 public void setNormaliseSequenceLogo(
2335 final boolean normaliseSequenceLogo) {
2336 this._normaliseSequenceLogo = normaliseSequenceLogo;
2337 this._has_normaliseSequenceLogo = true;
2341 * Sets the value of field 'pidSelected'.
2343 * @param pidSelected the value of field 'pidSelected'.
2345 public void setPidSelected(
2346 final boolean pidSelected) {
2347 this._pidSelected = pidSelected;
2348 this._has_pidSelected = true;
2352 * Sets the value of field 'pidThreshold'.
2354 * @param pidThreshold the value of field 'pidThreshold'.
2356 public void setPidThreshold(
2357 final int pidThreshold) {
2358 this._pidThreshold = pidThreshold;
2359 this._has_pidThreshold = true;
2363 * Sets the value of field 'renderGaps'.
2365 * @param renderGaps the value of field 'renderGaps'.
2367 public void setRenderGaps(
2368 final boolean renderGaps) {
2369 this._renderGaps = renderGaps;
2370 this._has_renderGaps = true;
2374 * Sets the value of field 'rightAlignIds'.
2376 * @param rightAlignIds the value of field 'rightAlignIds'.
2378 public void setRightAlignIds(
2379 final boolean rightAlignIds) {
2380 this._rightAlignIds = rightAlignIds;
2381 this._has_rightAlignIds = true;
2385 * Sets the value of field 'sequenceSetId'.
2387 * @param sequenceSetId the value of field 'sequenceSetId'.
2389 public void setSequenceSetId(
2390 final java.lang.String sequenceSetId) {
2391 this._sequenceSetId = sequenceSetId;
2395 * Sets the value of field 'showAnnotation'.
2397 * @param showAnnotation the value of field 'showAnnotation'.
2399 public void setShowAnnotation(
2400 final boolean showAnnotation) {
2401 this._showAnnotation = showAnnotation;
2402 this._has_showAnnotation = true;
2406 * Sets the value of field 'showBoxes'.
2408 * @param showBoxes the value of field 'showBoxes'.
2410 public void setShowBoxes(
2411 final boolean showBoxes) {
2412 this._showBoxes = showBoxes;
2413 this._has_showBoxes = true;
2417 * Sets the value of field 'showColourText'.
2419 * @param showColourText the value of field 'showColourText'.
2421 public void setShowColourText(
2422 final boolean showColourText) {
2423 this._showColourText = showColourText;
2424 this._has_showColourText = true;
2428 * Sets the value of field 'showConsensusHistogram'.
2430 * @param showConsensusHistogram the value of field
2431 * 'showConsensusHistogram'.
2433 public void setShowConsensusHistogram(
2434 final boolean showConsensusHistogram) {
2435 this._showConsensusHistogram = showConsensusHistogram;
2436 this._has_showConsensusHistogram = true;
2440 * Sets the value of field 'showDbRefTooltip'.
2442 * @param showDbRefTooltip the value of field 'showDbRefTooltip'
2444 public void setShowDbRefTooltip(
2445 final boolean showDbRefTooltip) {
2446 this._showDbRefTooltip = showDbRefTooltip;
2447 this._has_showDbRefTooltip = true;
2451 * Sets the value of field 'showFullId'.
2453 * @param showFullId the value of field 'showFullId'.
2455 public void setShowFullId(
2456 final boolean showFullId) {
2457 this._showFullId = showFullId;
2458 this._has_showFullId = true;
2462 * Sets the value of field 'showGroupConsensus'.
2464 * @param showGroupConsensus the value of field
2465 * 'showGroupConsensus'.
2467 public void setShowGroupConsensus(
2468 final boolean showGroupConsensus) {
2469 this._showGroupConsensus = showGroupConsensus;
2470 this._has_showGroupConsensus = true;
2474 * Sets the value of field 'showGroupConservation'.
2476 * @param showGroupConservation the value of field
2477 * 'showGroupConservation'.
2479 public void setShowGroupConservation(
2480 final boolean showGroupConservation) {
2481 this._showGroupConservation = showGroupConservation;
2482 this._has_showGroupConservation = true;
2486 * Sets the value of field 'showNPfeatureTooltip'.
2488 * @param showNPfeatureTooltip the value of field
2489 * 'showNPfeatureTooltip'.
2491 public void setShowNPfeatureTooltip(
2492 final boolean showNPfeatureTooltip) {
2493 this._showNPfeatureTooltip = showNPfeatureTooltip;
2494 this._has_showNPfeatureTooltip = true;
2498 * Sets the value of field 'showSequenceFeatures'.
2500 * @param showSequenceFeatures the value of field
2501 * 'showSequenceFeatures'.
2503 public void setShowSequenceFeatures(
2504 final boolean showSequenceFeatures) {
2505 this._showSequenceFeatures = showSequenceFeatures;
2506 this._has_showSequenceFeatures = true;
2510 * Sets the value of field 'showSequenceLogo'.
2512 * @param showSequenceLogo the value of field 'showSequenceLogo'
2514 public void setShowSequenceLogo(
2515 final boolean showSequenceLogo) {
2516 this._showSequenceLogo = showSequenceLogo;
2517 this._has_showSequenceLogo = true;
2521 * Sets the value of field 'showText'.
2523 * @param showText the value of field 'showText'.
2525 public void setShowText(
2526 final boolean showText) {
2527 this._showText = showText;
2528 this._has_showText = true;
2532 * Sets the value of field 'showUnconserved'.
2534 * @param showUnconserved the value of field 'showUnconserved'.
2536 public void setShowUnconserved(
2537 final boolean showUnconserved) {
2538 this._showUnconserved = showUnconserved;
2539 this._has_showUnconserved = true;
2543 * Sets the value of field 'startRes'.
2545 * @param startRes the value of field 'startRes'.
2547 public void setStartRes(
2548 final int startRes) {
2549 this._startRes = startRes;
2550 this._has_startRes = true;
2554 * Sets the value of field 'startSeq'.
2556 * @param startSeq the value of field 'startSeq'.
2558 public void setStartSeq(
2559 final int startSeq) {
2560 this._startSeq = startSeq;
2561 this._has_startSeq = true;
2565 * Sets the value of field 'textCol1'.
2567 * @param textCol1 the value of field 'textCol1'.
2569 public void setTextCol1(
2570 final int textCol1) {
2571 this._textCol1 = textCol1;
2572 this._has_textCol1 = true;
2576 * Sets the value of field 'textCol2'.
2578 * @param textCol2 the value of field 'textCol2'.
2580 public void setTextCol2(
2581 final int textCol2) {
2582 this._textCol2 = textCol2;
2583 this._has_textCol2 = true;
2587 * Sets the value of field 'textColThreshold'.
2589 * @param textColThreshold the value of field 'textColThreshold'
2591 public void setTextColThreshold(
2592 final int textColThreshold) {
2593 this._textColThreshold = textColThreshold;
2594 this._has_textColThreshold = true;
2598 * Sets the value of field 'title'.
2600 * @param title the value of field 'title'.
2602 public void setTitle(
2603 final java.lang.String title) {
2604 this._title = title;
2608 * Sets the value of field 'viewName'.
2610 * @param viewName the value of field 'viewName'.
2612 public void setViewName(
2613 final java.lang.String viewName) {
2614 this._viewName = viewName;
2618 * Sets the value of field 'width'.
2620 * @param width the value of field 'width'.
2622 public void setWidth(
2624 this._width = width;
2625 this._has_width = true;
2629 * Sets the value of field 'wrapAlignment'.
2631 * @param wrapAlignment the value of field 'wrapAlignment'.
2633 public void setWrapAlignment(
2634 final boolean wrapAlignment) {
2635 this._wrapAlignment = wrapAlignment;
2636 this._has_wrapAlignment = true;
2640 * Sets the value of field 'xpos'.
2642 * @param xpos the value of field 'xpos'.
2644 public void setXpos(
2647 this._has_xpos = true;
2651 * Sets the value of field 'ypos'.
2653 * @param ypos the value of field 'ypos'.
2655 public void setYpos(
2658 this._has_ypos = true;
2665 * @throws org.exolab.castor.xml.MarshalException if object is
2666 * null or if any SAXException is thrown during marshaling
2667 * @throws org.exolab.castor.xml.ValidationException if this
2668 * object is an invalid instance according to the schema
2669 * @return the unmarshaled
2670 * jalview.schemabinding.version2.Viewport
2672 public static jalview.schemabinding.version2.Viewport unmarshal(
2673 final java.io.Reader reader)
2674 throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
2675 return (jalview.schemabinding.version2.Viewport) Unmarshaller.unmarshal(jalview.schemabinding.version2.Viewport.class, reader);
2681 * @throws org.exolab.castor.xml.ValidationException if this
2682 * object is an invalid instance according to the schema
2684 public void validate(
2686 throws org.exolab.castor.xml.ValidationException {
2687 org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
2688 validator.validate(this);