1 /*******************************************************************************
2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
3 * Copyright (C) 2014 The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
11 * Jalview is distributed in the hope that it will be useful, but
12 * WITHOUT ANY WARRANTY; without even the implied warranty
13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
14 * PURPOSE. See the GNU General Public License for more details.
16 * You should have received a copy of the GNU General Public License along with Jalview.
17 * If not, see <http://www.gnu.org/licenses/>.
18 * The Jalview Authors are detailed in the 'AUTHORS' file.
19 ******************************************************************************/
21 * This class was automatically generated with
22 * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
27 package jalview.schemabinding.version2;
29 //---------------------------------/
30 //- Imported classes and packages -/
31 //---------------------------------/
33 import org.exolab.castor.xml.Marshaller;
34 import org.exolab.castor.xml.Unmarshaller;
39 * @version $Revision$ $Date$
41 public class Viewport implements java.io.Serializable
44 // --------------------------/
45 // - Class/Member Variables -/
46 // --------------------------/
49 * Field _conservationSelected.
51 private boolean _conservationSelected;
54 * keeps track of state for field: _conservationSelected
56 private boolean _has_conservationSelected;
61 private boolean _pidSelected;
64 * keeps track of state for field: _pidSelected
66 private boolean _has_pidSelected;
71 private java.lang.String _bgColour;
74 * Field _consThreshold.
76 private int _consThreshold;
79 * keeps track of state for field: _consThreshold
81 private boolean _has_consThreshold;
84 * Field _pidThreshold.
86 private int _pidThreshold;
89 * keeps track of state for field: _pidThreshold
91 private boolean _has_pidThreshold;
96 private java.lang.String _title;
101 private boolean _showFullId;
104 * keeps track of state for field: _showFullId
106 private boolean _has_showFullId;
109 * Field _rightAlignIds.
111 private boolean _rightAlignIds;
114 * keeps track of state for field: _rightAlignIds
116 private boolean _has_rightAlignIds;
121 private boolean _showText;
124 * keeps track of state for field: _showText
126 private boolean _has_showText;
129 * Field _showColourText.
131 private boolean _showColourText;
134 * keeps track of state for field: _showColourText
136 private boolean _has_showColourText;
139 * Field _showUnconserved.
141 private boolean _showUnconserved = false;
144 * keeps track of state for field: _showUnconserved
146 private boolean _has_showUnconserved;
151 private boolean _showBoxes;
154 * keeps track of state for field: _showBoxes
156 private boolean _has_showBoxes;
159 * Field _wrapAlignment.
161 private boolean _wrapAlignment;
164 * keeps track of state for field: _wrapAlignment
166 private boolean _has_wrapAlignment;
171 private boolean _renderGaps;
174 * keeps track of state for field: _renderGaps
176 private boolean _has_renderGaps;
179 * Field _showSequenceFeatures.
181 private boolean _showSequenceFeatures;
184 * keeps track of state for field: _showSequenceFeatures
186 private boolean _has_showSequenceFeatures;
189 * Field _showNPfeatureTooltip.
191 private boolean _showNPfeatureTooltip;
194 * keeps track of state for field: _showNPfeatureTooltip
196 private boolean _has_showNPfeatureTooltip;
199 * Field _showDbRefTooltip.
201 private boolean _showDbRefTooltip;
204 * keeps track of state for field: _showDbRefTooltip
206 private boolean _has_showDbRefTooltip;
209 * Field _followHighlight.
211 private boolean _followHighlight = true;
214 * keeps track of state for field: _followHighlight
216 private boolean _has_followHighlight;
219 * Field _followSelection.
221 private boolean _followSelection = true;
224 * keeps track of state for field: _followSelection
226 private boolean _has_followSelection;
229 * Field _showAnnotation.
231 private boolean _showAnnotation;
234 * keeps track of state for field: _showAnnotation
236 private boolean _has_showAnnotation;
239 * Field _centreColumnLabels.
241 private boolean _centreColumnLabels = false;
244 * keeps track of state for field: _centreColumnLabels
246 private boolean _has_centreColumnLabels;
249 * Field _showGroupConservation.
251 private boolean _showGroupConservation = false;
254 * keeps track of state for field: _showGroupConservation
256 private boolean _has_showGroupConservation;
259 * Field _showGroupConsensus.
261 private boolean _showGroupConsensus = false;
264 * keeps track of state for field: _showGroupConsensus
266 private boolean _has_showGroupConsensus;
269 * Field _showConsensusHistogram.
271 private boolean _showConsensusHistogram = true;
274 * keeps track of state for field: _showConsensusHistogram
276 private boolean _has_showConsensusHistogram;
279 * Field _showSequenceLogo.
281 private boolean _showSequenceLogo = false;
284 * keeps track of state for field: _showSequenceLogo
286 private boolean _has_showSequenceLogo;
289 * Field _normaliseSequenceLogo.
291 private boolean _normaliseSequenceLogo = false;
294 * keeps track of state for field: _normaliseSequenceLogo
296 private boolean _has_normaliseSequenceLogo;
299 * Field _ignoreGapsinConsensus.
301 private boolean _ignoreGapsinConsensus = true;
304 * keeps track of state for field: _ignoreGapsinConsensus
306 private boolean _has_ignoreGapsinConsensus;
311 private int _startRes;
314 * keeps track of state for field: _startRes
316 private boolean _has_startRes;
321 private int _startSeq;
324 * keeps track of state for field: _startSeq
326 private boolean _has_startSeq;
331 private java.lang.String _fontName;
336 private int _fontSize;
339 * keeps track of state for field: _fontSize
341 private boolean _has_fontSize;
346 private int _fontStyle;
349 * keeps track of state for field: _fontStyle
351 private boolean _has_fontStyle;
356 private java.lang.String _viewName;
359 * Field _sequenceSetId.
361 private java.lang.String _sequenceSetId;
364 * Field _gatheredViews.
366 private boolean _gatheredViews;
369 * keeps track of state for field: _gatheredViews
371 private boolean _has_gatheredViews;
376 private int _textCol1;
379 * keeps track of state for field: _textCol1
381 private boolean _has_textCol1;
386 private int _textCol2;
389 * keeps track of state for field: _textCol2
391 private boolean _has_textCol2;
394 * Field _textColThreshold.
396 private int _textColThreshold;
399 * keeps track of state for field: _textColThreshold
401 private boolean _has_textColThreshold;
404 * unique id used by jalview to synchronize between stored and instantiated
408 private java.lang.String _id;
416 * keeps track of state for field: _width
418 private boolean _has_width;
426 * keeps track of state for field: _height
428 private boolean _has_height;
436 * keeps track of state for field: _xpos
438 private boolean _has_xpos;
446 * keeps track of state for field: _ypos
448 private boolean _has_ypos;
451 * Field _annotationColours.
453 private jalview.schemabinding.version2.AnnotationColours _annotationColours;
456 * Field _hiddenColumnsList.
458 private java.util.Vector _hiddenColumnsList;
461 * Field _calcIdParamList.
463 private java.util.Vector _calcIdParamList;
472 this._hiddenColumnsList = new java.util.Vector();
473 this._calcIdParamList = new java.util.Vector();
483 * @param vCalcIdParam
484 * @throws java.lang.IndexOutOfBoundsException
485 * if the index given is outside the bounds of the collection
487 public void addCalcIdParam(
488 final jalview.schemabinding.version2.CalcIdParam vCalcIdParam)
489 throws java.lang.IndexOutOfBoundsException
491 this._calcIdParamList.addElement(vCalcIdParam);
498 * @param vCalcIdParam
499 * @throws java.lang.IndexOutOfBoundsException
500 * if the index given is outside the bounds of the collection
502 public void addCalcIdParam(final int index,
503 final jalview.schemabinding.version2.CalcIdParam vCalcIdParam)
504 throws java.lang.IndexOutOfBoundsException
506 this._calcIdParamList.add(index, vCalcIdParam);
512 * @param vHiddenColumns
513 * @throws java.lang.IndexOutOfBoundsException
514 * if the index given is outside the bounds of the collection
516 public void addHiddenColumns(
517 final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)
518 throws java.lang.IndexOutOfBoundsException
520 this._hiddenColumnsList.addElement(vHiddenColumns);
527 * @param vHiddenColumns
528 * @throws java.lang.IndexOutOfBoundsException
529 * if the index given is outside the bounds of the collection
531 public void addHiddenColumns(final int index,
532 final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)
533 throws java.lang.IndexOutOfBoundsException
535 this._hiddenColumnsList.add(index, vHiddenColumns);
540 public void deleteCentreColumnLabels()
542 this._has_centreColumnLabels = false;
547 public void deleteConsThreshold()
549 this._has_consThreshold = false;
554 public void deleteConservationSelected()
556 this._has_conservationSelected = false;
561 public void deleteFollowHighlight()
563 this._has_followHighlight = false;
568 public void deleteFollowSelection()
570 this._has_followSelection = false;
575 public void deleteFontSize()
577 this._has_fontSize = false;
582 public void deleteFontStyle()
584 this._has_fontStyle = false;
589 public void deleteGatheredViews()
591 this._has_gatheredViews = false;
596 public void deleteHeight()
598 this._has_height = false;
603 public void deleteIgnoreGapsinConsensus()
605 this._has_ignoreGapsinConsensus = false;
610 public void deleteNormaliseSequenceLogo()
612 this._has_normaliseSequenceLogo = false;
617 public void deletePidSelected()
619 this._has_pidSelected = false;
624 public void deletePidThreshold()
626 this._has_pidThreshold = false;
631 public void deleteRenderGaps()
633 this._has_renderGaps = false;
638 public void deleteRightAlignIds()
640 this._has_rightAlignIds = false;
645 public void deleteShowAnnotation()
647 this._has_showAnnotation = false;
652 public void deleteShowBoxes()
654 this._has_showBoxes = false;
659 public void deleteShowColourText()
661 this._has_showColourText = false;
666 public void deleteShowConsensusHistogram()
668 this._has_showConsensusHistogram = false;
673 public void deleteShowDbRefTooltip()
675 this._has_showDbRefTooltip = false;
680 public void deleteShowFullId()
682 this._has_showFullId = false;
687 public void deleteShowGroupConsensus()
689 this._has_showGroupConsensus = false;
694 public void deleteShowGroupConservation()
696 this._has_showGroupConservation = false;
701 public void deleteShowNPfeatureTooltip()
703 this._has_showNPfeatureTooltip = false;
708 public void deleteShowSequenceFeatures()
710 this._has_showSequenceFeatures = false;
715 public void deleteShowSequenceLogo()
717 this._has_showSequenceLogo = false;
722 public void deleteShowText()
724 this._has_showText = false;
729 public void deleteShowUnconserved()
731 this._has_showUnconserved = false;
736 public void deleteStartRes()
738 this._has_startRes = false;
743 public void deleteStartSeq()
745 this._has_startSeq = false;
750 public void deleteTextCol1()
752 this._has_textCol1 = false;
757 public void deleteTextCol2()
759 this._has_textCol2 = false;
764 public void deleteTextColThreshold()
766 this._has_textColThreshold = false;
771 public void deleteWidth()
773 this._has_width = false;
778 public void deleteWrapAlignment()
780 this._has_wrapAlignment = false;
785 public void deleteXpos()
787 this._has_xpos = false;
792 public void deleteYpos()
794 this._has_ypos = false;
798 * Method enumerateCalcIdParam.
800 * @return an Enumeration over all jalview.schemabinding.version2.CalcIdParam
803 public java.util.Enumeration enumerateCalcIdParam()
805 return this._calcIdParamList.elements();
809 * Method enumerateHiddenColumns.
811 * @return an Enumeration over all
812 * jalview.schemabinding.version2.HiddenColumns elements
814 public java.util.Enumeration enumerateHiddenColumns()
816 return this._hiddenColumnsList.elements();
820 * Returns the value of field 'annotationColours'.
822 * @return the value of field 'AnnotationColours'.
824 public jalview.schemabinding.version2.AnnotationColours getAnnotationColours()
826 return this._annotationColours;
830 * Returns the value of field 'bgColour'.
832 * @return the value of field 'BgColour'.
834 public java.lang.String getBgColour()
836 return this._bgColour;
840 * Method getCalcIdParam.
843 * @throws java.lang.IndexOutOfBoundsException
844 * if the index given is outside the bounds of the collection
845 * @return the value of the jalview.schemabinding.version2.CalcIdParam at the
848 public jalview.schemabinding.version2.CalcIdParam getCalcIdParam(
849 final int index) throws java.lang.IndexOutOfBoundsException
851 // check bounds for index
852 if (index < 0 || index >= this._calcIdParamList.size())
854 throw new IndexOutOfBoundsException("getCalcIdParam: Index value '"
855 + index + "' not in range [0.."
856 + (this._calcIdParamList.size() - 1) + "]");
859 return (jalview.schemabinding.version2.CalcIdParam) _calcIdParamList
864 * Method getCalcIdParam.Returns the contents of the collection in an Array.
866 * Note: Just in case the collection contents are changing in another thread,
867 * we pass a 0-length Array of the correct type into the API call. This way we
868 * <i>know</i> that the Array returned is of exactly the correct length.
870 * @return this collection as an Array
872 public jalview.schemabinding.version2.CalcIdParam[] getCalcIdParam()
874 jalview.schemabinding.version2.CalcIdParam[] array = new jalview.schemabinding.version2.CalcIdParam[0];
875 return (jalview.schemabinding.version2.CalcIdParam[]) this._calcIdParamList
880 * Method getCalcIdParamCount.
882 * @return the size of this collection
884 public int getCalcIdParamCount()
886 return this._calcIdParamList.size();
890 * Returns the value of field 'centreColumnLabels'.
892 * @return the value of field 'CentreColumnLabels'.
894 public boolean getCentreColumnLabels()
896 return this._centreColumnLabels;
900 * Returns the value of field 'consThreshold'.
902 * @return the value of field 'ConsThreshold'.
904 public int getConsThreshold()
906 return this._consThreshold;
910 * Returns the value of field 'conservationSelected'.
912 * @return the value of field 'ConservationSelected'.
914 public boolean getConservationSelected()
916 return this._conservationSelected;
920 * Returns the value of field 'followHighlight'.
922 * @return the value of field 'FollowHighlight'.
924 public boolean getFollowHighlight()
926 return this._followHighlight;
930 * Returns the value of field 'followSelection'.
932 * @return the value of field 'FollowSelection'.
934 public boolean getFollowSelection()
936 return this._followSelection;
940 * Returns the value of field 'fontName'.
942 * @return the value of field 'FontName'.
944 public java.lang.String getFontName()
946 return this._fontName;
950 * Returns the value of field 'fontSize'.
952 * @return the value of field 'FontSize'.
954 public int getFontSize()
956 return this._fontSize;
960 * Returns the value of field 'fontStyle'.
962 * @return the value of field 'FontStyle'.
964 public int getFontStyle()
966 return this._fontStyle;
970 * Returns the value of field 'gatheredViews'.
972 * @return the value of field 'GatheredViews'.
974 public boolean getGatheredViews()
976 return this._gatheredViews;
980 * Returns the value of field 'height'.
982 * @return the value of field 'Height'.
984 public int getHeight()
990 * Method getHiddenColumns.
993 * @throws java.lang.IndexOutOfBoundsException
994 * if the index given is outside the bounds of the collection
995 * @return the value of the jalview.schemabinding.version2.HiddenColumns at
998 public jalview.schemabinding.version2.HiddenColumns getHiddenColumns(
999 final int index) throws java.lang.IndexOutOfBoundsException
1001 // check bounds for index
1002 if (index < 0 || index >= this._hiddenColumnsList.size())
1004 throw new IndexOutOfBoundsException("getHiddenColumns: Index value '"
1005 + index + "' not in range [0.."
1006 + (this._hiddenColumnsList.size() - 1) + "]");
1009 return (jalview.schemabinding.version2.HiddenColumns) _hiddenColumnsList
1014 * Method getHiddenColumns.Returns the contents of the collection in an Array.
1016 * Note: Just in case the collection contents are changing in another thread,
1017 * we pass a 0-length Array of the correct type into the API call. This way we
1018 * <i>know</i> that the Array returned is of exactly the correct length.
1020 * @return this collection as an Array
1022 public jalview.schemabinding.version2.HiddenColumns[] getHiddenColumns()
1024 jalview.schemabinding.version2.HiddenColumns[] array = new jalview.schemabinding.version2.HiddenColumns[0];
1025 return (jalview.schemabinding.version2.HiddenColumns[]) this._hiddenColumnsList
1030 * Method getHiddenColumnsCount.
1032 * @return the size of this collection
1034 public int getHiddenColumnsCount()
1036 return this._hiddenColumnsList.size();
1040 * Returns the value of field 'id'. The field 'id' has the following
1041 * description: unique id used by jalview to synchronize between stored and
1042 * instantiated views
1045 * @return the value of field 'Id'.
1047 public java.lang.String getId()
1053 * Returns the value of field 'ignoreGapsinConsensus'.
1055 * @return the value of field 'IgnoreGapsinConsensus'.
1057 public boolean getIgnoreGapsinConsensus()
1059 return this._ignoreGapsinConsensus;
1063 * Returns the value of field 'normaliseSequenceLogo'.
1065 * @return the value of field 'NormaliseSequenceLogo'.
1067 public boolean getNormaliseSequenceLogo()
1069 return this._normaliseSequenceLogo;
1073 * Returns the value of field 'pidSelected'.
1075 * @return the value of field 'PidSelected'.
1077 public boolean getPidSelected()
1079 return this._pidSelected;
1083 * Returns the value of field 'pidThreshold'.
1085 * @return the value of field 'PidThreshold'.
1087 public int getPidThreshold()
1089 return this._pidThreshold;
1093 * Returns the value of field 'renderGaps'.
1095 * @return the value of field 'RenderGaps'.
1097 public boolean getRenderGaps()
1099 return this._renderGaps;
1103 * Returns the value of field 'rightAlignIds'.
1105 * @return the value of field 'RightAlignIds'.
1107 public boolean getRightAlignIds()
1109 return this._rightAlignIds;
1113 * Returns the value of field 'sequenceSetId'.
1115 * @return the value of field 'SequenceSetId'.
1117 public java.lang.String getSequenceSetId()
1119 return this._sequenceSetId;
1123 * Returns the value of field 'showAnnotation'.
1125 * @return the value of field 'ShowAnnotation'.
1127 public boolean getShowAnnotation()
1129 return this._showAnnotation;
1133 * Returns the value of field 'showBoxes'.
1135 * @return the value of field 'ShowBoxes'.
1137 public boolean getShowBoxes()
1139 return this._showBoxes;
1143 * Returns the value of field 'showColourText'.
1145 * @return the value of field 'ShowColourText'.
1147 public boolean getShowColourText()
1149 return this._showColourText;
1153 * Returns the value of field 'showConsensusHistogram'.
1155 * @return the value of field 'ShowConsensusHistogram'.
1157 public boolean getShowConsensusHistogram()
1159 return this._showConsensusHistogram;
1163 * Returns the value of field 'showDbRefTooltip'.
1165 * @return the value of field 'ShowDbRefTooltip'.
1167 public boolean getShowDbRefTooltip()
1169 return this._showDbRefTooltip;
1173 * Returns the value of field 'showFullId'.
1175 * @return the value of field 'ShowFullId'.
1177 public boolean getShowFullId()
1179 return this._showFullId;
1183 * Returns the value of field 'showGroupConsensus'.
1185 * @return the value of field 'ShowGroupConsensus'.
1187 public boolean getShowGroupConsensus()
1189 return this._showGroupConsensus;
1193 * Returns the value of field 'showGroupConservation'.
1195 * @return the value of field 'ShowGroupConservation'.
1197 public boolean getShowGroupConservation()
1199 return this._showGroupConservation;
1203 * Returns the value of field 'showNPfeatureTooltip'.
1205 * @return the value of field 'ShowNPfeatureTooltip'.
1207 public boolean getShowNPfeatureTooltip()
1209 return this._showNPfeatureTooltip;
1213 * Returns the value of field 'showSequenceFeatures'.
1215 * @return the value of field 'ShowSequenceFeatures'.
1217 public boolean getShowSequenceFeatures()
1219 return this._showSequenceFeatures;
1223 * Returns the value of field 'showSequenceLogo'.
1225 * @return the value of field 'ShowSequenceLogo'.
1227 public boolean getShowSequenceLogo()
1229 return this._showSequenceLogo;
1233 * Returns the value of field 'showText'.
1235 * @return the value of field 'ShowText'.
1237 public boolean getShowText()
1239 return this._showText;
1243 * Returns the value of field 'showUnconserved'.
1245 * @return the value of field 'ShowUnconserved'.
1247 public boolean getShowUnconserved()
1249 return this._showUnconserved;
1253 * Returns the value of field 'startRes'.
1255 * @return the value of field 'StartRes'.
1257 public int getStartRes()
1259 return this._startRes;
1263 * Returns the value of field 'startSeq'.
1265 * @return the value of field 'StartSeq'.
1267 public int getStartSeq()
1269 return this._startSeq;
1273 * Returns the value of field 'textCol1'.
1275 * @return the value of field 'TextCol1'.
1277 public int getTextCol1()
1279 return this._textCol1;
1283 * Returns the value of field 'textCol2'.
1285 * @return the value of field 'TextCol2'.
1287 public int getTextCol2()
1289 return this._textCol2;
1293 * Returns the value of field 'textColThreshold'.
1295 * @return the value of field 'TextColThreshold'.
1297 public int getTextColThreshold()
1299 return this._textColThreshold;
1303 * Returns the value of field 'title'.
1305 * @return the value of field 'Title'.
1307 public java.lang.String getTitle()
1313 * Returns the value of field 'viewName'.
1315 * @return the value of field 'ViewName'.
1317 public java.lang.String getViewName()
1319 return this._viewName;
1323 * Returns the value of field 'width'.
1325 * @return the value of field 'Width'.
1327 public int getWidth()
1333 * Returns the value of field 'wrapAlignment'.
1335 * @return the value of field 'WrapAlignment'.
1337 public boolean getWrapAlignment()
1339 return this._wrapAlignment;
1343 * Returns the value of field 'xpos'.
1345 * @return the value of field 'Xpos'.
1347 public int getXpos()
1353 * Returns the value of field 'ypos'.
1355 * @return the value of field 'Ypos'.
1357 public int getYpos()
1363 * Method hasCentreColumnLabels.
1365 * @return true if at least one CentreColumnLabels has been adde
1367 public boolean hasCentreColumnLabels()
1369 return this._has_centreColumnLabels;
1373 * Method hasConsThreshold.
1375 * @return true if at least one ConsThreshold has been added
1377 public boolean hasConsThreshold()
1379 return this._has_consThreshold;
1383 * Method hasConservationSelected.
1385 * @return true if at least one ConservationSelected has been added
1387 public boolean hasConservationSelected()
1389 return this._has_conservationSelected;
1393 * Method hasFollowHighlight.
1395 * @return true if at least one FollowHighlight has been added
1397 public boolean hasFollowHighlight()
1399 return this._has_followHighlight;
1403 * Method hasFollowSelection.
1405 * @return true if at least one FollowSelection has been added
1407 public boolean hasFollowSelection()
1409 return this._has_followSelection;
1413 * Method hasFontSize.
1415 * @return true if at least one FontSize has been added
1417 public boolean hasFontSize()
1419 return this._has_fontSize;
1423 * Method hasFontStyle.
1425 * @return true if at least one FontStyle has been added
1427 public boolean hasFontStyle()
1429 return this._has_fontStyle;
1433 * Method hasGatheredViews.
1435 * @return true if at least one GatheredViews has been added
1437 public boolean hasGatheredViews()
1439 return this._has_gatheredViews;
1445 * @return true if at least one Height has been added
1447 public boolean hasHeight()
1449 return this._has_height;
1453 * Method hasIgnoreGapsinConsensus.
1455 * @return true if at least one IgnoreGapsinConsensus has been added
1457 public boolean hasIgnoreGapsinConsensus()
1459 return this._has_ignoreGapsinConsensus;
1463 * Method hasNormaliseSequenceLogo.
1465 * @return true if at least one NormaliseSequenceLogo has been added
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 added
1547 public boolean hasShowConsensusHistogram()
1549 return this._has_showConsensusHistogram;
1553 * Method hasShowDbRefTooltip.
1555 * @return true if at least one ShowDbRefTooltip has been added
1557 public boolean hasShowDbRefTooltip()
1559 return this._has_showDbRefTooltip;
1563 * Method hasShowFullId.
1565 * @return true if at least one ShowFullId has been added
1567 public boolean hasShowFullId()
1569 return this._has_showFullId;
1573 * Method hasShowGroupConsensus.
1575 * @return true if at least one ShowGroupConsensus has been adde
1577 public boolean hasShowGroupConsensus()
1579 return this._has_showGroupConsensus;
1583 * Method hasShowGroupConservation.
1585 * @return true if at least one ShowGroupConservation has been added
1587 public boolean hasShowGroupConservation()
1589 return this._has_showGroupConservation;
1593 * Method hasShowNPfeatureTooltip.
1595 * @return true if at least one ShowNPfeatureTooltip has been added
1597 public boolean hasShowNPfeatureTooltip()
1599 return this._has_showNPfeatureTooltip;
1603 * Method hasShowSequenceFeatures.
1605 * @return true if at least one ShowSequenceFeatures has been added
1607 public boolean hasShowSequenceFeatures()
1609 return this._has_showSequenceFeatures;
1613 * Method hasShowSequenceLogo.
1615 * @return true if at least one ShowSequenceLogo has been added
1617 public boolean hasShowSequenceLogo()
1619 return this._has_showSequenceLogo;
1623 * Method hasShowText.
1625 * @return true if at least one ShowText has been added
1627 public boolean hasShowText()
1629 return this._has_showText;
1633 * Method hasShowUnconserved.
1635 * @return true if at least one ShowUnconserved has been added
1637 public boolean hasShowUnconserved()
1639 return this._has_showUnconserved;
1643 * Method hasStartRes.
1645 * @return true if at least one StartRes has been added
1647 public boolean hasStartRes()
1649 return this._has_startRes;
1653 * Method hasStartSeq.
1655 * @return true if at least one StartSeq has been added
1657 public boolean hasStartSeq()
1659 return this._has_startSeq;
1663 * Method hasTextCol1.
1665 * @return true if at least one TextCol1 has been added
1667 public boolean hasTextCol1()
1669 return this._has_textCol1;
1673 * Method hasTextCol2.
1675 * @return true if at least one TextCol2 has been added
1677 public boolean hasTextCol2()
1679 return this._has_textCol2;
1683 * Method hasTextColThreshold.
1685 * @return true if at least one TextColThreshold has been added
1687 public boolean hasTextColThreshold()
1689 return this._has_textColThreshold;
1695 * @return true if at least one Width has been added
1697 public boolean hasWidth()
1699 return this._has_width;
1703 * Method hasWrapAlignment.
1705 * @return true if at least one WrapAlignment has been added
1707 public boolean hasWrapAlignment()
1709 return this._has_wrapAlignment;
1715 * @return true if at least one Xpos has been added
1717 public boolean hasXpos()
1719 return this._has_xpos;
1725 * @return true if at least one Ypos has been added
1727 public boolean hasYpos()
1729 return this._has_ypos;
1733 * Returns the value of field 'centreColumnLabels'.
1735 * @return the value of field 'CentreColumnLabels'.
1737 public boolean isCentreColumnLabels()
1739 return this._centreColumnLabels;
1743 * Returns the value of field 'conservationSelected'.
1745 * @return the value of field 'ConservationSelected'.
1747 public boolean isConservationSelected()
1749 return this._conservationSelected;
1753 * Returns the value of field 'followHighlight'.
1755 * @return the value of field 'FollowHighlight'.
1757 public boolean isFollowHighlight()
1759 return this._followHighlight;
1763 * Returns the value of field 'followSelection'.
1765 * @return the value of field 'FollowSelection'.
1767 public boolean isFollowSelection()
1769 return this._followSelection;
1773 * Returns the value of field 'gatheredViews'.
1775 * @return the value of field 'GatheredViews'.
1777 public boolean isGatheredViews()
1779 return this._gatheredViews;
1783 * Returns the value of field 'ignoreGapsinConsensus'.
1785 * @return the value of field 'IgnoreGapsinConsensus'.
1787 public boolean isIgnoreGapsinConsensus()
1789 return this._ignoreGapsinConsensus;
1793 * Returns the value of field 'normaliseSequenceLogo'.
1795 * @return the value of field 'NormaliseSequenceLogo'.
1797 public boolean isNormaliseSequenceLogo()
1799 return this._normaliseSequenceLogo;
1803 * Returns the value of field 'pidSelected'.
1805 * @return the value of field 'PidSelected'.
1807 public boolean isPidSelected()
1809 return this._pidSelected;
1813 * Returns the value of field 'renderGaps'.
1815 * @return the value of field 'RenderGaps'.
1817 public boolean isRenderGaps()
1819 return this._renderGaps;
1823 * Returns the value of field 'rightAlignIds'.
1825 * @return the value of field 'RightAlignIds'.
1827 public boolean isRightAlignIds()
1829 return this._rightAlignIds;
1833 * Returns the value of field 'showAnnotation'.
1835 * @return the value of field 'ShowAnnotation'.
1837 public boolean isShowAnnotation()
1839 return this._showAnnotation;
1843 * Returns the value of field 'showBoxes'.
1845 * @return the value of field 'ShowBoxes'.
1847 public boolean isShowBoxes()
1849 return this._showBoxes;
1853 * Returns the value of field 'showColourText'.
1855 * @return the value of field 'ShowColourText'.
1857 public boolean isShowColourText()
1859 return this._showColourText;
1863 * Returns the value of field 'showConsensusHistogram'.
1865 * @return the value of field 'ShowConsensusHistogram'.
1867 public boolean isShowConsensusHistogram()
1869 return this._showConsensusHistogram;
1873 * Returns the value of field 'showDbRefTooltip'.
1875 * @return the value of field 'ShowDbRefTooltip'.
1877 public boolean isShowDbRefTooltip()
1879 return this._showDbRefTooltip;
1883 * Returns the value of field 'showFullId'.
1885 * @return the value of field 'ShowFullId'.
1887 public boolean isShowFullId()
1889 return this._showFullId;
1893 * Returns the value of field 'showGroupConsensus'.
1895 * @return the value of field 'ShowGroupConsensus'.
1897 public boolean isShowGroupConsensus()
1899 return this._showGroupConsensus;
1903 * Returns the value of field 'showGroupConservation'.
1905 * @return the value of field 'ShowGroupConservation'.
1907 public boolean isShowGroupConservation()
1909 return this._showGroupConservation;
1913 * Returns the value of field 'showNPfeatureTooltip'.
1915 * @return the value of field 'ShowNPfeatureTooltip'.
1917 public boolean isShowNPfeatureTooltip()
1919 return this._showNPfeatureTooltip;
1923 * Returns the value of field 'showSequenceFeatures'.
1925 * @return the value of field 'ShowSequenceFeatures'.
1927 public boolean isShowSequenceFeatures()
1929 return this._showSequenceFeatures;
1933 * Returns the value of field 'showSequenceLogo'.
1935 * @return the value of field 'ShowSequenceLogo'.
1937 public boolean isShowSequenceLogo()
1939 return this._showSequenceLogo;
1943 * Returns the value of field 'showText'.
1945 * @return the value of field 'ShowText'.
1947 public boolean isShowText()
1949 return this._showText;
1953 * Returns the value of field 'showUnconserved'.
1955 * @return the value of field 'ShowUnconserved'.
1957 public boolean isShowUnconserved()
1959 return this._showUnconserved;
1965 * @return true if this object is valid according to the schema
1967 public boolean isValid()
1972 } catch (org.exolab.castor.xml.ValidationException vex)
1980 * Returns the value of field 'wrapAlignment'.
1982 * @return the value of field 'WrapAlignment'.
1984 public boolean isWrapAlignment()
1986 return this._wrapAlignment;
1993 * @throws org.exolab.castor.xml.MarshalException
1994 * if object is null or if any SAXException is thrown during
1996 * @throws org.exolab.castor.xml.ValidationException
1997 * if this object is an invalid instance according to the schema
1999 public void marshal(final java.io.Writer out)
2000 throws org.exolab.castor.xml.MarshalException,
2001 org.exolab.castor.xml.ValidationException
2003 Marshaller.marshal(this, out);
2010 * @throws java.io.IOException
2011 * if an IOException occurs during marshaling
2012 * @throws org.exolab.castor.xml.ValidationException
2013 * if this object is an invalid instance according to the schema
2014 * @throws org.exolab.castor.xml.MarshalException
2015 * if object is null or if any SAXException is thrown during
2018 public void marshal(final org.xml.sax.ContentHandler handler)
2019 throws java.io.IOException,
2020 org.exolab.castor.xml.MarshalException,
2021 org.exolab.castor.xml.ValidationException
2023 Marshaller.marshal(this, handler);
2028 public void removeAllCalcIdParam()
2030 this._calcIdParamList.clear();
2035 public void removeAllHiddenColumns()
2037 this._hiddenColumnsList.clear();
2041 * Method removeCalcIdParam.
2043 * @param vCalcIdParam
2044 * @return true if the object was removed from the collection.
2046 public boolean removeCalcIdParam(
2047 final jalview.schemabinding.version2.CalcIdParam vCalcIdParam)
2049 boolean removed = _calcIdParamList.remove(vCalcIdParam);
2054 * Method removeCalcIdParamAt.
2057 * @return the element removed from the collection
2059 public jalview.schemabinding.version2.CalcIdParam removeCalcIdParamAt(
2062 java.lang.Object obj = this._calcIdParamList.remove(index);
2063 return (jalview.schemabinding.version2.CalcIdParam) obj;
2067 * Method removeHiddenColumns.
2069 * @param vHiddenColumns
2070 * @return true if the object was removed from the collection.
2072 public boolean removeHiddenColumns(
2073 final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)
2075 boolean removed = _hiddenColumnsList.remove(vHiddenColumns);
2080 * Method removeHiddenColumnsAt.
2083 * @return the element removed from the collection
2085 public jalview.schemabinding.version2.HiddenColumns removeHiddenColumnsAt(
2088 java.lang.Object obj = this._hiddenColumnsList.remove(index);
2089 return (jalview.schemabinding.version2.HiddenColumns) obj;
2093 * Sets the value of field 'annotationColours'.
2095 * @param annotationColours
2096 * the value of field 'annotationColours'.
2098 public void setAnnotationColours(
2099 final jalview.schemabinding.version2.AnnotationColours annotationColours)
2101 this._annotationColours = annotationColours;
2105 * Sets the value of field 'bgColour'.
2108 * the value of field 'bgColour'.
2110 public void setBgColour(final java.lang.String bgColour)
2112 this._bgColour = bgColour;
2119 * @param vCalcIdParam
2120 * @throws java.lang.IndexOutOfBoundsException
2121 * if the index given is outside the bounds of the collection
2123 public void setCalcIdParam(final int index,
2124 final jalview.schemabinding.version2.CalcIdParam vCalcIdParam)
2125 throws java.lang.IndexOutOfBoundsException
2127 // check bounds for index
2128 if (index < 0 || index >= this._calcIdParamList.size())
2130 throw new IndexOutOfBoundsException("setCalcIdParam: Index value '"
2131 + index + "' not in range [0.."
2132 + (this._calcIdParamList.size() - 1) + "]");
2135 this._calcIdParamList.set(index, vCalcIdParam);
2141 * @param vCalcIdParamArray
2143 public void setCalcIdParam(
2144 final jalview.schemabinding.version2.CalcIdParam[] vCalcIdParamArray)
2147 _calcIdParamList.clear();
2149 for (int i = 0; i < vCalcIdParamArray.length; i++)
2151 this._calcIdParamList.add(vCalcIdParamArray[i]);
2156 * Sets the value of field 'centreColumnLabels'.
2158 * @param centreColumnLabels
2159 * the value of field 'centreColumnLabels'.
2161 public void setCentreColumnLabels(final boolean centreColumnLabels)
2163 this._centreColumnLabels = centreColumnLabels;
2164 this._has_centreColumnLabels = true;
2168 * Sets the value of field 'consThreshold'.
2170 * @param consThreshold
2171 * the value of field 'consThreshold'.
2173 public void setConsThreshold(final int consThreshold)
2175 this._consThreshold = consThreshold;
2176 this._has_consThreshold = true;
2180 * Sets the value of field 'conservationSelected'.
2182 * @param conservationSelected
2183 * the value of field 'conservationSelected'.
2185 public void setConservationSelected(final boolean conservationSelected)
2187 this._conservationSelected = conservationSelected;
2188 this._has_conservationSelected = true;
2192 * Sets the value of field 'followHighlight'.
2194 * @param followHighlight
2195 * the value of field 'followHighlight'.
2197 public void setFollowHighlight(final boolean followHighlight)
2199 this._followHighlight = followHighlight;
2200 this._has_followHighlight = true;
2204 * Sets the value of field 'followSelection'.
2206 * @param followSelection
2207 * the value of field 'followSelection'.
2209 public void setFollowSelection(final boolean followSelection)
2211 this._followSelection = followSelection;
2212 this._has_followSelection = true;
2216 * Sets the value of field 'fontName'.
2219 * the value of field 'fontName'.
2221 public void setFontName(final java.lang.String fontName)
2223 this._fontName = fontName;
2227 * Sets the value of field 'fontSize'.
2230 * the value of field 'fontSize'.
2232 public void setFontSize(final int fontSize)
2234 this._fontSize = fontSize;
2235 this._has_fontSize = true;
2239 * Sets the value of field 'fontStyle'.
2242 * the value of field 'fontStyle'.
2244 public void setFontStyle(final int fontStyle)
2246 this._fontStyle = fontStyle;
2247 this._has_fontStyle = true;
2251 * Sets the value of field 'gatheredViews'.
2253 * @param gatheredViews
2254 * the value of field 'gatheredViews'.
2256 public void setGatheredViews(final boolean gatheredViews)
2258 this._gatheredViews = gatheredViews;
2259 this._has_gatheredViews = true;
2263 * Sets the value of field 'height'.
2266 * the value of field 'height'.
2268 public void setHeight(final int height)
2270 this._height = height;
2271 this._has_height = true;
2278 * @param vHiddenColumns
2279 * @throws java.lang.IndexOutOfBoundsException
2280 * if the index given is outside the bounds of the collection
2282 public void setHiddenColumns(final int index,
2283 final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)
2284 throws java.lang.IndexOutOfBoundsException
2286 // check bounds for index
2287 if (index < 0 || index >= this._hiddenColumnsList.size())
2289 throw new IndexOutOfBoundsException("setHiddenColumns: Index value '"
2290 + index + "' not in range [0.."
2291 + (this._hiddenColumnsList.size() - 1) + "]");
2294 this._hiddenColumnsList.set(index, vHiddenColumns);
2300 * @param vHiddenColumnsArray
2302 public void setHiddenColumns(
2303 final jalview.schemabinding.version2.HiddenColumns[] vHiddenColumnsArray)
2306 _hiddenColumnsList.clear();
2308 for (int i = 0; i < vHiddenColumnsArray.length; i++)
2310 this._hiddenColumnsList.add(vHiddenColumnsArray[i]);
2315 * Sets the value of field 'id'. The field 'id' has the following description:
2316 * unique id used by jalview to synchronize between stored and instantiated
2321 * the value of field 'id'.
2323 public void setId(final java.lang.String id)
2329 * Sets the value of field 'ignoreGapsinConsensus'.
2331 * @param ignoreGapsinConsensus
2332 * the value of field 'ignoreGapsinConsensus'.
2334 public void setIgnoreGapsinConsensus(final boolean ignoreGapsinConsensus)
2336 this._ignoreGapsinConsensus = ignoreGapsinConsensus;
2337 this._has_ignoreGapsinConsensus = true;
2341 * Sets the value of field 'normaliseSequenceLogo'.
2343 * @param normaliseSequenceLogo
2344 * the value of field 'normaliseSequenceLogo'.
2346 public void setNormaliseSequenceLogo(final boolean normaliseSequenceLogo)
2348 this._normaliseSequenceLogo = normaliseSequenceLogo;
2349 this._has_normaliseSequenceLogo = true;
2353 * Sets the value of field 'pidSelected'.
2355 * @param pidSelected
2356 * the value of field 'pidSelected'.
2358 public void setPidSelected(final boolean pidSelected)
2360 this._pidSelected = pidSelected;
2361 this._has_pidSelected = true;
2365 * Sets the value of field 'pidThreshold'.
2367 * @param pidThreshold
2368 * the value of field 'pidThreshold'.
2370 public void setPidThreshold(final int pidThreshold)
2372 this._pidThreshold = pidThreshold;
2373 this._has_pidThreshold = true;
2377 * Sets the value of field 'renderGaps'.
2380 * the value of field 'renderGaps'.
2382 public void setRenderGaps(final boolean renderGaps)
2384 this._renderGaps = renderGaps;
2385 this._has_renderGaps = true;
2389 * Sets the value of field 'rightAlignIds'.
2391 * @param rightAlignIds
2392 * the value of field 'rightAlignIds'.
2394 public void setRightAlignIds(final boolean rightAlignIds)
2396 this._rightAlignIds = rightAlignIds;
2397 this._has_rightAlignIds = true;
2401 * Sets the value of field 'sequenceSetId'.
2403 * @param sequenceSetId
2404 * the value of field 'sequenceSetId'.
2406 public void setSequenceSetId(final java.lang.String sequenceSetId)
2408 this._sequenceSetId = sequenceSetId;
2412 * Sets the value of field 'showAnnotation'.
2414 * @param showAnnotation
2415 * the value of field 'showAnnotation'.
2417 public void setShowAnnotation(final boolean showAnnotation)
2419 this._showAnnotation = showAnnotation;
2420 this._has_showAnnotation = true;
2424 * Sets the value of field 'showBoxes'.
2427 * the value of field 'showBoxes'.
2429 public void setShowBoxes(final boolean showBoxes)
2431 this._showBoxes = showBoxes;
2432 this._has_showBoxes = true;
2436 * Sets the value of field 'showColourText'.
2438 * @param showColourText
2439 * the value of field 'showColourText'.
2441 public void setShowColourText(final boolean showColourText)
2443 this._showColourText = showColourText;
2444 this._has_showColourText = true;
2448 * Sets the value of field 'showConsensusHistogram'.
2450 * @param showConsensusHistogram
2451 * the value of field 'showConsensusHistogram'.
2453 public void setShowConsensusHistogram(final boolean showConsensusHistogram)
2455 this._showConsensusHistogram = showConsensusHistogram;
2456 this._has_showConsensusHistogram = true;
2460 * Sets the value of field 'showDbRefTooltip'.
2462 * @param showDbRefTooltip
2463 * the value of field 'showDbRefTooltip'
2465 public void setShowDbRefTooltip(final boolean showDbRefTooltip)
2467 this._showDbRefTooltip = showDbRefTooltip;
2468 this._has_showDbRefTooltip = true;
2472 * Sets the value of field 'showFullId'.
2475 * the value of field 'showFullId'.
2477 public void setShowFullId(final boolean showFullId)
2479 this._showFullId = showFullId;
2480 this._has_showFullId = true;
2484 * Sets the value of field 'showGroupConsensus'.
2486 * @param showGroupConsensus
2487 * the value of field 'showGroupConsensus'.
2489 public void setShowGroupConsensus(final boolean showGroupConsensus)
2491 this._showGroupConsensus = showGroupConsensus;
2492 this._has_showGroupConsensus = true;
2496 * Sets the value of field 'showGroupConservation'.
2498 * @param showGroupConservation
2499 * the value of field 'showGroupConservation'.
2501 public void setShowGroupConservation(final boolean showGroupConservation)
2503 this._showGroupConservation = showGroupConservation;
2504 this._has_showGroupConservation = true;
2508 * Sets the value of field 'showNPfeatureTooltip'.
2510 * @param showNPfeatureTooltip
2511 * the value of field 'showNPfeatureTooltip'.
2513 public void setShowNPfeatureTooltip(final boolean showNPfeatureTooltip)
2515 this._showNPfeatureTooltip = showNPfeatureTooltip;
2516 this._has_showNPfeatureTooltip = true;
2520 * Sets the value of field 'showSequenceFeatures'.
2522 * @param showSequenceFeatures
2523 * the value of field 'showSequenceFeatures'.
2525 public void setShowSequenceFeatures(final boolean showSequenceFeatures)
2527 this._showSequenceFeatures = showSequenceFeatures;
2528 this._has_showSequenceFeatures = true;
2532 * Sets the value of field 'showSequenceLogo'.
2534 * @param showSequenceLogo
2535 * the value of field 'showSequenceLogo'
2537 public void setShowSequenceLogo(final boolean showSequenceLogo)
2539 this._showSequenceLogo = showSequenceLogo;
2540 this._has_showSequenceLogo = true;
2544 * Sets the value of field 'showText'.
2547 * the value of field 'showText'.
2549 public void setShowText(final boolean showText)
2551 this._showText = showText;
2552 this._has_showText = true;
2556 * Sets the value of field 'showUnconserved'.
2558 * @param showUnconserved
2559 * the value of field 'showUnconserved'.
2561 public void setShowUnconserved(final boolean showUnconserved)
2563 this._showUnconserved = showUnconserved;
2564 this._has_showUnconserved = true;
2568 * Sets the value of field 'startRes'.
2571 * the value of field 'startRes'.
2573 public void setStartRes(final int startRes)
2575 this._startRes = startRes;
2576 this._has_startRes = true;
2580 * Sets the value of field 'startSeq'.
2583 * the value of field 'startSeq'.
2585 public void setStartSeq(final int startSeq)
2587 this._startSeq = startSeq;
2588 this._has_startSeq = true;
2592 * Sets the value of field 'textCol1'.
2595 * the value of field 'textCol1'.
2597 public void setTextCol1(final int textCol1)
2599 this._textCol1 = textCol1;
2600 this._has_textCol1 = true;
2604 * Sets the value of field 'textCol2'.
2607 * the value of field 'textCol2'.
2609 public void setTextCol2(final int textCol2)
2611 this._textCol2 = textCol2;
2612 this._has_textCol2 = true;
2616 * Sets the value of field 'textColThreshold'.
2618 * @param textColThreshold
2619 * the value of field 'textColThreshold'
2621 public void setTextColThreshold(final int textColThreshold)
2623 this._textColThreshold = textColThreshold;
2624 this._has_textColThreshold = true;
2628 * Sets the value of field 'title'.
2631 * the value of field 'title'.
2633 public void setTitle(final java.lang.String title)
2635 this._title = title;
2639 * Sets the value of field 'viewName'.
2642 * the value of field 'viewName'.
2644 public void setViewName(final java.lang.String viewName)
2646 this._viewName = viewName;
2650 * Sets the value of field 'width'.
2653 * the value of field 'width'.
2655 public void setWidth(final int width)
2657 this._width = width;
2658 this._has_width = true;
2662 * Sets the value of field 'wrapAlignment'.
2664 * @param wrapAlignment
2665 * the value of field 'wrapAlignment'.
2667 public void setWrapAlignment(final boolean wrapAlignment)
2669 this._wrapAlignment = wrapAlignment;
2670 this._has_wrapAlignment = true;
2674 * Sets the value of field 'xpos'.
2677 * the value of field 'xpos'.
2679 public void setXpos(final int xpos)
2682 this._has_xpos = true;
2686 * Sets the value of field 'ypos'.
2689 * the value of field 'ypos'.
2691 public void setYpos(final int ypos)
2694 this._has_ypos = true;
2701 * @throws org.exolab.castor.xml.MarshalException
2702 * if object is null or if any SAXException is thrown during
2704 * @throws org.exolab.castor.xml.ValidationException
2705 * if this object is an invalid instance according to the schema
2706 * @return the unmarshaled jalview.schemabinding.version2.Viewport
2708 public static jalview.schemabinding.version2.Viewport unmarshal(
2709 final java.io.Reader reader)
2710 throws org.exolab.castor.xml.MarshalException,
2711 org.exolab.castor.xml.ValidationException
2713 return (jalview.schemabinding.version2.Viewport) Unmarshaller
2714 .unmarshal(jalview.schemabinding.version2.Viewport.class,
2721 * @throws org.exolab.castor.xml.ValidationException
2722 * if this object is an invalid instance according to the schema
2724 public void validate() throws org.exolab.castor.xml.ValidationException
2726 org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
2727 validator.validate(this);