2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
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. If not, see <http://www.gnu.org/licenses/>.
17 * The Jalview Authors are detailed in the 'AUTHORS' file.
19 package jalview.schemabinding.version2;
21 //---------------------------------/
22 //- Imported classes and packages -/
23 //---------------------------------/
25 import org.exolab.castor.xml.Marshaller;
26 import org.exolab.castor.xml.Unmarshaller;
31 * @version $Revision$ $Date$
33 public class Viewport implements java.io.Serializable
36 // --------------------------/
37 // - Class/Member Variables -/
38 // --------------------------/
41 * Field _conservationSelected.
43 private boolean _conservationSelected;
46 * keeps track of state for field: _conservationSelected
48 private boolean _has_conservationSelected;
53 private boolean _pidSelected;
56 * keeps track of state for field: _pidSelected
58 private boolean _has_pidSelected;
63 private java.lang.String _bgColour;
66 * Field _consThreshold.
68 private int _consThreshold;
71 * keeps track of state for field: _consThreshold
73 private boolean _has_consThreshold;
76 * Field _pidThreshold.
78 private int _pidThreshold;
81 * keeps track of state for field: _pidThreshold
83 private boolean _has_pidThreshold;
88 private java.lang.String _title;
93 private boolean _showFullId;
96 * keeps track of state for field: _showFullId
98 private boolean _has_showFullId;
101 * Field _rightAlignIds.
103 private boolean _rightAlignIds;
106 * keeps track of state for field: _rightAlignIds
108 private boolean _has_rightAlignIds;
113 private boolean _showText;
116 * keeps track of state for field: _showText
118 private boolean _has_showText;
121 * Field _showColourText.
123 private boolean _showColourText;
126 * keeps track of state for field: _showColourText
128 private boolean _has_showColourText;
131 * Field _showUnconserved.
133 private boolean _showUnconserved = false;
136 * keeps track of state for field: _showUnconserved
138 private boolean _has_showUnconserved;
143 private boolean _showBoxes;
146 * keeps track of state for field: _showBoxes
148 private boolean _has_showBoxes;
151 * Field _wrapAlignment.
153 private boolean _wrapAlignment;
156 * keeps track of state for field: _wrapAlignment
158 private boolean _has_wrapAlignment;
163 private boolean _renderGaps;
166 * keeps track of state for field: _renderGaps
168 private boolean _has_renderGaps;
171 * Field _showSequenceFeatures.
173 private boolean _showSequenceFeatures;
176 * keeps track of state for field: _showSequenceFeatures
178 private boolean _has_showSequenceFeatures;
181 * Field _showNPfeatureTooltip.
183 private boolean _showNPfeatureTooltip;
186 * keeps track of state for field: _showNPfeatureTooltip
188 private boolean _has_showNPfeatureTooltip;
191 * Field _showDbRefTooltip.
193 private boolean _showDbRefTooltip;
196 * keeps track of state for field: _showDbRefTooltip
198 private boolean _has_showDbRefTooltip;
201 * Field _followHighlight.
203 private boolean _followHighlight = true;
206 * keeps track of state for field: _followHighlight
208 private boolean _has_followHighlight;
211 * Field _followSelection.
213 private boolean _followSelection = true;
216 * keeps track of state for field: _followSelection
218 private boolean _has_followSelection;
221 * Field _showAnnotation.
223 private boolean _showAnnotation;
226 * keeps track of state for field: _showAnnotation
228 private boolean _has_showAnnotation;
231 * Field _centreColumnLabels.
233 private boolean _centreColumnLabels = false;
236 * keeps track of state for field: _centreColumnLabels
238 private boolean _has_centreColumnLabels;
241 * Field _showGroupConservation.
243 private boolean _showGroupConservation = false;
246 * keeps track of state for field: _showGroupConservation
248 private boolean _has_showGroupConservation;
251 * Field _showGroupConsensus.
253 private boolean _showGroupConsensus = false;
256 * keeps track of state for field: _showGroupConsensus
258 private boolean _has_showGroupConsensus;
261 * Field _showConsensusHistogram.
263 private boolean _showConsensusHistogram = true;
266 * keeps track of state for field: _showConsensusHistogram
268 private boolean _has_showConsensusHistogram;
271 * Field _showSequenceLogo.
273 private boolean _showSequenceLogo = false;
276 * keeps track of state for field: _showSequenceLogo
278 private boolean _has_showSequenceLogo;
281 * Field _normaliseSequenceLogo.
283 private boolean _normaliseSequenceLogo = false;
286 * keeps track of state for field: _normaliseSequenceLogo
288 private boolean _has_normaliseSequenceLogo;
291 * Field _ignoreGapsinConsensus.
293 private boolean _ignoreGapsinConsensus = true;
296 * keeps track of state for field: _ignoreGapsinConsensus
298 private boolean _has_ignoreGapsinConsensus;
303 private int _startRes;
306 * keeps track of state for field: _startRes
308 private boolean _has_startRes;
313 private int _startSeq;
316 * keeps track of state for field: _startSeq
318 private boolean _has_startSeq;
323 private java.lang.String _fontName;
328 private int _fontSize;
331 * keeps track of state for field: _fontSize
333 private boolean _has_fontSize;
338 private int _fontStyle;
341 * keeps track of state for field: _fontStyle
343 private boolean _has_fontStyle;
348 private java.lang.String _viewName;
351 * Field _sequenceSetId.
353 private java.lang.String _sequenceSetId;
356 * Field _gatheredViews.
358 private boolean _gatheredViews;
361 * keeps track of state for field: _gatheredViews
363 private boolean _has_gatheredViews;
368 private int _textCol1;
371 * keeps track of state for field: _textCol1
373 private boolean _has_textCol1;
378 private int _textCol2;
381 * keeps track of state for field: _textCol2
383 private boolean _has_textCol2;
386 * Field _textColThreshold.
388 private int _textColThreshold;
391 * keeps track of state for field: _textColThreshold
393 private boolean _has_textColThreshold;
396 * unique id used by jalview to synchronize between stored and instantiated
400 private java.lang.String _id;
408 * keeps track of state for field: _width
410 private boolean _has_width;
418 * keeps track of state for field: _height
420 private boolean _has_height;
428 * keeps track of state for field: _xpos
430 private boolean _has_xpos;
438 * keeps track of state for field: _ypos
440 private boolean _has_ypos;
443 * Field _annotationColours.
445 private jalview.schemabinding.version2.AnnotationColours _annotationColours;
448 * Field _hiddenColumnsList.
450 private java.util.Vector _hiddenColumnsList;
453 * Field _calcIdParamList.
455 private java.util.Vector _calcIdParamList;
464 this._hiddenColumnsList = new java.util.Vector();
465 this._calcIdParamList = new java.util.Vector();
475 * @param vCalcIdParam
476 * @throws java.lang.IndexOutOfBoundsException
477 * if the index given is outside the bounds of the collection
479 public void addCalcIdParam(
480 final jalview.schemabinding.version2.CalcIdParam vCalcIdParam)
481 throws java.lang.IndexOutOfBoundsException
483 this._calcIdParamList.addElement(vCalcIdParam);
490 * @param vCalcIdParam
491 * @throws java.lang.IndexOutOfBoundsException
492 * if the index given is outside the bounds of the collection
494 public void addCalcIdParam(final int index,
495 final jalview.schemabinding.version2.CalcIdParam vCalcIdParam)
496 throws java.lang.IndexOutOfBoundsException
498 this._calcIdParamList.add(index, vCalcIdParam);
504 * @param vHiddenColumns
505 * @throws java.lang.IndexOutOfBoundsException
506 * if the index given is outside the bounds of the collection
508 public void addHiddenColumns(
509 final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)
510 throws java.lang.IndexOutOfBoundsException
512 this._hiddenColumnsList.addElement(vHiddenColumns);
519 * @param vHiddenColumns
520 * @throws java.lang.IndexOutOfBoundsException
521 * if the index given is outside the bounds of the collection
523 public void addHiddenColumns(final int index,
524 final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)
525 throws java.lang.IndexOutOfBoundsException
527 this._hiddenColumnsList.add(index, vHiddenColumns);
532 public void deleteCentreColumnLabels()
534 this._has_centreColumnLabels = false;
539 public void deleteConsThreshold()
541 this._has_consThreshold = false;
546 public void deleteConservationSelected()
548 this._has_conservationSelected = false;
553 public void deleteFollowHighlight()
555 this._has_followHighlight = false;
560 public void deleteFollowSelection()
562 this._has_followSelection = false;
567 public void deleteFontSize()
569 this._has_fontSize = false;
574 public void deleteFontStyle()
576 this._has_fontStyle = false;
581 public void deleteGatheredViews()
583 this._has_gatheredViews = false;
588 public void deleteHeight()
590 this._has_height = false;
595 public void deleteIgnoreGapsinConsensus()
597 this._has_ignoreGapsinConsensus = false;
602 public void deleteNormaliseSequenceLogo()
604 this._has_normaliseSequenceLogo = false;
609 public void deletePidSelected()
611 this._has_pidSelected = false;
616 public void deletePidThreshold()
618 this._has_pidThreshold = false;
623 public void deleteRenderGaps()
625 this._has_renderGaps = false;
630 public void deleteRightAlignIds()
632 this._has_rightAlignIds = false;
637 public void deleteShowAnnotation()
639 this._has_showAnnotation = false;
644 public void deleteShowBoxes()
646 this._has_showBoxes = false;
651 public void deleteShowColourText()
653 this._has_showColourText = false;
658 public void deleteShowConsensusHistogram()
660 this._has_showConsensusHistogram = false;
665 public void deleteShowDbRefTooltip()
667 this._has_showDbRefTooltip = false;
672 public void deleteShowFullId()
674 this._has_showFullId = false;
679 public void deleteShowGroupConsensus()
681 this._has_showGroupConsensus = false;
686 public void deleteShowGroupConservation()
688 this._has_showGroupConservation = false;
693 public void deleteShowNPfeatureTooltip()
695 this._has_showNPfeatureTooltip = false;
700 public void deleteShowSequenceFeatures()
702 this._has_showSequenceFeatures = false;
707 public void deleteShowSequenceLogo()
709 this._has_showSequenceLogo = false;
714 public void deleteShowText()
716 this._has_showText = false;
721 public void deleteShowUnconserved()
723 this._has_showUnconserved = false;
728 public void deleteStartRes()
730 this._has_startRes = false;
735 public void deleteStartSeq()
737 this._has_startSeq = false;
742 public void deleteTextCol1()
744 this._has_textCol1 = false;
749 public void deleteTextCol2()
751 this._has_textCol2 = false;
756 public void deleteTextColThreshold()
758 this._has_textColThreshold = false;
763 public void deleteWidth()
765 this._has_width = false;
770 public void deleteWrapAlignment()
772 this._has_wrapAlignment = false;
777 public void deleteXpos()
779 this._has_xpos = false;
784 public void deleteYpos()
786 this._has_ypos = false;
790 * Method enumerateCalcIdParam.
792 * @return an Enumeration over all jalview.schemabinding.version2.CalcIdParam
795 public java.util.Enumeration enumerateCalcIdParam()
797 return this._calcIdParamList.elements();
801 * Method enumerateHiddenColumns.
803 * @return an Enumeration over all
804 * jalview.schemabinding.version2.HiddenColumns elements
806 public java.util.Enumeration enumerateHiddenColumns()
808 return this._hiddenColumnsList.elements();
812 * Returns the value of field 'annotationColours'.
814 * @return the value of field 'AnnotationColours'.
816 public jalview.schemabinding.version2.AnnotationColours getAnnotationColours()
818 return this._annotationColours;
822 * Returns the value of field 'bgColour'.
824 * @return the value of field 'BgColour'.
826 public java.lang.String getBgColour()
828 return this._bgColour;
832 * Method getCalcIdParam.
835 * @throws java.lang.IndexOutOfBoundsException
836 * if the index given is outside the bounds of the collection
837 * @return the value of the jalview.schemabinding.version2.CalcIdParam at the
840 public jalview.schemabinding.version2.CalcIdParam getCalcIdParam(
841 final int index) throws java.lang.IndexOutOfBoundsException
843 // check bounds for index
844 if (index < 0 || index >= this._calcIdParamList.size())
846 throw new IndexOutOfBoundsException("getCalcIdParam: Index value '"
847 + index + "' not in range [0.."
848 + (this._calcIdParamList.size() - 1) + "]");
851 return (jalview.schemabinding.version2.CalcIdParam) _calcIdParamList
856 * Method getCalcIdParam.Returns the contents of the collection in an Array.
858 * Note: Just in case the collection contents are changing in another thread,
859 * we pass a 0-length Array of the correct type into the API call. This way we
860 * <i>know</i> that the Array returned is of exactly the correct length.
862 * @return this collection as an Array
864 public jalview.schemabinding.version2.CalcIdParam[] getCalcIdParam()
866 jalview.schemabinding.version2.CalcIdParam[] array = new jalview.schemabinding.version2.CalcIdParam[0];
867 return (jalview.schemabinding.version2.CalcIdParam[]) this._calcIdParamList
872 * Method getCalcIdParamCount.
874 * @return the size of this collection
876 public int getCalcIdParamCount()
878 return this._calcIdParamList.size();
882 * Returns the value of field 'centreColumnLabels'.
884 * @return the value of field 'CentreColumnLabels'.
886 public boolean getCentreColumnLabels()
888 return this._centreColumnLabels;
892 * Returns the value of field 'consThreshold'.
894 * @return the value of field 'ConsThreshold'.
896 public int getConsThreshold()
898 return this._consThreshold;
902 * Returns the value of field 'conservationSelected'.
904 * @return the value of field 'ConservationSelected'.
906 public boolean getConservationSelected()
908 return this._conservationSelected;
912 * Returns the value of field 'followHighlight'.
914 * @return the value of field 'FollowHighlight'.
916 public boolean getFollowHighlight()
918 return this._followHighlight;
922 * Returns the value of field 'followSelection'.
924 * @return the value of field 'FollowSelection'.
926 public boolean getFollowSelection()
928 return this._followSelection;
932 * Returns the value of field 'fontName'.
934 * @return the value of field 'FontName'.
936 public java.lang.String getFontName()
938 return this._fontName;
942 * Returns the value of field 'fontSize'.
944 * @return the value of field 'FontSize'.
946 public int getFontSize()
948 return this._fontSize;
952 * Returns the value of field 'fontStyle'.
954 * @return the value of field 'FontStyle'.
956 public int getFontStyle()
958 return this._fontStyle;
962 * Returns the value of field 'gatheredViews'.
964 * @return the value of field 'GatheredViews'.
966 public boolean getGatheredViews()
968 return this._gatheredViews;
972 * Returns the value of field 'height'.
974 * @return the value of field 'Height'.
976 public int getHeight()
982 * Method getHiddenColumns.
985 * @throws java.lang.IndexOutOfBoundsException
986 * if the index given is outside the bounds of the collection
987 * @return the value of the jalview.schemabinding.version2.HiddenColumns at
990 public jalview.schemabinding.version2.HiddenColumns getHiddenColumns(
991 final int index) throws java.lang.IndexOutOfBoundsException
993 // check bounds for index
994 if (index < 0 || index >= this._hiddenColumnsList.size())
996 throw new IndexOutOfBoundsException("getHiddenColumns: Index value '"
997 + index + "' not in range [0.."
998 + (this._hiddenColumnsList.size() - 1) + "]");
1001 return (jalview.schemabinding.version2.HiddenColumns) _hiddenColumnsList
1006 * Method getHiddenColumns.Returns the contents of the collection in an Array.
1008 * Note: Just in case the collection contents are changing in another thread,
1009 * we pass a 0-length Array of the correct type into the API call. This way we
1010 * <i>know</i> that the Array returned is of exactly the correct length.
1012 * @return this collection as an Array
1014 public jalview.schemabinding.version2.HiddenColumns[] getHiddenColumns()
1016 jalview.schemabinding.version2.HiddenColumns[] array = new jalview.schemabinding.version2.HiddenColumns[0];
1017 return (jalview.schemabinding.version2.HiddenColumns[]) this._hiddenColumnsList
1022 * Method getHiddenColumnsCount.
1024 * @return the size of this collection
1026 public int getHiddenColumnsCount()
1028 return this._hiddenColumnsList.size();
1032 * Returns the value of field 'id'. The field 'id' has the following
1033 * description: unique id used by jalview to synchronize between stored and
1034 * instantiated views
1037 * @return the value of field 'Id'.
1039 public java.lang.String getId()
1045 * Returns the value of field 'ignoreGapsinConsensus'.
1047 * @return the value of field 'IgnoreGapsinConsensus'.
1049 public boolean getIgnoreGapsinConsensus()
1051 return this._ignoreGapsinConsensus;
1055 * Returns the value of field 'normaliseSequenceLogo'.
1057 * @return the value of field 'NormaliseSequenceLogo'.
1059 public boolean getNormaliseSequenceLogo()
1061 return this._normaliseSequenceLogo;
1065 * Returns the value of field 'pidSelected'.
1067 * @return the value of field 'PidSelected'.
1069 public boolean getPidSelected()
1071 return this._pidSelected;
1075 * Returns the value of field 'pidThreshold'.
1077 * @return the value of field 'PidThreshold'.
1079 public int getPidThreshold()
1081 return this._pidThreshold;
1085 * Returns the value of field 'renderGaps'.
1087 * @return the value of field 'RenderGaps'.
1089 public boolean getRenderGaps()
1091 return this._renderGaps;
1095 * Returns the value of field 'rightAlignIds'.
1097 * @return the value of field 'RightAlignIds'.
1099 public boolean getRightAlignIds()
1101 return this._rightAlignIds;
1105 * Returns the value of field 'sequenceSetId'.
1107 * @return the value of field 'SequenceSetId'.
1109 public java.lang.String getSequenceSetId()
1111 return this._sequenceSetId;
1115 * Returns the value of field 'showAnnotation'.
1117 * @return the value of field 'ShowAnnotation'.
1119 public boolean getShowAnnotation()
1121 return this._showAnnotation;
1125 * Returns the value of field 'showBoxes'.
1127 * @return the value of field 'ShowBoxes'.
1129 public boolean getShowBoxes()
1131 return this._showBoxes;
1135 * Returns the value of field 'showColourText'.
1137 * @return the value of field 'ShowColourText'.
1139 public boolean getShowColourText()
1141 return this._showColourText;
1145 * Returns the value of field 'showConsensusHistogram'.
1147 * @return the value of field 'ShowConsensusHistogram'.
1149 public boolean getShowConsensusHistogram()
1151 return this._showConsensusHistogram;
1155 * Returns the value of field 'showDbRefTooltip'.
1157 * @return the value of field 'ShowDbRefTooltip'.
1159 public boolean getShowDbRefTooltip()
1161 return this._showDbRefTooltip;
1165 * Returns the value of field 'showFullId'.
1167 * @return the value of field 'ShowFullId'.
1169 public boolean getShowFullId()
1171 return this._showFullId;
1175 * Returns the value of field 'showGroupConsensus'.
1177 * @return the value of field 'ShowGroupConsensus'.
1179 public boolean getShowGroupConsensus()
1181 return this._showGroupConsensus;
1185 * Returns the value of field 'showGroupConservation'.
1187 * @return the value of field 'ShowGroupConservation'.
1189 public boolean getShowGroupConservation()
1191 return this._showGroupConservation;
1195 * Returns the value of field 'showNPfeatureTooltip'.
1197 * @return the value of field 'ShowNPfeatureTooltip'.
1199 public boolean getShowNPfeatureTooltip()
1201 return this._showNPfeatureTooltip;
1205 * Returns the value of field 'showSequenceFeatures'.
1207 * @return the value of field 'ShowSequenceFeatures'.
1209 public boolean getShowSequenceFeatures()
1211 return this._showSequenceFeatures;
1215 * Returns the value of field 'showSequenceLogo'.
1217 * @return the value of field 'ShowSequenceLogo'.
1219 public boolean getShowSequenceLogo()
1221 return this._showSequenceLogo;
1225 * Returns the value of field 'showText'.
1227 * @return the value of field 'ShowText'.
1229 public boolean getShowText()
1231 return this._showText;
1235 * Returns the value of field 'showUnconserved'.
1237 * @return the value of field 'ShowUnconserved'.
1239 public boolean getShowUnconserved()
1241 return this._showUnconserved;
1245 * Returns the value of field 'startRes'.
1247 * @return the value of field 'StartRes'.
1249 public int getStartRes()
1251 return this._startRes;
1255 * Returns the value of field 'startSeq'.
1257 * @return the value of field 'StartSeq'.
1259 public int getStartSeq()
1261 return this._startSeq;
1265 * Returns the value of field 'textCol1'.
1267 * @return the value of field 'TextCol1'.
1269 public int getTextCol1()
1271 return this._textCol1;
1275 * Returns the value of field 'textCol2'.
1277 * @return the value of field 'TextCol2'.
1279 public int getTextCol2()
1281 return this._textCol2;
1285 * Returns the value of field 'textColThreshold'.
1287 * @return the value of field 'TextColThreshold'.
1289 public int getTextColThreshold()
1291 return this._textColThreshold;
1295 * Returns the value of field 'title'.
1297 * @return the value of field 'Title'.
1299 public java.lang.String getTitle()
1305 * Returns the value of field 'viewName'.
1307 * @return the value of field 'ViewName'.
1309 public java.lang.String getViewName()
1311 return this._viewName;
1315 * Returns the value of field 'width'.
1317 * @return the value of field 'Width'.
1319 public int getWidth()
1325 * Returns the value of field 'wrapAlignment'.
1327 * @return the value of field 'WrapAlignment'.
1329 public boolean getWrapAlignment()
1331 return this._wrapAlignment;
1335 * Returns the value of field 'xpos'.
1337 * @return the value of field 'Xpos'.
1339 public int getXpos()
1345 * Returns the value of field 'ypos'.
1347 * @return the value of field 'Ypos'.
1349 public int getYpos()
1355 * Method hasCentreColumnLabels.
1357 * @return true if at least one CentreColumnLabels has been adde
1359 public boolean hasCentreColumnLabels()
1361 return this._has_centreColumnLabels;
1365 * Method hasConsThreshold.
1367 * @return true if at least one ConsThreshold has been added
1369 public boolean hasConsThreshold()
1371 return this._has_consThreshold;
1375 * Method hasConservationSelected.
1377 * @return true if at least one ConservationSelected has been added
1379 public boolean hasConservationSelected()
1381 return this._has_conservationSelected;
1385 * Method hasFollowHighlight.
1387 * @return true if at least one FollowHighlight has been added
1389 public boolean hasFollowHighlight()
1391 return this._has_followHighlight;
1395 * Method hasFollowSelection.
1397 * @return true if at least one FollowSelection has been added
1399 public boolean hasFollowSelection()
1401 return this._has_followSelection;
1405 * Method hasFontSize.
1407 * @return true if at least one FontSize has been added
1409 public boolean hasFontSize()
1411 return this._has_fontSize;
1415 * Method hasFontStyle.
1417 * @return true if at least one FontStyle has been added
1419 public boolean hasFontStyle()
1421 return this._has_fontStyle;
1425 * Method hasGatheredViews.
1427 * @return true if at least one GatheredViews has been added
1429 public boolean hasGatheredViews()
1431 return this._has_gatheredViews;
1437 * @return true if at least one Height has been added
1439 public boolean hasHeight()
1441 return this._has_height;
1445 * Method hasIgnoreGapsinConsensus.
1447 * @return true if at least one IgnoreGapsinConsensus has been added
1449 public boolean hasIgnoreGapsinConsensus()
1451 return this._has_ignoreGapsinConsensus;
1455 * Method hasNormaliseSequenceLogo.
1457 * @return true if at least one NormaliseSequenceLogo has been added
1459 public boolean hasNormaliseSequenceLogo()
1461 return this._has_normaliseSequenceLogo;
1465 * Method hasPidSelected.
1467 * @return true if at least one PidSelected has been added
1469 public boolean hasPidSelected()
1471 return this._has_pidSelected;
1475 * Method hasPidThreshold.
1477 * @return true if at least one PidThreshold has been added
1479 public boolean hasPidThreshold()
1481 return this._has_pidThreshold;
1485 * Method hasRenderGaps.
1487 * @return true if at least one RenderGaps has been added
1489 public boolean hasRenderGaps()
1491 return this._has_renderGaps;
1495 * Method hasRightAlignIds.
1497 * @return true if at least one RightAlignIds has been added
1499 public boolean hasRightAlignIds()
1501 return this._has_rightAlignIds;
1505 * Method hasShowAnnotation.
1507 * @return true if at least one ShowAnnotation has been added
1509 public boolean hasShowAnnotation()
1511 return this._has_showAnnotation;
1515 * Method hasShowBoxes.
1517 * @return true if at least one ShowBoxes has been added
1519 public boolean hasShowBoxes()
1521 return this._has_showBoxes;
1525 * Method hasShowColourText.
1527 * @return true if at least one ShowColourText has been added
1529 public boolean hasShowColourText()
1531 return this._has_showColourText;
1535 * Method hasShowConsensusHistogram.
1537 * @return true if at least one ShowConsensusHistogram has been added
1539 public boolean hasShowConsensusHistogram()
1541 return this._has_showConsensusHistogram;
1545 * Method hasShowDbRefTooltip.
1547 * @return true if at least one ShowDbRefTooltip has been added
1549 public boolean hasShowDbRefTooltip()
1551 return this._has_showDbRefTooltip;
1555 * Method hasShowFullId.
1557 * @return true if at least one ShowFullId has been added
1559 public boolean hasShowFullId()
1561 return this._has_showFullId;
1565 * Method hasShowGroupConsensus.
1567 * @return true if at least one ShowGroupConsensus has been adde
1569 public boolean hasShowGroupConsensus()
1571 return this._has_showGroupConsensus;
1575 * Method hasShowGroupConservation.
1577 * @return true if at least one ShowGroupConservation has been added
1579 public boolean hasShowGroupConservation()
1581 return this._has_showGroupConservation;
1585 * Method hasShowNPfeatureTooltip.
1587 * @return true if at least one ShowNPfeatureTooltip has been added
1589 public boolean hasShowNPfeatureTooltip()
1591 return this._has_showNPfeatureTooltip;
1595 * Method hasShowSequenceFeatures.
1597 * @return true if at least one ShowSequenceFeatures has been added
1599 public boolean hasShowSequenceFeatures()
1601 return this._has_showSequenceFeatures;
1605 * Method hasShowSequenceLogo.
1607 * @return true if at least one ShowSequenceLogo has been added
1609 public boolean hasShowSequenceLogo()
1611 return this._has_showSequenceLogo;
1615 * Method hasShowText.
1617 * @return true if at least one ShowText has been added
1619 public boolean hasShowText()
1621 return this._has_showText;
1625 * Method hasShowUnconserved.
1627 * @return true if at least one ShowUnconserved has been added
1629 public boolean hasShowUnconserved()
1631 return this._has_showUnconserved;
1635 * Method hasStartRes.
1637 * @return true if at least one StartRes has been added
1639 public boolean hasStartRes()
1641 return this._has_startRes;
1645 * Method hasStartSeq.
1647 * @return true if at least one StartSeq has been added
1649 public boolean hasStartSeq()
1651 return this._has_startSeq;
1655 * Method hasTextCol1.
1657 * @return true if at least one TextCol1 has been added
1659 public boolean hasTextCol1()
1661 return this._has_textCol1;
1665 * Method hasTextCol2.
1667 * @return true if at least one TextCol2 has been added
1669 public boolean hasTextCol2()
1671 return this._has_textCol2;
1675 * Method hasTextColThreshold.
1677 * @return true if at least one TextColThreshold has been added
1679 public boolean hasTextColThreshold()
1681 return this._has_textColThreshold;
1687 * @return true if at least one Width has been added
1689 public boolean hasWidth()
1691 return this._has_width;
1695 * Method hasWrapAlignment.
1697 * @return true if at least one WrapAlignment has been added
1699 public boolean hasWrapAlignment()
1701 return this._has_wrapAlignment;
1707 * @return true if at least one Xpos has been added
1709 public boolean hasXpos()
1711 return this._has_xpos;
1717 * @return true if at least one Ypos has been added
1719 public boolean hasYpos()
1721 return this._has_ypos;
1725 * Returns the value of field 'centreColumnLabels'.
1727 * @return the value of field 'CentreColumnLabels'.
1729 public boolean isCentreColumnLabels()
1731 return this._centreColumnLabels;
1735 * Returns the value of field 'conservationSelected'.
1737 * @return the value of field 'ConservationSelected'.
1739 public boolean isConservationSelected()
1741 return this._conservationSelected;
1745 * Returns the value of field 'followHighlight'.
1747 * @return the value of field 'FollowHighlight'.
1749 public boolean isFollowHighlight()
1751 return this._followHighlight;
1755 * Returns the value of field 'followSelection'.
1757 * @return the value of field 'FollowSelection'.
1759 public boolean isFollowSelection()
1761 return this._followSelection;
1765 * Returns the value of field 'gatheredViews'.
1767 * @return the value of field 'GatheredViews'.
1769 public boolean isGatheredViews()
1771 return this._gatheredViews;
1775 * Returns the value of field 'ignoreGapsinConsensus'.
1777 * @return the value of field 'IgnoreGapsinConsensus'.
1779 public boolean isIgnoreGapsinConsensus()
1781 return this._ignoreGapsinConsensus;
1785 * Returns the value of field 'normaliseSequenceLogo'.
1787 * @return the value of field 'NormaliseSequenceLogo'.
1789 public boolean isNormaliseSequenceLogo()
1791 return this._normaliseSequenceLogo;
1795 * Returns the value of field 'pidSelected'.
1797 * @return the value of field 'PidSelected'.
1799 public boolean isPidSelected()
1801 return this._pidSelected;
1805 * Returns the value of field 'renderGaps'.
1807 * @return the value of field 'RenderGaps'.
1809 public boolean isRenderGaps()
1811 return this._renderGaps;
1815 * Returns the value of field 'rightAlignIds'.
1817 * @return the value of field 'RightAlignIds'.
1819 public boolean isRightAlignIds()
1821 return this._rightAlignIds;
1825 * Returns the value of field 'showAnnotation'.
1827 * @return the value of field 'ShowAnnotation'.
1829 public boolean isShowAnnotation()
1831 return this._showAnnotation;
1835 * Returns the value of field 'showBoxes'.
1837 * @return the value of field 'ShowBoxes'.
1839 public boolean isShowBoxes()
1841 return this._showBoxes;
1845 * Returns the value of field 'showColourText'.
1847 * @return the value of field 'ShowColourText'.
1849 public boolean isShowColourText()
1851 return this._showColourText;
1855 * Returns the value of field 'showConsensusHistogram'.
1857 * @return the value of field 'ShowConsensusHistogram'.
1859 public boolean isShowConsensusHistogram()
1861 return this._showConsensusHistogram;
1865 * Returns the value of field 'showDbRefTooltip'.
1867 * @return the value of field 'ShowDbRefTooltip'.
1869 public boolean isShowDbRefTooltip()
1871 return this._showDbRefTooltip;
1875 * Returns the value of field 'showFullId'.
1877 * @return the value of field 'ShowFullId'.
1879 public boolean isShowFullId()
1881 return this._showFullId;
1885 * Returns the value of field 'showGroupConsensus'.
1887 * @return the value of field 'ShowGroupConsensus'.
1889 public boolean isShowGroupConsensus()
1891 return this._showGroupConsensus;
1895 * Returns the value of field 'showGroupConservation'.
1897 * @return the value of field 'ShowGroupConservation'.
1899 public boolean isShowGroupConservation()
1901 return this._showGroupConservation;
1905 * Returns the value of field 'showNPfeatureTooltip'.
1907 * @return the value of field 'ShowNPfeatureTooltip'.
1909 public boolean isShowNPfeatureTooltip()
1911 return this._showNPfeatureTooltip;
1915 * Returns the value of field 'showSequenceFeatures'.
1917 * @return the value of field 'ShowSequenceFeatures'.
1919 public boolean isShowSequenceFeatures()
1921 return this._showSequenceFeatures;
1925 * Returns the value of field 'showSequenceLogo'.
1927 * @return the value of field 'ShowSequenceLogo'.
1929 public boolean isShowSequenceLogo()
1931 return this._showSequenceLogo;
1935 * Returns the value of field 'showText'.
1937 * @return the value of field 'ShowText'.
1939 public boolean isShowText()
1941 return this._showText;
1945 * Returns the value of field 'showUnconserved'.
1947 * @return the value of field 'ShowUnconserved'.
1949 public boolean isShowUnconserved()
1951 return this._showUnconserved;
1957 * @return true if this object is valid according to the schema
1959 public boolean isValid()
1964 } catch (org.exolab.castor.xml.ValidationException vex)
1972 * Returns the value of field 'wrapAlignment'.
1974 * @return the value of field 'WrapAlignment'.
1976 public boolean isWrapAlignment()
1978 return this._wrapAlignment;
1985 * @throws org.exolab.castor.xml.MarshalException
1986 * if object is null or if any SAXException is thrown during
1988 * @throws org.exolab.castor.xml.ValidationException
1989 * if this object is an invalid instance according to the schema
1991 public void marshal(final java.io.Writer out)
1992 throws org.exolab.castor.xml.MarshalException,
1993 org.exolab.castor.xml.ValidationException
1995 Marshaller.marshal(this, out);
2002 * @throws java.io.IOException
2003 * if an IOException occurs during marshaling
2004 * @throws org.exolab.castor.xml.ValidationException
2005 * if this object is an invalid instance according to the schema
2006 * @throws org.exolab.castor.xml.MarshalException
2007 * if object is null or if any SAXException is thrown during
2010 public void marshal(final org.xml.sax.ContentHandler handler)
2011 throws java.io.IOException,
2012 org.exolab.castor.xml.MarshalException,
2013 org.exolab.castor.xml.ValidationException
2015 Marshaller.marshal(this, handler);
2020 public void removeAllCalcIdParam()
2022 this._calcIdParamList.clear();
2027 public void removeAllHiddenColumns()
2029 this._hiddenColumnsList.clear();
2033 * Method removeCalcIdParam.
2035 * @param vCalcIdParam
2036 * @return true if the object was removed from the collection.
2038 public boolean removeCalcIdParam(
2039 final jalview.schemabinding.version2.CalcIdParam vCalcIdParam)
2041 boolean removed = _calcIdParamList.remove(vCalcIdParam);
2046 * Method removeCalcIdParamAt.
2049 * @return the element removed from the collection
2051 public jalview.schemabinding.version2.CalcIdParam removeCalcIdParamAt(
2054 java.lang.Object obj = this._calcIdParamList.remove(index);
2055 return (jalview.schemabinding.version2.CalcIdParam) obj;
2059 * Method removeHiddenColumns.
2061 * @param vHiddenColumns
2062 * @return true if the object was removed from the collection.
2064 public boolean removeHiddenColumns(
2065 final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)
2067 boolean removed = _hiddenColumnsList.remove(vHiddenColumns);
2072 * Method removeHiddenColumnsAt.
2075 * @return the element removed from the collection
2077 public jalview.schemabinding.version2.HiddenColumns removeHiddenColumnsAt(
2080 java.lang.Object obj = this._hiddenColumnsList.remove(index);
2081 return (jalview.schemabinding.version2.HiddenColumns) obj;
2085 * Sets the value of field 'annotationColours'.
2087 * @param annotationColours
2088 * the value of field 'annotationColours'.
2090 public void setAnnotationColours(
2091 final jalview.schemabinding.version2.AnnotationColours annotationColours)
2093 this._annotationColours = annotationColours;
2097 * Sets the value of field 'bgColour'.
2100 * the value of field 'bgColour'.
2102 public void setBgColour(final java.lang.String bgColour)
2104 this._bgColour = bgColour;
2111 * @param vCalcIdParam
2112 * @throws java.lang.IndexOutOfBoundsException
2113 * if the index given is outside the bounds of the collection
2115 public void setCalcIdParam(final int index,
2116 final jalview.schemabinding.version2.CalcIdParam vCalcIdParam)
2117 throws java.lang.IndexOutOfBoundsException
2119 // check bounds for index
2120 if (index < 0 || index >= this._calcIdParamList.size())
2122 throw new IndexOutOfBoundsException("setCalcIdParam: Index value '"
2123 + index + "' not in range [0.."
2124 + (this._calcIdParamList.size() - 1) + "]");
2127 this._calcIdParamList.set(index, vCalcIdParam);
2133 * @param vCalcIdParamArray
2135 public void setCalcIdParam(
2136 final jalview.schemabinding.version2.CalcIdParam[] vCalcIdParamArray)
2139 _calcIdParamList.clear();
2141 for (int i = 0; i < vCalcIdParamArray.length; i++)
2143 this._calcIdParamList.add(vCalcIdParamArray[i]);
2148 * Sets the value of field 'centreColumnLabels'.
2150 * @param centreColumnLabels
2151 * the value of field 'centreColumnLabels'.
2153 public void setCentreColumnLabels(final boolean centreColumnLabels)
2155 this._centreColumnLabels = centreColumnLabels;
2156 this._has_centreColumnLabels = true;
2160 * Sets the value of field 'consThreshold'.
2162 * @param consThreshold
2163 * the value of field 'consThreshold'.
2165 public void setConsThreshold(final int consThreshold)
2167 this._consThreshold = consThreshold;
2168 this._has_consThreshold = true;
2172 * Sets the value of field 'conservationSelected'.
2174 * @param conservationSelected
2175 * the value of field 'conservationSelected'.
2177 public void setConservationSelected(final boolean conservationSelected)
2179 this._conservationSelected = conservationSelected;
2180 this._has_conservationSelected = true;
2184 * Sets the value of field 'followHighlight'.
2186 * @param followHighlight
2187 * the value of field 'followHighlight'.
2189 public void setFollowHighlight(final boolean followHighlight)
2191 this._followHighlight = followHighlight;
2192 this._has_followHighlight = true;
2196 * Sets the value of field 'followSelection'.
2198 * @param followSelection
2199 * the value of field 'followSelection'.
2201 public void setFollowSelection(final boolean followSelection)
2203 this._followSelection = followSelection;
2204 this._has_followSelection = true;
2208 * Sets the value of field 'fontName'.
2211 * the value of field 'fontName'.
2213 public void setFontName(final java.lang.String fontName)
2215 this._fontName = fontName;
2219 * Sets the value of field 'fontSize'.
2222 * the value of field 'fontSize'.
2224 public void setFontSize(final int fontSize)
2226 this._fontSize = fontSize;
2227 this._has_fontSize = true;
2231 * Sets the value of field 'fontStyle'.
2234 * the value of field 'fontStyle'.
2236 public void setFontStyle(final int fontStyle)
2238 this._fontStyle = fontStyle;
2239 this._has_fontStyle = true;
2243 * Sets the value of field 'gatheredViews'.
2245 * @param gatheredViews
2246 * the value of field 'gatheredViews'.
2248 public void setGatheredViews(final boolean gatheredViews)
2250 this._gatheredViews = gatheredViews;
2251 this._has_gatheredViews = true;
2255 * Sets the value of field 'height'.
2258 * the value of field 'height'.
2260 public void setHeight(final int height)
2262 this._height = height;
2263 this._has_height = true;
2270 * @param vHiddenColumns
2271 * @throws java.lang.IndexOutOfBoundsException
2272 * if the index given is outside the bounds of the collection
2274 public void setHiddenColumns(final int index,
2275 final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)
2276 throws java.lang.IndexOutOfBoundsException
2278 // check bounds for index
2279 if (index < 0 || index >= this._hiddenColumnsList.size())
2281 throw new IndexOutOfBoundsException("setHiddenColumns: Index value '"
2282 + index + "' not in range [0.."
2283 + (this._hiddenColumnsList.size() - 1) + "]");
2286 this._hiddenColumnsList.set(index, vHiddenColumns);
2292 * @param vHiddenColumnsArray
2294 public void setHiddenColumns(
2295 final jalview.schemabinding.version2.HiddenColumns[] vHiddenColumnsArray)
2298 _hiddenColumnsList.clear();
2300 for (int i = 0; i < vHiddenColumnsArray.length; i++)
2302 this._hiddenColumnsList.add(vHiddenColumnsArray[i]);
2307 * Sets the value of field 'id'. The field 'id' has the following description:
2308 * unique id used by jalview to synchronize between stored and instantiated
2313 * the value of field 'id'.
2315 public void setId(final java.lang.String id)
2321 * Sets the value of field 'ignoreGapsinConsensus'.
2323 * @param ignoreGapsinConsensus
2324 * the value of field 'ignoreGapsinConsensus'.
2326 public void setIgnoreGapsinConsensus(final boolean ignoreGapsinConsensus)
2328 this._ignoreGapsinConsensus = ignoreGapsinConsensus;
2329 this._has_ignoreGapsinConsensus = true;
2333 * Sets the value of field 'normaliseSequenceLogo'.
2335 * @param normaliseSequenceLogo
2336 * the value of field 'normaliseSequenceLogo'.
2338 public void setNormaliseSequenceLogo(final boolean normaliseSequenceLogo)
2340 this._normaliseSequenceLogo = normaliseSequenceLogo;
2341 this._has_normaliseSequenceLogo = true;
2345 * Sets the value of field 'pidSelected'.
2347 * @param pidSelected
2348 * the value of field 'pidSelected'.
2350 public void setPidSelected(final boolean pidSelected)
2352 this._pidSelected = pidSelected;
2353 this._has_pidSelected = true;
2357 * Sets the value of field 'pidThreshold'.
2359 * @param pidThreshold
2360 * the value of field 'pidThreshold'.
2362 public void setPidThreshold(final int pidThreshold)
2364 this._pidThreshold = pidThreshold;
2365 this._has_pidThreshold = true;
2369 * Sets the value of field 'renderGaps'.
2372 * the value of field 'renderGaps'.
2374 public void setRenderGaps(final boolean renderGaps)
2376 this._renderGaps = renderGaps;
2377 this._has_renderGaps = true;
2381 * Sets the value of field 'rightAlignIds'.
2383 * @param rightAlignIds
2384 * the value of field 'rightAlignIds'.
2386 public void setRightAlignIds(final boolean rightAlignIds)
2388 this._rightAlignIds = rightAlignIds;
2389 this._has_rightAlignIds = true;
2393 * Sets the value of field 'sequenceSetId'.
2395 * @param sequenceSetId
2396 * the value of field 'sequenceSetId'.
2398 public void setSequenceSetId(final java.lang.String sequenceSetId)
2400 this._sequenceSetId = sequenceSetId;
2404 * Sets the value of field 'showAnnotation'.
2406 * @param showAnnotation
2407 * the value of field 'showAnnotation'.
2409 public void setShowAnnotation(final boolean showAnnotation)
2411 this._showAnnotation = showAnnotation;
2412 this._has_showAnnotation = true;
2416 * Sets the value of field 'showBoxes'.
2419 * the value of field 'showBoxes'.
2421 public void setShowBoxes(final boolean showBoxes)
2423 this._showBoxes = showBoxes;
2424 this._has_showBoxes = true;
2428 * Sets the value of field 'showColourText'.
2430 * @param showColourText
2431 * the value of field 'showColourText'.
2433 public void setShowColourText(final boolean showColourText)
2435 this._showColourText = showColourText;
2436 this._has_showColourText = true;
2440 * Sets the value of field 'showConsensusHistogram'.
2442 * @param showConsensusHistogram
2443 * the value of field 'showConsensusHistogram'.
2445 public void setShowConsensusHistogram(final boolean showConsensusHistogram)
2447 this._showConsensusHistogram = showConsensusHistogram;
2448 this._has_showConsensusHistogram = true;
2452 * Sets the value of field 'showDbRefTooltip'.
2454 * @param showDbRefTooltip
2455 * the value of field 'showDbRefTooltip'
2457 public void setShowDbRefTooltip(final boolean showDbRefTooltip)
2459 this._showDbRefTooltip = showDbRefTooltip;
2460 this._has_showDbRefTooltip = true;
2464 * Sets the value of field 'showFullId'.
2467 * the value of field 'showFullId'.
2469 public void setShowFullId(final boolean showFullId)
2471 this._showFullId = showFullId;
2472 this._has_showFullId = true;
2476 * Sets the value of field 'showGroupConsensus'.
2478 * @param showGroupConsensus
2479 * the value of field 'showGroupConsensus'.
2481 public void setShowGroupConsensus(final boolean showGroupConsensus)
2483 this._showGroupConsensus = showGroupConsensus;
2484 this._has_showGroupConsensus = true;
2488 * Sets the value of field 'showGroupConservation'.
2490 * @param showGroupConservation
2491 * the value of field 'showGroupConservation'.
2493 public void setShowGroupConservation(final boolean showGroupConservation)
2495 this._showGroupConservation = showGroupConservation;
2496 this._has_showGroupConservation = true;
2500 * Sets the value of field 'showNPfeatureTooltip'.
2502 * @param showNPfeatureTooltip
2503 * the value of field 'showNPfeatureTooltip'.
2505 public void setShowNPfeatureTooltip(final boolean showNPfeatureTooltip)
2507 this._showNPfeatureTooltip = showNPfeatureTooltip;
2508 this._has_showNPfeatureTooltip = true;
2512 * Sets the value of field 'showSequenceFeatures'.
2514 * @param showSequenceFeatures
2515 * the value of field 'showSequenceFeatures'.
2517 public void setShowSequenceFeatures(final boolean showSequenceFeatures)
2519 this._showSequenceFeatures = showSequenceFeatures;
2520 this._has_showSequenceFeatures = true;
2524 * Sets the value of field 'showSequenceLogo'.
2526 * @param showSequenceLogo
2527 * the value of field 'showSequenceLogo'
2529 public void setShowSequenceLogo(final boolean showSequenceLogo)
2531 this._showSequenceLogo = showSequenceLogo;
2532 this._has_showSequenceLogo = true;
2536 * Sets the value of field 'showText'.
2539 * the value of field 'showText'.
2541 public void setShowText(final boolean showText)
2543 this._showText = showText;
2544 this._has_showText = true;
2548 * Sets the value of field 'showUnconserved'.
2550 * @param showUnconserved
2551 * the value of field 'showUnconserved'.
2553 public void setShowUnconserved(final boolean showUnconserved)
2555 this._showUnconserved = showUnconserved;
2556 this._has_showUnconserved = true;
2560 * Sets the value of field 'startRes'.
2563 * the value of field 'startRes'.
2565 public void setStartRes(final int startRes)
2567 this._startRes = startRes;
2568 this._has_startRes = true;
2572 * Sets the value of field 'startSeq'.
2575 * the value of field 'startSeq'.
2577 public void setStartSeq(final int startSeq)
2579 this._startSeq = startSeq;
2580 this._has_startSeq = true;
2584 * Sets the value of field 'textCol1'.
2587 * the value of field 'textCol1'.
2589 public void setTextCol1(final int textCol1)
2591 this._textCol1 = textCol1;
2592 this._has_textCol1 = true;
2596 * Sets the value of field 'textCol2'.
2599 * the value of field 'textCol2'.
2601 public void setTextCol2(final int textCol2)
2603 this._textCol2 = textCol2;
2604 this._has_textCol2 = true;
2608 * Sets the value of field 'textColThreshold'.
2610 * @param textColThreshold
2611 * the value of field 'textColThreshold'
2613 public void setTextColThreshold(final int textColThreshold)
2615 this._textColThreshold = textColThreshold;
2616 this._has_textColThreshold = true;
2620 * Sets the value of field 'title'.
2623 * the value of field 'title'.
2625 public void setTitle(final java.lang.String title)
2627 this._title = title;
2631 * Sets the value of field 'viewName'.
2634 * the value of field 'viewName'.
2636 public void setViewName(final java.lang.String viewName)
2638 this._viewName = viewName;
2642 * Sets the value of field 'width'.
2645 * the value of field 'width'.
2647 public void setWidth(final int width)
2649 this._width = width;
2650 this._has_width = true;
2654 * Sets the value of field 'wrapAlignment'.
2656 * @param wrapAlignment
2657 * the value of field 'wrapAlignment'.
2659 public void setWrapAlignment(final boolean wrapAlignment)
2661 this._wrapAlignment = wrapAlignment;
2662 this._has_wrapAlignment = true;
2666 * Sets the value of field 'xpos'.
2669 * the value of field 'xpos'.
2671 public void setXpos(final int xpos)
2674 this._has_xpos = true;
2678 * Sets the value of field 'ypos'.
2681 * the value of field 'ypos'.
2683 public void setYpos(final int ypos)
2686 this._has_ypos = true;
2693 * @throws org.exolab.castor.xml.MarshalException
2694 * if object is null or if any SAXException is thrown during
2696 * @throws org.exolab.castor.xml.ValidationException
2697 * if this object is an invalid instance according to the schema
2698 * @return the unmarshaled jalview.schemabinding.version2.Viewport
2700 public static jalview.schemabinding.version2.Viewport unmarshal(
2701 final java.io.Reader reader)
2702 throws org.exolab.castor.xml.MarshalException,
2703 org.exolab.castor.xml.ValidationException
2705 return (jalview.schemabinding.version2.Viewport) Unmarshaller
2706 .unmarshal(jalview.schemabinding.version2.Viewport.class,
2713 * @throws org.exolab.castor.xml.ValidationException
2714 * if this object is an invalid instance according to the schema
2716 public void validate() throws org.exolab.castor.xml.ValidationException
2718 org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
2719 validator.validate(this);