2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
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
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 package jalview.schemabinding.version2;
23 //---------------------------------/
24 //- Imported classes and packages -/
25 //---------------------------------/
27 import org.exolab.castor.xml.Marshaller;
28 import org.exolab.castor.xml.Unmarshaller;
33 * @version $Revision$ $Date$
35 public class Viewport implements java.io.Serializable
38 // --------------------------/
39 // - Class/Member Variables -/
40 // --------------------------/
43 * Field _conservationSelected.
45 private boolean _conservationSelected;
48 * keeps track of state for field: _conservationSelected
50 private boolean _has_conservationSelected;
55 private boolean _pidSelected;
58 * keeps track of state for field: _pidSelected
60 private boolean _has_pidSelected;
65 private java.lang.String _bgColour;
68 * Field _consThreshold.
70 private int _consThreshold;
73 * keeps track of state for field: _consThreshold
75 private boolean _has_consThreshold;
78 * Field _pidThreshold.
80 private int _pidThreshold;
83 * keeps track of state for field: _pidThreshold
85 private boolean _has_pidThreshold;
90 private java.lang.String _title;
95 private boolean _showFullId;
98 * keeps track of state for field: _showFullId
100 private boolean _has_showFullId;
103 * Field _rightAlignIds.
105 private boolean _rightAlignIds;
108 * keeps track of state for field: _rightAlignIds
110 private boolean _has_rightAlignIds;
115 private boolean _showText;
118 * keeps track of state for field: _showText
120 private boolean _has_showText;
123 * Field _showColourText.
125 private boolean _showColourText;
128 * keeps track of state for field: _showColourText
130 private boolean _has_showColourText;
133 * Field _showUnconserved.
135 private boolean _showUnconserved = false;
138 * keeps track of state for field: _showUnconserved
140 private boolean _has_showUnconserved;
145 private boolean _showBoxes;
148 * keeps track of state for field: _showBoxes
150 private boolean _has_showBoxes;
153 * Field _wrapAlignment.
155 private boolean _wrapAlignment;
158 * keeps track of state for field: _wrapAlignment
160 private boolean _has_wrapAlignment;
165 private boolean _renderGaps;
168 * keeps track of state for field: _renderGaps
170 private boolean _has_renderGaps;
173 * Field _showSequenceFeatures.
175 private boolean _showSequenceFeatures;
178 * keeps track of state for field: _showSequenceFeatures
180 private boolean _has_showSequenceFeatures;
183 * Field _showNPfeatureTooltip.
185 private boolean _showNPfeatureTooltip;
188 * keeps track of state for field: _showNPfeatureTooltip
190 private boolean _has_showNPfeatureTooltip;
193 * Field _showDbRefTooltip.
195 private boolean _showDbRefTooltip;
198 * keeps track of state for field: _showDbRefTooltip
200 private boolean _has_showDbRefTooltip;
203 * Field _followHighlight.
205 private boolean _followHighlight = true;
208 * keeps track of state for field: _followHighlight
210 private boolean _has_followHighlight;
213 * Field _followSelection.
215 private boolean _followSelection = true;
218 * keeps track of state for field: _followSelection
220 private boolean _has_followSelection;
223 * Field _showAnnotation.
225 private boolean _showAnnotation;
228 * keeps track of state for field: _showAnnotation
230 private boolean _has_showAnnotation;
233 * Field _centreColumnLabels.
235 private boolean _centreColumnLabels = false;
238 * keeps track of state for field: _centreColumnLabels
240 private boolean _has_centreColumnLabels;
243 * Field _showGroupConservation.
245 private boolean _showGroupConservation = false;
248 * keeps track of state for field: _showGroupConservation
250 private boolean _has_showGroupConservation;
253 * Field _showGroupConsensus.
255 private boolean _showGroupConsensus = false;
258 * keeps track of state for field: _showGroupConsensus
260 private boolean _has_showGroupConsensus;
263 * Field _showConsensusHistogram.
265 private boolean _showConsensusHistogram = true;
268 * keeps track of state for field: _showConsensusHistogram
270 private boolean _has_showConsensusHistogram;
273 * Field _showSequenceLogo.
275 private boolean _showSequenceLogo = false;
278 * keeps track of state for field: _showSequenceLogo
280 private boolean _has_showSequenceLogo;
283 * Field _normaliseSequenceLogo.
285 private boolean _normaliseSequenceLogo = false;
288 * keeps track of state for field: _normaliseSequenceLogo
290 private boolean _has_normaliseSequenceLogo;
293 * Field _ignoreGapsinConsensus.
295 private boolean _ignoreGapsinConsensus = true;
298 * keeps track of state for field: _ignoreGapsinConsensus
300 private boolean _has_ignoreGapsinConsensus;
305 private int _startRes;
308 * keeps track of state for field: _startRes
310 private boolean _has_startRes;
315 private int _startSeq;
318 * keeps track of state for field: _startSeq
320 private boolean _has_startSeq;
325 private java.lang.String _fontName;
330 private int _fontSize;
333 * keeps track of state for field: _fontSize
335 private boolean _has_fontSize;
340 private int _fontStyle;
343 * keeps track of state for field: _fontStyle
345 private boolean _has_fontStyle;
350 private java.lang.String _viewName;
353 * Field _sequenceSetId.
355 private java.lang.String _sequenceSetId;
358 * Field _gatheredViews.
360 private boolean _gatheredViews;
363 * keeps track of state for field: _gatheredViews
365 private boolean _has_gatheredViews;
370 private int _textCol1;
373 * keeps track of state for field: _textCol1
375 private boolean _has_textCol1;
380 private int _textCol2;
383 * keeps track of state for field: _textCol2
385 private boolean _has_textCol2;
388 * Field _textColThreshold.
390 private int _textColThreshold;
393 * keeps track of state for field: _textColThreshold
395 private boolean _has_textColThreshold;
398 * unique id used by jalview to synchronize between stored and instantiated
402 private java.lang.String _id;
410 * keeps track of state for field: _width
412 private boolean _has_width;
420 * keeps track of state for field: _height
422 private boolean _has_height;
430 * keeps track of state for field: _xpos
432 private boolean _has_xpos;
440 * keeps track of state for field: _ypos
442 private boolean _has_ypos;
445 * Field _annotationColours.
447 private jalview.schemabinding.version2.AnnotationColours _annotationColours;
450 * Field _hiddenColumnsList.
452 private java.util.Vector _hiddenColumnsList;
455 * Field _calcIdParamList.
457 private java.util.Vector _calcIdParamList;
466 this._hiddenColumnsList = new java.util.Vector();
467 this._calcIdParamList = new java.util.Vector();
477 * @param vCalcIdParam
478 * @throws java.lang.IndexOutOfBoundsException
479 * if the index given is outside the bounds of the collection
481 public void addCalcIdParam(
482 final jalview.schemabinding.version2.CalcIdParam vCalcIdParam)
483 throws java.lang.IndexOutOfBoundsException
485 this._calcIdParamList.addElement(vCalcIdParam);
492 * @param vCalcIdParam
493 * @throws java.lang.IndexOutOfBoundsException
494 * if the index given is outside the bounds of the collection
496 public void addCalcIdParam(final int index,
497 final jalview.schemabinding.version2.CalcIdParam vCalcIdParam)
498 throws java.lang.IndexOutOfBoundsException
500 this._calcIdParamList.add(index, vCalcIdParam);
506 * @param vHiddenColumns
507 * @throws java.lang.IndexOutOfBoundsException
508 * if the index given is outside the bounds of the collection
510 public void addHiddenColumns(
511 final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)
512 throws java.lang.IndexOutOfBoundsException
514 this._hiddenColumnsList.addElement(vHiddenColumns);
521 * @param vHiddenColumns
522 * @throws java.lang.IndexOutOfBoundsException
523 * if the index given is outside the bounds of the collection
525 public void addHiddenColumns(final int index,
526 final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)
527 throws java.lang.IndexOutOfBoundsException
529 this._hiddenColumnsList.add(index, vHiddenColumns);
534 public void deleteCentreColumnLabels()
536 this._has_centreColumnLabels = false;
541 public void deleteConsThreshold()
543 this._has_consThreshold = false;
548 public void deleteConservationSelected()
550 this._has_conservationSelected = false;
555 public void deleteFollowHighlight()
557 this._has_followHighlight = false;
562 public void deleteFollowSelection()
564 this._has_followSelection = false;
569 public void deleteFontSize()
571 this._has_fontSize = false;
576 public void deleteFontStyle()
578 this._has_fontStyle = false;
583 public void deleteGatheredViews()
585 this._has_gatheredViews = false;
590 public void deleteHeight()
592 this._has_height = false;
597 public void deleteIgnoreGapsinConsensus()
599 this._has_ignoreGapsinConsensus = false;
604 public void deleteNormaliseSequenceLogo()
606 this._has_normaliseSequenceLogo = false;
611 public void deletePidSelected()
613 this._has_pidSelected = false;
618 public void deletePidThreshold()
620 this._has_pidThreshold = false;
625 public void deleteRenderGaps()
627 this._has_renderGaps = false;
632 public void deleteRightAlignIds()
634 this._has_rightAlignIds = false;
639 public void deleteShowAnnotation()
641 this._has_showAnnotation = false;
646 public void deleteShowBoxes()
648 this._has_showBoxes = false;
653 public void deleteShowColourText()
655 this._has_showColourText = false;
660 public void deleteShowConsensusHistogram()
662 this._has_showConsensusHistogram = false;
667 public void deleteShowDbRefTooltip()
669 this._has_showDbRefTooltip = false;
674 public void deleteShowFullId()
676 this._has_showFullId = false;
681 public void deleteShowGroupConsensus()
683 this._has_showGroupConsensus = false;
688 public void deleteShowGroupConservation()
690 this._has_showGroupConservation = false;
695 public void deleteShowNPfeatureTooltip()
697 this._has_showNPfeatureTooltip = false;
702 public void deleteShowSequenceFeatures()
704 this._has_showSequenceFeatures = false;
709 public void deleteShowSequenceLogo()
711 this._has_showSequenceLogo = false;
716 public void deleteShowText()
718 this._has_showText = false;
723 public void deleteShowUnconserved()
725 this._has_showUnconserved = false;
730 public void deleteStartRes()
732 this._has_startRes = false;
737 public void deleteStartSeq()
739 this._has_startSeq = false;
744 public void deleteTextCol1()
746 this._has_textCol1 = false;
751 public void deleteTextCol2()
753 this._has_textCol2 = false;
758 public void deleteTextColThreshold()
760 this._has_textColThreshold = false;
765 public void deleteWidth()
767 this._has_width = false;
772 public void deleteWrapAlignment()
774 this._has_wrapAlignment = false;
779 public void deleteXpos()
781 this._has_xpos = false;
786 public void deleteYpos()
788 this._has_ypos = false;
792 * Method enumerateCalcIdParam.
794 * @return an Enumeration over all jalview.schemabinding.version2.CalcIdParam
797 public java.util.Enumeration enumerateCalcIdParam()
799 return this._calcIdParamList.elements();
803 * Method enumerateHiddenColumns.
805 * @return an Enumeration over all
806 * jalview.schemabinding.version2.HiddenColumns elements
808 public java.util.Enumeration enumerateHiddenColumns()
810 return this._hiddenColumnsList.elements();
814 * Returns the value of field 'annotationColours'.
816 * @return the value of field 'AnnotationColours'.
818 public jalview.schemabinding.version2.AnnotationColours getAnnotationColours()
820 return this._annotationColours;
824 * Returns the value of field 'bgColour'.
826 * @return the value of field 'BgColour'.
828 public java.lang.String getBgColour()
830 return this._bgColour;
834 * Method getCalcIdParam.
837 * @throws java.lang.IndexOutOfBoundsException
838 * if the index given is outside the bounds of the collection
839 * @return the value of the jalview.schemabinding.version2.CalcIdParam at the
842 public jalview.schemabinding.version2.CalcIdParam getCalcIdParam(
843 final int index) throws java.lang.IndexOutOfBoundsException
845 // check bounds for index
846 if (index < 0 || index >= this._calcIdParamList.size())
848 throw new IndexOutOfBoundsException("getCalcIdParam: Index value '"
849 + index + "' not in range [0.."
850 + (this._calcIdParamList.size() - 1) + "]");
853 return (jalview.schemabinding.version2.CalcIdParam) _calcIdParamList
858 * Method getCalcIdParam.Returns the contents of the collection in an Array.
860 * Note: Just in case the collection contents are changing in another thread,
861 * we pass a 0-length Array of the correct type into the API call. This way we
862 * <i>know</i> that the Array returned is of exactly the correct length.
864 * @return this collection as an Array
866 public jalview.schemabinding.version2.CalcIdParam[] getCalcIdParam()
868 jalview.schemabinding.version2.CalcIdParam[] array = new jalview.schemabinding.version2.CalcIdParam[0];
869 return (jalview.schemabinding.version2.CalcIdParam[]) this._calcIdParamList
874 * Method getCalcIdParamCount.
876 * @return the size of this collection
878 public int getCalcIdParamCount()
880 return this._calcIdParamList.size();
884 * Returns the value of field 'centreColumnLabels'.
886 * @return the value of field 'CentreColumnLabels'.
888 public boolean getCentreColumnLabels()
890 return this._centreColumnLabels;
894 * Returns the value of field 'consThreshold'.
896 * @return the value of field 'ConsThreshold'.
898 public int getConsThreshold()
900 return this._consThreshold;
904 * Returns the value of field 'conservationSelected'.
906 * @return the value of field 'ConservationSelected'.
908 public boolean getConservationSelected()
910 return this._conservationSelected;
914 * Returns the value of field 'followHighlight'.
916 * @return the value of field 'FollowHighlight'.
918 public boolean getFollowHighlight()
920 return this._followHighlight;
924 * Returns the value of field 'followSelection'.
926 * @return the value of field 'FollowSelection'.
928 public boolean getFollowSelection()
930 return this._followSelection;
934 * Returns the value of field 'fontName'.
936 * @return the value of field 'FontName'.
938 public java.lang.String getFontName()
940 return this._fontName;
944 * Returns the value of field 'fontSize'.
946 * @return the value of field 'FontSize'.
948 public int getFontSize()
950 return this._fontSize;
954 * Returns the value of field 'fontStyle'.
956 * @return the value of field 'FontStyle'.
958 public int getFontStyle()
960 return this._fontStyle;
964 * Returns the value of field 'gatheredViews'.
966 * @return the value of field 'GatheredViews'.
968 public boolean getGatheredViews()
970 return this._gatheredViews;
974 * Returns the value of field 'height'.
976 * @return the value of field 'Height'.
978 public int getHeight()
984 * Method getHiddenColumns.
987 * @throws java.lang.IndexOutOfBoundsException
988 * if the index given is outside the bounds of the collection
989 * @return the value of the jalview.schemabinding.version2.HiddenColumns at
992 public jalview.schemabinding.version2.HiddenColumns getHiddenColumns(
993 final int index) throws java.lang.IndexOutOfBoundsException
995 // check bounds for index
996 if (index < 0 || index >= this._hiddenColumnsList.size())
998 throw new IndexOutOfBoundsException("getHiddenColumns: Index value '"
999 + index + "' not in range [0.."
1000 + (this._hiddenColumnsList.size() - 1) + "]");
1003 return (jalview.schemabinding.version2.HiddenColumns) _hiddenColumnsList
1008 * Method getHiddenColumns.Returns the contents of the collection in an Array.
1010 * Note: Just in case the collection contents are changing in another thread,
1011 * we pass a 0-length Array of the correct type into the API call. This way we
1012 * <i>know</i> that the Array returned is of exactly the correct length.
1014 * @return this collection as an Array
1016 public jalview.schemabinding.version2.HiddenColumns[] getHiddenColumns()
1018 jalview.schemabinding.version2.HiddenColumns[] array = new jalview.schemabinding.version2.HiddenColumns[0];
1019 return (jalview.schemabinding.version2.HiddenColumns[]) this._hiddenColumnsList
1024 * Method getHiddenColumnsCount.
1026 * @return the size of this collection
1028 public int getHiddenColumnsCount()
1030 return this._hiddenColumnsList.size();
1034 * Returns the value of field 'id'. The field 'id' has the following
1035 * description: unique id used by jalview to synchronize between stored and
1036 * instantiated views
1039 * @return the value of field 'Id'.
1041 public java.lang.String getId()
1047 * Returns the value of field 'ignoreGapsinConsensus'.
1049 * @return the value of field 'IgnoreGapsinConsensus'.
1051 public boolean getIgnoreGapsinConsensus()
1053 return this._ignoreGapsinConsensus;
1057 * Returns the value of field 'normaliseSequenceLogo'.
1059 * @return the value of field 'NormaliseSequenceLogo'.
1061 public boolean getNormaliseSequenceLogo()
1063 return this._normaliseSequenceLogo;
1067 * Returns the value of field 'pidSelected'.
1069 * @return the value of field 'PidSelected'.
1071 public boolean getPidSelected()
1073 return this._pidSelected;
1077 * Returns the value of field 'pidThreshold'.
1079 * @return the value of field 'PidThreshold'.
1081 public int getPidThreshold()
1083 return this._pidThreshold;
1087 * Returns the value of field 'renderGaps'.
1089 * @return the value of field 'RenderGaps'.
1091 public boolean getRenderGaps()
1093 return this._renderGaps;
1097 * Returns the value of field 'rightAlignIds'.
1099 * @return the value of field 'RightAlignIds'.
1101 public boolean getRightAlignIds()
1103 return this._rightAlignIds;
1107 * Returns the value of field 'sequenceSetId'.
1109 * @return the value of field 'SequenceSetId'.
1111 public java.lang.String getSequenceSetId()
1113 return this._sequenceSetId;
1117 * Returns the value of field 'showAnnotation'.
1119 * @return the value of field 'ShowAnnotation'.
1121 public boolean getShowAnnotation()
1123 return this._showAnnotation;
1127 * Returns the value of field 'showBoxes'.
1129 * @return the value of field 'ShowBoxes'.
1131 public boolean getShowBoxes()
1133 return this._showBoxes;
1137 * Returns the value of field 'showColourText'.
1139 * @return the value of field 'ShowColourText'.
1141 public boolean getShowColourText()
1143 return this._showColourText;
1147 * Returns the value of field 'showConsensusHistogram'.
1149 * @return the value of field 'ShowConsensusHistogram'.
1151 public boolean getShowConsensusHistogram()
1153 return this._showConsensusHistogram;
1157 * Returns the value of field 'showDbRefTooltip'.
1159 * @return the value of field 'ShowDbRefTooltip'.
1161 public boolean getShowDbRefTooltip()
1163 return this._showDbRefTooltip;
1167 * Returns the value of field 'showFullId'.
1169 * @return the value of field 'ShowFullId'.
1171 public boolean getShowFullId()
1173 return this._showFullId;
1177 * Returns the value of field 'showGroupConsensus'.
1179 * @return the value of field 'ShowGroupConsensus'.
1181 public boolean getShowGroupConsensus()
1183 return this._showGroupConsensus;
1187 * Returns the value of field 'showGroupConservation'.
1189 * @return the value of field 'ShowGroupConservation'.
1191 public boolean getShowGroupConservation()
1193 return this._showGroupConservation;
1197 * Returns the value of field 'showNPfeatureTooltip'.
1199 * @return the value of field 'ShowNPfeatureTooltip'.
1201 public boolean getShowNPfeatureTooltip()
1203 return this._showNPfeatureTooltip;
1207 * Returns the value of field 'showSequenceFeatures'.
1209 * @return the value of field 'ShowSequenceFeatures'.
1211 public boolean getShowSequenceFeatures()
1213 return this._showSequenceFeatures;
1217 * Returns the value of field 'showSequenceLogo'.
1219 * @return the value of field 'ShowSequenceLogo'.
1221 public boolean getShowSequenceLogo()
1223 return this._showSequenceLogo;
1227 * Returns the value of field 'showText'.
1229 * @return the value of field 'ShowText'.
1231 public boolean getShowText()
1233 return this._showText;
1237 * Returns the value of field 'showUnconserved'.
1239 * @return the value of field 'ShowUnconserved'.
1241 public boolean getShowUnconserved()
1243 return this._showUnconserved;
1247 * Returns the value of field 'startRes'.
1249 * @return the value of field 'StartRes'.
1251 public int getStartRes()
1253 return this._startRes;
1257 * Returns the value of field 'startSeq'.
1259 * @return the value of field 'StartSeq'.
1261 public int getStartSeq()
1263 return this._startSeq;
1267 * Returns the value of field 'textCol1'.
1269 * @return the value of field 'TextCol1'.
1271 public int getTextCol1()
1273 return this._textCol1;
1277 * Returns the value of field 'textCol2'.
1279 * @return the value of field 'TextCol2'.
1281 public int getTextCol2()
1283 return this._textCol2;
1287 * Returns the value of field 'textColThreshold'.
1289 * @return the value of field 'TextColThreshold'.
1291 public int getTextColThreshold()
1293 return this._textColThreshold;
1297 * Returns the value of field 'title'.
1299 * @return the value of field 'Title'.
1301 public java.lang.String getTitle()
1307 * Returns the value of field 'viewName'.
1309 * @return the value of field 'ViewName'.
1311 public java.lang.String getViewName()
1313 return this._viewName;
1317 * Returns the value of field 'width'.
1319 * @return the value of field 'Width'.
1321 public int getWidth()
1327 * Returns the value of field 'wrapAlignment'.
1329 * @return the value of field 'WrapAlignment'.
1331 public boolean getWrapAlignment()
1333 return this._wrapAlignment;
1337 * Returns the value of field 'xpos'.
1339 * @return the value of field 'Xpos'.
1341 public int getXpos()
1347 * Returns the value of field 'ypos'.
1349 * @return the value of field 'Ypos'.
1351 public int getYpos()
1357 * Method hasCentreColumnLabels.
1359 * @return true if at least one CentreColumnLabels has been adde
1361 public boolean hasCentreColumnLabels()
1363 return this._has_centreColumnLabels;
1367 * Method hasConsThreshold.
1369 * @return true if at least one ConsThreshold has been added
1371 public boolean hasConsThreshold()
1373 return this._has_consThreshold;
1377 * Method hasConservationSelected.
1379 * @return true if at least one ConservationSelected has been added
1381 public boolean hasConservationSelected()
1383 return this._has_conservationSelected;
1387 * Method hasFollowHighlight.
1389 * @return true if at least one FollowHighlight has been added
1391 public boolean hasFollowHighlight()
1393 return this._has_followHighlight;
1397 * Method hasFollowSelection.
1399 * @return true if at least one FollowSelection has been added
1401 public boolean hasFollowSelection()
1403 return this._has_followSelection;
1407 * Method hasFontSize.
1409 * @return true if at least one FontSize has been added
1411 public boolean hasFontSize()
1413 return this._has_fontSize;
1417 * Method hasFontStyle.
1419 * @return true if at least one FontStyle has been added
1421 public boolean hasFontStyle()
1423 return this._has_fontStyle;
1427 * Method hasGatheredViews.
1429 * @return true if at least one GatheredViews has been added
1431 public boolean hasGatheredViews()
1433 return this._has_gatheredViews;
1439 * @return true if at least one Height has been added
1441 public boolean hasHeight()
1443 return this._has_height;
1447 * Method hasIgnoreGapsinConsensus.
1449 * @return true if at least one IgnoreGapsinConsensus has been added
1451 public boolean hasIgnoreGapsinConsensus()
1453 return this._has_ignoreGapsinConsensus;
1457 * Method hasNormaliseSequenceLogo.
1459 * @return true if at least one NormaliseSequenceLogo has been added
1461 public boolean hasNormaliseSequenceLogo()
1463 return this._has_normaliseSequenceLogo;
1467 * Method hasPidSelected.
1469 * @return true if at least one PidSelected has been added
1471 public boolean hasPidSelected()
1473 return this._has_pidSelected;
1477 * Method hasPidThreshold.
1479 * @return true if at least one PidThreshold has been added
1481 public boolean hasPidThreshold()
1483 return this._has_pidThreshold;
1487 * Method hasRenderGaps.
1489 * @return true if at least one RenderGaps has been added
1491 public boolean hasRenderGaps()
1493 return this._has_renderGaps;
1497 * Method hasRightAlignIds.
1499 * @return true if at least one RightAlignIds has been added
1501 public boolean hasRightAlignIds()
1503 return this._has_rightAlignIds;
1507 * Method hasShowAnnotation.
1509 * @return true if at least one ShowAnnotation has been added
1511 public boolean hasShowAnnotation()
1513 return this._has_showAnnotation;
1517 * Method hasShowBoxes.
1519 * @return true if at least one ShowBoxes has been added
1521 public boolean hasShowBoxes()
1523 return this._has_showBoxes;
1527 * Method hasShowColourText.
1529 * @return true if at least one ShowColourText has been added
1531 public boolean hasShowColourText()
1533 return this._has_showColourText;
1537 * Method hasShowConsensusHistogram.
1539 * @return true if at least one ShowConsensusHistogram has been added
1541 public boolean hasShowConsensusHistogram()
1543 return this._has_showConsensusHistogram;
1547 * Method hasShowDbRefTooltip.
1549 * @return true if at least one ShowDbRefTooltip has been added
1551 public boolean hasShowDbRefTooltip()
1553 return this._has_showDbRefTooltip;
1557 * Method hasShowFullId.
1559 * @return true if at least one ShowFullId has been added
1561 public boolean hasShowFullId()
1563 return this._has_showFullId;
1567 * Method hasShowGroupConsensus.
1569 * @return true if at least one ShowGroupConsensus has been adde
1571 public boolean hasShowGroupConsensus()
1573 return this._has_showGroupConsensus;
1577 * Method hasShowGroupConservation.
1579 * @return true if at least one ShowGroupConservation has been added
1581 public boolean hasShowGroupConservation()
1583 return this._has_showGroupConservation;
1587 * Method hasShowNPfeatureTooltip.
1589 * @return true if at least one ShowNPfeatureTooltip has been added
1591 public boolean hasShowNPfeatureTooltip()
1593 return this._has_showNPfeatureTooltip;
1597 * Method hasShowSequenceFeatures.
1599 * @return true if at least one ShowSequenceFeatures has been added
1601 public boolean hasShowSequenceFeatures()
1603 return this._has_showSequenceFeatures;
1607 * Method hasShowSequenceLogo.
1609 * @return true if at least one ShowSequenceLogo has been added
1611 public boolean hasShowSequenceLogo()
1613 return this._has_showSequenceLogo;
1617 * Method hasShowText.
1619 * @return true if at least one ShowText has been added
1621 public boolean hasShowText()
1623 return this._has_showText;
1627 * Method hasShowUnconserved.
1629 * @return true if at least one ShowUnconserved has been added
1631 public boolean hasShowUnconserved()
1633 return this._has_showUnconserved;
1637 * Method hasStartRes.
1639 * @return true if at least one StartRes has been added
1641 public boolean hasStartRes()
1643 return this._has_startRes;
1647 * Method hasStartSeq.
1649 * @return true if at least one StartSeq has been added
1651 public boolean hasStartSeq()
1653 return this._has_startSeq;
1657 * Method hasTextCol1.
1659 * @return true if at least one TextCol1 has been added
1661 public boolean hasTextCol1()
1663 return this._has_textCol1;
1667 * Method hasTextCol2.
1669 * @return true if at least one TextCol2 has been added
1671 public boolean hasTextCol2()
1673 return this._has_textCol2;
1677 * Method hasTextColThreshold.
1679 * @return true if at least one TextColThreshold has been added
1681 public boolean hasTextColThreshold()
1683 return this._has_textColThreshold;
1689 * @return true if at least one Width has been added
1691 public boolean hasWidth()
1693 return this._has_width;
1697 * Method hasWrapAlignment.
1699 * @return true if at least one WrapAlignment has been added
1701 public boolean hasWrapAlignment()
1703 return this._has_wrapAlignment;
1709 * @return true if at least one Xpos has been added
1711 public boolean hasXpos()
1713 return this._has_xpos;
1719 * @return true if at least one Ypos has been added
1721 public boolean hasYpos()
1723 return this._has_ypos;
1727 * Returns the value of field 'centreColumnLabels'.
1729 * @return the value of field 'CentreColumnLabels'.
1731 public boolean isCentreColumnLabels()
1733 return this._centreColumnLabels;
1737 * Returns the value of field 'conservationSelected'.
1739 * @return the value of field 'ConservationSelected'.
1741 public boolean isConservationSelected()
1743 return this._conservationSelected;
1747 * Returns the value of field 'followHighlight'.
1749 * @return the value of field 'FollowHighlight'.
1751 public boolean isFollowHighlight()
1753 return this._followHighlight;
1757 * Returns the value of field 'followSelection'.
1759 * @return the value of field 'FollowSelection'.
1761 public boolean isFollowSelection()
1763 return this._followSelection;
1767 * Returns the value of field 'gatheredViews'.
1769 * @return the value of field 'GatheredViews'.
1771 public boolean isGatheredViews()
1773 return this._gatheredViews;
1777 * Returns the value of field 'ignoreGapsinConsensus'.
1779 * @return the value of field 'IgnoreGapsinConsensus'.
1781 public boolean isIgnoreGapsinConsensus()
1783 return this._ignoreGapsinConsensus;
1787 * Returns the value of field 'normaliseSequenceLogo'.
1789 * @return the value of field 'NormaliseSequenceLogo'.
1791 public boolean isNormaliseSequenceLogo()
1793 return this._normaliseSequenceLogo;
1797 * Returns the value of field 'pidSelected'.
1799 * @return the value of field 'PidSelected'.
1801 public boolean isPidSelected()
1803 return this._pidSelected;
1807 * Returns the value of field 'renderGaps'.
1809 * @return the value of field 'RenderGaps'.
1811 public boolean isRenderGaps()
1813 return this._renderGaps;
1817 * Returns the value of field 'rightAlignIds'.
1819 * @return the value of field 'RightAlignIds'.
1821 public boolean isRightAlignIds()
1823 return this._rightAlignIds;
1827 * Returns the value of field 'showAnnotation'.
1829 * @return the value of field 'ShowAnnotation'.
1831 public boolean isShowAnnotation()
1833 return this._showAnnotation;
1837 * Returns the value of field 'showBoxes'.
1839 * @return the value of field 'ShowBoxes'.
1841 public boolean isShowBoxes()
1843 return this._showBoxes;
1847 * Returns the value of field 'showColourText'.
1849 * @return the value of field 'ShowColourText'.
1851 public boolean isShowColourText()
1853 return this._showColourText;
1857 * Returns the value of field 'showConsensusHistogram'.
1859 * @return the value of field 'ShowConsensusHistogram'.
1861 public boolean isShowConsensusHistogram()
1863 return this._showConsensusHistogram;
1867 * Returns the value of field 'showDbRefTooltip'.
1869 * @return the value of field 'ShowDbRefTooltip'.
1871 public boolean isShowDbRefTooltip()
1873 return this._showDbRefTooltip;
1877 * Returns the value of field 'showFullId'.
1879 * @return the value of field 'ShowFullId'.
1881 public boolean isShowFullId()
1883 return this._showFullId;
1887 * Returns the value of field 'showGroupConsensus'.
1889 * @return the value of field 'ShowGroupConsensus'.
1891 public boolean isShowGroupConsensus()
1893 return this._showGroupConsensus;
1897 * Returns the value of field 'showGroupConservation'.
1899 * @return the value of field 'ShowGroupConservation'.
1901 public boolean isShowGroupConservation()
1903 return this._showGroupConservation;
1907 * Returns the value of field 'showNPfeatureTooltip'.
1909 * @return the value of field 'ShowNPfeatureTooltip'.
1911 public boolean isShowNPfeatureTooltip()
1913 return this._showNPfeatureTooltip;
1917 * Returns the value of field 'showSequenceFeatures'.
1919 * @return the value of field 'ShowSequenceFeatures'.
1921 public boolean isShowSequenceFeatures()
1923 return this._showSequenceFeatures;
1927 * Returns the value of field 'showSequenceLogo'.
1929 * @return the value of field 'ShowSequenceLogo'.
1931 public boolean isShowSequenceLogo()
1933 return this._showSequenceLogo;
1937 * Returns the value of field 'showText'.
1939 * @return the value of field 'ShowText'.
1941 public boolean isShowText()
1943 return this._showText;
1947 * Returns the value of field 'showUnconserved'.
1949 * @return the value of field 'ShowUnconserved'.
1951 public boolean isShowUnconserved()
1953 return this._showUnconserved;
1959 * @return true if this object is valid according to the schema
1961 public boolean isValid()
1966 } catch (org.exolab.castor.xml.ValidationException vex)
1974 * Returns the value of field 'wrapAlignment'.
1976 * @return the value of field 'WrapAlignment'.
1978 public boolean isWrapAlignment()
1980 return this._wrapAlignment;
1987 * @throws org.exolab.castor.xml.MarshalException
1988 * if object is null or if any SAXException is thrown during
1990 * @throws org.exolab.castor.xml.ValidationException
1991 * if this object is an invalid instance according to the schema
1993 public void marshal(final java.io.Writer out)
1994 throws org.exolab.castor.xml.MarshalException,
1995 org.exolab.castor.xml.ValidationException
1997 Marshaller.marshal(this, out);
2004 * @throws java.io.IOException
2005 * if an IOException occurs during marshaling
2006 * @throws org.exolab.castor.xml.ValidationException
2007 * if this object is an invalid instance according to the schema
2008 * @throws org.exolab.castor.xml.MarshalException
2009 * if object is null or if any SAXException is thrown during
2012 public void marshal(final org.xml.sax.ContentHandler handler)
2013 throws java.io.IOException,
2014 org.exolab.castor.xml.MarshalException,
2015 org.exolab.castor.xml.ValidationException
2017 Marshaller.marshal(this, handler);
2022 public void removeAllCalcIdParam()
2024 this._calcIdParamList.clear();
2029 public void removeAllHiddenColumns()
2031 this._hiddenColumnsList.clear();
2035 * Method removeCalcIdParam.
2037 * @param vCalcIdParam
2038 * @return true if the object was removed from the collection.
2040 public boolean removeCalcIdParam(
2041 final jalview.schemabinding.version2.CalcIdParam vCalcIdParam)
2043 boolean removed = _calcIdParamList.remove(vCalcIdParam);
2048 * Method removeCalcIdParamAt.
2051 * @return the element removed from the collection
2053 public jalview.schemabinding.version2.CalcIdParam removeCalcIdParamAt(
2056 java.lang.Object obj = this._calcIdParamList.remove(index);
2057 return (jalview.schemabinding.version2.CalcIdParam) obj;
2061 * Method removeHiddenColumns.
2063 * @param vHiddenColumns
2064 * @return true if the object was removed from the collection.
2066 public boolean removeHiddenColumns(
2067 final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)
2069 boolean removed = _hiddenColumnsList.remove(vHiddenColumns);
2074 * Method removeHiddenColumnsAt.
2077 * @return the element removed from the collection
2079 public jalview.schemabinding.version2.HiddenColumns removeHiddenColumnsAt(
2082 java.lang.Object obj = this._hiddenColumnsList.remove(index);
2083 return (jalview.schemabinding.version2.HiddenColumns) obj;
2087 * Sets the value of field 'annotationColours'.
2089 * @param annotationColours
2090 * the value of field 'annotationColours'.
2092 public void setAnnotationColours(
2093 final jalview.schemabinding.version2.AnnotationColours annotationColours)
2095 this._annotationColours = annotationColours;
2099 * Sets the value of field 'bgColour'.
2102 * the value of field 'bgColour'.
2104 public void setBgColour(final java.lang.String bgColour)
2106 this._bgColour = bgColour;
2113 * @param vCalcIdParam
2114 * @throws java.lang.IndexOutOfBoundsException
2115 * if the index given is outside the bounds of the collection
2117 public void setCalcIdParam(final int index,
2118 final jalview.schemabinding.version2.CalcIdParam vCalcIdParam)
2119 throws java.lang.IndexOutOfBoundsException
2121 // check bounds for index
2122 if (index < 0 || index >= this._calcIdParamList.size())
2124 throw new IndexOutOfBoundsException("setCalcIdParam: Index value '"
2125 + index + "' not in range [0.."
2126 + (this._calcIdParamList.size() - 1) + "]");
2129 this._calcIdParamList.set(index, vCalcIdParam);
2135 * @param vCalcIdParamArray
2137 public void setCalcIdParam(
2138 final jalview.schemabinding.version2.CalcIdParam[] vCalcIdParamArray)
2141 _calcIdParamList.clear();
2143 for (int i = 0; i < vCalcIdParamArray.length; i++)
2145 this._calcIdParamList.add(vCalcIdParamArray[i]);
2150 * Sets the value of field 'centreColumnLabels'.
2152 * @param centreColumnLabels
2153 * the value of field 'centreColumnLabels'.
2155 public void setCentreColumnLabels(final boolean centreColumnLabels)
2157 this._centreColumnLabels = centreColumnLabels;
2158 this._has_centreColumnLabels = true;
2162 * Sets the value of field 'consThreshold'.
2164 * @param consThreshold
2165 * the value of field 'consThreshold'.
2167 public void setConsThreshold(final int consThreshold)
2169 this._consThreshold = consThreshold;
2170 this._has_consThreshold = true;
2174 * Sets the value of field 'conservationSelected'.
2176 * @param conservationSelected
2177 * the value of field 'conservationSelected'.
2179 public void setConservationSelected(final boolean conservationSelected)
2181 this._conservationSelected = conservationSelected;
2182 this._has_conservationSelected = true;
2186 * Sets the value of field 'followHighlight'.
2188 * @param followHighlight
2189 * the value of field 'followHighlight'.
2191 public void setFollowHighlight(final boolean followHighlight)
2193 this._followHighlight = followHighlight;
2194 this._has_followHighlight = true;
2198 * Sets the value of field 'followSelection'.
2200 * @param followSelection
2201 * the value of field 'followSelection'.
2203 public void setFollowSelection(final boolean followSelection)
2205 this._followSelection = followSelection;
2206 this._has_followSelection = true;
2210 * Sets the value of field 'fontName'.
2213 * the value of field 'fontName'.
2215 public void setFontName(final java.lang.String fontName)
2217 this._fontName = fontName;
2221 * Sets the value of field 'fontSize'.
2224 * the value of field 'fontSize'.
2226 public void setFontSize(final int fontSize)
2228 this._fontSize = fontSize;
2229 this._has_fontSize = true;
2233 * Sets the value of field 'fontStyle'.
2236 * the value of field 'fontStyle'.
2238 public void setFontStyle(final int fontStyle)
2240 this._fontStyle = fontStyle;
2241 this._has_fontStyle = true;
2245 * Sets the value of field 'gatheredViews'.
2247 * @param gatheredViews
2248 * the value of field 'gatheredViews'.
2250 public void setGatheredViews(final boolean gatheredViews)
2252 this._gatheredViews = gatheredViews;
2253 this._has_gatheredViews = true;
2257 * Sets the value of field 'height'.
2260 * the value of field 'height'.
2262 public void setHeight(final int height)
2264 this._height = height;
2265 this._has_height = true;
2272 * @param vHiddenColumns
2273 * @throws java.lang.IndexOutOfBoundsException
2274 * if the index given is outside the bounds of the collection
2276 public void setHiddenColumns(final int index,
2277 final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)
2278 throws java.lang.IndexOutOfBoundsException
2280 // check bounds for index
2281 if (index < 0 || index >= this._hiddenColumnsList.size())
2283 throw new IndexOutOfBoundsException("setHiddenColumns: Index value '"
2284 + index + "' not in range [0.."
2285 + (this._hiddenColumnsList.size() - 1) + "]");
2288 this._hiddenColumnsList.set(index, vHiddenColumns);
2294 * @param vHiddenColumnsArray
2296 public void setHiddenColumns(
2297 final jalview.schemabinding.version2.HiddenColumns[] vHiddenColumnsArray)
2300 _hiddenColumnsList.clear();
2302 for (int i = 0; i < vHiddenColumnsArray.length; i++)
2304 this._hiddenColumnsList.add(vHiddenColumnsArray[i]);
2309 * Sets the value of field 'id'. The field 'id' has the following description:
2310 * unique id used by jalview to synchronize between stored and instantiated
2315 * the value of field 'id'.
2317 public void setId(final java.lang.String id)
2323 * Sets the value of field 'ignoreGapsinConsensus'.
2325 * @param ignoreGapsinConsensus
2326 * the value of field 'ignoreGapsinConsensus'.
2328 public void setIgnoreGapsinConsensus(final boolean ignoreGapsinConsensus)
2330 this._ignoreGapsinConsensus = ignoreGapsinConsensus;
2331 this._has_ignoreGapsinConsensus = true;
2335 * Sets the value of field 'normaliseSequenceLogo'.
2337 * @param normaliseSequenceLogo
2338 * the value of field 'normaliseSequenceLogo'.
2340 public void setNormaliseSequenceLogo(final boolean normaliseSequenceLogo)
2342 this._normaliseSequenceLogo = normaliseSequenceLogo;
2343 this._has_normaliseSequenceLogo = true;
2347 * Sets the value of field 'pidSelected'.
2349 * @param pidSelected
2350 * the value of field 'pidSelected'.
2352 public void setPidSelected(final boolean pidSelected)
2354 this._pidSelected = pidSelected;
2355 this._has_pidSelected = true;
2359 * Sets the value of field 'pidThreshold'.
2361 * @param pidThreshold
2362 * the value of field 'pidThreshold'.
2364 public void setPidThreshold(final int pidThreshold)
2366 this._pidThreshold = pidThreshold;
2367 this._has_pidThreshold = true;
2371 * Sets the value of field 'renderGaps'.
2374 * the value of field 'renderGaps'.
2376 public void setRenderGaps(final boolean renderGaps)
2378 this._renderGaps = renderGaps;
2379 this._has_renderGaps = true;
2383 * Sets the value of field 'rightAlignIds'.
2385 * @param rightAlignIds
2386 * the value of field 'rightAlignIds'.
2388 public void setRightAlignIds(final boolean rightAlignIds)
2390 this._rightAlignIds = rightAlignIds;
2391 this._has_rightAlignIds = true;
2395 * Sets the value of field 'sequenceSetId'.
2397 * @param sequenceSetId
2398 * the value of field 'sequenceSetId'.
2400 public void setSequenceSetId(final java.lang.String sequenceSetId)
2402 this._sequenceSetId = sequenceSetId;
2406 * Sets the value of field 'showAnnotation'.
2408 * @param showAnnotation
2409 * the value of field 'showAnnotation'.
2411 public void setShowAnnotation(final boolean showAnnotation)
2413 this._showAnnotation = showAnnotation;
2414 this._has_showAnnotation = true;
2418 * Sets the value of field 'showBoxes'.
2421 * the value of field 'showBoxes'.
2423 public void setShowBoxes(final boolean showBoxes)
2425 this._showBoxes = showBoxes;
2426 this._has_showBoxes = true;
2430 * Sets the value of field 'showColourText'.
2432 * @param showColourText
2433 * the value of field 'showColourText'.
2435 public void setShowColourText(final boolean showColourText)
2437 this._showColourText = showColourText;
2438 this._has_showColourText = true;
2442 * Sets the value of field 'showConsensusHistogram'.
2444 * @param showConsensusHistogram
2445 * the value of field 'showConsensusHistogram'.
2447 public void setShowConsensusHistogram(final boolean showConsensusHistogram)
2449 this._showConsensusHistogram = showConsensusHistogram;
2450 this._has_showConsensusHistogram = true;
2454 * Sets the value of field 'showDbRefTooltip'.
2456 * @param showDbRefTooltip
2457 * the value of field 'showDbRefTooltip'
2459 public void setShowDbRefTooltip(final boolean showDbRefTooltip)
2461 this._showDbRefTooltip = showDbRefTooltip;
2462 this._has_showDbRefTooltip = true;
2466 * Sets the value of field 'showFullId'.
2469 * the value of field 'showFullId'.
2471 public void setShowFullId(final boolean showFullId)
2473 this._showFullId = showFullId;
2474 this._has_showFullId = true;
2478 * Sets the value of field 'showGroupConsensus'.
2480 * @param showGroupConsensus
2481 * the value of field 'showGroupConsensus'.
2483 public void setShowGroupConsensus(final boolean showGroupConsensus)
2485 this._showGroupConsensus = showGroupConsensus;
2486 this._has_showGroupConsensus = true;
2490 * Sets the value of field 'showGroupConservation'.
2492 * @param showGroupConservation
2493 * the value of field 'showGroupConservation'.
2495 public void setShowGroupConservation(final boolean showGroupConservation)
2497 this._showGroupConservation = showGroupConservation;
2498 this._has_showGroupConservation = true;
2502 * Sets the value of field 'showNPfeatureTooltip'.
2504 * @param showNPfeatureTooltip
2505 * the value of field 'showNPfeatureTooltip'.
2507 public void setShowNPfeatureTooltip(final boolean showNPfeatureTooltip)
2509 this._showNPfeatureTooltip = showNPfeatureTooltip;
2510 this._has_showNPfeatureTooltip = true;
2514 * Sets the value of field 'showSequenceFeatures'.
2516 * @param showSequenceFeatures
2517 * the value of field 'showSequenceFeatures'.
2519 public void setShowSequenceFeatures(final boolean showSequenceFeatures)
2521 this._showSequenceFeatures = showSequenceFeatures;
2522 this._has_showSequenceFeatures = true;
2526 * Sets the value of field 'showSequenceLogo'.
2528 * @param showSequenceLogo
2529 * the value of field 'showSequenceLogo'
2531 public void setShowSequenceLogo(final boolean showSequenceLogo)
2533 this._showSequenceLogo = showSequenceLogo;
2534 this._has_showSequenceLogo = true;
2538 * Sets the value of field 'showText'.
2541 * the value of field 'showText'.
2543 public void setShowText(final boolean showText)
2545 this._showText = showText;
2546 this._has_showText = true;
2550 * Sets the value of field 'showUnconserved'.
2552 * @param showUnconserved
2553 * the value of field 'showUnconserved'.
2555 public void setShowUnconserved(final boolean showUnconserved)
2557 this._showUnconserved = showUnconserved;
2558 this._has_showUnconserved = true;
2562 * Sets the value of field 'startRes'.
2565 * the value of field 'startRes'.
2567 public void setStartRes(final int startRes)
2569 this._startRes = startRes;
2570 this._has_startRes = true;
2574 * Sets the value of field 'startSeq'.
2577 * the value of field 'startSeq'.
2579 public void setStartSeq(final int startSeq)
2581 this._startSeq = startSeq;
2582 this._has_startSeq = true;
2586 * Sets the value of field 'textCol1'.
2589 * the value of field 'textCol1'.
2591 public void setTextCol1(final int textCol1)
2593 this._textCol1 = textCol1;
2594 this._has_textCol1 = true;
2598 * Sets the value of field 'textCol2'.
2601 * the value of field 'textCol2'.
2603 public void setTextCol2(final int textCol2)
2605 this._textCol2 = textCol2;
2606 this._has_textCol2 = true;
2610 * Sets the value of field 'textColThreshold'.
2612 * @param textColThreshold
2613 * the value of field 'textColThreshold'
2615 public void setTextColThreshold(final int textColThreshold)
2617 this._textColThreshold = textColThreshold;
2618 this._has_textColThreshold = true;
2622 * Sets the value of field 'title'.
2625 * the value of field 'title'.
2627 public void setTitle(final java.lang.String title)
2629 this._title = title;
2633 * Sets the value of field 'viewName'.
2636 * the value of field 'viewName'.
2638 public void setViewName(final java.lang.String viewName)
2640 this._viewName = viewName;
2644 * Sets the value of field 'width'.
2647 * the value of field 'width'.
2649 public void setWidth(final int width)
2651 this._width = width;
2652 this._has_width = true;
2656 * Sets the value of field 'wrapAlignment'.
2658 * @param wrapAlignment
2659 * the value of field 'wrapAlignment'.
2661 public void setWrapAlignment(final boolean wrapAlignment)
2663 this._wrapAlignment = wrapAlignment;
2664 this._has_wrapAlignment = true;
2668 * Sets the value of field 'xpos'.
2671 * the value of field 'xpos'.
2673 public void setXpos(final int xpos)
2676 this._has_xpos = true;
2680 * Sets the value of field 'ypos'.
2683 * the value of field 'ypos'.
2685 public void setYpos(final int ypos)
2688 this._has_ypos = true;
2695 * @throws org.exolab.castor.xml.MarshalException
2696 * if object is null or if any SAXException is thrown during
2698 * @throws org.exolab.castor.xml.ValidationException
2699 * if this object is an invalid instance according to the schema
2700 * @return the unmarshaled jalview.schemabinding.version2.Viewport
2702 public static jalview.schemabinding.version2.Viewport unmarshal(
2703 final java.io.Reader reader)
2704 throws org.exolab.castor.xml.MarshalException,
2705 org.exolab.castor.xml.ValidationException
2707 return (jalview.schemabinding.version2.Viewport) Unmarshaller
2708 .unmarshal(jalview.schemabinding.version2.Viewport.class,
2715 * @throws org.exolab.castor.xml.ValidationException
2716 * if this object is an invalid instance according to the schema
2718 public void validate() throws org.exolab.castor.xml.ValidationException
2720 org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
2721 validator.validate(this);