2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
3 * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
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/>.
18 package jalview.schemabinding.version2;
20 //---------------------------------/
21 //- Imported classes and packages -/
22 //---------------------------------/
24 import org.exolab.castor.xml.Marshaller;
25 import org.exolab.castor.xml.Unmarshaller;
30 * @version $Revision$ $Date$
32 public class Viewport implements java.io.Serializable
35 // --------------------------/
36 // - Class/Member Variables -/
37 // --------------------------/
40 * Field _conservationSelected.
42 private boolean _conservationSelected;
45 * keeps track of state for field: _conservationSelected
47 private boolean _has_conservationSelected;
52 private boolean _pidSelected;
55 * keeps track of state for field: _pidSelected
57 private boolean _has_pidSelected;
62 private java.lang.String _bgColour;
65 * Field _consThreshold.
67 private int _consThreshold;
70 * keeps track of state for field: _consThreshold
72 private boolean _has_consThreshold;
75 * Field _pidThreshold.
77 private int _pidThreshold;
80 * keeps track of state for field: _pidThreshold
82 private boolean _has_pidThreshold;
87 private java.lang.String _title;
92 private boolean _showFullId;
95 * keeps track of state for field: _showFullId
97 private boolean _has_showFullId;
100 * Field _rightAlignIds.
102 private boolean _rightAlignIds;
105 * keeps track of state for field: _rightAlignIds
107 private boolean _has_rightAlignIds;
112 private boolean _showText;
115 * keeps track of state for field: _showText
117 private boolean _has_showText;
120 * Field _showColourText.
122 private boolean _showColourText;
125 * keeps track of state for field: _showColourText
127 private boolean _has_showColourText;
130 * Field _showUnconserved.
132 private boolean _showUnconserved = false;
135 * keeps track of state for field: _showUnconserved
137 private boolean _has_showUnconserved;
142 private boolean _showBoxes;
145 * keeps track of state for field: _showBoxes
147 private boolean _has_showBoxes;
150 * Field _wrapAlignment.
152 private boolean _wrapAlignment;
155 * keeps track of state for field: _wrapAlignment
157 private boolean _has_wrapAlignment;
162 private boolean _renderGaps;
165 * keeps track of state for field: _renderGaps
167 private boolean _has_renderGaps;
170 * Field _showSequenceFeatures.
172 private boolean _showSequenceFeatures;
175 * keeps track of state for field: _showSequenceFeatures
177 private boolean _has_showSequenceFeatures;
180 * Field _showNPfeatureTooltip.
182 private boolean _showNPfeatureTooltip;
185 * keeps track of state for field: _showNPfeatureTooltip
187 private boolean _has_showNPfeatureTooltip;
190 * Field _showDbRefTooltip.
192 private boolean _showDbRefTooltip;
195 * keeps track of state for field: _showDbRefTooltip
197 private boolean _has_showDbRefTooltip;
200 * Field _followHighlight.
202 private boolean _followHighlight = true;
205 * keeps track of state for field: _followHighlight
207 private boolean _has_followHighlight;
210 * Field _followSelection.
212 private boolean _followSelection = true;
215 * keeps track of state for field: _followSelection
217 private boolean _has_followSelection;
220 * Field _showAnnotation.
222 private boolean _showAnnotation;
225 * keeps track of state for field: _showAnnotation
227 private boolean _has_showAnnotation;
230 * Field _centreColumnLabels.
232 private boolean _centreColumnLabels = false;
235 * keeps track of state for field: _centreColumnLabels
237 private boolean _has_centreColumnLabels;
240 * Field _showGroupConservation.
242 private boolean _showGroupConservation = false;
245 * keeps track of state for field: _showGroupConservation
247 private boolean _has_showGroupConservation;
250 * Field _showGroupConsensus.
252 private boolean _showGroupConsensus = false;
255 * keeps track of state for field: _showGroupConsensus
257 private boolean _has_showGroupConsensus;
260 * Field _showConsensusHistogram.
262 private boolean _showConsensusHistogram = true;
265 * keeps track of state for field: _showConsensusHistogram
267 private boolean _has_showConsensusHistogram;
270 * Field _showSequenceLogo.
272 private boolean _showSequenceLogo = false;
275 * keeps track of state for field: _showSequenceLogo
277 private boolean _has_showSequenceLogo;
280 * Field _normaliseSequenceLogo.
282 private boolean _normaliseSequenceLogo = false;
285 * keeps track of state for field: _normaliseSequenceLogo
287 private boolean _has_normaliseSequenceLogo;
290 * Field _ignoreGapsinConsensus.
292 private boolean _ignoreGapsinConsensus = true;
295 * keeps track of state for field: _ignoreGapsinConsensus
297 private boolean _has_ignoreGapsinConsensus;
302 private int _startRes;
305 * keeps track of state for field: _startRes
307 private boolean _has_startRes;
312 private int _startSeq;
315 * keeps track of state for field: _startSeq
317 private boolean _has_startSeq;
322 private java.lang.String _fontName;
327 private int _fontSize;
330 * keeps track of state for field: _fontSize
332 private boolean _has_fontSize;
337 private int _fontStyle;
340 * keeps track of state for field: _fontStyle
342 private boolean _has_fontStyle;
347 private java.lang.String _viewName;
350 * Field _sequenceSetId.
352 private java.lang.String _sequenceSetId;
355 * Field _gatheredViews.
357 private boolean _gatheredViews;
360 * keeps track of state for field: _gatheredViews
362 private boolean _has_gatheredViews;
367 private int _textCol1;
370 * keeps track of state for field: _textCol1
372 private boolean _has_textCol1;
377 private int _textCol2;
380 * keeps track of state for field: _textCol2
382 private boolean _has_textCol2;
385 * Field _textColThreshold.
387 private int _textColThreshold;
390 * keeps track of state for field: _textColThreshold
392 private boolean _has_textColThreshold;
395 * unique id used by jalview to synchronize between stored and instantiated
399 private java.lang.String _id;
407 * keeps track of state for field: _width
409 private boolean _has_width;
417 * keeps track of state for field: _height
419 private boolean _has_height;
427 * keeps track of state for field: _xpos
429 private boolean _has_xpos;
437 * keeps track of state for field: _ypos
439 private boolean _has_ypos;
442 * Field _annotationColours.
444 private jalview.schemabinding.version2.AnnotationColours _annotationColours;
447 * Field _hiddenColumnsList.
449 private java.util.Vector _hiddenColumnsList;
452 * Field _calcIdParamList.
454 private java.util.Vector _calcIdParamList;
463 this._hiddenColumnsList = new java.util.Vector();
464 this._calcIdParamList = new java.util.Vector();
474 * @param vCalcIdParam
475 * @throws java.lang.IndexOutOfBoundsException
476 * if the index given is outside the bounds of the collection
478 public void addCalcIdParam(
479 final jalview.schemabinding.version2.CalcIdParam vCalcIdParam)
480 throws java.lang.IndexOutOfBoundsException
482 this._calcIdParamList.addElement(vCalcIdParam);
489 * @param vCalcIdParam
490 * @throws java.lang.IndexOutOfBoundsException
491 * if the index given is outside the bounds of the collection
493 public void addCalcIdParam(final int index,
494 final jalview.schemabinding.version2.CalcIdParam vCalcIdParam)
495 throws java.lang.IndexOutOfBoundsException
497 this._calcIdParamList.add(index, vCalcIdParam);
503 * @param vHiddenColumns
504 * @throws java.lang.IndexOutOfBoundsException
505 * if the index given is outside the bounds of the collection
507 public void addHiddenColumns(
508 final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)
509 throws java.lang.IndexOutOfBoundsException
511 this._hiddenColumnsList.addElement(vHiddenColumns);
518 * @param vHiddenColumns
519 * @throws java.lang.IndexOutOfBoundsException
520 * if the index given is outside the bounds of the collection
522 public void addHiddenColumns(final int index,
523 final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)
524 throws java.lang.IndexOutOfBoundsException
526 this._hiddenColumnsList.add(index, vHiddenColumns);
531 public void deleteCentreColumnLabels()
533 this._has_centreColumnLabels = false;
538 public void deleteConsThreshold()
540 this._has_consThreshold = false;
545 public void deleteConservationSelected()
547 this._has_conservationSelected = false;
552 public void deleteFollowHighlight()
554 this._has_followHighlight = false;
559 public void deleteFollowSelection()
561 this._has_followSelection = false;
566 public void deleteFontSize()
568 this._has_fontSize = false;
573 public void deleteFontStyle()
575 this._has_fontStyle = false;
580 public void deleteGatheredViews()
582 this._has_gatheredViews = false;
587 public void deleteHeight()
589 this._has_height = false;
594 public void deleteIgnoreGapsinConsensus()
596 this._has_ignoreGapsinConsensus = false;
601 public void deleteNormaliseSequenceLogo()
603 this._has_normaliseSequenceLogo = false;
608 public void deletePidSelected()
610 this._has_pidSelected = false;
615 public void deletePidThreshold()
617 this._has_pidThreshold = false;
622 public void deleteRenderGaps()
624 this._has_renderGaps = false;
629 public void deleteRightAlignIds()
631 this._has_rightAlignIds = false;
636 public void deleteShowAnnotation()
638 this._has_showAnnotation = false;
643 public void deleteShowBoxes()
645 this._has_showBoxes = false;
650 public void deleteShowColourText()
652 this._has_showColourText = false;
657 public void deleteShowConsensusHistogram()
659 this._has_showConsensusHistogram = false;
664 public void deleteShowDbRefTooltip()
666 this._has_showDbRefTooltip = false;
671 public void deleteShowFullId()
673 this._has_showFullId = false;
678 public void deleteShowGroupConsensus()
680 this._has_showGroupConsensus = false;
685 public void deleteShowGroupConservation()
687 this._has_showGroupConservation = false;
692 public void deleteShowNPfeatureTooltip()
694 this._has_showNPfeatureTooltip = false;
699 public void deleteShowSequenceFeatures()
701 this._has_showSequenceFeatures = false;
706 public void deleteShowSequenceLogo()
708 this._has_showSequenceLogo = false;
713 public void deleteShowText()
715 this._has_showText = false;
720 public void deleteShowUnconserved()
722 this._has_showUnconserved = false;
727 public void deleteStartRes()
729 this._has_startRes = false;
734 public void deleteStartSeq()
736 this._has_startSeq = false;
741 public void deleteTextCol1()
743 this._has_textCol1 = false;
748 public void deleteTextCol2()
750 this._has_textCol2 = false;
755 public void deleteTextColThreshold()
757 this._has_textColThreshold = false;
762 public void deleteWidth()
764 this._has_width = false;
769 public void deleteWrapAlignment()
771 this._has_wrapAlignment = false;
776 public void deleteXpos()
778 this._has_xpos = false;
783 public void deleteYpos()
785 this._has_ypos = false;
789 * Method enumerateCalcIdParam.
791 * @return an Enumeration over all jalview.schemabinding.version2.CalcIdParam
794 public java.util.Enumeration enumerateCalcIdParam()
796 return this._calcIdParamList.elements();
800 * Method enumerateHiddenColumns.
802 * @return an Enumeration over all
803 * jalview.schemabinding.version2.HiddenColumns elements
805 public java.util.Enumeration enumerateHiddenColumns()
807 return this._hiddenColumnsList.elements();
811 * Returns the value of field 'annotationColours'.
813 * @return the value of field 'AnnotationColours'.
815 public jalview.schemabinding.version2.AnnotationColours getAnnotationColours()
817 return this._annotationColours;
821 * Returns the value of field 'bgColour'.
823 * @return the value of field 'BgColour'.
825 public java.lang.String getBgColour()
827 return this._bgColour;
831 * Method getCalcIdParam.
834 * @throws java.lang.IndexOutOfBoundsException
835 * if the index given is outside the bounds of the collection
836 * @return the value of the jalview.schemabinding.version2.CalcIdParam at the
839 public jalview.schemabinding.version2.CalcIdParam getCalcIdParam(
840 final int index) throws java.lang.IndexOutOfBoundsException
842 // check bounds for index
843 if (index < 0 || index >= this._calcIdParamList.size())
845 throw new IndexOutOfBoundsException("getCalcIdParam: Index value '"
846 + index + "' not in range [0.."
847 + (this._calcIdParamList.size() - 1) + "]");
850 return (jalview.schemabinding.version2.CalcIdParam) _calcIdParamList
855 * Method getCalcIdParam.Returns the contents of the collection in an Array.
857 * Note: Just in case the collection contents are changing in another thread,
858 * we pass a 0-length Array of the correct type into the API call. This way we
859 * <i>know</i> that the Array returned is of exactly the correct length.
861 * @return this collection as an Array
863 public jalview.schemabinding.version2.CalcIdParam[] getCalcIdParam()
865 jalview.schemabinding.version2.CalcIdParam[] array = new jalview.schemabinding.version2.CalcIdParam[0];
866 return (jalview.schemabinding.version2.CalcIdParam[]) this._calcIdParamList
871 * Method getCalcIdParamCount.
873 * @return the size of this collection
875 public int getCalcIdParamCount()
877 return this._calcIdParamList.size();
881 * Returns the value of field 'centreColumnLabels'.
883 * @return the value of field 'CentreColumnLabels'.
885 public boolean getCentreColumnLabels()
887 return this._centreColumnLabels;
891 * Returns the value of field 'consThreshold'.
893 * @return the value of field 'ConsThreshold'.
895 public int getConsThreshold()
897 return this._consThreshold;
901 * Returns the value of field 'conservationSelected'.
903 * @return the value of field 'ConservationSelected'.
905 public boolean getConservationSelected()
907 return this._conservationSelected;
911 * Returns the value of field 'followHighlight'.
913 * @return the value of field 'FollowHighlight'.
915 public boolean getFollowHighlight()
917 return this._followHighlight;
921 * Returns the value of field 'followSelection'.
923 * @return the value of field 'FollowSelection'.
925 public boolean getFollowSelection()
927 return this._followSelection;
931 * Returns the value of field 'fontName'.
933 * @return the value of field 'FontName'.
935 public java.lang.String getFontName()
937 return this._fontName;
941 * Returns the value of field 'fontSize'.
943 * @return the value of field 'FontSize'.
945 public int getFontSize()
947 return this._fontSize;
951 * Returns the value of field 'fontStyle'.
953 * @return the value of field 'FontStyle'.
955 public int getFontStyle()
957 return this._fontStyle;
961 * Returns the value of field 'gatheredViews'.
963 * @return the value of field 'GatheredViews'.
965 public boolean getGatheredViews()
967 return this._gatheredViews;
971 * Returns the value of field 'height'.
973 * @return the value of field 'Height'.
975 public int getHeight()
981 * Method getHiddenColumns.
984 * @throws java.lang.IndexOutOfBoundsException
985 * if the index given is outside the bounds of the collection
986 * @return the value of the jalview.schemabinding.version2.HiddenColumns at
989 public jalview.schemabinding.version2.HiddenColumns getHiddenColumns(
990 final int index) throws java.lang.IndexOutOfBoundsException
992 // check bounds for index
993 if (index < 0 || index >= this._hiddenColumnsList.size())
995 throw new IndexOutOfBoundsException("getHiddenColumns: Index value '"
996 + index + "' not in range [0.."
997 + (this._hiddenColumnsList.size() - 1) + "]");
1000 return (jalview.schemabinding.version2.HiddenColumns) _hiddenColumnsList
1005 * Method getHiddenColumns.Returns the contents of the collection in an Array.
1007 * Note: Just in case the collection contents are changing in another thread,
1008 * we pass a 0-length Array of the correct type into the API call. This way we
1009 * <i>know</i> that the Array returned is of exactly the correct length.
1011 * @return this collection as an Array
1013 public jalview.schemabinding.version2.HiddenColumns[] getHiddenColumns()
1015 jalview.schemabinding.version2.HiddenColumns[] array = new jalview.schemabinding.version2.HiddenColumns[0];
1016 return (jalview.schemabinding.version2.HiddenColumns[]) this._hiddenColumnsList
1021 * Method getHiddenColumnsCount.
1023 * @return the size of this collection
1025 public int getHiddenColumnsCount()
1027 return this._hiddenColumnsList.size();
1031 * Returns the value of field 'id'. The field 'id' has the following
1032 * description: unique id used by jalview to synchronize between stored and
1033 * instantiated views
1036 * @return the value of field 'Id'.
1038 public java.lang.String getId()
1044 * Returns the value of field 'ignoreGapsinConsensus'.
1046 * @return the value of field 'IgnoreGapsinConsensus'.
1048 public boolean getIgnoreGapsinConsensus()
1050 return this._ignoreGapsinConsensus;
1054 * Returns the value of field 'normaliseSequenceLogo'.
1056 * @return the value of field 'NormaliseSequenceLogo'.
1058 public boolean getNormaliseSequenceLogo()
1060 return this._normaliseSequenceLogo;
1064 * Returns the value of field 'pidSelected'.
1066 * @return the value of field 'PidSelected'.
1068 public boolean getPidSelected()
1070 return this._pidSelected;
1074 * Returns the value of field 'pidThreshold'.
1076 * @return the value of field 'PidThreshold'.
1078 public int getPidThreshold()
1080 return this._pidThreshold;
1084 * Returns the value of field 'renderGaps'.
1086 * @return the value of field 'RenderGaps'.
1088 public boolean getRenderGaps()
1090 return this._renderGaps;
1094 * Returns the value of field 'rightAlignIds'.
1096 * @return the value of field 'RightAlignIds'.
1098 public boolean getRightAlignIds()
1100 return this._rightAlignIds;
1104 * Returns the value of field 'sequenceSetId'.
1106 * @return the value of field 'SequenceSetId'.
1108 public java.lang.String getSequenceSetId()
1110 return this._sequenceSetId;
1114 * Returns the value of field 'showAnnotation'.
1116 * @return the value of field 'ShowAnnotation'.
1118 public boolean getShowAnnotation()
1120 return this._showAnnotation;
1124 * Returns the value of field 'showBoxes'.
1126 * @return the value of field 'ShowBoxes'.
1128 public boolean getShowBoxes()
1130 return this._showBoxes;
1134 * Returns the value of field 'showColourText'.
1136 * @return the value of field 'ShowColourText'.
1138 public boolean getShowColourText()
1140 return this._showColourText;
1144 * Returns the value of field 'showConsensusHistogram'.
1146 * @return the value of field 'ShowConsensusHistogram'.
1148 public boolean getShowConsensusHistogram()
1150 return this._showConsensusHistogram;
1154 * Returns the value of field 'showDbRefTooltip'.
1156 * @return the value of field 'ShowDbRefTooltip'.
1158 public boolean getShowDbRefTooltip()
1160 return this._showDbRefTooltip;
1164 * Returns the value of field 'showFullId'.
1166 * @return the value of field 'ShowFullId'.
1168 public boolean getShowFullId()
1170 return this._showFullId;
1174 * Returns the value of field 'showGroupConsensus'.
1176 * @return the value of field 'ShowGroupConsensus'.
1178 public boolean getShowGroupConsensus()
1180 return this._showGroupConsensus;
1184 * Returns the value of field 'showGroupConservation'.
1186 * @return the value of field 'ShowGroupConservation'.
1188 public boolean getShowGroupConservation()
1190 return this._showGroupConservation;
1194 * Returns the value of field 'showNPfeatureTooltip'.
1196 * @return the value of field 'ShowNPfeatureTooltip'.
1198 public boolean getShowNPfeatureTooltip()
1200 return this._showNPfeatureTooltip;
1204 * Returns the value of field 'showSequenceFeatures'.
1206 * @return the value of field 'ShowSequenceFeatures'.
1208 public boolean getShowSequenceFeatures()
1210 return this._showSequenceFeatures;
1214 * Returns the value of field 'showSequenceLogo'.
1216 * @return the value of field 'ShowSequenceLogo'.
1218 public boolean getShowSequenceLogo()
1220 return this._showSequenceLogo;
1224 * Returns the value of field 'showText'.
1226 * @return the value of field 'ShowText'.
1228 public boolean getShowText()
1230 return this._showText;
1234 * Returns the value of field 'showUnconserved'.
1236 * @return the value of field 'ShowUnconserved'.
1238 public boolean getShowUnconserved()
1240 return this._showUnconserved;
1244 * Returns the value of field 'startRes'.
1246 * @return the value of field 'StartRes'.
1248 public int getStartRes()
1250 return this._startRes;
1254 * Returns the value of field 'startSeq'.
1256 * @return the value of field 'StartSeq'.
1258 public int getStartSeq()
1260 return this._startSeq;
1264 * Returns the value of field 'textCol1'.
1266 * @return the value of field 'TextCol1'.
1268 public int getTextCol1()
1270 return this._textCol1;
1274 * Returns the value of field 'textCol2'.
1276 * @return the value of field 'TextCol2'.
1278 public int getTextCol2()
1280 return this._textCol2;
1284 * Returns the value of field 'textColThreshold'.
1286 * @return the value of field 'TextColThreshold'.
1288 public int getTextColThreshold()
1290 return this._textColThreshold;
1294 * Returns the value of field 'title'.
1296 * @return the value of field 'Title'.
1298 public java.lang.String getTitle()
1304 * Returns the value of field 'viewName'.
1306 * @return the value of field 'ViewName'.
1308 public java.lang.String getViewName()
1310 return this._viewName;
1314 * Returns the value of field 'width'.
1316 * @return the value of field 'Width'.
1318 public int getWidth()
1324 * Returns the value of field 'wrapAlignment'.
1326 * @return the value of field 'WrapAlignment'.
1328 public boolean getWrapAlignment()
1330 return this._wrapAlignment;
1334 * Returns the value of field 'xpos'.
1336 * @return the value of field 'Xpos'.
1338 public int getXpos()
1344 * Returns the value of field 'ypos'.
1346 * @return the value of field 'Ypos'.
1348 public int getYpos()
1354 * Method hasCentreColumnLabels.
1356 * @return true if at least one CentreColumnLabels has been adde
1358 public boolean hasCentreColumnLabels()
1360 return this._has_centreColumnLabels;
1364 * Method hasConsThreshold.
1366 * @return true if at least one ConsThreshold has been added
1368 public boolean hasConsThreshold()
1370 return this._has_consThreshold;
1374 * Method hasConservationSelected.
1376 * @return true if at least one ConservationSelected has been added
1378 public boolean hasConservationSelected()
1380 return this._has_conservationSelected;
1384 * Method hasFollowHighlight.
1386 * @return true if at least one FollowHighlight has been added
1388 public boolean hasFollowHighlight()
1390 return this._has_followHighlight;
1394 * Method hasFollowSelection.
1396 * @return true if at least one FollowSelection has been added
1398 public boolean hasFollowSelection()
1400 return this._has_followSelection;
1404 * Method hasFontSize.
1406 * @return true if at least one FontSize has been added
1408 public boolean hasFontSize()
1410 return this._has_fontSize;
1414 * Method hasFontStyle.
1416 * @return true if at least one FontStyle has been added
1418 public boolean hasFontStyle()
1420 return this._has_fontStyle;
1424 * Method hasGatheredViews.
1426 * @return true if at least one GatheredViews has been added
1428 public boolean hasGatheredViews()
1430 return this._has_gatheredViews;
1436 * @return true if at least one Height has been added
1438 public boolean hasHeight()
1440 return this._has_height;
1444 * Method hasIgnoreGapsinConsensus.
1446 * @return true if at least one IgnoreGapsinConsensus has been added
1448 public boolean hasIgnoreGapsinConsensus()
1450 return this._has_ignoreGapsinConsensus;
1454 * Method hasNormaliseSequenceLogo.
1456 * @return true if at least one NormaliseSequenceLogo has been added
1458 public boolean hasNormaliseSequenceLogo()
1460 return this._has_normaliseSequenceLogo;
1464 * Method hasPidSelected.
1466 * @return true if at least one PidSelected has been added
1468 public boolean hasPidSelected()
1470 return this._has_pidSelected;
1474 * Method hasPidThreshold.
1476 * @return true if at least one PidThreshold has been added
1478 public boolean hasPidThreshold()
1480 return this._has_pidThreshold;
1484 * Method hasRenderGaps.
1486 * @return true if at least one RenderGaps has been added
1488 public boolean hasRenderGaps()
1490 return this._has_renderGaps;
1494 * Method hasRightAlignIds.
1496 * @return true if at least one RightAlignIds has been added
1498 public boolean hasRightAlignIds()
1500 return this._has_rightAlignIds;
1504 * Method hasShowAnnotation.
1506 * @return true if at least one ShowAnnotation has been added
1508 public boolean hasShowAnnotation()
1510 return this._has_showAnnotation;
1514 * Method hasShowBoxes.
1516 * @return true if at least one ShowBoxes has been added
1518 public boolean hasShowBoxes()
1520 return this._has_showBoxes;
1524 * Method hasShowColourText.
1526 * @return true if at least one ShowColourText has been added
1528 public boolean hasShowColourText()
1530 return this._has_showColourText;
1534 * Method hasShowConsensusHistogram.
1536 * @return true if at least one ShowConsensusHistogram has been added
1538 public boolean hasShowConsensusHistogram()
1540 return this._has_showConsensusHistogram;
1544 * Method hasShowDbRefTooltip.
1546 * @return true if at least one ShowDbRefTooltip has been added
1548 public boolean hasShowDbRefTooltip()
1550 return this._has_showDbRefTooltip;
1554 * Method hasShowFullId.
1556 * @return true if at least one ShowFullId has been added
1558 public boolean hasShowFullId()
1560 return this._has_showFullId;
1564 * Method hasShowGroupConsensus.
1566 * @return true if at least one ShowGroupConsensus has been adde
1568 public boolean hasShowGroupConsensus()
1570 return this._has_showGroupConsensus;
1574 * Method hasShowGroupConservation.
1576 * @return true if at least one ShowGroupConservation has been added
1578 public boolean hasShowGroupConservation()
1580 return this._has_showGroupConservation;
1584 * Method hasShowNPfeatureTooltip.
1586 * @return true if at least one ShowNPfeatureTooltip has been added
1588 public boolean hasShowNPfeatureTooltip()
1590 return this._has_showNPfeatureTooltip;
1594 * Method hasShowSequenceFeatures.
1596 * @return true if at least one ShowSequenceFeatures has been added
1598 public boolean hasShowSequenceFeatures()
1600 return this._has_showSequenceFeatures;
1604 * Method hasShowSequenceLogo.
1606 * @return true if at least one ShowSequenceLogo has been added
1608 public boolean hasShowSequenceLogo()
1610 return this._has_showSequenceLogo;
1614 * Method hasShowText.
1616 * @return true if at least one ShowText has been added
1618 public boolean hasShowText()
1620 return this._has_showText;
1624 * Method hasShowUnconserved.
1626 * @return true if at least one ShowUnconserved has been added
1628 public boolean hasShowUnconserved()
1630 return this._has_showUnconserved;
1634 * Method hasStartRes.
1636 * @return true if at least one StartRes has been added
1638 public boolean hasStartRes()
1640 return this._has_startRes;
1644 * Method hasStartSeq.
1646 * @return true if at least one StartSeq has been added
1648 public boolean hasStartSeq()
1650 return this._has_startSeq;
1654 * Method hasTextCol1.
1656 * @return true if at least one TextCol1 has been added
1658 public boolean hasTextCol1()
1660 return this._has_textCol1;
1664 * Method hasTextCol2.
1666 * @return true if at least one TextCol2 has been added
1668 public boolean hasTextCol2()
1670 return this._has_textCol2;
1674 * Method hasTextColThreshold.
1676 * @return true if at least one TextColThreshold has been added
1678 public boolean hasTextColThreshold()
1680 return this._has_textColThreshold;
1686 * @return true if at least one Width has been added
1688 public boolean hasWidth()
1690 return this._has_width;
1694 * Method hasWrapAlignment.
1696 * @return true if at least one WrapAlignment has been added
1698 public boolean hasWrapAlignment()
1700 return this._has_wrapAlignment;
1706 * @return true if at least one Xpos has been added
1708 public boolean hasXpos()
1710 return this._has_xpos;
1716 * @return true if at least one Ypos has been added
1718 public boolean hasYpos()
1720 return this._has_ypos;
1724 * Returns the value of field 'centreColumnLabels'.
1726 * @return the value of field 'CentreColumnLabels'.
1728 public boolean isCentreColumnLabels()
1730 return this._centreColumnLabels;
1734 * Returns the value of field 'conservationSelected'.
1736 * @return the value of field 'ConservationSelected'.
1738 public boolean isConservationSelected()
1740 return this._conservationSelected;
1744 * Returns the value of field 'followHighlight'.
1746 * @return the value of field 'FollowHighlight'.
1748 public boolean isFollowHighlight()
1750 return this._followHighlight;
1754 * Returns the value of field 'followSelection'.
1756 * @return the value of field 'FollowSelection'.
1758 public boolean isFollowSelection()
1760 return this._followSelection;
1764 * Returns the value of field 'gatheredViews'.
1766 * @return the value of field 'GatheredViews'.
1768 public boolean isGatheredViews()
1770 return this._gatheredViews;
1774 * Returns the value of field 'ignoreGapsinConsensus'.
1776 * @return the value of field 'IgnoreGapsinConsensus'.
1778 public boolean isIgnoreGapsinConsensus()
1780 return this._ignoreGapsinConsensus;
1784 * Returns the value of field 'normaliseSequenceLogo'.
1786 * @return the value of field 'NormaliseSequenceLogo'.
1788 public boolean isNormaliseSequenceLogo()
1790 return this._normaliseSequenceLogo;
1794 * Returns the value of field 'pidSelected'.
1796 * @return the value of field 'PidSelected'.
1798 public boolean isPidSelected()
1800 return this._pidSelected;
1804 * Returns the value of field 'renderGaps'.
1806 * @return the value of field 'RenderGaps'.
1808 public boolean isRenderGaps()
1810 return this._renderGaps;
1814 * Returns the value of field 'rightAlignIds'.
1816 * @return the value of field 'RightAlignIds'.
1818 public boolean isRightAlignIds()
1820 return this._rightAlignIds;
1824 * Returns the value of field 'showAnnotation'.
1826 * @return the value of field 'ShowAnnotation'.
1828 public boolean isShowAnnotation()
1830 return this._showAnnotation;
1834 * Returns the value of field 'showBoxes'.
1836 * @return the value of field 'ShowBoxes'.
1838 public boolean isShowBoxes()
1840 return this._showBoxes;
1844 * Returns the value of field 'showColourText'.
1846 * @return the value of field 'ShowColourText'.
1848 public boolean isShowColourText()
1850 return this._showColourText;
1854 * Returns the value of field 'showConsensusHistogram'.
1856 * @return the value of field 'ShowConsensusHistogram'.
1858 public boolean isShowConsensusHistogram()
1860 return this._showConsensusHistogram;
1864 * Returns the value of field 'showDbRefTooltip'.
1866 * @return the value of field 'ShowDbRefTooltip'.
1868 public boolean isShowDbRefTooltip()
1870 return this._showDbRefTooltip;
1874 * Returns the value of field 'showFullId'.
1876 * @return the value of field 'ShowFullId'.
1878 public boolean isShowFullId()
1880 return this._showFullId;
1884 * Returns the value of field 'showGroupConsensus'.
1886 * @return the value of field 'ShowGroupConsensus'.
1888 public boolean isShowGroupConsensus()
1890 return this._showGroupConsensus;
1894 * Returns the value of field 'showGroupConservation'.
1896 * @return the value of field 'ShowGroupConservation'.
1898 public boolean isShowGroupConservation()
1900 return this._showGroupConservation;
1904 * Returns the value of field 'showNPfeatureTooltip'.
1906 * @return the value of field 'ShowNPfeatureTooltip'.
1908 public boolean isShowNPfeatureTooltip()
1910 return this._showNPfeatureTooltip;
1914 * Returns the value of field 'showSequenceFeatures'.
1916 * @return the value of field 'ShowSequenceFeatures'.
1918 public boolean isShowSequenceFeatures()
1920 return this._showSequenceFeatures;
1924 * Returns the value of field 'showSequenceLogo'.
1926 * @return the value of field 'ShowSequenceLogo'.
1928 public boolean isShowSequenceLogo()
1930 return this._showSequenceLogo;
1934 * Returns the value of field 'showText'.
1936 * @return the value of field 'ShowText'.
1938 public boolean isShowText()
1940 return this._showText;
1944 * Returns the value of field 'showUnconserved'.
1946 * @return the value of field 'ShowUnconserved'.
1948 public boolean isShowUnconserved()
1950 return this._showUnconserved;
1956 * @return true if this object is valid according to the schema
1958 public boolean isValid()
1963 } catch (org.exolab.castor.xml.ValidationException vex)
1971 * Returns the value of field 'wrapAlignment'.
1973 * @return the value of field 'WrapAlignment'.
1975 public boolean isWrapAlignment()
1977 return this._wrapAlignment;
1984 * @throws org.exolab.castor.xml.MarshalException
1985 * if object is null or if any SAXException is thrown during
1987 * @throws org.exolab.castor.xml.ValidationException
1988 * if this object is an invalid instance according to the schema
1990 public void marshal(final java.io.Writer out)
1991 throws org.exolab.castor.xml.MarshalException,
1992 org.exolab.castor.xml.ValidationException
1994 Marshaller.marshal(this, out);
2001 * @throws java.io.IOException
2002 * if an IOException occurs during marshaling
2003 * @throws org.exolab.castor.xml.ValidationException
2004 * if this object is an invalid instance according to the schema
2005 * @throws org.exolab.castor.xml.MarshalException
2006 * if object is null or if any SAXException is thrown during
2009 public void marshal(final org.xml.sax.ContentHandler handler)
2010 throws java.io.IOException,
2011 org.exolab.castor.xml.MarshalException,
2012 org.exolab.castor.xml.ValidationException
2014 Marshaller.marshal(this, handler);
2019 public void removeAllCalcIdParam()
2021 this._calcIdParamList.clear();
2026 public void removeAllHiddenColumns()
2028 this._hiddenColumnsList.clear();
2032 * Method removeCalcIdParam.
2034 * @param vCalcIdParam
2035 * @return true if the object was removed from the collection.
2037 public boolean removeCalcIdParam(
2038 final jalview.schemabinding.version2.CalcIdParam vCalcIdParam)
2040 boolean removed = _calcIdParamList.remove(vCalcIdParam);
2045 * Method removeCalcIdParamAt.
2048 * @return the element removed from the collection
2050 public jalview.schemabinding.version2.CalcIdParam removeCalcIdParamAt(
2053 java.lang.Object obj = this._calcIdParamList.remove(index);
2054 return (jalview.schemabinding.version2.CalcIdParam) obj;
2058 * Method removeHiddenColumns.
2060 * @param vHiddenColumns
2061 * @return true if the object was removed from the collection.
2063 public boolean removeHiddenColumns(
2064 final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)
2066 boolean removed = _hiddenColumnsList.remove(vHiddenColumns);
2071 * Method removeHiddenColumnsAt.
2074 * @return the element removed from the collection
2076 public jalview.schemabinding.version2.HiddenColumns removeHiddenColumnsAt(
2079 java.lang.Object obj = this._hiddenColumnsList.remove(index);
2080 return (jalview.schemabinding.version2.HiddenColumns) obj;
2084 * Sets the value of field 'annotationColours'.
2086 * @param annotationColours
2087 * the value of field 'annotationColours'.
2089 public void setAnnotationColours(
2090 final jalview.schemabinding.version2.AnnotationColours annotationColours)
2092 this._annotationColours = annotationColours;
2096 * Sets the value of field 'bgColour'.
2099 * the value of field 'bgColour'.
2101 public void setBgColour(final java.lang.String bgColour)
2103 this._bgColour = bgColour;
2110 * @param vCalcIdParam
2111 * @throws java.lang.IndexOutOfBoundsException
2112 * if the index given is outside the bounds of the collection
2114 public void setCalcIdParam(final int index,
2115 final jalview.schemabinding.version2.CalcIdParam vCalcIdParam)
2116 throws java.lang.IndexOutOfBoundsException
2118 // check bounds for index
2119 if (index < 0 || index >= this._calcIdParamList.size())
2121 throw new IndexOutOfBoundsException("setCalcIdParam: Index value '"
2122 + index + "' not in range [0.."
2123 + (this._calcIdParamList.size() - 1) + "]");
2126 this._calcIdParamList.set(index, vCalcIdParam);
2132 * @param vCalcIdParamArray
2134 public void setCalcIdParam(
2135 final jalview.schemabinding.version2.CalcIdParam[] vCalcIdParamArray)
2138 _calcIdParamList.clear();
2140 for (int i = 0; i < vCalcIdParamArray.length; i++)
2142 this._calcIdParamList.add(vCalcIdParamArray[i]);
2147 * Sets the value of field 'centreColumnLabels'.
2149 * @param centreColumnLabels
2150 * the value of field 'centreColumnLabels'.
2152 public void setCentreColumnLabels(final boolean centreColumnLabels)
2154 this._centreColumnLabels = centreColumnLabels;
2155 this._has_centreColumnLabels = true;
2159 * Sets the value of field 'consThreshold'.
2161 * @param consThreshold
2162 * the value of field 'consThreshold'.
2164 public void setConsThreshold(final int consThreshold)
2166 this._consThreshold = consThreshold;
2167 this._has_consThreshold = true;
2171 * Sets the value of field 'conservationSelected'.
2173 * @param conservationSelected
2174 * the value of field 'conservationSelected'.
2176 public void setConservationSelected(final boolean conservationSelected)
2178 this._conservationSelected = conservationSelected;
2179 this._has_conservationSelected = true;
2183 * Sets the value of field 'followHighlight'.
2185 * @param followHighlight
2186 * the value of field 'followHighlight'.
2188 public void setFollowHighlight(final boolean followHighlight)
2190 this._followHighlight = followHighlight;
2191 this._has_followHighlight = true;
2195 * Sets the value of field 'followSelection'.
2197 * @param followSelection
2198 * the value of field 'followSelection'.
2200 public void setFollowSelection(final boolean followSelection)
2202 this._followSelection = followSelection;
2203 this._has_followSelection = true;
2207 * Sets the value of field 'fontName'.
2210 * the value of field 'fontName'.
2212 public void setFontName(final java.lang.String fontName)
2214 this._fontName = fontName;
2218 * Sets the value of field 'fontSize'.
2221 * the value of field 'fontSize'.
2223 public void setFontSize(final int fontSize)
2225 this._fontSize = fontSize;
2226 this._has_fontSize = true;
2230 * Sets the value of field 'fontStyle'.
2233 * the value of field 'fontStyle'.
2235 public void setFontStyle(final int fontStyle)
2237 this._fontStyle = fontStyle;
2238 this._has_fontStyle = true;
2242 * Sets the value of field 'gatheredViews'.
2244 * @param gatheredViews
2245 * the value of field 'gatheredViews'.
2247 public void setGatheredViews(final boolean gatheredViews)
2249 this._gatheredViews = gatheredViews;
2250 this._has_gatheredViews = true;
2254 * Sets the value of field 'height'.
2257 * the value of field 'height'.
2259 public void setHeight(final int height)
2261 this._height = height;
2262 this._has_height = true;
2269 * @param vHiddenColumns
2270 * @throws java.lang.IndexOutOfBoundsException
2271 * if the index given is outside the bounds of the collection
2273 public void setHiddenColumns(final int index,
2274 final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)
2275 throws java.lang.IndexOutOfBoundsException
2277 // check bounds for index
2278 if (index < 0 || index >= this._hiddenColumnsList.size())
2280 throw new IndexOutOfBoundsException("setHiddenColumns: Index value '"
2281 + index + "' not in range [0.."
2282 + (this._hiddenColumnsList.size() - 1) + "]");
2285 this._hiddenColumnsList.set(index, vHiddenColumns);
2291 * @param vHiddenColumnsArray
2293 public void setHiddenColumns(
2294 final jalview.schemabinding.version2.HiddenColumns[] vHiddenColumnsArray)
2297 _hiddenColumnsList.clear();
2299 for (int i = 0; i < vHiddenColumnsArray.length; i++)
2301 this._hiddenColumnsList.add(vHiddenColumnsArray[i]);
2306 * Sets the value of field 'id'. The field 'id' has the following description:
2307 * unique id used by jalview to synchronize between stored and instantiated
2312 * the value of field 'id'.
2314 public void setId(final java.lang.String id)
2320 * Sets the value of field 'ignoreGapsinConsensus'.
2322 * @param ignoreGapsinConsensus
2323 * the value of field 'ignoreGapsinConsensus'.
2325 public void setIgnoreGapsinConsensus(final boolean ignoreGapsinConsensus)
2327 this._ignoreGapsinConsensus = ignoreGapsinConsensus;
2328 this._has_ignoreGapsinConsensus = true;
2332 * Sets the value of field 'normaliseSequenceLogo'.
2334 * @param normaliseSequenceLogo
2335 * the value of field 'normaliseSequenceLogo'.
2337 public void setNormaliseSequenceLogo(final boolean normaliseSequenceLogo)
2339 this._normaliseSequenceLogo = normaliseSequenceLogo;
2340 this._has_normaliseSequenceLogo = true;
2344 * Sets the value of field 'pidSelected'.
2346 * @param pidSelected
2347 * the value of field 'pidSelected'.
2349 public void setPidSelected(final boolean pidSelected)
2351 this._pidSelected = pidSelected;
2352 this._has_pidSelected = true;
2356 * Sets the value of field 'pidThreshold'.
2358 * @param pidThreshold
2359 * the value of field 'pidThreshold'.
2361 public void setPidThreshold(final int pidThreshold)
2363 this._pidThreshold = pidThreshold;
2364 this._has_pidThreshold = true;
2368 * Sets the value of field 'renderGaps'.
2371 * the value of field 'renderGaps'.
2373 public void setRenderGaps(final boolean renderGaps)
2375 this._renderGaps = renderGaps;
2376 this._has_renderGaps = true;
2380 * Sets the value of field 'rightAlignIds'.
2382 * @param rightAlignIds
2383 * the value of field 'rightAlignIds'.
2385 public void setRightAlignIds(final boolean rightAlignIds)
2387 this._rightAlignIds = rightAlignIds;
2388 this._has_rightAlignIds = true;
2392 * Sets the value of field 'sequenceSetId'.
2394 * @param sequenceSetId
2395 * the value of field 'sequenceSetId'.
2397 public void setSequenceSetId(final java.lang.String sequenceSetId)
2399 this._sequenceSetId = sequenceSetId;
2403 * Sets the value of field 'showAnnotation'.
2405 * @param showAnnotation
2406 * the value of field 'showAnnotation'.
2408 public void setShowAnnotation(final boolean showAnnotation)
2410 this._showAnnotation = showAnnotation;
2411 this._has_showAnnotation = true;
2415 * Sets the value of field 'showBoxes'.
2418 * the value of field 'showBoxes'.
2420 public void setShowBoxes(final boolean showBoxes)
2422 this._showBoxes = showBoxes;
2423 this._has_showBoxes = true;
2427 * Sets the value of field 'showColourText'.
2429 * @param showColourText
2430 * the value of field 'showColourText'.
2432 public void setShowColourText(final boolean showColourText)
2434 this._showColourText = showColourText;
2435 this._has_showColourText = true;
2439 * Sets the value of field 'showConsensusHistogram'.
2441 * @param showConsensusHistogram
2442 * the value of field 'showConsensusHistogram'.
2444 public void setShowConsensusHistogram(final boolean showConsensusHistogram)
2446 this._showConsensusHistogram = showConsensusHistogram;
2447 this._has_showConsensusHistogram = true;
2451 * Sets the value of field 'showDbRefTooltip'.
2453 * @param showDbRefTooltip
2454 * the value of field 'showDbRefTooltip'
2456 public void setShowDbRefTooltip(final boolean showDbRefTooltip)
2458 this._showDbRefTooltip = showDbRefTooltip;
2459 this._has_showDbRefTooltip = true;
2463 * Sets the value of field 'showFullId'.
2466 * the value of field 'showFullId'.
2468 public void setShowFullId(final boolean showFullId)
2470 this._showFullId = showFullId;
2471 this._has_showFullId = true;
2475 * Sets the value of field 'showGroupConsensus'.
2477 * @param showGroupConsensus
2478 * the value of field 'showGroupConsensus'.
2480 public void setShowGroupConsensus(final boolean showGroupConsensus)
2482 this._showGroupConsensus = showGroupConsensus;
2483 this._has_showGroupConsensus = true;
2487 * Sets the value of field 'showGroupConservation'.
2489 * @param showGroupConservation
2490 * the value of field 'showGroupConservation'.
2492 public void setShowGroupConservation(final boolean showGroupConservation)
2494 this._showGroupConservation = showGroupConservation;
2495 this._has_showGroupConservation = true;
2499 * Sets the value of field 'showNPfeatureTooltip'.
2501 * @param showNPfeatureTooltip
2502 * the value of field 'showNPfeatureTooltip'.
2504 public void setShowNPfeatureTooltip(final boolean showNPfeatureTooltip)
2506 this._showNPfeatureTooltip = showNPfeatureTooltip;
2507 this._has_showNPfeatureTooltip = true;
2511 * Sets the value of field 'showSequenceFeatures'.
2513 * @param showSequenceFeatures
2514 * the value of field 'showSequenceFeatures'.
2516 public void setShowSequenceFeatures(final boolean showSequenceFeatures)
2518 this._showSequenceFeatures = showSequenceFeatures;
2519 this._has_showSequenceFeatures = true;
2523 * Sets the value of field 'showSequenceLogo'.
2525 * @param showSequenceLogo
2526 * the value of field 'showSequenceLogo'
2528 public void setShowSequenceLogo(final boolean showSequenceLogo)
2530 this._showSequenceLogo = showSequenceLogo;
2531 this._has_showSequenceLogo = true;
2535 * Sets the value of field 'showText'.
2538 * the value of field 'showText'.
2540 public void setShowText(final boolean showText)
2542 this._showText = showText;
2543 this._has_showText = true;
2547 * Sets the value of field 'showUnconserved'.
2549 * @param showUnconserved
2550 * the value of field 'showUnconserved'.
2552 public void setShowUnconserved(final boolean showUnconserved)
2554 this._showUnconserved = showUnconserved;
2555 this._has_showUnconserved = true;
2559 * Sets the value of field 'startRes'.
2562 * the value of field 'startRes'.
2564 public void setStartRes(final int startRes)
2566 this._startRes = startRes;
2567 this._has_startRes = true;
2571 * Sets the value of field 'startSeq'.
2574 * the value of field 'startSeq'.
2576 public void setStartSeq(final int startSeq)
2578 this._startSeq = startSeq;
2579 this._has_startSeq = true;
2583 * Sets the value of field 'textCol1'.
2586 * the value of field 'textCol1'.
2588 public void setTextCol1(final int textCol1)
2590 this._textCol1 = textCol1;
2591 this._has_textCol1 = true;
2595 * Sets the value of field 'textCol2'.
2598 * the value of field 'textCol2'.
2600 public void setTextCol2(final int textCol2)
2602 this._textCol2 = textCol2;
2603 this._has_textCol2 = true;
2607 * Sets the value of field 'textColThreshold'.
2609 * @param textColThreshold
2610 * the value of field 'textColThreshold'
2612 public void setTextColThreshold(final int textColThreshold)
2614 this._textColThreshold = textColThreshold;
2615 this._has_textColThreshold = true;
2619 * Sets the value of field 'title'.
2622 * the value of field 'title'.
2624 public void setTitle(final java.lang.String title)
2626 this._title = title;
2630 * Sets the value of field 'viewName'.
2633 * the value of field 'viewName'.
2635 public void setViewName(final java.lang.String viewName)
2637 this._viewName = viewName;
2641 * Sets the value of field 'width'.
2644 * the value of field 'width'.
2646 public void setWidth(final int width)
2648 this._width = width;
2649 this._has_width = true;
2653 * Sets the value of field 'wrapAlignment'.
2655 * @param wrapAlignment
2656 * the value of field 'wrapAlignment'.
2658 public void setWrapAlignment(final boolean wrapAlignment)
2660 this._wrapAlignment = wrapAlignment;
2661 this._has_wrapAlignment = true;
2665 * Sets the value of field 'xpos'.
2668 * the value of field 'xpos'.
2670 public void setXpos(final int xpos)
2673 this._has_xpos = true;
2677 * Sets the value of field 'ypos'.
2680 * the value of field 'ypos'.
2682 public void setYpos(final int ypos)
2685 this._has_ypos = true;
2692 * @throws org.exolab.castor.xml.MarshalException
2693 * if object is null or if any SAXException is thrown during
2695 * @throws org.exolab.castor.xml.ValidationException
2696 * if this object is an invalid instance according to the schema
2697 * @return the unmarshaled jalview.schemabinding.version2.Viewport
2699 public static jalview.schemabinding.version2.Viewport unmarshal(
2700 final java.io.Reader reader)
2701 throws org.exolab.castor.xml.MarshalException,
2702 org.exolab.castor.xml.ValidationException
2704 return (jalview.schemabinding.version2.Viewport) Unmarshaller
2705 .unmarshal(jalview.schemabinding.version2.Viewport.class,
2712 * @throws org.exolab.castor.xml.ValidationException
2713 * if this object is an invalid instance according to the schema
2715 public void validate() throws org.exolab.castor.xml.ValidationException
2717 org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
2718 validator.validate(this);