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 jalview.util.MessageManager;
29 import org.exolab.castor.xml.Marshaller;
30 import org.exolab.castor.xml.Unmarshaller;
35 * @version $Revision$ $Date$
37 public class Viewport implements java.io.Serializable
40 // --------------------------/
41 // - Class/Member Variables -/
42 // --------------------------/
45 * Field _conservationSelected.
47 private boolean _conservationSelected;
50 * keeps track of state for field: _conservationSelected
52 private boolean _has_conservationSelected;
57 private boolean _pidSelected;
60 * keeps track of state for field: _pidSelected
62 private boolean _has_pidSelected;
67 private java.lang.String _bgColour;
70 * Field _consThreshold.
72 private int _consThreshold;
75 * keeps track of state for field: _consThreshold
77 private boolean _has_consThreshold;
80 * Field _pidThreshold.
82 private int _pidThreshold;
85 * keeps track of state for field: _pidThreshold
87 private boolean _has_pidThreshold;
92 private java.lang.String _title;
97 private boolean _showFullId;
100 * keeps track of state for field: _showFullId
102 private boolean _has_showFullId;
105 * Field _rightAlignIds.
107 private boolean _rightAlignIds;
110 * keeps track of state for field: _rightAlignIds
112 private boolean _has_rightAlignIds;
117 private boolean _showText;
120 * keeps track of state for field: _showText
122 private boolean _has_showText;
125 * Field _showColourText.
127 private boolean _showColourText;
130 * keeps track of state for field: _showColourText
132 private boolean _has_showColourText;
135 * Field _showUnconserved.
137 private boolean _showUnconserved = false;
140 * keeps track of state for field: _showUnconserved
142 private boolean _has_showUnconserved;
147 private boolean _showBoxes;
150 * keeps track of state for field: _showBoxes
152 private boolean _has_showBoxes;
155 * Field _wrapAlignment.
157 private boolean _wrapAlignment;
160 * keeps track of state for field: _wrapAlignment
162 private boolean _has_wrapAlignment;
167 private boolean _renderGaps;
170 * keeps track of state for field: _renderGaps
172 private boolean _has_renderGaps;
175 * Field _showSequenceFeatures.
177 private boolean _showSequenceFeatures;
180 * keeps track of state for field: _showSequenceFeatures
182 private boolean _has_showSequenceFeatures;
185 * Field _showNPfeatureTooltip.
187 private boolean _showNPfeatureTooltip;
190 * keeps track of state for field: _showNPfeatureTooltip
192 private boolean _has_showNPfeatureTooltip;
195 * Field _showDbRefTooltip.
197 private boolean _showDbRefTooltip;
200 * keeps track of state for field: _showDbRefTooltip
202 private boolean _has_showDbRefTooltip;
205 * Field _followHighlight.
207 private boolean _followHighlight = true;
210 * keeps track of state for field: _followHighlight
212 private boolean _has_followHighlight;
215 * Field _followSelection.
217 private boolean _followSelection = true;
220 * keeps track of state for field: _followSelection
222 private boolean _has_followSelection;
225 * Field _showAnnotation.
227 private boolean _showAnnotation;
230 * keeps track of state for field: _showAnnotation
232 private boolean _has_showAnnotation;
235 * Field _centreColumnLabels.
237 private boolean _centreColumnLabels = false;
240 * keeps track of state for field: _centreColumnLabels
242 private boolean _has_centreColumnLabels;
245 * Field _showGroupConservation.
247 private boolean _showGroupConservation = false;
250 * keeps track of state for field: _showGroupConservation
252 private boolean _has_showGroupConservation;
255 * Field _showGroupConsensus.
257 private boolean _showGroupConsensus = false;
260 * keeps track of state for field: _showGroupConsensus
262 private boolean _has_showGroupConsensus;
265 * Field _showConsensusHistogram.
267 private boolean _showConsensusHistogram = true;
270 * keeps track of state for field: _showConsensusHistogram
272 private boolean _has_showConsensusHistogram;
275 * Field _showSequenceLogo.
277 private boolean _showSequenceLogo = false;
280 * keeps track of state for field: _showSequenceLogo
282 private boolean _has_showSequenceLogo;
285 * Field _normaliseSequenceLogo.
287 private boolean _normaliseSequenceLogo = false;
290 * keeps track of state for field: _normaliseSequenceLogo
292 private boolean _has_normaliseSequenceLogo;
295 * Field _ignoreGapsinConsensus.
297 private boolean _ignoreGapsinConsensus = true;
300 * keeps track of state for field: _ignoreGapsinConsensus
302 private boolean _has_ignoreGapsinConsensus;
307 private int _startRes;
310 * keeps track of state for field: _startRes
312 private boolean _has_startRes;
317 private int _startSeq;
320 * keeps track of state for field: _startSeq
322 private boolean _has_startSeq;
327 private java.lang.String _fontName;
332 private int _fontSize;
335 * keeps track of state for field: _fontSize
337 private boolean _has_fontSize;
342 private int _fontStyle;
345 * keeps track of state for field: _fontStyle
347 private boolean _has_fontStyle;
352 private java.lang.String _viewName;
355 * Field _sequenceSetId.
357 private java.lang.String _sequenceSetId;
360 * Field _gatheredViews.
362 private boolean _gatheredViews;
365 * keeps track of state for field: _gatheredViews
367 private boolean _has_gatheredViews;
372 private int _textCol1;
375 * keeps track of state for field: _textCol1
377 private boolean _has_textCol1;
382 private int _textCol2;
385 * keeps track of state for field: _textCol2
387 private boolean _has_textCol2;
390 * Field _textColThreshold.
392 private int _textColThreshold;
395 * keeps track of state for field: _textColThreshold
397 private boolean _has_textColThreshold;
400 * unique id used by jalview to synchronize between stored and instantiated
404 private java.lang.String _id;
412 * keeps track of state for field: _width
414 private boolean _has_width;
422 * keeps track of state for field: _height
424 private boolean _has_height;
432 * keeps track of state for field: _xpos
434 private boolean _has_xpos;
442 * keeps track of state for field: _ypos
444 private boolean _has_ypos;
447 * Field _annotationColours.
449 private jalview.schemabinding.version2.AnnotationColours _annotationColours;
452 * Field _hiddenColumnsList.
454 private java.util.Vector _hiddenColumnsList;
457 * Field _calcIdParamList.
459 private java.util.Vector _calcIdParamList;
468 this._hiddenColumnsList = new java.util.Vector();
469 this._calcIdParamList = new java.util.Vector();
479 * @param vCalcIdParam
480 * @throws java.lang.IndexOutOfBoundsException
481 * if the index given is outside the bounds of the collection
483 public void addCalcIdParam(
484 final jalview.schemabinding.version2.CalcIdParam vCalcIdParam)
485 throws java.lang.IndexOutOfBoundsException
487 this._calcIdParamList.addElement(vCalcIdParam);
494 * @param vCalcIdParam
495 * @throws java.lang.IndexOutOfBoundsException
496 * if the index given is outside the bounds of the collection
498 public void addCalcIdParam(final int index,
499 final jalview.schemabinding.version2.CalcIdParam vCalcIdParam)
500 throws java.lang.IndexOutOfBoundsException
502 this._calcIdParamList.add(index, vCalcIdParam);
508 * @param vHiddenColumns
509 * @throws java.lang.IndexOutOfBoundsException
510 * if the index given is outside the bounds of the collection
512 public void addHiddenColumns(
513 final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)
514 throws java.lang.IndexOutOfBoundsException
516 this._hiddenColumnsList.addElement(vHiddenColumns);
523 * @param vHiddenColumns
524 * @throws java.lang.IndexOutOfBoundsException
525 * if the index given is outside the bounds of the collection
527 public void addHiddenColumns(final int index,
528 final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)
529 throws java.lang.IndexOutOfBoundsException
531 this._hiddenColumnsList.add(index, vHiddenColumns);
536 public void deleteCentreColumnLabels()
538 this._has_centreColumnLabels = false;
543 public void deleteConsThreshold()
545 this._has_consThreshold = false;
550 public void deleteConservationSelected()
552 this._has_conservationSelected = false;
557 public void deleteFollowHighlight()
559 this._has_followHighlight = false;
564 public void deleteFollowSelection()
566 this._has_followSelection = false;
571 public void deleteFontSize()
573 this._has_fontSize = false;
578 public void deleteFontStyle()
580 this._has_fontStyle = false;
585 public void deleteGatheredViews()
587 this._has_gatheredViews = false;
592 public void deleteHeight()
594 this._has_height = false;
599 public void deleteIgnoreGapsinConsensus()
601 this._has_ignoreGapsinConsensus = false;
606 public void deleteNormaliseSequenceLogo()
608 this._has_normaliseSequenceLogo = false;
613 public void deletePidSelected()
615 this._has_pidSelected = false;
620 public void deletePidThreshold()
622 this._has_pidThreshold = false;
627 public void deleteRenderGaps()
629 this._has_renderGaps = false;
634 public void deleteRightAlignIds()
636 this._has_rightAlignIds = false;
641 public void deleteShowAnnotation()
643 this._has_showAnnotation = false;
648 public void deleteShowBoxes()
650 this._has_showBoxes = false;
655 public void deleteShowColourText()
657 this._has_showColourText = false;
662 public void deleteShowConsensusHistogram()
664 this._has_showConsensusHistogram = false;
669 public void deleteShowDbRefTooltip()
671 this._has_showDbRefTooltip = false;
676 public void deleteShowFullId()
678 this._has_showFullId = false;
683 public void deleteShowGroupConsensus()
685 this._has_showGroupConsensus = false;
690 public void deleteShowGroupConservation()
692 this._has_showGroupConservation = false;
697 public void deleteShowNPfeatureTooltip()
699 this._has_showNPfeatureTooltip = false;
704 public void deleteShowSequenceFeatures()
706 this._has_showSequenceFeatures = false;
711 public void deleteShowSequenceLogo()
713 this._has_showSequenceLogo = false;
718 public void deleteShowText()
720 this._has_showText = false;
725 public void deleteShowUnconserved()
727 this._has_showUnconserved = false;
732 public void deleteStartRes()
734 this._has_startRes = false;
739 public void deleteStartSeq()
741 this._has_startSeq = false;
746 public void deleteTextCol1()
748 this._has_textCol1 = false;
753 public void deleteTextCol2()
755 this._has_textCol2 = false;
760 public void deleteTextColThreshold()
762 this._has_textColThreshold = false;
767 public void deleteWidth()
769 this._has_width = false;
774 public void deleteWrapAlignment()
776 this._has_wrapAlignment = false;
781 public void deleteXpos()
783 this._has_xpos = false;
788 public void deleteYpos()
790 this._has_ypos = false;
794 * Method enumerateCalcIdParam.
796 * @return an Enumeration over all jalview.schemabinding.version2.CalcIdParam
799 public java.util.Enumeration enumerateCalcIdParam()
801 return this._calcIdParamList.elements();
805 * Method enumerateHiddenColumns.
807 * @return an Enumeration over all
808 * jalview.schemabinding.version2.HiddenColumns elements
810 public java.util.Enumeration enumerateHiddenColumns()
812 return this._hiddenColumnsList.elements();
816 * Returns the value of field 'annotationColours'.
818 * @return the value of field 'AnnotationColours'.
820 public jalview.schemabinding.version2.AnnotationColours getAnnotationColours()
822 return this._annotationColours;
826 * Returns the value of field 'bgColour'.
828 * @return the value of field 'BgColour'.
830 public java.lang.String getBgColour()
832 return this._bgColour;
836 * Method getCalcIdParam.
839 * @throws java.lang.IndexOutOfBoundsException
840 * if the index given is outside the bounds of the collection
841 * @return the value of the jalview.schemabinding.version2.CalcIdParam at the
844 public jalview.schemabinding.version2.CalcIdParam getCalcIdParam(
845 final int index) throws java.lang.IndexOutOfBoundsException
847 // check bounds for index
848 if (index < 0 || index >= this._calcIdParamList.size())
850 throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
852 Integer.valueOf(index).toString(),
853 Integer.valueOf((this._calcIdParamList.size() - 1)).toString()
857 return (jalview.schemabinding.version2.CalcIdParam) _calcIdParamList
862 * Method getCalcIdParam.Returns the contents of the collection in an Array.
864 * Note: Just in case the collection contents are changing in another thread,
865 * we pass a 0-length Array of the correct type into the API call. This way we
866 * <i>know</i> that the Array returned is of exactly the correct length.
868 * @return this collection as an Array
870 public jalview.schemabinding.version2.CalcIdParam[] getCalcIdParam()
872 jalview.schemabinding.version2.CalcIdParam[] array = new jalview.schemabinding.version2.CalcIdParam[0];
873 return (jalview.schemabinding.version2.CalcIdParam[]) this._calcIdParamList
878 * Method getCalcIdParamCount.
880 * @return the size of this collection
882 public int getCalcIdParamCount()
884 return this._calcIdParamList.size();
888 * Returns the value of field 'centreColumnLabels'.
890 * @return the value of field 'CentreColumnLabels'.
892 public boolean getCentreColumnLabels()
894 return this._centreColumnLabels;
898 * Returns the value of field 'consThreshold'.
900 * @return the value of field 'ConsThreshold'.
902 public int getConsThreshold()
904 return this._consThreshold;
908 * Returns the value of field 'conservationSelected'.
910 * @return the value of field 'ConservationSelected'.
912 public boolean getConservationSelected()
914 return this._conservationSelected;
918 * Returns the value of field 'followHighlight'.
920 * @return the value of field 'FollowHighlight'.
922 public boolean getFollowHighlight()
924 return this._followHighlight;
928 * Returns the value of field 'followSelection'.
930 * @return the value of field 'FollowSelection'.
932 public boolean getFollowSelection()
934 return this._followSelection;
938 * Returns the value of field 'fontName'.
940 * @return the value of field 'FontName'.
942 public java.lang.String getFontName()
944 return this._fontName;
948 * Returns the value of field 'fontSize'.
950 * @return the value of field 'FontSize'.
952 public int getFontSize()
954 return this._fontSize;
958 * Returns the value of field 'fontStyle'.
960 * @return the value of field 'FontStyle'.
962 public int getFontStyle()
964 return this._fontStyle;
968 * Returns the value of field 'gatheredViews'.
970 * @return the value of field 'GatheredViews'.
972 public boolean getGatheredViews()
974 return this._gatheredViews;
978 * Returns the value of field 'height'.
980 * @return the value of field 'Height'.
982 public int getHeight()
988 * Method getHiddenColumns.
991 * @throws java.lang.IndexOutOfBoundsException
992 * if the index given is outside the bounds of the collection
993 * @return the value of the jalview.schemabinding.version2.HiddenColumns at
996 public jalview.schemabinding.version2.HiddenColumns getHiddenColumns(
997 final int index) throws java.lang.IndexOutOfBoundsException
999 // check bounds for index
1000 if (index < 0 || index >= this._hiddenColumnsList.size())
1002 throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
1004 Integer.valueOf(index).toString(),
1005 Integer.valueOf((this._hiddenColumnsList.size() - 1)).toString()
1009 return (jalview.schemabinding.version2.HiddenColumns) _hiddenColumnsList
1014 * Method getHiddenColumns.Returns the contents of the collection in an Array.
1016 * Note: Just in case the collection contents are changing in another thread,
1017 * we pass a 0-length Array of the correct type into the API call. This way we
1018 * <i>know</i> that the Array returned is of exactly the correct length.
1020 * @return this collection as an Array
1022 public jalview.schemabinding.version2.HiddenColumns[] getHiddenColumns()
1024 jalview.schemabinding.version2.HiddenColumns[] array = new jalview.schemabinding.version2.HiddenColumns[0];
1025 return (jalview.schemabinding.version2.HiddenColumns[]) this._hiddenColumnsList
1030 * Method getHiddenColumnsCount.
1032 * @return the size of this collection
1034 public int getHiddenColumnsCount()
1036 return this._hiddenColumnsList.size();
1040 * Returns the value of field 'id'. The field 'id' has the following
1041 * description: unique id used by jalview to synchronize between stored and
1042 * instantiated views
1045 * @return the value of field 'Id'.
1047 public java.lang.String getId()
1053 * Returns the value of field 'ignoreGapsinConsensus'.
1055 * @return the value of field 'IgnoreGapsinConsensus'.
1057 public boolean getIgnoreGapsinConsensus()
1059 return this._ignoreGapsinConsensus;
1063 * Returns the value of field 'normaliseSequenceLogo'.
1065 * @return the value of field 'NormaliseSequenceLogo'.
1067 public boolean getNormaliseSequenceLogo()
1069 return this._normaliseSequenceLogo;
1073 * Returns the value of field 'pidSelected'.
1075 * @return the value of field 'PidSelected'.
1077 public boolean getPidSelected()
1079 return this._pidSelected;
1083 * Returns the value of field 'pidThreshold'.
1085 * @return the value of field 'PidThreshold'.
1087 public int getPidThreshold()
1089 return this._pidThreshold;
1093 * Returns the value of field 'renderGaps'.
1095 * @return the value of field 'RenderGaps'.
1097 public boolean getRenderGaps()
1099 return this._renderGaps;
1103 * Returns the value of field 'rightAlignIds'.
1105 * @return the value of field 'RightAlignIds'.
1107 public boolean getRightAlignIds()
1109 return this._rightAlignIds;
1113 * Returns the value of field 'sequenceSetId'.
1115 * @return the value of field 'SequenceSetId'.
1117 public java.lang.String getSequenceSetId()
1119 return this._sequenceSetId;
1123 * Returns the value of field 'showAnnotation'.
1125 * @return the value of field 'ShowAnnotation'.
1127 public boolean getShowAnnotation()
1129 return this._showAnnotation;
1133 * Returns the value of field 'showBoxes'.
1135 * @return the value of field 'ShowBoxes'.
1137 public boolean getShowBoxes()
1139 return this._showBoxes;
1143 * Returns the value of field 'showColourText'.
1145 * @return the value of field 'ShowColourText'.
1147 public boolean getShowColourText()
1149 return this._showColourText;
1153 * Returns the value of field 'showConsensusHistogram'.
1155 * @return the value of field 'ShowConsensusHistogram'.
1157 public boolean getShowConsensusHistogram()
1159 return this._showConsensusHistogram;
1163 * Returns the value of field 'showDbRefTooltip'.
1165 * @return the value of field 'ShowDbRefTooltip'.
1167 public boolean getShowDbRefTooltip()
1169 return this._showDbRefTooltip;
1173 * Returns the value of field 'showFullId'.
1175 * @return the value of field 'ShowFullId'.
1177 public boolean getShowFullId()
1179 return this._showFullId;
1183 * Returns the value of field 'showGroupConsensus'.
1185 * @return the value of field 'ShowGroupConsensus'.
1187 public boolean getShowGroupConsensus()
1189 return this._showGroupConsensus;
1193 * Returns the value of field 'showGroupConservation'.
1195 * @return the value of field 'ShowGroupConservation'.
1197 public boolean getShowGroupConservation()
1199 return this._showGroupConservation;
1203 * Returns the value of field 'showNPfeatureTooltip'.
1205 * @return the value of field 'ShowNPfeatureTooltip'.
1207 public boolean getShowNPfeatureTooltip()
1209 return this._showNPfeatureTooltip;
1213 * Returns the value of field 'showSequenceFeatures'.
1215 * @return the value of field 'ShowSequenceFeatures'.
1217 public boolean getShowSequenceFeatures()
1219 return this._showSequenceFeatures;
1223 * Returns the value of field 'showSequenceLogo'.
1225 * @return the value of field 'ShowSequenceLogo'.
1227 public boolean getShowSequenceLogo()
1229 return this._showSequenceLogo;
1233 * Returns the value of field 'showText'.
1235 * @return the value of field 'ShowText'.
1237 public boolean getShowText()
1239 return this._showText;
1243 * Returns the value of field 'showUnconserved'.
1245 * @return the value of field 'ShowUnconserved'.
1247 public boolean getShowUnconserved()
1249 return this._showUnconserved;
1253 * Returns the value of field 'startRes'.
1255 * @return the value of field 'StartRes'.
1257 public int getStartRes()
1259 return this._startRes;
1263 * Returns the value of field 'startSeq'.
1265 * @return the value of field 'StartSeq'.
1267 public int getStartSeq()
1269 return this._startSeq;
1273 * Returns the value of field 'textCol1'.
1275 * @return the value of field 'TextCol1'.
1277 public int getTextCol1()
1279 return this._textCol1;
1283 * Returns the value of field 'textCol2'.
1285 * @return the value of field 'TextCol2'.
1287 public int getTextCol2()
1289 return this._textCol2;
1293 * Returns the value of field 'textColThreshold'.
1295 * @return the value of field 'TextColThreshold'.
1297 public int getTextColThreshold()
1299 return this._textColThreshold;
1303 * Returns the value of field 'title'.
1305 * @return the value of field 'Title'.
1307 public java.lang.String getTitle()
1313 * Returns the value of field 'viewName'.
1315 * @return the value of field 'ViewName'.
1317 public java.lang.String getViewName()
1319 return this._viewName;
1323 * Returns the value of field 'width'.
1325 * @return the value of field 'Width'.
1327 public int getWidth()
1333 * Returns the value of field 'wrapAlignment'.
1335 * @return the value of field 'WrapAlignment'.
1337 public boolean getWrapAlignment()
1339 return this._wrapAlignment;
1343 * Returns the value of field 'xpos'.
1345 * @return the value of field 'Xpos'.
1347 public int getXpos()
1353 * Returns the value of field 'ypos'.
1355 * @return the value of field 'Ypos'.
1357 public int getYpos()
1363 * Method hasCentreColumnLabels.
1365 * @return true if at least one CentreColumnLabels has been adde
1367 public boolean hasCentreColumnLabels()
1369 return this._has_centreColumnLabels;
1373 * Method hasConsThreshold.
1375 * @return true if at least one ConsThreshold has been added
1377 public boolean hasConsThreshold()
1379 return this._has_consThreshold;
1383 * Method hasConservationSelected.
1385 * @return true if at least one ConservationSelected has been added
1387 public boolean hasConservationSelected()
1389 return this._has_conservationSelected;
1393 * Method hasFollowHighlight.
1395 * @return true if at least one FollowHighlight has been added
1397 public boolean hasFollowHighlight()
1399 return this._has_followHighlight;
1403 * Method hasFollowSelection.
1405 * @return true if at least one FollowSelection has been added
1407 public boolean hasFollowSelection()
1409 return this._has_followSelection;
1413 * Method hasFontSize.
1415 * @return true if at least one FontSize has been added
1417 public boolean hasFontSize()
1419 return this._has_fontSize;
1423 * Method hasFontStyle.
1425 * @return true if at least one FontStyle has been added
1427 public boolean hasFontStyle()
1429 return this._has_fontStyle;
1433 * Method hasGatheredViews.
1435 * @return true if at least one GatheredViews has been added
1437 public boolean hasGatheredViews()
1439 return this._has_gatheredViews;
1445 * @return true if at least one Height has been added
1447 public boolean hasHeight()
1449 return this._has_height;
1453 * Method hasIgnoreGapsinConsensus.
1455 * @return true if at least one IgnoreGapsinConsensus has been added
1457 public boolean hasIgnoreGapsinConsensus()
1459 return this._has_ignoreGapsinConsensus;
1463 * Method hasNormaliseSequenceLogo.
1465 * @return true if at least one NormaliseSequenceLogo has been added
1467 public boolean hasNormaliseSequenceLogo()
1469 return this._has_normaliseSequenceLogo;
1473 * Method hasPidSelected.
1475 * @return true if at least one PidSelected has been added
1477 public boolean hasPidSelected()
1479 return this._has_pidSelected;
1483 * Method hasPidThreshold.
1485 * @return true if at least one PidThreshold has been added
1487 public boolean hasPidThreshold()
1489 return this._has_pidThreshold;
1493 * Method hasRenderGaps.
1495 * @return true if at least one RenderGaps has been added
1497 public boolean hasRenderGaps()
1499 return this._has_renderGaps;
1503 * Method hasRightAlignIds.
1505 * @return true if at least one RightAlignIds has been added
1507 public boolean hasRightAlignIds()
1509 return this._has_rightAlignIds;
1513 * Method hasShowAnnotation.
1515 * @return true if at least one ShowAnnotation has been added
1517 public boolean hasShowAnnotation()
1519 return this._has_showAnnotation;
1523 * Method hasShowBoxes.
1525 * @return true if at least one ShowBoxes has been added
1527 public boolean hasShowBoxes()
1529 return this._has_showBoxes;
1533 * Method hasShowColourText.
1535 * @return true if at least one ShowColourText has been added
1537 public boolean hasShowColourText()
1539 return this._has_showColourText;
1543 * Method hasShowConsensusHistogram.
1545 * @return true if at least one ShowConsensusHistogram has been added
1547 public boolean hasShowConsensusHistogram()
1549 return this._has_showConsensusHistogram;
1553 * Method hasShowDbRefTooltip.
1555 * @return true if at least one ShowDbRefTooltip has been added
1557 public boolean hasShowDbRefTooltip()
1559 return this._has_showDbRefTooltip;
1563 * Method hasShowFullId.
1565 * @return true if at least one ShowFullId has been added
1567 public boolean hasShowFullId()
1569 return this._has_showFullId;
1573 * Method hasShowGroupConsensus.
1575 * @return true if at least one ShowGroupConsensus has been adde
1577 public boolean hasShowGroupConsensus()
1579 return this._has_showGroupConsensus;
1583 * Method hasShowGroupConservation.
1585 * @return true if at least one ShowGroupConservation has been added
1587 public boolean hasShowGroupConservation()
1589 return this._has_showGroupConservation;
1593 * Method hasShowNPfeatureTooltip.
1595 * @return true if at least one ShowNPfeatureTooltip has been added
1597 public boolean hasShowNPfeatureTooltip()
1599 return this._has_showNPfeatureTooltip;
1603 * Method hasShowSequenceFeatures.
1605 * @return true if at least one ShowSequenceFeatures has been added
1607 public boolean hasShowSequenceFeatures()
1609 return this._has_showSequenceFeatures;
1613 * Method hasShowSequenceLogo.
1615 * @return true if at least one ShowSequenceLogo has been added
1617 public boolean hasShowSequenceLogo()
1619 return this._has_showSequenceLogo;
1623 * Method hasShowText.
1625 * @return true if at least one ShowText has been added
1627 public boolean hasShowText()
1629 return this._has_showText;
1633 * Method hasShowUnconserved.
1635 * @return true if at least one ShowUnconserved has been added
1637 public boolean hasShowUnconserved()
1639 return this._has_showUnconserved;
1643 * Method hasStartRes.
1645 * @return true if at least one StartRes has been added
1647 public boolean hasStartRes()
1649 return this._has_startRes;
1653 * Method hasStartSeq.
1655 * @return true if at least one StartSeq has been added
1657 public boolean hasStartSeq()
1659 return this._has_startSeq;
1663 * Method hasTextCol1.
1665 * @return true if at least one TextCol1 has been added
1667 public boolean hasTextCol1()
1669 return this._has_textCol1;
1673 * Method hasTextCol2.
1675 * @return true if at least one TextCol2 has been added
1677 public boolean hasTextCol2()
1679 return this._has_textCol2;
1683 * Method hasTextColThreshold.
1685 * @return true if at least one TextColThreshold has been added
1687 public boolean hasTextColThreshold()
1689 return this._has_textColThreshold;
1695 * @return true if at least one Width has been added
1697 public boolean hasWidth()
1699 return this._has_width;
1703 * Method hasWrapAlignment.
1705 * @return true if at least one WrapAlignment has been added
1707 public boolean hasWrapAlignment()
1709 return this._has_wrapAlignment;
1715 * @return true if at least one Xpos has been added
1717 public boolean hasXpos()
1719 return this._has_xpos;
1725 * @return true if at least one Ypos has been added
1727 public boolean hasYpos()
1729 return this._has_ypos;
1733 * Returns the value of field 'centreColumnLabels'.
1735 * @return the value of field 'CentreColumnLabels'.
1737 public boolean isCentreColumnLabels()
1739 return this._centreColumnLabels;
1743 * Returns the value of field 'conservationSelected'.
1745 * @return the value of field 'ConservationSelected'.
1747 public boolean isConservationSelected()
1749 return this._conservationSelected;
1753 * Returns the value of field 'followHighlight'.
1755 * @return the value of field 'FollowHighlight'.
1757 public boolean isFollowHighlight()
1759 return this._followHighlight;
1763 * Returns the value of field 'followSelection'.
1765 * @return the value of field 'FollowSelection'.
1767 public boolean isFollowSelection()
1769 return this._followSelection;
1773 * Returns the value of field 'gatheredViews'.
1775 * @return the value of field 'GatheredViews'.
1777 public boolean isGatheredViews()
1779 return this._gatheredViews;
1783 * Returns the value of field 'ignoreGapsinConsensus'.
1785 * @return the value of field 'IgnoreGapsinConsensus'.
1787 public boolean isIgnoreGapsinConsensus()
1789 return this._ignoreGapsinConsensus;
1793 * Returns the value of field 'normaliseSequenceLogo'.
1795 * @return the value of field 'NormaliseSequenceLogo'.
1797 public boolean isNormaliseSequenceLogo()
1799 return this._normaliseSequenceLogo;
1803 * Returns the value of field 'pidSelected'.
1805 * @return the value of field 'PidSelected'.
1807 public boolean isPidSelected()
1809 return this._pidSelected;
1813 * Returns the value of field 'renderGaps'.
1815 * @return the value of field 'RenderGaps'.
1817 public boolean isRenderGaps()
1819 return this._renderGaps;
1823 * Returns the value of field 'rightAlignIds'.
1825 * @return the value of field 'RightAlignIds'.
1827 public boolean isRightAlignIds()
1829 return this._rightAlignIds;
1833 * Returns the value of field 'showAnnotation'.
1835 * @return the value of field 'ShowAnnotation'.
1837 public boolean isShowAnnotation()
1839 return this._showAnnotation;
1843 * Returns the value of field 'showBoxes'.
1845 * @return the value of field 'ShowBoxes'.
1847 public boolean isShowBoxes()
1849 return this._showBoxes;
1853 * Returns the value of field 'showColourText'.
1855 * @return the value of field 'ShowColourText'.
1857 public boolean isShowColourText()
1859 return this._showColourText;
1863 * Returns the value of field 'showConsensusHistogram'.
1865 * @return the value of field 'ShowConsensusHistogram'.
1867 public boolean isShowConsensusHistogram()
1869 return this._showConsensusHistogram;
1873 * Returns the value of field 'showDbRefTooltip'.
1875 * @return the value of field 'ShowDbRefTooltip'.
1877 public boolean isShowDbRefTooltip()
1879 return this._showDbRefTooltip;
1883 * Returns the value of field 'showFullId'.
1885 * @return the value of field 'ShowFullId'.
1887 public boolean isShowFullId()
1889 return this._showFullId;
1893 * Returns the value of field 'showGroupConsensus'.
1895 * @return the value of field 'ShowGroupConsensus'.
1897 public boolean isShowGroupConsensus()
1899 return this._showGroupConsensus;
1903 * Returns the value of field 'showGroupConservation'.
1905 * @return the value of field 'ShowGroupConservation'.
1907 public boolean isShowGroupConservation()
1909 return this._showGroupConservation;
1913 * Returns the value of field 'showNPfeatureTooltip'.
1915 * @return the value of field 'ShowNPfeatureTooltip'.
1917 public boolean isShowNPfeatureTooltip()
1919 return this._showNPfeatureTooltip;
1923 * Returns the value of field 'showSequenceFeatures'.
1925 * @return the value of field 'ShowSequenceFeatures'.
1927 public boolean isShowSequenceFeatures()
1929 return this._showSequenceFeatures;
1933 * Returns the value of field 'showSequenceLogo'.
1935 * @return the value of field 'ShowSequenceLogo'.
1937 public boolean isShowSequenceLogo()
1939 return this._showSequenceLogo;
1943 * Returns the value of field 'showText'.
1945 * @return the value of field 'ShowText'.
1947 public boolean isShowText()
1949 return this._showText;
1953 * Returns the value of field 'showUnconserved'.
1955 * @return the value of field 'ShowUnconserved'.
1957 public boolean isShowUnconserved()
1959 return this._showUnconserved;
1965 * @return true if this object is valid according to the schema
1967 public boolean isValid()
1972 } catch (org.exolab.castor.xml.ValidationException vex)
1980 * Returns the value of field 'wrapAlignment'.
1982 * @return the value of field 'WrapAlignment'.
1984 public boolean isWrapAlignment()
1986 return this._wrapAlignment;
1993 * @throws org.exolab.castor.xml.MarshalException
1994 * if object is null or if any SAXException is thrown during
1996 * @throws org.exolab.castor.xml.ValidationException
1997 * if this object is an invalid instance according to the schema
1999 public void marshal(final java.io.Writer out)
2000 throws org.exolab.castor.xml.MarshalException,
2001 org.exolab.castor.xml.ValidationException
2003 Marshaller.marshal(this, out);
2010 * @throws java.io.IOException
2011 * if an IOException occurs during marshaling
2012 * @throws org.exolab.castor.xml.ValidationException
2013 * if this object is an invalid instance according to the schema
2014 * @throws org.exolab.castor.xml.MarshalException
2015 * if object is null or if any SAXException is thrown during
2018 public void marshal(final org.xml.sax.ContentHandler handler)
2019 throws java.io.IOException,
2020 org.exolab.castor.xml.MarshalException,
2021 org.exolab.castor.xml.ValidationException
2023 Marshaller.marshal(this, handler);
2028 public void removeAllCalcIdParam()
2030 this._calcIdParamList.clear();
2035 public void removeAllHiddenColumns()
2037 this._hiddenColumnsList.clear();
2041 * Method removeCalcIdParam.
2043 * @param vCalcIdParam
2044 * @return true if the object was removed from the collection.
2046 public boolean removeCalcIdParam(
2047 final jalview.schemabinding.version2.CalcIdParam vCalcIdParam)
2049 boolean removed = _calcIdParamList.remove(vCalcIdParam);
2054 * Method removeCalcIdParamAt.
2057 * @return the element removed from the collection
2059 public jalview.schemabinding.version2.CalcIdParam removeCalcIdParamAt(
2062 java.lang.Object obj = this._calcIdParamList.remove(index);
2063 return (jalview.schemabinding.version2.CalcIdParam) obj;
2067 * Method removeHiddenColumns.
2069 * @param vHiddenColumns
2070 * @return true if the object was removed from the collection.
2072 public boolean removeHiddenColumns(
2073 final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)
2075 boolean removed = _hiddenColumnsList.remove(vHiddenColumns);
2080 * Method removeHiddenColumnsAt.
2083 * @return the element removed from the collection
2085 public jalview.schemabinding.version2.HiddenColumns removeHiddenColumnsAt(
2088 java.lang.Object obj = this._hiddenColumnsList.remove(index);
2089 return (jalview.schemabinding.version2.HiddenColumns) obj;
2093 * Sets the value of field 'annotationColours'.
2095 * @param annotationColours
2096 * the value of field 'annotationColours'.
2098 public void setAnnotationColours(
2099 final jalview.schemabinding.version2.AnnotationColours annotationColours)
2101 this._annotationColours = annotationColours;
2105 * Sets the value of field 'bgColour'.
2108 * the value of field 'bgColour'.
2110 public void setBgColour(final java.lang.String bgColour)
2112 this._bgColour = bgColour;
2119 * @param vCalcIdParam
2120 * @throws java.lang.IndexOutOfBoundsException
2121 * if the index given is outside the bounds of the collection
2123 public void setCalcIdParam(final int index,
2124 final jalview.schemabinding.version2.CalcIdParam vCalcIdParam)
2125 throws java.lang.IndexOutOfBoundsException
2127 // check bounds for index
2128 if (index < 0 || index >= this._calcIdParamList.size())
2130 throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
2132 Integer.valueOf(index).toString(),
2133 Integer.valueOf((this._calcIdParamList.size() - 1)).toString()
2137 this._calcIdParamList.set(index, vCalcIdParam);
2143 * @param vCalcIdParamArray
2145 public void setCalcIdParam(
2146 final jalview.schemabinding.version2.CalcIdParam[] vCalcIdParamArray)
2149 _calcIdParamList.clear();
2151 for (int i = 0; i < vCalcIdParamArray.length; i++)
2153 this._calcIdParamList.add(vCalcIdParamArray[i]);
2158 * Sets the value of field 'centreColumnLabels'.
2160 * @param centreColumnLabels
2161 * the value of field 'centreColumnLabels'.
2163 public void setCentreColumnLabels(final boolean centreColumnLabels)
2165 this._centreColumnLabels = centreColumnLabels;
2166 this._has_centreColumnLabels = true;
2170 * Sets the value of field 'consThreshold'.
2172 * @param consThreshold
2173 * the value of field 'consThreshold'.
2175 public void setConsThreshold(final int consThreshold)
2177 this._consThreshold = consThreshold;
2178 this._has_consThreshold = true;
2182 * Sets the value of field 'conservationSelected'.
2184 * @param conservationSelected
2185 * the value of field 'conservationSelected'.
2187 public void setConservationSelected(final boolean conservationSelected)
2189 this._conservationSelected = conservationSelected;
2190 this._has_conservationSelected = true;
2194 * Sets the value of field 'followHighlight'.
2196 * @param followHighlight
2197 * the value of field 'followHighlight'.
2199 public void setFollowHighlight(final boolean followHighlight)
2201 this._followHighlight = followHighlight;
2202 this._has_followHighlight = true;
2206 * Sets the value of field 'followSelection'.
2208 * @param followSelection
2209 * the value of field 'followSelection'.
2211 public void setFollowSelection(final boolean followSelection)
2213 this._followSelection = followSelection;
2214 this._has_followSelection = true;
2218 * Sets the value of field 'fontName'.
2221 * the value of field 'fontName'.
2223 public void setFontName(final java.lang.String fontName)
2225 this._fontName = fontName;
2229 * Sets the value of field 'fontSize'.
2232 * the value of field 'fontSize'.
2234 public void setFontSize(final int fontSize)
2236 this._fontSize = fontSize;
2237 this._has_fontSize = true;
2241 * Sets the value of field 'fontStyle'.
2244 * the value of field 'fontStyle'.
2246 public void setFontStyle(final int fontStyle)
2248 this._fontStyle = fontStyle;
2249 this._has_fontStyle = true;
2253 * Sets the value of field 'gatheredViews'.
2255 * @param gatheredViews
2256 * the value of field 'gatheredViews'.
2258 public void setGatheredViews(final boolean gatheredViews)
2260 this._gatheredViews = gatheredViews;
2261 this._has_gatheredViews = true;
2265 * Sets the value of field 'height'.
2268 * the value of field 'height'.
2270 public void setHeight(final int height)
2272 this._height = height;
2273 this._has_height = true;
2280 * @param vHiddenColumns
2281 * @throws java.lang.IndexOutOfBoundsException
2282 * if the index given is outside the bounds of the collection
2284 public void setHiddenColumns(final int index,
2285 final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)
2286 throws java.lang.IndexOutOfBoundsException
2288 // check bounds for index
2289 if (index < 0 || index >= this._hiddenColumnsList.size())
2291 throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
2293 Integer.valueOf(index).toString(),
2294 Integer.valueOf((this._hiddenColumnsList.size() - 1)).toString()
2298 this._hiddenColumnsList.set(index, vHiddenColumns);
2304 * @param vHiddenColumnsArray
2306 public void setHiddenColumns(
2307 final jalview.schemabinding.version2.HiddenColumns[] vHiddenColumnsArray)
2310 _hiddenColumnsList.clear();
2312 for (int i = 0; i < vHiddenColumnsArray.length; i++)
2314 this._hiddenColumnsList.add(vHiddenColumnsArray[i]);
2319 * Sets the value of field 'id'. The field 'id' has the following description:
2320 * unique id used by jalview to synchronize between stored and instantiated
2325 * the value of field 'id'.
2327 public void setId(final java.lang.String id)
2333 * Sets the value of field 'ignoreGapsinConsensus'.
2335 * @param ignoreGapsinConsensus
2336 * the value of field 'ignoreGapsinConsensus'.
2338 public void setIgnoreGapsinConsensus(final boolean ignoreGapsinConsensus)
2340 this._ignoreGapsinConsensus = ignoreGapsinConsensus;
2341 this._has_ignoreGapsinConsensus = true;
2345 * Sets the value of field 'normaliseSequenceLogo'.
2347 * @param normaliseSequenceLogo
2348 * the value of field 'normaliseSequenceLogo'.
2350 public void setNormaliseSequenceLogo(final boolean normaliseSequenceLogo)
2352 this._normaliseSequenceLogo = normaliseSequenceLogo;
2353 this._has_normaliseSequenceLogo = true;
2357 * Sets the value of field 'pidSelected'.
2359 * @param pidSelected
2360 * the value of field 'pidSelected'.
2362 public void setPidSelected(final boolean pidSelected)
2364 this._pidSelected = pidSelected;
2365 this._has_pidSelected = true;
2369 * Sets the value of field 'pidThreshold'.
2371 * @param pidThreshold
2372 * the value of field 'pidThreshold'.
2374 public void setPidThreshold(final int pidThreshold)
2376 this._pidThreshold = pidThreshold;
2377 this._has_pidThreshold = true;
2381 * Sets the value of field 'renderGaps'.
2384 * the value of field 'renderGaps'.
2386 public void setRenderGaps(final boolean renderGaps)
2388 this._renderGaps = renderGaps;
2389 this._has_renderGaps = true;
2393 * Sets the value of field 'rightAlignIds'.
2395 * @param rightAlignIds
2396 * the value of field 'rightAlignIds'.
2398 public void setRightAlignIds(final boolean rightAlignIds)
2400 this._rightAlignIds = rightAlignIds;
2401 this._has_rightAlignIds = true;
2405 * Sets the value of field 'sequenceSetId'.
2407 * @param sequenceSetId
2408 * the value of field 'sequenceSetId'.
2410 public void setSequenceSetId(final java.lang.String sequenceSetId)
2412 this._sequenceSetId = sequenceSetId;
2416 * Sets the value of field 'showAnnotation'.
2418 * @param showAnnotation
2419 * the value of field 'showAnnotation'.
2421 public void setShowAnnotation(final boolean showAnnotation)
2423 this._showAnnotation = showAnnotation;
2424 this._has_showAnnotation = true;
2428 * Sets the value of field 'showBoxes'.
2431 * the value of field 'showBoxes'.
2433 public void setShowBoxes(final boolean showBoxes)
2435 this._showBoxes = showBoxes;
2436 this._has_showBoxes = true;
2440 * Sets the value of field 'showColourText'.
2442 * @param showColourText
2443 * the value of field 'showColourText'.
2445 public void setShowColourText(final boolean showColourText)
2447 this._showColourText = showColourText;
2448 this._has_showColourText = true;
2452 * Sets the value of field 'showConsensusHistogram'.
2454 * @param showConsensusHistogram
2455 * the value of field 'showConsensusHistogram'.
2457 public void setShowConsensusHistogram(final boolean showConsensusHistogram)
2459 this._showConsensusHistogram = showConsensusHistogram;
2460 this._has_showConsensusHistogram = true;
2464 * Sets the value of field 'showDbRefTooltip'.
2466 * @param showDbRefTooltip
2467 * the value of field 'showDbRefTooltip'
2469 public void setShowDbRefTooltip(final boolean showDbRefTooltip)
2471 this._showDbRefTooltip = showDbRefTooltip;
2472 this._has_showDbRefTooltip = true;
2476 * Sets the value of field 'showFullId'.
2479 * the value of field 'showFullId'.
2481 public void setShowFullId(final boolean showFullId)
2483 this._showFullId = showFullId;
2484 this._has_showFullId = true;
2488 * Sets the value of field 'showGroupConsensus'.
2490 * @param showGroupConsensus
2491 * the value of field 'showGroupConsensus'.
2493 public void setShowGroupConsensus(final boolean showGroupConsensus)
2495 this._showGroupConsensus = showGroupConsensus;
2496 this._has_showGroupConsensus = true;
2500 * Sets the value of field 'showGroupConservation'.
2502 * @param showGroupConservation
2503 * the value of field 'showGroupConservation'.
2505 public void setShowGroupConservation(final boolean showGroupConservation)
2507 this._showGroupConservation = showGroupConservation;
2508 this._has_showGroupConservation = true;
2512 * Sets the value of field 'showNPfeatureTooltip'.
2514 * @param showNPfeatureTooltip
2515 * the value of field 'showNPfeatureTooltip'.
2517 public void setShowNPfeatureTooltip(final boolean showNPfeatureTooltip)
2519 this._showNPfeatureTooltip = showNPfeatureTooltip;
2520 this._has_showNPfeatureTooltip = true;
2524 * Sets the value of field 'showSequenceFeatures'.
2526 * @param showSequenceFeatures
2527 * the value of field 'showSequenceFeatures'.
2529 public void setShowSequenceFeatures(final boolean showSequenceFeatures)
2531 this._showSequenceFeatures = showSequenceFeatures;
2532 this._has_showSequenceFeatures = true;
2536 * Sets the value of field 'showSequenceLogo'.
2538 * @param showSequenceLogo
2539 * the value of field 'showSequenceLogo'
2541 public void setShowSequenceLogo(final boolean showSequenceLogo)
2543 this._showSequenceLogo = showSequenceLogo;
2544 this._has_showSequenceLogo = true;
2548 * Sets the value of field 'showText'.
2551 * the value of field 'showText'.
2553 public void setShowText(final boolean showText)
2555 this._showText = showText;
2556 this._has_showText = true;
2560 * Sets the value of field 'showUnconserved'.
2562 * @param showUnconserved
2563 * the value of field 'showUnconserved'.
2565 public void setShowUnconserved(final boolean showUnconserved)
2567 this._showUnconserved = showUnconserved;
2568 this._has_showUnconserved = true;
2572 * Sets the value of field 'startRes'.
2575 * the value of field 'startRes'.
2577 public void setStartRes(final int startRes)
2579 this._startRes = startRes;
2580 this._has_startRes = true;
2584 * Sets the value of field 'startSeq'.
2587 * the value of field 'startSeq'.
2589 public void setStartSeq(final int startSeq)
2591 this._startSeq = startSeq;
2592 this._has_startSeq = true;
2596 * Sets the value of field 'textCol1'.
2599 * the value of field 'textCol1'.
2601 public void setTextCol1(final int textCol1)
2603 this._textCol1 = textCol1;
2604 this._has_textCol1 = true;
2608 * Sets the value of field 'textCol2'.
2611 * the value of field 'textCol2'.
2613 public void setTextCol2(final int textCol2)
2615 this._textCol2 = textCol2;
2616 this._has_textCol2 = true;
2620 * Sets the value of field 'textColThreshold'.
2622 * @param textColThreshold
2623 * the value of field 'textColThreshold'
2625 public void setTextColThreshold(final int textColThreshold)
2627 this._textColThreshold = textColThreshold;
2628 this._has_textColThreshold = true;
2632 * Sets the value of field 'title'.
2635 * the value of field 'title'.
2637 public void setTitle(final java.lang.String title)
2639 this._title = title;
2643 * Sets the value of field 'viewName'.
2646 * the value of field 'viewName'.
2648 public void setViewName(final java.lang.String viewName)
2650 this._viewName = viewName;
2654 * Sets the value of field 'width'.
2657 * the value of field 'width'.
2659 public void setWidth(final int width)
2661 this._width = width;
2662 this._has_width = true;
2666 * Sets the value of field 'wrapAlignment'.
2668 * @param wrapAlignment
2669 * the value of field 'wrapAlignment'.
2671 public void setWrapAlignment(final boolean wrapAlignment)
2673 this._wrapAlignment = wrapAlignment;
2674 this._has_wrapAlignment = true;
2678 * Sets the value of field 'xpos'.
2681 * the value of field 'xpos'.
2683 public void setXpos(final int xpos)
2686 this._has_xpos = true;
2690 * Sets the value of field 'ypos'.
2693 * the value of field 'ypos'.
2695 public void setYpos(final int ypos)
2698 this._has_ypos = true;
2705 * @throws org.exolab.castor.xml.MarshalException
2706 * if object is null or if any SAXException is thrown during
2708 * @throws org.exolab.castor.xml.ValidationException
2709 * if this object is an invalid instance according to the schema
2710 * @return the unmarshaled jalview.schemabinding.version2.Viewport
2712 public static jalview.schemabinding.version2.Viewport unmarshal(
2713 final java.io.Reader reader)
2714 throws org.exolab.castor.xml.MarshalException,
2715 org.exolab.castor.xml.ValidationException
2717 return (jalview.schemabinding.version2.Viewport) Unmarshaller
2718 .unmarshal(jalview.schemabinding.version2.Viewport.class,
2725 * @throws org.exolab.castor.xml.ValidationException
2726 * if this object is an invalid instance according to the schema
2728 public void validate() throws org.exolab.castor.xml.ValidationException
2730 org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
2731 validator.validate(this);