2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 package jalview.schemabinding.version2;
23 //---------------------------------/
24 //- Imported classes and packages -/
25 //---------------------------------/
27 import org.exolab.castor.xml.Marshaller;
28 import org.exolab.castor.xml.Unmarshaller;
33 * @version $Revision$ $Date$
35 public class Viewport implements java.io.Serializable {
38 //--------------------------/
39 //- Class/Member Variables -/
40 //--------------------------/
43 * Field _conservationSelected.
45 private boolean _conservationSelected;
48 * keeps track of state for field: _conservationSelected
50 private boolean _has_conservationSelected;
55 private boolean _pidSelected;
58 * keeps track of state for field: _pidSelected
60 private boolean _has_pidSelected;
65 private java.lang.String _bgColour;
68 * Field _consThreshold.
70 private int _consThreshold;
73 * keeps track of state for field: _consThreshold
75 private boolean _has_consThreshold;
78 * Field _pidThreshold.
80 private int _pidThreshold;
83 * keeps track of state for field: _pidThreshold
85 private boolean _has_pidThreshold;
90 private java.lang.String _title;
95 private boolean _showFullId;
98 * keeps track of state for field: _showFullId
100 private boolean _has_showFullId;
103 * Field _rightAlignIds.
105 private boolean _rightAlignIds;
108 * keeps track of state for field: _rightAlignIds
110 private boolean _has_rightAlignIds;
115 private boolean _showText;
118 * keeps track of state for field: _showText
120 private boolean _has_showText;
123 * Field _showColourText.
125 private boolean _showColourText;
128 * keeps track of state for field: _showColourText
130 private boolean _has_showColourText;
133 * Field _showUnconserved.
135 private boolean _showUnconserved = false;
138 * keeps track of state for field: _showUnconserved
140 private boolean _has_showUnconserved;
145 private boolean _showBoxes;
148 * keeps track of state for field: _showBoxes
150 private boolean _has_showBoxes;
153 * Field _wrapAlignment.
155 private boolean _wrapAlignment;
158 * keeps track of state for field: _wrapAlignment
160 private boolean _has_wrapAlignment;
165 private boolean _renderGaps;
168 * keeps track of state for field: _renderGaps
170 private boolean _has_renderGaps;
173 * Field _showSequenceFeatures.
175 private boolean _showSequenceFeatures;
178 * keeps track of state for field: _showSequenceFeatures
180 private boolean _has_showSequenceFeatures;
183 * Field _showNPfeatureTooltip.
185 private boolean _showNPfeatureTooltip;
188 * keeps track of state for field: _showNPfeatureTooltip
190 private boolean _has_showNPfeatureTooltip;
193 * Field _showDbRefTooltip.
195 private boolean _showDbRefTooltip;
198 * keeps track of state for field: _showDbRefTooltip
200 private boolean _has_showDbRefTooltip;
203 * Field _followHighlight.
205 private boolean _followHighlight = true;
208 * keeps track of state for field: _followHighlight
210 private boolean _has_followHighlight;
213 * Field _followSelection.
215 private boolean _followSelection = true;
218 * keeps track of state for field: _followSelection
220 private boolean _has_followSelection;
223 * Field _showAnnotation.
225 private boolean _showAnnotation;
228 * keeps track of state for field: _showAnnotation
230 private boolean _has_showAnnotation;
233 * Field _centreColumnLabels.
235 private boolean _centreColumnLabels = false;
238 * keeps track of state for field: _centreColumnLabels
240 private boolean _has_centreColumnLabels;
243 * Field _showGroupConservation.
245 private boolean _showGroupConservation = false;
248 * keeps track of state for field: _showGroupConservation
250 private boolean _has_showGroupConservation;
253 * Field _showGroupConsensus.
255 private boolean _showGroupConsensus = false;
258 * keeps track of state for field: _showGroupConsensus
260 private boolean _has_showGroupConsensus;
263 * Field _showConsensusHistogram.
265 private boolean _showConsensusHistogram = true;
268 * keeps track of state for field: _showConsensusHistogram
270 private boolean _has_showConsensusHistogram;
273 * Field _showSequenceLogo.
275 private boolean _showSequenceLogo = false;
278 * keeps track of state for field: _showSequenceLogo
280 private boolean _has_showSequenceLogo;
283 * Field _normaliseSequenceLogo.
285 private boolean _normaliseSequenceLogo = false;
288 * keeps track of state for field: _normaliseSequenceLogo
290 private boolean _has_normaliseSequenceLogo;
293 * Field _ignoreGapsinConsensus.
295 private boolean _ignoreGapsinConsensus = true;
298 * keeps track of state for field: _ignoreGapsinConsensus
300 private boolean _has_ignoreGapsinConsensus;
305 private int _startRes;
308 * keeps track of state for field: _startRes
310 private boolean _has_startRes;
315 private int _startSeq;
318 * keeps track of state for field: _startSeq
320 private boolean _has_startSeq;
325 private java.lang.String _fontName;
330 private int _fontSize;
333 * keeps track of state for field: _fontSize
335 private boolean _has_fontSize;
340 private int _fontStyle;
343 * keeps track of state for field: _fontStyle
345 private boolean _has_fontStyle;
350 private java.lang.String _viewName;
353 * Field _sequenceSetId.
355 private java.lang.String _sequenceSetId;
358 * Field _gatheredViews.
360 private boolean _gatheredViews;
363 * keeps track of state for field: _gatheredViews
365 private boolean _has_gatheredViews;
370 private int _textCol1;
373 * keeps track of state for field: _textCol1
375 private boolean _has_textCol1;
380 private int _textCol2;
383 * keeps track of state for field: _textCol2
385 private boolean _has_textCol2;
388 * Field _textColThreshold.
390 private int _textColThreshold;
393 * keeps track of state for field: _textColThreshold
395 private boolean _has_textColThreshold;
398 * unique id used by jalview to
399 * synchronize between stored and
403 private java.lang.String _id;
406 * The viewport id of this viewport's (cdna/protein) coding
410 private java.lang.String _complementId;
418 * keeps track of state for field: _width
420 private boolean _has_width;
428 * keeps track of state for field: _height
430 private boolean _has_height;
438 * keeps track of state for field: _xpos
440 private boolean _has_xpos;
448 * keeps track of state for field: _ypos
450 private boolean _has_ypos;
453 * Field _annotationColours.
455 private jalview.schemabinding.version2.AnnotationColours _annotationColours;
458 * Field _hiddenColumnsList.
460 private java.util.Vector _hiddenColumnsList;
463 * Field _calcIdParamList.
465 private java.util.Vector _calcIdParamList;
474 this._hiddenColumnsList = new java.util.Vector();
475 this._calcIdParamList = new java.util.Vector();
486 * @param vCalcIdParam
487 * @throws java.lang.IndexOutOfBoundsException if the index
488 * given is outside the bounds of the collection
490 public void addCalcIdParam(
491 final jalview.schemabinding.version2.CalcIdParam vCalcIdParam)
492 throws java.lang.IndexOutOfBoundsException {
493 this._calcIdParamList.addElement(vCalcIdParam);
500 * @param vCalcIdParam
501 * @throws java.lang.IndexOutOfBoundsException if the index
502 * given is outside the bounds of the collection
504 public void addCalcIdParam(
506 final jalview.schemabinding.version2.CalcIdParam vCalcIdParam)
507 throws java.lang.IndexOutOfBoundsException {
508 this._calcIdParamList.add(index, vCalcIdParam);
514 * @param vHiddenColumns
515 * @throws java.lang.IndexOutOfBoundsException if the index
516 * given is outside the bounds of the collection
518 public void addHiddenColumns(
519 final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)
520 throws java.lang.IndexOutOfBoundsException {
521 this._hiddenColumnsList.addElement(vHiddenColumns);
528 * @param vHiddenColumns
529 * @throws java.lang.IndexOutOfBoundsException if the index
530 * given is outside the bounds of the collection
532 public void addHiddenColumns(
534 final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)
535 throws java.lang.IndexOutOfBoundsException {
536 this._hiddenColumnsList.add(index, vHiddenColumns);
541 public void deleteCentreColumnLabels(
543 this._has_centreColumnLabels= false;
548 public void deleteConsThreshold(
550 this._has_consThreshold= false;
555 public void deleteConservationSelected(
557 this._has_conservationSelected= false;
562 public void deleteFollowHighlight(
564 this._has_followHighlight= false;
569 public void deleteFollowSelection(
571 this._has_followSelection= false;
576 public void deleteFontSize(
578 this._has_fontSize= false;
583 public void deleteFontStyle(
585 this._has_fontStyle= false;
590 public void deleteGatheredViews(
592 this._has_gatheredViews= false;
597 public void deleteHeight(
599 this._has_height= false;
604 public void deleteIgnoreGapsinConsensus(
606 this._has_ignoreGapsinConsensus= false;
611 public void deleteNormaliseSequenceLogo(
613 this._has_normaliseSequenceLogo= false;
618 public void deletePidSelected(
620 this._has_pidSelected= false;
625 public void deletePidThreshold(
627 this._has_pidThreshold= false;
632 public void deleteRenderGaps(
634 this._has_renderGaps= false;
639 public void deleteRightAlignIds(
641 this._has_rightAlignIds= false;
646 public void deleteShowAnnotation(
648 this._has_showAnnotation= false;
653 public void deleteShowBoxes(
655 this._has_showBoxes= false;
660 public void deleteShowColourText(
662 this._has_showColourText= false;
667 public void deleteShowConsensusHistogram(
669 this._has_showConsensusHistogram= false;
674 public void deleteShowDbRefTooltip(
676 this._has_showDbRefTooltip= false;
681 public void deleteShowFullId(
683 this._has_showFullId= false;
688 public void deleteShowGroupConsensus(
690 this._has_showGroupConsensus= false;
695 public void deleteShowGroupConservation(
697 this._has_showGroupConservation= false;
702 public void deleteShowNPfeatureTooltip(
704 this._has_showNPfeatureTooltip= false;
709 public void deleteShowSequenceFeatures(
711 this._has_showSequenceFeatures= false;
716 public void deleteShowSequenceLogo(
718 this._has_showSequenceLogo= false;
723 public void deleteShowText(
725 this._has_showText= false;
730 public void deleteShowUnconserved(
732 this._has_showUnconserved= false;
737 public void deleteStartRes(
739 this._has_startRes= false;
744 public void deleteStartSeq(
746 this._has_startSeq= false;
751 public void deleteTextCol1(
753 this._has_textCol1= false;
758 public void deleteTextCol2(
760 this._has_textCol2= false;
765 public void deleteTextColThreshold(
767 this._has_textColThreshold= false;
772 public void deleteWidth(
774 this._has_width= false;
779 public void deleteWrapAlignment(
781 this._has_wrapAlignment= false;
786 public void deleteXpos(
788 this._has_xpos= false;
793 public void deleteYpos(
795 this._has_ypos= false;
799 * Method enumerateCalcIdParam.
801 * @return an Enumeration over all
802 * jalview.schemabinding.version2.CalcIdParam elements
804 public java.util.Enumeration enumerateCalcIdParam(
806 return this._calcIdParamList.elements();
810 * Method enumerateHiddenColumns.
812 * @return an Enumeration over all
813 * jalview.schemabinding.version2.HiddenColumns elements
815 public java.util.Enumeration enumerateHiddenColumns(
817 return this._hiddenColumnsList.elements();
821 * Returns the value of field 'annotationColours'.
823 * @return the value of field 'AnnotationColours'.
825 public jalview.schemabinding.version2.AnnotationColours getAnnotationColours(
827 return this._annotationColours;
831 * Returns the value of field 'bgColour'.
833 * @return the value of field 'BgColour'.
835 public java.lang.String getBgColour(
837 return this._bgColour;
841 * Method getCalcIdParam.
844 * @throws java.lang.IndexOutOfBoundsException if the index
845 * given is outside the bounds of the collection
846 * @return the value of the
847 * jalview.schemabinding.version2.CalcIdParam at the given index
849 public jalview.schemabinding.version2.CalcIdParam getCalcIdParam(
851 throws java.lang.IndexOutOfBoundsException {
852 // check bounds for index
853 if (index < 0 || index >= this._calcIdParamList.size()) {
854 throw new IndexOutOfBoundsException("getCalcIdParam: Index value '" + index + "' not in range [0.." + (this._calcIdParamList.size() - 1) + "]");
857 return (jalview.schemabinding.version2.CalcIdParam) _calcIdParamList.get(index);
861 * Method getCalcIdParam.Returns the contents of the collection
862 * in an Array. <p>Note: Just in case the collection contents
863 * are changing in another thread, we pass a 0-length Array of
864 * the correct type into the API call. This way we <i>know</i>
865 * that the Array returned is of exactly the correct length.
867 * @return this collection as an Array
869 public jalview.schemabinding.version2.CalcIdParam[] getCalcIdParam(
871 jalview.schemabinding.version2.CalcIdParam[] array = new jalview.schemabinding.version2.CalcIdParam[0];
872 return (jalview.schemabinding.version2.CalcIdParam[]) this._calcIdParamList.toArray(array);
876 * Method getCalcIdParamCount.
878 * @return the size of this collection
880 public int getCalcIdParamCount(
882 return this._calcIdParamList.size();
886 * Returns the value of field 'centreColumnLabels'.
888 * @return the value of field 'CentreColumnLabels'.
890 public boolean getCentreColumnLabels(
892 return this._centreColumnLabels;
896 * Returns the value of field 'complementId'. The field
897 * 'complementId' has the following description: The viewport
898 * id of this viewport's (cdna/protein) coding complement, if
902 * @return the value of field 'ComplementId'.
904 public java.lang.String getComplementId(
906 return this._complementId;
910 * Returns the value of field 'consThreshold'.
912 * @return the value of field 'ConsThreshold'.
914 public int getConsThreshold(
916 return this._consThreshold;
920 * Returns the value of field 'conservationSelected'.
922 * @return the value of field 'ConservationSelected'.
924 public boolean getConservationSelected(
926 return this._conservationSelected;
930 * Returns the value of field 'followHighlight'.
932 * @return the value of field 'FollowHighlight'.
934 public boolean getFollowHighlight(
936 return this._followHighlight;
940 * Returns the value of field 'followSelection'.
942 * @return the value of field 'FollowSelection'.
944 public boolean getFollowSelection(
946 return this._followSelection;
950 * Returns the value of field 'fontName'.
952 * @return the value of field 'FontName'.
954 public java.lang.String getFontName(
956 return this._fontName;
960 * Returns the value of field 'fontSize'.
962 * @return the value of field 'FontSize'.
964 public int getFontSize(
966 return this._fontSize;
970 * Returns the value of field 'fontStyle'.
972 * @return the value of field 'FontStyle'.
974 public int getFontStyle(
976 return this._fontStyle;
980 * Returns the value of field 'gatheredViews'.
982 * @return the value of field 'GatheredViews'.
984 public boolean getGatheredViews(
986 return this._gatheredViews;
990 * Returns the value of field 'height'.
992 * @return the value of field 'Height'.
994 public int getHeight(
1000 * Method getHiddenColumns.
1003 * @throws java.lang.IndexOutOfBoundsException if the index
1004 * given is outside the bounds of the collection
1005 * @return the value of the
1006 * jalview.schemabinding.version2.HiddenColumns at the given
1009 public jalview.schemabinding.version2.HiddenColumns getHiddenColumns(
1011 throws java.lang.IndexOutOfBoundsException {
1012 // check bounds for index
1013 if (index < 0 || index >= this._hiddenColumnsList.size()) {
1014 throw new IndexOutOfBoundsException("getHiddenColumns: Index value '" + index + "' not in range [0.." + (this._hiddenColumnsList.size() - 1) + "]");
1017 return (jalview.schemabinding.version2.HiddenColumns) _hiddenColumnsList.get(index);
1021 * Method getHiddenColumns.Returns the contents of the
1022 * collection in an Array. <p>Note: Just in case the
1023 * collection contents are changing in another thread, we pass
1024 * a 0-length Array of the correct type into the API call.
1025 * This way we <i>know</i> that the Array returned is of
1026 * exactly the correct length.
1028 * @return this collection as an Array
1030 public jalview.schemabinding.version2.HiddenColumns[] getHiddenColumns(
1032 jalview.schemabinding.version2.HiddenColumns[] array = new jalview.schemabinding.version2.HiddenColumns[0];
1033 return (jalview.schemabinding.version2.HiddenColumns[]) this._hiddenColumnsList.toArray(array);
1037 * Method getHiddenColumnsCount.
1039 * @return the size of this collection
1041 public int getHiddenColumnsCount(
1043 return this._hiddenColumnsList.size();
1047 * Returns the value of field 'id'. The field 'id' has the
1048 * following description: unique id used by jalview to
1049 * synchronize between stored and
1050 * instantiated views
1053 * @return the value of field 'Id'.
1055 public java.lang.String getId(
1061 * Returns the value of field 'ignoreGapsinConsensus'.
1063 * @return the value of field 'IgnoreGapsinConsensus'.
1065 public boolean getIgnoreGapsinConsensus(
1067 return this._ignoreGapsinConsensus;
1071 * Returns the value of field 'normaliseSequenceLogo'.
1073 * @return the value of field 'NormaliseSequenceLogo'.
1075 public boolean getNormaliseSequenceLogo(
1077 return this._normaliseSequenceLogo;
1081 * Returns the value of field 'pidSelected'.
1083 * @return the value of field 'PidSelected'.
1085 public boolean getPidSelected(
1087 return this._pidSelected;
1091 * Returns the value of field 'pidThreshold'.
1093 * @return the value of field 'PidThreshold'.
1095 public int getPidThreshold(
1097 return this._pidThreshold;
1101 * Returns the value of field 'renderGaps'.
1103 * @return the value of field 'RenderGaps'.
1105 public boolean getRenderGaps(
1107 return this._renderGaps;
1111 * Returns the value of field 'rightAlignIds'.
1113 * @return the value of field 'RightAlignIds'.
1115 public boolean getRightAlignIds(
1117 return this._rightAlignIds;
1121 * Returns the value of field 'sequenceSetId'.
1123 * @return the value of field 'SequenceSetId'.
1125 public java.lang.String getSequenceSetId(
1127 return this._sequenceSetId;
1131 * Returns the value of field 'showAnnotation'.
1133 * @return the value of field 'ShowAnnotation'.
1135 public boolean getShowAnnotation(
1137 return this._showAnnotation;
1141 * Returns the value of field 'showBoxes'.
1143 * @return the value of field 'ShowBoxes'.
1145 public boolean getShowBoxes(
1147 return this._showBoxes;
1151 * Returns the value of field 'showColourText'.
1153 * @return the value of field 'ShowColourText'.
1155 public boolean getShowColourText(
1157 return this._showColourText;
1161 * Returns the value of field 'showConsensusHistogram'.
1163 * @return the value of field 'ShowConsensusHistogram'.
1165 public boolean getShowConsensusHistogram(
1167 return this._showConsensusHistogram;
1171 * Returns the value of field 'showDbRefTooltip'.
1173 * @return the value of field 'ShowDbRefTooltip'.
1175 public boolean getShowDbRefTooltip(
1177 return this._showDbRefTooltip;
1181 * Returns the value of field 'showFullId'.
1183 * @return the value of field 'ShowFullId'.
1185 public boolean getShowFullId(
1187 return this._showFullId;
1191 * Returns the value of field 'showGroupConsensus'.
1193 * @return the value of field 'ShowGroupConsensus'.
1195 public boolean getShowGroupConsensus(
1197 return this._showGroupConsensus;
1201 * Returns the value of field 'showGroupConservation'.
1203 * @return the value of field 'ShowGroupConservation'.
1205 public boolean getShowGroupConservation(
1207 return this._showGroupConservation;
1211 * Returns the value of field 'showNPfeatureTooltip'.
1213 * @return the value of field 'ShowNPfeatureTooltip'.
1215 public boolean getShowNPfeatureTooltip(
1217 return this._showNPfeatureTooltip;
1221 * Returns the value of field 'showSequenceFeatures'.
1223 * @return the value of field 'ShowSequenceFeatures'.
1225 public boolean getShowSequenceFeatures(
1227 return this._showSequenceFeatures;
1231 * Returns the value of field 'showSequenceLogo'.
1233 * @return the value of field 'ShowSequenceLogo'.
1235 public boolean getShowSequenceLogo(
1237 return this._showSequenceLogo;
1241 * Returns the value of field 'showText'.
1243 * @return the value of field 'ShowText'.
1245 public boolean getShowText(
1247 return this._showText;
1251 * Returns the value of field 'showUnconserved'.
1253 * @return the value of field 'ShowUnconserved'.
1255 public boolean getShowUnconserved(
1257 return this._showUnconserved;
1261 * Returns the value of field 'startRes'.
1263 * @return the value of field 'StartRes'.
1265 public int getStartRes(
1267 return this._startRes;
1271 * Returns the value of field 'startSeq'.
1273 * @return the value of field 'StartSeq'.
1275 public int getStartSeq(
1277 return this._startSeq;
1281 * Returns the value of field 'textCol1'.
1283 * @return the value of field 'TextCol1'.
1285 public int getTextCol1(
1287 return this._textCol1;
1291 * Returns the value of field 'textCol2'.
1293 * @return the value of field 'TextCol2'.
1295 public int getTextCol2(
1297 return this._textCol2;
1301 * Returns the value of field 'textColThreshold'.
1303 * @return the value of field 'TextColThreshold'.
1305 public int getTextColThreshold(
1307 return this._textColThreshold;
1311 * Returns the value of field 'title'.
1313 * @return the value of field 'Title'.
1315 public java.lang.String getTitle(
1321 * Returns the value of field 'viewName'.
1323 * @return the value of field 'ViewName'.
1325 public java.lang.String getViewName(
1327 return this._viewName;
1331 * Returns the value of field 'width'.
1333 * @return the value of field 'Width'.
1335 public int getWidth(
1341 * Returns the value of field 'wrapAlignment'.
1343 * @return the value of field 'WrapAlignment'.
1345 public boolean getWrapAlignment(
1347 return this._wrapAlignment;
1351 * Returns the value of field 'xpos'.
1353 * @return the value of field 'Xpos'.
1361 * Returns the value of field 'ypos'.
1363 * @return the value of field 'Ypos'.
1371 * Method hasCentreColumnLabels.
1373 * @return true if at least one CentreColumnLabels has been adde
1375 public boolean hasCentreColumnLabels(
1377 return this._has_centreColumnLabels;
1381 * Method hasConsThreshold.
1383 * @return true if at least one ConsThreshold has been added
1385 public boolean hasConsThreshold(
1387 return this._has_consThreshold;
1391 * Method hasConservationSelected.
1393 * @return true if at least one ConservationSelected has been
1396 public boolean hasConservationSelected(
1398 return this._has_conservationSelected;
1402 * Method hasFollowHighlight.
1404 * @return true if at least one FollowHighlight has been added
1406 public boolean hasFollowHighlight(
1408 return this._has_followHighlight;
1412 * Method hasFollowSelection.
1414 * @return true if at least one FollowSelection has been added
1416 public boolean hasFollowSelection(
1418 return this._has_followSelection;
1422 * Method hasFontSize.
1424 * @return true if at least one FontSize has been added
1426 public boolean hasFontSize(
1428 return this._has_fontSize;
1432 * Method hasFontStyle.
1434 * @return true if at least one FontStyle has been added
1436 public boolean hasFontStyle(
1438 return this._has_fontStyle;
1442 * Method hasGatheredViews.
1444 * @return true if at least one GatheredViews has been added
1446 public boolean hasGatheredViews(
1448 return this._has_gatheredViews;
1454 * @return true if at least one Height has been added
1456 public boolean hasHeight(
1458 return this._has_height;
1462 * Method hasIgnoreGapsinConsensus.
1464 * @return true if at least one IgnoreGapsinConsensus has been
1467 public boolean hasIgnoreGapsinConsensus(
1469 return this._has_ignoreGapsinConsensus;
1473 * Method hasNormaliseSequenceLogo.
1475 * @return true if at least one NormaliseSequenceLogo has been
1478 public boolean hasNormaliseSequenceLogo(
1480 return this._has_normaliseSequenceLogo;
1484 * Method hasPidSelected.
1486 * @return true if at least one PidSelected has been added
1488 public boolean hasPidSelected(
1490 return this._has_pidSelected;
1494 * Method hasPidThreshold.
1496 * @return true if at least one PidThreshold has been added
1498 public boolean hasPidThreshold(
1500 return this._has_pidThreshold;
1504 * Method hasRenderGaps.
1506 * @return true if at least one RenderGaps has been added
1508 public boolean hasRenderGaps(
1510 return this._has_renderGaps;
1514 * Method hasRightAlignIds.
1516 * @return true if at least one RightAlignIds has been added
1518 public boolean hasRightAlignIds(
1520 return this._has_rightAlignIds;
1524 * Method hasShowAnnotation.
1526 * @return true if at least one ShowAnnotation has been added
1528 public boolean hasShowAnnotation(
1530 return this._has_showAnnotation;
1534 * Method hasShowBoxes.
1536 * @return true if at least one ShowBoxes has been added
1538 public boolean hasShowBoxes(
1540 return this._has_showBoxes;
1544 * Method hasShowColourText.
1546 * @return true if at least one ShowColourText has been added
1548 public boolean hasShowColourText(
1550 return this._has_showColourText;
1554 * Method hasShowConsensusHistogram.
1556 * @return true if at least one ShowConsensusHistogram has been
1559 public boolean hasShowConsensusHistogram(
1561 return this._has_showConsensusHistogram;
1565 * Method hasShowDbRefTooltip.
1567 * @return true if at least one ShowDbRefTooltip has been added
1569 public boolean hasShowDbRefTooltip(
1571 return this._has_showDbRefTooltip;
1575 * Method hasShowFullId.
1577 * @return true if at least one ShowFullId has been added
1579 public boolean hasShowFullId(
1581 return this._has_showFullId;
1585 * Method hasShowGroupConsensus.
1587 * @return true if at least one ShowGroupConsensus has been adde
1589 public boolean hasShowGroupConsensus(
1591 return this._has_showGroupConsensus;
1595 * Method hasShowGroupConservation.
1597 * @return true if at least one ShowGroupConservation has been
1600 public boolean hasShowGroupConservation(
1602 return this._has_showGroupConservation;
1606 * Method hasShowNPfeatureTooltip.
1608 * @return true if at least one ShowNPfeatureTooltip has been
1611 public boolean hasShowNPfeatureTooltip(
1613 return this._has_showNPfeatureTooltip;
1617 * Method hasShowSequenceFeatures.
1619 * @return true if at least one ShowSequenceFeatures has been
1622 public boolean hasShowSequenceFeatures(
1624 return this._has_showSequenceFeatures;
1628 * Method hasShowSequenceLogo.
1630 * @return true if at least one ShowSequenceLogo has been added
1632 public boolean hasShowSequenceLogo(
1634 return this._has_showSequenceLogo;
1638 * Method hasShowText.
1640 * @return true if at least one ShowText has been added
1642 public boolean hasShowText(
1644 return this._has_showText;
1648 * Method hasShowUnconserved.
1650 * @return true if at least one ShowUnconserved has been added
1652 public boolean hasShowUnconserved(
1654 return this._has_showUnconserved;
1658 * Method hasStartRes.
1660 * @return true if at least one StartRes has been added
1662 public boolean hasStartRes(
1664 return this._has_startRes;
1668 * Method hasStartSeq.
1670 * @return true if at least one StartSeq has been added
1672 public boolean hasStartSeq(
1674 return this._has_startSeq;
1678 * Method hasTextCol1.
1680 * @return true if at least one TextCol1 has been added
1682 public boolean hasTextCol1(
1684 return this._has_textCol1;
1688 * Method hasTextCol2.
1690 * @return true if at least one TextCol2 has been added
1692 public boolean hasTextCol2(
1694 return this._has_textCol2;
1698 * Method hasTextColThreshold.
1700 * @return true if at least one TextColThreshold has been added
1702 public boolean hasTextColThreshold(
1704 return this._has_textColThreshold;
1710 * @return true if at least one Width has been added
1712 public boolean hasWidth(
1714 return this._has_width;
1718 * Method hasWrapAlignment.
1720 * @return true if at least one WrapAlignment has been added
1722 public boolean hasWrapAlignment(
1724 return this._has_wrapAlignment;
1730 * @return true if at least one Xpos has been added
1732 public boolean hasXpos(
1734 return this._has_xpos;
1740 * @return true if at least one Ypos has been added
1742 public boolean hasYpos(
1744 return this._has_ypos;
1748 * Returns the value of field 'centreColumnLabels'.
1750 * @return the value of field 'CentreColumnLabels'.
1752 public boolean isCentreColumnLabels(
1754 return this._centreColumnLabels;
1758 * Returns the value of field 'conservationSelected'.
1760 * @return the value of field 'ConservationSelected'.
1762 public boolean isConservationSelected(
1764 return this._conservationSelected;
1768 * Returns the value of field 'followHighlight'.
1770 * @return the value of field 'FollowHighlight'.
1772 public boolean isFollowHighlight(
1774 return this._followHighlight;
1778 * Returns the value of field 'followSelection'.
1780 * @return the value of field 'FollowSelection'.
1782 public boolean isFollowSelection(
1784 return this._followSelection;
1788 * Returns the value of field 'gatheredViews'.
1790 * @return the value of field 'GatheredViews'.
1792 public boolean isGatheredViews(
1794 return this._gatheredViews;
1798 * Returns the value of field 'ignoreGapsinConsensus'.
1800 * @return the value of field 'IgnoreGapsinConsensus'.
1802 public boolean isIgnoreGapsinConsensus(
1804 return this._ignoreGapsinConsensus;
1808 * Returns the value of field 'normaliseSequenceLogo'.
1810 * @return the value of field 'NormaliseSequenceLogo'.
1812 public boolean isNormaliseSequenceLogo(
1814 return this._normaliseSequenceLogo;
1818 * Returns the value of field 'pidSelected'.
1820 * @return the value of field 'PidSelected'.
1822 public boolean isPidSelected(
1824 return this._pidSelected;
1828 * Returns the value of field 'renderGaps'.
1830 * @return the value of field 'RenderGaps'.
1832 public boolean isRenderGaps(
1834 return this._renderGaps;
1838 * Returns the value of field 'rightAlignIds'.
1840 * @return the value of field 'RightAlignIds'.
1842 public boolean isRightAlignIds(
1844 return this._rightAlignIds;
1848 * Returns the value of field 'showAnnotation'.
1850 * @return the value of field 'ShowAnnotation'.
1852 public boolean isShowAnnotation(
1854 return this._showAnnotation;
1858 * Returns the value of field 'showBoxes'.
1860 * @return the value of field 'ShowBoxes'.
1862 public boolean isShowBoxes(
1864 return this._showBoxes;
1868 * Returns the value of field 'showColourText'.
1870 * @return the value of field 'ShowColourText'.
1872 public boolean isShowColourText(
1874 return this._showColourText;
1878 * Returns the value of field 'showConsensusHistogram'.
1880 * @return the value of field 'ShowConsensusHistogram'.
1882 public boolean isShowConsensusHistogram(
1884 return this._showConsensusHistogram;
1888 * Returns the value of field 'showDbRefTooltip'.
1890 * @return the value of field 'ShowDbRefTooltip'.
1892 public boolean isShowDbRefTooltip(
1894 return this._showDbRefTooltip;
1898 * Returns the value of field 'showFullId'.
1900 * @return the value of field 'ShowFullId'.
1902 public boolean isShowFullId(
1904 return this._showFullId;
1908 * Returns the value of field 'showGroupConsensus'.
1910 * @return the value of field 'ShowGroupConsensus'.
1912 public boolean isShowGroupConsensus(
1914 return this._showGroupConsensus;
1918 * Returns the value of field 'showGroupConservation'.
1920 * @return the value of field 'ShowGroupConservation'.
1922 public boolean isShowGroupConservation(
1924 return this._showGroupConservation;
1928 * Returns the value of field 'showNPfeatureTooltip'.
1930 * @return the value of field 'ShowNPfeatureTooltip'.
1932 public boolean isShowNPfeatureTooltip(
1934 return this._showNPfeatureTooltip;
1938 * Returns the value of field 'showSequenceFeatures'.
1940 * @return the value of field 'ShowSequenceFeatures'.
1942 public boolean isShowSequenceFeatures(
1944 return this._showSequenceFeatures;
1948 * Returns the value of field 'showSequenceLogo'.
1950 * @return the value of field 'ShowSequenceLogo'.
1952 public boolean isShowSequenceLogo(
1954 return this._showSequenceLogo;
1958 * Returns the value of field 'showText'.
1960 * @return the value of field 'ShowText'.
1962 public boolean isShowText(
1964 return this._showText;
1968 * Returns the value of field 'showUnconserved'.
1970 * @return the value of field 'ShowUnconserved'.
1972 public boolean isShowUnconserved(
1974 return this._showUnconserved;
1980 * @return true if this object is valid according to the schema
1982 public boolean isValid(
1986 } catch (org.exolab.castor.xml.ValidationException vex) {
1993 * Returns the value of field 'wrapAlignment'.
1995 * @return the value of field 'WrapAlignment'.
1997 public boolean isWrapAlignment(
1999 return this._wrapAlignment;
2006 * @throws org.exolab.castor.xml.MarshalException if object is
2007 * null or if any SAXException is thrown during marshaling
2008 * @throws org.exolab.castor.xml.ValidationException if this
2009 * object is an invalid instance according to the schema
2011 public void marshal(
2012 final java.io.Writer out)
2013 throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
2014 Marshaller.marshal(this, out);
2021 * @throws java.io.IOException if an IOException occurs during
2023 * @throws org.exolab.castor.xml.ValidationException if this
2024 * object is an invalid instance according to the schema
2025 * @throws org.exolab.castor.xml.MarshalException if object is
2026 * null or if any SAXException is thrown during marshaling
2028 public void marshal(
2029 final org.xml.sax.ContentHandler handler)
2030 throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
2031 Marshaller.marshal(this, handler);
2036 public void removeAllCalcIdParam(
2038 this._calcIdParamList.clear();
2043 public void removeAllHiddenColumns(
2045 this._hiddenColumnsList.clear();
2049 * Method removeCalcIdParam.
2051 * @param vCalcIdParam
2052 * @return true if the object was removed from the collection.
2054 public boolean removeCalcIdParam(
2055 final jalview.schemabinding.version2.CalcIdParam vCalcIdParam) {
2056 boolean removed = _calcIdParamList.remove(vCalcIdParam);
2061 * Method removeCalcIdParamAt.
2064 * @return the element removed from the collection
2066 public jalview.schemabinding.version2.CalcIdParam removeCalcIdParamAt(
2068 java.lang.Object obj = this._calcIdParamList.remove(index);
2069 return (jalview.schemabinding.version2.CalcIdParam) obj;
2073 * Method removeHiddenColumns.
2075 * @param vHiddenColumns
2076 * @return true if the object was removed from the collection.
2078 public boolean removeHiddenColumns(
2079 final jalview.schemabinding.version2.HiddenColumns vHiddenColumns) {
2080 boolean removed = _hiddenColumnsList.remove(vHiddenColumns);
2085 * Method removeHiddenColumnsAt.
2088 * @return the element removed from the collection
2090 public jalview.schemabinding.version2.HiddenColumns removeHiddenColumnsAt(
2092 java.lang.Object obj = this._hiddenColumnsList.remove(index);
2093 return (jalview.schemabinding.version2.HiddenColumns) obj;
2097 * Sets the value of field 'annotationColours'.
2099 * @param annotationColours the value of field
2100 * 'annotationColours'.
2102 public void setAnnotationColours(
2103 final jalview.schemabinding.version2.AnnotationColours annotationColours) {
2104 this._annotationColours = annotationColours;
2108 * Sets the value of field 'bgColour'.
2110 * @param bgColour the value of field 'bgColour'.
2112 public void setBgColour(
2113 final java.lang.String bgColour) {
2114 this._bgColour = bgColour;
2121 * @param vCalcIdParam
2122 * @throws java.lang.IndexOutOfBoundsException if the index
2123 * given is outside the bounds of the collection
2125 public void setCalcIdParam(
2127 final jalview.schemabinding.version2.CalcIdParam vCalcIdParam)
2128 throws java.lang.IndexOutOfBoundsException {
2129 // check bounds for index
2130 if (index < 0 || index >= this._calcIdParamList.size()) {
2131 throw new IndexOutOfBoundsException("setCalcIdParam: Index value '" + index + "' not in range [0.." + (this._calcIdParamList.size() - 1) + "]");
2134 this._calcIdParamList.set(index, vCalcIdParam);
2140 * @param vCalcIdParamArray
2142 public void setCalcIdParam(
2143 final jalview.schemabinding.version2.CalcIdParam[] vCalcIdParamArray) {
2145 _calcIdParamList.clear();
2147 for (int i = 0; i < vCalcIdParamArray.length; i++) {
2148 this._calcIdParamList.add(vCalcIdParamArray[i]);
2153 * Sets the value of field 'centreColumnLabels'.
2155 * @param centreColumnLabels the value of field
2156 * 'centreColumnLabels'.
2158 public void setCentreColumnLabels(
2159 final boolean centreColumnLabels) {
2160 this._centreColumnLabels = centreColumnLabels;
2161 this._has_centreColumnLabels = true;
2165 * Sets the value of field 'complementId'. The field
2166 * 'complementId' has the following description: The viewport
2167 * id of this viewport's (cdna/protein) coding complement, if
2171 * @param complementId the value of field 'complementId'.
2173 public void setComplementId(
2174 final java.lang.String complementId) {
2175 this._complementId = complementId;
2179 * Sets the value of field 'consThreshold'.
2181 * @param consThreshold the value of field 'consThreshold'.
2183 public void setConsThreshold(
2184 final int consThreshold) {
2185 this._consThreshold = consThreshold;
2186 this._has_consThreshold = true;
2190 * Sets the value of field 'conservationSelected'.
2192 * @param conservationSelected the value of field
2193 * 'conservationSelected'.
2195 public void setConservationSelected(
2196 final boolean conservationSelected) {
2197 this._conservationSelected = conservationSelected;
2198 this._has_conservationSelected = true;
2202 * Sets the value of field 'followHighlight'.
2204 * @param followHighlight the value of field 'followHighlight'.
2206 public void setFollowHighlight(
2207 final boolean followHighlight) {
2208 this._followHighlight = followHighlight;
2209 this._has_followHighlight = true;
2213 * Sets the value of field 'followSelection'.
2215 * @param followSelection the value of field 'followSelection'.
2217 public void setFollowSelection(
2218 final boolean followSelection) {
2219 this._followSelection = followSelection;
2220 this._has_followSelection = true;
2224 * Sets the value of field 'fontName'.
2226 * @param fontName the value of field 'fontName'.
2228 public void setFontName(
2229 final java.lang.String fontName) {
2230 this._fontName = fontName;
2234 * Sets the value of field 'fontSize'.
2236 * @param fontSize the value of field 'fontSize'.
2238 public void setFontSize(
2239 final int fontSize) {
2240 this._fontSize = fontSize;
2241 this._has_fontSize = true;
2245 * Sets the value of field 'fontStyle'.
2247 * @param fontStyle the value of field 'fontStyle'.
2249 public void setFontStyle(
2250 final int fontStyle) {
2251 this._fontStyle = fontStyle;
2252 this._has_fontStyle = true;
2256 * Sets the value of field 'gatheredViews'.
2258 * @param gatheredViews the value of field 'gatheredViews'.
2260 public void setGatheredViews(
2261 final boolean gatheredViews) {
2262 this._gatheredViews = gatheredViews;
2263 this._has_gatheredViews = true;
2267 * Sets the value of field 'height'.
2269 * @param height the value of field 'height'.
2271 public void setHeight(
2273 this._height = height;
2274 this._has_height = true;
2281 * @param vHiddenColumns
2282 * @throws java.lang.IndexOutOfBoundsException if the index
2283 * given is outside the bounds of the collection
2285 public void setHiddenColumns(
2287 final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)
2288 throws java.lang.IndexOutOfBoundsException {
2289 // check bounds for index
2290 if (index < 0 || index >= this._hiddenColumnsList.size()) {
2291 throw new IndexOutOfBoundsException("setHiddenColumns: Index value '" + index + "' not in range [0.." + (this._hiddenColumnsList.size() - 1) + "]");
2294 this._hiddenColumnsList.set(index, vHiddenColumns);
2300 * @param vHiddenColumnsArray
2302 public void setHiddenColumns(
2303 final jalview.schemabinding.version2.HiddenColumns[] vHiddenColumnsArray) {
2305 _hiddenColumnsList.clear();
2307 for (int i = 0; i < vHiddenColumnsArray.length; i++) {
2308 this._hiddenColumnsList.add(vHiddenColumnsArray[i]);
2313 * Sets the value of field 'id'. The field 'id' has the
2314 * following description: unique id used by jalview to
2315 * synchronize between stored and
2316 * instantiated views
2319 * @param id the value of field 'id'.
2322 final java.lang.String id) {
2327 * Sets the value of field 'ignoreGapsinConsensus'.
2329 * @param ignoreGapsinConsensus the value of field
2330 * 'ignoreGapsinConsensus'.
2332 public void setIgnoreGapsinConsensus(
2333 final boolean ignoreGapsinConsensus) {
2334 this._ignoreGapsinConsensus = ignoreGapsinConsensus;
2335 this._has_ignoreGapsinConsensus = true;
2339 * Sets the value of field 'normaliseSequenceLogo'.
2341 * @param normaliseSequenceLogo the value of field
2342 * 'normaliseSequenceLogo'.
2344 public void setNormaliseSequenceLogo(
2345 final boolean normaliseSequenceLogo) {
2346 this._normaliseSequenceLogo = normaliseSequenceLogo;
2347 this._has_normaliseSequenceLogo = true;
2351 * Sets the value of field 'pidSelected'.
2353 * @param pidSelected the value of field 'pidSelected'.
2355 public void setPidSelected(
2356 final boolean pidSelected) {
2357 this._pidSelected = pidSelected;
2358 this._has_pidSelected = true;
2362 * Sets the value of field 'pidThreshold'.
2364 * @param pidThreshold the value of field 'pidThreshold'.
2366 public void setPidThreshold(
2367 final int pidThreshold) {
2368 this._pidThreshold = pidThreshold;
2369 this._has_pidThreshold = true;
2373 * Sets the value of field 'renderGaps'.
2375 * @param renderGaps the value of field 'renderGaps'.
2377 public void setRenderGaps(
2378 final boolean renderGaps) {
2379 this._renderGaps = renderGaps;
2380 this._has_renderGaps = true;
2384 * Sets the value of field 'rightAlignIds'.
2386 * @param rightAlignIds the value of field 'rightAlignIds'.
2388 public void setRightAlignIds(
2389 final boolean rightAlignIds) {
2390 this._rightAlignIds = rightAlignIds;
2391 this._has_rightAlignIds = true;
2395 * Sets the value of field 'sequenceSetId'.
2397 * @param sequenceSetId the value of field 'sequenceSetId'.
2399 public void setSequenceSetId(
2400 final java.lang.String sequenceSetId) {
2401 this._sequenceSetId = sequenceSetId;
2405 * Sets the value of field 'showAnnotation'.
2407 * @param showAnnotation the value of field 'showAnnotation'.
2409 public void setShowAnnotation(
2410 final boolean showAnnotation) {
2411 this._showAnnotation = showAnnotation;
2412 this._has_showAnnotation = true;
2416 * Sets the value of field 'showBoxes'.
2418 * @param showBoxes the value of field 'showBoxes'.
2420 public void setShowBoxes(
2421 final boolean showBoxes) {
2422 this._showBoxes = showBoxes;
2423 this._has_showBoxes = true;
2427 * Sets the value of field 'showColourText'.
2429 * @param showColourText the value of field 'showColourText'.
2431 public void setShowColourText(
2432 final boolean showColourText) {
2433 this._showColourText = showColourText;
2434 this._has_showColourText = true;
2438 * Sets the value of field 'showConsensusHistogram'.
2440 * @param showConsensusHistogram the value of field
2441 * 'showConsensusHistogram'.
2443 public void setShowConsensusHistogram(
2444 final boolean showConsensusHistogram) {
2445 this._showConsensusHistogram = showConsensusHistogram;
2446 this._has_showConsensusHistogram = true;
2450 * Sets the value of field 'showDbRefTooltip'.
2452 * @param showDbRefTooltip the value of field 'showDbRefTooltip'
2454 public void setShowDbRefTooltip(
2455 final boolean showDbRefTooltip) {
2456 this._showDbRefTooltip = showDbRefTooltip;
2457 this._has_showDbRefTooltip = true;
2461 * Sets the value of field 'showFullId'.
2463 * @param showFullId the value of field 'showFullId'.
2465 public void setShowFullId(
2466 final boolean showFullId) {
2467 this._showFullId = showFullId;
2468 this._has_showFullId = true;
2472 * Sets the value of field 'showGroupConsensus'.
2474 * @param showGroupConsensus the value of field
2475 * 'showGroupConsensus'.
2477 public void setShowGroupConsensus(
2478 final boolean showGroupConsensus) {
2479 this._showGroupConsensus = showGroupConsensus;
2480 this._has_showGroupConsensus = true;
2484 * Sets the value of field 'showGroupConservation'.
2486 * @param showGroupConservation the value of field
2487 * 'showGroupConservation'.
2489 public void setShowGroupConservation(
2490 final boolean showGroupConservation) {
2491 this._showGroupConservation = showGroupConservation;
2492 this._has_showGroupConservation = true;
2496 * Sets the value of field 'showNPfeatureTooltip'.
2498 * @param showNPfeatureTooltip the value of field
2499 * 'showNPfeatureTooltip'.
2501 public void setShowNPfeatureTooltip(
2502 final boolean showNPfeatureTooltip) {
2503 this._showNPfeatureTooltip = showNPfeatureTooltip;
2504 this._has_showNPfeatureTooltip = true;
2508 * Sets the value of field 'showSequenceFeatures'.
2510 * @param showSequenceFeatures the value of field
2511 * 'showSequenceFeatures'.
2513 public void setShowSequenceFeatures(
2514 final boolean showSequenceFeatures) {
2515 this._showSequenceFeatures = showSequenceFeatures;
2516 this._has_showSequenceFeatures = true;
2520 * Sets the value of field 'showSequenceLogo'.
2522 * @param showSequenceLogo the value of field 'showSequenceLogo'
2524 public void setShowSequenceLogo(
2525 final boolean showSequenceLogo) {
2526 this._showSequenceLogo = showSequenceLogo;
2527 this._has_showSequenceLogo = true;
2531 * Sets the value of field 'showText'.
2533 * @param showText the value of field 'showText'.
2535 public void setShowText(
2536 final boolean showText) {
2537 this._showText = showText;
2538 this._has_showText = true;
2542 * Sets the value of field 'showUnconserved'.
2544 * @param showUnconserved the value of field 'showUnconserved'.
2546 public void setShowUnconserved(
2547 final boolean showUnconserved) {
2548 this._showUnconserved = showUnconserved;
2549 this._has_showUnconserved = true;
2553 * Sets the value of field 'startRes'.
2555 * @param startRes the value of field 'startRes'.
2557 public void setStartRes(
2558 final int startRes) {
2559 this._startRes = startRes;
2560 this._has_startRes = true;
2564 * Sets the value of field 'startSeq'.
2566 * @param startSeq the value of field 'startSeq'.
2568 public void setStartSeq(
2569 final int startSeq) {
2570 this._startSeq = startSeq;
2571 this._has_startSeq = true;
2575 * Sets the value of field 'textCol1'.
2577 * @param textCol1 the value of field 'textCol1'.
2579 public void setTextCol1(
2580 final int textCol1) {
2581 this._textCol1 = textCol1;
2582 this._has_textCol1 = true;
2586 * Sets the value of field 'textCol2'.
2588 * @param textCol2 the value of field 'textCol2'.
2590 public void setTextCol2(
2591 final int textCol2) {
2592 this._textCol2 = textCol2;
2593 this._has_textCol2 = true;
2597 * Sets the value of field 'textColThreshold'.
2599 * @param textColThreshold the value of field 'textColThreshold'
2601 public void setTextColThreshold(
2602 final int textColThreshold) {
2603 this._textColThreshold = textColThreshold;
2604 this._has_textColThreshold = true;
2608 * Sets the value of field 'title'.
2610 * @param title the value of field 'title'.
2612 public void setTitle(
2613 final java.lang.String title) {
2614 this._title = title;
2618 * Sets the value of field 'viewName'.
2620 * @param viewName the value of field 'viewName'.
2622 public void setViewName(
2623 final java.lang.String viewName) {
2624 this._viewName = viewName;
2628 * Sets the value of field 'width'.
2630 * @param width the value of field 'width'.
2632 public void setWidth(
2634 this._width = width;
2635 this._has_width = true;
2639 * Sets the value of field 'wrapAlignment'.
2641 * @param wrapAlignment the value of field 'wrapAlignment'.
2643 public void setWrapAlignment(
2644 final boolean wrapAlignment) {
2645 this._wrapAlignment = wrapAlignment;
2646 this._has_wrapAlignment = true;
2650 * Sets the value of field 'xpos'.
2652 * @param xpos the value of field 'xpos'.
2654 public void setXpos(
2657 this._has_xpos = true;
2661 * Sets the value of field 'ypos'.
2663 * @param ypos the value of field 'ypos'.
2665 public void setYpos(
2668 this._has_ypos = true;
2675 * @throws org.exolab.castor.xml.MarshalException if object is
2676 * null or if any SAXException is thrown during marshaling
2677 * @throws org.exolab.castor.xml.ValidationException if this
2678 * object is an invalid instance according to the schema
2679 * @return the unmarshaled
2680 * jalview.schemabinding.version2.Viewport
2682 public static jalview.schemabinding.version2.Viewport unmarshal(
2683 final java.io.Reader reader)
2684 throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
2685 return (jalview.schemabinding.version2.Viewport) Unmarshaller.unmarshal(jalview.schemabinding.version2.Viewport.class, reader);
2691 * @throws org.exolab.castor.xml.ValidationException if this
2692 * object is an invalid instance according to the schema
2694 public void validate(
2696 throws org.exolab.castor.xml.ValidationException {
2697 org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
2698 validator.validate(this);