2 * This class was automatically generated with
3 * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
8 package jalview.schemabinding.version2;
10 //---------------------------------/
11 //- Imported classes and packages -/
12 //---------------------------------/
14 import org.exolab.castor.xml.Marshaller;
15 import org.exolab.castor.xml.Unmarshaller;
20 * @version $Revision$ $Date$
22 public class Viewport implements java.io.Serializable {
25 //--------------------------/
26 //- Class/Member Variables -/
27 //--------------------------/
30 * Field _conservationSelected.
32 private boolean _conservationSelected;
35 * keeps track of state for field: _conservationSelected
37 private boolean _has_conservationSelected;
42 private boolean _pidSelected;
45 * keeps track of state for field: _pidSelected
47 private boolean _has_pidSelected;
52 private java.lang.String _bgColour;
55 * Field _consThreshold.
57 private int _consThreshold;
60 * keeps track of state for field: _consThreshold
62 private boolean _has_consThreshold;
65 * Field _pidThreshold.
67 private int _pidThreshold;
70 * keeps track of state for field: _pidThreshold
72 private boolean _has_pidThreshold;
77 private java.lang.String _title;
82 private boolean _showFullId;
85 * keeps track of state for field: _showFullId
87 private boolean _has_showFullId;
90 * Field _rightAlignIds.
92 private boolean _rightAlignIds;
95 * keeps track of state for field: _rightAlignIds
97 private boolean _has_rightAlignIds;
102 private boolean _showText;
105 * keeps track of state for field: _showText
107 private boolean _has_showText;
110 * Field _showColourText.
112 private boolean _showColourText;
115 * keeps track of state for field: _showColourText
117 private boolean _has_showColourText;
120 * Field _showUnconserved.
122 private boolean _showUnconserved = false;
125 * keeps track of state for field: _showUnconserved
127 private boolean _has_showUnconserved;
132 private boolean _showBoxes;
135 * keeps track of state for field: _showBoxes
137 private boolean _has_showBoxes;
140 * Field _wrapAlignment.
142 private boolean _wrapAlignment;
145 * keeps track of state for field: _wrapAlignment
147 private boolean _has_wrapAlignment;
152 private boolean _renderGaps;
155 * keeps track of state for field: _renderGaps
157 private boolean _has_renderGaps;
160 * Field _showSequenceFeatures.
162 private boolean _showSequenceFeatures;
165 * keeps track of state for field: _showSequenceFeatures
167 private boolean _has_showSequenceFeatures;
170 * Field _showNPfeatureTooltip.
172 private boolean _showNPfeatureTooltip;
175 * keeps track of state for field: _showNPfeatureTooltip
177 private boolean _has_showNPfeatureTooltip;
180 * Field _showDbRefTooltip.
182 private boolean _showDbRefTooltip;
185 * keeps track of state for field: _showDbRefTooltip
187 private boolean _has_showDbRefTooltip;
190 * Field _followHighlight.
192 private boolean _followHighlight = true;
195 * keeps track of state for field: _followHighlight
197 private boolean _has_followHighlight;
200 * Field _followSelection.
202 private boolean _followSelection = true;
205 * keeps track of state for field: _followSelection
207 private boolean _has_followSelection;
210 * Field _showAnnotation.
212 private boolean _showAnnotation;
215 * keeps track of state for field: _showAnnotation
217 private boolean _has_showAnnotation;
220 * Field _centreColumnLabels.
222 private boolean _centreColumnLabels = false;
225 * keeps track of state for field: _centreColumnLabels
227 private boolean _has_centreColumnLabels;
230 * Field _showGroupConservation.
232 private boolean _showGroupConservation = false;
235 * keeps track of state for field: _showGroupConservation
237 private boolean _has_showGroupConservation;
240 * Field _showGroupConsensus.
242 private boolean _showGroupConsensus = false;
245 * keeps track of state for field: _showGroupConsensus
247 private boolean _has_showGroupConsensus;
250 * Field _showConsensusHistogram.
252 private boolean _showConsensusHistogram = true;
255 * keeps track of state for field: _showConsensusHistogram
257 private boolean _has_showConsensusHistogram;
260 * Field _showSequenceLogo.
262 private boolean _showSequenceLogo = false;
265 * keeps track of state for field: _showSequenceLogo
267 private boolean _has_showSequenceLogo;
270 * Field _normaliseSequenceLogo.
272 private boolean _normaliseSequenceLogo = false;
275 * keeps track of state for field: _normaliseSequenceLogo
277 private boolean _has_normaliseSequenceLogo;
280 * Field _ignoreGapsinConsensus.
282 private boolean _ignoreGapsinConsensus = true;
285 * keeps track of state for field: _ignoreGapsinConsensus
287 private boolean _has_ignoreGapsinConsensus;
292 private int _startRes;
295 * keeps track of state for field: _startRes
297 private boolean _has_startRes;
302 private int _startSeq;
305 * keeps track of state for field: _startSeq
307 private boolean _has_startSeq;
312 private java.lang.String _fontName;
317 private int _fontSize;
320 * keeps track of state for field: _fontSize
322 private boolean _has_fontSize;
327 private int _fontStyle;
330 * keeps track of state for field: _fontStyle
332 private boolean _has_fontStyle;
335 * Field _scaleProteinAsCdna.
337 private boolean _scaleProteinAsCdna = true;
340 * keeps track of state for field: _scaleProteinAsCdna
342 private boolean _has_scaleProteinAsCdna;
347 private java.lang.String _viewName;
350 * Field _sequenceSetId.
352 private java.lang.String _sequenceSetId;
355 * Field _gatheredViews.
357 private boolean _gatheredViews;
360 * keeps track of state for field: _gatheredViews
362 private boolean _has_gatheredViews;
367 private int _textCol1;
370 * keeps track of state for field: _textCol1
372 private boolean _has_textCol1;
377 private int _textCol2;
380 * keeps track of state for field: _textCol2
382 private boolean _has_textCol2;
385 * Field _textColThreshold.
387 private int _textColThreshold;
390 * keeps track of state for field: _textColThreshold
392 private boolean _has_textColThreshold;
395 * unique id used by jalview to
401 private java.lang.String _id;
404 * The viewport id of this viewport's
405 * (cdna/protein) coding complement, if any
408 private java.lang.String _complementId;
416 * keeps track of state for field: _width
418 private boolean _has_width;
426 * keeps track of state for field: _height
428 private boolean _has_height;
436 * keeps track of state for field: _xpos
438 private boolean _has_xpos;
446 * keeps track of state for field: _ypos
448 private boolean _has_ypos;
451 * Field _annotationColours.
453 private jalview.schemabinding.version2.AnnotationColours _annotationColours;
456 * Field _hiddenColumnsList.
458 private java.util.Vector _hiddenColumnsList;
461 * Field _calcIdParamList.
463 private java.util.Vector _calcIdParamList;
472 this._hiddenColumnsList = new java.util.Vector();
473 this._calcIdParamList = new java.util.Vector();
484 * @param vCalcIdParam
485 * @throws java.lang.IndexOutOfBoundsException if the index
486 * given is outside the bounds of the collection
488 public void addCalcIdParam(
489 final jalview.schemabinding.version2.CalcIdParam vCalcIdParam)
490 throws java.lang.IndexOutOfBoundsException {
491 this._calcIdParamList.addElement(vCalcIdParam);
498 * @param vCalcIdParam
499 * @throws java.lang.IndexOutOfBoundsException if the index
500 * given is outside the bounds of the collection
502 public void addCalcIdParam(
504 final jalview.schemabinding.version2.CalcIdParam vCalcIdParam)
505 throws java.lang.IndexOutOfBoundsException {
506 this._calcIdParamList.add(index, vCalcIdParam);
512 * @param vHiddenColumns
513 * @throws java.lang.IndexOutOfBoundsException if the index
514 * given is outside the bounds of the collection
516 public void addHiddenColumns(
517 final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)
518 throws java.lang.IndexOutOfBoundsException {
519 this._hiddenColumnsList.addElement(vHiddenColumns);
526 * @param vHiddenColumns
527 * @throws java.lang.IndexOutOfBoundsException if the index
528 * given is outside the bounds of the collection
530 public void addHiddenColumns(
532 final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)
533 throws java.lang.IndexOutOfBoundsException {
534 this._hiddenColumnsList.add(index, vHiddenColumns);
539 public void deleteCentreColumnLabels(
541 this._has_centreColumnLabels= false;
546 public void deleteConsThreshold(
548 this._has_consThreshold= false;
553 public void deleteConservationSelected(
555 this._has_conservationSelected= false;
560 public void deleteFollowHighlight(
562 this._has_followHighlight= false;
567 public void deleteFollowSelection(
569 this._has_followSelection= false;
574 public void deleteFontSize(
576 this._has_fontSize= false;
581 public void deleteFontStyle(
583 this._has_fontStyle= false;
588 public void deleteGatheredViews(
590 this._has_gatheredViews= false;
595 public void deleteHeight(
597 this._has_height= false;
602 public void deleteIgnoreGapsinConsensus(
604 this._has_ignoreGapsinConsensus= false;
609 public void deleteNormaliseSequenceLogo(
611 this._has_normaliseSequenceLogo= false;
616 public void deletePidSelected(
618 this._has_pidSelected= false;
623 public void deletePidThreshold(
625 this._has_pidThreshold= false;
630 public void deleteRenderGaps(
632 this._has_renderGaps= false;
637 public void deleteRightAlignIds(
639 this._has_rightAlignIds= false;
644 public void deleteScaleProteinAsCdna(
646 this._has_scaleProteinAsCdna= false;
651 public void deleteShowAnnotation(
653 this._has_showAnnotation= false;
658 public void deleteShowBoxes(
660 this._has_showBoxes= false;
665 public void deleteShowColourText(
667 this._has_showColourText= false;
672 public void deleteShowConsensusHistogram(
674 this._has_showConsensusHistogram= false;
679 public void deleteShowDbRefTooltip(
681 this._has_showDbRefTooltip= false;
686 public void deleteShowFullId(
688 this._has_showFullId= false;
693 public void deleteShowGroupConsensus(
695 this._has_showGroupConsensus= false;
700 public void deleteShowGroupConservation(
702 this._has_showGroupConservation= false;
707 public void deleteShowNPfeatureTooltip(
709 this._has_showNPfeatureTooltip= false;
714 public void deleteShowSequenceFeatures(
716 this._has_showSequenceFeatures= false;
721 public void deleteShowSequenceLogo(
723 this._has_showSequenceLogo= false;
728 public void deleteShowText(
730 this._has_showText= false;
735 public void deleteShowUnconserved(
737 this._has_showUnconserved= false;
742 public void deleteStartRes(
744 this._has_startRes= false;
749 public void deleteStartSeq(
751 this._has_startSeq= false;
756 public void deleteTextCol1(
758 this._has_textCol1= false;
763 public void deleteTextCol2(
765 this._has_textCol2= false;
770 public void deleteTextColThreshold(
772 this._has_textColThreshold= false;
777 public void deleteWidth(
779 this._has_width= false;
784 public void deleteWrapAlignment(
786 this._has_wrapAlignment= false;
791 public void deleteXpos(
793 this._has_xpos= false;
798 public void deleteYpos(
800 this._has_ypos= false;
804 * Method enumerateCalcIdParam.
806 * @return an Enumeration over all
807 * jalview.schemabinding.version2.CalcIdParam elements
809 public java.util.Enumeration enumerateCalcIdParam(
811 return this._calcIdParamList.elements();
815 * Method enumerateHiddenColumns.
817 * @return an Enumeration over all
818 * jalview.schemabinding.version2.HiddenColumns elements
820 public java.util.Enumeration enumerateHiddenColumns(
822 return this._hiddenColumnsList.elements();
826 * Returns the value of field 'annotationColours'.
828 * @return the value of field 'AnnotationColours'.
830 public jalview.schemabinding.version2.AnnotationColours getAnnotationColours(
832 return this._annotationColours;
836 * Returns the value of field 'bgColour'.
838 * @return the value of field 'BgColour'.
840 public java.lang.String getBgColour(
842 return this._bgColour;
846 * Method getCalcIdParam.
849 * @throws java.lang.IndexOutOfBoundsException if the index
850 * given is outside the bounds of the collection
851 * @return the value of the
852 * jalview.schemabinding.version2.CalcIdParam at the given index
854 public jalview.schemabinding.version2.CalcIdParam getCalcIdParam(
856 throws java.lang.IndexOutOfBoundsException {
857 // check bounds for index
858 if (index < 0 || index >= this._calcIdParamList.size()) {
859 throw new IndexOutOfBoundsException("getCalcIdParam: Index value '" + index + "' not in range [0.." + (this._calcIdParamList.size() - 1) + "]");
862 return (jalview.schemabinding.version2.CalcIdParam) _calcIdParamList.get(index);
866 * Method getCalcIdParam.Returns the contents of the collection
867 * in an Array. <p>Note: Just in case the collection contents
868 * are changing in another thread, we pass a 0-length Array of
869 * the correct type into the API call. This way we <i>know</i>
870 * that the Array returned is of exactly the correct length.
872 * @return this collection as an Array
874 public jalview.schemabinding.version2.CalcIdParam[] getCalcIdParam(
876 jalview.schemabinding.version2.CalcIdParam[] array = new jalview.schemabinding.version2.CalcIdParam[0];
877 return (jalview.schemabinding.version2.CalcIdParam[]) this._calcIdParamList.toArray(array);
881 * Method getCalcIdParamCount.
883 * @return the size of this collection
885 public int getCalcIdParamCount(
887 return this._calcIdParamList.size();
891 * Returns the value of field 'centreColumnLabels'.
893 * @return the value of field 'CentreColumnLabels'.
895 public boolean getCentreColumnLabels(
897 return this._centreColumnLabels;
901 * Returns the value of field 'complementId'. The field
902 * 'complementId' has the following description: The viewport
903 * id of this viewport's
904 * (cdna/protein) coding complement, if any
907 * @return the value of field 'ComplementId'.
909 public java.lang.String getComplementId(
911 return this._complementId;
915 * Returns the value of field 'consThreshold'.
917 * @return the value of field 'ConsThreshold'.
919 public int getConsThreshold(
921 return this._consThreshold;
925 * Returns the value of field 'conservationSelected'.
927 * @return the value of field 'ConservationSelected'.
929 public boolean getConservationSelected(
931 return this._conservationSelected;
935 * Returns the value of field 'followHighlight'.
937 * @return the value of field 'FollowHighlight'.
939 public boolean getFollowHighlight(
941 return this._followHighlight;
945 * Returns the value of field 'followSelection'.
947 * @return the value of field 'FollowSelection'.
949 public boolean getFollowSelection(
951 return this._followSelection;
955 * Returns the value of field 'fontName'.
957 * @return the value of field 'FontName'.
959 public java.lang.String getFontName(
961 return this._fontName;
965 * Returns the value of field 'fontSize'.
967 * @return the value of field 'FontSize'.
969 public int getFontSize(
971 return this._fontSize;
975 * Returns the value of field 'fontStyle'.
977 * @return the value of field 'FontStyle'.
979 public int getFontStyle(
981 return this._fontStyle;
985 * Returns the value of field 'gatheredViews'.
987 * @return the value of field 'GatheredViews'.
989 public boolean getGatheredViews(
991 return this._gatheredViews;
995 * Returns the value of field 'height'.
997 * @return the value of field 'Height'.
999 public int getHeight(
1001 return this._height;
1005 * Method getHiddenColumns.
1008 * @throws java.lang.IndexOutOfBoundsException if the index
1009 * given is outside the bounds of the collection
1010 * @return the value of the
1011 * jalview.schemabinding.version2.HiddenColumns at the given
1014 public jalview.schemabinding.version2.HiddenColumns getHiddenColumns(
1016 throws java.lang.IndexOutOfBoundsException {
1017 // check bounds for index
1018 if (index < 0 || index >= this._hiddenColumnsList.size()) {
1019 throw new IndexOutOfBoundsException("getHiddenColumns: Index value '" + index + "' not in range [0.." + (this._hiddenColumnsList.size() - 1) + "]");
1022 return (jalview.schemabinding.version2.HiddenColumns) _hiddenColumnsList.get(index);
1026 * Method getHiddenColumns.Returns the contents of the
1027 * collection in an Array. <p>Note: Just in case the
1028 * collection contents are changing in another thread, we pass
1029 * a 0-length Array of the correct type into the API call.
1030 * This way we <i>know</i> that the Array returned is of
1031 * exactly the correct length.
1033 * @return this collection as an Array
1035 public jalview.schemabinding.version2.HiddenColumns[] getHiddenColumns(
1037 jalview.schemabinding.version2.HiddenColumns[] array = new jalview.schemabinding.version2.HiddenColumns[0];
1038 return (jalview.schemabinding.version2.HiddenColumns[]) this._hiddenColumnsList.toArray(array);
1042 * Method getHiddenColumnsCount.
1044 * @return the size of this collection
1046 public int getHiddenColumnsCount(
1048 return this._hiddenColumnsList.size();
1052 * Returns the value of field 'id'. The field 'id' has the
1053 * following description: unique id used by jalview to
1055 * between stored and
1056 * instantiated views
1059 * @return the value of field 'Id'.
1061 public java.lang.String getId(
1067 * Returns the value of field 'ignoreGapsinConsensus'.
1069 * @return the value of field 'IgnoreGapsinConsensus'.
1071 public boolean getIgnoreGapsinConsensus(
1073 return this._ignoreGapsinConsensus;
1077 * Returns the value of field 'normaliseSequenceLogo'.
1079 * @return the value of field 'NormaliseSequenceLogo'.
1081 public boolean getNormaliseSequenceLogo(
1083 return this._normaliseSequenceLogo;
1087 * Returns the value of field 'pidSelected'.
1089 * @return the value of field 'PidSelected'.
1091 public boolean getPidSelected(
1093 return this._pidSelected;
1097 * Returns the value of field 'pidThreshold'.
1099 * @return the value of field 'PidThreshold'.
1101 public int getPidThreshold(
1103 return this._pidThreshold;
1107 * Returns the value of field 'renderGaps'.
1109 * @return the value of field 'RenderGaps'.
1111 public boolean getRenderGaps(
1113 return this._renderGaps;
1117 * Returns the value of field 'rightAlignIds'.
1119 * @return the value of field 'RightAlignIds'.
1121 public boolean getRightAlignIds(
1123 return this._rightAlignIds;
1127 * Returns the value of field 'scaleProteinAsCdna'.
1129 * @return the value of field 'ScaleProteinAsCdna'.
1131 public boolean getScaleProteinAsCdna(
1133 return this._scaleProteinAsCdna;
1137 * Returns the value of field 'sequenceSetId'.
1139 * @return the value of field 'SequenceSetId'.
1141 public java.lang.String getSequenceSetId(
1143 return this._sequenceSetId;
1147 * Returns the value of field 'showAnnotation'.
1149 * @return the value of field 'ShowAnnotation'.
1151 public boolean getShowAnnotation(
1153 return this._showAnnotation;
1157 * Returns the value of field 'showBoxes'.
1159 * @return the value of field 'ShowBoxes'.
1161 public boolean getShowBoxes(
1163 return this._showBoxes;
1167 * Returns the value of field 'showColourText'.
1169 * @return the value of field 'ShowColourText'.
1171 public boolean getShowColourText(
1173 return this._showColourText;
1177 * Returns the value of field 'showConsensusHistogram'.
1179 * @return the value of field 'ShowConsensusHistogram'.
1181 public boolean getShowConsensusHistogram(
1183 return this._showConsensusHistogram;
1187 * Returns the value of field 'showDbRefTooltip'.
1189 * @return the value of field 'ShowDbRefTooltip'.
1191 public boolean getShowDbRefTooltip(
1193 return this._showDbRefTooltip;
1197 * Returns the value of field 'showFullId'.
1199 * @return the value of field 'ShowFullId'.
1201 public boolean getShowFullId(
1203 return this._showFullId;
1207 * Returns the value of field 'showGroupConsensus'.
1209 * @return the value of field 'ShowGroupConsensus'.
1211 public boolean getShowGroupConsensus(
1213 return this._showGroupConsensus;
1217 * Returns the value of field 'showGroupConservation'.
1219 * @return the value of field 'ShowGroupConservation'.
1221 public boolean getShowGroupConservation(
1223 return this._showGroupConservation;
1227 * Returns the value of field 'showNPfeatureTooltip'.
1229 * @return the value of field 'ShowNPfeatureTooltip'.
1231 public boolean getShowNPfeatureTooltip(
1233 return this._showNPfeatureTooltip;
1237 * Returns the value of field 'showSequenceFeatures'.
1239 * @return the value of field 'ShowSequenceFeatures'.
1241 public boolean getShowSequenceFeatures(
1243 return this._showSequenceFeatures;
1247 * Returns the value of field 'showSequenceLogo'.
1249 * @return the value of field 'ShowSequenceLogo'.
1251 public boolean getShowSequenceLogo(
1253 return this._showSequenceLogo;
1257 * Returns the value of field 'showText'.
1259 * @return the value of field 'ShowText'.
1261 public boolean getShowText(
1263 return this._showText;
1267 * Returns the value of field 'showUnconserved'.
1269 * @return the value of field 'ShowUnconserved'.
1271 public boolean getShowUnconserved(
1273 return this._showUnconserved;
1277 * Returns the value of field 'startRes'.
1279 * @return the value of field 'StartRes'.
1281 public int getStartRes(
1283 return this._startRes;
1287 * Returns the value of field 'startSeq'.
1289 * @return the value of field 'StartSeq'.
1291 public int getStartSeq(
1293 return this._startSeq;
1297 * Returns the value of field 'textCol1'.
1299 * @return the value of field 'TextCol1'.
1301 public int getTextCol1(
1303 return this._textCol1;
1307 * Returns the value of field 'textCol2'.
1309 * @return the value of field 'TextCol2'.
1311 public int getTextCol2(
1313 return this._textCol2;
1317 * Returns the value of field 'textColThreshold'.
1319 * @return the value of field 'TextColThreshold'.
1321 public int getTextColThreshold(
1323 return this._textColThreshold;
1327 * Returns the value of field 'title'.
1329 * @return the value of field 'Title'.
1331 public java.lang.String getTitle(
1337 * Returns the value of field 'viewName'.
1339 * @return the value of field 'ViewName'.
1341 public java.lang.String getViewName(
1343 return this._viewName;
1347 * Returns the value of field 'width'.
1349 * @return the value of field 'Width'.
1351 public int getWidth(
1357 * Returns the value of field 'wrapAlignment'.
1359 * @return the value of field 'WrapAlignment'.
1361 public boolean getWrapAlignment(
1363 return this._wrapAlignment;
1367 * Returns the value of field 'xpos'.
1369 * @return the value of field 'Xpos'.
1377 * Returns the value of field 'ypos'.
1379 * @return the value of field 'Ypos'.
1387 * Method hasCentreColumnLabels.
1389 * @return true if at least one CentreColumnLabels has been adde
1391 public boolean hasCentreColumnLabels(
1393 return this._has_centreColumnLabels;
1397 * Method hasConsThreshold.
1399 * @return true if at least one ConsThreshold has been added
1401 public boolean hasConsThreshold(
1403 return this._has_consThreshold;
1407 * Method hasConservationSelected.
1409 * @return true if at least one ConservationSelected has been
1412 public boolean hasConservationSelected(
1414 return this._has_conservationSelected;
1418 * Method hasFollowHighlight.
1420 * @return true if at least one FollowHighlight has been added
1422 public boolean hasFollowHighlight(
1424 return this._has_followHighlight;
1428 * Method hasFollowSelection.
1430 * @return true if at least one FollowSelection has been added
1432 public boolean hasFollowSelection(
1434 return this._has_followSelection;
1438 * Method hasFontSize.
1440 * @return true if at least one FontSize has been added
1442 public boolean hasFontSize(
1444 return this._has_fontSize;
1448 * Method hasFontStyle.
1450 * @return true if at least one FontStyle has been added
1452 public boolean hasFontStyle(
1454 return this._has_fontStyle;
1458 * Method hasGatheredViews.
1460 * @return true if at least one GatheredViews has been added
1462 public boolean hasGatheredViews(
1464 return this._has_gatheredViews;
1470 * @return true if at least one Height has been added
1472 public boolean hasHeight(
1474 return this._has_height;
1478 * Method hasIgnoreGapsinConsensus.
1480 * @return true if at least one IgnoreGapsinConsensus has been
1483 public boolean hasIgnoreGapsinConsensus(
1485 return this._has_ignoreGapsinConsensus;
1489 * Method hasNormaliseSequenceLogo.
1491 * @return true if at least one NormaliseSequenceLogo has been
1494 public boolean hasNormaliseSequenceLogo(
1496 return this._has_normaliseSequenceLogo;
1500 * Method hasPidSelected.
1502 * @return true if at least one PidSelected has been added
1504 public boolean hasPidSelected(
1506 return this._has_pidSelected;
1510 * Method hasPidThreshold.
1512 * @return true if at least one PidThreshold has been added
1514 public boolean hasPidThreshold(
1516 return this._has_pidThreshold;
1520 * Method hasRenderGaps.
1522 * @return true if at least one RenderGaps has been added
1524 public boolean hasRenderGaps(
1526 return this._has_renderGaps;
1530 * Method hasRightAlignIds.
1532 * @return true if at least one RightAlignIds has been added
1534 public boolean hasRightAlignIds(
1536 return this._has_rightAlignIds;
1540 * Method hasScaleProteinAsCdna.
1542 * @return true if at least one ScaleProteinAsCdna has been adde
1544 public boolean hasScaleProteinAsCdna(
1546 return this._has_scaleProteinAsCdna;
1550 * Method hasShowAnnotation.
1552 * @return true if at least one ShowAnnotation has been added
1554 public boolean hasShowAnnotation(
1556 return this._has_showAnnotation;
1560 * Method hasShowBoxes.
1562 * @return true if at least one ShowBoxes has been added
1564 public boolean hasShowBoxes(
1566 return this._has_showBoxes;
1570 * Method hasShowColourText.
1572 * @return true if at least one ShowColourText has been added
1574 public boolean hasShowColourText(
1576 return this._has_showColourText;
1580 * Method hasShowConsensusHistogram.
1582 * @return true if at least one ShowConsensusHistogram has been
1585 public boolean hasShowConsensusHistogram(
1587 return this._has_showConsensusHistogram;
1591 * Method hasShowDbRefTooltip.
1593 * @return true if at least one ShowDbRefTooltip has been added
1595 public boolean hasShowDbRefTooltip(
1597 return this._has_showDbRefTooltip;
1601 * Method hasShowFullId.
1603 * @return true if at least one ShowFullId has been added
1605 public boolean hasShowFullId(
1607 return this._has_showFullId;
1611 * Method hasShowGroupConsensus.
1613 * @return true if at least one ShowGroupConsensus has been adde
1615 public boolean hasShowGroupConsensus(
1617 return this._has_showGroupConsensus;
1621 * Method hasShowGroupConservation.
1623 * @return true if at least one ShowGroupConservation has been
1626 public boolean hasShowGroupConservation(
1628 return this._has_showGroupConservation;
1632 * Method hasShowNPfeatureTooltip.
1634 * @return true if at least one ShowNPfeatureTooltip has been
1637 public boolean hasShowNPfeatureTooltip(
1639 return this._has_showNPfeatureTooltip;
1643 * Method hasShowSequenceFeatures.
1645 * @return true if at least one ShowSequenceFeatures has been
1648 public boolean hasShowSequenceFeatures(
1650 return this._has_showSequenceFeatures;
1654 * Method hasShowSequenceLogo.
1656 * @return true if at least one ShowSequenceLogo has been added
1658 public boolean hasShowSequenceLogo(
1660 return this._has_showSequenceLogo;
1664 * Method hasShowText.
1666 * @return true if at least one ShowText has been added
1668 public boolean hasShowText(
1670 return this._has_showText;
1674 * Method hasShowUnconserved.
1676 * @return true if at least one ShowUnconserved has been added
1678 public boolean hasShowUnconserved(
1680 return this._has_showUnconserved;
1684 * Method hasStartRes.
1686 * @return true if at least one StartRes has been added
1688 public boolean hasStartRes(
1690 return this._has_startRes;
1694 * Method hasStartSeq.
1696 * @return true if at least one StartSeq has been added
1698 public boolean hasStartSeq(
1700 return this._has_startSeq;
1704 * Method hasTextCol1.
1706 * @return true if at least one TextCol1 has been added
1708 public boolean hasTextCol1(
1710 return this._has_textCol1;
1714 * Method hasTextCol2.
1716 * @return true if at least one TextCol2 has been added
1718 public boolean hasTextCol2(
1720 return this._has_textCol2;
1724 * Method hasTextColThreshold.
1726 * @return true if at least one TextColThreshold has been added
1728 public boolean hasTextColThreshold(
1730 return this._has_textColThreshold;
1736 * @return true if at least one Width has been added
1738 public boolean hasWidth(
1740 return this._has_width;
1744 * Method hasWrapAlignment.
1746 * @return true if at least one WrapAlignment has been added
1748 public boolean hasWrapAlignment(
1750 return this._has_wrapAlignment;
1756 * @return true if at least one Xpos has been added
1758 public boolean hasXpos(
1760 return this._has_xpos;
1766 * @return true if at least one Ypos has been added
1768 public boolean hasYpos(
1770 return this._has_ypos;
1774 * Returns the value of field 'centreColumnLabels'.
1776 * @return the value of field 'CentreColumnLabels'.
1778 public boolean isCentreColumnLabels(
1780 return this._centreColumnLabels;
1784 * Returns the value of field 'conservationSelected'.
1786 * @return the value of field 'ConservationSelected'.
1788 public boolean isConservationSelected(
1790 return this._conservationSelected;
1794 * Returns the value of field 'followHighlight'.
1796 * @return the value of field 'FollowHighlight'.
1798 public boolean isFollowHighlight(
1800 return this._followHighlight;
1804 * Returns the value of field 'followSelection'.
1806 * @return the value of field 'FollowSelection'.
1808 public boolean isFollowSelection(
1810 return this._followSelection;
1814 * Returns the value of field 'gatheredViews'.
1816 * @return the value of field 'GatheredViews'.
1818 public boolean isGatheredViews(
1820 return this._gatheredViews;
1824 * Returns the value of field 'ignoreGapsinConsensus'.
1826 * @return the value of field 'IgnoreGapsinConsensus'.
1828 public boolean isIgnoreGapsinConsensus(
1830 return this._ignoreGapsinConsensus;
1834 * Returns the value of field 'normaliseSequenceLogo'.
1836 * @return the value of field 'NormaliseSequenceLogo'.
1838 public boolean isNormaliseSequenceLogo(
1840 return this._normaliseSequenceLogo;
1844 * Returns the value of field 'pidSelected'.
1846 * @return the value of field 'PidSelected'.
1848 public boolean isPidSelected(
1850 return this._pidSelected;
1854 * Returns the value of field 'renderGaps'.
1856 * @return the value of field 'RenderGaps'.
1858 public boolean isRenderGaps(
1860 return this._renderGaps;
1864 * Returns the value of field 'rightAlignIds'.
1866 * @return the value of field 'RightAlignIds'.
1868 public boolean isRightAlignIds(
1870 return this._rightAlignIds;
1874 * Returns the value of field 'scaleProteinAsCdna'.
1876 * @return the value of field 'ScaleProteinAsCdna'.
1878 public boolean isScaleProteinAsCdna(
1880 return this._scaleProteinAsCdna;
1884 * Returns the value of field 'showAnnotation'.
1886 * @return the value of field 'ShowAnnotation'.
1888 public boolean isShowAnnotation(
1890 return this._showAnnotation;
1894 * Returns the value of field 'showBoxes'.
1896 * @return the value of field 'ShowBoxes'.
1898 public boolean isShowBoxes(
1900 return this._showBoxes;
1904 * Returns the value of field 'showColourText'.
1906 * @return the value of field 'ShowColourText'.
1908 public boolean isShowColourText(
1910 return this._showColourText;
1914 * Returns the value of field 'showConsensusHistogram'.
1916 * @return the value of field 'ShowConsensusHistogram'.
1918 public boolean isShowConsensusHistogram(
1920 return this._showConsensusHistogram;
1924 * Returns the value of field 'showDbRefTooltip'.
1926 * @return the value of field 'ShowDbRefTooltip'.
1928 public boolean isShowDbRefTooltip(
1930 return this._showDbRefTooltip;
1934 * Returns the value of field 'showFullId'.
1936 * @return the value of field 'ShowFullId'.
1938 public boolean isShowFullId(
1940 return this._showFullId;
1944 * Returns the value of field 'showGroupConsensus'.
1946 * @return the value of field 'ShowGroupConsensus'.
1948 public boolean isShowGroupConsensus(
1950 return this._showGroupConsensus;
1954 * Returns the value of field 'showGroupConservation'.
1956 * @return the value of field 'ShowGroupConservation'.
1958 public boolean isShowGroupConservation(
1960 return this._showGroupConservation;
1964 * Returns the value of field 'showNPfeatureTooltip'.
1966 * @return the value of field 'ShowNPfeatureTooltip'.
1968 public boolean isShowNPfeatureTooltip(
1970 return this._showNPfeatureTooltip;
1974 * Returns the value of field 'showSequenceFeatures'.
1976 * @return the value of field 'ShowSequenceFeatures'.
1978 public boolean isShowSequenceFeatures(
1980 return this._showSequenceFeatures;
1984 * Returns the value of field 'showSequenceLogo'.
1986 * @return the value of field 'ShowSequenceLogo'.
1988 public boolean isShowSequenceLogo(
1990 return this._showSequenceLogo;
1994 * Returns the value of field 'showText'.
1996 * @return the value of field 'ShowText'.
1998 public boolean isShowText(
2000 return this._showText;
2004 * Returns the value of field 'showUnconserved'.
2006 * @return the value of field 'ShowUnconserved'.
2008 public boolean isShowUnconserved(
2010 return this._showUnconserved;
2016 * @return true if this object is valid according to the schema
2018 public boolean isValid(
2022 } catch (org.exolab.castor.xml.ValidationException vex) {
2029 * Returns the value of field 'wrapAlignment'.
2031 * @return the value of field 'WrapAlignment'.
2033 public boolean isWrapAlignment(
2035 return this._wrapAlignment;
2042 * @throws org.exolab.castor.xml.MarshalException if object is
2043 * null or if any SAXException is thrown during marshaling
2044 * @throws org.exolab.castor.xml.ValidationException if this
2045 * object is an invalid instance according to the schema
2047 public void marshal(
2048 final java.io.Writer out)
2049 throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
2050 Marshaller.marshal(this, out);
2057 * @throws java.io.IOException if an IOException occurs during
2059 * @throws org.exolab.castor.xml.ValidationException if this
2060 * object is an invalid instance according to the schema
2061 * @throws org.exolab.castor.xml.MarshalException if object is
2062 * null or if any SAXException is thrown during marshaling
2064 public void marshal(
2065 final org.xml.sax.ContentHandler handler)
2066 throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
2067 Marshaller.marshal(this, handler);
2072 public void removeAllCalcIdParam(
2074 this._calcIdParamList.clear();
2079 public void removeAllHiddenColumns(
2081 this._hiddenColumnsList.clear();
2085 * Method removeCalcIdParam.
2087 * @param vCalcIdParam
2088 * @return true if the object was removed from the collection.
2090 public boolean removeCalcIdParam(
2091 final jalview.schemabinding.version2.CalcIdParam vCalcIdParam) {
2092 boolean removed = _calcIdParamList.remove(vCalcIdParam);
2097 * Method removeCalcIdParamAt.
2100 * @return the element removed from the collection
2102 public jalview.schemabinding.version2.CalcIdParam removeCalcIdParamAt(
2104 java.lang.Object obj = this._calcIdParamList.remove(index);
2105 return (jalview.schemabinding.version2.CalcIdParam) obj;
2109 * Method removeHiddenColumns.
2111 * @param vHiddenColumns
2112 * @return true if the object was removed from the collection.
2114 public boolean removeHiddenColumns(
2115 final jalview.schemabinding.version2.HiddenColumns vHiddenColumns) {
2116 boolean removed = _hiddenColumnsList.remove(vHiddenColumns);
2121 * Method removeHiddenColumnsAt.
2124 * @return the element removed from the collection
2126 public jalview.schemabinding.version2.HiddenColumns removeHiddenColumnsAt(
2128 java.lang.Object obj = this._hiddenColumnsList.remove(index);
2129 return (jalview.schemabinding.version2.HiddenColumns) obj;
2133 * Sets the value of field 'annotationColours'.
2135 * @param annotationColours the value of field
2136 * 'annotationColours'.
2138 public void setAnnotationColours(
2139 final jalview.schemabinding.version2.AnnotationColours annotationColours) {
2140 this._annotationColours = annotationColours;
2144 * Sets the value of field 'bgColour'.
2146 * @param bgColour the value of field 'bgColour'.
2148 public void setBgColour(
2149 final java.lang.String bgColour) {
2150 this._bgColour = bgColour;
2157 * @param vCalcIdParam
2158 * @throws java.lang.IndexOutOfBoundsException if the index
2159 * given is outside the bounds of the collection
2161 public void setCalcIdParam(
2163 final jalview.schemabinding.version2.CalcIdParam vCalcIdParam)
2164 throws java.lang.IndexOutOfBoundsException {
2165 // check bounds for index
2166 if (index < 0 || index >= this._calcIdParamList.size()) {
2167 throw new IndexOutOfBoundsException("setCalcIdParam: Index value '" + index + "' not in range [0.." + (this._calcIdParamList.size() - 1) + "]");
2170 this._calcIdParamList.set(index, vCalcIdParam);
2176 * @param vCalcIdParamArray
2178 public void setCalcIdParam(
2179 final jalview.schemabinding.version2.CalcIdParam[] vCalcIdParamArray) {
2181 _calcIdParamList.clear();
2183 for (int i = 0; i < vCalcIdParamArray.length; i++) {
2184 this._calcIdParamList.add(vCalcIdParamArray[i]);
2189 * Sets the value of field 'centreColumnLabels'.
2191 * @param centreColumnLabels the value of field
2192 * 'centreColumnLabels'.
2194 public void setCentreColumnLabels(
2195 final boolean centreColumnLabels) {
2196 this._centreColumnLabels = centreColumnLabels;
2197 this._has_centreColumnLabels = true;
2201 * Sets the value of field 'complementId'. The field
2202 * 'complementId' has the following description: The viewport
2203 * id of this viewport's
2204 * (cdna/protein) coding complement, if any
2207 * @param complementId the value of field 'complementId'.
2209 public void setComplementId(
2210 final java.lang.String complementId) {
2211 this._complementId = complementId;
2215 * Sets the value of field 'consThreshold'.
2217 * @param consThreshold the value of field 'consThreshold'.
2219 public void setConsThreshold(
2220 final int consThreshold) {
2221 this._consThreshold = consThreshold;
2222 this._has_consThreshold = true;
2226 * Sets the value of field 'conservationSelected'.
2228 * @param conservationSelected the value of field
2229 * 'conservationSelected'.
2231 public void setConservationSelected(
2232 final boolean conservationSelected) {
2233 this._conservationSelected = conservationSelected;
2234 this._has_conservationSelected = true;
2238 * Sets the value of field 'followHighlight'.
2240 * @param followHighlight the value of field 'followHighlight'.
2242 public void setFollowHighlight(
2243 final boolean followHighlight) {
2244 this._followHighlight = followHighlight;
2245 this._has_followHighlight = true;
2249 * Sets the value of field 'followSelection'.
2251 * @param followSelection the value of field 'followSelection'.
2253 public void setFollowSelection(
2254 final boolean followSelection) {
2255 this._followSelection = followSelection;
2256 this._has_followSelection = true;
2260 * Sets the value of field 'fontName'.
2262 * @param fontName the value of field 'fontName'.
2264 public void setFontName(
2265 final java.lang.String fontName) {
2266 this._fontName = fontName;
2270 * Sets the value of field 'fontSize'.
2272 * @param fontSize the value of field 'fontSize'.
2274 public void setFontSize(
2275 final int fontSize) {
2276 this._fontSize = fontSize;
2277 this._has_fontSize = true;
2281 * Sets the value of field 'fontStyle'.
2283 * @param fontStyle the value of field 'fontStyle'.
2285 public void setFontStyle(
2286 final int fontStyle) {
2287 this._fontStyle = fontStyle;
2288 this._has_fontStyle = true;
2292 * Sets the value of field 'gatheredViews'.
2294 * @param gatheredViews the value of field 'gatheredViews'.
2296 public void setGatheredViews(
2297 final boolean gatheredViews) {
2298 this._gatheredViews = gatheredViews;
2299 this._has_gatheredViews = true;
2303 * Sets the value of field 'height'.
2305 * @param height the value of field 'height'.
2307 public void setHeight(
2309 this._height = height;
2310 this._has_height = true;
2317 * @param vHiddenColumns
2318 * @throws java.lang.IndexOutOfBoundsException if the index
2319 * given is outside the bounds of the collection
2321 public void setHiddenColumns(
2323 final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)
2324 throws java.lang.IndexOutOfBoundsException {
2325 // check bounds for index
2326 if (index < 0 || index >= this._hiddenColumnsList.size()) {
2327 throw new IndexOutOfBoundsException("setHiddenColumns: Index value '" + index + "' not in range [0.." + (this._hiddenColumnsList.size() - 1) + "]");
2330 this._hiddenColumnsList.set(index, vHiddenColumns);
2336 * @param vHiddenColumnsArray
2338 public void setHiddenColumns(
2339 final jalview.schemabinding.version2.HiddenColumns[] vHiddenColumnsArray) {
2341 _hiddenColumnsList.clear();
2343 for (int i = 0; i < vHiddenColumnsArray.length; i++) {
2344 this._hiddenColumnsList.add(vHiddenColumnsArray[i]);
2349 * Sets the value of field 'id'. The field 'id' has the
2350 * following description: unique id used by jalview to
2352 * between stored and
2353 * instantiated views
2356 * @param id the value of field 'id'.
2359 final java.lang.String id) {
2364 * Sets the value of field 'ignoreGapsinConsensus'.
2366 * @param ignoreGapsinConsensus the value of field
2367 * 'ignoreGapsinConsensus'.
2369 public void setIgnoreGapsinConsensus(
2370 final boolean ignoreGapsinConsensus) {
2371 this._ignoreGapsinConsensus = ignoreGapsinConsensus;
2372 this._has_ignoreGapsinConsensus = true;
2376 * Sets the value of field 'normaliseSequenceLogo'.
2378 * @param normaliseSequenceLogo the value of field
2379 * 'normaliseSequenceLogo'.
2381 public void setNormaliseSequenceLogo(
2382 final boolean normaliseSequenceLogo) {
2383 this._normaliseSequenceLogo = normaliseSequenceLogo;
2384 this._has_normaliseSequenceLogo = true;
2388 * Sets the value of field 'pidSelected'.
2390 * @param pidSelected the value of field 'pidSelected'.
2392 public void setPidSelected(
2393 final boolean pidSelected) {
2394 this._pidSelected = pidSelected;
2395 this._has_pidSelected = true;
2399 * Sets the value of field 'pidThreshold'.
2401 * @param pidThreshold the value of field 'pidThreshold'.
2403 public void setPidThreshold(
2404 final int pidThreshold) {
2405 this._pidThreshold = pidThreshold;
2406 this._has_pidThreshold = true;
2410 * Sets the value of field 'renderGaps'.
2412 * @param renderGaps the value of field 'renderGaps'.
2414 public void setRenderGaps(
2415 final boolean renderGaps) {
2416 this._renderGaps = renderGaps;
2417 this._has_renderGaps = true;
2421 * Sets the value of field 'rightAlignIds'.
2423 * @param rightAlignIds the value of field 'rightAlignIds'.
2425 public void setRightAlignIds(
2426 final boolean rightAlignIds) {
2427 this._rightAlignIds = rightAlignIds;
2428 this._has_rightAlignIds = true;
2432 * Sets the value of field 'scaleProteinAsCdna'.
2434 * @param scaleProteinAsCdna the value of field
2435 * 'scaleProteinAsCdna'.
2437 public void setScaleProteinAsCdna(
2438 final boolean scaleProteinAsCdna) {
2439 this._scaleProteinAsCdna = scaleProteinAsCdna;
2440 this._has_scaleProteinAsCdna = true;
2444 * Sets the value of field 'sequenceSetId'.
2446 * @param sequenceSetId the value of field 'sequenceSetId'.
2448 public void setSequenceSetId(
2449 final java.lang.String sequenceSetId) {
2450 this._sequenceSetId = sequenceSetId;
2454 * Sets the value of field 'showAnnotation'.
2456 * @param showAnnotation the value of field 'showAnnotation'.
2458 public void setShowAnnotation(
2459 final boolean showAnnotation) {
2460 this._showAnnotation = showAnnotation;
2461 this._has_showAnnotation = true;
2465 * Sets the value of field 'showBoxes'.
2467 * @param showBoxes the value of field 'showBoxes'.
2469 public void setShowBoxes(
2470 final boolean showBoxes) {
2471 this._showBoxes = showBoxes;
2472 this._has_showBoxes = true;
2476 * Sets the value of field 'showColourText'.
2478 * @param showColourText the value of field 'showColourText'.
2480 public void setShowColourText(
2481 final boolean showColourText) {
2482 this._showColourText = showColourText;
2483 this._has_showColourText = true;
2487 * Sets the value of field 'showConsensusHistogram'.
2489 * @param showConsensusHistogram the value of field
2490 * 'showConsensusHistogram'.
2492 public void setShowConsensusHistogram(
2493 final boolean showConsensusHistogram) {
2494 this._showConsensusHistogram = showConsensusHistogram;
2495 this._has_showConsensusHistogram = true;
2499 * Sets the value of field 'showDbRefTooltip'.
2501 * @param showDbRefTooltip the value of field 'showDbRefTooltip'
2503 public void setShowDbRefTooltip(
2504 final boolean showDbRefTooltip) {
2505 this._showDbRefTooltip = showDbRefTooltip;
2506 this._has_showDbRefTooltip = true;
2510 * Sets the value of field 'showFullId'.
2512 * @param showFullId the value of field 'showFullId'.
2514 public void setShowFullId(
2515 final boolean showFullId) {
2516 this._showFullId = showFullId;
2517 this._has_showFullId = true;
2521 * Sets the value of field 'showGroupConsensus'.
2523 * @param showGroupConsensus the value of field
2524 * 'showGroupConsensus'.
2526 public void setShowGroupConsensus(
2527 final boolean showGroupConsensus) {
2528 this._showGroupConsensus = showGroupConsensus;
2529 this._has_showGroupConsensus = true;
2533 * Sets the value of field 'showGroupConservation'.
2535 * @param showGroupConservation the value of field
2536 * 'showGroupConservation'.
2538 public void setShowGroupConservation(
2539 final boolean showGroupConservation) {
2540 this._showGroupConservation = showGroupConservation;
2541 this._has_showGroupConservation = true;
2545 * Sets the value of field 'showNPfeatureTooltip'.
2547 * @param showNPfeatureTooltip the value of field
2548 * 'showNPfeatureTooltip'.
2550 public void setShowNPfeatureTooltip(
2551 final boolean showNPfeatureTooltip) {
2552 this._showNPfeatureTooltip = showNPfeatureTooltip;
2553 this._has_showNPfeatureTooltip = true;
2557 * Sets the value of field 'showSequenceFeatures'.
2559 * @param showSequenceFeatures the value of field
2560 * 'showSequenceFeatures'.
2562 public void setShowSequenceFeatures(
2563 final boolean showSequenceFeatures) {
2564 this._showSequenceFeatures = showSequenceFeatures;
2565 this._has_showSequenceFeatures = true;
2569 * Sets the value of field 'showSequenceLogo'.
2571 * @param showSequenceLogo the value of field 'showSequenceLogo'
2573 public void setShowSequenceLogo(
2574 final boolean showSequenceLogo) {
2575 this._showSequenceLogo = showSequenceLogo;
2576 this._has_showSequenceLogo = true;
2580 * Sets the value of field 'showText'.
2582 * @param showText the value of field 'showText'.
2584 public void setShowText(
2585 final boolean showText) {
2586 this._showText = showText;
2587 this._has_showText = true;
2591 * Sets the value of field 'showUnconserved'.
2593 * @param showUnconserved the value of field 'showUnconserved'.
2595 public void setShowUnconserved(
2596 final boolean showUnconserved) {
2597 this._showUnconserved = showUnconserved;
2598 this._has_showUnconserved = true;
2602 * Sets the value of field 'startRes'.
2604 * @param startRes the value of field 'startRes'.
2606 public void setStartRes(
2607 final int startRes) {
2608 this._startRes = startRes;
2609 this._has_startRes = true;
2613 * Sets the value of field 'startSeq'.
2615 * @param startSeq the value of field 'startSeq'.
2617 public void setStartSeq(
2618 final int startSeq) {
2619 this._startSeq = startSeq;
2620 this._has_startSeq = true;
2624 * Sets the value of field 'textCol1'.
2626 * @param textCol1 the value of field 'textCol1'.
2628 public void setTextCol1(
2629 final int textCol1) {
2630 this._textCol1 = textCol1;
2631 this._has_textCol1 = true;
2635 * Sets the value of field 'textCol2'.
2637 * @param textCol2 the value of field 'textCol2'.
2639 public void setTextCol2(
2640 final int textCol2) {
2641 this._textCol2 = textCol2;
2642 this._has_textCol2 = true;
2646 * Sets the value of field 'textColThreshold'.
2648 * @param textColThreshold the value of field 'textColThreshold'
2650 public void setTextColThreshold(
2651 final int textColThreshold) {
2652 this._textColThreshold = textColThreshold;
2653 this._has_textColThreshold = true;
2657 * Sets the value of field 'title'.
2659 * @param title the value of field 'title'.
2661 public void setTitle(
2662 final java.lang.String title) {
2663 this._title = title;
2667 * Sets the value of field 'viewName'.
2669 * @param viewName the value of field 'viewName'.
2671 public void setViewName(
2672 final java.lang.String viewName) {
2673 this._viewName = viewName;
2677 * Sets the value of field 'width'.
2679 * @param width the value of field 'width'.
2681 public void setWidth(
2683 this._width = width;
2684 this._has_width = true;
2688 * Sets the value of field 'wrapAlignment'.
2690 * @param wrapAlignment the value of field 'wrapAlignment'.
2692 public void setWrapAlignment(
2693 final boolean wrapAlignment) {
2694 this._wrapAlignment = wrapAlignment;
2695 this._has_wrapAlignment = true;
2699 * Sets the value of field 'xpos'.
2701 * @param xpos the value of field 'xpos'.
2703 public void setXpos(
2706 this._has_xpos = true;
2710 * Sets the value of field 'ypos'.
2712 * @param ypos the value of field 'ypos'.
2714 public void setYpos(
2717 this._has_ypos = true;
2724 * @throws org.exolab.castor.xml.MarshalException if object is
2725 * null or if any SAXException is thrown during marshaling
2726 * @throws org.exolab.castor.xml.ValidationException if this
2727 * object is an invalid instance according to the schema
2728 * @return the unmarshaled
2729 * jalview.schemabinding.version2.Viewport
2731 public static jalview.schemabinding.version2.Viewport unmarshal(
2732 final java.io.Reader reader)
2733 throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
2734 return (jalview.schemabinding.version2.Viewport) Unmarshaller.unmarshal(jalview.schemabinding.version2.Viewport.class, reader);
2740 * @throws org.exolab.castor.xml.ValidationException if this
2741 * object is an invalid instance according to the schema
2743 public void validate(
2745 throws org.exolab.castor.xml.ValidationException {
2746 org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
2747 validator.validate(this);