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 synchronize between stored and instantiated
399 private java.lang.String _id;
402 * The viewport id of this viewport's (cdna/protein) coding complement, if any
405 private java.lang.String _complementId;
413 * keeps track of state for field: _width
415 private boolean _has_width;
423 * keeps track of state for field: _height
425 private boolean _has_height;
433 * keeps track of state for field: _xpos
435 private boolean _has_xpos;
443 * keeps track of state for field: _ypos
445 private boolean _has_ypos;
448 * Field _annotationColours.
450 private jalview.schemabinding.version2.AnnotationColours _annotationColours;
453 * Field _hiddenColumnsList.
455 private java.util.Vector _hiddenColumnsList;
458 * Field _calcIdParamList.
460 private java.util.Vector _calcIdParamList;
469 this._hiddenColumnsList = new java.util.Vector();
470 this._calcIdParamList = new java.util.Vector();
480 * @param vCalcIdParam
481 * @throws java.lang.IndexOutOfBoundsException
482 * if the index given is outside the bounds of the collection
484 public void addCalcIdParam(
485 final jalview.schemabinding.version2.CalcIdParam vCalcIdParam)
486 throws java.lang.IndexOutOfBoundsException
488 this._calcIdParamList.addElement(vCalcIdParam);
495 * @param vCalcIdParam
496 * @throws java.lang.IndexOutOfBoundsException
497 * if the index given is outside the bounds of the collection
499 public void addCalcIdParam(final int index,
500 final jalview.schemabinding.version2.CalcIdParam vCalcIdParam)
501 throws java.lang.IndexOutOfBoundsException
503 this._calcIdParamList.add(index, vCalcIdParam);
509 * @param vHiddenColumns
510 * @throws java.lang.IndexOutOfBoundsException
511 * if the index given is outside the bounds of the collection
513 public void addHiddenColumns(
514 final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)
515 throws java.lang.IndexOutOfBoundsException
517 this._hiddenColumnsList.addElement(vHiddenColumns);
524 * @param vHiddenColumns
525 * @throws java.lang.IndexOutOfBoundsException
526 * if the index given is outside the bounds of the collection
528 public void addHiddenColumns(final int index,
529 final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)
530 throws java.lang.IndexOutOfBoundsException
532 this._hiddenColumnsList.add(index, vHiddenColumns);
537 public void deleteCentreColumnLabels()
539 this._has_centreColumnLabels = false;
544 public void deleteConsThreshold()
546 this._has_consThreshold = false;
551 public void deleteConservationSelected()
553 this._has_conservationSelected = false;
558 public void deleteFollowHighlight()
560 this._has_followHighlight = false;
565 public void deleteFollowSelection()
567 this._has_followSelection = false;
572 public void deleteFontSize()
574 this._has_fontSize = false;
579 public void deleteFontStyle()
581 this._has_fontStyle = false;
586 public void deleteGatheredViews()
588 this._has_gatheredViews = false;
593 public void deleteHeight()
595 this._has_height = false;
600 public void deleteIgnoreGapsinConsensus()
602 this._has_ignoreGapsinConsensus = false;
607 public void deleteNormaliseSequenceLogo()
609 this._has_normaliseSequenceLogo = false;
614 public void deletePidSelected()
616 this._has_pidSelected = false;
621 public void deletePidThreshold()
623 this._has_pidThreshold = false;
628 public void deleteRenderGaps()
630 this._has_renderGaps = false;
635 public void deleteRightAlignIds()
637 this._has_rightAlignIds = false;
642 public void deleteScaleProteinAsCdna()
644 this._has_scaleProteinAsCdna = false;
649 public void deleteShowAnnotation()
651 this._has_showAnnotation = false;
656 public void deleteShowBoxes()
658 this._has_showBoxes = false;
663 public void deleteShowColourText()
665 this._has_showColourText = false;
670 public void deleteShowConsensusHistogram()
672 this._has_showConsensusHistogram = false;
677 public void deleteShowDbRefTooltip()
679 this._has_showDbRefTooltip = false;
684 public void deleteShowFullId()
686 this._has_showFullId = false;
691 public void deleteShowGroupConsensus()
693 this._has_showGroupConsensus = false;
698 public void deleteShowGroupConservation()
700 this._has_showGroupConservation = false;
705 public void deleteShowNPfeatureTooltip()
707 this._has_showNPfeatureTooltip = false;
712 public void deleteShowSequenceFeatures()
714 this._has_showSequenceFeatures = false;
719 public void deleteShowSequenceLogo()
721 this._has_showSequenceLogo = false;
726 public void deleteShowText()
728 this._has_showText = false;
733 public void deleteShowUnconserved()
735 this._has_showUnconserved = false;
740 public void deleteStartRes()
742 this._has_startRes = false;
747 public void deleteStartSeq()
749 this._has_startSeq = false;
754 public void deleteTextCol1()
756 this._has_textCol1 = false;
761 public void deleteTextCol2()
763 this._has_textCol2 = false;
768 public void deleteTextColThreshold()
770 this._has_textColThreshold = false;
775 public void deleteWidth()
777 this._has_width = false;
782 public void deleteWrapAlignment()
784 this._has_wrapAlignment = false;
789 public void deleteXpos()
791 this._has_xpos = false;
796 public void deleteYpos()
798 this._has_ypos = false;
802 * Method enumerateCalcIdParam.
804 * @return an Enumeration over all jalview.schemabinding.version2.CalcIdParam
807 public java.util.Enumeration enumerateCalcIdParam()
809 return this._calcIdParamList.elements();
813 * Method enumerateHiddenColumns.
815 * @return an Enumeration over all
816 * jalview.schemabinding.version2.HiddenColumns elements
818 public java.util.Enumeration enumerateHiddenColumns()
820 return this._hiddenColumnsList.elements();
824 * Returns the value of field 'annotationColours'.
826 * @return the value of field 'AnnotationColours'.
828 public jalview.schemabinding.version2.AnnotationColours getAnnotationColours()
830 return this._annotationColours;
834 * Returns the value of field 'bgColour'.
836 * @return the value of field 'BgColour'.
838 public java.lang.String getBgColour()
840 return this._bgColour;
844 * Method getCalcIdParam.
847 * @throws java.lang.IndexOutOfBoundsException
848 * if the index given is outside the bounds of the collection
849 * @return the value of the jalview.schemabinding.version2.CalcIdParam at the
852 public jalview.schemabinding.version2.CalcIdParam getCalcIdParam(
853 final int index) throws java.lang.IndexOutOfBoundsException
855 // check bounds for index
856 if (index < 0 || index >= this._calcIdParamList.size())
858 throw new IndexOutOfBoundsException("getCalcIdParam: Index value '"
859 + index + "' not in range [0.."
860 + (this._calcIdParamList.size() - 1) + "]");
863 return (jalview.schemabinding.version2.CalcIdParam) _calcIdParamList
868 * Method getCalcIdParam.Returns the contents of the collection in an Array.
870 * Note: Just in case the collection contents are changing in another thread,
871 * we pass a 0-length Array of the correct type into the API call. This way we
872 * <i>know</i> that the Array returned is of exactly the correct length.
874 * @return this collection as an Array
876 public jalview.schemabinding.version2.CalcIdParam[] getCalcIdParam()
878 jalview.schemabinding.version2.CalcIdParam[] array = new jalview.schemabinding.version2.CalcIdParam[0];
879 return (jalview.schemabinding.version2.CalcIdParam[]) this._calcIdParamList
884 * Method getCalcIdParamCount.
886 * @return the size of this collection
888 public int getCalcIdParamCount()
890 return this._calcIdParamList.size();
894 * Returns the value of field 'centreColumnLabels'.
896 * @return the value of field 'CentreColumnLabels'.
898 public boolean getCentreColumnLabels()
900 return this._centreColumnLabels;
904 * Returns the value of field 'complementId'. The field 'complementId' has the
905 * following description: The viewport id of this viewport's (cdna/protein)
906 * coding complement, if any
909 * @return the value of field 'ComplementId'.
911 public java.lang.String getComplementId()
913 return this._complementId;
917 * Returns the value of field 'consThreshold'.
919 * @return the value of field 'ConsThreshold'.
921 public int getConsThreshold()
923 return this._consThreshold;
927 * Returns the value of field 'conservationSelected'.
929 * @return the value of field 'ConservationSelected'.
931 public boolean getConservationSelected()
933 return this._conservationSelected;
937 * Returns the value of field 'followHighlight'.
939 * @return the value of field 'FollowHighlight'.
941 public boolean getFollowHighlight()
943 return this._followHighlight;
947 * Returns the value of field 'followSelection'.
949 * @return the value of field 'FollowSelection'.
951 public boolean getFollowSelection()
953 return this._followSelection;
957 * Returns the value of field 'fontName'.
959 * @return the value of field 'FontName'.
961 public java.lang.String getFontName()
963 return this._fontName;
967 * Returns the value of field 'fontSize'.
969 * @return the value of field 'FontSize'.
971 public int getFontSize()
973 return this._fontSize;
977 * Returns the value of field 'fontStyle'.
979 * @return the value of field 'FontStyle'.
981 public int getFontStyle()
983 return this._fontStyle;
987 * Returns the value of field 'gatheredViews'.
989 * @return the value of field 'GatheredViews'.
991 public boolean getGatheredViews()
993 return this._gatheredViews;
997 * Returns the value of field 'height'.
999 * @return the value of field 'Height'.
1001 public int getHeight()
1003 return this._height;
1007 * Method getHiddenColumns.
1010 * @throws java.lang.IndexOutOfBoundsException
1011 * if the index given is outside the bounds of the collection
1012 * @return the value of the jalview.schemabinding.version2.HiddenColumns at
1015 public jalview.schemabinding.version2.HiddenColumns getHiddenColumns(
1016 final int index) throws java.lang.IndexOutOfBoundsException
1018 // check bounds for index
1019 if (index < 0 || index >= this._hiddenColumnsList.size())
1021 throw new IndexOutOfBoundsException("getHiddenColumns: Index value '"
1022 + index + "' not in range [0.."
1023 + (this._hiddenColumnsList.size() - 1) + "]");
1026 return (jalview.schemabinding.version2.HiddenColumns) _hiddenColumnsList
1031 * Method getHiddenColumns.Returns the contents of the collection in an Array.
1033 * Note: Just in case the collection contents are changing in another thread,
1034 * we pass a 0-length Array of the correct type into the API call. This way we
1035 * <i>know</i> that the Array returned is of exactly the correct length.
1037 * @return this collection as an Array
1039 public jalview.schemabinding.version2.HiddenColumns[] getHiddenColumns()
1041 jalview.schemabinding.version2.HiddenColumns[] array = new jalview.schemabinding.version2.HiddenColumns[0];
1042 return (jalview.schemabinding.version2.HiddenColumns[]) this._hiddenColumnsList
1047 * Method getHiddenColumnsCount.
1049 * @return the size of this collection
1051 public int getHiddenColumnsCount()
1053 return this._hiddenColumnsList.size();
1057 * Returns the value of field 'id'. The field 'id' has the following
1058 * description: unique id used by jalview to synchronize between stored and
1059 * instantiated views
1062 * @return the value of field 'Id'.
1064 public java.lang.String getId()
1070 * Returns the value of field 'ignoreGapsinConsensus'.
1072 * @return the value of field 'IgnoreGapsinConsensus'.
1074 public boolean getIgnoreGapsinConsensus()
1076 return this._ignoreGapsinConsensus;
1080 * Returns the value of field 'normaliseSequenceLogo'.
1082 * @return the value of field 'NormaliseSequenceLogo'.
1084 public boolean getNormaliseSequenceLogo()
1086 return this._normaliseSequenceLogo;
1090 * Returns the value of field 'pidSelected'.
1092 * @return the value of field 'PidSelected'.
1094 public boolean getPidSelected()
1096 return this._pidSelected;
1100 * Returns the value of field 'pidThreshold'.
1102 * @return the value of field 'PidThreshold'.
1104 public int getPidThreshold()
1106 return this._pidThreshold;
1110 * Returns the value of field 'renderGaps'.
1112 * @return the value of field 'RenderGaps'.
1114 public boolean getRenderGaps()
1116 return this._renderGaps;
1120 * Returns the value of field 'rightAlignIds'.
1122 * @return the value of field 'RightAlignIds'.
1124 public boolean getRightAlignIds()
1126 return this._rightAlignIds;
1130 * Returns the value of field 'scaleProteinAsCdna'.
1132 * @return the value of field 'ScaleProteinAsCdna'.
1134 public boolean getScaleProteinAsCdna()
1136 return this._scaleProteinAsCdna;
1140 * Returns the value of field 'sequenceSetId'.
1142 * @return the value of field 'SequenceSetId'.
1144 public java.lang.String getSequenceSetId()
1146 return this._sequenceSetId;
1150 * Returns the value of field 'showAnnotation'.
1152 * @return the value of field 'ShowAnnotation'.
1154 public boolean getShowAnnotation()
1156 return this._showAnnotation;
1160 * Returns the value of field 'showBoxes'.
1162 * @return the value of field 'ShowBoxes'.
1164 public boolean getShowBoxes()
1166 return this._showBoxes;
1170 * Returns the value of field 'showColourText'.
1172 * @return the value of field 'ShowColourText'.
1174 public boolean getShowColourText()
1176 return this._showColourText;
1180 * Returns the value of field 'showConsensusHistogram'.
1182 * @return the value of field 'ShowConsensusHistogram'.
1184 public boolean getShowConsensusHistogram()
1186 return this._showConsensusHistogram;
1190 * Returns the value of field 'showDbRefTooltip'.
1192 * @return the value of field 'ShowDbRefTooltip'.
1194 public boolean getShowDbRefTooltip()
1196 return this._showDbRefTooltip;
1200 * Returns the value of field 'showFullId'.
1202 * @return the value of field 'ShowFullId'.
1204 public boolean getShowFullId()
1206 return this._showFullId;
1210 * Returns the value of field 'showGroupConsensus'.
1212 * @return the value of field 'ShowGroupConsensus'.
1214 public boolean getShowGroupConsensus()
1216 return this._showGroupConsensus;
1220 * Returns the value of field 'showGroupConservation'.
1222 * @return the value of field 'ShowGroupConservation'.
1224 public boolean getShowGroupConservation()
1226 return this._showGroupConservation;
1230 * Returns the value of field 'showNPfeatureTooltip'.
1232 * @return the value of field 'ShowNPfeatureTooltip'.
1234 public boolean getShowNPfeatureTooltip()
1236 return this._showNPfeatureTooltip;
1240 * Returns the value of field 'showSequenceFeatures'.
1242 * @return the value of field 'ShowSequenceFeatures'.
1244 public boolean getShowSequenceFeatures()
1246 return this._showSequenceFeatures;
1250 * Returns the value of field 'showSequenceLogo'.
1252 * @return the value of field 'ShowSequenceLogo'.
1254 public boolean getShowSequenceLogo()
1256 return this._showSequenceLogo;
1260 * Returns the value of field 'showText'.
1262 * @return the value of field 'ShowText'.
1264 public boolean getShowText()
1266 return this._showText;
1270 * Returns the value of field 'showUnconserved'.
1272 * @return the value of field 'ShowUnconserved'.
1274 public boolean getShowUnconserved()
1276 return this._showUnconserved;
1280 * Returns the value of field 'startRes'.
1282 * @return the value of field 'StartRes'.
1284 public int getStartRes()
1286 return this._startRes;
1290 * Returns the value of field 'startSeq'.
1292 * @return the value of field 'StartSeq'.
1294 public int getStartSeq()
1296 return this._startSeq;
1300 * Returns the value of field 'textCol1'.
1302 * @return the value of field 'TextCol1'.
1304 public int getTextCol1()
1306 return this._textCol1;
1310 * Returns the value of field 'textCol2'.
1312 * @return the value of field 'TextCol2'.
1314 public int getTextCol2()
1316 return this._textCol2;
1320 * Returns the value of field 'textColThreshold'.
1322 * @return the value of field 'TextColThreshold'.
1324 public int getTextColThreshold()
1326 return this._textColThreshold;
1330 * Returns the value of field 'title'.
1332 * @return the value of field 'Title'.
1334 public java.lang.String getTitle()
1340 * Returns the value of field 'viewName'.
1342 * @return the value of field 'ViewName'.
1344 public java.lang.String getViewName()
1346 return this._viewName;
1350 * Returns the value of field 'width'.
1352 * @return the value of field 'Width'.
1354 public int getWidth()
1360 * Returns the value of field 'wrapAlignment'.
1362 * @return the value of field 'WrapAlignment'.
1364 public boolean getWrapAlignment()
1366 return this._wrapAlignment;
1370 * Returns the value of field 'xpos'.
1372 * @return the value of field 'Xpos'.
1374 public int getXpos()
1380 * Returns the value of field 'ypos'.
1382 * @return the value of field 'Ypos'.
1384 public int getYpos()
1390 * Method hasCentreColumnLabels.
1392 * @return true if at least one CentreColumnLabels has been adde
1394 public boolean hasCentreColumnLabels()
1396 return this._has_centreColumnLabels;
1400 * Method hasConsThreshold.
1402 * @return true if at least one ConsThreshold has been added
1404 public boolean hasConsThreshold()
1406 return this._has_consThreshold;
1410 * Method hasConservationSelected.
1412 * @return true if at least one ConservationSelected has been added
1414 public boolean hasConservationSelected()
1416 return this._has_conservationSelected;
1420 * Method hasFollowHighlight.
1422 * @return true if at least one FollowHighlight has been added
1424 public boolean hasFollowHighlight()
1426 return this._has_followHighlight;
1430 * Method hasFollowSelection.
1432 * @return true if at least one FollowSelection has been added
1434 public boolean hasFollowSelection()
1436 return this._has_followSelection;
1440 * Method hasFontSize.
1442 * @return true if at least one FontSize has been added
1444 public boolean hasFontSize()
1446 return this._has_fontSize;
1450 * Method hasFontStyle.
1452 * @return true if at least one FontStyle has been added
1454 public boolean hasFontStyle()
1456 return this._has_fontStyle;
1460 * Method hasGatheredViews.
1462 * @return true if at least one GatheredViews has been added
1464 public boolean hasGatheredViews()
1466 return this._has_gatheredViews;
1472 * @return true if at least one Height has been added
1474 public boolean hasHeight()
1476 return this._has_height;
1480 * Method hasIgnoreGapsinConsensus.
1482 * @return true if at least one IgnoreGapsinConsensus has been added
1484 public boolean hasIgnoreGapsinConsensus()
1486 return this._has_ignoreGapsinConsensus;
1490 * Method hasNormaliseSequenceLogo.
1492 * @return true if at least one NormaliseSequenceLogo has been added
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 added
1584 public boolean hasShowConsensusHistogram()
1586 return this._has_showConsensusHistogram;
1590 * Method hasShowDbRefTooltip.
1592 * @return true if at least one ShowDbRefTooltip has been added
1594 public boolean hasShowDbRefTooltip()
1596 return this._has_showDbRefTooltip;
1600 * Method hasShowFullId.
1602 * @return true if at least one ShowFullId has been added
1604 public boolean hasShowFullId()
1606 return this._has_showFullId;
1610 * Method hasShowGroupConsensus.
1612 * @return true if at least one ShowGroupConsensus has been adde
1614 public boolean hasShowGroupConsensus()
1616 return this._has_showGroupConsensus;
1620 * Method hasShowGroupConservation.
1622 * @return true if at least one ShowGroupConservation has been added
1624 public boolean hasShowGroupConservation()
1626 return this._has_showGroupConservation;
1630 * Method hasShowNPfeatureTooltip.
1632 * @return true if at least one ShowNPfeatureTooltip has been added
1634 public boolean hasShowNPfeatureTooltip()
1636 return this._has_showNPfeatureTooltip;
1640 * Method hasShowSequenceFeatures.
1642 * @return true if at least one ShowSequenceFeatures has been added
1644 public boolean hasShowSequenceFeatures()
1646 return this._has_showSequenceFeatures;
1650 * Method hasShowSequenceLogo.
1652 * @return true if at least one ShowSequenceLogo has been added
1654 public boolean hasShowSequenceLogo()
1656 return this._has_showSequenceLogo;
1660 * Method hasShowText.
1662 * @return true if at least one ShowText has been added
1664 public boolean hasShowText()
1666 return this._has_showText;
1670 * Method hasShowUnconserved.
1672 * @return true if at least one ShowUnconserved has been added
1674 public boolean hasShowUnconserved()
1676 return this._has_showUnconserved;
1680 * Method hasStartRes.
1682 * @return true if at least one StartRes has been added
1684 public boolean hasStartRes()
1686 return this._has_startRes;
1690 * Method hasStartSeq.
1692 * @return true if at least one StartSeq has been added
1694 public boolean hasStartSeq()
1696 return this._has_startSeq;
1700 * Method hasTextCol1.
1702 * @return true if at least one TextCol1 has been added
1704 public boolean hasTextCol1()
1706 return this._has_textCol1;
1710 * Method hasTextCol2.
1712 * @return true if at least one TextCol2 has been added
1714 public boolean hasTextCol2()
1716 return this._has_textCol2;
1720 * Method hasTextColThreshold.
1722 * @return true if at least one TextColThreshold has been added
1724 public boolean hasTextColThreshold()
1726 return this._has_textColThreshold;
1732 * @return true if at least one Width has been added
1734 public boolean hasWidth()
1736 return this._has_width;
1740 * Method hasWrapAlignment.
1742 * @return true if at least one WrapAlignment has been added
1744 public boolean hasWrapAlignment()
1746 return this._has_wrapAlignment;
1752 * @return true if at least one Xpos has been added
1754 public boolean hasXpos()
1756 return this._has_xpos;
1762 * @return true if at least one Ypos has been added
1764 public boolean hasYpos()
1766 return this._has_ypos;
1770 * Returns the value of field 'centreColumnLabels'.
1772 * @return the value of field 'CentreColumnLabels'.
1774 public boolean isCentreColumnLabels()
1776 return this._centreColumnLabels;
1780 * Returns the value of field 'conservationSelected'.
1782 * @return the value of field 'ConservationSelected'.
1784 public boolean isConservationSelected()
1786 return this._conservationSelected;
1790 * Returns the value of field 'followHighlight'.
1792 * @return the value of field 'FollowHighlight'.
1794 public boolean isFollowHighlight()
1796 return this._followHighlight;
1800 * Returns the value of field 'followSelection'.
1802 * @return the value of field 'FollowSelection'.
1804 public boolean isFollowSelection()
1806 return this._followSelection;
1810 * Returns the value of field 'gatheredViews'.
1812 * @return the value of field 'GatheredViews'.
1814 public boolean isGatheredViews()
1816 return this._gatheredViews;
1820 * Returns the value of field 'ignoreGapsinConsensus'.
1822 * @return the value of field 'IgnoreGapsinConsensus'.
1824 public boolean isIgnoreGapsinConsensus()
1826 return this._ignoreGapsinConsensus;
1830 * Returns the value of field 'normaliseSequenceLogo'.
1832 * @return the value of field 'NormaliseSequenceLogo'.
1834 public boolean isNormaliseSequenceLogo()
1836 return this._normaliseSequenceLogo;
1840 * Returns the value of field 'pidSelected'.
1842 * @return the value of field 'PidSelected'.
1844 public boolean isPidSelected()
1846 return this._pidSelected;
1850 * Returns the value of field 'renderGaps'.
1852 * @return the value of field 'RenderGaps'.
1854 public boolean isRenderGaps()
1856 return this._renderGaps;
1860 * Returns the value of field 'rightAlignIds'.
1862 * @return the value of field 'RightAlignIds'.
1864 public boolean isRightAlignIds()
1866 return this._rightAlignIds;
1870 * Returns the value of field 'scaleProteinAsCdna'.
1872 * @return the value of field 'ScaleProteinAsCdna'.
1874 public boolean isScaleProteinAsCdna()
1876 return this._scaleProteinAsCdna;
1880 * Returns the value of field 'showAnnotation'.
1882 * @return the value of field 'ShowAnnotation'.
1884 public boolean isShowAnnotation()
1886 return this._showAnnotation;
1890 * Returns the value of field 'showBoxes'.
1892 * @return the value of field 'ShowBoxes'.
1894 public boolean isShowBoxes()
1896 return this._showBoxes;
1900 * Returns the value of field 'showColourText'.
1902 * @return the value of field 'ShowColourText'.
1904 public boolean isShowColourText()
1906 return this._showColourText;
1910 * Returns the value of field 'showConsensusHistogram'.
1912 * @return the value of field 'ShowConsensusHistogram'.
1914 public boolean isShowConsensusHistogram()
1916 return this._showConsensusHistogram;
1920 * Returns the value of field 'showDbRefTooltip'.
1922 * @return the value of field 'ShowDbRefTooltip'.
1924 public boolean isShowDbRefTooltip()
1926 return this._showDbRefTooltip;
1930 * Returns the value of field 'showFullId'.
1932 * @return the value of field 'ShowFullId'.
1934 public boolean isShowFullId()
1936 return this._showFullId;
1940 * Returns the value of field 'showGroupConsensus'.
1942 * @return the value of field 'ShowGroupConsensus'.
1944 public boolean isShowGroupConsensus()
1946 return this._showGroupConsensus;
1950 * Returns the value of field 'showGroupConservation'.
1952 * @return the value of field 'ShowGroupConservation'.
1954 public boolean isShowGroupConservation()
1956 return this._showGroupConservation;
1960 * Returns the value of field 'showNPfeatureTooltip'.
1962 * @return the value of field 'ShowNPfeatureTooltip'.
1964 public boolean isShowNPfeatureTooltip()
1966 return this._showNPfeatureTooltip;
1970 * Returns the value of field 'showSequenceFeatures'.
1972 * @return the value of field 'ShowSequenceFeatures'.
1974 public boolean isShowSequenceFeatures()
1976 return this._showSequenceFeatures;
1980 * Returns the value of field 'showSequenceLogo'.
1982 * @return the value of field 'ShowSequenceLogo'.
1984 public boolean isShowSequenceLogo()
1986 return this._showSequenceLogo;
1990 * Returns the value of field 'showText'.
1992 * @return the value of field 'ShowText'.
1994 public boolean isShowText()
1996 return this._showText;
2000 * Returns the value of field 'showUnconserved'.
2002 * @return the value of field 'ShowUnconserved'.
2004 public boolean isShowUnconserved()
2006 return this._showUnconserved;
2012 * @return true if this object is valid according to the schema
2014 public boolean isValid()
2019 } catch (org.exolab.castor.xml.ValidationException vex)
2027 * Returns the value of field 'wrapAlignment'.
2029 * @return the value of field 'WrapAlignment'.
2031 public boolean isWrapAlignment()
2033 return this._wrapAlignment;
2040 * @throws org.exolab.castor.xml.MarshalException
2041 * if object is null or if any SAXException is thrown during
2043 * @throws org.exolab.castor.xml.ValidationException
2044 * if this object is an invalid instance according to the schema
2046 public void marshal(final java.io.Writer out)
2047 throws org.exolab.castor.xml.MarshalException,
2048 org.exolab.castor.xml.ValidationException
2050 Marshaller.marshal(this, out);
2057 * @throws java.io.IOException
2058 * if an IOException occurs during marshaling
2059 * @throws org.exolab.castor.xml.ValidationException
2060 * if this object is an invalid instance according to the schema
2061 * @throws org.exolab.castor.xml.MarshalException
2062 * if object is null or if any SAXException is thrown during
2065 public void marshal(final org.xml.sax.ContentHandler handler)
2066 throws java.io.IOException,
2067 org.exolab.castor.xml.MarshalException,
2068 org.exolab.castor.xml.ValidationException
2070 Marshaller.marshal(this, handler);
2075 public void removeAllCalcIdParam()
2077 this._calcIdParamList.clear();
2082 public void removeAllHiddenColumns()
2084 this._hiddenColumnsList.clear();
2088 * Method removeCalcIdParam.
2090 * @param vCalcIdParam
2091 * @return true if the object was removed from the collection.
2093 public boolean removeCalcIdParam(
2094 final jalview.schemabinding.version2.CalcIdParam vCalcIdParam)
2096 boolean removed = _calcIdParamList.remove(vCalcIdParam);
2101 * Method removeCalcIdParamAt.
2104 * @return the element removed from the collection
2106 public jalview.schemabinding.version2.CalcIdParam removeCalcIdParamAt(
2109 java.lang.Object obj = this._calcIdParamList.remove(index);
2110 return (jalview.schemabinding.version2.CalcIdParam) obj;
2114 * Method removeHiddenColumns.
2116 * @param vHiddenColumns
2117 * @return true if the object was removed from the collection.
2119 public boolean removeHiddenColumns(
2120 final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)
2122 boolean removed = _hiddenColumnsList.remove(vHiddenColumns);
2127 * Method removeHiddenColumnsAt.
2130 * @return the element removed from the collection
2132 public jalview.schemabinding.version2.HiddenColumns removeHiddenColumnsAt(
2135 java.lang.Object obj = this._hiddenColumnsList.remove(index);
2136 return (jalview.schemabinding.version2.HiddenColumns) obj;
2140 * Sets the value of field 'annotationColours'.
2142 * @param annotationColours
2143 * the value of field 'annotationColours'.
2145 public void setAnnotationColours(
2146 final jalview.schemabinding.version2.AnnotationColours annotationColours)
2148 this._annotationColours = annotationColours;
2152 * Sets the value of field 'bgColour'.
2155 * the value of field 'bgColour'.
2157 public void setBgColour(final java.lang.String bgColour)
2159 this._bgColour = bgColour;
2166 * @param vCalcIdParam
2167 * @throws java.lang.IndexOutOfBoundsException
2168 * if the index given is outside the bounds of the collection
2170 public void setCalcIdParam(final int index,
2171 final jalview.schemabinding.version2.CalcIdParam vCalcIdParam)
2172 throws java.lang.IndexOutOfBoundsException
2174 // check bounds for index
2175 if (index < 0 || index >= this._calcIdParamList.size())
2177 throw new IndexOutOfBoundsException("setCalcIdParam: Index value '"
2178 + index + "' not in range [0.."
2179 + (this._calcIdParamList.size() - 1) + "]");
2182 this._calcIdParamList.set(index, vCalcIdParam);
2188 * @param vCalcIdParamArray
2190 public void setCalcIdParam(
2191 final jalview.schemabinding.version2.CalcIdParam[] vCalcIdParamArray)
2194 _calcIdParamList.clear();
2196 for (int i = 0; i < vCalcIdParamArray.length; i++)
2198 this._calcIdParamList.add(vCalcIdParamArray[i]);
2203 * Sets the value of field 'centreColumnLabels'.
2205 * @param centreColumnLabels
2206 * the value of field 'centreColumnLabels'.
2208 public void setCentreColumnLabels(final boolean centreColumnLabels)
2210 this._centreColumnLabels = centreColumnLabels;
2211 this._has_centreColumnLabels = true;
2215 * Sets the value of field 'complementId'. The field 'complementId' has the
2216 * following description: The viewport id of this viewport's (cdna/protein)
2217 * coding complement, if any
2220 * @param complementId
2221 * the value of field 'complementId'.
2223 public void setComplementId(final java.lang.String complementId)
2225 this._complementId = complementId;
2229 * Sets the value of field 'consThreshold'.
2231 * @param consThreshold
2232 * the value of field 'consThreshold'.
2234 public void setConsThreshold(final int consThreshold)
2236 this._consThreshold = consThreshold;
2237 this._has_consThreshold = true;
2241 * Sets the value of field 'conservationSelected'.
2243 * @param conservationSelected
2244 * the value of field 'conservationSelected'.
2246 public void setConservationSelected(final boolean conservationSelected)
2248 this._conservationSelected = conservationSelected;
2249 this._has_conservationSelected = true;
2253 * Sets the value of field 'followHighlight'.
2255 * @param followHighlight
2256 * the value of field 'followHighlight'.
2258 public void setFollowHighlight(final boolean followHighlight)
2260 this._followHighlight = followHighlight;
2261 this._has_followHighlight = true;
2265 * Sets the value of field 'followSelection'.
2267 * @param followSelection
2268 * the value of field 'followSelection'.
2270 public void setFollowSelection(final boolean followSelection)
2272 this._followSelection = followSelection;
2273 this._has_followSelection = true;
2277 * Sets the value of field 'fontName'.
2280 * the value of field 'fontName'.
2282 public void setFontName(final java.lang.String fontName)
2284 this._fontName = fontName;
2288 * Sets the value of field 'fontSize'.
2291 * the value of field 'fontSize'.
2293 public void setFontSize(final int fontSize)
2295 this._fontSize = fontSize;
2296 this._has_fontSize = true;
2300 * Sets the value of field 'fontStyle'.
2303 * the value of field 'fontStyle'.
2305 public void setFontStyle(final int fontStyle)
2307 this._fontStyle = fontStyle;
2308 this._has_fontStyle = true;
2312 * Sets the value of field 'gatheredViews'.
2314 * @param gatheredViews
2315 * the value of field 'gatheredViews'.
2317 public void setGatheredViews(final boolean gatheredViews)
2319 this._gatheredViews = gatheredViews;
2320 this._has_gatheredViews = true;
2324 * Sets the value of field 'height'.
2327 * the value of field 'height'.
2329 public void setHeight(final int height)
2331 this._height = height;
2332 this._has_height = true;
2339 * @param vHiddenColumns
2340 * @throws java.lang.IndexOutOfBoundsException
2341 * if the index given is outside the bounds of the collection
2343 public void setHiddenColumns(final int index,
2344 final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)
2345 throws java.lang.IndexOutOfBoundsException
2347 // check bounds for index
2348 if (index < 0 || index >= this._hiddenColumnsList.size())
2350 throw new IndexOutOfBoundsException("setHiddenColumns: Index value '"
2351 + index + "' not in range [0.."
2352 + (this._hiddenColumnsList.size() - 1) + "]");
2355 this._hiddenColumnsList.set(index, vHiddenColumns);
2361 * @param vHiddenColumnsArray
2363 public void setHiddenColumns(
2364 final jalview.schemabinding.version2.HiddenColumns[] vHiddenColumnsArray)
2367 _hiddenColumnsList.clear();
2369 for (int i = 0; i < vHiddenColumnsArray.length; i++)
2371 this._hiddenColumnsList.add(vHiddenColumnsArray[i]);
2376 * Sets the value of field 'id'. The field 'id' has the following description:
2377 * unique id used by jalview to synchronize between stored and instantiated
2382 * the value of field 'id'.
2384 public void setId(final java.lang.String id)
2390 * Sets the value of field 'ignoreGapsinConsensus'.
2392 * @param ignoreGapsinConsensus
2393 * the value of field 'ignoreGapsinConsensus'.
2395 public void setIgnoreGapsinConsensus(final boolean ignoreGapsinConsensus)
2397 this._ignoreGapsinConsensus = ignoreGapsinConsensus;
2398 this._has_ignoreGapsinConsensus = true;
2402 * Sets the value of field 'normaliseSequenceLogo'.
2404 * @param normaliseSequenceLogo
2405 * the value of field 'normaliseSequenceLogo'.
2407 public void setNormaliseSequenceLogo(final boolean normaliseSequenceLogo)
2409 this._normaliseSequenceLogo = normaliseSequenceLogo;
2410 this._has_normaliseSequenceLogo = true;
2414 * Sets the value of field 'pidSelected'.
2416 * @param pidSelected
2417 * the value of field 'pidSelected'.
2419 public void setPidSelected(final boolean pidSelected)
2421 this._pidSelected = pidSelected;
2422 this._has_pidSelected = true;
2426 * Sets the value of field 'pidThreshold'.
2428 * @param pidThreshold
2429 * the value of field 'pidThreshold'.
2431 public void setPidThreshold(final int pidThreshold)
2433 this._pidThreshold = pidThreshold;
2434 this._has_pidThreshold = true;
2438 * Sets the value of field 'renderGaps'.
2441 * the value of field 'renderGaps'.
2443 public void setRenderGaps(final boolean renderGaps)
2445 this._renderGaps = renderGaps;
2446 this._has_renderGaps = true;
2450 * Sets the value of field 'rightAlignIds'.
2452 * @param rightAlignIds
2453 * the value of field 'rightAlignIds'.
2455 public void setRightAlignIds(final boolean rightAlignIds)
2457 this._rightAlignIds = rightAlignIds;
2458 this._has_rightAlignIds = true;
2462 * Sets the value of field 'scaleProteinAsCdna'.
2464 * @param scaleProteinAsCdna
2465 * the value of field 'scaleProteinAsCdna'.
2467 public void setScaleProteinAsCdna(final boolean scaleProteinAsCdna)
2469 this._scaleProteinAsCdna = scaleProteinAsCdna;
2470 this._has_scaleProteinAsCdna = true;
2474 * Sets the value of field 'sequenceSetId'.
2476 * @param sequenceSetId
2477 * the value of field 'sequenceSetId'.
2479 public void setSequenceSetId(final java.lang.String sequenceSetId)
2481 this._sequenceSetId = sequenceSetId;
2485 * Sets the value of field 'showAnnotation'.
2487 * @param showAnnotation
2488 * the value of field 'showAnnotation'.
2490 public void setShowAnnotation(final boolean showAnnotation)
2492 this._showAnnotation = showAnnotation;
2493 this._has_showAnnotation = true;
2497 * Sets the value of field 'showBoxes'.
2500 * the value of field 'showBoxes'.
2502 public void setShowBoxes(final boolean showBoxes)
2504 this._showBoxes = showBoxes;
2505 this._has_showBoxes = true;
2509 * Sets the value of field 'showColourText'.
2511 * @param showColourText
2512 * the value of field 'showColourText'.
2514 public void setShowColourText(final boolean showColourText)
2516 this._showColourText = showColourText;
2517 this._has_showColourText = true;
2521 * Sets the value of field 'showConsensusHistogram'.
2523 * @param showConsensusHistogram
2524 * the value of field 'showConsensusHistogram'.
2526 public void setShowConsensusHistogram(final boolean showConsensusHistogram)
2528 this._showConsensusHistogram = showConsensusHistogram;
2529 this._has_showConsensusHistogram = true;
2533 * Sets the value of field 'showDbRefTooltip'.
2535 * @param showDbRefTooltip
2536 * the value of field 'showDbRefTooltip'
2538 public void setShowDbRefTooltip(final boolean showDbRefTooltip)
2540 this._showDbRefTooltip = showDbRefTooltip;
2541 this._has_showDbRefTooltip = true;
2545 * Sets the value of field 'showFullId'.
2548 * the value of field 'showFullId'.
2550 public void setShowFullId(final boolean showFullId)
2552 this._showFullId = showFullId;
2553 this._has_showFullId = true;
2557 * Sets the value of field 'showGroupConsensus'.
2559 * @param showGroupConsensus
2560 * the value of field 'showGroupConsensus'.
2562 public void setShowGroupConsensus(final boolean showGroupConsensus)
2564 this._showGroupConsensus = showGroupConsensus;
2565 this._has_showGroupConsensus = true;
2569 * Sets the value of field 'showGroupConservation'.
2571 * @param showGroupConservation
2572 * the value of field 'showGroupConservation'.
2574 public void setShowGroupConservation(final boolean showGroupConservation)
2576 this._showGroupConservation = showGroupConservation;
2577 this._has_showGroupConservation = true;
2581 * Sets the value of field 'showNPfeatureTooltip'.
2583 * @param showNPfeatureTooltip
2584 * the value of field 'showNPfeatureTooltip'.
2586 public void setShowNPfeatureTooltip(final boolean showNPfeatureTooltip)
2588 this._showNPfeatureTooltip = showNPfeatureTooltip;
2589 this._has_showNPfeatureTooltip = true;
2593 * Sets the value of field 'showSequenceFeatures'.
2595 * @param showSequenceFeatures
2596 * the value of field 'showSequenceFeatures'.
2598 public void setShowSequenceFeatures(final boolean showSequenceFeatures)
2600 this._showSequenceFeatures = showSequenceFeatures;
2601 this._has_showSequenceFeatures = true;
2605 * Sets the value of field 'showSequenceLogo'.
2607 * @param showSequenceLogo
2608 * the value of field 'showSequenceLogo'
2610 public void setShowSequenceLogo(final boolean showSequenceLogo)
2612 this._showSequenceLogo = showSequenceLogo;
2613 this._has_showSequenceLogo = true;
2617 * Sets the value of field 'showText'.
2620 * the value of field 'showText'.
2622 public void setShowText(final boolean showText)
2624 this._showText = showText;
2625 this._has_showText = true;
2629 * Sets the value of field 'showUnconserved'.
2631 * @param showUnconserved
2632 * the value of field 'showUnconserved'.
2634 public void setShowUnconserved(final boolean showUnconserved)
2636 this._showUnconserved = showUnconserved;
2637 this._has_showUnconserved = true;
2641 * Sets the value of field 'startRes'.
2644 * the value of field 'startRes'.
2646 public void setStartRes(final int startRes)
2648 this._startRes = startRes;
2649 this._has_startRes = true;
2653 * Sets the value of field 'startSeq'.
2656 * the value of field 'startSeq'.
2658 public void setStartSeq(final int startSeq)
2660 this._startSeq = startSeq;
2661 this._has_startSeq = true;
2665 * Sets the value of field 'textCol1'.
2668 * the value of field 'textCol1'.
2670 public void setTextCol1(final int textCol1)
2672 this._textCol1 = textCol1;
2673 this._has_textCol1 = true;
2677 * Sets the value of field 'textCol2'.
2680 * the value of field 'textCol2'.
2682 public void setTextCol2(final int textCol2)
2684 this._textCol2 = textCol2;
2685 this._has_textCol2 = true;
2689 * Sets the value of field 'textColThreshold'.
2691 * @param textColThreshold
2692 * the value of field 'textColThreshold'
2694 public void setTextColThreshold(final int textColThreshold)
2696 this._textColThreshold = textColThreshold;
2697 this._has_textColThreshold = true;
2701 * Sets the value of field 'title'.
2704 * the value of field 'title'.
2706 public void setTitle(final java.lang.String title)
2708 this._title = title;
2712 * Sets the value of field 'viewName'.
2715 * the value of field 'viewName'.
2717 public void setViewName(final java.lang.String viewName)
2719 this._viewName = viewName;
2723 * Sets the value of field 'width'.
2726 * the value of field 'width'.
2728 public void setWidth(final int width)
2730 this._width = width;
2731 this._has_width = true;
2735 * Sets the value of field 'wrapAlignment'.
2737 * @param wrapAlignment
2738 * the value of field 'wrapAlignment'.
2740 public void setWrapAlignment(final boolean wrapAlignment)
2742 this._wrapAlignment = wrapAlignment;
2743 this._has_wrapAlignment = true;
2747 * Sets the value of field 'xpos'.
2750 * the value of field 'xpos'.
2752 public void setXpos(final int xpos)
2755 this._has_xpos = true;
2759 * Sets the value of field 'ypos'.
2762 * the value of field 'ypos'.
2764 public void setYpos(final int ypos)
2767 this._has_ypos = true;
2774 * @throws org.exolab.castor.xml.MarshalException
2775 * if object is null or if any SAXException is thrown during
2777 * @throws org.exolab.castor.xml.ValidationException
2778 * if this object is an invalid instance according to the schema
2779 * @return the unmarshaled jalview.schemabinding.version2.Viewport
2781 public static jalview.schemabinding.version2.Viewport unmarshal(
2782 final java.io.Reader reader)
2783 throws org.exolab.castor.xml.MarshalException,
2784 org.exolab.castor.xml.ValidationException
2786 return (jalview.schemabinding.version2.Viewport) Unmarshaller
2787 .unmarshal(jalview.schemabinding.version2.Viewport.class,
2794 * @throws org.exolab.castor.xml.ValidationException
2795 * if this object is an invalid instance according to the schema
2797 public void validate() throws org.exolab.castor.xml.ValidationException
2799 org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
2800 validator.validate(this);