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 _ignoreGapsinConsensus.
272 private boolean _ignoreGapsinConsensus = true;
275 * keeps track of state for field: _ignoreGapsinConsensus
277 private boolean _has_ignoreGapsinConsensus;
285 * keeps track of state for field: _xpos
287 private boolean _has_xpos;
295 * keeps track of state for field: _ypos
297 private boolean _has_ypos;
305 * keeps track of state for field: _width
307 private boolean _has_width;
315 * keeps track of state for field: _height
317 private boolean _has_height;
322 private int _startRes;
325 * keeps track of state for field: _startRes
327 private boolean _has_startRes;
332 private int _startSeq;
335 * keeps track of state for field: _startSeq
337 private boolean _has_startSeq;
342 private java.lang.String _fontName;
347 private int _fontSize;
350 * keeps track of state for field: _fontSize
352 private boolean _has_fontSize;
357 private int _fontStyle;
360 * keeps track of state for field: _fontStyle
362 private boolean _has_fontStyle;
367 private java.lang.String _viewName;
370 * Field _sequenceSetId.
372 private java.lang.String _sequenceSetId;
375 * Field _gatheredViews.
377 private boolean _gatheredViews;
380 * keeps track of state for field: _gatheredViews
382 private boolean _has_gatheredViews;
387 private int _textCol1;
390 * keeps track of state for field: _textCol1
392 private boolean _has_textCol1;
397 private int _textCol2;
400 * keeps track of state for field: _textCol2
402 private boolean _has_textCol2;
405 * Field _textColThreshold.
407 private int _textColThreshold;
410 * keeps track of state for field: _textColThreshold
412 private boolean _has_textColThreshold;
415 * unique id used by jalview to synchronize between stored and
419 private java.lang.String _id;
422 * Field _annotationColours.
424 private jalview.schemabinding.version2.AnnotationColours _annotationColours;
427 * Field _hiddenColumnsList.
429 private java.util.Vector _hiddenColumnsList;
438 this._hiddenColumnsList = new java.util.Vector();
449 * @param vHiddenColumns
450 * @throws java.lang.IndexOutOfBoundsException if the index
451 * given is outside the bounds of the collection
453 public void addHiddenColumns(
454 final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)
455 throws java.lang.IndexOutOfBoundsException {
456 this._hiddenColumnsList.addElement(vHiddenColumns);
463 * @param vHiddenColumns
464 * @throws java.lang.IndexOutOfBoundsException if the index
465 * given is outside the bounds of the collection
467 public void addHiddenColumns(
469 final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)
470 throws java.lang.IndexOutOfBoundsException {
471 this._hiddenColumnsList.add(index, vHiddenColumns);
476 public void deleteCentreColumnLabels(
478 this._has_centreColumnLabels= false;
483 public void deleteConsThreshold(
485 this._has_consThreshold= false;
490 public void deleteConservationSelected(
492 this._has_conservationSelected= false;
497 public void deleteFollowHighlight(
499 this._has_followHighlight= false;
504 public void deleteFollowSelection(
506 this._has_followSelection= false;
511 public void deleteFontSize(
513 this._has_fontSize= false;
518 public void deleteFontStyle(
520 this._has_fontStyle= false;
525 public void deleteGatheredViews(
527 this._has_gatheredViews= false;
532 public void deleteHeight(
534 this._has_height= false;
539 public void deleteIgnoreGapsinConsensus(
541 this._has_ignoreGapsinConsensus= false;
546 public void deletePidSelected(
548 this._has_pidSelected= false;
553 public void deletePidThreshold(
555 this._has_pidThreshold= false;
560 public void deleteRenderGaps(
562 this._has_renderGaps= false;
567 public void deleteRightAlignIds(
569 this._has_rightAlignIds= false;
574 public void deleteShowAnnotation(
576 this._has_showAnnotation= false;
581 public void deleteShowBoxes(
583 this._has_showBoxes= false;
588 public void deleteShowColourText(
590 this._has_showColourText= false;
595 public void deleteShowConsensusHistogram(
597 this._has_showConsensusHistogram= false;
602 public void deleteShowDbRefTooltip(
604 this._has_showDbRefTooltip= false;
609 public void deleteShowFullId(
611 this._has_showFullId= false;
616 public void deleteShowGroupConsensus(
618 this._has_showGroupConsensus= false;
623 public void deleteShowGroupConservation(
625 this._has_showGroupConservation= false;
630 public void deleteShowNPfeatureTooltip(
632 this._has_showNPfeatureTooltip= false;
637 public void deleteShowSequenceFeatures(
639 this._has_showSequenceFeatures= false;
644 public void deleteShowSequenceLogo(
646 this._has_showSequenceLogo= false;
651 public void deleteShowText(
653 this._has_showText= false;
658 public void deleteShowUnconserved(
660 this._has_showUnconserved= false;
665 public void deleteStartRes(
667 this._has_startRes= false;
672 public void deleteStartSeq(
674 this._has_startSeq= false;
679 public void deleteTextCol1(
681 this._has_textCol1= false;
686 public void deleteTextCol2(
688 this._has_textCol2= false;
693 public void deleteTextColThreshold(
695 this._has_textColThreshold= false;
700 public void deleteWidth(
702 this._has_width= false;
707 public void deleteWrapAlignment(
709 this._has_wrapAlignment= false;
714 public void deleteXpos(
716 this._has_xpos= false;
721 public void deleteYpos(
723 this._has_ypos= false;
727 * Method enumerateHiddenColumns.
729 * @return an Enumeration over all
730 * jalview.schemabinding.version2.HiddenColumns elements
732 public java.util.Enumeration enumerateHiddenColumns(
734 return this._hiddenColumnsList.elements();
738 * Returns the value of field 'annotationColours'.
740 * @return the value of field 'AnnotationColours'.
742 public jalview.schemabinding.version2.AnnotationColours getAnnotationColours(
744 return this._annotationColours;
748 * Returns the value of field 'bgColour'.
750 * @return the value of field 'BgColour'.
752 public java.lang.String getBgColour(
754 return this._bgColour;
758 * Returns the value of field 'centreColumnLabels'.
760 * @return the value of field 'CentreColumnLabels'.
762 public boolean getCentreColumnLabels(
764 return this._centreColumnLabels;
768 * Returns the value of field 'consThreshold'.
770 * @return the value of field 'ConsThreshold'.
772 public int getConsThreshold(
774 return this._consThreshold;
778 * Returns the value of field 'conservationSelected'.
780 * @return the value of field 'ConservationSelected'.
782 public boolean getConservationSelected(
784 return this._conservationSelected;
788 * Returns the value of field 'followHighlight'.
790 * @return the value of field 'FollowHighlight'.
792 public boolean getFollowHighlight(
794 return this._followHighlight;
798 * Returns the value of field 'followSelection'.
800 * @return the value of field 'FollowSelection'.
802 public boolean getFollowSelection(
804 return this._followSelection;
808 * Returns the value of field 'fontName'.
810 * @return the value of field 'FontName'.
812 public java.lang.String getFontName(
814 return this._fontName;
818 * Returns the value of field 'fontSize'.
820 * @return the value of field 'FontSize'.
822 public int getFontSize(
824 return this._fontSize;
828 * Returns the value of field 'fontStyle'.
830 * @return the value of field 'FontStyle'.
832 public int getFontStyle(
834 return this._fontStyle;
838 * Returns the value of field 'gatheredViews'.
840 * @return the value of field 'GatheredViews'.
842 public boolean getGatheredViews(
844 return this._gatheredViews;
848 * Returns the value of field 'height'.
850 * @return the value of field 'Height'.
852 public int getHeight(
858 * Method getHiddenColumns.
861 * @throws java.lang.IndexOutOfBoundsException if the index
862 * given is outside the bounds of the collection
863 * @return the value of the
864 * jalview.schemabinding.version2.HiddenColumns at the given
867 public jalview.schemabinding.version2.HiddenColumns getHiddenColumns(
869 throws java.lang.IndexOutOfBoundsException {
870 // check bounds for index
871 if (index < 0 || index >= this._hiddenColumnsList.size()) {
872 throw new IndexOutOfBoundsException("getHiddenColumns: Index value '" + index + "' not in range [0.." + (this._hiddenColumnsList.size() - 1) + "]");
875 return (jalview.schemabinding.version2.HiddenColumns) _hiddenColumnsList.get(index);
879 * Method getHiddenColumns.Returns the contents of the
880 * collection in an Array. <p>Note: Just in case the
881 * collection contents are changing in another thread, we pass
882 * a 0-length Array of the correct type into the API call.
883 * This way we <i>know</i> that the Array returned is of
884 * exactly the correct length.
886 * @return this collection as an Array
888 public jalview.schemabinding.version2.HiddenColumns[] getHiddenColumns(
890 jalview.schemabinding.version2.HiddenColumns[] array = new jalview.schemabinding.version2.HiddenColumns[0];
891 return (jalview.schemabinding.version2.HiddenColumns[]) this._hiddenColumnsList.toArray(array);
895 * Method getHiddenColumnsCount.
897 * @return the size of this collection
899 public int getHiddenColumnsCount(
901 return this._hiddenColumnsList.size();
905 * Returns the value of field 'id'. The field 'id' has the
906 * following description: unique id used by jalview to
907 * synchronize between stored and instantiated views
910 * @return the value of field 'Id'.
912 public java.lang.String getId(
918 * Returns the value of field 'ignoreGapsinConsensus'.
920 * @return the value of field 'IgnoreGapsinConsensus'.
922 public boolean getIgnoreGapsinConsensus(
924 return this._ignoreGapsinConsensus;
928 * Returns the value of field 'pidSelected'.
930 * @return the value of field 'PidSelected'.
932 public boolean getPidSelected(
934 return this._pidSelected;
938 * Returns the value of field 'pidThreshold'.
940 * @return the value of field 'PidThreshold'.
942 public int getPidThreshold(
944 return this._pidThreshold;
948 * Returns the value of field 'renderGaps'.
950 * @return the value of field 'RenderGaps'.
952 public boolean getRenderGaps(
954 return this._renderGaps;
958 * Returns the value of field 'rightAlignIds'.
960 * @return the value of field 'RightAlignIds'.
962 public boolean getRightAlignIds(
964 return this._rightAlignIds;
968 * Returns the value of field 'sequenceSetId'.
970 * @return the value of field 'SequenceSetId'.
972 public java.lang.String getSequenceSetId(
974 return this._sequenceSetId;
978 * Returns the value of field 'showAnnotation'.
980 * @return the value of field 'ShowAnnotation'.
982 public boolean getShowAnnotation(
984 return this._showAnnotation;
988 * Returns the value of field 'showBoxes'.
990 * @return the value of field 'ShowBoxes'.
992 public boolean getShowBoxes(
994 return this._showBoxes;
998 * Returns the value of field 'showColourText'.
1000 * @return the value of field 'ShowColourText'.
1002 public boolean getShowColourText(
1004 return this._showColourText;
1008 * Returns the value of field 'showConsensusHistogram'.
1010 * @return the value of field 'ShowConsensusHistogram'.
1012 public boolean getShowConsensusHistogram(
1014 return this._showConsensusHistogram;
1018 * Returns the value of field 'showDbRefTooltip'.
1020 * @return the value of field 'ShowDbRefTooltip'.
1022 public boolean getShowDbRefTooltip(
1024 return this._showDbRefTooltip;
1028 * Returns the value of field 'showFullId'.
1030 * @return the value of field 'ShowFullId'.
1032 public boolean getShowFullId(
1034 return this._showFullId;
1038 * Returns the value of field 'showGroupConsensus'.
1040 * @return the value of field 'ShowGroupConsensus'.
1042 public boolean getShowGroupConsensus(
1044 return this._showGroupConsensus;
1048 * Returns the value of field 'showGroupConservation'.
1050 * @return the value of field 'ShowGroupConservation'.
1052 public boolean getShowGroupConservation(
1054 return this._showGroupConservation;
1058 * Returns the value of field 'showNPfeatureTooltip'.
1060 * @return the value of field 'ShowNPfeatureTooltip'.
1062 public boolean getShowNPfeatureTooltip(
1064 return this._showNPfeatureTooltip;
1068 * Returns the value of field 'showSequenceFeatures'.
1070 * @return the value of field 'ShowSequenceFeatures'.
1072 public boolean getShowSequenceFeatures(
1074 return this._showSequenceFeatures;
1078 * Returns the value of field 'showSequenceLogo'.
1080 * @return the value of field 'ShowSequenceLogo'.
1082 public boolean getShowSequenceLogo(
1084 return this._showSequenceLogo;
1088 * Returns the value of field 'showText'.
1090 * @return the value of field 'ShowText'.
1092 public boolean getShowText(
1094 return this._showText;
1098 * Returns the value of field 'showUnconserved'.
1100 * @return the value of field 'ShowUnconserved'.
1102 public boolean getShowUnconserved(
1104 return this._showUnconserved;
1108 * Returns the value of field 'startRes'.
1110 * @return the value of field 'StartRes'.
1112 public int getStartRes(
1114 return this._startRes;
1118 * Returns the value of field 'startSeq'.
1120 * @return the value of field 'StartSeq'.
1122 public int getStartSeq(
1124 return this._startSeq;
1128 * Returns the value of field 'textCol1'.
1130 * @return the value of field 'TextCol1'.
1132 public int getTextCol1(
1134 return this._textCol1;
1138 * Returns the value of field 'textCol2'.
1140 * @return the value of field 'TextCol2'.
1142 public int getTextCol2(
1144 return this._textCol2;
1148 * Returns the value of field 'textColThreshold'.
1150 * @return the value of field 'TextColThreshold'.
1152 public int getTextColThreshold(
1154 return this._textColThreshold;
1158 * Returns the value of field 'title'.
1160 * @return the value of field 'Title'.
1162 public java.lang.String getTitle(
1168 * Returns the value of field 'viewName'.
1170 * @return the value of field 'ViewName'.
1172 public java.lang.String getViewName(
1174 return this._viewName;
1178 * Returns the value of field 'width'.
1180 * @return the value of field 'Width'.
1182 public int getWidth(
1188 * Returns the value of field 'wrapAlignment'.
1190 * @return the value of field 'WrapAlignment'.
1192 public boolean getWrapAlignment(
1194 return this._wrapAlignment;
1198 * Returns the value of field 'xpos'.
1200 * @return the value of field 'Xpos'.
1208 * Returns the value of field 'ypos'.
1210 * @return the value of field 'Ypos'.
1218 * Method hasCentreColumnLabels.
1220 * @return true if at least one CentreColumnLabels has been adde
1222 public boolean hasCentreColumnLabels(
1224 return this._has_centreColumnLabels;
1228 * Method hasConsThreshold.
1230 * @return true if at least one ConsThreshold has been added
1232 public boolean hasConsThreshold(
1234 return this._has_consThreshold;
1238 * Method hasConservationSelected.
1240 * @return true if at least one ConservationSelected has been
1243 public boolean hasConservationSelected(
1245 return this._has_conservationSelected;
1249 * Method hasFollowHighlight.
1251 * @return true if at least one FollowHighlight has been added
1253 public boolean hasFollowHighlight(
1255 return this._has_followHighlight;
1259 * Method hasFollowSelection.
1261 * @return true if at least one FollowSelection has been added
1263 public boolean hasFollowSelection(
1265 return this._has_followSelection;
1269 * Method hasFontSize.
1271 * @return true if at least one FontSize has been added
1273 public boolean hasFontSize(
1275 return this._has_fontSize;
1279 * Method hasFontStyle.
1281 * @return true if at least one FontStyle has been added
1283 public boolean hasFontStyle(
1285 return this._has_fontStyle;
1289 * Method hasGatheredViews.
1291 * @return true if at least one GatheredViews has been added
1293 public boolean hasGatheredViews(
1295 return this._has_gatheredViews;
1301 * @return true if at least one Height has been added
1303 public boolean hasHeight(
1305 return this._has_height;
1309 * Method hasIgnoreGapsinConsensus.
1311 * @return true if at least one IgnoreGapsinConsensus has been
1314 public boolean hasIgnoreGapsinConsensus(
1316 return this._has_ignoreGapsinConsensus;
1320 * Method hasPidSelected.
1322 * @return true if at least one PidSelected has been added
1324 public boolean hasPidSelected(
1326 return this._has_pidSelected;
1330 * Method hasPidThreshold.
1332 * @return true if at least one PidThreshold has been added
1334 public boolean hasPidThreshold(
1336 return this._has_pidThreshold;
1340 * Method hasRenderGaps.
1342 * @return true if at least one RenderGaps has been added
1344 public boolean hasRenderGaps(
1346 return this._has_renderGaps;
1350 * Method hasRightAlignIds.
1352 * @return true if at least one RightAlignIds has been added
1354 public boolean hasRightAlignIds(
1356 return this._has_rightAlignIds;
1360 * Method hasShowAnnotation.
1362 * @return true if at least one ShowAnnotation has been added
1364 public boolean hasShowAnnotation(
1366 return this._has_showAnnotation;
1370 * Method hasShowBoxes.
1372 * @return true if at least one ShowBoxes has been added
1374 public boolean hasShowBoxes(
1376 return this._has_showBoxes;
1380 * Method hasShowColourText.
1382 * @return true if at least one ShowColourText has been added
1384 public boolean hasShowColourText(
1386 return this._has_showColourText;
1390 * Method hasShowConsensusHistogram.
1392 * @return true if at least one ShowConsensusHistogram has been
1395 public boolean hasShowConsensusHistogram(
1397 return this._has_showConsensusHistogram;
1401 * Method hasShowDbRefTooltip.
1403 * @return true if at least one ShowDbRefTooltip has been added
1405 public boolean hasShowDbRefTooltip(
1407 return this._has_showDbRefTooltip;
1411 * Method hasShowFullId.
1413 * @return true if at least one ShowFullId has been added
1415 public boolean hasShowFullId(
1417 return this._has_showFullId;
1421 * Method hasShowGroupConsensus.
1423 * @return true if at least one ShowGroupConsensus has been adde
1425 public boolean hasShowGroupConsensus(
1427 return this._has_showGroupConsensus;
1431 * Method hasShowGroupConservation.
1433 * @return true if at least one ShowGroupConservation has been
1436 public boolean hasShowGroupConservation(
1438 return this._has_showGroupConservation;
1442 * Method hasShowNPfeatureTooltip.
1444 * @return true if at least one ShowNPfeatureTooltip has been
1447 public boolean hasShowNPfeatureTooltip(
1449 return this._has_showNPfeatureTooltip;
1453 * Method hasShowSequenceFeatures.
1455 * @return true if at least one ShowSequenceFeatures has been
1458 public boolean hasShowSequenceFeatures(
1460 return this._has_showSequenceFeatures;
1464 * Method hasShowSequenceLogo.
1466 * @return true if at least one ShowSequenceLogo has been added
1468 public boolean hasShowSequenceLogo(
1470 return this._has_showSequenceLogo;
1474 * Method hasShowText.
1476 * @return true if at least one ShowText has been added
1478 public boolean hasShowText(
1480 return this._has_showText;
1484 * Method hasShowUnconserved.
1486 * @return true if at least one ShowUnconserved has been added
1488 public boolean hasShowUnconserved(
1490 return this._has_showUnconserved;
1494 * Method hasStartRes.
1496 * @return true if at least one StartRes has been added
1498 public boolean hasStartRes(
1500 return this._has_startRes;
1504 * Method hasStartSeq.
1506 * @return true if at least one StartSeq has been added
1508 public boolean hasStartSeq(
1510 return this._has_startSeq;
1514 * Method hasTextCol1.
1516 * @return true if at least one TextCol1 has been added
1518 public boolean hasTextCol1(
1520 return this._has_textCol1;
1524 * Method hasTextCol2.
1526 * @return true if at least one TextCol2 has been added
1528 public boolean hasTextCol2(
1530 return this._has_textCol2;
1534 * Method hasTextColThreshold.
1536 * @return true if at least one TextColThreshold has been added
1538 public boolean hasTextColThreshold(
1540 return this._has_textColThreshold;
1546 * @return true if at least one Width has been added
1548 public boolean hasWidth(
1550 return this._has_width;
1554 * Method hasWrapAlignment.
1556 * @return true if at least one WrapAlignment has been added
1558 public boolean hasWrapAlignment(
1560 return this._has_wrapAlignment;
1566 * @return true if at least one Xpos has been added
1568 public boolean hasXpos(
1570 return this._has_xpos;
1576 * @return true if at least one Ypos has been added
1578 public boolean hasYpos(
1580 return this._has_ypos;
1584 * Returns the value of field 'centreColumnLabels'.
1586 * @return the value of field 'CentreColumnLabels'.
1588 public boolean isCentreColumnLabels(
1590 return this._centreColumnLabels;
1594 * Returns the value of field 'conservationSelected'.
1596 * @return the value of field 'ConservationSelected'.
1598 public boolean isConservationSelected(
1600 return this._conservationSelected;
1604 * Returns the value of field 'followHighlight'.
1606 * @return the value of field 'FollowHighlight'.
1608 public boolean isFollowHighlight(
1610 return this._followHighlight;
1614 * Returns the value of field 'followSelection'.
1616 * @return the value of field 'FollowSelection'.
1618 public boolean isFollowSelection(
1620 return this._followSelection;
1624 * Returns the value of field 'gatheredViews'.
1626 * @return the value of field 'GatheredViews'.
1628 public boolean isGatheredViews(
1630 return this._gatheredViews;
1634 * Returns the value of field 'ignoreGapsinConsensus'.
1636 * @return the value of field 'IgnoreGapsinConsensus'.
1638 public boolean isIgnoreGapsinConsensus(
1640 return this._ignoreGapsinConsensus;
1644 * Returns the value of field 'pidSelected'.
1646 * @return the value of field 'PidSelected'.
1648 public boolean isPidSelected(
1650 return this._pidSelected;
1654 * Returns the value of field 'renderGaps'.
1656 * @return the value of field 'RenderGaps'.
1658 public boolean isRenderGaps(
1660 return this._renderGaps;
1664 * Returns the value of field 'rightAlignIds'.
1666 * @return the value of field 'RightAlignIds'.
1668 public boolean isRightAlignIds(
1670 return this._rightAlignIds;
1674 * Returns the value of field 'showAnnotation'.
1676 * @return the value of field 'ShowAnnotation'.
1678 public boolean isShowAnnotation(
1680 return this._showAnnotation;
1684 * Returns the value of field 'showBoxes'.
1686 * @return the value of field 'ShowBoxes'.
1688 public boolean isShowBoxes(
1690 return this._showBoxes;
1694 * Returns the value of field 'showColourText'.
1696 * @return the value of field 'ShowColourText'.
1698 public boolean isShowColourText(
1700 return this._showColourText;
1704 * Returns the value of field 'showConsensusHistogram'.
1706 * @return the value of field 'ShowConsensusHistogram'.
1708 public boolean isShowConsensusHistogram(
1710 return this._showConsensusHistogram;
1714 * Returns the value of field 'showDbRefTooltip'.
1716 * @return the value of field 'ShowDbRefTooltip'.
1718 public boolean isShowDbRefTooltip(
1720 return this._showDbRefTooltip;
1724 * Returns the value of field 'showFullId'.
1726 * @return the value of field 'ShowFullId'.
1728 public boolean isShowFullId(
1730 return this._showFullId;
1734 * Returns the value of field 'showGroupConsensus'.
1736 * @return the value of field 'ShowGroupConsensus'.
1738 public boolean isShowGroupConsensus(
1740 return this._showGroupConsensus;
1744 * Returns the value of field 'showGroupConservation'.
1746 * @return the value of field 'ShowGroupConservation'.
1748 public boolean isShowGroupConservation(
1750 return this._showGroupConservation;
1754 * Returns the value of field 'showNPfeatureTooltip'.
1756 * @return the value of field 'ShowNPfeatureTooltip'.
1758 public boolean isShowNPfeatureTooltip(
1760 return this._showNPfeatureTooltip;
1764 * Returns the value of field 'showSequenceFeatures'.
1766 * @return the value of field 'ShowSequenceFeatures'.
1768 public boolean isShowSequenceFeatures(
1770 return this._showSequenceFeatures;
1774 * Returns the value of field 'showSequenceLogo'.
1776 * @return the value of field 'ShowSequenceLogo'.
1778 public boolean isShowSequenceLogo(
1780 return this._showSequenceLogo;
1784 * Returns the value of field 'showText'.
1786 * @return the value of field 'ShowText'.
1788 public boolean isShowText(
1790 return this._showText;
1794 * Returns the value of field 'showUnconserved'.
1796 * @return the value of field 'ShowUnconserved'.
1798 public boolean isShowUnconserved(
1800 return this._showUnconserved;
1806 * @return true if this object is valid according to the schema
1808 public boolean isValid(
1812 } catch (org.exolab.castor.xml.ValidationException vex) {
1819 * Returns the value of field 'wrapAlignment'.
1821 * @return the value of field 'WrapAlignment'.
1823 public boolean isWrapAlignment(
1825 return this._wrapAlignment;
1832 * @throws org.exolab.castor.xml.MarshalException if object is
1833 * null or if any SAXException is thrown during marshaling
1834 * @throws org.exolab.castor.xml.ValidationException if this
1835 * object is an invalid instance according to the schema
1837 public void marshal(
1838 final java.io.Writer out)
1839 throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
1840 Marshaller.marshal(this, out);
1847 * @throws java.io.IOException if an IOException occurs during
1849 * @throws org.exolab.castor.xml.ValidationException if this
1850 * object is an invalid instance according to the schema
1851 * @throws org.exolab.castor.xml.MarshalException if object is
1852 * null or if any SAXException is thrown during marshaling
1854 public void marshal(
1855 final org.xml.sax.ContentHandler handler)
1856 throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
1857 Marshaller.marshal(this, handler);
1862 public void removeAllHiddenColumns(
1864 this._hiddenColumnsList.clear();
1868 * Method removeHiddenColumns.
1870 * @param vHiddenColumns
1871 * @return true if the object was removed from the collection.
1873 public boolean removeHiddenColumns(
1874 final jalview.schemabinding.version2.HiddenColumns vHiddenColumns) {
1875 boolean removed = _hiddenColumnsList.remove(vHiddenColumns);
1880 * Method removeHiddenColumnsAt.
1883 * @return the element removed from the collection
1885 public jalview.schemabinding.version2.HiddenColumns removeHiddenColumnsAt(
1887 java.lang.Object obj = this._hiddenColumnsList.remove(index);
1888 return (jalview.schemabinding.version2.HiddenColumns) obj;
1892 * Sets the value of field 'annotationColours'.
1894 * @param annotationColours the value of field
1895 * 'annotationColours'.
1897 public void setAnnotationColours(
1898 final jalview.schemabinding.version2.AnnotationColours annotationColours) {
1899 this._annotationColours = annotationColours;
1903 * Sets the value of field 'bgColour'.
1905 * @param bgColour the value of field 'bgColour'.
1907 public void setBgColour(
1908 final java.lang.String bgColour) {
1909 this._bgColour = bgColour;
1913 * Sets the value of field 'centreColumnLabels'.
1915 * @param centreColumnLabels the value of field
1916 * 'centreColumnLabels'.
1918 public void setCentreColumnLabels(
1919 final boolean centreColumnLabels) {
1920 this._centreColumnLabels = centreColumnLabels;
1921 this._has_centreColumnLabels = true;
1925 * Sets the value of field 'consThreshold'.
1927 * @param consThreshold the value of field 'consThreshold'.
1929 public void setConsThreshold(
1930 final int consThreshold) {
1931 this._consThreshold = consThreshold;
1932 this._has_consThreshold = true;
1936 * Sets the value of field 'conservationSelected'.
1938 * @param conservationSelected the value of field
1939 * 'conservationSelected'.
1941 public void setConservationSelected(
1942 final boolean conservationSelected) {
1943 this._conservationSelected = conservationSelected;
1944 this._has_conservationSelected = true;
1948 * Sets the value of field 'followHighlight'.
1950 * @param followHighlight the value of field 'followHighlight'.
1952 public void setFollowHighlight(
1953 final boolean followHighlight) {
1954 this._followHighlight = followHighlight;
1955 this._has_followHighlight = true;
1959 * Sets the value of field 'followSelection'.
1961 * @param followSelection the value of field 'followSelection'.
1963 public void setFollowSelection(
1964 final boolean followSelection) {
1965 this._followSelection = followSelection;
1966 this._has_followSelection = true;
1970 * Sets the value of field 'fontName'.
1972 * @param fontName the value of field 'fontName'.
1974 public void setFontName(
1975 final java.lang.String fontName) {
1976 this._fontName = fontName;
1980 * Sets the value of field 'fontSize'.
1982 * @param fontSize the value of field 'fontSize'.
1984 public void setFontSize(
1985 final int fontSize) {
1986 this._fontSize = fontSize;
1987 this._has_fontSize = true;
1991 * Sets the value of field 'fontStyle'.
1993 * @param fontStyle the value of field 'fontStyle'.
1995 public void setFontStyle(
1996 final int fontStyle) {
1997 this._fontStyle = fontStyle;
1998 this._has_fontStyle = true;
2002 * Sets the value of field 'gatheredViews'.
2004 * @param gatheredViews the value of field 'gatheredViews'.
2006 public void setGatheredViews(
2007 final boolean gatheredViews) {
2008 this._gatheredViews = gatheredViews;
2009 this._has_gatheredViews = true;
2013 * Sets the value of field 'height'.
2015 * @param height the value of field 'height'.
2017 public void setHeight(
2019 this._height = height;
2020 this._has_height = true;
2027 * @param vHiddenColumns
2028 * @throws java.lang.IndexOutOfBoundsException if the index
2029 * given is outside the bounds of the collection
2031 public void setHiddenColumns(
2033 final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)
2034 throws java.lang.IndexOutOfBoundsException {
2035 // check bounds for index
2036 if (index < 0 || index >= this._hiddenColumnsList.size()) {
2037 throw new IndexOutOfBoundsException("setHiddenColumns: Index value '" + index + "' not in range [0.." + (this._hiddenColumnsList.size() - 1) + "]");
2040 this._hiddenColumnsList.set(index, vHiddenColumns);
2046 * @param vHiddenColumnsArray
2048 public void setHiddenColumns(
2049 final jalview.schemabinding.version2.HiddenColumns[] vHiddenColumnsArray) {
2051 _hiddenColumnsList.clear();
2053 for (int i = 0; i < vHiddenColumnsArray.length; i++) {
2054 this._hiddenColumnsList.add(vHiddenColumnsArray[i]);
2059 * Sets the value of field 'id'. The field 'id' has the
2060 * following description: unique id used by jalview to
2061 * synchronize between stored and instantiated views
2064 * @param id the value of field 'id'.
2067 final java.lang.String id) {
2072 * Sets the value of field 'ignoreGapsinConsensus'.
2074 * @param ignoreGapsinConsensus the value of field
2075 * 'ignoreGapsinConsensus'.
2077 public void setIgnoreGapsinConsensus(
2078 final boolean ignoreGapsinConsensus) {
2079 this._ignoreGapsinConsensus = ignoreGapsinConsensus;
2080 this._has_ignoreGapsinConsensus = true;
2084 * Sets the value of field 'pidSelected'.
2086 * @param pidSelected the value of field 'pidSelected'.
2088 public void setPidSelected(
2089 final boolean pidSelected) {
2090 this._pidSelected = pidSelected;
2091 this._has_pidSelected = true;
2095 * Sets the value of field 'pidThreshold'.
2097 * @param pidThreshold the value of field 'pidThreshold'.
2099 public void setPidThreshold(
2100 final int pidThreshold) {
2101 this._pidThreshold = pidThreshold;
2102 this._has_pidThreshold = true;
2106 * Sets the value of field 'renderGaps'.
2108 * @param renderGaps the value of field 'renderGaps'.
2110 public void setRenderGaps(
2111 final boolean renderGaps) {
2112 this._renderGaps = renderGaps;
2113 this._has_renderGaps = true;
2117 * Sets the value of field 'rightAlignIds'.
2119 * @param rightAlignIds the value of field 'rightAlignIds'.
2121 public void setRightAlignIds(
2122 final boolean rightAlignIds) {
2123 this._rightAlignIds = rightAlignIds;
2124 this._has_rightAlignIds = true;
2128 * Sets the value of field 'sequenceSetId'.
2130 * @param sequenceSetId the value of field 'sequenceSetId'.
2132 public void setSequenceSetId(
2133 final java.lang.String sequenceSetId) {
2134 this._sequenceSetId = sequenceSetId;
2138 * Sets the value of field 'showAnnotation'.
2140 * @param showAnnotation the value of field 'showAnnotation'.
2142 public void setShowAnnotation(
2143 final boolean showAnnotation) {
2144 this._showAnnotation = showAnnotation;
2145 this._has_showAnnotation = true;
2149 * Sets the value of field 'showBoxes'.
2151 * @param showBoxes the value of field 'showBoxes'.
2153 public void setShowBoxes(
2154 final boolean showBoxes) {
2155 this._showBoxes = showBoxes;
2156 this._has_showBoxes = true;
2160 * Sets the value of field 'showColourText'.
2162 * @param showColourText the value of field 'showColourText'.
2164 public void setShowColourText(
2165 final boolean showColourText) {
2166 this._showColourText = showColourText;
2167 this._has_showColourText = true;
2171 * Sets the value of field 'showConsensusHistogram'.
2173 * @param showConsensusHistogram the value of field
2174 * 'showConsensusHistogram'.
2176 public void setShowConsensusHistogram(
2177 final boolean showConsensusHistogram) {
2178 this._showConsensusHistogram = showConsensusHistogram;
2179 this._has_showConsensusHistogram = true;
2183 * Sets the value of field 'showDbRefTooltip'.
2185 * @param showDbRefTooltip the value of field 'showDbRefTooltip'
2187 public void setShowDbRefTooltip(
2188 final boolean showDbRefTooltip) {
2189 this._showDbRefTooltip = showDbRefTooltip;
2190 this._has_showDbRefTooltip = true;
2194 * Sets the value of field 'showFullId'.
2196 * @param showFullId the value of field 'showFullId'.
2198 public void setShowFullId(
2199 final boolean showFullId) {
2200 this._showFullId = showFullId;
2201 this._has_showFullId = true;
2205 * Sets the value of field 'showGroupConsensus'.
2207 * @param showGroupConsensus the value of field
2208 * 'showGroupConsensus'.
2210 public void setShowGroupConsensus(
2211 final boolean showGroupConsensus) {
2212 this._showGroupConsensus = showGroupConsensus;
2213 this._has_showGroupConsensus = true;
2217 * Sets the value of field 'showGroupConservation'.
2219 * @param showGroupConservation the value of field
2220 * 'showGroupConservation'.
2222 public void setShowGroupConservation(
2223 final boolean showGroupConservation) {
2224 this._showGroupConservation = showGroupConservation;
2225 this._has_showGroupConservation = true;
2229 * Sets the value of field 'showNPfeatureTooltip'.
2231 * @param showNPfeatureTooltip the value of field
2232 * 'showNPfeatureTooltip'.
2234 public void setShowNPfeatureTooltip(
2235 final boolean showNPfeatureTooltip) {
2236 this._showNPfeatureTooltip = showNPfeatureTooltip;
2237 this._has_showNPfeatureTooltip = true;
2241 * Sets the value of field 'showSequenceFeatures'.
2243 * @param showSequenceFeatures the value of field
2244 * 'showSequenceFeatures'.
2246 public void setShowSequenceFeatures(
2247 final boolean showSequenceFeatures) {
2248 this._showSequenceFeatures = showSequenceFeatures;
2249 this._has_showSequenceFeatures = true;
2253 * Sets the value of field 'showSequenceLogo'.
2255 * @param showSequenceLogo the value of field 'showSequenceLogo'
2257 public void setShowSequenceLogo(
2258 final boolean showSequenceLogo) {
2259 this._showSequenceLogo = showSequenceLogo;
2260 this._has_showSequenceLogo = true;
2264 * Sets the value of field 'showText'.
2266 * @param showText the value of field 'showText'.
2268 public void setShowText(
2269 final boolean showText) {
2270 this._showText = showText;
2271 this._has_showText = true;
2275 * Sets the value of field 'showUnconserved'.
2277 * @param showUnconserved the value of field 'showUnconserved'.
2279 public void setShowUnconserved(
2280 final boolean showUnconserved) {
2281 this._showUnconserved = showUnconserved;
2282 this._has_showUnconserved = true;
2286 * Sets the value of field 'startRes'.
2288 * @param startRes the value of field 'startRes'.
2290 public void setStartRes(
2291 final int startRes) {
2292 this._startRes = startRes;
2293 this._has_startRes = true;
2297 * Sets the value of field 'startSeq'.
2299 * @param startSeq the value of field 'startSeq'.
2301 public void setStartSeq(
2302 final int startSeq) {
2303 this._startSeq = startSeq;
2304 this._has_startSeq = true;
2308 * Sets the value of field 'textCol1'.
2310 * @param textCol1 the value of field 'textCol1'.
2312 public void setTextCol1(
2313 final int textCol1) {
2314 this._textCol1 = textCol1;
2315 this._has_textCol1 = true;
2319 * Sets the value of field 'textCol2'.
2321 * @param textCol2 the value of field 'textCol2'.
2323 public void setTextCol2(
2324 final int textCol2) {
2325 this._textCol2 = textCol2;
2326 this._has_textCol2 = true;
2330 * Sets the value of field 'textColThreshold'.
2332 * @param textColThreshold the value of field 'textColThreshold'
2334 public void setTextColThreshold(
2335 final int textColThreshold) {
2336 this._textColThreshold = textColThreshold;
2337 this._has_textColThreshold = true;
2341 * Sets the value of field 'title'.
2343 * @param title the value of field 'title'.
2345 public void setTitle(
2346 final java.lang.String title) {
2347 this._title = title;
2351 * Sets the value of field 'viewName'.
2353 * @param viewName the value of field 'viewName'.
2355 public void setViewName(
2356 final java.lang.String viewName) {
2357 this._viewName = viewName;
2361 * Sets the value of field 'width'.
2363 * @param width the value of field 'width'.
2365 public void setWidth(
2367 this._width = width;
2368 this._has_width = true;
2372 * Sets the value of field 'wrapAlignment'.
2374 * @param wrapAlignment the value of field 'wrapAlignment'.
2376 public void setWrapAlignment(
2377 final boolean wrapAlignment) {
2378 this._wrapAlignment = wrapAlignment;
2379 this._has_wrapAlignment = true;
2383 * Sets the value of field 'xpos'.
2385 * @param xpos the value of field 'xpos'.
2387 public void setXpos(
2390 this._has_xpos = true;
2394 * Sets the value of field 'ypos'.
2396 * @param ypos the value of field 'ypos'.
2398 public void setYpos(
2401 this._has_ypos = true;
2408 * @throws org.exolab.castor.xml.MarshalException if object is
2409 * null or if any SAXException is thrown during marshaling
2410 * @throws org.exolab.castor.xml.ValidationException if this
2411 * object is an invalid instance according to the schema
2412 * @return the unmarshaled
2413 * jalview.schemabinding.version2.Viewport
2415 public static jalview.schemabinding.version2.Viewport unmarshal(
2416 final java.io.Reader reader)
2417 throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
2418 return (jalview.schemabinding.version2.Viewport) Unmarshaller.unmarshal(jalview.schemabinding.version2.Viewport.class, reader);
2424 * @throws org.exolab.castor.xml.ValidationException if this
2425 * object is an invalid instance according to the schema
2427 public void validate(
2429 throws org.exolab.castor.xml.ValidationException {
2430 org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
2431 validator.validate(this);