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;
282 private int _startRes;
285 * keeps track of state for field: _startRes
287 private boolean _has_startRes;
292 private int _startSeq;
295 * keeps track of state for field: _startSeq
297 private boolean _has_startSeq;
302 private java.lang.String _fontName;
307 private int _fontSize;
310 * keeps track of state for field: _fontSize
312 private boolean _has_fontSize;
317 private int _fontStyle;
320 * keeps track of state for field: _fontStyle
322 private boolean _has_fontStyle;
327 private java.lang.String _viewName;
330 * Field _sequenceSetId.
332 private java.lang.String _sequenceSetId;
335 * Field _gatheredViews.
337 private boolean _gatheredViews;
340 * keeps track of state for field: _gatheredViews
342 private boolean _has_gatheredViews;
347 private int _textCol1;
350 * keeps track of state for field: _textCol1
352 private boolean _has_textCol1;
357 private int _textCol2;
360 * keeps track of state for field: _textCol2
362 private boolean _has_textCol2;
365 * Field _textColThreshold.
367 private int _textColThreshold;
370 * keeps track of state for field: _textColThreshold
372 private boolean _has_textColThreshold;
375 * unique id used by jalview to
376 * synchronize between stored and
380 private java.lang.String _id;
388 * keeps track of state for field: _width
390 private boolean _has_width;
398 * keeps track of state for field: _height
400 private boolean _has_height;
408 * keeps track of state for field: _xpos
410 private boolean _has_xpos;
418 * keeps track of state for field: _ypos
420 private boolean _has_ypos;
423 * Field _annotationColours.
425 private jalview.schemabinding.version2.AnnotationColours _annotationColours;
428 * Field _hiddenColumnsList.
430 private java.util.Vector _hiddenColumnsList;
433 * Field _calcIdParamList.
435 private java.util.Vector _calcIdParamList;
444 this._hiddenColumnsList = new java.util.Vector();
445 this._calcIdParamList = new java.util.Vector();
456 * @param vCalcIdParam
457 * @throws java.lang.IndexOutOfBoundsException if the index
458 * given is outside the bounds of the collection
460 public void addCalcIdParam(
461 final jalview.schemabinding.version2.CalcIdParam vCalcIdParam)
462 throws java.lang.IndexOutOfBoundsException {
463 this._calcIdParamList.addElement(vCalcIdParam);
470 * @param vCalcIdParam
471 * @throws java.lang.IndexOutOfBoundsException if the index
472 * given is outside the bounds of the collection
474 public void addCalcIdParam(
476 final jalview.schemabinding.version2.CalcIdParam vCalcIdParam)
477 throws java.lang.IndexOutOfBoundsException {
478 this._calcIdParamList.add(index, vCalcIdParam);
484 * @param vHiddenColumns
485 * @throws java.lang.IndexOutOfBoundsException if the index
486 * given is outside the bounds of the collection
488 public void addHiddenColumns(
489 final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)
490 throws java.lang.IndexOutOfBoundsException {
491 this._hiddenColumnsList.addElement(vHiddenColumns);
498 * @param vHiddenColumns
499 * @throws java.lang.IndexOutOfBoundsException if the index
500 * given is outside the bounds of the collection
502 public void addHiddenColumns(
504 final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)
505 throws java.lang.IndexOutOfBoundsException {
506 this._hiddenColumnsList.add(index, vHiddenColumns);
511 public void deleteCentreColumnLabels(
513 this._has_centreColumnLabels= false;
518 public void deleteConsThreshold(
520 this._has_consThreshold= false;
525 public void deleteConservationSelected(
527 this._has_conservationSelected= false;
532 public void deleteFollowHighlight(
534 this._has_followHighlight= false;
539 public void deleteFollowSelection(
541 this._has_followSelection= false;
546 public void deleteFontSize(
548 this._has_fontSize= false;
553 public void deleteFontStyle(
555 this._has_fontStyle= false;
560 public void deleteGatheredViews(
562 this._has_gatheredViews= false;
567 public void deleteHeight(
569 this._has_height= false;
574 public void deleteIgnoreGapsinConsensus(
576 this._has_ignoreGapsinConsensus= false;
581 public void deletePidSelected(
583 this._has_pidSelected= false;
588 public void deletePidThreshold(
590 this._has_pidThreshold= false;
595 public void deleteRenderGaps(
597 this._has_renderGaps= false;
602 public void deleteRightAlignIds(
604 this._has_rightAlignIds= false;
609 public void deleteShowAnnotation(
611 this._has_showAnnotation= false;
616 public void deleteShowBoxes(
618 this._has_showBoxes= false;
623 public void deleteShowColourText(
625 this._has_showColourText= false;
630 public void deleteShowConsensusHistogram(
632 this._has_showConsensusHistogram= false;
637 public void deleteShowDbRefTooltip(
639 this._has_showDbRefTooltip= false;
644 public void deleteShowFullId(
646 this._has_showFullId= false;
651 public void deleteShowGroupConsensus(
653 this._has_showGroupConsensus= false;
658 public void deleteShowGroupConservation(
660 this._has_showGroupConservation= false;
665 public void deleteShowNPfeatureTooltip(
667 this._has_showNPfeatureTooltip= false;
672 public void deleteShowSequenceFeatures(
674 this._has_showSequenceFeatures= false;
679 public void deleteShowSequenceLogo(
681 this._has_showSequenceLogo= false;
686 public void deleteShowText(
688 this._has_showText= false;
693 public void deleteShowUnconserved(
695 this._has_showUnconserved= false;
700 public void deleteStartRes(
702 this._has_startRes= false;
707 public void deleteStartSeq(
709 this._has_startSeq= false;
714 public void deleteTextCol1(
716 this._has_textCol1= false;
721 public void deleteTextCol2(
723 this._has_textCol2= false;
728 public void deleteTextColThreshold(
730 this._has_textColThreshold= false;
735 public void deleteWidth(
737 this._has_width= false;
742 public void deleteWrapAlignment(
744 this._has_wrapAlignment= false;
749 public void deleteXpos(
751 this._has_xpos= false;
756 public void deleteYpos(
758 this._has_ypos= false;
762 * Method enumerateCalcIdParam.
764 * @return an Enumeration over all
765 * jalview.schemabinding.version2.CalcIdParam elements
767 public java.util.Enumeration enumerateCalcIdParam(
769 return this._calcIdParamList.elements();
773 * Method enumerateHiddenColumns.
775 * @return an Enumeration over all
776 * jalview.schemabinding.version2.HiddenColumns elements
778 public java.util.Enumeration enumerateHiddenColumns(
780 return this._hiddenColumnsList.elements();
784 * Returns the value of field 'annotationColours'.
786 * @return the value of field 'AnnotationColours'.
788 public jalview.schemabinding.version2.AnnotationColours getAnnotationColours(
790 return this._annotationColours;
794 * Returns the value of field 'bgColour'.
796 * @return the value of field 'BgColour'.
798 public java.lang.String getBgColour(
800 return this._bgColour;
804 * Method getCalcIdParam.
807 * @throws java.lang.IndexOutOfBoundsException if the index
808 * given is outside the bounds of the collection
809 * @return the value of the
810 * jalview.schemabinding.version2.CalcIdParam at the given index
812 public jalview.schemabinding.version2.CalcIdParam getCalcIdParam(
814 throws java.lang.IndexOutOfBoundsException {
815 // check bounds for index
816 if (index < 0 || index >= this._calcIdParamList.size()) {
817 throw new IndexOutOfBoundsException("getCalcIdParam: Index value '" + index + "' not in range [0.." + (this._calcIdParamList.size() - 1) + "]");
820 return (jalview.schemabinding.version2.CalcIdParam) _calcIdParamList.get(index);
824 * Method getCalcIdParam.Returns the contents of the collection
825 * in an Array. <p>Note: Just in case the collection contents
826 * are changing in another thread, we pass a 0-length Array of
827 * the correct type into the API call. This way we <i>know</i>
828 * that the Array returned is of exactly the correct length.
830 * @return this collection as an Array
832 public jalview.schemabinding.version2.CalcIdParam[] getCalcIdParam(
834 jalview.schemabinding.version2.CalcIdParam[] array = new jalview.schemabinding.version2.CalcIdParam[0];
835 return (jalview.schemabinding.version2.CalcIdParam[]) this._calcIdParamList.toArray(array);
839 * Method getCalcIdParamCount.
841 * @return the size of this collection
843 public int getCalcIdParamCount(
845 return this._calcIdParamList.size();
849 * Returns the value of field 'centreColumnLabels'.
851 * @return the value of field 'CentreColumnLabels'.
853 public boolean getCentreColumnLabels(
855 return this._centreColumnLabels;
859 * Returns the value of field 'consThreshold'.
861 * @return the value of field 'ConsThreshold'.
863 public int getConsThreshold(
865 return this._consThreshold;
869 * Returns the value of field 'conservationSelected'.
871 * @return the value of field 'ConservationSelected'.
873 public boolean getConservationSelected(
875 return this._conservationSelected;
879 * Returns the value of field 'followHighlight'.
881 * @return the value of field 'FollowHighlight'.
883 public boolean getFollowHighlight(
885 return this._followHighlight;
889 * Returns the value of field 'followSelection'.
891 * @return the value of field 'FollowSelection'.
893 public boolean getFollowSelection(
895 return this._followSelection;
899 * Returns the value of field 'fontName'.
901 * @return the value of field 'FontName'.
903 public java.lang.String getFontName(
905 return this._fontName;
909 * Returns the value of field 'fontSize'.
911 * @return the value of field 'FontSize'.
913 public int getFontSize(
915 return this._fontSize;
919 * Returns the value of field 'fontStyle'.
921 * @return the value of field 'FontStyle'.
923 public int getFontStyle(
925 return this._fontStyle;
929 * Returns the value of field 'gatheredViews'.
931 * @return the value of field 'GatheredViews'.
933 public boolean getGatheredViews(
935 return this._gatheredViews;
939 * Returns the value of field 'height'.
941 * @return the value of field 'Height'.
943 public int getHeight(
949 * Method getHiddenColumns.
952 * @throws java.lang.IndexOutOfBoundsException if the index
953 * given is outside the bounds of the collection
954 * @return the value of the
955 * jalview.schemabinding.version2.HiddenColumns at the given
958 public jalview.schemabinding.version2.HiddenColumns getHiddenColumns(
960 throws java.lang.IndexOutOfBoundsException {
961 // check bounds for index
962 if (index < 0 || index >= this._hiddenColumnsList.size()) {
963 throw new IndexOutOfBoundsException("getHiddenColumns: Index value '" + index + "' not in range [0.." + (this._hiddenColumnsList.size() - 1) + "]");
966 return (jalview.schemabinding.version2.HiddenColumns) _hiddenColumnsList.get(index);
970 * Method getHiddenColumns.Returns the contents of the
971 * collection in an Array. <p>Note: Just in case the
972 * collection contents are changing in another thread, we pass
973 * a 0-length Array of the correct type into the API call.
974 * This way we <i>know</i> that the Array returned is of
975 * exactly the correct length.
977 * @return this collection as an Array
979 public jalview.schemabinding.version2.HiddenColumns[] getHiddenColumns(
981 jalview.schemabinding.version2.HiddenColumns[] array = new jalview.schemabinding.version2.HiddenColumns[0];
982 return (jalview.schemabinding.version2.HiddenColumns[]) this._hiddenColumnsList.toArray(array);
986 * Method getHiddenColumnsCount.
988 * @return the size of this collection
990 public int getHiddenColumnsCount(
992 return this._hiddenColumnsList.size();
996 * Returns the value of field 'id'. The field 'id' has the
997 * following description: unique id used by jalview to
998 * synchronize between stored and
1002 * @return the value of field 'Id'.
1004 public java.lang.String getId(
1010 * Returns the value of field 'ignoreGapsinConsensus'.
1012 * @return the value of field 'IgnoreGapsinConsensus'.
1014 public boolean getIgnoreGapsinConsensus(
1016 return this._ignoreGapsinConsensus;
1020 * Returns the value of field 'pidSelected'.
1022 * @return the value of field 'PidSelected'.
1024 public boolean getPidSelected(
1026 return this._pidSelected;
1030 * Returns the value of field 'pidThreshold'.
1032 * @return the value of field 'PidThreshold'.
1034 public int getPidThreshold(
1036 return this._pidThreshold;
1040 * Returns the value of field 'renderGaps'.
1042 * @return the value of field 'RenderGaps'.
1044 public boolean getRenderGaps(
1046 return this._renderGaps;
1050 * Returns the value of field 'rightAlignIds'.
1052 * @return the value of field 'RightAlignIds'.
1054 public boolean getRightAlignIds(
1056 return this._rightAlignIds;
1060 * Returns the value of field 'sequenceSetId'.
1062 * @return the value of field 'SequenceSetId'.
1064 public java.lang.String getSequenceSetId(
1066 return this._sequenceSetId;
1070 * Returns the value of field 'showAnnotation'.
1072 * @return the value of field 'ShowAnnotation'.
1074 public boolean getShowAnnotation(
1076 return this._showAnnotation;
1080 * Returns the value of field 'showBoxes'.
1082 * @return the value of field 'ShowBoxes'.
1084 public boolean getShowBoxes(
1086 return this._showBoxes;
1090 * Returns the value of field 'showColourText'.
1092 * @return the value of field 'ShowColourText'.
1094 public boolean getShowColourText(
1096 return this._showColourText;
1100 * Returns the value of field 'showConsensusHistogram'.
1102 * @return the value of field 'ShowConsensusHistogram'.
1104 public boolean getShowConsensusHistogram(
1106 return this._showConsensusHistogram;
1110 * Returns the value of field 'showDbRefTooltip'.
1112 * @return the value of field 'ShowDbRefTooltip'.
1114 public boolean getShowDbRefTooltip(
1116 return this._showDbRefTooltip;
1120 * Returns the value of field 'showFullId'.
1122 * @return the value of field 'ShowFullId'.
1124 public boolean getShowFullId(
1126 return this._showFullId;
1130 * Returns the value of field 'showGroupConsensus'.
1132 * @return the value of field 'ShowGroupConsensus'.
1134 public boolean getShowGroupConsensus(
1136 return this._showGroupConsensus;
1140 * Returns the value of field 'showGroupConservation'.
1142 * @return the value of field 'ShowGroupConservation'.
1144 public boolean getShowGroupConservation(
1146 return this._showGroupConservation;
1150 * Returns the value of field 'showNPfeatureTooltip'.
1152 * @return the value of field 'ShowNPfeatureTooltip'.
1154 public boolean getShowNPfeatureTooltip(
1156 return this._showNPfeatureTooltip;
1160 * Returns the value of field 'showSequenceFeatures'.
1162 * @return the value of field 'ShowSequenceFeatures'.
1164 public boolean getShowSequenceFeatures(
1166 return this._showSequenceFeatures;
1170 * Returns the value of field 'showSequenceLogo'.
1172 * @return the value of field 'ShowSequenceLogo'.
1174 public boolean getShowSequenceLogo(
1176 return this._showSequenceLogo;
1180 * Returns the value of field 'showText'.
1182 * @return the value of field 'ShowText'.
1184 public boolean getShowText(
1186 return this._showText;
1190 * Returns the value of field 'showUnconserved'.
1192 * @return the value of field 'ShowUnconserved'.
1194 public boolean getShowUnconserved(
1196 return this._showUnconserved;
1200 * Returns the value of field 'startRes'.
1202 * @return the value of field 'StartRes'.
1204 public int getStartRes(
1206 return this._startRes;
1210 * Returns the value of field 'startSeq'.
1212 * @return the value of field 'StartSeq'.
1214 public int getStartSeq(
1216 return this._startSeq;
1220 * Returns the value of field 'textCol1'.
1222 * @return the value of field 'TextCol1'.
1224 public int getTextCol1(
1226 return this._textCol1;
1230 * Returns the value of field 'textCol2'.
1232 * @return the value of field 'TextCol2'.
1234 public int getTextCol2(
1236 return this._textCol2;
1240 * Returns the value of field 'textColThreshold'.
1242 * @return the value of field 'TextColThreshold'.
1244 public int getTextColThreshold(
1246 return this._textColThreshold;
1250 * Returns the value of field 'title'.
1252 * @return the value of field 'Title'.
1254 public java.lang.String getTitle(
1260 * Returns the value of field 'viewName'.
1262 * @return the value of field 'ViewName'.
1264 public java.lang.String getViewName(
1266 return this._viewName;
1270 * Returns the value of field 'width'.
1272 * @return the value of field 'Width'.
1274 public int getWidth(
1280 * Returns the value of field 'wrapAlignment'.
1282 * @return the value of field 'WrapAlignment'.
1284 public boolean getWrapAlignment(
1286 return this._wrapAlignment;
1290 * Returns the value of field 'xpos'.
1292 * @return the value of field 'Xpos'.
1300 * Returns the value of field 'ypos'.
1302 * @return the value of field 'Ypos'.
1310 * Method hasCentreColumnLabels.
1312 * @return true if at least one CentreColumnLabels has been adde
1314 public boolean hasCentreColumnLabels(
1316 return this._has_centreColumnLabels;
1320 * Method hasConsThreshold.
1322 * @return true if at least one ConsThreshold has been added
1324 public boolean hasConsThreshold(
1326 return this._has_consThreshold;
1330 * Method hasConservationSelected.
1332 * @return true if at least one ConservationSelected has been
1335 public boolean hasConservationSelected(
1337 return this._has_conservationSelected;
1341 * Method hasFollowHighlight.
1343 * @return true if at least one FollowHighlight has been added
1345 public boolean hasFollowHighlight(
1347 return this._has_followHighlight;
1351 * Method hasFollowSelection.
1353 * @return true if at least one FollowSelection has been added
1355 public boolean hasFollowSelection(
1357 return this._has_followSelection;
1361 * Method hasFontSize.
1363 * @return true if at least one FontSize has been added
1365 public boolean hasFontSize(
1367 return this._has_fontSize;
1371 * Method hasFontStyle.
1373 * @return true if at least one FontStyle has been added
1375 public boolean hasFontStyle(
1377 return this._has_fontStyle;
1381 * Method hasGatheredViews.
1383 * @return true if at least one GatheredViews has been added
1385 public boolean hasGatheredViews(
1387 return this._has_gatheredViews;
1393 * @return true if at least one Height has been added
1395 public boolean hasHeight(
1397 return this._has_height;
1401 * Method hasIgnoreGapsinConsensus.
1403 * @return true if at least one IgnoreGapsinConsensus has been
1406 public boolean hasIgnoreGapsinConsensus(
1408 return this._has_ignoreGapsinConsensus;
1412 * Method hasPidSelected.
1414 * @return true if at least one PidSelected has been added
1416 public boolean hasPidSelected(
1418 return this._has_pidSelected;
1422 * Method hasPidThreshold.
1424 * @return true if at least one PidThreshold has been added
1426 public boolean hasPidThreshold(
1428 return this._has_pidThreshold;
1432 * Method hasRenderGaps.
1434 * @return true if at least one RenderGaps has been added
1436 public boolean hasRenderGaps(
1438 return this._has_renderGaps;
1442 * Method hasRightAlignIds.
1444 * @return true if at least one RightAlignIds has been added
1446 public boolean hasRightAlignIds(
1448 return this._has_rightAlignIds;
1452 * Method hasShowAnnotation.
1454 * @return true if at least one ShowAnnotation has been added
1456 public boolean hasShowAnnotation(
1458 return this._has_showAnnotation;
1462 * Method hasShowBoxes.
1464 * @return true if at least one ShowBoxes has been added
1466 public boolean hasShowBoxes(
1468 return this._has_showBoxes;
1472 * Method hasShowColourText.
1474 * @return true if at least one ShowColourText has been added
1476 public boolean hasShowColourText(
1478 return this._has_showColourText;
1482 * Method hasShowConsensusHistogram.
1484 * @return true if at least one ShowConsensusHistogram has been
1487 public boolean hasShowConsensusHistogram(
1489 return this._has_showConsensusHistogram;
1493 * Method hasShowDbRefTooltip.
1495 * @return true if at least one ShowDbRefTooltip has been added
1497 public boolean hasShowDbRefTooltip(
1499 return this._has_showDbRefTooltip;
1503 * Method hasShowFullId.
1505 * @return true if at least one ShowFullId has been added
1507 public boolean hasShowFullId(
1509 return this._has_showFullId;
1513 * Method hasShowGroupConsensus.
1515 * @return true if at least one ShowGroupConsensus has been adde
1517 public boolean hasShowGroupConsensus(
1519 return this._has_showGroupConsensus;
1523 * Method hasShowGroupConservation.
1525 * @return true if at least one ShowGroupConservation has been
1528 public boolean hasShowGroupConservation(
1530 return this._has_showGroupConservation;
1534 * Method hasShowNPfeatureTooltip.
1536 * @return true if at least one ShowNPfeatureTooltip has been
1539 public boolean hasShowNPfeatureTooltip(
1541 return this._has_showNPfeatureTooltip;
1545 * Method hasShowSequenceFeatures.
1547 * @return true if at least one ShowSequenceFeatures has been
1550 public boolean hasShowSequenceFeatures(
1552 return this._has_showSequenceFeatures;
1556 * Method hasShowSequenceLogo.
1558 * @return true if at least one ShowSequenceLogo has been added
1560 public boolean hasShowSequenceLogo(
1562 return this._has_showSequenceLogo;
1566 * Method hasShowText.
1568 * @return true if at least one ShowText has been added
1570 public boolean hasShowText(
1572 return this._has_showText;
1576 * Method hasShowUnconserved.
1578 * @return true if at least one ShowUnconserved has been added
1580 public boolean hasShowUnconserved(
1582 return this._has_showUnconserved;
1586 * Method hasStartRes.
1588 * @return true if at least one StartRes has been added
1590 public boolean hasStartRes(
1592 return this._has_startRes;
1596 * Method hasStartSeq.
1598 * @return true if at least one StartSeq has been added
1600 public boolean hasStartSeq(
1602 return this._has_startSeq;
1606 * Method hasTextCol1.
1608 * @return true if at least one TextCol1 has been added
1610 public boolean hasTextCol1(
1612 return this._has_textCol1;
1616 * Method hasTextCol2.
1618 * @return true if at least one TextCol2 has been added
1620 public boolean hasTextCol2(
1622 return this._has_textCol2;
1626 * Method hasTextColThreshold.
1628 * @return true if at least one TextColThreshold has been added
1630 public boolean hasTextColThreshold(
1632 return this._has_textColThreshold;
1638 * @return true if at least one Width has been added
1640 public boolean hasWidth(
1642 return this._has_width;
1646 * Method hasWrapAlignment.
1648 * @return true if at least one WrapAlignment has been added
1650 public boolean hasWrapAlignment(
1652 return this._has_wrapAlignment;
1658 * @return true if at least one Xpos has been added
1660 public boolean hasXpos(
1662 return this._has_xpos;
1668 * @return true if at least one Ypos has been added
1670 public boolean hasYpos(
1672 return this._has_ypos;
1676 * Returns the value of field 'centreColumnLabels'.
1678 * @return the value of field 'CentreColumnLabels'.
1680 public boolean isCentreColumnLabels(
1682 return this._centreColumnLabels;
1686 * Returns the value of field 'conservationSelected'.
1688 * @return the value of field 'ConservationSelected'.
1690 public boolean isConservationSelected(
1692 return this._conservationSelected;
1696 * Returns the value of field 'followHighlight'.
1698 * @return the value of field 'FollowHighlight'.
1700 public boolean isFollowHighlight(
1702 return this._followHighlight;
1706 * Returns the value of field 'followSelection'.
1708 * @return the value of field 'FollowSelection'.
1710 public boolean isFollowSelection(
1712 return this._followSelection;
1716 * Returns the value of field 'gatheredViews'.
1718 * @return the value of field 'GatheredViews'.
1720 public boolean isGatheredViews(
1722 return this._gatheredViews;
1726 * Returns the value of field 'ignoreGapsinConsensus'.
1728 * @return the value of field 'IgnoreGapsinConsensus'.
1730 public boolean isIgnoreGapsinConsensus(
1732 return this._ignoreGapsinConsensus;
1736 * Returns the value of field 'pidSelected'.
1738 * @return the value of field 'PidSelected'.
1740 public boolean isPidSelected(
1742 return this._pidSelected;
1746 * Returns the value of field 'renderGaps'.
1748 * @return the value of field 'RenderGaps'.
1750 public boolean isRenderGaps(
1752 return this._renderGaps;
1756 * Returns the value of field 'rightAlignIds'.
1758 * @return the value of field 'RightAlignIds'.
1760 public boolean isRightAlignIds(
1762 return this._rightAlignIds;
1766 * Returns the value of field 'showAnnotation'.
1768 * @return the value of field 'ShowAnnotation'.
1770 public boolean isShowAnnotation(
1772 return this._showAnnotation;
1776 * Returns the value of field 'showBoxes'.
1778 * @return the value of field 'ShowBoxes'.
1780 public boolean isShowBoxes(
1782 return this._showBoxes;
1786 * Returns the value of field 'showColourText'.
1788 * @return the value of field 'ShowColourText'.
1790 public boolean isShowColourText(
1792 return this._showColourText;
1796 * Returns the value of field 'showConsensusHistogram'.
1798 * @return the value of field 'ShowConsensusHistogram'.
1800 public boolean isShowConsensusHistogram(
1802 return this._showConsensusHistogram;
1806 * Returns the value of field 'showDbRefTooltip'.
1808 * @return the value of field 'ShowDbRefTooltip'.
1810 public boolean isShowDbRefTooltip(
1812 return this._showDbRefTooltip;
1816 * Returns the value of field 'showFullId'.
1818 * @return the value of field 'ShowFullId'.
1820 public boolean isShowFullId(
1822 return this._showFullId;
1826 * Returns the value of field 'showGroupConsensus'.
1828 * @return the value of field 'ShowGroupConsensus'.
1830 public boolean isShowGroupConsensus(
1832 return this._showGroupConsensus;
1836 * Returns the value of field 'showGroupConservation'.
1838 * @return the value of field 'ShowGroupConservation'.
1840 public boolean isShowGroupConservation(
1842 return this._showGroupConservation;
1846 * Returns the value of field 'showNPfeatureTooltip'.
1848 * @return the value of field 'ShowNPfeatureTooltip'.
1850 public boolean isShowNPfeatureTooltip(
1852 return this._showNPfeatureTooltip;
1856 * Returns the value of field 'showSequenceFeatures'.
1858 * @return the value of field 'ShowSequenceFeatures'.
1860 public boolean isShowSequenceFeatures(
1862 return this._showSequenceFeatures;
1866 * Returns the value of field 'showSequenceLogo'.
1868 * @return the value of field 'ShowSequenceLogo'.
1870 public boolean isShowSequenceLogo(
1872 return this._showSequenceLogo;
1876 * Returns the value of field 'showText'.
1878 * @return the value of field 'ShowText'.
1880 public boolean isShowText(
1882 return this._showText;
1886 * Returns the value of field 'showUnconserved'.
1888 * @return the value of field 'ShowUnconserved'.
1890 public boolean isShowUnconserved(
1892 return this._showUnconserved;
1898 * @return true if this object is valid according to the schema
1900 public boolean isValid(
1904 } catch (org.exolab.castor.xml.ValidationException vex) {
1911 * Returns the value of field 'wrapAlignment'.
1913 * @return the value of field 'WrapAlignment'.
1915 public boolean isWrapAlignment(
1917 return this._wrapAlignment;
1924 * @throws org.exolab.castor.xml.MarshalException if object is
1925 * null or if any SAXException is thrown during marshaling
1926 * @throws org.exolab.castor.xml.ValidationException if this
1927 * object is an invalid instance according to the schema
1929 public void marshal(
1930 final java.io.Writer out)
1931 throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
1932 Marshaller.marshal(this, out);
1939 * @throws java.io.IOException if an IOException occurs during
1941 * @throws org.exolab.castor.xml.ValidationException if this
1942 * object is an invalid instance according to the schema
1943 * @throws org.exolab.castor.xml.MarshalException if object is
1944 * null or if any SAXException is thrown during marshaling
1946 public void marshal(
1947 final org.xml.sax.ContentHandler handler)
1948 throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
1949 Marshaller.marshal(this, handler);
1954 public void removeAllCalcIdParam(
1956 this._calcIdParamList.clear();
1961 public void removeAllHiddenColumns(
1963 this._hiddenColumnsList.clear();
1967 * Method removeCalcIdParam.
1969 * @param vCalcIdParam
1970 * @return true if the object was removed from the collection.
1972 public boolean removeCalcIdParam(
1973 final jalview.schemabinding.version2.CalcIdParam vCalcIdParam) {
1974 boolean removed = _calcIdParamList.remove(vCalcIdParam);
1979 * Method removeCalcIdParamAt.
1982 * @return the element removed from the collection
1984 public jalview.schemabinding.version2.CalcIdParam removeCalcIdParamAt(
1986 java.lang.Object obj = this._calcIdParamList.remove(index);
1987 return (jalview.schemabinding.version2.CalcIdParam) obj;
1991 * Method removeHiddenColumns.
1993 * @param vHiddenColumns
1994 * @return true if the object was removed from the collection.
1996 public boolean removeHiddenColumns(
1997 final jalview.schemabinding.version2.HiddenColumns vHiddenColumns) {
1998 boolean removed = _hiddenColumnsList.remove(vHiddenColumns);
2003 * Method removeHiddenColumnsAt.
2006 * @return the element removed from the collection
2008 public jalview.schemabinding.version2.HiddenColumns removeHiddenColumnsAt(
2010 java.lang.Object obj = this._hiddenColumnsList.remove(index);
2011 return (jalview.schemabinding.version2.HiddenColumns) obj;
2015 * Sets the value of field 'annotationColours'.
2017 * @param annotationColours the value of field
2018 * 'annotationColours'.
2020 public void setAnnotationColours(
2021 final jalview.schemabinding.version2.AnnotationColours annotationColours) {
2022 this._annotationColours = annotationColours;
2026 * Sets the value of field 'bgColour'.
2028 * @param bgColour the value of field 'bgColour'.
2030 public void setBgColour(
2031 final java.lang.String bgColour) {
2032 this._bgColour = bgColour;
2039 * @param vCalcIdParam
2040 * @throws java.lang.IndexOutOfBoundsException if the index
2041 * given is outside the bounds of the collection
2043 public void setCalcIdParam(
2045 final jalview.schemabinding.version2.CalcIdParam vCalcIdParam)
2046 throws java.lang.IndexOutOfBoundsException {
2047 // check bounds for index
2048 if (index < 0 || index >= this._calcIdParamList.size()) {
2049 throw new IndexOutOfBoundsException("setCalcIdParam: Index value '" + index + "' not in range [0.." + (this._calcIdParamList.size() - 1) + "]");
2052 this._calcIdParamList.set(index, vCalcIdParam);
2058 * @param vCalcIdParamArray
2060 public void setCalcIdParam(
2061 final jalview.schemabinding.version2.CalcIdParam[] vCalcIdParamArray) {
2063 _calcIdParamList.clear();
2065 for (int i = 0; i < vCalcIdParamArray.length; i++) {
2066 this._calcIdParamList.add(vCalcIdParamArray[i]);
2071 * Sets the value of field 'centreColumnLabels'.
2073 * @param centreColumnLabels the value of field
2074 * 'centreColumnLabels'.
2076 public void setCentreColumnLabels(
2077 final boolean centreColumnLabels) {
2078 this._centreColumnLabels = centreColumnLabels;
2079 this._has_centreColumnLabels = true;
2083 * Sets the value of field 'consThreshold'.
2085 * @param consThreshold the value of field 'consThreshold'.
2087 public void setConsThreshold(
2088 final int consThreshold) {
2089 this._consThreshold = consThreshold;
2090 this._has_consThreshold = true;
2094 * Sets the value of field 'conservationSelected'.
2096 * @param conservationSelected the value of field
2097 * 'conservationSelected'.
2099 public void setConservationSelected(
2100 final boolean conservationSelected) {
2101 this._conservationSelected = conservationSelected;
2102 this._has_conservationSelected = true;
2106 * Sets the value of field 'followHighlight'.
2108 * @param followHighlight the value of field 'followHighlight'.
2110 public void setFollowHighlight(
2111 final boolean followHighlight) {
2112 this._followHighlight = followHighlight;
2113 this._has_followHighlight = true;
2117 * Sets the value of field 'followSelection'.
2119 * @param followSelection the value of field 'followSelection'.
2121 public void setFollowSelection(
2122 final boolean followSelection) {
2123 this._followSelection = followSelection;
2124 this._has_followSelection = true;
2128 * Sets the value of field 'fontName'.
2130 * @param fontName the value of field 'fontName'.
2132 public void setFontName(
2133 final java.lang.String fontName) {
2134 this._fontName = fontName;
2138 * Sets the value of field 'fontSize'.
2140 * @param fontSize the value of field 'fontSize'.
2142 public void setFontSize(
2143 final int fontSize) {
2144 this._fontSize = fontSize;
2145 this._has_fontSize = true;
2149 * Sets the value of field 'fontStyle'.
2151 * @param fontStyle the value of field 'fontStyle'.
2153 public void setFontStyle(
2154 final int fontStyle) {
2155 this._fontStyle = fontStyle;
2156 this._has_fontStyle = true;
2160 * Sets the value of field 'gatheredViews'.
2162 * @param gatheredViews the value of field 'gatheredViews'.
2164 public void setGatheredViews(
2165 final boolean gatheredViews) {
2166 this._gatheredViews = gatheredViews;
2167 this._has_gatheredViews = true;
2171 * Sets the value of field 'height'.
2173 * @param height the value of field 'height'.
2175 public void setHeight(
2177 this._height = height;
2178 this._has_height = true;
2185 * @param vHiddenColumns
2186 * @throws java.lang.IndexOutOfBoundsException if the index
2187 * given is outside the bounds of the collection
2189 public void setHiddenColumns(
2191 final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)
2192 throws java.lang.IndexOutOfBoundsException {
2193 // check bounds for index
2194 if (index < 0 || index >= this._hiddenColumnsList.size()) {
2195 throw new IndexOutOfBoundsException("setHiddenColumns: Index value '" + index + "' not in range [0.." + (this._hiddenColumnsList.size() - 1) + "]");
2198 this._hiddenColumnsList.set(index, vHiddenColumns);
2204 * @param vHiddenColumnsArray
2206 public void setHiddenColumns(
2207 final jalview.schemabinding.version2.HiddenColumns[] vHiddenColumnsArray) {
2209 _hiddenColumnsList.clear();
2211 for (int i = 0; i < vHiddenColumnsArray.length; i++) {
2212 this._hiddenColumnsList.add(vHiddenColumnsArray[i]);
2217 * Sets the value of field 'id'. The field 'id' has the
2218 * following description: unique id used by jalview to
2219 * synchronize between stored and
2220 * instantiated views
2223 * @param id the value of field 'id'.
2226 final java.lang.String id) {
2231 * Sets the value of field 'ignoreGapsinConsensus'.
2233 * @param ignoreGapsinConsensus the value of field
2234 * 'ignoreGapsinConsensus'.
2236 public void setIgnoreGapsinConsensus(
2237 final boolean ignoreGapsinConsensus) {
2238 this._ignoreGapsinConsensus = ignoreGapsinConsensus;
2239 this._has_ignoreGapsinConsensus = true;
2243 * Sets the value of field 'pidSelected'.
2245 * @param pidSelected the value of field 'pidSelected'.
2247 public void setPidSelected(
2248 final boolean pidSelected) {
2249 this._pidSelected = pidSelected;
2250 this._has_pidSelected = true;
2254 * Sets the value of field 'pidThreshold'.
2256 * @param pidThreshold the value of field 'pidThreshold'.
2258 public void setPidThreshold(
2259 final int pidThreshold) {
2260 this._pidThreshold = pidThreshold;
2261 this._has_pidThreshold = true;
2265 * Sets the value of field 'renderGaps'.
2267 * @param renderGaps the value of field 'renderGaps'.
2269 public void setRenderGaps(
2270 final boolean renderGaps) {
2271 this._renderGaps = renderGaps;
2272 this._has_renderGaps = true;
2276 * Sets the value of field 'rightAlignIds'.
2278 * @param rightAlignIds the value of field 'rightAlignIds'.
2280 public void setRightAlignIds(
2281 final boolean rightAlignIds) {
2282 this._rightAlignIds = rightAlignIds;
2283 this._has_rightAlignIds = true;
2287 * Sets the value of field 'sequenceSetId'.
2289 * @param sequenceSetId the value of field 'sequenceSetId'.
2291 public void setSequenceSetId(
2292 final java.lang.String sequenceSetId) {
2293 this._sequenceSetId = sequenceSetId;
2297 * Sets the value of field 'showAnnotation'.
2299 * @param showAnnotation the value of field 'showAnnotation'.
2301 public void setShowAnnotation(
2302 final boolean showAnnotation) {
2303 this._showAnnotation = showAnnotation;
2304 this._has_showAnnotation = true;
2308 * Sets the value of field 'showBoxes'.
2310 * @param showBoxes the value of field 'showBoxes'.
2312 public void setShowBoxes(
2313 final boolean showBoxes) {
2314 this._showBoxes = showBoxes;
2315 this._has_showBoxes = true;
2319 * Sets the value of field 'showColourText'.
2321 * @param showColourText the value of field 'showColourText'.
2323 public void setShowColourText(
2324 final boolean showColourText) {
2325 this._showColourText = showColourText;
2326 this._has_showColourText = true;
2330 * Sets the value of field 'showConsensusHistogram'.
2332 * @param showConsensusHistogram the value of field
2333 * 'showConsensusHistogram'.
2335 public void setShowConsensusHistogram(
2336 final boolean showConsensusHistogram) {
2337 this._showConsensusHistogram = showConsensusHistogram;
2338 this._has_showConsensusHistogram = true;
2342 * Sets the value of field 'showDbRefTooltip'.
2344 * @param showDbRefTooltip the value of field 'showDbRefTooltip'
2346 public void setShowDbRefTooltip(
2347 final boolean showDbRefTooltip) {
2348 this._showDbRefTooltip = showDbRefTooltip;
2349 this._has_showDbRefTooltip = true;
2353 * Sets the value of field 'showFullId'.
2355 * @param showFullId the value of field 'showFullId'.
2357 public void setShowFullId(
2358 final boolean showFullId) {
2359 this._showFullId = showFullId;
2360 this._has_showFullId = true;
2364 * Sets the value of field 'showGroupConsensus'.
2366 * @param showGroupConsensus the value of field
2367 * 'showGroupConsensus'.
2369 public void setShowGroupConsensus(
2370 final boolean showGroupConsensus) {
2371 this._showGroupConsensus = showGroupConsensus;
2372 this._has_showGroupConsensus = true;
2376 * Sets the value of field 'showGroupConservation'.
2378 * @param showGroupConservation the value of field
2379 * 'showGroupConservation'.
2381 public void setShowGroupConservation(
2382 final boolean showGroupConservation) {
2383 this._showGroupConservation = showGroupConservation;
2384 this._has_showGroupConservation = true;
2388 * Sets the value of field 'showNPfeatureTooltip'.
2390 * @param showNPfeatureTooltip the value of field
2391 * 'showNPfeatureTooltip'.
2393 public void setShowNPfeatureTooltip(
2394 final boolean showNPfeatureTooltip) {
2395 this._showNPfeatureTooltip = showNPfeatureTooltip;
2396 this._has_showNPfeatureTooltip = true;
2400 * Sets the value of field 'showSequenceFeatures'.
2402 * @param showSequenceFeatures the value of field
2403 * 'showSequenceFeatures'.
2405 public void setShowSequenceFeatures(
2406 final boolean showSequenceFeatures) {
2407 this._showSequenceFeatures = showSequenceFeatures;
2408 this._has_showSequenceFeatures = true;
2412 * Sets the value of field 'showSequenceLogo'.
2414 * @param showSequenceLogo the value of field 'showSequenceLogo'
2416 public void setShowSequenceLogo(
2417 final boolean showSequenceLogo) {
2418 this._showSequenceLogo = showSequenceLogo;
2419 this._has_showSequenceLogo = true;
2423 * Sets the value of field 'showText'.
2425 * @param showText the value of field 'showText'.
2427 public void setShowText(
2428 final boolean showText) {
2429 this._showText = showText;
2430 this._has_showText = true;
2434 * Sets the value of field 'showUnconserved'.
2436 * @param showUnconserved the value of field 'showUnconserved'.
2438 public void setShowUnconserved(
2439 final boolean showUnconserved) {
2440 this._showUnconserved = showUnconserved;
2441 this._has_showUnconserved = true;
2445 * Sets the value of field 'startRes'.
2447 * @param startRes the value of field 'startRes'.
2449 public void setStartRes(
2450 final int startRes) {
2451 this._startRes = startRes;
2452 this._has_startRes = true;
2456 * Sets the value of field 'startSeq'.
2458 * @param startSeq the value of field 'startSeq'.
2460 public void setStartSeq(
2461 final int startSeq) {
2462 this._startSeq = startSeq;
2463 this._has_startSeq = true;
2467 * Sets the value of field 'textCol1'.
2469 * @param textCol1 the value of field 'textCol1'.
2471 public void setTextCol1(
2472 final int textCol1) {
2473 this._textCol1 = textCol1;
2474 this._has_textCol1 = true;
2478 * Sets the value of field 'textCol2'.
2480 * @param textCol2 the value of field 'textCol2'.
2482 public void setTextCol2(
2483 final int textCol2) {
2484 this._textCol2 = textCol2;
2485 this._has_textCol2 = true;
2489 * Sets the value of field 'textColThreshold'.
2491 * @param textColThreshold the value of field 'textColThreshold'
2493 public void setTextColThreshold(
2494 final int textColThreshold) {
2495 this._textColThreshold = textColThreshold;
2496 this._has_textColThreshold = true;
2500 * Sets the value of field 'title'.
2502 * @param title the value of field 'title'.
2504 public void setTitle(
2505 final java.lang.String title) {
2506 this._title = title;
2510 * Sets the value of field 'viewName'.
2512 * @param viewName the value of field 'viewName'.
2514 public void setViewName(
2515 final java.lang.String viewName) {
2516 this._viewName = viewName;
2520 * Sets the value of field 'width'.
2522 * @param width the value of field 'width'.
2524 public void setWidth(
2526 this._width = width;
2527 this._has_width = true;
2531 * Sets the value of field 'wrapAlignment'.
2533 * @param wrapAlignment the value of field 'wrapAlignment'.
2535 public void setWrapAlignment(
2536 final boolean wrapAlignment) {
2537 this._wrapAlignment = wrapAlignment;
2538 this._has_wrapAlignment = true;
2542 * Sets the value of field 'xpos'.
2544 * @param xpos the value of field 'xpos'.
2546 public void setXpos(
2549 this._has_xpos = true;
2553 * Sets the value of field 'ypos'.
2555 * @param ypos the value of field 'ypos'.
2557 public void setYpos(
2560 this._has_ypos = true;
2567 * @throws org.exolab.castor.xml.MarshalException if object is
2568 * null or if any SAXException is thrown during marshaling
2569 * @throws org.exolab.castor.xml.ValidationException if this
2570 * object is an invalid instance according to the schema
2571 * @return the unmarshaled
2572 * jalview.schemabinding.version2.Viewport
2574 public static jalview.schemabinding.version2.Viewport unmarshal(
2575 final java.io.Reader reader)
2576 throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
2577 return (jalview.schemabinding.version2.Viewport) Unmarshaller.unmarshal(jalview.schemabinding.version2.Viewport.class, reader);
2583 * @throws org.exolab.castor.xml.ValidationException if this
2584 * object is an invalid instance according to the schema
2586 public void validate(
2588 throws org.exolab.castor.xml.ValidationException {
2589 org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
2590 validator.validate(this);