1 /*******************************************************************************
2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
3 * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
11 * Jalview is distributed in the hope that it will be useful, but
12 * WITHOUT ANY WARRANTY; without even the implied warranty
13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
14 * PURPOSE. See the GNU General Public License for more details.
16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
17 *******************************************************************************/
19 * This class was automatically generated with
20 * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
25 package jalview.schemabinding.version2;
27 //---------------------------------/
28 //- Imported classes and packages -/
29 //---------------------------------/
31 import org.exolab.castor.xml.Marshaller;
32 import org.exolab.castor.xml.Unmarshaller;
37 * @version $Revision$ $Date$
39 public class Viewport implements java.io.Serializable {
42 //--------------------------/
43 //- Class/Member Variables -/
44 //--------------------------/
47 * Field _conservationSelected.
49 private boolean _conservationSelected;
52 * keeps track of state for field: _conservationSelected
54 private boolean _has_conservationSelected;
59 private boolean _pidSelected;
62 * keeps track of state for field: _pidSelected
64 private boolean _has_pidSelected;
69 private java.lang.String _bgColour;
72 * Field _consThreshold.
74 private int _consThreshold;
77 * keeps track of state for field: _consThreshold
79 private boolean _has_consThreshold;
82 * Field _pidThreshold.
84 private int _pidThreshold;
87 * keeps track of state for field: _pidThreshold
89 private boolean _has_pidThreshold;
94 private java.lang.String _title;
99 private boolean _showFullId;
102 * keeps track of state for field: _showFullId
104 private boolean _has_showFullId;
107 * Field _rightAlignIds.
109 private boolean _rightAlignIds;
112 * keeps track of state for field: _rightAlignIds
114 private boolean _has_rightAlignIds;
119 private boolean _showText;
122 * keeps track of state for field: _showText
124 private boolean _has_showText;
127 * Field _showColourText.
129 private boolean _showColourText;
132 * keeps track of state for field: _showColourText
134 private boolean _has_showColourText;
137 * Field _showUnconserved.
139 private boolean _showUnconserved = false;
142 * keeps track of state for field: _showUnconserved
144 private boolean _has_showUnconserved;
149 private boolean _showBoxes;
152 * keeps track of state for field: _showBoxes
154 private boolean _has_showBoxes;
157 * Field _wrapAlignment.
159 private boolean _wrapAlignment;
162 * keeps track of state for field: _wrapAlignment
164 private boolean _has_wrapAlignment;
169 private boolean _renderGaps;
172 * keeps track of state for field: _renderGaps
174 private boolean _has_renderGaps;
177 * Field _showSequenceFeatures.
179 private boolean _showSequenceFeatures;
182 * keeps track of state for field: _showSequenceFeatures
184 private boolean _has_showSequenceFeatures;
187 * Field _showNPfeatureTooltip.
189 private boolean _showNPfeatureTooltip;
192 * keeps track of state for field: _showNPfeatureTooltip
194 private boolean _has_showNPfeatureTooltip;
197 * Field _showDbRefTooltip.
199 private boolean _showDbRefTooltip;
202 * keeps track of state for field: _showDbRefTooltip
204 private boolean _has_showDbRefTooltip;
207 * Field _followHighlight.
209 private boolean _followHighlight = true;
212 * keeps track of state for field: _followHighlight
214 private boolean _has_followHighlight;
217 * Field _followSelection.
219 private boolean _followSelection = true;
222 * keeps track of state for field: _followSelection
224 private boolean _has_followSelection;
227 * Field _showAnnotation.
229 private boolean _showAnnotation;
232 * keeps track of state for field: _showAnnotation
234 private boolean _has_showAnnotation;
237 * Field _centreColumnLabels.
239 private boolean _centreColumnLabels = false;
242 * keeps track of state for field: _centreColumnLabels
244 private boolean _has_centreColumnLabels;
247 * Field _showGroupConservation.
249 private boolean _showGroupConservation = false;
252 * keeps track of state for field: _showGroupConservation
254 private boolean _has_showGroupConservation;
257 * Field _showGroupConsensus.
259 private boolean _showGroupConsensus = false;
262 * keeps track of state for field: _showGroupConsensus
264 private boolean _has_showGroupConsensus;
267 * Field _showConsensusHistogram.
269 private boolean _showConsensusHistogram = true;
272 * keeps track of state for field: _showConsensusHistogram
274 private boolean _has_showConsensusHistogram;
277 * Field _showSequenceLogo.
279 private boolean _showSequenceLogo = false;
282 * keeps track of state for field: _showSequenceLogo
284 private boolean _has_showSequenceLogo;
287 * Field _ignoreGapsinConsensus.
289 private boolean _ignoreGapsinConsensus = true;
292 * keeps track of state for field: _ignoreGapsinConsensus
294 private boolean _has_ignoreGapsinConsensus;
299 private int _startRes;
302 * keeps track of state for field: _startRes
304 private boolean _has_startRes;
309 private int _startSeq;
312 * keeps track of state for field: _startSeq
314 private boolean _has_startSeq;
319 private java.lang.String _fontName;
324 private int _fontSize;
327 * keeps track of state for field: _fontSize
329 private boolean _has_fontSize;
334 private int _fontStyle;
337 * keeps track of state for field: _fontStyle
339 private boolean _has_fontStyle;
344 private java.lang.String _viewName;
347 * Field _sequenceSetId.
349 private java.lang.String _sequenceSetId;
352 * Field _gatheredViews.
354 private boolean _gatheredViews;
357 * keeps track of state for field: _gatheredViews
359 private boolean _has_gatheredViews;
364 private int _textCol1;
367 * keeps track of state for field: _textCol1
369 private boolean _has_textCol1;
374 private int _textCol2;
377 * keeps track of state for field: _textCol2
379 private boolean _has_textCol2;
382 * Field _textColThreshold.
384 private int _textColThreshold;
387 * keeps track of state for field: _textColThreshold
389 private boolean _has_textColThreshold;
392 * unique id used by jalview to synchronize between stored and
396 private java.lang.String _id;
404 * keeps track of state for field: _width
406 private boolean _has_width;
414 * keeps track of state for field: _height
416 private boolean _has_height;
424 * keeps track of state for field: _xpos
426 private boolean _has_xpos;
434 * keeps track of state for field: _ypos
436 private boolean _has_ypos;
439 * Field _annotationColours.
441 private jalview.schemabinding.version2.AnnotationColours _annotationColours;
444 * Field _hiddenColumnsList.
446 private java.util.Vector _hiddenColumnsList;
455 this._hiddenColumnsList = new java.util.Vector();
466 * @param vHiddenColumns
467 * @throws java.lang.IndexOutOfBoundsException if the index
468 * given is outside the bounds of the collection
470 public void addHiddenColumns(
471 final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)
472 throws java.lang.IndexOutOfBoundsException {
473 this._hiddenColumnsList.addElement(vHiddenColumns);
480 * @param vHiddenColumns
481 * @throws java.lang.IndexOutOfBoundsException if the index
482 * given is outside the bounds of the collection
484 public void addHiddenColumns(
486 final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)
487 throws java.lang.IndexOutOfBoundsException {
488 this._hiddenColumnsList.add(index, vHiddenColumns);
493 public void deleteCentreColumnLabels(
495 this._has_centreColumnLabels= false;
500 public void deleteConsThreshold(
502 this._has_consThreshold= false;
507 public void deleteConservationSelected(
509 this._has_conservationSelected= false;
514 public void deleteFollowHighlight(
516 this._has_followHighlight= false;
521 public void deleteFollowSelection(
523 this._has_followSelection= false;
528 public void deleteFontSize(
530 this._has_fontSize= false;
535 public void deleteFontStyle(
537 this._has_fontStyle= false;
542 public void deleteGatheredViews(
544 this._has_gatheredViews= false;
549 public void deleteHeight(
551 this._has_height= false;
556 public void deleteIgnoreGapsinConsensus(
558 this._has_ignoreGapsinConsensus= false;
563 public void deletePidSelected(
565 this._has_pidSelected= false;
570 public void deletePidThreshold(
572 this._has_pidThreshold= false;
577 public void deleteRenderGaps(
579 this._has_renderGaps= false;
584 public void deleteRightAlignIds(
586 this._has_rightAlignIds= false;
591 public void deleteShowAnnotation(
593 this._has_showAnnotation= false;
598 public void deleteShowBoxes(
600 this._has_showBoxes= false;
605 public void deleteShowColourText(
607 this._has_showColourText= false;
612 public void deleteShowConsensusHistogram(
614 this._has_showConsensusHistogram= false;
619 public void deleteShowDbRefTooltip(
621 this._has_showDbRefTooltip= false;
626 public void deleteShowFullId(
628 this._has_showFullId= false;
633 public void deleteShowGroupConsensus(
635 this._has_showGroupConsensus= false;
640 public void deleteShowGroupConservation(
642 this._has_showGroupConservation= false;
647 public void deleteShowNPfeatureTooltip(
649 this._has_showNPfeatureTooltip= false;
654 public void deleteShowSequenceFeatures(
656 this._has_showSequenceFeatures= false;
661 public void deleteShowSequenceLogo(
663 this._has_showSequenceLogo= false;
668 public void deleteShowText(
670 this._has_showText= false;
675 public void deleteShowUnconserved(
677 this._has_showUnconserved= false;
682 public void deleteStartRes(
684 this._has_startRes= false;
689 public void deleteStartSeq(
691 this._has_startSeq= false;
696 public void deleteTextCol1(
698 this._has_textCol1= false;
703 public void deleteTextCol2(
705 this._has_textCol2= false;
710 public void deleteTextColThreshold(
712 this._has_textColThreshold= false;
717 public void deleteWidth(
719 this._has_width= false;
724 public void deleteWrapAlignment(
726 this._has_wrapAlignment= false;
731 public void deleteXpos(
733 this._has_xpos= false;
738 public void deleteYpos(
740 this._has_ypos= false;
744 * Method enumerateHiddenColumns.
746 * @return an Enumeration over all
747 * jalview.schemabinding.version2.HiddenColumns elements
749 public java.util.Enumeration enumerateHiddenColumns(
751 return this._hiddenColumnsList.elements();
755 * Returns the value of field 'annotationColours'.
757 * @return the value of field 'AnnotationColours'.
759 public jalview.schemabinding.version2.AnnotationColours getAnnotationColours(
761 return this._annotationColours;
765 * Returns the value of field 'bgColour'.
767 * @return the value of field 'BgColour'.
769 public java.lang.String getBgColour(
771 return this._bgColour;
775 * Returns the value of field 'centreColumnLabels'.
777 * @return the value of field 'CentreColumnLabels'.
779 public boolean getCentreColumnLabels(
781 return this._centreColumnLabels;
785 * Returns the value of field 'consThreshold'.
787 * @return the value of field 'ConsThreshold'.
789 public int getConsThreshold(
791 return this._consThreshold;
795 * Returns the value of field 'conservationSelected'.
797 * @return the value of field 'ConservationSelected'.
799 public boolean getConservationSelected(
801 return this._conservationSelected;
805 * Returns the value of field 'followHighlight'.
807 * @return the value of field 'FollowHighlight'.
809 public boolean getFollowHighlight(
811 return this._followHighlight;
815 * Returns the value of field 'followSelection'.
817 * @return the value of field 'FollowSelection'.
819 public boolean getFollowSelection(
821 return this._followSelection;
825 * Returns the value of field 'fontName'.
827 * @return the value of field 'FontName'.
829 public java.lang.String getFontName(
831 return this._fontName;
835 * Returns the value of field 'fontSize'.
837 * @return the value of field 'FontSize'.
839 public int getFontSize(
841 return this._fontSize;
845 * Returns the value of field 'fontStyle'.
847 * @return the value of field 'FontStyle'.
849 public int getFontStyle(
851 return this._fontStyle;
855 * Returns the value of field 'gatheredViews'.
857 * @return the value of field 'GatheredViews'.
859 public boolean getGatheredViews(
861 return this._gatheredViews;
865 * Returns the value of field 'height'.
867 * @return the value of field 'Height'.
869 public int getHeight(
875 * Method getHiddenColumns.
878 * @throws java.lang.IndexOutOfBoundsException if the index
879 * given is outside the bounds of the collection
880 * @return the value of the
881 * jalview.schemabinding.version2.HiddenColumns at the given
884 public jalview.schemabinding.version2.HiddenColumns getHiddenColumns(
886 throws java.lang.IndexOutOfBoundsException {
887 // check bounds for index
888 if (index < 0 || index >= this._hiddenColumnsList.size()) {
889 throw new IndexOutOfBoundsException("getHiddenColumns: Index value '" + index + "' not in range [0.." + (this._hiddenColumnsList.size() - 1) + "]");
892 return (jalview.schemabinding.version2.HiddenColumns) _hiddenColumnsList.get(index);
896 * Method getHiddenColumns.Returns the contents of the
897 * collection in an Array. <p>Note: Just in case the
898 * collection contents are changing in another thread, we pass
899 * a 0-length Array of the correct type into the API call.
900 * This way we <i>know</i> that the Array returned is of
901 * exactly the correct length.
903 * @return this collection as an Array
905 public jalview.schemabinding.version2.HiddenColumns[] getHiddenColumns(
907 jalview.schemabinding.version2.HiddenColumns[] array = new jalview.schemabinding.version2.HiddenColumns[0];
908 return (jalview.schemabinding.version2.HiddenColumns[]) this._hiddenColumnsList.toArray(array);
912 * Method getHiddenColumnsCount.
914 * @return the size of this collection
916 public int getHiddenColumnsCount(
918 return this._hiddenColumnsList.size();
922 * Returns the value of field 'id'. The field 'id' has the
923 * following description: unique id used by jalview to
924 * synchronize between stored and instantiated views
927 * @return the value of field 'Id'.
929 public java.lang.String getId(
935 * Returns the value of field 'ignoreGapsinConsensus'.
937 * @return the value of field 'IgnoreGapsinConsensus'.
939 public boolean getIgnoreGapsinConsensus(
941 return this._ignoreGapsinConsensus;
945 * Returns the value of field 'pidSelected'.
947 * @return the value of field 'PidSelected'.
949 public boolean getPidSelected(
951 return this._pidSelected;
955 * Returns the value of field 'pidThreshold'.
957 * @return the value of field 'PidThreshold'.
959 public int getPidThreshold(
961 return this._pidThreshold;
965 * Returns the value of field 'renderGaps'.
967 * @return the value of field 'RenderGaps'.
969 public boolean getRenderGaps(
971 return this._renderGaps;
975 * Returns the value of field 'rightAlignIds'.
977 * @return the value of field 'RightAlignIds'.
979 public boolean getRightAlignIds(
981 return this._rightAlignIds;
985 * Returns the value of field 'sequenceSetId'.
987 * @return the value of field 'SequenceSetId'.
989 public java.lang.String getSequenceSetId(
991 return this._sequenceSetId;
995 * Returns the value of field 'showAnnotation'.
997 * @return the value of field 'ShowAnnotation'.
999 public boolean getShowAnnotation(
1001 return this._showAnnotation;
1005 * Returns the value of field 'showBoxes'.
1007 * @return the value of field 'ShowBoxes'.
1009 public boolean getShowBoxes(
1011 return this._showBoxes;
1015 * Returns the value of field 'showColourText'.
1017 * @return the value of field 'ShowColourText'.
1019 public boolean getShowColourText(
1021 return this._showColourText;
1025 * Returns the value of field 'showConsensusHistogram'.
1027 * @return the value of field 'ShowConsensusHistogram'.
1029 public boolean getShowConsensusHistogram(
1031 return this._showConsensusHistogram;
1035 * Returns the value of field 'showDbRefTooltip'.
1037 * @return the value of field 'ShowDbRefTooltip'.
1039 public boolean getShowDbRefTooltip(
1041 return this._showDbRefTooltip;
1045 * Returns the value of field 'showFullId'.
1047 * @return the value of field 'ShowFullId'.
1049 public boolean getShowFullId(
1051 return this._showFullId;
1055 * Returns the value of field 'showGroupConsensus'.
1057 * @return the value of field 'ShowGroupConsensus'.
1059 public boolean getShowGroupConsensus(
1061 return this._showGroupConsensus;
1065 * Returns the value of field 'showGroupConservation'.
1067 * @return the value of field 'ShowGroupConservation'.
1069 public boolean getShowGroupConservation(
1071 return this._showGroupConservation;
1075 * Returns the value of field 'showNPfeatureTooltip'.
1077 * @return the value of field 'ShowNPfeatureTooltip'.
1079 public boolean getShowNPfeatureTooltip(
1081 return this._showNPfeatureTooltip;
1085 * Returns the value of field 'showSequenceFeatures'.
1087 * @return the value of field 'ShowSequenceFeatures'.
1089 public boolean getShowSequenceFeatures(
1091 return this._showSequenceFeatures;
1095 * Returns the value of field 'showSequenceLogo'.
1097 * @return the value of field 'ShowSequenceLogo'.
1099 public boolean getShowSequenceLogo(
1101 return this._showSequenceLogo;
1105 * Returns the value of field 'showText'.
1107 * @return the value of field 'ShowText'.
1109 public boolean getShowText(
1111 return this._showText;
1115 * Returns the value of field 'showUnconserved'.
1117 * @return the value of field 'ShowUnconserved'.
1119 public boolean getShowUnconserved(
1121 return this._showUnconserved;
1125 * Returns the value of field 'startRes'.
1127 * @return the value of field 'StartRes'.
1129 public int getStartRes(
1131 return this._startRes;
1135 * Returns the value of field 'startSeq'.
1137 * @return the value of field 'StartSeq'.
1139 public int getStartSeq(
1141 return this._startSeq;
1145 * Returns the value of field 'textCol1'.
1147 * @return the value of field 'TextCol1'.
1149 public int getTextCol1(
1151 return this._textCol1;
1155 * Returns the value of field 'textCol2'.
1157 * @return the value of field 'TextCol2'.
1159 public int getTextCol2(
1161 return this._textCol2;
1165 * Returns the value of field 'textColThreshold'.
1167 * @return the value of field 'TextColThreshold'.
1169 public int getTextColThreshold(
1171 return this._textColThreshold;
1175 * Returns the value of field 'title'.
1177 * @return the value of field 'Title'.
1179 public java.lang.String getTitle(
1185 * Returns the value of field 'viewName'.
1187 * @return the value of field 'ViewName'.
1189 public java.lang.String getViewName(
1191 return this._viewName;
1195 * Returns the value of field 'width'.
1197 * @return the value of field 'Width'.
1199 public int getWidth(
1205 * Returns the value of field 'wrapAlignment'.
1207 * @return the value of field 'WrapAlignment'.
1209 public boolean getWrapAlignment(
1211 return this._wrapAlignment;
1215 * Returns the value of field 'xpos'.
1217 * @return the value of field 'Xpos'.
1225 * Returns the value of field 'ypos'.
1227 * @return the value of field 'Ypos'.
1235 * Method hasCentreColumnLabels.
1237 * @return true if at least one CentreColumnLabels has been adde
1239 public boolean hasCentreColumnLabels(
1241 return this._has_centreColumnLabels;
1245 * Method hasConsThreshold.
1247 * @return true if at least one ConsThreshold has been added
1249 public boolean hasConsThreshold(
1251 return this._has_consThreshold;
1255 * Method hasConservationSelected.
1257 * @return true if at least one ConservationSelected has been
1260 public boolean hasConservationSelected(
1262 return this._has_conservationSelected;
1266 * Method hasFollowHighlight.
1268 * @return true if at least one FollowHighlight has been added
1270 public boolean hasFollowHighlight(
1272 return this._has_followHighlight;
1276 * Method hasFollowSelection.
1278 * @return true if at least one FollowSelection has been added
1280 public boolean hasFollowSelection(
1282 return this._has_followSelection;
1286 * Method hasFontSize.
1288 * @return true if at least one FontSize has been added
1290 public boolean hasFontSize(
1292 return this._has_fontSize;
1296 * Method hasFontStyle.
1298 * @return true if at least one FontStyle has been added
1300 public boolean hasFontStyle(
1302 return this._has_fontStyle;
1306 * Method hasGatheredViews.
1308 * @return true if at least one GatheredViews has been added
1310 public boolean hasGatheredViews(
1312 return this._has_gatheredViews;
1318 * @return true if at least one Height has been added
1320 public boolean hasHeight(
1322 return this._has_height;
1326 * Method hasIgnoreGapsinConsensus.
1328 * @return true if at least one IgnoreGapsinConsensus has been
1331 public boolean hasIgnoreGapsinConsensus(
1333 return this._has_ignoreGapsinConsensus;
1337 * Method hasPidSelected.
1339 * @return true if at least one PidSelected has been added
1341 public boolean hasPidSelected(
1343 return this._has_pidSelected;
1347 * Method hasPidThreshold.
1349 * @return true if at least one PidThreshold has been added
1351 public boolean hasPidThreshold(
1353 return this._has_pidThreshold;
1357 * Method hasRenderGaps.
1359 * @return true if at least one RenderGaps has been added
1361 public boolean hasRenderGaps(
1363 return this._has_renderGaps;
1367 * Method hasRightAlignIds.
1369 * @return true if at least one RightAlignIds has been added
1371 public boolean hasRightAlignIds(
1373 return this._has_rightAlignIds;
1377 * Method hasShowAnnotation.
1379 * @return true if at least one ShowAnnotation has been added
1381 public boolean hasShowAnnotation(
1383 return this._has_showAnnotation;
1387 * Method hasShowBoxes.
1389 * @return true if at least one ShowBoxes has been added
1391 public boolean hasShowBoxes(
1393 return this._has_showBoxes;
1397 * Method hasShowColourText.
1399 * @return true if at least one ShowColourText has been added
1401 public boolean hasShowColourText(
1403 return this._has_showColourText;
1407 * Method hasShowConsensusHistogram.
1409 * @return true if at least one ShowConsensusHistogram has been
1412 public boolean hasShowConsensusHistogram(
1414 return this._has_showConsensusHistogram;
1418 * Method hasShowDbRefTooltip.
1420 * @return true if at least one ShowDbRefTooltip has been added
1422 public boolean hasShowDbRefTooltip(
1424 return this._has_showDbRefTooltip;
1428 * Method hasShowFullId.
1430 * @return true if at least one ShowFullId has been added
1432 public boolean hasShowFullId(
1434 return this._has_showFullId;
1438 * Method hasShowGroupConsensus.
1440 * @return true if at least one ShowGroupConsensus has been adde
1442 public boolean hasShowGroupConsensus(
1444 return this._has_showGroupConsensus;
1448 * Method hasShowGroupConservation.
1450 * @return true if at least one ShowGroupConservation has been
1453 public boolean hasShowGroupConservation(
1455 return this._has_showGroupConservation;
1459 * Method hasShowNPfeatureTooltip.
1461 * @return true if at least one ShowNPfeatureTooltip has been
1464 public boolean hasShowNPfeatureTooltip(
1466 return this._has_showNPfeatureTooltip;
1470 * Method hasShowSequenceFeatures.
1472 * @return true if at least one ShowSequenceFeatures has been
1475 public boolean hasShowSequenceFeatures(
1477 return this._has_showSequenceFeatures;
1481 * Method hasShowSequenceLogo.
1483 * @return true if at least one ShowSequenceLogo has been added
1485 public boolean hasShowSequenceLogo(
1487 return this._has_showSequenceLogo;
1491 * Method hasShowText.
1493 * @return true if at least one ShowText has been added
1495 public boolean hasShowText(
1497 return this._has_showText;
1501 * Method hasShowUnconserved.
1503 * @return true if at least one ShowUnconserved has been added
1505 public boolean hasShowUnconserved(
1507 return this._has_showUnconserved;
1511 * Method hasStartRes.
1513 * @return true if at least one StartRes has been added
1515 public boolean hasStartRes(
1517 return this._has_startRes;
1521 * Method hasStartSeq.
1523 * @return true if at least one StartSeq has been added
1525 public boolean hasStartSeq(
1527 return this._has_startSeq;
1531 * Method hasTextCol1.
1533 * @return true if at least one TextCol1 has been added
1535 public boolean hasTextCol1(
1537 return this._has_textCol1;
1541 * Method hasTextCol2.
1543 * @return true if at least one TextCol2 has been added
1545 public boolean hasTextCol2(
1547 return this._has_textCol2;
1551 * Method hasTextColThreshold.
1553 * @return true if at least one TextColThreshold has been added
1555 public boolean hasTextColThreshold(
1557 return this._has_textColThreshold;
1563 * @return true if at least one Width has been added
1565 public boolean hasWidth(
1567 return this._has_width;
1571 * Method hasWrapAlignment.
1573 * @return true if at least one WrapAlignment has been added
1575 public boolean hasWrapAlignment(
1577 return this._has_wrapAlignment;
1583 * @return true if at least one Xpos has been added
1585 public boolean hasXpos(
1587 return this._has_xpos;
1593 * @return true if at least one Ypos has been added
1595 public boolean hasYpos(
1597 return this._has_ypos;
1601 * Returns the value of field 'centreColumnLabels'.
1603 * @return the value of field 'CentreColumnLabels'.
1605 public boolean isCentreColumnLabels(
1607 return this._centreColumnLabels;
1611 * Returns the value of field 'conservationSelected'.
1613 * @return the value of field 'ConservationSelected'.
1615 public boolean isConservationSelected(
1617 return this._conservationSelected;
1621 * Returns the value of field 'followHighlight'.
1623 * @return the value of field 'FollowHighlight'.
1625 public boolean isFollowHighlight(
1627 return this._followHighlight;
1631 * Returns the value of field 'followSelection'.
1633 * @return the value of field 'FollowSelection'.
1635 public boolean isFollowSelection(
1637 return this._followSelection;
1641 * Returns the value of field 'gatheredViews'.
1643 * @return the value of field 'GatheredViews'.
1645 public boolean isGatheredViews(
1647 return this._gatheredViews;
1651 * Returns the value of field 'ignoreGapsinConsensus'.
1653 * @return the value of field 'IgnoreGapsinConsensus'.
1655 public boolean isIgnoreGapsinConsensus(
1657 return this._ignoreGapsinConsensus;
1661 * Returns the value of field 'pidSelected'.
1663 * @return the value of field 'PidSelected'.
1665 public boolean isPidSelected(
1667 return this._pidSelected;
1671 * Returns the value of field 'renderGaps'.
1673 * @return the value of field 'RenderGaps'.
1675 public boolean isRenderGaps(
1677 return this._renderGaps;
1681 * Returns the value of field 'rightAlignIds'.
1683 * @return the value of field 'RightAlignIds'.
1685 public boolean isRightAlignIds(
1687 return this._rightAlignIds;
1691 * Returns the value of field 'showAnnotation'.
1693 * @return the value of field 'ShowAnnotation'.
1695 public boolean isShowAnnotation(
1697 return this._showAnnotation;
1701 * Returns the value of field 'showBoxes'.
1703 * @return the value of field 'ShowBoxes'.
1705 public boolean isShowBoxes(
1707 return this._showBoxes;
1711 * Returns the value of field 'showColourText'.
1713 * @return the value of field 'ShowColourText'.
1715 public boolean isShowColourText(
1717 return this._showColourText;
1721 * Returns the value of field 'showConsensusHistogram'.
1723 * @return the value of field 'ShowConsensusHistogram'.
1725 public boolean isShowConsensusHistogram(
1727 return this._showConsensusHistogram;
1731 * Returns the value of field 'showDbRefTooltip'.
1733 * @return the value of field 'ShowDbRefTooltip'.
1735 public boolean isShowDbRefTooltip(
1737 return this._showDbRefTooltip;
1741 * Returns the value of field 'showFullId'.
1743 * @return the value of field 'ShowFullId'.
1745 public boolean isShowFullId(
1747 return this._showFullId;
1751 * Returns the value of field 'showGroupConsensus'.
1753 * @return the value of field 'ShowGroupConsensus'.
1755 public boolean isShowGroupConsensus(
1757 return this._showGroupConsensus;
1761 * Returns the value of field 'showGroupConservation'.
1763 * @return the value of field 'ShowGroupConservation'.
1765 public boolean isShowGroupConservation(
1767 return this._showGroupConservation;
1771 * Returns the value of field 'showNPfeatureTooltip'.
1773 * @return the value of field 'ShowNPfeatureTooltip'.
1775 public boolean isShowNPfeatureTooltip(
1777 return this._showNPfeatureTooltip;
1781 * Returns the value of field 'showSequenceFeatures'.
1783 * @return the value of field 'ShowSequenceFeatures'.
1785 public boolean isShowSequenceFeatures(
1787 return this._showSequenceFeatures;
1791 * Returns the value of field 'showSequenceLogo'.
1793 * @return the value of field 'ShowSequenceLogo'.
1795 public boolean isShowSequenceLogo(
1797 return this._showSequenceLogo;
1801 * Returns the value of field 'showText'.
1803 * @return the value of field 'ShowText'.
1805 public boolean isShowText(
1807 return this._showText;
1811 * Returns the value of field 'showUnconserved'.
1813 * @return the value of field 'ShowUnconserved'.
1815 public boolean isShowUnconserved(
1817 return this._showUnconserved;
1823 * @return true if this object is valid according to the schema
1825 public boolean isValid(
1829 } catch (org.exolab.castor.xml.ValidationException vex) {
1836 * Returns the value of field 'wrapAlignment'.
1838 * @return the value of field 'WrapAlignment'.
1840 public boolean isWrapAlignment(
1842 return this._wrapAlignment;
1849 * @throws org.exolab.castor.xml.MarshalException if object is
1850 * null or if any SAXException is thrown during marshaling
1851 * @throws org.exolab.castor.xml.ValidationException if this
1852 * object is an invalid instance according to the schema
1854 public void marshal(
1855 final java.io.Writer out)
1856 throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
1857 Marshaller.marshal(this, out);
1864 * @throws java.io.IOException if an IOException occurs during
1866 * @throws org.exolab.castor.xml.ValidationException if this
1867 * object is an invalid instance according to the schema
1868 * @throws org.exolab.castor.xml.MarshalException if object is
1869 * null or if any SAXException is thrown during marshaling
1871 public void marshal(
1872 final org.xml.sax.ContentHandler handler)
1873 throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
1874 Marshaller.marshal(this, handler);
1879 public void removeAllHiddenColumns(
1881 this._hiddenColumnsList.clear();
1885 * Method removeHiddenColumns.
1887 * @param vHiddenColumns
1888 * @return true if the object was removed from the collection.
1890 public boolean removeHiddenColumns(
1891 final jalview.schemabinding.version2.HiddenColumns vHiddenColumns) {
1892 boolean removed = _hiddenColumnsList.remove(vHiddenColumns);
1897 * Method removeHiddenColumnsAt.
1900 * @return the element removed from the collection
1902 public jalview.schemabinding.version2.HiddenColumns removeHiddenColumnsAt(
1904 java.lang.Object obj = this._hiddenColumnsList.remove(index);
1905 return (jalview.schemabinding.version2.HiddenColumns) obj;
1909 * Sets the value of field 'annotationColours'.
1911 * @param annotationColours the value of field
1912 * 'annotationColours'.
1914 public void setAnnotationColours(
1915 final jalview.schemabinding.version2.AnnotationColours annotationColours) {
1916 this._annotationColours = annotationColours;
1920 * Sets the value of field 'bgColour'.
1922 * @param bgColour the value of field 'bgColour'.
1924 public void setBgColour(
1925 final java.lang.String bgColour) {
1926 this._bgColour = bgColour;
1930 * Sets the value of field 'centreColumnLabels'.
1932 * @param centreColumnLabels the value of field
1933 * 'centreColumnLabels'.
1935 public void setCentreColumnLabels(
1936 final boolean centreColumnLabels) {
1937 this._centreColumnLabels = centreColumnLabels;
1938 this._has_centreColumnLabels = true;
1942 * Sets the value of field 'consThreshold'.
1944 * @param consThreshold the value of field 'consThreshold'.
1946 public void setConsThreshold(
1947 final int consThreshold) {
1948 this._consThreshold = consThreshold;
1949 this._has_consThreshold = true;
1953 * Sets the value of field 'conservationSelected'.
1955 * @param conservationSelected the value of field
1956 * 'conservationSelected'.
1958 public void setConservationSelected(
1959 final boolean conservationSelected) {
1960 this._conservationSelected = conservationSelected;
1961 this._has_conservationSelected = true;
1965 * Sets the value of field 'followHighlight'.
1967 * @param followHighlight the value of field 'followHighlight'.
1969 public void setFollowHighlight(
1970 final boolean followHighlight) {
1971 this._followHighlight = followHighlight;
1972 this._has_followHighlight = true;
1976 * Sets the value of field 'followSelection'.
1978 * @param followSelection the value of field 'followSelection'.
1980 public void setFollowSelection(
1981 final boolean followSelection) {
1982 this._followSelection = followSelection;
1983 this._has_followSelection = true;
1987 * Sets the value of field 'fontName'.
1989 * @param fontName the value of field 'fontName'.
1991 public void setFontName(
1992 final java.lang.String fontName) {
1993 this._fontName = fontName;
1997 * Sets the value of field 'fontSize'.
1999 * @param fontSize the value of field 'fontSize'.
2001 public void setFontSize(
2002 final int fontSize) {
2003 this._fontSize = fontSize;
2004 this._has_fontSize = true;
2008 * Sets the value of field 'fontStyle'.
2010 * @param fontStyle the value of field 'fontStyle'.
2012 public void setFontStyle(
2013 final int fontStyle) {
2014 this._fontStyle = fontStyle;
2015 this._has_fontStyle = true;
2019 * Sets the value of field 'gatheredViews'.
2021 * @param gatheredViews the value of field 'gatheredViews'.
2023 public void setGatheredViews(
2024 final boolean gatheredViews) {
2025 this._gatheredViews = gatheredViews;
2026 this._has_gatheredViews = true;
2030 * Sets the value of field 'height'.
2032 * @param height the value of field 'height'.
2034 public void setHeight(
2036 this._height = height;
2037 this._has_height = true;
2044 * @param vHiddenColumns
2045 * @throws java.lang.IndexOutOfBoundsException if the index
2046 * given is outside the bounds of the collection
2048 public void setHiddenColumns(
2050 final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)
2051 throws java.lang.IndexOutOfBoundsException {
2052 // check bounds for index
2053 if (index < 0 || index >= this._hiddenColumnsList.size()) {
2054 throw new IndexOutOfBoundsException("setHiddenColumns: Index value '" + index + "' not in range [0.." + (this._hiddenColumnsList.size() - 1) + "]");
2057 this._hiddenColumnsList.set(index, vHiddenColumns);
2063 * @param vHiddenColumnsArray
2065 public void setHiddenColumns(
2066 final jalview.schemabinding.version2.HiddenColumns[] vHiddenColumnsArray) {
2068 _hiddenColumnsList.clear();
2070 for (int i = 0; i < vHiddenColumnsArray.length; i++) {
2071 this._hiddenColumnsList.add(vHiddenColumnsArray[i]);
2076 * Sets the value of field 'id'. The field 'id' has the
2077 * following description: unique id used by jalview to
2078 * synchronize between stored and instantiated views
2081 * @param id the value of field 'id'.
2084 final java.lang.String id) {
2089 * Sets the value of field 'ignoreGapsinConsensus'.
2091 * @param ignoreGapsinConsensus the value of field
2092 * 'ignoreGapsinConsensus'.
2094 public void setIgnoreGapsinConsensus(
2095 final boolean ignoreGapsinConsensus) {
2096 this._ignoreGapsinConsensus = ignoreGapsinConsensus;
2097 this._has_ignoreGapsinConsensus = true;
2101 * Sets the value of field 'pidSelected'.
2103 * @param pidSelected the value of field 'pidSelected'.
2105 public void setPidSelected(
2106 final boolean pidSelected) {
2107 this._pidSelected = pidSelected;
2108 this._has_pidSelected = true;
2112 * Sets the value of field 'pidThreshold'.
2114 * @param pidThreshold the value of field 'pidThreshold'.
2116 public void setPidThreshold(
2117 final int pidThreshold) {
2118 this._pidThreshold = pidThreshold;
2119 this._has_pidThreshold = true;
2123 * Sets the value of field 'renderGaps'.
2125 * @param renderGaps the value of field 'renderGaps'.
2127 public void setRenderGaps(
2128 final boolean renderGaps) {
2129 this._renderGaps = renderGaps;
2130 this._has_renderGaps = true;
2134 * Sets the value of field 'rightAlignIds'.
2136 * @param rightAlignIds the value of field 'rightAlignIds'.
2138 public void setRightAlignIds(
2139 final boolean rightAlignIds) {
2140 this._rightAlignIds = rightAlignIds;
2141 this._has_rightAlignIds = true;
2145 * Sets the value of field 'sequenceSetId'.
2147 * @param sequenceSetId the value of field 'sequenceSetId'.
2149 public void setSequenceSetId(
2150 final java.lang.String sequenceSetId) {
2151 this._sequenceSetId = sequenceSetId;
2155 * Sets the value of field 'showAnnotation'.
2157 * @param showAnnotation the value of field 'showAnnotation'.
2159 public void setShowAnnotation(
2160 final boolean showAnnotation) {
2161 this._showAnnotation = showAnnotation;
2162 this._has_showAnnotation = true;
2166 * Sets the value of field 'showBoxes'.
2168 * @param showBoxes the value of field 'showBoxes'.
2170 public void setShowBoxes(
2171 final boolean showBoxes) {
2172 this._showBoxes = showBoxes;
2173 this._has_showBoxes = true;
2177 * Sets the value of field 'showColourText'.
2179 * @param showColourText the value of field 'showColourText'.
2181 public void setShowColourText(
2182 final boolean showColourText) {
2183 this._showColourText = showColourText;
2184 this._has_showColourText = true;
2188 * Sets the value of field 'showConsensusHistogram'.
2190 * @param showConsensusHistogram the value of field
2191 * 'showConsensusHistogram'.
2193 public void setShowConsensusHistogram(
2194 final boolean showConsensusHistogram) {
2195 this._showConsensusHistogram = showConsensusHistogram;
2196 this._has_showConsensusHistogram = true;
2200 * Sets the value of field 'showDbRefTooltip'.
2202 * @param showDbRefTooltip the value of field 'showDbRefTooltip'
2204 public void setShowDbRefTooltip(
2205 final boolean showDbRefTooltip) {
2206 this._showDbRefTooltip = showDbRefTooltip;
2207 this._has_showDbRefTooltip = true;
2211 * Sets the value of field 'showFullId'.
2213 * @param showFullId the value of field 'showFullId'.
2215 public void setShowFullId(
2216 final boolean showFullId) {
2217 this._showFullId = showFullId;
2218 this._has_showFullId = true;
2222 * Sets the value of field 'showGroupConsensus'.
2224 * @param showGroupConsensus the value of field
2225 * 'showGroupConsensus'.
2227 public void setShowGroupConsensus(
2228 final boolean showGroupConsensus) {
2229 this._showGroupConsensus = showGroupConsensus;
2230 this._has_showGroupConsensus = true;
2234 * Sets the value of field 'showGroupConservation'.
2236 * @param showGroupConservation the value of field
2237 * 'showGroupConservation'.
2239 public void setShowGroupConservation(
2240 final boolean showGroupConservation) {
2241 this._showGroupConservation = showGroupConservation;
2242 this._has_showGroupConservation = true;
2246 * Sets the value of field 'showNPfeatureTooltip'.
2248 * @param showNPfeatureTooltip the value of field
2249 * 'showNPfeatureTooltip'.
2251 public void setShowNPfeatureTooltip(
2252 final boolean showNPfeatureTooltip) {
2253 this._showNPfeatureTooltip = showNPfeatureTooltip;
2254 this._has_showNPfeatureTooltip = true;
2258 * Sets the value of field 'showSequenceFeatures'.
2260 * @param showSequenceFeatures the value of field
2261 * 'showSequenceFeatures'.
2263 public void setShowSequenceFeatures(
2264 final boolean showSequenceFeatures) {
2265 this._showSequenceFeatures = showSequenceFeatures;
2266 this._has_showSequenceFeatures = true;
2270 * Sets the value of field 'showSequenceLogo'.
2272 * @param showSequenceLogo the value of field 'showSequenceLogo'
2274 public void setShowSequenceLogo(
2275 final boolean showSequenceLogo) {
2276 this._showSequenceLogo = showSequenceLogo;
2277 this._has_showSequenceLogo = true;
2281 * Sets the value of field 'showText'.
2283 * @param showText the value of field 'showText'.
2285 public void setShowText(
2286 final boolean showText) {
2287 this._showText = showText;
2288 this._has_showText = true;
2292 * Sets the value of field 'showUnconserved'.
2294 * @param showUnconserved the value of field 'showUnconserved'.
2296 public void setShowUnconserved(
2297 final boolean showUnconserved) {
2298 this._showUnconserved = showUnconserved;
2299 this._has_showUnconserved = true;
2303 * Sets the value of field 'startRes'.
2305 * @param startRes the value of field 'startRes'.
2307 public void setStartRes(
2308 final int startRes) {
2309 this._startRes = startRes;
2310 this._has_startRes = true;
2314 * Sets the value of field 'startSeq'.
2316 * @param startSeq the value of field 'startSeq'.
2318 public void setStartSeq(
2319 final int startSeq) {
2320 this._startSeq = startSeq;
2321 this._has_startSeq = true;
2325 * Sets the value of field 'textCol1'.
2327 * @param textCol1 the value of field 'textCol1'.
2329 public void setTextCol1(
2330 final int textCol1) {
2331 this._textCol1 = textCol1;
2332 this._has_textCol1 = true;
2336 * Sets the value of field 'textCol2'.
2338 * @param textCol2 the value of field 'textCol2'.
2340 public void setTextCol2(
2341 final int textCol2) {
2342 this._textCol2 = textCol2;
2343 this._has_textCol2 = true;
2347 * Sets the value of field 'textColThreshold'.
2349 * @param textColThreshold the value of field 'textColThreshold'
2351 public void setTextColThreshold(
2352 final int textColThreshold) {
2353 this._textColThreshold = textColThreshold;
2354 this._has_textColThreshold = true;
2358 * Sets the value of field 'title'.
2360 * @param title the value of field 'title'.
2362 public void setTitle(
2363 final java.lang.String title) {
2364 this._title = title;
2368 * Sets the value of field 'viewName'.
2370 * @param viewName the value of field 'viewName'.
2372 public void setViewName(
2373 final java.lang.String viewName) {
2374 this._viewName = viewName;
2378 * Sets the value of field 'width'.
2380 * @param width the value of field 'width'.
2382 public void setWidth(
2384 this._width = width;
2385 this._has_width = true;
2389 * Sets the value of field 'wrapAlignment'.
2391 * @param wrapAlignment the value of field 'wrapAlignment'.
2393 public void setWrapAlignment(
2394 final boolean wrapAlignment) {
2395 this._wrapAlignment = wrapAlignment;
2396 this._has_wrapAlignment = true;
2400 * Sets the value of field 'xpos'.
2402 * @param xpos the value of field 'xpos'.
2404 public void setXpos(
2407 this._has_xpos = true;
2411 * Sets the value of field 'ypos'.
2413 * @param ypos the value of field 'ypos'.
2415 public void setYpos(
2418 this._has_ypos = true;
2425 * @throws org.exolab.castor.xml.MarshalException if object is
2426 * null or if any SAXException is thrown during marshaling
2427 * @throws org.exolab.castor.xml.ValidationException if this
2428 * object is an invalid instance according to the schema
2429 * @return the unmarshaled
2430 * jalview.schemabinding.version2.Viewport
2432 public static jalview.schemabinding.version2.Viewport unmarshal(
2433 final java.io.Reader reader)
2434 throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
2435 return (jalview.schemabinding.version2.Viewport) Unmarshaller.unmarshal(jalview.schemabinding.version2.Viewport.class, reader);
2441 * @throws org.exolab.castor.xml.ValidationException if this
2442 * object is an invalid instance according to the schema
2444 public void validate(
2446 throws org.exolab.castor.xml.ValidationException {
2447 org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
2448 validator.validate(this);