1 /*******************************************************************************
2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $(date) The Jalview Authors
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
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
20 *******************************************************************************/
22 * This class was automatically generated with
23 * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
28 package jalview.schemabinding.version2;
30 //---------------------------------/
31 //- Imported classes and packages -/
32 //---------------------------------/
34 import org.exolab.castor.xml.Marshaller;
35 import org.exolab.castor.xml.Unmarshaller;
40 * @version $Revision$ $Date$
42 public class Viewport implements java.io.Serializable
45 // --------------------------/
46 // - Class/Member Variables -/
47 // --------------------------/
50 * Field _conservationSelected.
52 private boolean _conservationSelected;
55 * keeps track of state for field: _conservationSelected
57 private boolean _has_conservationSelected;
62 private boolean _pidSelected;
65 * keeps track of state for field: _pidSelected
67 private boolean _has_pidSelected;
72 private java.lang.String _bgColour;
75 * Field _consThreshold.
77 private int _consThreshold;
80 * keeps track of state for field: _consThreshold
82 private boolean _has_consThreshold;
85 * Field _pidThreshold.
87 private int _pidThreshold;
90 * keeps track of state for field: _pidThreshold
92 private boolean _has_pidThreshold;
97 private java.lang.String _title;
102 private boolean _showFullId;
105 * keeps track of state for field: _showFullId
107 private boolean _has_showFullId;
110 * Field _rightAlignIds.
112 private boolean _rightAlignIds;
115 * keeps track of state for field: _rightAlignIds
117 private boolean _has_rightAlignIds;
122 private boolean _showText;
125 * keeps track of state for field: _showText
127 private boolean _has_showText;
130 * Field _showColourText.
132 private boolean _showColourText;
135 * keeps track of state for field: _showColourText
137 private boolean _has_showColourText;
140 * Field _showUnconserved.
142 private boolean _showUnconserved = false;
145 * keeps track of state for field: _showUnconserved
147 private boolean _has_showUnconserved;
152 private boolean _showBoxes;
155 * keeps track of state for field: _showBoxes
157 private boolean _has_showBoxes;
160 * Field _wrapAlignment.
162 private boolean _wrapAlignment;
165 * keeps track of state for field: _wrapAlignment
167 private boolean _has_wrapAlignment;
172 private boolean _renderGaps;
175 * keeps track of state for field: _renderGaps
177 private boolean _has_renderGaps;
180 * Field _showSequenceFeatures.
182 private boolean _showSequenceFeatures;
185 * keeps track of state for field: _showSequenceFeatures
187 private boolean _has_showSequenceFeatures;
190 * Field _showNPfeatureTooltip.
192 private boolean _showNPfeatureTooltip;
195 * keeps track of state for field: _showNPfeatureTooltip
197 private boolean _has_showNPfeatureTooltip;
200 * Field _showDbRefTooltip.
202 private boolean _showDbRefTooltip;
205 * keeps track of state for field: _showDbRefTooltip
207 private boolean _has_showDbRefTooltip;
210 * Field _followHighlight.
212 private boolean _followHighlight = true;
215 * keeps track of state for field: _followHighlight
217 private boolean _has_followHighlight;
220 * Field _followSelection.
222 private boolean _followSelection = true;
225 * keeps track of state for field: _followSelection
227 private boolean _has_followSelection;
230 * Field _showAnnotation.
232 private boolean _showAnnotation;
235 * keeps track of state for field: _showAnnotation
237 private boolean _has_showAnnotation;
240 * Field _centreColumnLabels.
242 private boolean _centreColumnLabels = false;
245 * keeps track of state for field: _centreColumnLabels
247 private boolean _has_centreColumnLabels;
250 * Field _showGroupConservation.
252 private boolean _showGroupConservation = false;
255 * keeps track of state for field: _showGroupConservation
257 private boolean _has_showGroupConservation;
260 * Field _showGroupConsensus.
262 private boolean _showGroupConsensus = false;
265 * keeps track of state for field: _showGroupConsensus
267 private boolean _has_showGroupConsensus;
270 * Field _showConsensusHistogram.
272 private boolean _showConsensusHistogram = true;
275 * keeps track of state for field: _showConsensusHistogram
277 private boolean _has_showConsensusHistogram;
280 * Field _showSequenceLogo.
282 private boolean _showSequenceLogo = false;
285 * keeps track of state for field: _showSequenceLogo
287 private boolean _has_showSequenceLogo;
290 * Field _normaliseSequenceLogo.
292 private boolean _normaliseSequenceLogo = false;
295 * keeps track of state for field: _normaliseSequenceLogo
297 private boolean _has_normaliseSequenceLogo;
300 * Field _ignoreGapsinConsensus.
302 private boolean _ignoreGapsinConsensus = true;
305 * keeps track of state for field: _ignoreGapsinConsensus
307 private boolean _has_ignoreGapsinConsensus;
312 private int _startRes;
315 * keeps track of state for field: _startRes
317 private boolean _has_startRes;
322 private int _startSeq;
325 * keeps track of state for field: _startSeq
327 private boolean _has_startSeq;
332 private java.lang.String _fontName;
337 private int _fontSize;
340 * keeps track of state for field: _fontSize
342 private boolean _has_fontSize;
347 private int _fontStyle;
350 * keeps track of state for field: _fontStyle
352 private boolean _has_fontStyle;
355 * Field _scaleProteinAsCdna.
357 private boolean _scaleProteinAsCdna = true;
360 * keeps track of state for field: _scaleProteinAsCdna
362 private boolean _has_scaleProteinAsCdna;
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 instantiated
419 private java.lang.String _id;
422 * The viewport id of this viewport's (cdna/protein) coding complement, if any
425 private java.lang.String _complementId;
433 * keeps track of state for field: _width
435 private boolean _has_width;
443 * keeps track of state for field: _height
445 private boolean _has_height;
453 * keeps track of state for field: _xpos
455 private boolean _has_xpos;
463 * keeps track of state for field: _ypos
465 private boolean _has_ypos;
468 * Field _annotationColours.
470 private jalview.schemabinding.version2.AnnotationColours _annotationColours;
473 * Field _hiddenColumnsList.
475 private java.util.Vector _hiddenColumnsList;
478 * Field _calcIdParamList.
480 private java.util.Vector _calcIdParamList;
489 this._hiddenColumnsList = new java.util.Vector();
490 this._calcIdParamList = new java.util.Vector();
500 * @param vCalcIdParam
501 * @throws java.lang.IndexOutOfBoundsException
502 * if the index given is outside the bounds of the collection
504 public void addCalcIdParam(
505 final jalview.schemabinding.version2.CalcIdParam vCalcIdParam)
506 throws java.lang.IndexOutOfBoundsException
508 this._calcIdParamList.addElement(vCalcIdParam);
515 * @param vCalcIdParam
516 * @throws java.lang.IndexOutOfBoundsException
517 * if the index given is outside the bounds of the collection
519 public void addCalcIdParam(final int index,
520 final jalview.schemabinding.version2.CalcIdParam vCalcIdParam)
521 throws java.lang.IndexOutOfBoundsException
523 this._calcIdParamList.add(index, vCalcIdParam);
529 * @param vHiddenColumns
530 * @throws java.lang.IndexOutOfBoundsException
531 * if the index given is outside the bounds of the collection
533 public void addHiddenColumns(
534 final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)
535 throws java.lang.IndexOutOfBoundsException
537 this._hiddenColumnsList.addElement(vHiddenColumns);
544 * @param vHiddenColumns
545 * @throws java.lang.IndexOutOfBoundsException
546 * if the index given is outside the bounds of the collection
548 public void addHiddenColumns(final int index,
549 final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)
550 throws java.lang.IndexOutOfBoundsException
552 this._hiddenColumnsList.add(index, vHiddenColumns);
557 public void deleteCentreColumnLabels()
559 this._has_centreColumnLabels = false;
564 public void deleteConsThreshold()
566 this._has_consThreshold = false;
571 public void deleteConservationSelected()
573 this._has_conservationSelected = false;
578 public void deleteFollowHighlight()
580 this._has_followHighlight = false;
585 public void deleteFollowSelection()
587 this._has_followSelection = false;
592 public void deleteFontSize()
594 this._has_fontSize = false;
599 public void deleteFontStyle()
601 this._has_fontStyle = false;
606 public void deleteGatheredViews()
608 this._has_gatheredViews = false;
613 public void deleteHeight()
615 this._has_height = false;
620 public void deleteIgnoreGapsinConsensus()
622 this._has_ignoreGapsinConsensus = false;
627 public void deleteNormaliseSequenceLogo()
629 this._has_normaliseSequenceLogo = false;
634 public void deletePidSelected()
636 this._has_pidSelected = false;
641 public void deletePidThreshold()
643 this._has_pidThreshold = false;
648 public void deleteRenderGaps()
650 this._has_renderGaps = false;
655 public void deleteRightAlignIds()
657 this._has_rightAlignIds = false;
662 public void deleteScaleProteinAsCdna()
664 this._has_scaleProteinAsCdna = false;
669 public void deleteShowAnnotation()
671 this._has_showAnnotation = false;
676 public void deleteShowBoxes()
678 this._has_showBoxes = false;
683 public void deleteShowColourText()
685 this._has_showColourText = false;
690 public void deleteShowConsensusHistogram()
692 this._has_showConsensusHistogram = false;
697 public void deleteShowDbRefTooltip()
699 this._has_showDbRefTooltip = false;
704 public void deleteShowFullId()
706 this._has_showFullId = false;
711 public void deleteShowGroupConsensus()
713 this._has_showGroupConsensus = false;
718 public void deleteShowGroupConservation()
720 this._has_showGroupConservation = false;
725 public void deleteShowNPfeatureTooltip()
727 this._has_showNPfeatureTooltip = false;
732 public void deleteShowSequenceFeatures()
734 this._has_showSequenceFeatures = false;
739 public void deleteShowSequenceLogo()
741 this._has_showSequenceLogo = false;
746 public void deleteShowText()
748 this._has_showText = false;
753 public void deleteShowUnconserved()
755 this._has_showUnconserved = false;
760 public void deleteStartRes()
762 this._has_startRes = false;
767 public void deleteStartSeq()
769 this._has_startSeq = false;
774 public void deleteTextCol1()
776 this._has_textCol1 = false;
781 public void deleteTextCol2()
783 this._has_textCol2 = false;
788 public void deleteTextColThreshold()
790 this._has_textColThreshold = false;
795 public void deleteWidth()
797 this._has_width = false;
802 public void deleteWrapAlignment()
804 this._has_wrapAlignment = false;
809 public void deleteXpos()
811 this._has_xpos = false;
816 public void deleteYpos()
818 this._has_ypos = false;
822 * Method enumerateCalcIdParam.
824 * @return an Enumeration over all jalview.schemabinding.version2.CalcIdParam
827 public java.util.Enumeration enumerateCalcIdParam()
829 return this._calcIdParamList.elements();
833 * Method enumerateHiddenColumns.
835 * @return an Enumeration over all
836 * jalview.schemabinding.version2.HiddenColumns elements
838 public java.util.Enumeration enumerateHiddenColumns()
840 return this._hiddenColumnsList.elements();
844 * Returns the value of field 'annotationColours'.
846 * @return the value of field 'AnnotationColours'.
848 public jalview.schemabinding.version2.AnnotationColours getAnnotationColours()
850 return this._annotationColours;
854 * Returns the value of field 'bgColour'.
856 * @return the value of field 'BgColour'.
858 public java.lang.String getBgColour()
860 return this._bgColour;
864 * Method getCalcIdParam.
867 * @throws java.lang.IndexOutOfBoundsException
868 * if the index given is outside the bounds of the collection
869 * @return the value of the jalview.schemabinding.version2.CalcIdParam at the
872 public jalview.schemabinding.version2.CalcIdParam getCalcIdParam(
873 final int index) throws java.lang.IndexOutOfBoundsException
875 // check bounds for index
876 if (index < 0 || index >= this._calcIdParamList.size())
878 throw new IndexOutOfBoundsException("getCalcIdParam: Index value '"
879 + index + "' not in range [0.."
880 + (this._calcIdParamList.size() - 1) + "]");
883 return (jalview.schemabinding.version2.CalcIdParam) _calcIdParamList
888 * Method getCalcIdParam.Returns the contents of the collection in an Array.
890 * Note: Just in case the collection contents are changing in another thread,
891 * we pass a 0-length Array of the correct type into the API call. This way we
892 * <i>know</i> that the Array returned is of exactly the correct length.
894 * @return this collection as an Array
896 public jalview.schemabinding.version2.CalcIdParam[] getCalcIdParam()
898 jalview.schemabinding.version2.CalcIdParam[] array = new jalview.schemabinding.version2.CalcIdParam[0];
899 return (jalview.schemabinding.version2.CalcIdParam[]) this._calcIdParamList
904 * Method getCalcIdParamCount.
906 * @return the size of this collection
908 public int getCalcIdParamCount()
910 return this._calcIdParamList.size();
914 * Returns the value of field 'centreColumnLabels'.
916 * @return the value of field 'CentreColumnLabels'.
918 public boolean getCentreColumnLabels()
920 return this._centreColumnLabels;
924 * Returns the value of field 'complementId'. The field 'complementId' has the
925 * following description: The viewport id of this viewport's (cdna/protein)
926 * coding complement, if any
929 * @return the value of field 'ComplementId'.
931 public java.lang.String getComplementId()
933 return this._complementId;
937 * Returns the value of field 'consThreshold'.
939 * @return the value of field 'ConsThreshold'.
941 public int getConsThreshold()
943 return this._consThreshold;
947 * Returns the value of field 'conservationSelected'.
949 * @return the value of field 'ConservationSelected'.
951 public boolean getConservationSelected()
953 return this._conservationSelected;
957 * Returns the value of field 'followHighlight'.
959 * @return the value of field 'FollowHighlight'.
961 public boolean getFollowHighlight()
963 return this._followHighlight;
967 * Returns the value of field 'followSelection'.
969 * @return the value of field 'FollowSelection'.
971 public boolean getFollowSelection()
973 return this._followSelection;
977 * Returns the value of field 'fontName'.
979 * @return the value of field 'FontName'.
981 public java.lang.String getFontName()
983 return this._fontName;
987 * Returns the value of field 'fontSize'.
989 * @return the value of field 'FontSize'.
991 public int getFontSize()
993 return this._fontSize;
997 * Returns the value of field 'fontStyle'.
999 * @return the value of field 'FontStyle'.
1001 public int getFontStyle()
1003 return this._fontStyle;
1007 * Returns the value of field 'gatheredViews'.
1009 * @return the value of field 'GatheredViews'.
1011 public boolean getGatheredViews()
1013 return this._gatheredViews;
1017 * Returns the value of field 'height'.
1019 * @return the value of field 'Height'.
1021 public int getHeight()
1023 return this._height;
1027 * Method getHiddenColumns.
1030 * @throws java.lang.IndexOutOfBoundsException
1031 * if the index given is outside the bounds of the collection
1032 * @return the value of the jalview.schemabinding.version2.HiddenColumns at
1035 public jalview.schemabinding.version2.HiddenColumns getHiddenColumns(
1036 final int index) throws java.lang.IndexOutOfBoundsException
1038 // check bounds for index
1039 if (index < 0 || index >= this._hiddenColumnsList.size())
1041 throw new IndexOutOfBoundsException("getHiddenColumns: Index value '"
1042 + index + "' not in range [0.."
1043 + (this._hiddenColumnsList.size() - 1) + "]");
1046 return (jalview.schemabinding.version2.HiddenColumns) _hiddenColumnsList
1051 * Method getHiddenColumns.Returns the contents of the collection in an Array.
1053 * Note: Just in case the collection contents are changing in another thread,
1054 * we pass a 0-length Array of the correct type into the API call. This way we
1055 * <i>know</i> that the Array returned is of exactly the correct length.
1057 * @return this collection as an Array
1059 public jalview.schemabinding.version2.HiddenColumns[] getHiddenColumns()
1061 jalview.schemabinding.version2.HiddenColumns[] array = new jalview.schemabinding.version2.HiddenColumns[0];
1062 return (jalview.schemabinding.version2.HiddenColumns[]) this._hiddenColumnsList
1067 * Method getHiddenColumnsCount.
1069 * @return the size of this collection
1071 public int getHiddenColumnsCount()
1073 return this._hiddenColumnsList.size();
1077 * Returns the value of field 'id'. The field 'id' has the following
1078 * description: unique id used by jalview to synchronize between stored and
1079 * instantiated views
1082 * @return the value of field 'Id'.
1084 public java.lang.String getId()
1090 * Returns the value of field 'ignoreGapsinConsensus'.
1092 * @return the value of field 'IgnoreGapsinConsensus'.
1094 public boolean getIgnoreGapsinConsensus()
1096 return this._ignoreGapsinConsensus;
1100 * Returns the value of field 'normaliseSequenceLogo'.
1102 * @return the value of field 'NormaliseSequenceLogo'.
1104 public boolean getNormaliseSequenceLogo()
1106 return this._normaliseSequenceLogo;
1110 * Returns the value of field 'pidSelected'.
1112 * @return the value of field 'PidSelected'.
1114 public boolean getPidSelected()
1116 return this._pidSelected;
1120 * Returns the value of field 'pidThreshold'.
1122 * @return the value of field 'PidThreshold'.
1124 public int getPidThreshold()
1126 return this._pidThreshold;
1130 * Returns the value of field 'renderGaps'.
1132 * @return the value of field 'RenderGaps'.
1134 public boolean getRenderGaps()
1136 return this._renderGaps;
1140 * Returns the value of field 'rightAlignIds'.
1142 * @return the value of field 'RightAlignIds'.
1144 public boolean getRightAlignIds()
1146 return this._rightAlignIds;
1150 * Returns the value of field 'scaleProteinAsCdna'.
1152 * @return the value of field 'ScaleProteinAsCdna'.
1154 public boolean getScaleProteinAsCdna()
1156 return this._scaleProteinAsCdna;
1160 * Returns the value of field 'sequenceSetId'.
1162 * @return the value of field 'SequenceSetId'.
1164 public java.lang.String getSequenceSetId()
1166 return this._sequenceSetId;
1170 * Returns the value of field 'showAnnotation'.
1172 * @return the value of field 'ShowAnnotation'.
1174 public boolean getShowAnnotation()
1176 return this._showAnnotation;
1180 * Returns the value of field 'showBoxes'.
1182 * @return the value of field 'ShowBoxes'.
1184 public boolean getShowBoxes()
1186 return this._showBoxes;
1190 * Returns the value of field 'showColourText'.
1192 * @return the value of field 'ShowColourText'.
1194 public boolean getShowColourText()
1196 return this._showColourText;
1200 * Returns the value of field 'showConsensusHistogram'.
1202 * @return the value of field 'ShowConsensusHistogram'.
1204 public boolean getShowConsensusHistogram()
1206 return this._showConsensusHistogram;
1210 * Returns the value of field 'showDbRefTooltip'.
1212 * @return the value of field 'ShowDbRefTooltip'.
1214 public boolean getShowDbRefTooltip()
1216 return this._showDbRefTooltip;
1220 * Returns the value of field 'showFullId'.
1222 * @return the value of field 'ShowFullId'.
1224 public boolean getShowFullId()
1226 return this._showFullId;
1230 * Returns the value of field 'showGroupConsensus'.
1232 * @return the value of field 'ShowGroupConsensus'.
1234 public boolean getShowGroupConsensus()
1236 return this._showGroupConsensus;
1240 * Returns the value of field 'showGroupConservation'.
1242 * @return the value of field 'ShowGroupConservation'.
1244 public boolean getShowGroupConservation()
1246 return this._showGroupConservation;
1250 * Returns the value of field 'showNPfeatureTooltip'.
1252 * @return the value of field 'ShowNPfeatureTooltip'.
1254 public boolean getShowNPfeatureTooltip()
1256 return this._showNPfeatureTooltip;
1260 * Returns the value of field 'showSequenceFeatures'.
1262 * @return the value of field 'ShowSequenceFeatures'.
1264 public boolean getShowSequenceFeatures()
1266 return this._showSequenceFeatures;
1270 * Returns the value of field 'showSequenceLogo'.
1272 * @return the value of field 'ShowSequenceLogo'.
1274 public boolean getShowSequenceLogo()
1276 return this._showSequenceLogo;
1280 * Returns the value of field 'showText'.
1282 * @return the value of field 'ShowText'.
1284 public boolean getShowText()
1286 return this._showText;
1290 * Returns the value of field 'showUnconserved'.
1292 * @return the value of field 'ShowUnconserved'.
1294 public boolean getShowUnconserved()
1296 return this._showUnconserved;
1300 * Returns the value of field 'startRes'.
1302 * @return the value of field 'StartRes'.
1304 public int getStartRes()
1306 return this._startRes;
1310 * Returns the value of field 'startSeq'.
1312 * @return the value of field 'StartSeq'.
1314 public int getStartSeq()
1316 return this._startSeq;
1320 * Returns the value of field 'textCol1'.
1322 * @return the value of field 'TextCol1'.
1324 public int getTextCol1()
1326 return this._textCol1;
1330 * Returns the value of field 'textCol2'.
1332 * @return the value of field 'TextCol2'.
1334 public int getTextCol2()
1336 return this._textCol2;
1340 * Returns the value of field 'textColThreshold'.
1342 * @return the value of field 'TextColThreshold'.
1344 public int getTextColThreshold()
1346 return this._textColThreshold;
1350 * Returns the value of field 'title'.
1352 * @return the value of field 'Title'.
1354 public java.lang.String getTitle()
1360 * Returns the value of field 'viewName'.
1362 * @return the value of field 'ViewName'.
1364 public java.lang.String getViewName()
1366 return this._viewName;
1370 * Returns the value of field 'width'.
1372 * @return the value of field 'Width'.
1374 public int getWidth()
1380 * Returns the value of field 'wrapAlignment'.
1382 * @return the value of field 'WrapAlignment'.
1384 public boolean getWrapAlignment()
1386 return this._wrapAlignment;
1390 * Returns the value of field 'xpos'.
1392 * @return the value of field 'Xpos'.
1394 public int getXpos()
1400 * Returns the value of field 'ypos'.
1402 * @return the value of field 'Ypos'.
1404 public int getYpos()
1410 * Method hasCentreColumnLabels.
1412 * @return true if at least one CentreColumnLabels has been adde
1414 public boolean hasCentreColumnLabels()
1416 return this._has_centreColumnLabels;
1420 * Method hasConsThreshold.
1422 * @return true if at least one ConsThreshold has been added
1424 public boolean hasConsThreshold()
1426 return this._has_consThreshold;
1430 * Method hasConservationSelected.
1432 * @return true if at least one ConservationSelected has been added
1434 public boolean hasConservationSelected()
1436 return this._has_conservationSelected;
1440 * Method hasFollowHighlight.
1442 * @return true if at least one FollowHighlight has been added
1444 public boolean hasFollowHighlight()
1446 return this._has_followHighlight;
1450 * Method hasFollowSelection.
1452 * @return true if at least one FollowSelection has been added
1454 public boolean hasFollowSelection()
1456 return this._has_followSelection;
1460 * Method hasFontSize.
1462 * @return true if at least one FontSize has been added
1464 public boolean hasFontSize()
1466 return this._has_fontSize;
1470 * Method hasFontStyle.
1472 * @return true if at least one FontStyle has been added
1474 public boolean hasFontStyle()
1476 return this._has_fontStyle;
1480 * Method hasGatheredViews.
1482 * @return true if at least one GatheredViews has been added
1484 public boolean hasGatheredViews()
1486 return this._has_gatheredViews;
1492 * @return true if at least one Height has been added
1494 public boolean hasHeight()
1496 return this._has_height;
1500 * Method hasIgnoreGapsinConsensus.
1502 * @return true if at least one IgnoreGapsinConsensus has been added
1504 public boolean hasIgnoreGapsinConsensus()
1506 return this._has_ignoreGapsinConsensus;
1510 * Method hasNormaliseSequenceLogo.
1512 * @return true if at least one NormaliseSequenceLogo has been added
1514 public boolean hasNormaliseSequenceLogo()
1516 return this._has_normaliseSequenceLogo;
1520 * Method hasPidSelected.
1522 * @return true if at least one PidSelected has been added
1524 public boolean hasPidSelected()
1526 return this._has_pidSelected;
1530 * Method hasPidThreshold.
1532 * @return true if at least one PidThreshold has been added
1534 public boolean hasPidThreshold()
1536 return this._has_pidThreshold;
1540 * Method hasRenderGaps.
1542 * @return true if at least one RenderGaps has been added
1544 public boolean hasRenderGaps()
1546 return this._has_renderGaps;
1550 * Method hasRightAlignIds.
1552 * @return true if at least one RightAlignIds has been added
1554 public boolean hasRightAlignIds()
1556 return this._has_rightAlignIds;
1560 * Method hasScaleProteinAsCdna.
1562 * @return true if at least one ScaleProteinAsCdna has been adde
1564 public boolean hasScaleProteinAsCdna()
1566 return this._has_scaleProteinAsCdna;
1570 * Method hasShowAnnotation.
1572 * @return true if at least one ShowAnnotation has been added
1574 public boolean hasShowAnnotation()
1576 return this._has_showAnnotation;
1580 * Method hasShowBoxes.
1582 * @return true if at least one ShowBoxes has been added
1584 public boolean hasShowBoxes()
1586 return this._has_showBoxes;
1590 * Method hasShowColourText.
1592 * @return true if at least one ShowColourText has been added
1594 public boolean hasShowColourText()
1596 return this._has_showColourText;
1600 * Method hasShowConsensusHistogram.
1602 * @return true if at least one ShowConsensusHistogram has been added
1604 public boolean hasShowConsensusHistogram()
1606 return this._has_showConsensusHistogram;
1610 * Method hasShowDbRefTooltip.
1612 * @return true if at least one ShowDbRefTooltip has been added
1614 public boolean hasShowDbRefTooltip()
1616 return this._has_showDbRefTooltip;
1620 * Method hasShowFullId.
1622 * @return true if at least one ShowFullId has been added
1624 public boolean hasShowFullId()
1626 return this._has_showFullId;
1630 * Method hasShowGroupConsensus.
1632 * @return true if at least one ShowGroupConsensus has been adde
1634 public boolean hasShowGroupConsensus()
1636 return this._has_showGroupConsensus;
1640 * Method hasShowGroupConservation.
1642 * @return true if at least one ShowGroupConservation has been added
1644 public boolean hasShowGroupConservation()
1646 return this._has_showGroupConservation;
1650 * Method hasShowNPfeatureTooltip.
1652 * @return true if at least one ShowNPfeatureTooltip has been added
1654 public boolean hasShowNPfeatureTooltip()
1656 return this._has_showNPfeatureTooltip;
1660 * Method hasShowSequenceFeatures.
1662 * @return true if at least one ShowSequenceFeatures has been added
1664 public boolean hasShowSequenceFeatures()
1666 return this._has_showSequenceFeatures;
1670 * Method hasShowSequenceLogo.
1672 * @return true if at least one ShowSequenceLogo has been added
1674 public boolean hasShowSequenceLogo()
1676 return this._has_showSequenceLogo;
1680 * Method hasShowText.
1682 * @return true if at least one ShowText has been added
1684 public boolean hasShowText()
1686 return this._has_showText;
1690 * Method hasShowUnconserved.
1692 * @return true if at least one ShowUnconserved has been added
1694 public boolean hasShowUnconserved()
1696 return this._has_showUnconserved;
1700 * Method hasStartRes.
1702 * @return true if at least one StartRes has been added
1704 public boolean hasStartRes()
1706 return this._has_startRes;
1710 * Method hasStartSeq.
1712 * @return true if at least one StartSeq has been added
1714 public boolean hasStartSeq()
1716 return this._has_startSeq;
1720 * Method hasTextCol1.
1722 * @return true if at least one TextCol1 has been added
1724 public boolean hasTextCol1()
1726 return this._has_textCol1;
1730 * Method hasTextCol2.
1732 * @return true if at least one TextCol2 has been added
1734 public boolean hasTextCol2()
1736 return this._has_textCol2;
1740 * Method hasTextColThreshold.
1742 * @return true if at least one TextColThreshold has been added
1744 public boolean hasTextColThreshold()
1746 return this._has_textColThreshold;
1752 * @return true if at least one Width has been added
1754 public boolean hasWidth()
1756 return this._has_width;
1760 * Method hasWrapAlignment.
1762 * @return true if at least one WrapAlignment has been added
1764 public boolean hasWrapAlignment()
1766 return this._has_wrapAlignment;
1772 * @return true if at least one Xpos has been added
1774 public boolean hasXpos()
1776 return this._has_xpos;
1782 * @return true if at least one Ypos has been added
1784 public boolean hasYpos()
1786 return this._has_ypos;
1790 * Returns the value of field 'centreColumnLabels'.
1792 * @return the value of field 'CentreColumnLabels'.
1794 public boolean isCentreColumnLabels()
1796 return this._centreColumnLabels;
1800 * Returns the value of field 'conservationSelected'.
1802 * @return the value of field 'ConservationSelected'.
1804 public boolean isConservationSelected()
1806 return this._conservationSelected;
1810 * Returns the value of field 'followHighlight'.
1812 * @return the value of field 'FollowHighlight'.
1814 public boolean isFollowHighlight()
1816 return this._followHighlight;
1820 * Returns the value of field 'followSelection'.
1822 * @return the value of field 'FollowSelection'.
1824 public boolean isFollowSelection()
1826 return this._followSelection;
1830 * Returns the value of field 'gatheredViews'.
1832 * @return the value of field 'GatheredViews'.
1834 public boolean isGatheredViews()
1836 return this._gatheredViews;
1840 * Returns the value of field 'ignoreGapsinConsensus'.
1842 * @return the value of field 'IgnoreGapsinConsensus'.
1844 public boolean isIgnoreGapsinConsensus()
1846 return this._ignoreGapsinConsensus;
1850 * Returns the value of field 'normaliseSequenceLogo'.
1852 * @return the value of field 'NormaliseSequenceLogo'.
1854 public boolean isNormaliseSequenceLogo()
1856 return this._normaliseSequenceLogo;
1860 * Returns the value of field 'pidSelected'.
1862 * @return the value of field 'PidSelected'.
1864 public boolean isPidSelected()
1866 return this._pidSelected;
1870 * Returns the value of field 'renderGaps'.
1872 * @return the value of field 'RenderGaps'.
1874 public boolean isRenderGaps()
1876 return this._renderGaps;
1880 * Returns the value of field 'rightAlignIds'.
1882 * @return the value of field 'RightAlignIds'.
1884 public boolean isRightAlignIds()
1886 return this._rightAlignIds;
1890 * Returns the value of field 'scaleProteinAsCdna'.
1892 * @return the value of field 'ScaleProteinAsCdna'.
1894 public boolean isScaleProteinAsCdna()
1896 return this._scaleProteinAsCdna;
1900 * Returns the value of field 'showAnnotation'.
1902 * @return the value of field 'ShowAnnotation'.
1904 public boolean isShowAnnotation()
1906 return this._showAnnotation;
1910 * Returns the value of field 'showBoxes'.
1912 * @return the value of field 'ShowBoxes'.
1914 public boolean isShowBoxes()
1916 return this._showBoxes;
1920 * Returns the value of field 'showColourText'.
1922 * @return the value of field 'ShowColourText'.
1924 public boolean isShowColourText()
1926 return this._showColourText;
1930 * Returns the value of field 'showConsensusHistogram'.
1932 * @return the value of field 'ShowConsensusHistogram'.
1934 public boolean isShowConsensusHistogram()
1936 return this._showConsensusHistogram;
1940 * Returns the value of field 'showDbRefTooltip'.
1942 * @return the value of field 'ShowDbRefTooltip'.
1944 public boolean isShowDbRefTooltip()
1946 return this._showDbRefTooltip;
1950 * Returns the value of field 'showFullId'.
1952 * @return the value of field 'ShowFullId'.
1954 public boolean isShowFullId()
1956 return this._showFullId;
1960 * Returns the value of field 'showGroupConsensus'.
1962 * @return the value of field 'ShowGroupConsensus'.
1964 public boolean isShowGroupConsensus()
1966 return this._showGroupConsensus;
1970 * Returns the value of field 'showGroupConservation'.
1972 * @return the value of field 'ShowGroupConservation'.
1974 public boolean isShowGroupConservation()
1976 return this._showGroupConservation;
1980 * Returns the value of field 'showNPfeatureTooltip'.
1982 * @return the value of field 'ShowNPfeatureTooltip'.
1984 public boolean isShowNPfeatureTooltip()
1986 return this._showNPfeatureTooltip;
1990 * Returns the value of field 'showSequenceFeatures'.
1992 * @return the value of field 'ShowSequenceFeatures'.
1994 public boolean isShowSequenceFeatures()
1996 return this._showSequenceFeatures;
2000 * Returns the value of field 'showSequenceLogo'.
2002 * @return the value of field 'ShowSequenceLogo'.
2004 public boolean isShowSequenceLogo()
2006 return this._showSequenceLogo;
2010 * Returns the value of field 'showText'.
2012 * @return the value of field 'ShowText'.
2014 public boolean isShowText()
2016 return this._showText;
2020 * Returns the value of field 'showUnconserved'.
2022 * @return the value of field 'ShowUnconserved'.
2024 public boolean isShowUnconserved()
2026 return this._showUnconserved;
2032 * @return true if this object is valid according to the schema
2034 public boolean isValid()
2039 } catch (org.exolab.castor.xml.ValidationException vex)
2047 * Returns the value of field 'wrapAlignment'.
2049 * @return the value of field 'WrapAlignment'.
2051 public boolean isWrapAlignment()
2053 return this._wrapAlignment;
2060 * @throws org.exolab.castor.xml.MarshalException
2061 * if object is null or if any SAXException is thrown during
2063 * @throws org.exolab.castor.xml.ValidationException
2064 * if this object is an invalid instance according to the schema
2066 public void marshal(final java.io.Writer out)
2067 throws org.exolab.castor.xml.MarshalException,
2068 org.exolab.castor.xml.ValidationException
2070 Marshaller.marshal(this, out);
2077 * @throws java.io.IOException
2078 * if an IOException occurs during marshaling
2079 * @throws org.exolab.castor.xml.ValidationException
2080 * if this object is an invalid instance according to the schema
2081 * @throws org.exolab.castor.xml.MarshalException
2082 * if object is null or if any SAXException is thrown during
2085 public void marshal(final org.xml.sax.ContentHandler handler)
2086 throws java.io.IOException,
2087 org.exolab.castor.xml.MarshalException,
2088 org.exolab.castor.xml.ValidationException
2090 Marshaller.marshal(this, handler);
2095 public void removeAllCalcIdParam()
2097 this._calcIdParamList.clear();
2102 public void removeAllHiddenColumns()
2104 this._hiddenColumnsList.clear();
2108 * Method removeCalcIdParam.
2110 * @param vCalcIdParam
2111 * @return true if the object was removed from the collection.
2113 public boolean removeCalcIdParam(
2114 final jalview.schemabinding.version2.CalcIdParam vCalcIdParam)
2116 boolean removed = _calcIdParamList.remove(vCalcIdParam);
2121 * Method removeCalcIdParamAt.
2124 * @return the element removed from the collection
2126 public jalview.schemabinding.version2.CalcIdParam removeCalcIdParamAt(
2129 java.lang.Object obj = this._calcIdParamList.remove(index);
2130 return (jalview.schemabinding.version2.CalcIdParam) obj;
2134 * Method removeHiddenColumns.
2136 * @param vHiddenColumns
2137 * @return true if the object was removed from the collection.
2139 public boolean removeHiddenColumns(
2140 final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)
2142 boolean removed = _hiddenColumnsList.remove(vHiddenColumns);
2147 * Method removeHiddenColumnsAt.
2150 * @return the element removed from the collection
2152 public jalview.schemabinding.version2.HiddenColumns removeHiddenColumnsAt(
2155 java.lang.Object obj = this._hiddenColumnsList.remove(index);
2156 return (jalview.schemabinding.version2.HiddenColumns) obj;
2160 * Sets the value of field 'annotationColours'.
2162 * @param annotationColours
2163 * the value of field 'annotationColours'.
2165 public void setAnnotationColours(
2166 final jalview.schemabinding.version2.AnnotationColours annotationColours)
2168 this._annotationColours = annotationColours;
2172 * Sets the value of field 'bgColour'.
2175 * the value of field 'bgColour'.
2177 public void setBgColour(final java.lang.String bgColour)
2179 this._bgColour = bgColour;
2186 * @param vCalcIdParam
2187 * @throws java.lang.IndexOutOfBoundsException
2188 * if the index given is outside the bounds of the collection
2190 public void setCalcIdParam(final int index,
2191 final jalview.schemabinding.version2.CalcIdParam vCalcIdParam)
2192 throws java.lang.IndexOutOfBoundsException
2194 // check bounds for index
2195 if (index < 0 || index >= this._calcIdParamList.size())
2197 throw new IndexOutOfBoundsException("setCalcIdParam: Index value '"
2198 + index + "' not in range [0.."
2199 + (this._calcIdParamList.size() - 1) + "]");
2202 this._calcIdParamList.set(index, vCalcIdParam);
2208 * @param vCalcIdParamArray
2210 public void setCalcIdParam(
2211 final jalview.schemabinding.version2.CalcIdParam[] vCalcIdParamArray)
2214 _calcIdParamList.clear();
2216 for (int i = 0; i < vCalcIdParamArray.length; i++)
2218 this._calcIdParamList.add(vCalcIdParamArray[i]);
2223 * Sets the value of field 'centreColumnLabels'.
2225 * @param centreColumnLabels
2226 * the value of field 'centreColumnLabels'.
2228 public void setCentreColumnLabels(final boolean centreColumnLabels)
2230 this._centreColumnLabels = centreColumnLabels;
2231 this._has_centreColumnLabels = true;
2235 * Sets the value of field 'complementId'. The field 'complementId' has the
2236 * following description: The viewport id of this viewport's (cdna/protein)
2237 * coding complement, if any
2240 * @param complementId
2241 * the value of field 'complementId'.
2243 public void setComplementId(final java.lang.String complementId)
2245 this._complementId = complementId;
2249 * Sets the value of field 'consThreshold'.
2251 * @param consThreshold
2252 * the value of field 'consThreshold'.
2254 public void setConsThreshold(final int consThreshold)
2256 this._consThreshold = consThreshold;
2257 this._has_consThreshold = true;
2261 * Sets the value of field 'conservationSelected'.
2263 * @param conservationSelected
2264 * the value of field 'conservationSelected'.
2266 public void setConservationSelected(final boolean conservationSelected)
2268 this._conservationSelected = conservationSelected;
2269 this._has_conservationSelected = true;
2273 * Sets the value of field 'followHighlight'.
2275 * @param followHighlight
2276 * the value of field 'followHighlight'.
2278 public void setFollowHighlight(final boolean followHighlight)
2280 this._followHighlight = followHighlight;
2281 this._has_followHighlight = true;
2285 * Sets the value of field 'followSelection'.
2287 * @param followSelection
2288 * the value of field 'followSelection'.
2290 public void setFollowSelection(final boolean followSelection)
2292 this._followSelection = followSelection;
2293 this._has_followSelection = true;
2297 * Sets the value of field 'fontName'.
2300 * the value of field 'fontName'.
2302 public void setFontName(final java.lang.String fontName)
2304 this._fontName = fontName;
2308 * Sets the value of field 'fontSize'.
2311 * the value of field 'fontSize'.
2313 public void setFontSize(final int fontSize)
2315 this._fontSize = fontSize;
2316 this._has_fontSize = true;
2320 * Sets the value of field 'fontStyle'.
2323 * the value of field 'fontStyle'.
2325 public void setFontStyle(final int fontStyle)
2327 this._fontStyle = fontStyle;
2328 this._has_fontStyle = true;
2332 * Sets the value of field 'gatheredViews'.
2334 * @param gatheredViews
2335 * the value of field 'gatheredViews'.
2337 public void setGatheredViews(final boolean gatheredViews)
2339 this._gatheredViews = gatheredViews;
2340 this._has_gatheredViews = true;
2344 * Sets the value of field 'height'.
2347 * the value of field 'height'.
2349 public void setHeight(final int height)
2351 this._height = height;
2352 this._has_height = true;
2359 * @param vHiddenColumns
2360 * @throws java.lang.IndexOutOfBoundsException
2361 * if the index given is outside the bounds of the collection
2363 public void setHiddenColumns(final int index,
2364 final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)
2365 throws java.lang.IndexOutOfBoundsException
2367 // check bounds for index
2368 if (index < 0 || index >= this._hiddenColumnsList.size())
2370 throw new IndexOutOfBoundsException("setHiddenColumns: Index value '"
2371 + index + "' not in range [0.."
2372 + (this._hiddenColumnsList.size() - 1) + "]");
2375 this._hiddenColumnsList.set(index, vHiddenColumns);
2381 * @param vHiddenColumnsArray
2383 public void setHiddenColumns(
2384 final jalview.schemabinding.version2.HiddenColumns[] vHiddenColumnsArray)
2387 _hiddenColumnsList.clear();
2389 for (int i = 0; i < vHiddenColumnsArray.length; i++)
2391 this._hiddenColumnsList.add(vHiddenColumnsArray[i]);
2396 * Sets the value of field 'id'. The field 'id' has the following description:
2397 * unique id used by jalview to synchronize between stored and instantiated
2402 * the value of field 'id'.
2404 public void setId(final java.lang.String id)
2410 * Sets the value of field 'ignoreGapsinConsensus'.
2412 * @param ignoreGapsinConsensus
2413 * the value of field 'ignoreGapsinConsensus'.
2415 public void setIgnoreGapsinConsensus(final boolean ignoreGapsinConsensus)
2417 this._ignoreGapsinConsensus = ignoreGapsinConsensus;
2418 this._has_ignoreGapsinConsensus = true;
2422 * Sets the value of field 'normaliseSequenceLogo'.
2424 * @param normaliseSequenceLogo
2425 * the value of field 'normaliseSequenceLogo'.
2427 public void setNormaliseSequenceLogo(final boolean normaliseSequenceLogo)
2429 this._normaliseSequenceLogo = normaliseSequenceLogo;
2430 this._has_normaliseSequenceLogo = true;
2434 * Sets the value of field 'pidSelected'.
2436 * @param pidSelected
2437 * the value of field 'pidSelected'.
2439 public void setPidSelected(final boolean pidSelected)
2441 this._pidSelected = pidSelected;
2442 this._has_pidSelected = true;
2446 * Sets the value of field 'pidThreshold'.
2448 * @param pidThreshold
2449 * the value of field 'pidThreshold'.
2451 public void setPidThreshold(final int pidThreshold)
2453 this._pidThreshold = pidThreshold;
2454 this._has_pidThreshold = true;
2458 * Sets the value of field 'renderGaps'.
2461 * the value of field 'renderGaps'.
2463 public void setRenderGaps(final boolean renderGaps)
2465 this._renderGaps = renderGaps;
2466 this._has_renderGaps = true;
2470 * Sets the value of field 'rightAlignIds'.
2472 * @param rightAlignIds
2473 * the value of field 'rightAlignIds'.
2475 public void setRightAlignIds(final boolean rightAlignIds)
2477 this._rightAlignIds = rightAlignIds;
2478 this._has_rightAlignIds = true;
2482 * Sets the value of field 'scaleProteinAsCdna'.
2484 * @param scaleProteinAsCdna
2485 * the value of field 'scaleProteinAsCdna'.
2487 public void setScaleProteinAsCdna(final boolean scaleProteinAsCdna)
2489 this._scaleProteinAsCdna = scaleProteinAsCdna;
2490 this._has_scaleProteinAsCdna = true;
2494 * Sets the value of field 'sequenceSetId'.
2496 * @param sequenceSetId
2497 * the value of field 'sequenceSetId'.
2499 public void setSequenceSetId(final java.lang.String sequenceSetId)
2501 this._sequenceSetId = sequenceSetId;
2505 * Sets the value of field 'showAnnotation'.
2507 * @param showAnnotation
2508 * the value of field 'showAnnotation'.
2510 public void setShowAnnotation(final boolean showAnnotation)
2512 this._showAnnotation = showAnnotation;
2513 this._has_showAnnotation = true;
2517 * Sets the value of field 'showBoxes'.
2520 * the value of field 'showBoxes'.
2522 public void setShowBoxes(final boolean showBoxes)
2524 this._showBoxes = showBoxes;
2525 this._has_showBoxes = true;
2529 * Sets the value of field 'showColourText'.
2531 * @param showColourText
2532 * the value of field 'showColourText'.
2534 public void setShowColourText(final boolean showColourText)
2536 this._showColourText = showColourText;
2537 this._has_showColourText = true;
2541 * Sets the value of field 'showConsensusHistogram'.
2543 * @param showConsensusHistogram
2544 * the value of field 'showConsensusHistogram'.
2546 public void setShowConsensusHistogram(final boolean showConsensusHistogram)
2548 this._showConsensusHistogram = showConsensusHistogram;
2549 this._has_showConsensusHistogram = true;
2553 * Sets the value of field 'showDbRefTooltip'.
2555 * @param showDbRefTooltip
2556 * the value of field 'showDbRefTooltip'
2558 public void setShowDbRefTooltip(final boolean showDbRefTooltip)
2560 this._showDbRefTooltip = showDbRefTooltip;
2561 this._has_showDbRefTooltip = true;
2565 * Sets the value of field 'showFullId'.
2568 * the value of field 'showFullId'.
2570 public void setShowFullId(final boolean showFullId)
2572 this._showFullId = showFullId;
2573 this._has_showFullId = true;
2577 * Sets the value of field 'showGroupConsensus'.
2579 * @param showGroupConsensus
2580 * the value of field 'showGroupConsensus'.
2582 public void setShowGroupConsensus(final boolean showGroupConsensus)
2584 this._showGroupConsensus = showGroupConsensus;
2585 this._has_showGroupConsensus = true;
2589 * Sets the value of field 'showGroupConservation'.
2591 * @param showGroupConservation
2592 * the value of field 'showGroupConservation'.
2594 public void setShowGroupConservation(final boolean showGroupConservation)
2596 this._showGroupConservation = showGroupConservation;
2597 this._has_showGroupConservation = true;
2601 * Sets the value of field 'showNPfeatureTooltip'.
2603 * @param showNPfeatureTooltip
2604 * the value of field 'showNPfeatureTooltip'.
2606 public void setShowNPfeatureTooltip(final boolean showNPfeatureTooltip)
2608 this._showNPfeatureTooltip = showNPfeatureTooltip;
2609 this._has_showNPfeatureTooltip = true;
2613 * Sets the value of field 'showSequenceFeatures'.
2615 * @param showSequenceFeatures
2616 * the value of field 'showSequenceFeatures'.
2618 public void setShowSequenceFeatures(final boolean showSequenceFeatures)
2620 this._showSequenceFeatures = showSequenceFeatures;
2621 this._has_showSequenceFeatures = true;
2625 * Sets the value of field 'showSequenceLogo'.
2627 * @param showSequenceLogo
2628 * the value of field 'showSequenceLogo'
2630 public void setShowSequenceLogo(final boolean showSequenceLogo)
2632 this._showSequenceLogo = showSequenceLogo;
2633 this._has_showSequenceLogo = true;
2637 * Sets the value of field 'showText'.
2640 * the value of field 'showText'.
2642 public void setShowText(final boolean showText)
2644 this._showText = showText;
2645 this._has_showText = true;
2649 * Sets the value of field 'showUnconserved'.
2651 * @param showUnconserved
2652 * the value of field 'showUnconserved'.
2654 public void setShowUnconserved(final boolean showUnconserved)
2656 this._showUnconserved = showUnconserved;
2657 this._has_showUnconserved = true;
2661 * Sets the value of field 'startRes'.
2664 * the value of field 'startRes'.
2666 public void setStartRes(final int startRes)
2668 this._startRes = startRes;
2669 this._has_startRes = true;
2673 * Sets the value of field 'startSeq'.
2676 * the value of field 'startSeq'.
2678 public void setStartSeq(final int startSeq)
2680 this._startSeq = startSeq;
2681 this._has_startSeq = true;
2685 * Sets the value of field 'textCol1'.
2688 * the value of field 'textCol1'.
2690 public void setTextCol1(final int textCol1)
2692 this._textCol1 = textCol1;
2693 this._has_textCol1 = true;
2697 * Sets the value of field 'textCol2'.
2700 * the value of field 'textCol2'.
2702 public void setTextCol2(final int textCol2)
2704 this._textCol2 = textCol2;
2705 this._has_textCol2 = true;
2709 * Sets the value of field 'textColThreshold'.
2711 * @param textColThreshold
2712 * the value of field 'textColThreshold'
2714 public void setTextColThreshold(final int textColThreshold)
2716 this._textColThreshold = textColThreshold;
2717 this._has_textColThreshold = true;
2721 * Sets the value of field 'title'.
2724 * the value of field 'title'.
2726 public void setTitle(final java.lang.String title)
2728 this._title = title;
2732 * Sets the value of field 'viewName'.
2735 * the value of field 'viewName'.
2737 public void setViewName(final java.lang.String viewName)
2739 this._viewName = viewName;
2743 * Sets the value of field 'width'.
2746 * the value of field 'width'.
2748 public void setWidth(final int width)
2750 this._width = width;
2751 this._has_width = true;
2755 * Sets the value of field 'wrapAlignment'.
2757 * @param wrapAlignment
2758 * the value of field 'wrapAlignment'.
2760 public void setWrapAlignment(final boolean wrapAlignment)
2762 this._wrapAlignment = wrapAlignment;
2763 this._has_wrapAlignment = true;
2767 * Sets the value of field 'xpos'.
2770 * the value of field 'xpos'.
2772 public void setXpos(final int xpos)
2775 this._has_xpos = true;
2779 * Sets the value of field 'ypos'.
2782 * the value of field 'ypos'.
2784 public void setYpos(final int ypos)
2787 this._has_ypos = true;
2794 * @throws org.exolab.castor.xml.MarshalException
2795 * if object is null or if any SAXException is thrown during
2797 * @throws org.exolab.castor.xml.ValidationException
2798 * if this object is an invalid instance according to the schema
2799 * @return the unmarshaled jalview.schemabinding.version2.Viewport
2801 public static jalview.schemabinding.version2.Viewport unmarshal(
2802 final java.io.Reader reader)
2803 throws org.exolab.castor.xml.MarshalException,
2804 org.exolab.castor.xml.ValidationException
2806 return (jalview.schemabinding.version2.Viewport) Unmarshaller
2807 .unmarshal(jalview.schemabinding.version2.Viewport.class,
2814 * @throws org.exolab.castor.xml.ValidationException
2815 * if this object is an invalid instance according to the schema
2817 public void validate() throws org.exolab.castor.xml.ValidationException
2819 org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
2820 validator.validate(this);