2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
\r
3 * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
\r
5 * This file is part of Jalview.
\r
7 * Jalview is free software: you can redistribute it and/or
\r
8 * modify it under the terms of the GNU General Public License
\r
9 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
\r
11 * Jalview is distributed in the hope that it will be useful, but
\r
12 * WITHOUT ANY WARRANTY; without even the implied warranty
\r
13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
\r
14 * PURPOSE. See the GNU General Public License for more details.
\r
16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
\r
18 package jalview.schemabinding.version2;
\r
20 //---------------------------------/
\r
21 //- Imported classes and packages -/
\r
22 //---------------------------------/
\r
24 import org.exolab.castor.xml.Marshaller;
\r
25 import org.exolab.castor.xml.Unmarshaller;
\r
30 * @version $Revision$ $Date$
\r
32 public class Viewport implements java.io.Serializable
\r
35 // --------------------------/
\r
36 // - Class/Member Variables -/
\r
37 // --------------------------/
\r
40 * Field _conservationSelected.
\r
42 private boolean _conservationSelected;
\r
45 * keeps track of state for field: _conservationSelected
\r
47 private boolean _has_conservationSelected;
\r
50 * Field _pidSelected.
\r
52 private boolean _pidSelected;
\r
55 * keeps track of state for field: _pidSelected
\r
57 private boolean _has_pidSelected;
\r
62 private java.lang.String _bgColour;
\r
65 * Field _consThreshold.
\r
67 private int _consThreshold;
\r
70 * keeps track of state for field: _consThreshold
\r
72 private boolean _has_consThreshold;
\r
75 * Field _pidThreshold.
\r
77 private int _pidThreshold;
\r
80 * keeps track of state for field: _pidThreshold
\r
82 private boolean _has_pidThreshold;
\r
87 private java.lang.String _title;
\r
90 * Field _showFullId.
\r
92 private boolean _showFullId;
\r
95 * keeps track of state for field: _showFullId
\r
97 private boolean _has_showFullId;
\r
100 * Field _rightAlignIds.
\r
102 private boolean _rightAlignIds;
\r
105 * keeps track of state for field: _rightAlignIds
\r
107 private boolean _has_rightAlignIds;
\r
112 private boolean _showText;
\r
115 * keeps track of state for field: _showText
\r
117 private boolean _has_showText;
\r
120 * Field _showColourText.
\r
122 private boolean _showColourText;
\r
125 * keeps track of state for field: _showColourText
\r
127 private boolean _has_showColourText;
\r
130 * Field _showUnconserved.
\r
132 private boolean _showUnconserved = false;
\r
135 * keeps track of state for field: _showUnconserved
\r
137 private boolean _has_showUnconserved;
\r
140 * Field _showBoxes.
\r
142 private boolean _showBoxes;
\r
145 * keeps track of state for field: _showBoxes
\r
147 private boolean _has_showBoxes;
\r
150 * Field _wrapAlignment.
\r
152 private boolean _wrapAlignment;
\r
155 * keeps track of state for field: _wrapAlignment
\r
157 private boolean _has_wrapAlignment;
\r
160 * Field _renderGaps.
\r
162 private boolean _renderGaps;
\r
165 * keeps track of state for field: _renderGaps
\r
167 private boolean _has_renderGaps;
\r
170 * Field _showSequenceFeatures.
\r
172 private boolean _showSequenceFeatures;
\r
175 * keeps track of state for field: _showSequenceFeatures
\r
177 private boolean _has_showSequenceFeatures;
\r
180 * Field _showNPfeatureTooltip.
\r
182 private boolean _showNPfeatureTooltip;
\r
185 * keeps track of state for field: _showNPfeatureTooltip
\r
187 private boolean _has_showNPfeatureTooltip;
\r
190 * Field _showDbRefTooltip.
\r
192 private boolean _showDbRefTooltip;
\r
195 * keeps track of state for field: _showDbRefTooltip
\r
197 private boolean _has_showDbRefTooltip;
\r
200 * Field _followHighlight.
\r
202 private boolean _followHighlight = true;
\r
205 * keeps track of state for field: _followHighlight
\r
207 private boolean _has_followHighlight;
\r
210 * Field _followSelection.
\r
212 private boolean _followSelection = true;
\r
215 * keeps track of state for field: _followSelection
\r
217 private boolean _has_followSelection;
\r
220 * Field _showAnnotation.
\r
222 private boolean _showAnnotation;
\r
225 * keeps track of state for field: _showAnnotation
\r
227 private boolean _has_showAnnotation;
\r
230 * Field _centreColumnLabels.
\r
232 private boolean _centreColumnLabels = false;
\r
235 * keeps track of state for field: _centreColumnLabels
\r
237 private boolean _has_centreColumnLabels;
\r
240 * Field _showGroupConservation.
\r
242 private boolean _showGroupConservation = false;
\r
245 * keeps track of state for field: _showGroupConservation
\r
247 private boolean _has_showGroupConservation;
\r
250 * Field _showGroupConsensus.
\r
252 private boolean _showGroupConsensus = false;
\r
255 * keeps track of state for field: _showGroupConsensus
\r
257 private boolean _has_showGroupConsensus;
\r
260 * Field _showConsensusHistogram.
\r
262 private boolean _showConsensusHistogram = true;
\r
265 * keeps track of state for field: _showConsensusHistogram
\r
267 private boolean _has_showConsensusHistogram;
\r
270 * Field _showSequenceLogo.
\r
272 private boolean _showSequenceLogo = false;
\r
275 * keeps track of state for field: _showSequenceLogo
\r
277 private boolean _has_showSequenceLogo;
\r
280 * Field _ignoreGapsinConsensus.
\r
282 private boolean _ignoreGapsinConsensus = true;
\r
285 * keeps track of state for field: _ignoreGapsinConsensus
\r
287 private boolean _has_ignoreGapsinConsensus;
\r
295 * keeps track of state for field: _xpos
\r
297 private boolean _has_xpos;
\r
305 * keeps track of state for field: _ypos
\r
307 private boolean _has_ypos;
\r
312 private int _width;
\r
315 * keeps track of state for field: _width
\r
317 private boolean _has_width;
\r
322 private int _height;
\r
325 * keeps track of state for field: _height
\r
327 private boolean _has_height;
\r
332 private int _startRes;
\r
335 * keeps track of state for field: _startRes
\r
337 private boolean _has_startRes;
\r
342 private int _startSeq;
\r
345 * keeps track of state for field: _startSeq
\r
347 private boolean _has_startSeq;
\r
352 private java.lang.String _fontName;
\r
357 private int _fontSize;
\r
360 * keeps track of state for field: _fontSize
\r
362 private boolean _has_fontSize;
\r
365 * Field _fontStyle.
\r
367 private int _fontStyle;
\r
370 * keeps track of state for field: _fontStyle
\r
372 private boolean _has_fontStyle;
\r
377 private java.lang.String _viewName;
\r
380 * Field _sequenceSetId.
\r
382 private java.lang.String _sequenceSetId;
\r
385 * Field _gatheredViews.
\r
387 private boolean _gatheredViews;
\r
390 * keeps track of state for field: _gatheredViews
\r
392 private boolean _has_gatheredViews;
\r
397 private int _textCol1;
\r
400 * keeps track of state for field: _textCol1
\r
402 private boolean _has_textCol1;
\r
407 private int _textCol2;
\r
410 * keeps track of state for field: _textCol2
\r
412 private boolean _has_textCol2;
\r
415 * Field _textColThreshold.
\r
417 private int _textColThreshold;
\r
420 * keeps track of state for field: _textColThreshold
\r
422 private boolean _has_textColThreshold;
\r
425 * unique id used by jalview to synchronize between stored and instantiated
\r
429 private java.lang.String _id;
\r
432 * Field _annotationColours.
\r
434 private jalview.schemabinding.version2.AnnotationColours _annotationColours;
\r
437 * Field _hiddenColumnsList.
\r
439 private java.util.Vector _hiddenColumnsList;
\r
441 // ----------------/
\r
442 // - Constructors -/
\r
443 // ----------------/
\r
448 this._hiddenColumnsList = new java.util.Vector();
\r
458 * @param vHiddenColumns
\r
459 * @throws java.lang.IndexOutOfBoundsException
\r
460 * if the index given is outside the bounds of the collection
\r
462 public void addHiddenColumns(
\r
463 final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)
\r
464 throws java.lang.IndexOutOfBoundsException
\r
466 this._hiddenColumnsList.addElement(vHiddenColumns);
\r
473 * @param vHiddenColumns
\r
474 * @throws java.lang.IndexOutOfBoundsException
\r
475 * if the index given is outside the bounds of the collection
\r
477 public void addHiddenColumns(final int index,
\r
478 final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)
\r
479 throws java.lang.IndexOutOfBoundsException
\r
481 this._hiddenColumnsList.add(index, vHiddenColumns);
\r
486 public void deleteCentreColumnLabels()
\r
488 this._has_centreColumnLabels = false;
\r
493 public void deleteConsThreshold()
\r
495 this._has_consThreshold = false;
\r
500 public void deleteConservationSelected()
\r
502 this._has_conservationSelected = false;
\r
507 public void deleteFollowHighlight()
\r
509 this._has_followHighlight = false;
\r
514 public void deleteFollowSelection()
\r
516 this._has_followSelection = false;
\r
521 public void deleteFontSize()
\r
523 this._has_fontSize = false;
\r
528 public void deleteFontStyle()
\r
530 this._has_fontStyle = false;
\r
535 public void deleteGatheredViews()
\r
537 this._has_gatheredViews = false;
\r
542 public void deleteHeight()
\r
544 this._has_height = false;
\r
549 public void deleteIgnoreGapsinConsensus()
\r
551 this._has_ignoreGapsinConsensus = false;
\r
556 public void deletePidSelected()
\r
558 this._has_pidSelected = false;
\r
563 public void deletePidThreshold()
\r
565 this._has_pidThreshold = false;
\r
570 public void deleteRenderGaps()
\r
572 this._has_renderGaps = false;
\r
577 public void deleteRightAlignIds()
\r
579 this._has_rightAlignIds = false;
\r
584 public void deleteShowAnnotation()
\r
586 this._has_showAnnotation = false;
\r
591 public void deleteShowBoxes()
\r
593 this._has_showBoxes = false;
\r
598 public void deleteShowColourText()
\r
600 this._has_showColourText = false;
\r
605 public void deleteShowConsensusHistogram()
\r
607 this._has_showConsensusHistogram = false;
\r
612 public void deleteShowDbRefTooltip()
\r
614 this._has_showDbRefTooltip = false;
\r
619 public void deleteShowFullId()
\r
621 this._has_showFullId = false;
\r
626 public void deleteShowGroupConsensus()
\r
628 this._has_showGroupConsensus = false;
\r
633 public void deleteShowGroupConservation()
\r
635 this._has_showGroupConservation = false;
\r
640 public void deleteShowNPfeatureTooltip()
\r
642 this._has_showNPfeatureTooltip = false;
\r
647 public void deleteShowSequenceFeatures()
\r
649 this._has_showSequenceFeatures = false;
\r
654 public void deleteShowSequenceLogo()
\r
656 this._has_showSequenceLogo = false;
\r
661 public void deleteShowText()
\r
663 this._has_showText = false;
\r
668 public void deleteShowUnconserved()
\r
670 this._has_showUnconserved = false;
\r
675 public void deleteStartRes()
\r
677 this._has_startRes = false;
\r
682 public void deleteStartSeq()
\r
684 this._has_startSeq = false;
\r
689 public void deleteTextCol1()
\r
691 this._has_textCol1 = false;
\r
696 public void deleteTextCol2()
\r
698 this._has_textCol2 = false;
\r
703 public void deleteTextColThreshold()
\r
705 this._has_textColThreshold = false;
\r
710 public void deleteWidth()
\r
712 this._has_width = false;
\r
717 public void deleteWrapAlignment()
\r
719 this._has_wrapAlignment = false;
\r
724 public void deleteXpos()
\r
726 this._has_xpos = false;
\r
731 public void deleteYpos()
\r
733 this._has_ypos = false;
\r
737 * Method enumerateHiddenColumns.
\r
739 * @return an Enumeration over all
\r
740 * jalview.schemabinding.version2.HiddenColumns elements
\r
742 public java.util.Enumeration enumerateHiddenColumns()
\r
744 return this._hiddenColumnsList.elements();
\r
748 * Returns the value of field 'annotationColours'.
\r
750 * @return the value of field 'AnnotationColours'.
\r
752 public jalview.schemabinding.version2.AnnotationColours getAnnotationColours()
\r
754 return this._annotationColours;
\r
758 * Returns the value of field 'bgColour'.
\r
760 * @return the value of field 'BgColour'.
\r
762 public java.lang.String getBgColour()
\r
764 return this._bgColour;
\r
768 * Returns the value of field 'centreColumnLabels'.
\r
770 * @return the value of field 'CentreColumnLabels'.
\r
772 public boolean getCentreColumnLabels()
\r
774 return this._centreColumnLabels;
\r
778 * Returns the value of field 'consThreshold'.
\r
780 * @return the value of field 'ConsThreshold'.
\r
782 public int getConsThreshold()
\r
784 return this._consThreshold;
\r
788 * Returns the value of field 'conservationSelected'.
\r
790 * @return the value of field 'ConservationSelected'.
\r
792 public boolean getConservationSelected()
\r
794 return this._conservationSelected;
\r
798 * Returns the value of field 'followHighlight'.
\r
800 * @return the value of field 'FollowHighlight'.
\r
802 public boolean getFollowHighlight()
\r
804 return this._followHighlight;
\r
808 * Returns the value of field 'followSelection'.
\r
810 * @return the value of field 'FollowSelection'.
\r
812 public boolean getFollowSelection()
\r
814 return this._followSelection;
\r
818 * Returns the value of field 'fontName'.
\r
820 * @return the value of field 'FontName'.
\r
822 public java.lang.String getFontName()
\r
824 return this._fontName;
\r
828 * Returns the value of field 'fontSize'.
\r
830 * @return the value of field 'FontSize'.
\r
832 public int getFontSize()
\r
834 return this._fontSize;
\r
838 * Returns the value of field 'fontStyle'.
\r
840 * @return the value of field 'FontStyle'.
\r
842 public int getFontStyle()
\r
844 return this._fontStyle;
\r
848 * Returns the value of field 'gatheredViews'.
\r
850 * @return the value of field 'GatheredViews'.
\r
852 public boolean getGatheredViews()
\r
854 return this._gatheredViews;
\r
858 * Returns the value of field 'height'.
\r
860 * @return the value of field 'Height'.
\r
862 public int getHeight()
\r
864 return this._height;
\r
868 * Method getHiddenColumns.
\r
871 * @throws java.lang.IndexOutOfBoundsException
\r
872 * if the index given is outside the bounds of the collection
\r
873 * @return the value of the jalview.schemabinding.version2.HiddenColumns at
\r
876 public jalview.schemabinding.version2.HiddenColumns getHiddenColumns(
\r
877 final int index) throws java.lang.IndexOutOfBoundsException
\r
879 // check bounds for index
\r
880 if (index < 0 || index >= this._hiddenColumnsList.size())
\r
882 throw new IndexOutOfBoundsException("getHiddenColumns: Index value '"
\r
883 + index + "' not in range [0.."
\r
884 + (this._hiddenColumnsList.size() - 1) + "]");
\r
887 return (jalview.schemabinding.version2.HiddenColumns) _hiddenColumnsList
\r
892 * Method getHiddenColumns.Returns the contents of the collection in an Array.
\r
894 * Note: Just in case the collection contents are changing in another thread,
\r
895 * we pass a 0-length Array of the correct type into the API call. This way we
\r
896 * <i>know</i> that the Array returned is of exactly the correct length.
\r
898 * @return this collection as an Array
\r
900 public jalview.schemabinding.version2.HiddenColumns[] getHiddenColumns()
\r
902 jalview.schemabinding.version2.HiddenColumns[] array = new jalview.schemabinding.version2.HiddenColumns[0];
\r
903 return (jalview.schemabinding.version2.HiddenColumns[]) this._hiddenColumnsList
\r
908 * Method getHiddenColumnsCount.
\r
910 * @return the size of this collection
\r
912 public int getHiddenColumnsCount()
\r
914 return this._hiddenColumnsList.size();
\r
918 * Returns the value of field 'id'. The field 'id' has the following
\r
919 * description: unique id used by jalview to synchronize between stored and
\r
920 * instantiated views
\r
923 * @return the value of field 'Id'.
\r
925 public java.lang.String getId()
\r
931 * Returns the value of field 'ignoreGapsinConsensus'.
\r
933 * @return the value of field 'IgnoreGapsinConsensus'.
\r
935 public boolean getIgnoreGapsinConsensus()
\r
937 return this._ignoreGapsinConsensus;
\r
941 * Returns the value of field 'pidSelected'.
\r
943 * @return the value of field 'PidSelected'.
\r
945 public boolean getPidSelected()
\r
947 return this._pidSelected;
\r
951 * Returns the value of field 'pidThreshold'.
\r
953 * @return the value of field 'PidThreshold'.
\r
955 public int getPidThreshold()
\r
957 return this._pidThreshold;
\r
961 * Returns the value of field 'renderGaps'.
\r
963 * @return the value of field 'RenderGaps'.
\r
965 public boolean getRenderGaps()
\r
967 return this._renderGaps;
\r
971 * Returns the value of field 'rightAlignIds'.
\r
973 * @return the value of field 'RightAlignIds'.
\r
975 public boolean getRightAlignIds()
\r
977 return this._rightAlignIds;
\r
981 * Returns the value of field 'sequenceSetId'.
\r
983 * @return the value of field 'SequenceSetId'.
\r
985 public java.lang.String getSequenceSetId()
\r
987 return this._sequenceSetId;
\r
991 * Returns the value of field 'showAnnotation'.
\r
993 * @return the value of field 'ShowAnnotation'.
\r
995 public boolean getShowAnnotation()
\r
997 return this._showAnnotation;
\r
1001 * Returns the value of field 'showBoxes'.
\r
1003 * @return the value of field 'ShowBoxes'.
\r
1005 public boolean getShowBoxes()
\r
1007 return this._showBoxes;
\r
1011 * Returns the value of field 'showColourText'.
\r
1013 * @return the value of field 'ShowColourText'.
\r
1015 public boolean getShowColourText()
\r
1017 return this._showColourText;
\r
1021 * Returns the value of field 'showConsensusHistogram'.
\r
1023 * @return the value of field 'ShowConsensusHistogram'.
\r
1025 public boolean getShowConsensusHistogram()
\r
1027 return this._showConsensusHistogram;
\r
1031 * Returns the value of field 'showDbRefTooltip'.
\r
1033 * @return the value of field 'ShowDbRefTooltip'.
\r
1035 public boolean getShowDbRefTooltip()
\r
1037 return this._showDbRefTooltip;
\r
1041 * Returns the value of field 'showFullId'.
\r
1043 * @return the value of field 'ShowFullId'.
\r
1045 public boolean getShowFullId()
\r
1047 return this._showFullId;
\r
1051 * Returns the value of field 'showGroupConsensus'.
\r
1053 * @return the value of field 'ShowGroupConsensus'.
\r
1055 public boolean getShowGroupConsensus()
\r
1057 return this._showGroupConsensus;
\r
1061 * Returns the value of field 'showGroupConservation'.
\r
1063 * @return the value of field 'ShowGroupConservation'.
\r
1065 public boolean getShowGroupConservation()
\r
1067 return this._showGroupConservation;
\r
1071 * Returns the value of field 'showNPfeatureTooltip'.
\r
1073 * @return the value of field 'ShowNPfeatureTooltip'.
\r
1075 public boolean getShowNPfeatureTooltip()
\r
1077 return this._showNPfeatureTooltip;
\r
1081 * Returns the value of field 'showSequenceFeatures'.
\r
1083 * @return the value of field 'ShowSequenceFeatures'.
\r
1085 public boolean getShowSequenceFeatures()
\r
1087 return this._showSequenceFeatures;
\r
1091 * Returns the value of field 'showSequenceLogo'.
\r
1093 * @return the value of field 'ShowSequenceLogo'.
\r
1095 public boolean getShowSequenceLogo()
\r
1097 return this._showSequenceLogo;
\r
1101 * Returns the value of field 'showText'.
\r
1103 * @return the value of field 'ShowText'.
\r
1105 public boolean getShowText()
\r
1107 return this._showText;
\r
1111 * Returns the value of field 'showUnconserved'.
\r
1113 * @return the value of field 'ShowUnconserved'.
\r
1115 public boolean getShowUnconserved()
\r
1117 return this._showUnconserved;
\r
1121 * Returns the value of field 'startRes'.
\r
1123 * @return the value of field 'StartRes'.
\r
1125 public int getStartRes()
\r
1127 return this._startRes;
\r
1131 * Returns the value of field 'startSeq'.
\r
1133 * @return the value of field 'StartSeq'.
\r
1135 public int getStartSeq()
\r
1137 return this._startSeq;
\r
1141 * Returns the value of field 'textCol1'.
\r
1143 * @return the value of field 'TextCol1'.
\r
1145 public int getTextCol1()
\r
1147 return this._textCol1;
\r
1151 * Returns the value of field 'textCol2'.
\r
1153 * @return the value of field 'TextCol2'.
\r
1155 public int getTextCol2()
\r
1157 return this._textCol2;
\r
1161 * Returns the value of field 'textColThreshold'.
\r
1163 * @return the value of field 'TextColThreshold'.
\r
1165 public int getTextColThreshold()
\r
1167 return this._textColThreshold;
\r
1171 * Returns the value of field 'title'.
\r
1173 * @return the value of field 'Title'.
\r
1175 public java.lang.String getTitle()
\r
1177 return this._title;
\r
1181 * Returns the value of field 'viewName'.
\r
1183 * @return the value of field 'ViewName'.
\r
1185 public java.lang.String getViewName()
\r
1187 return this._viewName;
\r
1191 * Returns the value of field 'width'.
\r
1193 * @return the value of field 'Width'.
\r
1195 public int getWidth()
\r
1197 return this._width;
\r
1201 * Returns the value of field 'wrapAlignment'.
\r
1203 * @return the value of field 'WrapAlignment'.
\r
1205 public boolean getWrapAlignment()
\r
1207 return this._wrapAlignment;
\r
1211 * Returns the value of field 'xpos'.
\r
1213 * @return the value of field 'Xpos'.
\r
1215 public int getXpos()
\r
1217 return this._xpos;
\r
1221 * Returns the value of field 'ypos'.
\r
1223 * @return the value of field 'Ypos'.
\r
1225 public int getYpos()
\r
1227 return this._ypos;
\r
1231 * Method hasCentreColumnLabels.
\r
1233 * @return true if at least one CentreColumnLabels has been adde
\r
1235 public boolean hasCentreColumnLabels()
\r
1237 return this._has_centreColumnLabels;
\r
1241 * Method hasConsThreshold.
\r
1243 * @return true if at least one ConsThreshold has been added
\r
1245 public boolean hasConsThreshold()
\r
1247 return this._has_consThreshold;
\r
1251 * Method hasConservationSelected.
\r
1253 * @return true if at least one ConservationSelected has been added
\r
1255 public boolean hasConservationSelected()
\r
1257 return this._has_conservationSelected;
\r
1261 * Method hasFollowHighlight.
\r
1263 * @return true if at least one FollowHighlight has been added
\r
1265 public boolean hasFollowHighlight()
\r
1267 return this._has_followHighlight;
\r
1271 * Method hasFollowSelection.
\r
1273 * @return true if at least one FollowSelection has been added
\r
1275 public boolean hasFollowSelection()
\r
1277 return this._has_followSelection;
\r
1281 * Method hasFontSize.
\r
1283 * @return true if at least one FontSize has been added
\r
1285 public boolean hasFontSize()
\r
1287 return this._has_fontSize;
\r
1291 * Method hasFontStyle.
\r
1293 * @return true if at least one FontStyle has been added
\r
1295 public boolean hasFontStyle()
\r
1297 return this._has_fontStyle;
\r
1301 * Method hasGatheredViews.
\r
1303 * @return true if at least one GatheredViews has been added
\r
1305 public boolean hasGatheredViews()
\r
1307 return this._has_gatheredViews;
\r
1311 * Method hasHeight.
\r
1313 * @return true if at least one Height has been added
\r
1315 public boolean hasHeight()
\r
1317 return this._has_height;
\r
1321 * Method hasIgnoreGapsinConsensus.
\r
1323 * @return true if at least one IgnoreGapsinConsensus has been added
\r
1325 public boolean hasIgnoreGapsinConsensus()
\r
1327 return this._has_ignoreGapsinConsensus;
\r
1331 * Method hasPidSelected.
\r
1333 * @return true if at least one PidSelected has been added
\r
1335 public boolean hasPidSelected()
\r
1337 return this._has_pidSelected;
\r
1341 * Method hasPidThreshold.
\r
1343 * @return true if at least one PidThreshold has been added
\r
1345 public boolean hasPidThreshold()
\r
1347 return this._has_pidThreshold;
\r
1351 * Method hasRenderGaps.
\r
1353 * @return true if at least one RenderGaps has been added
\r
1355 public boolean hasRenderGaps()
\r
1357 return this._has_renderGaps;
\r
1361 * Method hasRightAlignIds.
\r
1363 * @return true if at least one RightAlignIds has been added
\r
1365 public boolean hasRightAlignIds()
\r
1367 return this._has_rightAlignIds;
\r
1371 * Method hasShowAnnotation.
\r
1373 * @return true if at least one ShowAnnotation has been added
\r
1375 public boolean hasShowAnnotation()
\r
1377 return this._has_showAnnotation;
\r
1381 * Method hasShowBoxes.
\r
1383 * @return true if at least one ShowBoxes has been added
\r
1385 public boolean hasShowBoxes()
\r
1387 return this._has_showBoxes;
\r
1391 * Method hasShowColourText.
\r
1393 * @return true if at least one ShowColourText has been added
\r
1395 public boolean hasShowColourText()
\r
1397 return this._has_showColourText;
\r
1401 * Method hasShowConsensusHistogram.
\r
1403 * @return true if at least one ShowConsensusHistogram has been added
\r
1405 public boolean hasShowConsensusHistogram()
\r
1407 return this._has_showConsensusHistogram;
\r
1411 * Method hasShowDbRefTooltip.
\r
1413 * @return true if at least one ShowDbRefTooltip has been added
\r
1415 public boolean hasShowDbRefTooltip()
\r
1417 return this._has_showDbRefTooltip;
\r
1421 * Method hasShowFullId.
\r
1423 * @return true if at least one ShowFullId has been added
\r
1425 public boolean hasShowFullId()
\r
1427 return this._has_showFullId;
\r
1431 * Method hasShowGroupConsensus.
\r
1433 * @return true if at least one ShowGroupConsensus has been adde
\r
1435 public boolean hasShowGroupConsensus()
\r
1437 return this._has_showGroupConsensus;
\r
1441 * Method hasShowGroupConservation.
\r
1443 * @return true if at least one ShowGroupConservation has been added
\r
1445 public boolean hasShowGroupConservation()
\r
1447 return this._has_showGroupConservation;
\r
1451 * Method hasShowNPfeatureTooltip.
\r
1453 * @return true if at least one ShowNPfeatureTooltip has been added
\r
1455 public boolean hasShowNPfeatureTooltip()
\r
1457 return this._has_showNPfeatureTooltip;
\r
1461 * Method hasShowSequenceFeatures.
\r
1463 * @return true if at least one ShowSequenceFeatures has been added
\r
1465 public boolean hasShowSequenceFeatures()
\r
1467 return this._has_showSequenceFeatures;
\r
1471 * Method hasShowSequenceLogo.
\r
1473 * @return true if at least one ShowSequenceLogo has been added
\r
1475 public boolean hasShowSequenceLogo()
\r
1477 return this._has_showSequenceLogo;
\r
1481 * Method hasShowText.
\r
1483 * @return true if at least one ShowText has been added
\r
1485 public boolean hasShowText()
\r
1487 return this._has_showText;
\r
1491 * Method hasShowUnconserved.
\r
1493 * @return true if at least one ShowUnconserved has been added
\r
1495 public boolean hasShowUnconserved()
\r
1497 return this._has_showUnconserved;
\r
1501 * Method hasStartRes.
\r
1503 * @return true if at least one StartRes has been added
\r
1505 public boolean hasStartRes()
\r
1507 return this._has_startRes;
\r
1511 * Method hasStartSeq.
\r
1513 * @return true if at least one StartSeq has been added
\r
1515 public boolean hasStartSeq()
\r
1517 return this._has_startSeq;
\r
1521 * Method hasTextCol1.
\r
1523 * @return true if at least one TextCol1 has been added
\r
1525 public boolean hasTextCol1()
\r
1527 return this._has_textCol1;
\r
1531 * Method hasTextCol2.
\r
1533 * @return true if at least one TextCol2 has been added
\r
1535 public boolean hasTextCol2()
\r
1537 return this._has_textCol2;
\r
1541 * Method hasTextColThreshold.
\r
1543 * @return true if at least one TextColThreshold has been added
\r
1545 public boolean hasTextColThreshold()
\r
1547 return this._has_textColThreshold;
\r
1551 * Method hasWidth.
\r
1553 * @return true if at least one Width has been added
\r
1555 public boolean hasWidth()
\r
1557 return this._has_width;
\r
1561 * Method hasWrapAlignment.
\r
1563 * @return true if at least one WrapAlignment has been added
\r
1565 public boolean hasWrapAlignment()
\r
1567 return this._has_wrapAlignment;
\r
1573 * @return true if at least one Xpos has been added
\r
1575 public boolean hasXpos()
\r
1577 return this._has_xpos;
\r
1583 * @return true if at least one Ypos has been added
\r
1585 public boolean hasYpos()
\r
1587 return this._has_ypos;
\r
1591 * Returns the value of field 'centreColumnLabels'.
\r
1593 * @return the value of field 'CentreColumnLabels'.
\r
1595 public boolean isCentreColumnLabels()
\r
1597 return this._centreColumnLabels;
\r
1601 * Returns the value of field 'conservationSelected'.
\r
1603 * @return the value of field 'ConservationSelected'.
\r
1605 public boolean isConservationSelected()
\r
1607 return this._conservationSelected;
\r
1611 * Returns the value of field 'followHighlight'.
\r
1613 * @return the value of field 'FollowHighlight'.
\r
1615 public boolean isFollowHighlight()
\r
1617 return this._followHighlight;
\r
1621 * Returns the value of field 'followSelection'.
\r
1623 * @return the value of field 'FollowSelection'.
\r
1625 public boolean isFollowSelection()
\r
1627 return this._followSelection;
\r
1631 * Returns the value of field 'gatheredViews'.
\r
1633 * @return the value of field 'GatheredViews'.
\r
1635 public boolean isGatheredViews()
\r
1637 return this._gatheredViews;
\r
1641 * Returns the value of field 'ignoreGapsinConsensus'.
\r
1643 * @return the value of field 'IgnoreGapsinConsensus'.
\r
1645 public boolean isIgnoreGapsinConsensus()
\r
1647 return this._ignoreGapsinConsensus;
\r
1651 * Returns the value of field 'pidSelected'.
\r
1653 * @return the value of field 'PidSelected'.
\r
1655 public boolean isPidSelected()
\r
1657 return this._pidSelected;
\r
1661 * Returns the value of field 'renderGaps'.
\r
1663 * @return the value of field 'RenderGaps'.
\r
1665 public boolean isRenderGaps()
\r
1667 return this._renderGaps;
\r
1671 * Returns the value of field 'rightAlignIds'.
\r
1673 * @return the value of field 'RightAlignIds'.
\r
1675 public boolean isRightAlignIds()
\r
1677 return this._rightAlignIds;
\r
1681 * Returns the value of field 'showAnnotation'.
\r
1683 * @return the value of field 'ShowAnnotation'.
\r
1685 public boolean isShowAnnotation()
\r
1687 return this._showAnnotation;
\r
1691 * Returns the value of field 'showBoxes'.
\r
1693 * @return the value of field 'ShowBoxes'.
\r
1695 public boolean isShowBoxes()
\r
1697 return this._showBoxes;
\r
1701 * Returns the value of field 'showColourText'.
\r
1703 * @return the value of field 'ShowColourText'.
\r
1705 public boolean isShowColourText()
\r
1707 return this._showColourText;
\r
1711 * Returns the value of field 'showConsensusHistogram'.
\r
1713 * @return the value of field 'ShowConsensusHistogram'.
\r
1715 public boolean isShowConsensusHistogram()
\r
1717 return this._showConsensusHistogram;
\r
1721 * Returns the value of field 'showDbRefTooltip'.
\r
1723 * @return the value of field 'ShowDbRefTooltip'.
\r
1725 public boolean isShowDbRefTooltip()
\r
1727 return this._showDbRefTooltip;
\r
1731 * Returns the value of field 'showFullId'.
\r
1733 * @return the value of field 'ShowFullId'.
\r
1735 public boolean isShowFullId()
\r
1737 return this._showFullId;
\r
1741 * Returns the value of field 'showGroupConsensus'.
\r
1743 * @return the value of field 'ShowGroupConsensus'.
\r
1745 public boolean isShowGroupConsensus()
\r
1747 return this._showGroupConsensus;
\r
1751 * Returns the value of field 'showGroupConservation'.
\r
1753 * @return the value of field 'ShowGroupConservation'.
\r
1755 public boolean isShowGroupConservation()
\r
1757 return this._showGroupConservation;
\r
1761 * Returns the value of field 'showNPfeatureTooltip'.
\r
1763 * @return the value of field 'ShowNPfeatureTooltip'.
\r
1765 public boolean isShowNPfeatureTooltip()
\r
1767 return this._showNPfeatureTooltip;
\r
1771 * Returns the value of field 'showSequenceFeatures'.
\r
1773 * @return the value of field 'ShowSequenceFeatures'.
\r
1775 public boolean isShowSequenceFeatures()
\r
1777 return this._showSequenceFeatures;
\r
1781 * Returns the value of field 'showSequenceLogo'.
\r
1783 * @return the value of field 'ShowSequenceLogo'.
\r
1785 public boolean isShowSequenceLogo()
\r
1787 return this._showSequenceLogo;
\r
1791 * Returns the value of field 'showText'.
\r
1793 * @return the value of field 'ShowText'.
\r
1795 public boolean isShowText()
\r
1797 return this._showText;
\r
1801 * Returns the value of field 'showUnconserved'.
\r
1803 * @return the value of field 'ShowUnconserved'.
\r
1805 public boolean isShowUnconserved()
\r
1807 return this._showUnconserved;
\r
1813 * @return true if this object is valid according to the schema
\r
1815 public boolean isValid()
\r
1820 } catch (org.exolab.castor.xml.ValidationException vex)
\r
1828 * Returns the value of field 'wrapAlignment'.
\r
1830 * @return the value of field 'WrapAlignment'.
\r
1832 public boolean isWrapAlignment()
\r
1834 return this._wrapAlignment;
\r
1841 * @throws org.exolab.castor.xml.MarshalException
\r
1842 * if object is null or if any SAXException is thrown during
\r
1844 * @throws org.exolab.castor.xml.ValidationException
\r
1845 * if this object is an invalid instance according to the schema
\r
1847 public void marshal(final java.io.Writer out)
\r
1848 throws org.exolab.castor.xml.MarshalException,
\r
1849 org.exolab.castor.xml.ValidationException
\r
1851 Marshaller.marshal(this, out);
\r
1858 * @throws java.io.IOException
\r
1859 * if an IOException occurs during marshaling
\r
1860 * @throws org.exolab.castor.xml.ValidationException
\r
1861 * if this object is an invalid instance according to the schema
\r
1862 * @throws org.exolab.castor.xml.MarshalException
\r
1863 * if object is null or if any SAXException is thrown during
\r
1866 public void marshal(final org.xml.sax.ContentHandler handler)
\r
1867 throws java.io.IOException,
\r
1868 org.exolab.castor.xml.MarshalException,
\r
1869 org.exolab.castor.xml.ValidationException
\r
1871 Marshaller.marshal(this, handler);
\r
1876 public void removeAllHiddenColumns()
\r
1878 this._hiddenColumnsList.clear();
\r
1882 * Method removeHiddenColumns.
\r
1884 * @param vHiddenColumns
\r
1885 * @return true if the object was removed from the collection.
\r
1887 public boolean removeHiddenColumns(
\r
1888 final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)
\r
1890 boolean removed = _hiddenColumnsList.remove(vHiddenColumns);
\r
1895 * Method removeHiddenColumnsAt.
\r
1898 * @return the element removed from the collection
\r
1900 public jalview.schemabinding.version2.HiddenColumns removeHiddenColumnsAt(
\r
1903 java.lang.Object obj = this._hiddenColumnsList.remove(index);
\r
1904 return (jalview.schemabinding.version2.HiddenColumns) obj;
\r
1908 * Sets the value of field 'annotationColours'.
\r
1910 * @param annotationColours
\r
1911 * the value of field 'annotationColours'.
\r
1913 public void setAnnotationColours(
\r
1914 final jalview.schemabinding.version2.AnnotationColours annotationColours)
\r
1916 this._annotationColours = annotationColours;
\r
1920 * Sets the value of field 'bgColour'.
\r
1923 * the value of field 'bgColour'.
\r
1925 public void setBgColour(final java.lang.String bgColour)
\r
1927 this._bgColour = bgColour;
\r
1931 * Sets the value of field 'centreColumnLabels'.
\r
1933 * @param centreColumnLabels
\r
1934 * the value of field 'centreColumnLabels'.
\r
1936 public void setCentreColumnLabels(final boolean centreColumnLabels)
\r
1938 this._centreColumnLabels = centreColumnLabels;
\r
1939 this._has_centreColumnLabels = true;
\r
1943 * Sets the value of field 'consThreshold'.
\r
1945 * @param consThreshold
\r
1946 * the value of field 'consThreshold'.
\r
1948 public void setConsThreshold(final int consThreshold)
\r
1950 this._consThreshold = consThreshold;
\r
1951 this._has_consThreshold = true;
\r
1955 * Sets the value of field 'conservationSelected'.
\r
1957 * @param conservationSelected
\r
1958 * the value of field 'conservationSelected'.
\r
1960 public void setConservationSelected(final boolean conservationSelected)
\r
1962 this._conservationSelected = conservationSelected;
\r
1963 this._has_conservationSelected = true;
\r
1967 * Sets the value of field 'followHighlight'.
\r
1969 * @param followHighlight
\r
1970 * the value of field 'followHighlight'.
\r
1972 public void setFollowHighlight(final boolean followHighlight)
\r
1974 this._followHighlight = followHighlight;
\r
1975 this._has_followHighlight = true;
\r
1979 * Sets the value of field 'followSelection'.
\r
1981 * @param followSelection
\r
1982 * the value of field 'followSelection'.
\r
1984 public void setFollowSelection(final boolean followSelection)
\r
1986 this._followSelection = followSelection;
\r
1987 this._has_followSelection = true;
\r
1991 * Sets the value of field 'fontName'.
\r
1994 * the value of field 'fontName'.
\r
1996 public void setFontName(final java.lang.String fontName)
\r
1998 this._fontName = fontName;
\r
2002 * Sets the value of field 'fontSize'.
\r
2005 * the value of field 'fontSize'.
\r
2007 public void setFontSize(final int fontSize)
\r
2009 this._fontSize = fontSize;
\r
2010 this._has_fontSize = true;
\r
2014 * Sets the value of field 'fontStyle'.
\r
2016 * @param fontStyle
\r
2017 * the value of field 'fontStyle'.
\r
2019 public void setFontStyle(final int fontStyle)
\r
2021 this._fontStyle = fontStyle;
\r
2022 this._has_fontStyle = true;
\r
2026 * Sets the value of field 'gatheredViews'.
\r
2028 * @param gatheredViews
\r
2029 * the value of field 'gatheredViews'.
\r
2031 public void setGatheredViews(final boolean gatheredViews)
\r
2033 this._gatheredViews = gatheredViews;
\r
2034 this._has_gatheredViews = true;
\r
2038 * Sets the value of field 'height'.
\r
2041 * the value of field 'height'.
\r
2043 public void setHeight(final int height)
\r
2045 this._height = height;
\r
2046 this._has_height = true;
\r
2053 * @param vHiddenColumns
\r
2054 * @throws java.lang.IndexOutOfBoundsException
\r
2055 * if the index given is outside the bounds of the collection
\r
2057 public void setHiddenColumns(final int index,
\r
2058 final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)
\r
2059 throws java.lang.IndexOutOfBoundsException
\r
2061 // check bounds for index
\r
2062 if (index < 0 || index >= this._hiddenColumnsList.size())
\r
2064 throw new IndexOutOfBoundsException("setHiddenColumns: Index value '"
\r
2065 + index + "' not in range [0.."
\r
2066 + (this._hiddenColumnsList.size() - 1) + "]");
\r
2069 this._hiddenColumnsList.set(index, vHiddenColumns);
\r
2075 * @param vHiddenColumnsArray
\r
2077 public void setHiddenColumns(
\r
2078 final jalview.schemabinding.version2.HiddenColumns[] vHiddenColumnsArray)
\r
2081 _hiddenColumnsList.clear();
\r
2083 for (int i = 0; i < vHiddenColumnsArray.length; i++)
\r
2085 this._hiddenColumnsList.add(vHiddenColumnsArray[i]);
\r
2090 * Sets the value of field 'id'. The field 'id' has the following description:
\r
2091 * unique id used by jalview to synchronize between stored and instantiated
\r
2096 * the value of field 'id'.
\r
2098 public void setId(final java.lang.String id)
\r
2104 * Sets the value of field 'ignoreGapsinConsensus'.
\r
2106 * @param ignoreGapsinConsensus
\r
2107 * the value of field 'ignoreGapsinConsensus'.
\r
2109 public void setIgnoreGapsinConsensus(final boolean ignoreGapsinConsensus)
\r
2111 this._ignoreGapsinConsensus = ignoreGapsinConsensus;
\r
2112 this._has_ignoreGapsinConsensus = true;
\r
2116 * Sets the value of field 'pidSelected'.
\r
2118 * @param pidSelected
\r
2119 * the value of field 'pidSelected'.
\r
2121 public void setPidSelected(final boolean pidSelected)
\r
2123 this._pidSelected = pidSelected;
\r
2124 this._has_pidSelected = true;
\r
2128 * Sets the value of field 'pidThreshold'.
\r
2130 * @param pidThreshold
\r
2131 * the value of field 'pidThreshold'.
\r
2133 public void setPidThreshold(final int pidThreshold)
\r
2135 this._pidThreshold = pidThreshold;
\r
2136 this._has_pidThreshold = true;
\r
2140 * Sets the value of field 'renderGaps'.
\r
2142 * @param renderGaps
\r
2143 * the value of field 'renderGaps'.
\r
2145 public void setRenderGaps(final boolean renderGaps)
\r
2147 this._renderGaps = renderGaps;
\r
2148 this._has_renderGaps = true;
\r
2152 * Sets the value of field 'rightAlignIds'.
\r
2154 * @param rightAlignIds
\r
2155 * the value of field 'rightAlignIds'.
\r
2157 public void setRightAlignIds(final boolean rightAlignIds)
\r
2159 this._rightAlignIds = rightAlignIds;
\r
2160 this._has_rightAlignIds = true;
\r
2164 * Sets the value of field 'sequenceSetId'.
\r
2166 * @param sequenceSetId
\r
2167 * the value of field 'sequenceSetId'.
\r
2169 public void setSequenceSetId(final java.lang.String sequenceSetId)
\r
2171 this._sequenceSetId = sequenceSetId;
\r
2175 * Sets the value of field 'showAnnotation'.
\r
2177 * @param showAnnotation
\r
2178 * the value of field 'showAnnotation'.
\r
2180 public void setShowAnnotation(final boolean showAnnotation)
\r
2182 this._showAnnotation = showAnnotation;
\r
2183 this._has_showAnnotation = true;
\r
2187 * Sets the value of field 'showBoxes'.
\r
2189 * @param showBoxes
\r
2190 * the value of field 'showBoxes'.
\r
2192 public void setShowBoxes(final boolean showBoxes)
\r
2194 this._showBoxes = showBoxes;
\r
2195 this._has_showBoxes = true;
\r
2199 * Sets the value of field 'showColourText'.
\r
2201 * @param showColourText
\r
2202 * the value of field 'showColourText'.
\r
2204 public void setShowColourText(final boolean showColourText)
\r
2206 this._showColourText = showColourText;
\r
2207 this._has_showColourText = true;
\r
2211 * Sets the value of field 'showConsensusHistogram'.
\r
2213 * @param showConsensusHistogram
\r
2214 * the value of field 'showConsensusHistogram'.
\r
2216 public void setShowConsensusHistogram(final boolean showConsensusHistogram)
\r
2218 this._showConsensusHistogram = showConsensusHistogram;
\r
2219 this._has_showConsensusHistogram = true;
\r
2223 * Sets the value of field 'showDbRefTooltip'.
\r
2225 * @param showDbRefTooltip
\r
2226 * the value of field 'showDbRefTooltip'
\r
2228 public void setShowDbRefTooltip(final boolean showDbRefTooltip)
\r
2230 this._showDbRefTooltip = showDbRefTooltip;
\r
2231 this._has_showDbRefTooltip = true;
\r
2235 * Sets the value of field 'showFullId'.
\r
2237 * @param showFullId
\r
2238 * the value of field 'showFullId'.
\r
2240 public void setShowFullId(final boolean showFullId)
\r
2242 this._showFullId = showFullId;
\r
2243 this._has_showFullId = true;
\r
2247 * Sets the value of field 'showGroupConsensus'.
\r
2249 * @param showGroupConsensus
\r
2250 * the value of field 'showGroupConsensus'.
\r
2252 public void setShowGroupConsensus(final boolean showGroupConsensus)
\r
2254 this._showGroupConsensus = showGroupConsensus;
\r
2255 this._has_showGroupConsensus = true;
\r
2259 * Sets the value of field 'showGroupConservation'.
\r
2261 * @param showGroupConservation
\r
2262 * the value of field 'showGroupConservation'.
\r
2264 public void setShowGroupConservation(final boolean showGroupConservation)
\r
2266 this._showGroupConservation = showGroupConservation;
\r
2267 this._has_showGroupConservation = true;
\r
2271 * Sets the value of field 'showNPfeatureTooltip'.
\r
2273 * @param showNPfeatureTooltip
\r
2274 * the value of field 'showNPfeatureTooltip'.
\r
2276 public void setShowNPfeatureTooltip(final boolean showNPfeatureTooltip)
\r
2278 this._showNPfeatureTooltip = showNPfeatureTooltip;
\r
2279 this._has_showNPfeatureTooltip = true;
\r
2283 * Sets the value of field 'showSequenceFeatures'.
\r
2285 * @param showSequenceFeatures
\r
2286 * the value of field 'showSequenceFeatures'.
\r
2288 public void setShowSequenceFeatures(final boolean showSequenceFeatures)
\r
2290 this._showSequenceFeatures = showSequenceFeatures;
\r
2291 this._has_showSequenceFeatures = true;
\r
2295 * Sets the value of field 'showSequenceLogo'.
\r
2297 * @param showSequenceLogo
\r
2298 * the value of field 'showSequenceLogo'
\r
2300 public void setShowSequenceLogo(final boolean showSequenceLogo)
\r
2302 this._showSequenceLogo = showSequenceLogo;
\r
2303 this._has_showSequenceLogo = true;
\r
2307 * Sets the value of field 'showText'.
\r
2310 * the value of field 'showText'.
\r
2312 public void setShowText(final boolean showText)
\r
2314 this._showText = showText;
\r
2315 this._has_showText = true;
\r
2319 * Sets the value of field 'showUnconserved'.
\r
2321 * @param showUnconserved
\r
2322 * the value of field 'showUnconserved'.
\r
2324 public void setShowUnconserved(final boolean showUnconserved)
\r
2326 this._showUnconserved = showUnconserved;
\r
2327 this._has_showUnconserved = true;
\r
2331 * Sets the value of field 'startRes'.
\r
2334 * the value of field 'startRes'.
\r
2336 public void setStartRes(final int startRes)
\r
2338 this._startRes = startRes;
\r
2339 this._has_startRes = true;
\r
2343 * Sets the value of field 'startSeq'.
\r
2346 * the value of field 'startSeq'.
\r
2348 public void setStartSeq(final int startSeq)
\r
2350 this._startSeq = startSeq;
\r
2351 this._has_startSeq = true;
\r
2355 * Sets the value of field 'textCol1'.
\r
2358 * the value of field 'textCol1'.
\r
2360 public void setTextCol1(final int textCol1)
\r
2362 this._textCol1 = textCol1;
\r
2363 this._has_textCol1 = true;
\r
2367 * Sets the value of field 'textCol2'.
\r
2370 * the value of field 'textCol2'.
\r
2372 public void setTextCol2(final int textCol2)
\r
2374 this._textCol2 = textCol2;
\r
2375 this._has_textCol2 = true;
\r
2379 * Sets the value of field 'textColThreshold'.
\r
2381 * @param textColThreshold
\r
2382 * the value of field 'textColThreshold'
\r
2384 public void setTextColThreshold(final int textColThreshold)
\r
2386 this._textColThreshold = textColThreshold;
\r
2387 this._has_textColThreshold = true;
\r
2391 * Sets the value of field 'title'.
\r
2394 * the value of field 'title'.
\r
2396 public void setTitle(final java.lang.String title)
\r
2398 this._title = title;
\r
2402 * Sets the value of field 'viewName'.
\r
2405 * the value of field 'viewName'.
\r
2407 public void setViewName(final java.lang.String viewName)
\r
2409 this._viewName = viewName;
\r
2413 * Sets the value of field 'width'.
\r
2416 * the value of field 'width'.
\r
2418 public void setWidth(final int width)
\r
2420 this._width = width;
\r
2421 this._has_width = true;
\r
2425 * Sets the value of field 'wrapAlignment'.
\r
2427 * @param wrapAlignment
\r
2428 * the value of field 'wrapAlignment'.
\r
2430 public void setWrapAlignment(final boolean wrapAlignment)
\r
2432 this._wrapAlignment = wrapAlignment;
\r
2433 this._has_wrapAlignment = true;
\r
2437 * Sets the value of field 'xpos'.
\r
2440 * the value of field 'xpos'.
\r
2442 public void setXpos(final int xpos)
\r
2444 this._xpos = xpos;
\r
2445 this._has_xpos = true;
\r
2449 * Sets the value of field 'ypos'.
\r
2452 * the value of field 'ypos'.
\r
2454 public void setYpos(final int ypos)
\r
2456 this._ypos = ypos;
\r
2457 this._has_ypos = true;
\r
2461 * Method unmarshal.
\r
2464 * @throws org.exolab.castor.xml.MarshalException
\r
2465 * if object is null or if any SAXException is thrown during
\r
2467 * @throws org.exolab.castor.xml.ValidationException
\r
2468 * if this object is an invalid instance according to the schema
\r
2469 * @return the unmarshaled jalview.schemabinding.version2.Viewport
\r
2471 public static jalview.schemabinding.version2.Viewport unmarshal(
\r
2472 final java.io.Reader reader)
\r
2473 throws org.exolab.castor.xml.MarshalException,
\r
2474 org.exolab.castor.xml.ValidationException
\r
2476 return (jalview.schemabinding.version2.Viewport) Unmarshaller
\r
2477 .unmarshal(jalview.schemabinding.version2.Viewport.class,
\r
2484 * @throws org.exolab.castor.xml.ValidationException
\r
2485 * if this object is an invalid instance according to the schema
\r
2487 public void validate() throws org.exolab.castor.xml.ValidationException
\r
2489 org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
\r
2490 validator.validate(this);
\r