2 * This class was automatically generated with
\r
3 * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
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8 package jalview.schemabinding.version2;
\r
10 //---------------------------------/
\r
11 //- Imported classes and packages -/
\r
12 //---------------------------------/
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14 import org.exolab.castor.xml.Marshaller;
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15 import org.exolab.castor.xml.Unmarshaller;
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20 * @version $Revision$ $Date$
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22 public class Viewport implements java.io.Serializable {
\r
25 //--------------------------/
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26 //- Class/Member Variables -/
\r
27 //--------------------------/
\r
30 * Field _conservationSelected.
\r
32 private boolean _conservationSelected;
\r
35 * keeps track of state for field: _conservationSelected
\r
37 private boolean _has_conservationSelected;
\r
40 * Field _pidSelected.
\r
42 private boolean _pidSelected;
\r
45 * keeps track of state for field: _pidSelected
\r
47 private boolean _has_pidSelected;
\r
52 private java.lang.String _bgColour;
\r
55 * Field _consThreshold.
\r
57 private int _consThreshold;
\r
60 * keeps track of state for field: _consThreshold
\r
62 private boolean _has_consThreshold;
\r
65 * Field _pidThreshold.
\r
67 private int _pidThreshold;
\r
70 * keeps track of state for field: _pidThreshold
\r
72 private boolean _has_pidThreshold;
\r
77 private java.lang.String _title;
\r
80 * Field _showFullId.
\r
82 private boolean _showFullId;
\r
85 * keeps track of state for field: _showFullId
\r
87 private boolean _has_showFullId;
\r
90 * Field _rightAlignIds.
\r
92 private boolean _rightAlignIds;
\r
95 * keeps track of state for field: _rightAlignIds
\r
97 private boolean _has_rightAlignIds;
\r
102 private boolean _showText;
\r
105 * keeps track of state for field: _showText
\r
107 private boolean _has_showText;
\r
110 * Field _showColourText.
\r
112 private boolean _showColourText;
\r
115 * keeps track of state for field: _showColourText
\r
117 private boolean _has_showColourText;
\r
120 * Field _showUnconserved.
\r
122 private boolean _showUnconserved;
\r
125 * keeps track of state for field: _showUnconserved
\r
127 private boolean _has_showUnconserved;
\r
130 * Field _showBoxes.
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132 private boolean _showBoxes;
\r
135 * keeps track of state for field: _showBoxes
\r
137 private boolean _has_showBoxes;
\r
140 * Field _wrapAlignment.
\r
142 private boolean _wrapAlignment;
\r
145 * keeps track of state for field: _wrapAlignment
\r
147 private boolean _has_wrapAlignment;
\r
150 * Field _renderGaps.
\r
152 private boolean _renderGaps;
\r
155 * keeps track of state for field: _renderGaps
\r
157 private boolean _has_renderGaps;
\r
160 * Field _showSequenceFeatures.
\r
162 private boolean _showSequenceFeatures;
\r
165 * keeps track of state for field: _showSequenceFeatures
\r
167 private boolean _has_showSequenceFeatures;
\r
170 * Field _showAnnotation.
\r
172 private boolean _showAnnotation;
\r
175 * keeps track of state for field: _showAnnotation
\r
177 private boolean _has_showAnnotation;
\r
185 * keeps track of state for field: _xpos
\r
187 private boolean _has_xpos;
\r
195 * keeps track of state for field: _ypos
\r
197 private boolean _has_ypos;
\r
202 private int _width;
\r
205 * keeps track of state for field: _width
\r
207 private boolean _has_width;
\r
212 private int _height;
\r
215 * keeps track of state for field: _height
\r
217 private boolean _has_height;
\r
222 private int _startRes;
\r
225 * keeps track of state for field: _startRes
\r
227 private boolean _has_startRes;
\r
232 private int _startSeq;
\r
235 * keeps track of state for field: _startSeq
\r
237 private boolean _has_startSeq;
\r
242 private java.lang.String _fontName;
\r
247 private int _fontSize;
\r
250 * keeps track of state for field: _fontSize
\r
252 private boolean _has_fontSize;
\r
255 * Field _fontStyle.
\r
257 private int _fontStyle;
\r
260 * keeps track of state for field: _fontStyle
\r
262 private boolean _has_fontStyle;
\r
267 private java.lang.String _viewName;
\r
270 * Field _sequenceSetId.
\r
272 private java.lang.String _sequenceSetId;
\r
275 * Field _gatheredViews.
\r
277 private boolean _gatheredViews;
\r
280 * keeps track of state for field: _gatheredViews
\r
282 private boolean _has_gatheredViews;
\r
287 private int _textCol1;
\r
290 * keeps track of state for field: _textCol1
\r
292 private boolean _has_textCol1;
\r
297 private int _textCol2;
\r
300 * keeps track of state for field: _textCol2
\r
302 private boolean _has_textCol2;
\r
305 * Field _textColThreshold.
\r
307 private int _textColThreshold;
\r
310 * keeps track of state for field: _textColThreshold
\r
312 private boolean _has_textColThreshold;
\r
315 * unique id used by jalview to synchronize between stored and
\r
316 * instantiated views
\r
319 private java.lang.String _id;
\r
322 * Field _annotationColours.
\r
324 private jalview.schemabinding.version2.AnnotationColours _annotationColours;
\r
327 * Field _hiddenColumnsList.
\r
329 private java.util.Vector _hiddenColumnsList;
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332 //----------------/
\r
333 //- Constructors -/
\r
334 //----------------/
\r
336 public Viewport() {
\r
338 this._hiddenColumnsList = new java.util.Vector();
\r
349 * @param vHiddenColumns
\r
350 * @throws java.lang.IndexOutOfBoundsException if the index
\r
351 * given is outside the bounds of the collection
\r
353 public void addHiddenColumns(
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354 final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)
\r
355 throws java.lang.IndexOutOfBoundsException {
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356 this._hiddenColumnsList.addElement(vHiddenColumns);
\r
363 * @param vHiddenColumns
\r
364 * @throws java.lang.IndexOutOfBoundsException if the index
\r
365 * given is outside the bounds of the collection
\r
367 public void addHiddenColumns(
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369 final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)
\r
370 throws java.lang.IndexOutOfBoundsException {
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371 this._hiddenColumnsList.add(index, vHiddenColumns);
\r
376 public void deleteConsThreshold(
\r
378 this._has_consThreshold= false;
\r
383 public void deleteConservationSelected(
\r
385 this._has_conservationSelected= false;
\r
390 public void deleteFontSize(
\r
392 this._has_fontSize= false;
\r
397 public void deleteFontStyle(
\r
399 this._has_fontStyle= false;
\r
404 public void deleteGatheredViews(
\r
406 this._has_gatheredViews= false;
\r
411 public void deleteHeight(
\r
413 this._has_height= false;
\r
418 public void deletePidSelected(
\r
420 this._has_pidSelected= false;
\r
425 public void deletePidThreshold(
\r
427 this._has_pidThreshold= false;
\r
432 public void deleteRenderGaps(
\r
434 this._has_renderGaps= false;
\r
439 public void deleteRightAlignIds(
\r
441 this._has_rightAlignIds= false;
\r
446 public void deleteShowAnnotation(
\r
448 this._has_showAnnotation= false;
\r
453 public void deleteShowBoxes(
\r
455 this._has_showBoxes= false;
\r
460 public void deleteShowColourText(
\r
462 this._has_showColourText= false;
\r
467 public void deleteShowFullId(
\r
469 this._has_showFullId= false;
\r
474 public void deleteShowSequenceFeatures(
\r
476 this._has_showSequenceFeatures= false;
\r
481 public void deleteShowText(
\r
483 this._has_showText= false;
\r
488 public void deleteShowUnconserved(
\r
490 this._has_showUnconserved= false;
\r
495 public void deleteStartRes(
\r
497 this._has_startRes= false;
\r
502 public void deleteStartSeq(
\r
504 this._has_startSeq= false;
\r
509 public void deleteTextCol1(
\r
511 this._has_textCol1= false;
\r
516 public void deleteTextCol2(
\r
518 this._has_textCol2= false;
\r
523 public void deleteTextColThreshold(
\r
525 this._has_textColThreshold= false;
\r
530 public void deleteWidth(
\r
532 this._has_width= false;
\r
537 public void deleteWrapAlignment(
\r
539 this._has_wrapAlignment= false;
\r
544 public void deleteXpos(
\r
546 this._has_xpos= false;
\r
551 public void deleteYpos(
\r
553 this._has_ypos= false;
\r
557 * Method enumerateHiddenColumns.
\r
559 * @return an Enumeration over all
\r
560 * jalview.schemabinding.version2.HiddenColumns elements
\r
562 public java.util.Enumeration enumerateHiddenColumns(
\r
564 return this._hiddenColumnsList.elements();
\r
568 * Returns the value of field 'annotationColours'.
\r
570 * @return the value of field 'AnnotationColours'.
\r
572 public jalview.schemabinding.version2.AnnotationColours getAnnotationColours(
\r
574 return this._annotationColours;
\r
578 * Returns the value of field 'bgColour'.
\r
580 * @return the value of field 'BgColour'.
\r
582 public java.lang.String getBgColour(
\r
584 return this._bgColour;
\r
588 * Returns the value of field 'consThreshold'.
\r
590 * @return the value of field 'ConsThreshold'.
\r
592 public int getConsThreshold(
\r
594 return this._consThreshold;
\r
598 * Returns the value of field 'conservationSelected'.
\r
600 * @return the value of field 'ConservationSelected'.
\r
602 public boolean getConservationSelected(
\r
604 return this._conservationSelected;
\r
608 * Returns the value of field 'fontName'.
\r
610 * @return the value of field 'FontName'.
\r
612 public java.lang.String getFontName(
\r
614 return this._fontName;
\r
618 * Returns the value of field 'fontSize'.
\r
620 * @return the value of field 'FontSize'.
\r
622 public int getFontSize(
\r
624 return this._fontSize;
\r
628 * Returns the value of field 'fontStyle'.
\r
630 * @return the value of field 'FontStyle'.
\r
632 public int getFontStyle(
\r
634 return this._fontStyle;
\r
638 * Returns the value of field 'gatheredViews'.
\r
640 * @return the value of field 'GatheredViews'.
\r
642 public boolean getGatheredViews(
\r
644 return this._gatheredViews;
\r
648 * Returns the value of field 'height'.
\r
650 * @return the value of field 'Height'.
\r
652 public int getHeight(
\r
654 return this._height;
\r
658 * Method getHiddenColumns.
\r
661 * @throws java.lang.IndexOutOfBoundsException if the index
\r
662 * given is outside the bounds of the collection
\r
663 * @return the value of the
\r
664 * jalview.schemabinding.version2.HiddenColumns at the given
\r
667 public jalview.schemabinding.version2.HiddenColumns getHiddenColumns(
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669 throws java.lang.IndexOutOfBoundsException {
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670 // check bounds for index
\r
671 if (index < 0 || index >= this._hiddenColumnsList.size()) {
\r
672 throw new IndexOutOfBoundsException("getHiddenColumns: Index value '" + index + "' not in range [0.." + (this._hiddenColumnsList.size() - 1) + "]");
\r
675 return (jalview.schemabinding.version2.HiddenColumns) _hiddenColumnsList.get(index);
\r
679 * Method getHiddenColumns.Returns the contents of the
\r
680 * collection in an Array. <p>Note: Just in case the
\r
681 * collection contents are changing in another thread, we pass
\r
682 * a 0-length Array of the correct type into the API call.
\r
683 * This way we <i>know</i> that the Array returned is of
\r
684 * exactly the correct length.
\r
686 * @return this collection as an Array
\r
688 public jalview.schemabinding.version2.HiddenColumns[] getHiddenColumns(
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690 jalview.schemabinding.version2.HiddenColumns[] array = new jalview.schemabinding.version2.HiddenColumns[0];
\r
691 return (jalview.schemabinding.version2.HiddenColumns[]) this._hiddenColumnsList.toArray(array);
\r
695 * Method getHiddenColumnsCount.
\r
697 * @return the size of this collection
\r
699 public int getHiddenColumnsCount(
\r
701 return this._hiddenColumnsList.size();
\r
705 * Returns the value of field 'id'. The field 'id' has the
\r
706 * following description: unique id used by jalview to
\r
707 * synchronize between stored and instantiated views
\r
710 * @return the value of field 'Id'.
\r
712 public java.lang.String getId(
\r
718 * Returns the value of field 'pidSelected'.
\r
720 * @return the value of field 'PidSelected'.
\r
722 public boolean getPidSelected(
\r
724 return this._pidSelected;
\r
728 * Returns the value of field 'pidThreshold'.
\r
730 * @return the value of field 'PidThreshold'.
\r
732 public int getPidThreshold(
\r
734 return this._pidThreshold;
\r
738 * Returns the value of field 'renderGaps'.
\r
740 * @return the value of field 'RenderGaps'.
\r
742 public boolean getRenderGaps(
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744 return this._renderGaps;
\r
748 * Returns the value of field 'rightAlignIds'.
\r
750 * @return the value of field 'RightAlignIds'.
\r
752 public boolean getRightAlignIds(
\r
754 return this._rightAlignIds;
\r
758 * Returns the value of field 'sequenceSetId'.
\r
760 * @return the value of field 'SequenceSetId'.
\r
762 public java.lang.String getSequenceSetId(
\r
764 return this._sequenceSetId;
\r
768 * Returns the value of field 'showAnnotation'.
\r
770 * @return the value of field 'ShowAnnotation'.
\r
772 public boolean getShowAnnotation(
\r
774 return this._showAnnotation;
\r
778 * Returns the value of field 'showBoxes'.
\r
780 * @return the value of field 'ShowBoxes'.
\r
782 public boolean getShowBoxes(
\r
784 return this._showBoxes;
\r
788 * Returns the value of field 'showColourText'.
\r
790 * @return the value of field 'ShowColourText'.
\r
792 public boolean getShowColourText(
\r
794 return this._showColourText;
\r
798 * Returns the value of field 'showFullId'.
\r
800 * @return the value of field 'ShowFullId'.
\r
802 public boolean getShowFullId(
\r
804 return this._showFullId;
\r
808 * Returns the value of field 'showSequenceFeatures'.
\r
810 * @return the value of field 'ShowSequenceFeatures'.
\r
812 public boolean getShowSequenceFeatures(
\r
814 return this._showSequenceFeatures;
\r
818 * Returns the value of field 'showText'.
\r
820 * @return the value of field 'ShowText'.
\r
822 public boolean getShowText(
\r
824 return this._showText;
\r
828 * Returns the value of field 'showUnconserved'.
\r
830 * @return the value of field 'ShowUnconserved'.
\r
832 public boolean getShowUnconserved(
\r
834 return this._showUnconserved;
\r
838 * Returns the value of field 'startRes'.
\r
840 * @return the value of field 'StartRes'.
\r
842 public int getStartRes(
\r
844 return this._startRes;
\r
848 * Returns the value of field 'startSeq'.
\r
850 * @return the value of field 'StartSeq'.
\r
852 public int getStartSeq(
\r
854 return this._startSeq;
\r
858 * Returns the value of field 'textCol1'.
\r
860 * @return the value of field 'TextCol1'.
\r
862 public int getTextCol1(
\r
864 return this._textCol1;
\r
868 * Returns the value of field 'textCol2'.
\r
870 * @return the value of field 'TextCol2'.
\r
872 public int getTextCol2(
\r
874 return this._textCol2;
\r
878 * Returns the value of field 'textColThreshold'.
\r
880 * @return the value of field 'TextColThreshold'.
\r
882 public int getTextColThreshold(
\r
884 return this._textColThreshold;
\r
888 * Returns the value of field 'title'.
\r
890 * @return the value of field 'Title'.
\r
892 public java.lang.String getTitle(
\r
894 return this._title;
\r
898 * Returns the value of field 'viewName'.
\r
900 * @return the value of field 'ViewName'.
\r
902 public java.lang.String getViewName(
\r
904 return this._viewName;
\r
908 * Returns the value of field 'width'.
\r
910 * @return the value of field 'Width'.
\r
912 public int getWidth(
\r
914 return this._width;
\r
918 * Returns the value of field 'wrapAlignment'.
\r
920 * @return the value of field 'WrapAlignment'.
\r
922 public boolean getWrapAlignment(
\r
924 return this._wrapAlignment;
\r
928 * Returns the value of field 'xpos'.
\r
930 * @return the value of field 'Xpos'.
\r
932 public int getXpos(
\r
938 * Returns the value of field 'ypos'.
\r
940 * @return the value of field 'Ypos'.
\r
942 public int getYpos(
\r
948 * Method hasConsThreshold.
\r
950 * @return true if at least one ConsThreshold has been added
\r
952 public boolean hasConsThreshold(
\r
954 return this._has_consThreshold;
\r
958 * Method hasConservationSelected.
\r
960 * @return true if at least one ConservationSelected has been
\r
963 public boolean hasConservationSelected(
\r
965 return this._has_conservationSelected;
\r
969 * Method hasFontSize.
\r
971 * @return true if at least one FontSize has been added
\r
973 public boolean hasFontSize(
\r
975 return this._has_fontSize;
\r
979 * Method hasFontStyle.
\r
981 * @return true if at least one FontStyle has been added
\r
983 public boolean hasFontStyle(
\r
985 return this._has_fontStyle;
\r
989 * Method hasGatheredViews.
\r
991 * @return true if at least one GatheredViews has been added
\r
993 public boolean hasGatheredViews(
\r
995 return this._has_gatheredViews;
\r
999 * Method hasHeight.
\r
1001 * @return true if at least one Height has been added
\r
1003 public boolean hasHeight(
\r
1005 return this._has_height;
\r
1009 * Method hasPidSelected.
\r
1011 * @return true if at least one PidSelected has been added
\r
1013 public boolean hasPidSelected(
\r
1015 return this._has_pidSelected;
\r
1019 * Method hasPidThreshold.
\r
1021 * @return true if at least one PidThreshold has been added
\r
1023 public boolean hasPidThreshold(
\r
1025 return this._has_pidThreshold;
\r
1029 * Method hasRenderGaps.
\r
1031 * @return true if at least one RenderGaps has been added
\r
1033 public boolean hasRenderGaps(
\r
1035 return this._has_renderGaps;
\r
1039 * Method hasRightAlignIds.
\r
1041 * @return true if at least one RightAlignIds has been added
\r
1043 public boolean hasRightAlignIds(
\r
1045 return this._has_rightAlignIds;
\r
1049 * Method hasShowAnnotation.
\r
1051 * @return true if at least one ShowAnnotation has been added
\r
1053 public boolean hasShowAnnotation(
\r
1055 return this._has_showAnnotation;
\r
1059 * Method hasShowBoxes.
\r
1061 * @return true if at least one ShowBoxes has been added
\r
1063 public boolean hasShowBoxes(
\r
1065 return this._has_showBoxes;
\r
1069 * Method hasShowColourText.
\r
1071 * @return true if at least one ShowColourText has been added
\r
1073 public boolean hasShowColourText(
\r
1075 return this._has_showColourText;
\r
1079 * Method hasShowFullId.
\r
1081 * @return true if at least one ShowFullId has been added
\r
1083 public boolean hasShowFullId(
\r
1085 return this._has_showFullId;
\r
1089 * Method hasShowSequenceFeatures.
\r
1091 * @return true if at least one ShowSequenceFeatures has been
\r
1094 public boolean hasShowSequenceFeatures(
\r
1096 return this._has_showSequenceFeatures;
\r
1100 * Method hasShowText.
\r
1102 * @return true if at least one ShowText has been added
\r
1104 public boolean hasShowText(
\r
1106 return this._has_showText;
\r
1110 * Method hasShowUnconserved.
\r
1112 * @return true if at least one ShowUnconserved has been added
\r
1114 public boolean hasShowUnconserved(
\r
1116 return this._has_showUnconserved;
\r
1120 * Method hasStartRes.
\r
1122 * @return true if at least one StartRes has been added
\r
1124 public boolean hasStartRes(
\r
1126 return this._has_startRes;
\r
1130 * Method hasStartSeq.
\r
1132 * @return true if at least one StartSeq has been added
\r
1134 public boolean hasStartSeq(
\r
1136 return this._has_startSeq;
\r
1140 * Method hasTextCol1.
\r
1142 * @return true if at least one TextCol1 has been added
\r
1144 public boolean hasTextCol1(
\r
1146 return this._has_textCol1;
\r
1150 * Method hasTextCol2.
\r
1152 * @return true if at least one TextCol2 has been added
\r
1154 public boolean hasTextCol2(
\r
1156 return this._has_textCol2;
\r
1160 * Method hasTextColThreshold.
\r
1162 * @return true if at least one TextColThreshold has been added
\r
1164 public boolean hasTextColThreshold(
\r
1166 return this._has_textColThreshold;
\r
1170 * Method hasWidth.
\r
1172 * @return true if at least one Width has been added
\r
1174 public boolean hasWidth(
\r
1176 return this._has_width;
\r
1180 * Method hasWrapAlignment.
\r
1182 * @return true if at least one WrapAlignment has been added
\r
1184 public boolean hasWrapAlignment(
\r
1186 return this._has_wrapAlignment;
\r
1192 * @return true if at least one Xpos has been added
\r
1194 public boolean hasXpos(
\r
1196 return this._has_xpos;
\r
1202 * @return true if at least one Ypos has been added
\r
1204 public boolean hasYpos(
\r
1206 return this._has_ypos;
\r
1210 * Returns the value of field 'conservationSelected'.
\r
1212 * @return the value of field 'ConservationSelected'.
\r
1214 public boolean isConservationSelected(
\r
1216 return this._conservationSelected;
\r
1220 * Returns the value of field 'gatheredViews'.
\r
1222 * @return the value of field 'GatheredViews'.
\r
1224 public boolean isGatheredViews(
\r
1226 return this._gatheredViews;
\r
1230 * Returns the value of field 'pidSelected'.
\r
1232 * @return the value of field 'PidSelected'.
\r
1234 public boolean isPidSelected(
\r
1236 return this._pidSelected;
\r
1240 * Returns the value of field 'renderGaps'.
\r
1242 * @return the value of field 'RenderGaps'.
\r
1244 public boolean isRenderGaps(
\r
1246 return this._renderGaps;
\r
1250 * Returns the value of field 'rightAlignIds'.
\r
1252 * @return the value of field 'RightAlignIds'.
\r
1254 public boolean isRightAlignIds(
\r
1256 return this._rightAlignIds;
\r
1260 * Returns the value of field 'showAnnotation'.
\r
1262 * @return the value of field 'ShowAnnotation'.
\r
1264 public boolean isShowAnnotation(
\r
1266 return this._showAnnotation;
\r
1270 * Returns the value of field 'showBoxes'.
\r
1272 * @return the value of field 'ShowBoxes'.
\r
1274 public boolean isShowBoxes(
\r
1276 return this._showBoxes;
\r
1280 * Returns the value of field 'showColourText'.
\r
1282 * @return the value of field 'ShowColourText'.
\r
1284 public boolean isShowColourText(
\r
1286 return this._showColourText;
\r
1290 * Returns the value of field 'showFullId'.
\r
1292 * @return the value of field 'ShowFullId'.
\r
1294 public boolean isShowFullId(
\r
1296 return this._showFullId;
\r
1300 * Returns the value of field 'showSequenceFeatures'.
\r
1302 * @return the value of field 'ShowSequenceFeatures'.
\r
1304 public boolean isShowSequenceFeatures(
\r
1306 return this._showSequenceFeatures;
\r
1310 * Returns the value of field 'showText'.
\r
1312 * @return the value of field 'ShowText'.
\r
1314 public boolean isShowText(
\r
1316 return this._showText;
\r
1320 * Returns the value of field 'showUnconserved'.
\r
1322 * @return the value of field 'ShowUnconserved'.
\r
1324 public boolean isShowUnconserved(
\r
1326 return this._showUnconserved;
\r
1332 * @return true if this object is valid according to the schema
\r
1334 public boolean isValid(
\r
1338 } catch (org.exolab.castor.xml.ValidationException vex) {
\r
1345 * Returns the value of field 'wrapAlignment'.
\r
1347 * @return the value of field 'WrapAlignment'.
\r
1349 public boolean isWrapAlignment(
\r
1351 return this._wrapAlignment;
\r
1358 * @throws org.exolab.castor.xml.MarshalException if object is
\r
1359 * null or if any SAXException is thrown during marshaling
\r
1360 * @throws org.exolab.castor.xml.ValidationException if this
\r
1361 * object is an invalid instance according to the schema
\r
1363 public void marshal(
\r
1364 final java.io.Writer out)
\r
1365 throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
\r
1366 Marshaller.marshal(this, out);
\r
1373 * @throws java.io.IOException if an IOException occurs during
\r
1375 * @throws org.exolab.castor.xml.ValidationException if this
\r
1376 * object is an invalid instance according to the schema
\r
1377 * @throws org.exolab.castor.xml.MarshalException if object is
\r
1378 * null or if any SAXException is thrown during marshaling
\r
1380 public void marshal(
\r
1381 final org.xml.sax.ContentHandler handler)
\r
1382 throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
\r
1383 Marshaller.marshal(this, handler);
\r
1388 public void removeAllHiddenColumns(
\r
1390 this._hiddenColumnsList.clear();
\r
1394 * Method removeHiddenColumns.
\r
1396 * @param vHiddenColumns
\r
1397 * @return true if the object was removed from the collection.
\r
1399 public boolean removeHiddenColumns(
\r
1400 final jalview.schemabinding.version2.HiddenColumns vHiddenColumns) {
\r
1401 boolean removed = _hiddenColumnsList.remove(vHiddenColumns);
\r
1406 * Method removeHiddenColumnsAt.
\r
1409 * @return the element removed from the collection
\r
1411 public jalview.schemabinding.version2.HiddenColumns removeHiddenColumnsAt(
\r
1412 final int index) {
\r
1413 java.lang.Object obj = this._hiddenColumnsList.remove(index);
\r
1414 return (jalview.schemabinding.version2.HiddenColumns) obj;
\r
1418 * Sets the value of field 'annotationColours'.
\r
1420 * @param annotationColours the value of field
\r
1421 * 'annotationColours'.
\r
1423 public void setAnnotationColours(
\r
1424 final jalview.schemabinding.version2.AnnotationColours annotationColours) {
\r
1425 this._annotationColours = annotationColours;
\r
1429 * Sets the value of field 'bgColour'.
\r
1431 * @param bgColour the value of field 'bgColour'.
\r
1433 public void setBgColour(
\r
1434 final java.lang.String bgColour) {
\r
1435 this._bgColour = bgColour;
\r
1439 * Sets the value of field 'consThreshold'.
\r
1441 * @param consThreshold the value of field 'consThreshold'.
\r
1443 public void setConsThreshold(
\r
1444 final int consThreshold) {
\r
1445 this._consThreshold = consThreshold;
\r
1446 this._has_consThreshold = true;
\r
1450 * Sets the value of field 'conservationSelected'.
\r
1452 * @param conservationSelected the value of field
\r
1453 * 'conservationSelected'.
\r
1455 public void setConservationSelected(
\r
1456 final boolean conservationSelected) {
\r
1457 this._conservationSelected = conservationSelected;
\r
1458 this._has_conservationSelected = true;
\r
1462 * Sets the value of field 'fontName'.
\r
1464 * @param fontName the value of field 'fontName'.
\r
1466 public void setFontName(
\r
1467 final java.lang.String fontName) {
\r
1468 this._fontName = fontName;
\r
1472 * Sets the value of field 'fontSize'.
\r
1474 * @param fontSize the value of field 'fontSize'.
\r
1476 public void setFontSize(
\r
1477 final int fontSize) {
\r
1478 this._fontSize = fontSize;
\r
1479 this._has_fontSize = true;
\r
1483 * Sets the value of field 'fontStyle'.
\r
1485 * @param fontStyle the value of field 'fontStyle'.
\r
1487 public void setFontStyle(
\r
1488 final int fontStyle) {
\r
1489 this._fontStyle = fontStyle;
\r
1490 this._has_fontStyle = true;
\r
1494 * Sets the value of field 'gatheredViews'.
\r
1496 * @param gatheredViews the value of field 'gatheredViews'.
\r
1498 public void setGatheredViews(
\r
1499 final boolean gatheredViews) {
\r
1500 this._gatheredViews = gatheredViews;
\r
1501 this._has_gatheredViews = true;
\r
1505 * Sets the value of field 'height'.
\r
1507 * @param height the value of field 'height'.
\r
1509 public void setHeight(
\r
1510 final int height) {
\r
1511 this._height = height;
\r
1512 this._has_height = true;
\r
1519 * @param vHiddenColumns
\r
1520 * @throws java.lang.IndexOutOfBoundsException if the index
\r
1521 * given is outside the bounds of the collection
\r
1523 public void setHiddenColumns(
\r
1525 final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)
\r
1526 throws java.lang.IndexOutOfBoundsException {
\r
1527 // check bounds for index
\r
1528 if (index < 0 || index >= this._hiddenColumnsList.size()) {
\r
1529 throw new IndexOutOfBoundsException("setHiddenColumns: Index value '" + index + "' not in range [0.." + (this._hiddenColumnsList.size() - 1) + "]");
\r
1532 this._hiddenColumnsList.set(index, vHiddenColumns);
\r
1538 * @param vHiddenColumnsArray
\r
1540 public void setHiddenColumns(
\r
1541 final jalview.schemabinding.version2.HiddenColumns[] vHiddenColumnsArray) {
\r
1543 _hiddenColumnsList.clear();
\r
1545 for (int i = 0; i < vHiddenColumnsArray.length; i++) {
\r
1546 this._hiddenColumnsList.add(vHiddenColumnsArray[i]);
\r
1551 * Sets the value of field 'id'. The field 'id' has the
\r
1552 * following description: unique id used by jalview to
\r
1553 * synchronize between stored and instantiated views
\r
1556 * @param id the value of field 'id'.
\r
1558 public void setId(
\r
1559 final java.lang.String id) {
\r
1564 * Sets the value of field 'pidSelected'.
\r
1566 * @param pidSelected the value of field 'pidSelected'.
\r
1568 public void setPidSelected(
\r
1569 final boolean pidSelected) {
\r
1570 this._pidSelected = pidSelected;
\r
1571 this._has_pidSelected = true;
\r
1575 * Sets the value of field 'pidThreshold'.
\r
1577 * @param pidThreshold the value of field 'pidThreshold'.
\r
1579 public void setPidThreshold(
\r
1580 final int pidThreshold) {
\r
1581 this._pidThreshold = pidThreshold;
\r
1582 this._has_pidThreshold = true;
\r
1586 * Sets the value of field 'renderGaps'.
\r
1588 * @param renderGaps the value of field 'renderGaps'.
\r
1590 public void setRenderGaps(
\r
1591 final boolean renderGaps) {
\r
1592 this._renderGaps = renderGaps;
\r
1593 this._has_renderGaps = true;
\r
1597 * Sets the value of field 'rightAlignIds'.
\r
1599 * @param rightAlignIds the value of field 'rightAlignIds'.
\r
1601 public void setRightAlignIds(
\r
1602 final boolean rightAlignIds) {
\r
1603 this._rightAlignIds = rightAlignIds;
\r
1604 this._has_rightAlignIds = true;
\r
1608 * Sets the value of field 'sequenceSetId'.
\r
1610 * @param sequenceSetId the value of field 'sequenceSetId'.
\r
1612 public void setSequenceSetId(
\r
1613 final java.lang.String sequenceSetId) {
\r
1614 this._sequenceSetId = sequenceSetId;
\r
1618 * Sets the value of field 'showAnnotation'.
\r
1620 * @param showAnnotation the value of field 'showAnnotation'.
\r
1622 public void setShowAnnotation(
\r
1623 final boolean showAnnotation) {
\r
1624 this._showAnnotation = showAnnotation;
\r
1625 this._has_showAnnotation = true;
\r
1629 * Sets the value of field 'showBoxes'.
\r
1631 * @param showBoxes the value of field 'showBoxes'.
\r
1633 public void setShowBoxes(
\r
1634 final boolean showBoxes) {
\r
1635 this._showBoxes = showBoxes;
\r
1636 this._has_showBoxes = true;
\r
1640 * Sets the value of field 'showColourText'.
\r
1642 * @param showColourText the value of field 'showColourText'.
\r
1644 public void setShowColourText(
\r
1645 final boolean showColourText) {
\r
1646 this._showColourText = showColourText;
\r
1647 this._has_showColourText = true;
\r
1651 * Sets the value of field 'showFullId'.
\r
1653 * @param showFullId the value of field 'showFullId'.
\r
1655 public void setShowFullId(
\r
1656 final boolean showFullId) {
\r
1657 this._showFullId = showFullId;
\r
1658 this._has_showFullId = true;
\r
1662 * Sets the value of field 'showSequenceFeatures'.
\r
1664 * @param showSequenceFeatures the value of field
\r
1665 * 'showSequenceFeatures'.
\r
1667 public void setShowSequenceFeatures(
\r
1668 final boolean showSequenceFeatures) {
\r
1669 this._showSequenceFeatures = showSequenceFeatures;
\r
1670 this._has_showSequenceFeatures = true;
\r
1674 * Sets the value of field 'showText'.
\r
1676 * @param showText the value of field 'showText'.
\r
1678 public void setShowText(
\r
1679 final boolean showText) {
\r
1680 this._showText = showText;
\r
1681 this._has_showText = true;
\r
1685 * Sets the value of field 'showUnconserved'.
\r
1687 * @param showUnconserved the value of field 'showUnconserved'.
\r
1689 public void setShowUnconserved(
\r
1690 final boolean showUnconserved) {
\r
1691 this._showUnconserved = showUnconserved;
\r
1692 this._has_showUnconserved = true;
\r
1696 * Sets the value of field 'startRes'.
\r
1698 * @param startRes the value of field 'startRes'.
\r
1700 public void setStartRes(
\r
1701 final int startRes) {
\r
1702 this._startRes = startRes;
\r
1703 this._has_startRes = true;
\r
1707 * Sets the value of field 'startSeq'.
\r
1709 * @param startSeq the value of field 'startSeq'.
\r
1711 public void setStartSeq(
\r
1712 final int startSeq) {
\r
1713 this._startSeq = startSeq;
\r
1714 this._has_startSeq = true;
\r
1718 * Sets the value of field 'textCol1'.
\r
1720 * @param textCol1 the value of field 'textCol1'.
\r
1722 public void setTextCol1(
\r
1723 final int textCol1) {
\r
1724 this._textCol1 = textCol1;
\r
1725 this._has_textCol1 = true;
\r
1729 * Sets the value of field 'textCol2'.
\r
1731 * @param textCol2 the value of field 'textCol2'.
\r
1733 public void setTextCol2(
\r
1734 final int textCol2) {
\r
1735 this._textCol2 = textCol2;
\r
1736 this._has_textCol2 = true;
\r
1740 * Sets the value of field 'textColThreshold'.
\r
1742 * @param textColThreshold the value of field 'textColThreshold'
\r
1744 public void setTextColThreshold(
\r
1745 final int textColThreshold) {
\r
1746 this._textColThreshold = textColThreshold;
\r
1747 this._has_textColThreshold = true;
\r
1751 * Sets the value of field 'title'.
\r
1753 * @param title the value of field 'title'.
\r
1755 public void setTitle(
\r
1756 final java.lang.String title) {
\r
1757 this._title = title;
\r
1761 * Sets the value of field 'viewName'.
\r
1763 * @param viewName the value of field 'viewName'.
\r
1765 public void setViewName(
\r
1766 final java.lang.String viewName) {
\r
1767 this._viewName = viewName;
\r
1771 * Sets the value of field 'width'.
\r
1773 * @param width the value of field 'width'.
\r
1775 public void setWidth(
\r
1776 final int width) {
\r
1777 this._width = width;
\r
1778 this._has_width = true;
\r
1782 * Sets the value of field 'wrapAlignment'.
\r
1784 * @param wrapAlignment the value of field 'wrapAlignment'.
\r
1786 public void setWrapAlignment(
\r
1787 final boolean wrapAlignment) {
\r
1788 this._wrapAlignment = wrapAlignment;
\r
1789 this._has_wrapAlignment = true;
\r
1793 * Sets the value of field 'xpos'.
\r
1795 * @param xpos the value of field 'xpos'.
\r
1797 public void setXpos(
\r
1799 this._xpos = xpos;
\r
1800 this._has_xpos = true;
\r
1804 * Sets the value of field 'ypos'.
\r
1806 * @param ypos the value of field 'ypos'.
\r
1808 public void setYpos(
\r
1810 this._ypos = ypos;
\r
1811 this._has_ypos = true;
\r
1815 * Method unmarshal.
\r
1818 * @throws org.exolab.castor.xml.MarshalException if object is
\r
1819 * null or if any SAXException is thrown during marshaling
\r
1820 * @throws org.exolab.castor.xml.ValidationException if this
\r
1821 * object is an invalid instance according to the schema
\r
1822 * @return the unmarshaled
\r
1823 * jalview.schemabinding.version2.Viewport
\r
1825 public static jalview.schemabinding.version2.Viewport unmarshal(
\r
1826 final java.io.Reader reader)
\r
1827 throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
\r
1828 return (jalview.schemabinding.version2.Viewport) Unmarshaller.unmarshal(jalview.schemabinding.version2.Viewport.class, reader);
\r
1834 * @throws org.exolab.castor.xml.ValidationException if this
\r
1835 * object is an invalid instance according to the schema
\r
1837 public void validate(
\r
1839 throws org.exolab.castor.xml.ValidationException {
\r
1840 org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
\r
1841 validator.validate(this);
\r