2 * This class was automatically generated with
3 * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
8 package jalview.schemabinding.version2;
10 //---------------------------------/
11 //- Imported classes and packages -/
12 //---------------------------------/
14 import org.exolab.castor.xml.Marshaller;
15 import org.exolab.castor.xml.Unmarshaller;
20 * @version $Revision$ $Date$
22 public class Tree implements java.io.Serializable {
25 //--------------------------/
26 //- Class/Member Variables -/
27 //--------------------------/
32 private java.lang.String _fontName;
37 private int _fontSize;
40 * keeps track of state for field: _fontSize
42 private boolean _has_fontSize;
47 private int _fontStyle;
50 * keeps track of state for field: _fontStyle
52 private boolean _has_fontStyle;
57 private float _threshold;
60 * keeps track of state for field: _threshold
62 private boolean _has_threshold;
65 * Field _showBootstrap.
67 private boolean _showBootstrap;
70 * keeps track of state for field: _showBootstrap
72 private boolean _has_showBootstrap;
75 * Field _showDistances.
77 private boolean _showDistances;
80 * keeps track of state for field: _showDistances
82 private boolean _has_showDistances;
85 * Field _markUnlinked.
87 private boolean _markUnlinked;
90 * keeps track of state for field: _markUnlinked
92 private boolean _has_markUnlinked;
97 private boolean _fitToWindow;
100 * keeps track of state for field: _fitToWindow
102 private boolean _has_fitToWindow;
105 * Field _currentTree.
107 private boolean _currentTree;
110 * keeps track of state for field: _currentTree
112 private boolean _has_currentTree;
115 * Tree ID added for binding tree
118 * document trees in jalview 2.4.1
121 private java.lang.String _id;
124 * Field _linkToAllViews.
126 private boolean _linkToAllViews = false;
129 * keeps track of state for field: _linkToAllViews
131 private boolean _has_linkToAllViews;
139 * keeps track of state for field: _width
141 private boolean _has_width;
149 * keeps track of state for field: _height
151 private boolean _has_height;
159 * keeps track of state for field: _xpos
161 private boolean _has_xpos;
169 * keeps track of state for field: _ypos
171 private boolean _has_ypos;
176 private java.lang.String _title;
181 private java.lang.String _newick;
199 public void deleteCurrentTree(
201 this._has_currentTree= false;
206 public void deleteFitToWindow(
208 this._has_fitToWindow= false;
213 public void deleteFontSize(
215 this._has_fontSize= false;
220 public void deleteFontStyle(
222 this._has_fontStyle= false;
227 public void deleteHeight(
229 this._has_height= false;
234 public void deleteLinkToAllViews(
236 this._has_linkToAllViews= false;
241 public void deleteMarkUnlinked(
243 this._has_markUnlinked= false;
248 public void deleteShowBootstrap(
250 this._has_showBootstrap= false;
255 public void deleteShowDistances(
257 this._has_showDistances= false;
262 public void deleteThreshold(
264 this._has_threshold= false;
269 public void deleteWidth(
271 this._has_width= false;
276 public void deleteXpos(
278 this._has_xpos= false;
283 public void deleteYpos(
285 this._has_ypos= false;
289 * Returns the value of field 'currentTree'.
291 * @return the value of field 'CurrentTree'.
293 public boolean getCurrentTree(
295 return this._currentTree;
299 * Returns the value of field 'fitToWindow'.
301 * @return the value of field 'FitToWindow'.
303 public boolean getFitToWindow(
305 return this._fitToWindow;
309 * Returns the value of field 'fontName'.
311 * @return the value of field 'FontName'.
313 public java.lang.String getFontName(
315 return this._fontName;
319 * Returns the value of field 'fontSize'.
321 * @return the value of field 'FontSize'.
323 public int getFontSize(
325 return this._fontSize;
329 * Returns the value of field 'fontStyle'.
331 * @return the value of field 'FontStyle'.
333 public int getFontStyle(
335 return this._fontStyle;
339 * Returns the value of field 'height'.
341 * @return the value of field 'Height'.
343 public int getHeight(
349 * Returns the value of field 'id'. The field 'id' has the
350 * following description: Tree ID added for binding tree
353 * document trees in jalview 2.4.1
356 * @return the value of field 'Id'.
358 public java.lang.String getId(
364 * Returns the value of field 'linkToAllViews'.
366 * @return the value of field 'LinkToAllViews'.
368 public boolean getLinkToAllViews(
370 return this._linkToAllViews;
374 * Returns the value of field 'markUnlinked'.
376 * @return the value of field 'MarkUnlinked'.
378 public boolean getMarkUnlinked(
380 return this._markUnlinked;
384 * Returns the value of field 'newick'.
386 * @return the value of field 'Newick'.
388 public java.lang.String getNewick(
394 * Returns the value of field 'showBootstrap'.
396 * @return the value of field 'ShowBootstrap'.
398 public boolean getShowBootstrap(
400 return this._showBootstrap;
404 * Returns the value of field 'showDistances'.
406 * @return the value of field 'ShowDistances'.
408 public boolean getShowDistances(
410 return this._showDistances;
414 * Returns the value of field 'threshold'.
416 * @return the value of field 'Threshold'.
418 public float getThreshold(
420 return this._threshold;
424 * Returns the value of field 'title'.
426 * @return the value of field 'Title'.
428 public java.lang.String getTitle(
434 * Returns the value of field 'width'.
436 * @return the value of field 'Width'.
444 * Returns the value of field 'xpos'.
446 * @return the value of field 'Xpos'.
454 * Returns the value of field 'ypos'.
456 * @return the value of field 'Ypos'.
464 * Method hasCurrentTree.
466 * @return true if at least one CurrentTree has been added
468 public boolean hasCurrentTree(
470 return this._has_currentTree;
474 * Method hasFitToWindow.
476 * @return true if at least one FitToWindow has been added
478 public boolean hasFitToWindow(
480 return this._has_fitToWindow;
484 * Method hasFontSize.
486 * @return true if at least one FontSize has been added
488 public boolean hasFontSize(
490 return this._has_fontSize;
494 * Method hasFontStyle.
496 * @return true if at least one FontStyle has been added
498 public boolean hasFontStyle(
500 return this._has_fontStyle;
506 * @return true if at least one Height has been added
508 public boolean hasHeight(
510 return this._has_height;
514 * Method hasLinkToAllViews.
516 * @return true if at least one LinkToAllViews has been added
518 public boolean hasLinkToAllViews(
520 return this._has_linkToAllViews;
524 * Method hasMarkUnlinked.
526 * @return true if at least one MarkUnlinked has been added
528 public boolean hasMarkUnlinked(
530 return this._has_markUnlinked;
534 * Method hasShowBootstrap.
536 * @return true if at least one ShowBootstrap has been added
538 public boolean hasShowBootstrap(
540 return this._has_showBootstrap;
544 * Method hasShowDistances.
546 * @return true if at least one ShowDistances has been added
548 public boolean hasShowDistances(
550 return this._has_showDistances;
554 * Method hasThreshold.
556 * @return true if at least one Threshold has been added
558 public boolean hasThreshold(
560 return this._has_threshold;
566 * @return true if at least one Width has been added
568 public boolean hasWidth(
570 return this._has_width;
576 * @return true if at least one Xpos has been added
578 public boolean hasXpos(
580 return this._has_xpos;
586 * @return true if at least one Ypos has been added
588 public boolean hasYpos(
590 return this._has_ypos;
594 * Returns the value of field 'currentTree'.
596 * @return the value of field 'CurrentTree'.
598 public boolean isCurrentTree(
600 return this._currentTree;
604 * Returns the value of field 'fitToWindow'.
606 * @return the value of field 'FitToWindow'.
608 public boolean isFitToWindow(
610 return this._fitToWindow;
614 * Returns the value of field 'linkToAllViews'.
616 * @return the value of field 'LinkToAllViews'.
618 public boolean isLinkToAllViews(
620 return this._linkToAllViews;
624 * Returns the value of field 'markUnlinked'.
626 * @return the value of field 'MarkUnlinked'.
628 public boolean isMarkUnlinked(
630 return this._markUnlinked;
634 * Returns the value of field 'showBootstrap'.
636 * @return the value of field 'ShowBootstrap'.
638 public boolean isShowBootstrap(
640 return this._showBootstrap;
644 * Returns the value of field 'showDistances'.
646 * @return the value of field 'ShowDistances'.
648 public boolean isShowDistances(
650 return this._showDistances;
656 * @return true if this object is valid according to the schema
658 public boolean isValid(
662 } catch (org.exolab.castor.xml.ValidationException vex) {
672 * @throws org.exolab.castor.xml.MarshalException if object is
673 * null or if any SAXException is thrown during marshaling
674 * @throws org.exolab.castor.xml.ValidationException if this
675 * object is an invalid instance according to the schema
678 final java.io.Writer out)
679 throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
680 Marshaller.marshal(this, out);
687 * @throws java.io.IOException if an IOException occurs during
689 * @throws org.exolab.castor.xml.ValidationException if this
690 * object is an invalid instance according to the schema
691 * @throws org.exolab.castor.xml.MarshalException if object is
692 * null or if any SAXException is thrown during marshaling
695 final org.xml.sax.ContentHandler handler)
696 throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
697 Marshaller.marshal(this, handler);
701 * Sets the value of field 'currentTree'.
703 * @param currentTree the value of field 'currentTree'.
705 public void setCurrentTree(
706 final boolean currentTree) {
707 this._currentTree = currentTree;
708 this._has_currentTree = true;
712 * Sets the value of field 'fitToWindow'.
714 * @param fitToWindow the value of field 'fitToWindow'.
716 public void setFitToWindow(
717 final boolean fitToWindow) {
718 this._fitToWindow = fitToWindow;
719 this._has_fitToWindow = true;
723 * Sets the value of field 'fontName'.
725 * @param fontName the value of field 'fontName'.
727 public void setFontName(
728 final java.lang.String fontName) {
729 this._fontName = fontName;
733 * Sets the value of field 'fontSize'.
735 * @param fontSize the value of field 'fontSize'.
737 public void setFontSize(
738 final int fontSize) {
739 this._fontSize = fontSize;
740 this._has_fontSize = true;
744 * Sets the value of field 'fontStyle'.
746 * @param fontStyle the value of field 'fontStyle'.
748 public void setFontStyle(
749 final int fontStyle) {
750 this._fontStyle = fontStyle;
751 this._has_fontStyle = true;
755 * Sets the value of field 'height'.
757 * @param height the value of field 'height'.
759 public void setHeight(
761 this._height = height;
762 this._has_height = true;
766 * Sets the value of field 'id'. The field 'id' has the
767 * following description: Tree ID added for binding tree
770 * document trees in jalview 2.4.1
773 * @param id the value of field 'id'.
776 final java.lang.String id) {
781 * Sets the value of field 'linkToAllViews'.
783 * @param linkToAllViews the value of field 'linkToAllViews'.
785 public void setLinkToAllViews(
786 final boolean linkToAllViews) {
787 this._linkToAllViews = linkToAllViews;
788 this._has_linkToAllViews = true;
792 * Sets the value of field 'markUnlinked'.
794 * @param markUnlinked the value of field 'markUnlinked'.
796 public void setMarkUnlinked(
797 final boolean markUnlinked) {
798 this._markUnlinked = markUnlinked;
799 this._has_markUnlinked = true;
803 * Sets the value of field 'newick'.
805 * @param newick the value of field 'newick'.
807 public void setNewick(
808 final java.lang.String newick) {
809 this._newick = newick;
813 * Sets the value of field 'showBootstrap'.
815 * @param showBootstrap the value of field 'showBootstrap'.
817 public void setShowBootstrap(
818 final boolean showBootstrap) {
819 this._showBootstrap = showBootstrap;
820 this._has_showBootstrap = true;
824 * Sets the value of field 'showDistances'.
826 * @param showDistances the value of field 'showDistances'.
828 public void setShowDistances(
829 final boolean showDistances) {
830 this._showDistances = showDistances;
831 this._has_showDistances = true;
835 * Sets the value of field 'threshold'.
837 * @param threshold the value of field 'threshold'.
839 public void setThreshold(
840 final float threshold) {
841 this._threshold = threshold;
842 this._has_threshold = true;
846 * Sets the value of field 'title'.
848 * @param title the value of field 'title'.
850 public void setTitle(
851 final java.lang.String title) {
856 * Sets the value of field 'width'.
858 * @param width the value of field 'width'.
860 public void setWidth(
863 this._has_width = true;
867 * Sets the value of field 'xpos'.
869 * @param xpos the value of field 'xpos'.
874 this._has_xpos = true;
878 * Sets the value of field 'ypos'.
880 * @param ypos the value of field 'ypos'.
885 this._has_ypos = true;
892 * @throws org.exolab.castor.xml.MarshalException if object is
893 * null or if any SAXException is thrown during marshaling
894 * @throws org.exolab.castor.xml.ValidationException if this
895 * object is an invalid instance according to the schema
896 * @return the unmarshaled jalview.schemabinding.version2.Tree
898 public static jalview.schemabinding.version2.Tree unmarshal(
899 final java.io.Reader reader)
900 throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
901 return (jalview.schemabinding.version2.Tree) Unmarshaller.unmarshal(jalview.schemabinding.version2.Tree.class, reader);
907 * @throws org.exolab.castor.xml.ValidationException if this
908 * object is an invalid instance according to the schema
910 public void validate(
912 throws org.exolab.castor.xml.ValidationException {
913 org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
914 validator.validate(this);