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 visualization settings to
116 * vamsas document trees in jalview 2.4.1
118 private java.lang.String _id;
126 * keeps track of state for field: _width
128 private boolean _has_width;
136 * keeps track of state for field: _height
138 private boolean _has_height;
146 * keeps track of state for field: _xpos
148 private boolean _has_xpos;
156 * keeps track of state for field: _ypos
158 private boolean _has_ypos;
163 private java.lang.String _title;
168 private java.lang.String _newick;
186 public void deleteCurrentTree(
188 this._has_currentTree= false;
193 public void deleteFitToWindow(
195 this._has_fitToWindow= false;
200 public void deleteFontSize(
202 this._has_fontSize= false;
207 public void deleteFontStyle(
209 this._has_fontStyle= false;
214 public void deleteHeight(
216 this._has_height= false;
221 public void deleteMarkUnlinked(
223 this._has_markUnlinked= false;
228 public void deleteShowBootstrap(
230 this._has_showBootstrap= false;
235 public void deleteShowDistances(
237 this._has_showDistances= false;
242 public void deleteThreshold(
244 this._has_threshold= false;
249 public void deleteWidth(
251 this._has_width= false;
256 public void deleteXpos(
258 this._has_xpos= false;
263 public void deleteYpos(
265 this._has_ypos= false;
269 * Returns the value of field 'currentTree'.
271 * @return the value of field 'CurrentTree'.
273 public boolean getCurrentTree(
275 return this._currentTree;
279 * Returns the value of field 'fitToWindow'.
281 * @return the value of field 'FitToWindow'.
283 public boolean getFitToWindow(
285 return this._fitToWindow;
289 * Returns the value of field 'fontName'.
291 * @return the value of field 'FontName'.
293 public java.lang.String getFontName(
295 return this._fontName;
299 * Returns the value of field 'fontSize'.
301 * @return the value of field 'FontSize'.
303 public int getFontSize(
305 return this._fontSize;
309 * Returns the value of field 'fontStyle'.
311 * @return the value of field 'FontStyle'.
313 public int getFontStyle(
315 return this._fontStyle;
319 * Returns the value of field 'height'.
321 * @return the value of field 'Height'.
323 public int getHeight(
329 * Returns the value of field 'id'. The field 'id' has the
330 * following description: Tree ID added for binding tree
331 * visualization settings to vamsas document trees in jalview
334 * @return the value of field 'Id'.
336 public java.lang.String getId(
342 * Returns the value of field 'markUnlinked'.
344 * @return the value of field 'MarkUnlinked'.
346 public boolean getMarkUnlinked(
348 return this._markUnlinked;
352 * Returns the value of field 'newick'.
354 * @return the value of field 'Newick'.
356 public java.lang.String getNewick(
362 * Returns the value of field 'showBootstrap'.
364 * @return the value of field 'ShowBootstrap'.
366 public boolean getShowBootstrap(
368 return this._showBootstrap;
372 * Returns the value of field 'showDistances'.
374 * @return the value of field 'ShowDistances'.
376 public boolean getShowDistances(
378 return this._showDistances;
382 * Returns the value of field 'threshold'.
384 * @return the value of field 'Threshold'.
386 public float getThreshold(
388 return this._threshold;
392 * Returns the value of field 'title'.
394 * @return the value of field 'Title'.
396 public java.lang.String getTitle(
402 * Returns the value of field 'width'.
404 * @return the value of field 'Width'.
412 * Returns the value of field 'xpos'.
414 * @return the value of field 'Xpos'.
422 * Returns the value of field 'ypos'.
424 * @return the value of field 'Ypos'.
432 * Method hasCurrentTree.
434 * @return true if at least one CurrentTree has been added
436 public boolean hasCurrentTree(
438 return this._has_currentTree;
442 * Method hasFitToWindow.
444 * @return true if at least one FitToWindow has been added
446 public boolean hasFitToWindow(
448 return this._has_fitToWindow;
452 * Method hasFontSize.
454 * @return true if at least one FontSize has been added
456 public boolean hasFontSize(
458 return this._has_fontSize;
462 * Method hasFontStyle.
464 * @return true if at least one FontStyle has been added
466 public boolean hasFontStyle(
468 return this._has_fontStyle;
474 * @return true if at least one Height has been added
476 public boolean hasHeight(
478 return this._has_height;
482 * Method hasMarkUnlinked.
484 * @return true if at least one MarkUnlinked has been added
486 public boolean hasMarkUnlinked(
488 return this._has_markUnlinked;
492 * Method hasShowBootstrap.
494 * @return true if at least one ShowBootstrap has been added
496 public boolean hasShowBootstrap(
498 return this._has_showBootstrap;
502 * Method hasShowDistances.
504 * @return true if at least one ShowDistances has been added
506 public boolean hasShowDistances(
508 return this._has_showDistances;
512 * Method hasThreshold.
514 * @return true if at least one Threshold has been added
516 public boolean hasThreshold(
518 return this._has_threshold;
524 * @return true if at least one Width has been added
526 public boolean hasWidth(
528 return this._has_width;
534 * @return true if at least one Xpos has been added
536 public boolean hasXpos(
538 return this._has_xpos;
544 * @return true if at least one Ypos has been added
546 public boolean hasYpos(
548 return this._has_ypos;
552 * Returns the value of field 'currentTree'.
554 * @return the value of field 'CurrentTree'.
556 public boolean isCurrentTree(
558 return this._currentTree;
562 * Returns the value of field 'fitToWindow'.
564 * @return the value of field 'FitToWindow'.
566 public boolean isFitToWindow(
568 return this._fitToWindow;
572 * Returns the value of field 'markUnlinked'.
574 * @return the value of field 'MarkUnlinked'.
576 public boolean isMarkUnlinked(
578 return this._markUnlinked;
582 * Returns the value of field 'showBootstrap'.
584 * @return the value of field 'ShowBootstrap'.
586 public boolean isShowBootstrap(
588 return this._showBootstrap;
592 * Returns the value of field 'showDistances'.
594 * @return the value of field 'ShowDistances'.
596 public boolean isShowDistances(
598 return this._showDistances;
604 * @return true if this object is valid according to the schema
606 public boolean isValid(
610 } catch (org.exolab.castor.xml.ValidationException vex) {
620 * @throws org.exolab.castor.xml.MarshalException if object is
621 * null or if any SAXException is thrown during marshaling
622 * @throws org.exolab.castor.xml.ValidationException if this
623 * object is an invalid instance according to the schema
626 final java.io.Writer out)
627 throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
628 Marshaller.marshal(this, out);
635 * @throws java.io.IOException if an IOException occurs during
637 * @throws org.exolab.castor.xml.ValidationException if this
638 * object is an invalid instance according to the schema
639 * @throws org.exolab.castor.xml.MarshalException if object is
640 * null or if any SAXException is thrown during marshaling
643 final org.xml.sax.ContentHandler handler)
644 throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
645 Marshaller.marshal(this, handler);
649 * Sets the value of field 'currentTree'.
651 * @param currentTree the value of field 'currentTree'.
653 public void setCurrentTree(
654 final boolean currentTree) {
655 this._currentTree = currentTree;
656 this._has_currentTree = true;
660 * Sets the value of field 'fitToWindow'.
662 * @param fitToWindow the value of field 'fitToWindow'.
664 public void setFitToWindow(
665 final boolean fitToWindow) {
666 this._fitToWindow = fitToWindow;
667 this._has_fitToWindow = true;
671 * Sets the value of field 'fontName'.
673 * @param fontName the value of field 'fontName'.
675 public void setFontName(
676 final java.lang.String fontName) {
677 this._fontName = fontName;
681 * Sets the value of field 'fontSize'.
683 * @param fontSize the value of field 'fontSize'.
685 public void setFontSize(
686 final int fontSize) {
687 this._fontSize = fontSize;
688 this._has_fontSize = true;
692 * Sets the value of field 'fontStyle'.
694 * @param fontStyle the value of field 'fontStyle'.
696 public void setFontStyle(
697 final int fontStyle) {
698 this._fontStyle = fontStyle;
699 this._has_fontStyle = true;
703 * Sets the value of field 'height'.
705 * @param height the value of field 'height'.
707 public void setHeight(
709 this._height = height;
710 this._has_height = true;
714 * Sets the value of field 'id'. The field 'id' has the
715 * following description: Tree ID added for binding tree
716 * visualization settings to vamsas document trees in jalview
719 * @param id the value of field 'id'.
722 final java.lang.String id) {
727 * Sets the value of field 'markUnlinked'.
729 * @param markUnlinked the value of field 'markUnlinked'.
731 public void setMarkUnlinked(
732 final boolean markUnlinked) {
733 this._markUnlinked = markUnlinked;
734 this._has_markUnlinked = true;
738 * Sets the value of field 'newick'.
740 * @param newick the value of field 'newick'.
742 public void setNewick(
743 final java.lang.String newick) {
744 this._newick = newick;
748 * Sets the value of field 'showBootstrap'.
750 * @param showBootstrap the value of field 'showBootstrap'.
752 public void setShowBootstrap(
753 final boolean showBootstrap) {
754 this._showBootstrap = showBootstrap;
755 this._has_showBootstrap = true;
759 * Sets the value of field 'showDistances'.
761 * @param showDistances the value of field 'showDistances'.
763 public void setShowDistances(
764 final boolean showDistances) {
765 this._showDistances = showDistances;
766 this._has_showDistances = true;
770 * Sets the value of field 'threshold'.
772 * @param threshold the value of field 'threshold'.
774 public void setThreshold(
775 final float threshold) {
776 this._threshold = threshold;
777 this._has_threshold = true;
781 * Sets the value of field 'title'.
783 * @param title the value of field 'title'.
785 public void setTitle(
786 final java.lang.String title) {
791 * Sets the value of field 'width'.
793 * @param width the value of field 'width'.
795 public void setWidth(
798 this._has_width = true;
802 * Sets the value of field 'xpos'.
804 * @param xpos the value of field 'xpos'.
809 this._has_xpos = true;
813 * Sets the value of field 'ypos'.
815 * @param ypos the value of field 'ypos'.
820 this._has_ypos = true;
827 * @throws org.exolab.castor.xml.MarshalException if object is
828 * null or if any SAXException is thrown during marshaling
829 * @throws org.exolab.castor.xml.ValidationException if this
830 * object is an invalid instance according to the schema
831 * @return the unmarshaled jalview.schemabinding.version2.Tree
833 public static jalview.schemabinding.version2.Tree unmarshal(
834 final java.io.Reader reader)
835 throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
836 return (jalview.schemabinding.version2.Tree) Unmarshaller.unmarshal(jalview.schemabinding.version2.Tree.class, reader);
842 * @throws org.exolab.castor.xml.ValidationException if this
843 * object is an invalid instance according to the schema
845 public void validate(
847 throws org.exolab.castor.xml.ValidationException {
848 org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
849 validator.validate(this);