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
116 * visualization settings to vamsas
117 * document trees in jalview 2.4.1
120 private java.lang.String _id;
128 * keeps track of state for field: _width
130 private boolean _has_width;
138 * keeps track of state for field: _height
140 private boolean _has_height;
148 * keeps track of state for field: _xpos
150 private boolean _has_xpos;
158 * keeps track of state for field: _ypos
160 private boolean _has_ypos;
165 private java.lang.String _title;
170 private java.lang.String _newick;
188 public void deleteCurrentTree(
190 this._has_currentTree= false;
195 public void deleteFitToWindow(
197 this._has_fitToWindow= false;
202 public void deleteFontSize(
204 this._has_fontSize= false;
209 public void deleteFontStyle(
211 this._has_fontStyle= false;
216 public void deleteHeight(
218 this._has_height= false;
223 public void deleteMarkUnlinked(
225 this._has_markUnlinked= false;
230 public void deleteShowBootstrap(
232 this._has_showBootstrap= false;
237 public void deleteShowDistances(
239 this._has_showDistances= false;
244 public void deleteThreshold(
246 this._has_threshold= false;
251 public void deleteWidth(
253 this._has_width= false;
258 public void deleteXpos(
260 this._has_xpos= false;
265 public void deleteYpos(
267 this._has_ypos= false;
271 * Returns the value of field 'currentTree'.
273 * @return the value of field 'CurrentTree'.
275 public boolean getCurrentTree(
277 return this._currentTree;
281 * Returns the value of field 'fitToWindow'.
283 * @return the value of field 'FitToWindow'.
285 public boolean getFitToWindow(
287 return this._fitToWindow;
291 * Returns the value of field 'fontName'.
293 * @return the value of field 'FontName'.
295 public java.lang.String getFontName(
297 return this._fontName;
301 * Returns the value of field 'fontSize'.
303 * @return the value of field 'FontSize'.
305 public int getFontSize(
307 return this._fontSize;
311 * Returns the value of field 'fontStyle'.
313 * @return the value of field 'FontStyle'.
315 public int getFontStyle(
317 return this._fontStyle;
321 * Returns the value of field 'height'.
323 * @return the value of field 'Height'.
325 public int getHeight(
331 * Returns the value of field 'id'. The field 'id' has the
332 * following description: Tree ID added for binding tree
333 * visualization settings to vamsas
334 * document trees in jalview 2.4.1
337 * @return the value of field 'Id'.
339 public java.lang.String getId(
345 * Returns the value of field 'markUnlinked'.
347 * @return the value of field 'MarkUnlinked'.
349 public boolean getMarkUnlinked(
351 return this._markUnlinked;
355 * Returns the value of field 'newick'.
357 * @return the value of field 'Newick'.
359 public java.lang.String getNewick(
365 * Returns the value of field 'showBootstrap'.
367 * @return the value of field 'ShowBootstrap'.
369 public boolean getShowBootstrap(
371 return this._showBootstrap;
375 * Returns the value of field 'showDistances'.
377 * @return the value of field 'ShowDistances'.
379 public boolean getShowDistances(
381 return this._showDistances;
385 * Returns the value of field 'threshold'.
387 * @return the value of field 'Threshold'.
389 public float getThreshold(
391 return this._threshold;
395 * Returns the value of field 'title'.
397 * @return the value of field 'Title'.
399 public java.lang.String getTitle(
405 * Returns the value of field 'width'.
407 * @return the value of field 'Width'.
415 * Returns the value of field 'xpos'.
417 * @return the value of field 'Xpos'.
425 * Returns the value of field 'ypos'.
427 * @return the value of field 'Ypos'.
435 * Method hasCurrentTree.
437 * @return true if at least one CurrentTree has been added
439 public boolean hasCurrentTree(
441 return this._has_currentTree;
445 * Method hasFitToWindow.
447 * @return true if at least one FitToWindow has been added
449 public boolean hasFitToWindow(
451 return this._has_fitToWindow;
455 * Method hasFontSize.
457 * @return true if at least one FontSize has been added
459 public boolean hasFontSize(
461 return this._has_fontSize;
465 * Method hasFontStyle.
467 * @return true if at least one FontStyle has been added
469 public boolean hasFontStyle(
471 return this._has_fontStyle;
477 * @return true if at least one Height has been added
479 public boolean hasHeight(
481 return this._has_height;
485 * Method hasMarkUnlinked.
487 * @return true if at least one MarkUnlinked has been added
489 public boolean hasMarkUnlinked(
491 return this._has_markUnlinked;
495 * Method hasShowBootstrap.
497 * @return true if at least one ShowBootstrap has been added
499 public boolean hasShowBootstrap(
501 return this._has_showBootstrap;
505 * Method hasShowDistances.
507 * @return true if at least one ShowDistances has been added
509 public boolean hasShowDistances(
511 return this._has_showDistances;
515 * Method hasThreshold.
517 * @return true if at least one Threshold has been added
519 public boolean hasThreshold(
521 return this._has_threshold;
527 * @return true if at least one Width has been added
529 public boolean hasWidth(
531 return this._has_width;
537 * @return true if at least one Xpos has been added
539 public boolean hasXpos(
541 return this._has_xpos;
547 * @return true if at least one Ypos has been added
549 public boolean hasYpos(
551 return this._has_ypos;
555 * Returns the value of field 'currentTree'.
557 * @return the value of field 'CurrentTree'.
559 public boolean isCurrentTree(
561 return this._currentTree;
565 * Returns the value of field 'fitToWindow'.
567 * @return the value of field 'FitToWindow'.
569 public boolean isFitToWindow(
571 return this._fitToWindow;
575 * Returns the value of field 'markUnlinked'.
577 * @return the value of field 'MarkUnlinked'.
579 public boolean isMarkUnlinked(
581 return this._markUnlinked;
585 * Returns the value of field 'showBootstrap'.
587 * @return the value of field 'ShowBootstrap'.
589 public boolean isShowBootstrap(
591 return this._showBootstrap;
595 * Returns the value of field 'showDistances'.
597 * @return the value of field 'ShowDistances'.
599 public boolean isShowDistances(
601 return this._showDistances;
607 * @return true if this object is valid according to the schema
609 public boolean isValid(
613 } catch (org.exolab.castor.xml.ValidationException vex) {
623 * @throws org.exolab.castor.xml.MarshalException if object is
624 * null or if any SAXException is thrown during marshaling
625 * @throws org.exolab.castor.xml.ValidationException if this
626 * object is an invalid instance according to the schema
629 final java.io.Writer out)
630 throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
631 Marshaller.marshal(this, out);
638 * @throws java.io.IOException if an IOException occurs during
640 * @throws org.exolab.castor.xml.ValidationException if this
641 * object is an invalid instance according to the schema
642 * @throws org.exolab.castor.xml.MarshalException if object is
643 * null or if any SAXException is thrown during marshaling
646 final org.xml.sax.ContentHandler handler)
647 throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
648 Marshaller.marshal(this, handler);
652 * Sets the value of field 'currentTree'.
654 * @param currentTree the value of field 'currentTree'.
656 public void setCurrentTree(
657 final boolean currentTree) {
658 this._currentTree = currentTree;
659 this._has_currentTree = true;
663 * Sets the value of field 'fitToWindow'.
665 * @param fitToWindow the value of field 'fitToWindow'.
667 public void setFitToWindow(
668 final boolean fitToWindow) {
669 this._fitToWindow = fitToWindow;
670 this._has_fitToWindow = true;
674 * Sets the value of field 'fontName'.
676 * @param fontName the value of field 'fontName'.
678 public void setFontName(
679 final java.lang.String fontName) {
680 this._fontName = fontName;
684 * Sets the value of field 'fontSize'.
686 * @param fontSize the value of field 'fontSize'.
688 public void setFontSize(
689 final int fontSize) {
690 this._fontSize = fontSize;
691 this._has_fontSize = true;
695 * Sets the value of field 'fontStyle'.
697 * @param fontStyle the value of field 'fontStyle'.
699 public void setFontStyle(
700 final int fontStyle) {
701 this._fontStyle = fontStyle;
702 this._has_fontStyle = true;
706 * Sets the value of field 'height'.
708 * @param height the value of field 'height'.
710 public void setHeight(
712 this._height = height;
713 this._has_height = true;
717 * Sets the value of field 'id'. The field 'id' has the
718 * following description: Tree ID added for binding tree
719 * visualization settings to vamsas
720 * document trees in jalview 2.4.1
723 * @param id the value of field 'id'.
726 final java.lang.String id) {
731 * Sets the value of field 'markUnlinked'.
733 * @param markUnlinked the value of field 'markUnlinked'.
735 public void setMarkUnlinked(
736 final boolean markUnlinked) {
737 this._markUnlinked = markUnlinked;
738 this._has_markUnlinked = true;
742 * Sets the value of field 'newick'.
744 * @param newick the value of field 'newick'.
746 public void setNewick(
747 final java.lang.String newick) {
748 this._newick = newick;
752 * Sets the value of field 'showBootstrap'.
754 * @param showBootstrap the value of field 'showBootstrap'.
756 public void setShowBootstrap(
757 final boolean showBootstrap) {
758 this._showBootstrap = showBootstrap;
759 this._has_showBootstrap = true;
763 * Sets the value of field 'showDistances'.
765 * @param showDistances the value of field 'showDistances'.
767 public void setShowDistances(
768 final boolean showDistances) {
769 this._showDistances = showDistances;
770 this._has_showDistances = true;
774 * Sets the value of field 'threshold'.
776 * @param threshold the value of field 'threshold'.
778 public void setThreshold(
779 final float threshold) {
780 this._threshold = threshold;
781 this._has_threshold = true;
785 * Sets the value of field 'title'.
787 * @param title the value of field 'title'.
789 public void setTitle(
790 final java.lang.String title) {
795 * Sets the value of field 'width'.
797 * @param width the value of field 'width'.
799 public void setWidth(
802 this._has_width = true;
806 * Sets the value of field 'xpos'.
808 * @param xpos the value of field 'xpos'.
813 this._has_xpos = true;
817 * Sets the value of field 'ypos'.
819 * @param ypos the value of field 'ypos'.
824 this._has_ypos = true;
831 * @throws org.exolab.castor.xml.MarshalException if object is
832 * null or if any SAXException is thrown during marshaling
833 * @throws org.exolab.castor.xml.ValidationException if this
834 * object is an invalid instance according to the schema
835 * @return the unmarshaled jalview.schemabinding.version2.Tree
837 public static jalview.schemabinding.version2.Tree unmarshal(
838 final java.io.Reader reader)
839 throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
840 return (jalview.schemabinding.version2.Tree) Unmarshaller.unmarshal(jalview.schemabinding.version2.Tree.class, reader);
846 * @throws org.exolab.castor.xml.ValidationException if this
847 * object is an invalid instance according to the schema
849 public void validate(
851 throws org.exolab.castor.xml.ValidationException {
852 org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
853 validator.validate(this);