Classes

Class	Line #	Total Statements	Complexity	Uncovered Elements	TOTAL Coverage	Actions
Tree	22	83	68	48	0.6868%	Show methods

Class Tree

Class Tree	Line # 22	Total Statements 83	Complexity 68	Uncovered Elements 48	TOTAL Coverage 0.6868%
Tree()   Tree()	175175	1.01	1.01	0.00	1.0 1.0100%
deleteCurrentTree() : void   deleteCurrentTree() : void	186186	1.01	1.01	1.01	0.0 0.00%
deleteFitToWindow() : void   deleteFitToWindow() : void	193193	1.01	1.01	1.01	0.0 0.00%
deleteFontSize() : void   deleteFontSize() : void	200200	1.01	1.01	1.01	0.0 0.00%
deleteFontStyle() : void   deleteFontStyle() : void	207207	1.01	1.01	1.01	0.0 0.00%
deleteHeight() : void   deleteHeight() : void	214214	1.01	1.01	1.01	0.0 0.00%
deleteMarkUnlinked() : void   deleteMarkUnlinked() : void	221221	1.01	1.01	1.01	0.0 0.00%
deleteShowBootstrap() : void   deleteShowBootstrap() : void	228228	1.01	1.01	1.01	0.0 0.00%
deleteShowDistances() : void   deleteShowDistances() : void	235235	1.01	1.01	1.01	0.0 0.00%
deleteThreshold() : void   deleteThreshold() : void	242242	1.01	1.01	1.01	0.0 0.00%
deleteWidth() : void   deleteWidth() : void	249249	1.01	1.01	1.01	0.0 0.00%
deleteXpos() : void   deleteXpos() : void	256256	1.01	1.01	1.01	0.0 0.00%
deleteYpos() : void   deleteYpos() : void	263263	1.01	1.01	1.01	0.0 0.00%
getCurrentTree() : boolean   getCurrentTree() : boolean	273273	1.01	1.01	0.00	1.0 1.0100%
getFitToWindow() : boolean   getFitToWindow() : boolean	283283	1.01	1.01	0.00	1.0 1.0100%
getFontName() : java.lang.String   getFontName() : java.lang.String	293293	1.01	1.01	0.00	1.0 1.0100%
getFontSize() : int   getFontSize() : int	303303	1.01	1.01	0.00	1.0 1.0100%
getFontStyle() : int   getFontStyle() : int	313313	1.01	1.01	0.00	1.0 1.0100%
getHeight() : int   getHeight() : int	323323	1.01	1.01	0.00	1.0 1.0100%
getId() : java.lang.String   getId() : java.lang.String	336336	1.01	1.01	0.00	1.0 1.0100%
getMarkUnlinked() : boolean   getMarkUnlinked() : boolean	346346	1.01	1.01	0.00	1.0 1.0100%
getNewick() : java.lang.String   getNewick() : java.lang.String	356356	1.01	1.01	0.00	1.0 1.0100%
getShowBootstrap() : boolean   getShowBootstrap() : boolean	366366	1.01	1.01	0.00	1.0 1.0100%
getShowDistances() : boolean   getShowDistances() : boolean	376376	1.01	1.01	0.00	1.0 1.0100%
getThreshold() : float   getThreshold() : float	386386	1.01	1.01	0.00	1.0 1.0100%
getTitle() : java.lang.String   getTitle() : java.lang.String	396396	1.01	1.01	0.00	1.0 1.0100%
getWidth() : int   getWidth() : int	406406	1.01	1.01	0.00	1.0 1.0100%
getXpos() : int   getXpos() : int	416416	1.01	1.01	0.00	1.0 1.0100%
getYpos() : int   getYpos() : int	426426	1.01	1.01	0.00	1.0 1.0100%
hasCurrentTree() : boolean   hasCurrentTree() : boolean	436436	1.01	1.01	0.00	1.0 1.0100%
hasFitToWindow() : boolean   hasFitToWindow() : boolean	446446	1.01	1.01	0.00	1.0 1.0100%
hasFontSize() : boolean   hasFontSize() : boolean	456456	1.01	1.01	0.00	1.0 1.0100%
hasFontStyle() : boolean   hasFontStyle() : boolean	466466	1.01	1.01	0.00	1.0 1.0100%
hasHeight() : boolean   hasHeight() : boolean	476476	1.01	1.01	0.00	1.0 1.0100%
hasMarkUnlinked() : boolean   hasMarkUnlinked() : boolean	486486	1.01	1.01	0.00	1.0 1.0100%
hasShowBootstrap() : boolean   hasShowBootstrap() : boolean	496496	1.01	1.01	0.00	1.0 1.0100%
hasShowDistances() : boolean   hasShowDistances() : boolean	506506	1.01	1.01	0.00	1.0 1.0100%
hasThreshold() : boolean   hasThreshold() : boolean	516516	1.01	1.01	0.00	1.0 1.0100%
hasWidth() : boolean   hasWidth() : boolean	526526	1.01	1.01	0.00	1.0 1.0100%
hasXpos() : boolean   hasXpos() : boolean	536536	1.01	1.01	0.00	1.0 1.0100%
hasYpos() : boolean   hasYpos() : boolean	546546	1.01	1.01	0.00	1.0 1.0100%
isCurrentTree() : boolean   isCurrentTree() : boolean	556556	1.01	1.01	1.01	0.0 0.00%
isFitToWindow() : boolean   isFitToWindow() : boolean	566566	1.01	1.01	1.01	0.0 0.00%
isMarkUnlinked() : boolean   isMarkUnlinked() : boolean	576576	1.01	1.01	1.01	0.0 0.00%
isShowBootstrap() : boolean   isShowBootstrap() : boolean	586586	1.01	1.01	1.01	0.0 0.00%
isShowDistances() : boolean   isShowDistances() : boolean	596596	1.01	1.01	1.01	0.0 0.00%
isValid() : boolean   isValid() : boolean	606606	4.04	2.02	4.04	0.0 0.00%
marshal(java.io.Writer) : void   marshal(java.io.Writer) : void	628628	1.01	1.01	1.01	0.0 0.00%
marshal(org.xml.sax.ContentHandler) : void   marshal(org.xml.sax.ContentHandler) : void	647647	1.01	1.01	1.01	0.0 0.00%
setCurrentTree(boolean) : void   setCurrentTree(boolean) : void	661661	2.02	1.01	0.00	1.0 1.0100%
setFitToWindow(boolean) : void   setFitToWindow(boolean) : void	673673	2.02	1.01	0.00	1.0 1.0100%
setFontName(java.lang.String) : void   setFontName(java.lang.String) : void	685685	1.01	1.01	0.00	1.0 1.0100%
setFontSize(int) : void   setFontSize(int) : void	696696	2.02	1.01	0.00	1.0 1.0100%
setFontStyle(int) : void   setFontStyle(int) : void	708708	2.02	1.01	0.00	1.0 1.0100%
setHeight(int) : void   setHeight(int) : void	720720	2.02	1.01	0.00	1.0 1.0100%
setId(java.lang.String) : void   setId(java.lang.String) : void	735735	1.01	1.01	0.00	1.0 1.0100%
setMarkUnlinked(boolean) : void   setMarkUnlinked(boolean) : void	746746	2.02	1.01	0.00	1.0 1.0100%
setNewick(java.lang.String) : void   setNewick(java.lang.String) : void	758758	1.01	1.01	0.00	1.0 1.0100%
setShowBootstrap(boolean) : void   setShowBootstrap(boolean) : void	769769	2.02	1.01	0.00	1.0 1.0100%
setShowDistances(boolean) : void   setShowDistances(boolean) : void	781781	2.02	1.01	0.00	1.0 1.0100%
setThreshold(float) : void   setThreshold(float) : void	793793	2.02	1.01	0.00	1.0 1.0100%
setTitle(java.lang.String) : void   setTitle(java.lang.String) : void	805805	1.01	1.01	0.00	1.0 1.0100%
setWidth(int) : void   setWidth(int) : void	816816	2.02	1.01	0.00	1.0 1.0100%
setXpos(int) : void   setXpos(int) : void	828828	2.02	1.01	0.00	1.0 1.0100%
setYpos(int) : void   setYpos(int) : void	840840	2.02	1.01	0.00	1.0 1.0100%
unmarshal(java.io.Reader) : jalview.schemabinding.version2.Tree   unmarshal(java.io.Reader) : jalview.schemabinding.version2.Tree	857857	1.01	1.01	1.01	0.0 0.00%
validate() : void   validate() : void	872872	2.02	1.01	2.02	0.0 0.00%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.68	jalview.io.Jalview2xmlTests.testStoreAndRecoverExpandedviewsjalview.io.Jalview2xmlTests.testStoreAndRecoverExpandedviews	1PASS
	0.68	jalview.io.Jalview2xmlTests.testStoreAndRecoverReferenceSeqSettingsjalview.io.Jalview2xmlTests.testStoreAndRecoverReferenceSeqSettings	1PASS
	0.50666666	jalview.io.Jalview2xmlTests.gatherViewsHerejalview.io.Jalview2xmlTests.gatherViewsHere	1PASS
	0.50666666	jalview.io.Jalview2xmlTests.viewRefPdbAnnotationjalview.io.Jalview2xmlTests.viewRefPdbAnnotation	1PASS
	0.50666666	jalview.io.Jalview2xmlTests.testCopyViewSettingsjalview.io.Jalview2xmlTests.testCopyViewSettings	1PASS
	0.50666666	jalview.io.Jalview2xmlTests.noDuplicatePdbMappingsMadejalview.io.Jalview2xmlTests.noDuplicatePdbMappingsMade	1PASS

 

Source view

1		/*
2		* This class was automatically generated with
3		* <a href="http://www.castor.org">Castor 1.1</a>, using an XML
4		* Schema.
5		* $Id$
6		*/
7
8		package jalview.schemabinding.version2;
9
10		//---------------------------------/
11		//- Imported classes and packages -/
12		//---------------------------------/
13
14		import org.exolab.castor.xml.Marshaller;
15		import org.exolab.castor.xml.Unmarshaller;
16
17		/**
18		* Class Tree.
19		*
20		* @version $Revision$ $Date$
21		*/
		68% Uncovered Elements: 48 (150) Complexity: 68 Complexity Density: 0.82
22		public class Tree implements java.io.Serializable
23		{
24
25		// --------------------------/
26		// - Class/Member Variables -/
27		// --------------------------/
28
29		/**
30		* Field _fontName.
31		*/
32		private java.lang.String _fontName;
33
34		/**
35		* Field _fontSize.
36		*/
37		private int _fontSize;
38
39		/**
40		* keeps track of state for field: _fontSize
41		*/
42		private boolean _has_fontSize;
43
44		/**
45		* Field _fontStyle.
46		*/
47		private int _fontStyle;
48
49		/**
50		* keeps track of state for field: _fontStyle
51		*/
52		private boolean _has_fontStyle;
53
54		/**
55		* Field _threshold.
56		*/
57		private float _threshold;
58
59		/**
60		* keeps track of state for field: _threshold
61		*/
62		private boolean _has_threshold;
63
64		/**
65		* Field _showBootstrap.
66		*/
67		private boolean _showBootstrap;
68
69		/**
70		* keeps track of state for field: _showBootstrap
71		*/
72		private boolean _has_showBootstrap;
73
74		/**
75		* Field _showDistances.
76		*/
77		private boolean _showDistances;
78
79		/**
80		* keeps track of state for field: _showDistances
81		*/
82		private boolean _has_showDistances;
83
84		/**
85		* Field _markUnlinked.
86		*/
87		private boolean _markUnlinked;
88
89		/**
90		* keeps track of state for field: _markUnlinked
91		*/
92		private boolean _has_markUnlinked;
93
94		/**
95		* Field _fitToWindow.
96		*/
97		private boolean _fitToWindow;
98
99		/**
100		* keeps track of state for field: _fitToWindow
101		*/
102		private boolean _has_fitToWindow;
103
104		/**
105		* Field _currentTree.
106		*/
107		private boolean _currentTree;
108
109		/**
110		* keeps track of state for field: _currentTree
111		*/
112		private boolean _has_currentTree;
113
114		/**
115		* Tree ID added for binding tree visualization settings to vamsas document
116		* trees in jalview 2.4.1
117		*
118		*/
119		private java.lang.String _id;
120
121		/**
122		* Field _width.
123		*/
124		private int _width;
125
126		/**
127		* keeps track of state for field: _width
128		*/
129		private boolean _has_width;
130
131		/**
132		* Field _height.
133		*/
134		private int _height;
135
136		/**
137		* keeps track of state for field: _height
138		*/
139		private boolean _has_height;
140
141		/**
142		* Field _xpos.
143		*/
144		private int _xpos;
145
146		/**
147		* keeps track of state for field: _xpos
148		*/
149		private boolean _has_xpos;
150
151		/**
152		* Field _ypos.
153		*/
154		private int _ypos;
155
156		/**
157		* keeps track of state for field: _ypos
158		*/
159		private boolean _has_ypos;
160
161		/**
162		* Field _title.
163		*/
164		private java.lang.String _title;
165
166		/**
167		* Field _newick.
168		*/
169		private java.lang.String _newick;
170
171		// ----------------/
172		// - Constructors -/
173		// ----------------/
174
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
175	14	public Tree()...
176		{
177	14	super();
178		}
179
180		// -----------/
181		// - Methods -/
182		// -----------/
183
184		/**
185		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
186	0	public void deleteCurrentTree()...
187		{
188	0	this._has_currentTree = false;
189		}
190
191		/**
192		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
193	0	public void deleteFitToWindow()...
194		{
195	0	this._has_fitToWindow = false;
196		}
197
198		/**
199		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
200	0	public void deleteFontSize()...
201		{
202	0	this._has_fontSize = false;
203		}
204
205		/**
206		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
207	0	public void deleteFontStyle()...
208		{
209	0	this._has_fontStyle = false;
210		}
211
212		/**
213		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
214	0	public void deleteHeight()...
215		{
216	0	this._has_height = false;
217		}
218
219		/**
220		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
221	0	public void deleteMarkUnlinked()...
222		{
223	0	this._has_markUnlinked = false;
224		}
225
226		/**
227		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
228	0	public void deleteShowBootstrap()...
229		{
230	0	this._has_showBootstrap = false;
231		}
232
233		/**
234		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
235	0	public void deleteShowDistances()...
236		{
237	0	this._has_showDistances = false;
238		}
239
240		/**
241		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
242	0	public void deleteThreshold()...
243		{
244	0	this._has_threshold = false;
245		}
246
247		/**
248		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
249	0	public void deleteWidth()...
250		{
251	0	this._has_width = false;
252		}
253
254		/**
255		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
256	0	public void deleteXpos()...
257		{
258	0	this._has_xpos = false;
259		}
260
261		/**
262		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
263	0	public void deleteYpos()...
264		{
265	0	this._has_ypos = false;
266		}
267
268		/**
269		* Returns the value of field 'currentTree'.
270		*
271		* @return the value of field 'CurrentTree'.
272		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
273	16	public boolean getCurrentTree()...
274		{
275	16	return this._currentTree;
276		}
277
278		/**
279		* Returns the value of field 'fitToWindow'.
280		*
281		* @return the value of field 'FitToWindow'.
282		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
283	16	public boolean getFitToWindow()...
284		{
285	16	return this._fitToWindow;
286		}
287
288		/**
289		* Returns the value of field 'fontName'.
290		*
291		* @return the value of field 'FontName'.
292		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
293	28	public java.lang.String getFontName()...
294		{
295	28	return this._fontName;
296		}
297
298		/**
299		* Returns the value of field 'fontSize'.
300		*
301		* @return the value of field 'FontSize'.
302		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
303	16	public int getFontSize()...
304		{
305	16	return this._fontSize;
306		}
307
308		/**
309		* Returns the value of field 'fontStyle'.
310		*
311		* @return the value of field 'FontStyle'.
312		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
313	16	public int getFontStyle()...
314		{
315	16	return this._fontStyle;
316		}
317
318		/**
319		* Returns the value of field 'height'.
320		*
321		* @return the value of field 'Height'.
322		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
323	16	public int getHeight()...
324		{
325	16	return this._height;
326		}
327
328		/**
329		* Returns the value of field 'id'. The field 'id' has the following
330		* description: Tree ID added for binding tree visualization settings to
331		* vamsas document trees in jalview 2.4.1
332		*
333		*
334		* @return the value of field 'Id'.
335		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
336	28	public java.lang.String getId()...
337		{
338	28	return this._id;
339		}
340
341		/**
342		* Returns the value of field 'markUnlinked'.
343		*
344		* @return the value of field 'MarkUnlinked'.
345		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
346	16	public boolean getMarkUnlinked()...
347		{
348	16	return this._markUnlinked;
349		}
350
351		/**
352		* Returns the value of field 'newick'.
353		*
354		* @return the value of field 'Newick'.
355		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
356	16	public java.lang.String getNewick()...
357		{
358	16	return this._newick;
359		}
360
361		/**
362		* Returns the value of field 'showBootstrap'.
363		*
364		* @return the value of field 'ShowBootstrap'.
365		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
366	16	public boolean getShowBootstrap()...
367		{
368	16	return this._showBootstrap;
369		}
370
371		/**
372		* Returns the value of field 'showDistances'.
373		*
374		* @return the value of field 'ShowDistances'.
375		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
376	16	public boolean getShowDistances()...
377		{
378	16	return this._showDistances;
379		}
380
381		/**
382		* Returns the value of field 'threshold'.
383		*
384		* @return the value of field 'Threshold'.
385		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
386	16	public float getThreshold()...
387		{
388	16	return this._threshold;
389		}
390
391		/**
392		* Returns the value of field 'title'.
393		*
394		* @return the value of field 'Title'.
395		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
396	16	public java.lang.String getTitle()...
397		{
398	16	return this._title;
399		}
400
401		/**
402		* Returns the value of field 'width'.
403		*
404		* @return the value of field 'Width'.
405		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
406	16	public int getWidth()...
407		{
408	16	return this._width;
409		}
410
411		/**
412		* Returns the value of field 'xpos'.
413		*
414		* @return the value of field 'Xpos'.
415		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
416	16	public int getXpos()...
417		{
418	16	return this._xpos;
419		}
420
421		/**
422		* Returns the value of field 'ypos'.
423		*
424		* @return the value of field 'Ypos'.
425		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
426	16	public int getYpos()...
427		{
428	16	return this._ypos;
429		}
430
431		/**
432		* Method hasCurrentTree.
433		*
434		* @return true if at least one CurrentTree has been added
435		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
436	4	public boolean hasCurrentTree()...
437		{
438	4	return this._has_currentTree;
439		}
440
441		/**
442		* Method hasFitToWindow.
443		*
444		* @return true if at least one FitToWindow has been added
445		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
446	4	public boolean hasFitToWindow()...
447		{
448	4	return this._has_fitToWindow;
449		}
450
451		/**
452		* Method hasFontSize.
453		*
454		* @return true if at least one FontSize has been added
455		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
456	4	public boolean hasFontSize()...
457		{
458	4	return this._has_fontSize;
459		}
460
461		/**
462		* Method hasFontStyle.
463		*
464		* @return true if at least one FontStyle has been added
465		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
466	4	public boolean hasFontStyle()...
467		{
468	4	return this._has_fontStyle;
469		}
470
471		/**
472		* Method hasHeight.
473		*
474		* @return true if at least one Height has been added
475		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
476	4	public boolean hasHeight()...
477		{
478	4	return this._has_height;
479		}
480
481		/**
482		* Method hasMarkUnlinked.
483		*
484		* @return true if at least one MarkUnlinked has been added
485		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
486	4	public boolean hasMarkUnlinked()...
487		{
488	4	return this._has_markUnlinked;
489		}
490
491		/**
492		* Method hasShowBootstrap.
493		*
494		* @return true if at least one ShowBootstrap has been added
495		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
496	4	public boolean hasShowBootstrap()...
497		{
498	4	return this._has_showBootstrap;
499		}
500
501		/**
502		* Method hasShowDistances.
503		*
504		* @return true if at least one ShowDistances has been added
505		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
506	4	public boolean hasShowDistances()...
507		{
508	4	return this._has_showDistances;
509		}
510
511		/**
512		* Method hasThreshold.
513		*
514		* @return true if at least one Threshold has been added
515		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
516	4	public boolean hasThreshold()...
517		{
518	4	return this._has_threshold;
519		}
520
521		/**
522		* Method hasWidth.
523		*
524		* @return true if at least one Width has been added
525		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
526	4	public boolean hasWidth()...
527		{
528	4	return this._has_width;
529		}
530
531		/**
532		* Method hasXpos.
533		*
534		* @return true if at least one Xpos has been added
535		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
536	4	public boolean hasXpos()...
537		{
538	4	return this._has_xpos;
539		}
540
541		/**
542		* Method hasYpos.
543		*
544		* @return true if at least one Ypos has been added
545		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
546	4	public boolean hasYpos()...
547		{
548	4	return this._has_ypos;
549		}
550
551		/**
552		* Returns the value of field 'currentTree'.
553		*
554		* @return the value of field 'CurrentTree'.
555		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
556	0	public boolean isCurrentTree()...
557		{
558	0	return this._currentTree;
559		}
560
561		/**
562		* Returns the value of field 'fitToWindow'.
563		*
564		* @return the value of field 'FitToWindow'.
565		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
566	0	public boolean isFitToWindow()...
567		{
568	0	return this._fitToWindow;
569		}
570
571		/**
572		* Returns the value of field 'markUnlinked'.
573		*
574		* @return the value of field 'MarkUnlinked'.
575		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
576	0	public boolean isMarkUnlinked()...
577		{
578	0	return this._markUnlinked;
579		}
580
581		/**
582		* Returns the value of field 'showBootstrap'.
583		*
584		* @return the value of field 'ShowBootstrap'.
585		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
586	0	public boolean isShowBootstrap()...
587		{
588	0	return this._showBootstrap;
589		}
590
591		/**
592		* Returns the value of field 'showDistances'.
593		*
594		* @return the value of field 'ShowDistances'.
595		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
596	0	public boolean isShowDistances()...
597		{
598	0	return this._showDistances;
599		}
600
601		/**
602		* Method isValid.
603		*
604		* @return true if this object is valid according to the schema
605		*/
		0% Uncovered Elements: 4 (4) Complexity: 2 Complexity Density: 0.5
606	0	public boolean isValid()...
607		{
608	0	try
609		{
610	0	validate();
611		} catch (org.exolab.castor.xml.ValidationException vex)
612		{
613	0	return false;
614		}
615	0	return true;
616		}
617
618		/**
619		*
620		*
621		* @param out
622		* @throws org.exolab.castor.xml.MarshalException
623		* if object is null or if any SAXException is thrown during
624		* marshaling
625		* @throws org.exolab.castor.xml.ValidationException
626		* if this object is an invalid instance according to the schema
627		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
628	0	public void marshal(final java.io.Writer out)...
629		throws org.exolab.castor.xml.MarshalException,
630		org.exolab.castor.xml.ValidationException
631		{
632	0	Marshaller.marshal(this, out);
633		}
634
635		/**
636		*
637		*
638		* @param handler
639		* @throws java.io.IOException
640		* if an IOException occurs during marshaling
641		* @throws org.exolab.castor.xml.ValidationException
642		* if this object is an invalid instance according to the schema
643		* @throws org.exolab.castor.xml.MarshalException
644		* if object is null or if any SAXException is thrown during
645		* marshaling
646		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
647	0	public void marshal(final org.xml.sax.ContentHandler handler)...
648		throws java.io.IOException,
649		org.exolab.castor.xml.MarshalException,
650		org.exolab.castor.xml.ValidationException
651		{
652	0	Marshaller.marshal(this, handler);
653		}
654
655		/**
656		* Sets the value of field 'currentTree'.
657		*
658		* @param currentTree
659		* the value of field 'currentTree'.
660		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
661	14	public void setCurrentTree(final boolean currentTree)...
662		{
663	14	this._currentTree = currentTree;
664	14	this._has_currentTree = true;
665		}
666
667		/**
668		* Sets the value of field 'fitToWindow'.
669		*
670		* @param fitToWindow
671		* the value of field 'fitToWindow'.
672		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
673	14	public void setFitToWindow(final boolean fitToWindow)...
674		{
675	14	this._fitToWindow = fitToWindow;
676	14	this._has_fitToWindow = true;
677		}
678
679		/**
680		* Sets the value of field 'fontName'.
681		*
682		* @param fontName
683		* the value of field 'fontName'.
684		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
685	14	public void setFontName(final java.lang.String fontName)...
686		{
687	14	this._fontName = fontName;
688		}
689
690		/**
691		* Sets the value of field 'fontSize'.
692		*
693		* @param fontSize
694		* the value of field 'fontSize'.
695		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
696	14	public void setFontSize(final int fontSize)...
697		{
698	14	this._fontSize = fontSize;
699	14	this._has_fontSize = true;
700		}
701
702		/**
703		* Sets the value of field 'fontStyle'.
704		*
705		* @param fontStyle
706		* the value of field 'fontStyle'.
707		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
708	14	public void setFontStyle(final int fontStyle)...
709		{
710	14	this._fontStyle = fontStyle;
711	14	this._has_fontStyle = true;
712		}
713
714		/**
715		* Sets the value of field 'height'.
716		*
717		* @param height
718		* the value of field 'height'.
719		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
720	14	public void setHeight(final int height)...
721		{
722	14	this._height = height;
723	14	this._has_height = true;
724		}
725
726		/**
727		* Sets the value of field 'id'. The field 'id' has the following description:
728		* Tree ID added for binding tree visualization settings to vamsas document
729		* trees in jalview 2.4.1
730		*
731		*
732		* @param id
733		* the value of field 'id'.
734		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
735	2	public void setId(final java.lang.String id)...
736		{
737	2	this._id = id;
738		}
739
740		/**
741		* Sets the value of field 'markUnlinked'.
742		*
743		* @param markUnlinked
744		* the value of field 'markUnlinked'.
745		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
746	14	public void setMarkUnlinked(final boolean markUnlinked)...
747		{
748	14	this._markUnlinked = markUnlinked;
749	14	this._has_markUnlinked = true;
750		}
751
752		/**
753		* Sets the value of field 'newick'.
754		*
755		* @param newick
756		* the value of field 'newick'.
757		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
758	14	public void setNewick(final java.lang.String newick)...
759		{
760	14	this._newick = newick;
761		}
762
763		/**
764		* Sets the value of field 'showBootstrap'.
765		*
766		* @param showBootstrap
767		* the value of field 'showBootstrap'.
768		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
769	14	public void setShowBootstrap(final boolean showBootstrap)...
770		{
771	14	this._showBootstrap = showBootstrap;
772	14	this._has_showBootstrap = true;
773		}
774
775		/**
776		* Sets the value of field 'showDistances'.
777		*
778		* @param showDistances
779		* the value of field 'showDistances'.
780		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
781	14	public void setShowDistances(final boolean showDistances)...
782		{
783	14	this._showDistances = showDistances;
784	14	this._has_showDistances = true;
785		}
786
787		/**
788		* Sets the value of field 'threshold'.
789		*
790		* @param threshold
791		* the value of field 'threshold'.
792		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
793	14	public void setThreshold(final float threshold)...
794		{
795	14	this._threshold = threshold;
796	14	this._has_threshold = true;
797		}
798
799		/**
800		* Sets the value of field 'title'.
801		*
802		* @param title
803		* the value of field 'title'.
804		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
805	14	public void setTitle(final java.lang.String title)...
806		{
807	14	this._title = title;
808		}
809
810		/**
811		* Sets the value of field 'width'.
812		*
813		* @param width
814		* the value of field 'width'.
815		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
816	14	public void setWidth(final int width)...
817		{
818	14	this._width = width;
819	14	this._has_width = true;
820		}
821
822		/**
823		* Sets the value of field 'xpos'.
824		*
825		* @param xpos
826		* the value of field 'xpos'.
827		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
828	14	public void setXpos(final int xpos)...
829		{
830	14	this._xpos = xpos;
831	14	this._has_xpos = true;
832		}
833
834		/**
835		* Sets the value of field 'ypos'.
836		*
837		* @param ypos
838		* the value of field 'ypos'.
839		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
840	14	public void setYpos(final int ypos)...
841		{
842	14	this._ypos = ypos;
843	14	this._has_ypos = true;
844		}
845
846		/**
847		* Method unmarshal.
848		*
849		* @param reader
850		* @throws org.exolab.castor.xml.MarshalException
851		* if object is null or if any SAXException is thrown during
852		* marshaling
853		* @throws org.exolab.castor.xml.ValidationException
854		* if this object is an invalid instance according to the schema
855		* @return the unmarshaled jalview.schemabinding.version2.Tree
856		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
857	0	public static jalview.schemabinding.version2.Tree unmarshal(...
858		final java.io.Reader reader)
859		throws org.exolab.castor.xml.MarshalException,
860		org.exolab.castor.xml.ValidationException
861		{
862	0	return (jalview.schemabinding.version2.Tree) Unmarshaller.unmarshal(
863		jalview.schemabinding.version2.Tree.class, reader);
864		}
865
866		/**
867		*
868		*
869		* @throws org.exolab.castor.xml.ValidationException
870		* if this object is an invalid instance according to the schema
871		*/
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
872	0	public void validate() throws org.exolab.castor.xml.ValidationException...
873		{
874	0	org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
875	0	validator.validate(this);
876		}
877
878		}