Classes

Class	Line #	Total Statements	Complexity	Uncovered Elements	TOTAL Coverage	Actions
StructureState	22	61	49	38	0.651376165.1%	Show methods

Class StructureState

Class StructureState	Line # 22	Total Statements 61	Complexity 49	Uncovered Elements 38	TOTAL Coverage 0.651376165.1%
StructureState()   StructureState()	141141	2.02	1.01	0.00	1.0 1.0100%
deleteAlignwithAlignPanel() : void   deleteAlignwithAlignPanel() : void	153153	1.01	1.01	1.01	0.0 0.00%
deleteColourByJmol() : void   deleteColourByJmol() : void	160160	1.01	1.01	1.01	0.0 0.00%
deleteColourwithAlignPanel() : void   deleteColourwithAlignPanel() : void	167167	1.01	1.01	1.01	0.0 0.00%
deleteHeight() : void   deleteHeight() : void	174174	1.01	1.01	1.01	0.0 0.00%
deleteVisible() : void   deleteVisible() : void	181181	1.01	1.01	1.01	0.0 0.00%
deleteWidth() : void   deleteWidth() : void	188188	1.01	1.01	1.01	0.0 0.00%
deleteXpos() : void   deleteXpos() : void	195195	1.01	1.01	1.01	0.0 0.00%
deleteYpos() : void   deleteYpos() : void	202202	1.01	1.01	1.01	0.0 0.00%
getAlignwithAlignPanel() : boolean   getAlignwithAlignPanel() : boolean	216216	1.01	1.01	0.00	1.0 1.0100%
getColourByJmol() : boolean   getColourByJmol() : boolean	229229	1.01	1.01	0.00	1.0 1.0100%
getColourwithAlignPanel() : boolean   getColourwithAlignPanel() : boolean	243243	1.01	1.01	0.00	1.0 1.0100%
getContent() : java.lang.String   getContent() : java.lang.String	254254	1.01	1.01	0.00	1.0 1.0100%
getHeight() : int   getHeight() : int	264264	1.01	1.01	0.00	1.0 1.0100%
getType() : java.lang.String   getType() : java.lang.String	277277	1.01	1.01	0.00	1.0 1.0100%
getViewId() : java.lang.String   getViewId() : java.lang.String	293293	1.01	1.01	0.00	1.0 1.0100%
getVisible() : boolean   getVisible() : boolean	303303	1.01	1.01	0.00	1.0 1.0100%
getWidth() : int   getWidth() : int	313313	1.01	1.01	0.00	1.0 1.0100%
getXpos() : int   getXpos() : int	323323	1.01	1.01	0.00	1.0 1.0100%
getYpos() : int   getYpos() : int	333333	1.01	1.01	0.00	1.0 1.0100%
hasAlignwithAlignPanel() : boolean   hasAlignwithAlignPanel() : boolean	343343	1.01	1.01	0.00	1.0 1.0100%
hasColourByJmol() : boolean   hasColourByJmol() : boolean	353353	1.01	1.01	0.00	1.0 1.0100%
hasColourwithAlignPanel() : boolean   hasColourwithAlignPanel() : boolean	363363	1.01	1.01	0.00	1.0 1.0100%
hasHeight() : boolean   hasHeight() : boolean	373373	1.01	1.01	0.00	1.0 1.0100%
hasVisible() : boolean   hasVisible() : boolean	383383	1.01	1.01	0.00	1.0 1.0100%
hasWidth() : boolean   hasWidth() : boolean	393393	1.01	1.01	0.00	1.0 1.0100%
hasXpos() : boolean   hasXpos() : boolean	403403	1.01	1.01	0.00	1.0 1.0100%
hasYpos() : boolean   hasYpos() : boolean	413413	1.01	1.01	0.00	1.0 1.0100%
isAlignwithAlignPanel() : boolean   isAlignwithAlignPanel() : boolean	427427	1.01	1.01	1.01	0.0 0.00%
isColourByJmol() : boolean   isColourByJmol() : boolean	440440	1.01	1.01	1.01	0.0 0.00%
isColourwithAlignPanel() : boolean   isColourwithAlignPanel() : boolean	454454	1.01	1.01	1.01	0.0 0.00%
isValid() : boolean   isValid() : boolean	464464	4.04	2.02	4.04	0.0 0.00%
isVisible() : boolean   isVisible() : boolean	481481	1.01	1.01	1.01	0.0 0.00%
marshal(java.io.Writer) : void   marshal(java.io.Writer) : void	496496	1.01	1.01	1.01	0.0 0.00%
marshal(org.xml.sax.ContentHandler) : void   marshal(org.xml.sax.ContentHandler) : void	515515	1.01	1.01	1.01	0.0 0.00%
setAlignwithAlignPanel(boolean) : void   setAlignwithAlignPanel(boolean) : void	533533	2.02	1.01	0.00	1.0 1.0100%
setColourByJmol(boolean) : void   setColourByJmol(boolean) : void	548548	2.02	1.01	0.00	1.0 1.0100%
setColourwithAlignPanel(boolean) : void   setColourwithAlignPanel(boolean) : void	564564	2.02	1.01	0.00	1.0 1.0100%
setContent(java.lang.String) : void   setContent(java.lang.String) : void	577577	1.01	1.01	0.00	1.0 1.0100%
setHeight(int) : void   setHeight(int) : void	588588	2.02	1.01	0.00	1.0 1.0100%
setType(java.lang.String) : void   setType(java.lang.String) : void	603603	1.01	1.01	0.00	1.0 1.0100%
setViewId(java.lang.String) : void   setViewId(java.lang.String) : void	620620	1.01	1.01	0.00	1.0 1.0100%
setVisible(boolean) : void   setVisible(boolean) : void	631631	2.02	1.01	0.00	1.0 1.0100%
setWidth(int) : void   setWidth(int) : void	643643	2.02	1.01	0.00	1.0 1.0100%
setXpos(int) : void   setXpos(int) : void	655655	2.02	1.01	0.00	1.0 1.0100%
setYpos(int) : void   setYpos(int) : void	667667	2.02	1.01	0.00	1.0 1.0100%
unmarshal(java.io.Reader) : jalview.schemabinding.version2.StructureState   unmarshal(java.io.Reader) : jalview.schemabinding.version2.StructureState	684684	1.01	1.01	1.01	0.0 0.00%
validate() : void   validate() : void	700700	2.02	1.01	2.02	0.0 0.00%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.6513761	jalview.io.Jalview2xmlTests.testStoreAndRecoverExpandedviewsjalview.io.Jalview2xmlTests.testStoreAndRecoverExpandedviews	1PASS
	0.6513761	jalview.io.Jalview2xmlTests.testStoreAndRecoverReferenceSeqSettingsjalview.io.Jalview2xmlTests.testStoreAndRecoverReferenceSeqSettings	1PASS
	0.5229358	jalview.io.Jalview2xmlTests.gatherViewsHerejalview.io.Jalview2xmlTests.gatherViewsHere	1PASS
	0.5229358	jalview.io.Jalview2xmlTests.viewRefPdbAnnotationjalview.io.Jalview2xmlTests.viewRefPdbAnnotation	1PASS
	0.5229358	jalview.io.Jalview2xmlTests.testCopyViewSettingsjalview.io.Jalview2xmlTests.testCopyViewSettings	1PASS
	0.5229358	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 StructureState.
19		*
20		* @version $Revision$ $Date$
21		*/
		65.1% Uncovered Elements: 38 (109) Complexity: 49 Complexity Density: 0.8
22		public class StructureState implements java.io.Serializable
23		{
24
25		// --------------------------/
26		// - Class/Member Variables -/
27		// --------------------------/
28
29		/**
30		* internal content storage
31		*/
32		private java.lang.String _content = "";
33
34		/**
35		* Field _visible.
36		*/
37		private boolean _visible;
38
39		/**
40		* keeps track of state for field: _visible
41		*/
42		private boolean _has_visible;
43
44		/**
45		* additional identifier which properly disambiguates the structure view from
46		* any other view with the same attributes. This is not an ID, because it is
47		* possible to have many references to the same physical structure view from
48		* different sequences in an alignment. A structureState element citing the
49		* same viewId will appear for each instance.
50		*
51		*/
52		private java.lang.String _viewId;
53
54		/**
55		* Flag set if the alignment panel containing this JSeq should be included in
56		* those used to perform a structure superposition (since Jalview 2.7).
57		*
58		*/
59		private boolean _alignwithAlignPanel = true;
60
61		/**
62		* keeps track of state for field: _alignwithAlignPanel
63		*/
64		private boolean _has_alignwithAlignPanel;
65
66		/**
67		* Flag set if the alignment panel containing this JSeq should be included in
68		* those used to colour its associated sequences in this structureState(since
69		* Jalview 2.7).
70		*
71		*/
72		private boolean _colourwithAlignPanel = false;
73
74		/**
75		* keeps track of state for field: _colourwithAlignPanel
76		*/
77		private boolean _has_colourwithAlignPanel;
78
79		/**
80		* Flag set if the structure display is coloured by the Jmol state, rather
81		* than by one or more linked alignment views.
82		*
83		*/
84		private boolean _colourByJmol = true;
85
86		/**
87		* keeps track of state for field: _colourByJmol
88		*/
89		private boolean _has_colourByJmol;
90
91		/**
92		* An identifier for the viewer type, currently either JMOL or CHIMERA
93		*
94		*/
95		private java.lang.String _type;
96
97		/**
98		* Field _width.
99		*/
100		private int _width;
101
102		/**
103		* keeps track of state for field: _width
104		*/
105		private boolean _has_width;
106
107		/**
108		* Field _height.
109		*/
110		private int _height;
111
112		/**
113		* keeps track of state for field: _height
114		*/
115		private boolean _has_height;
116
117		/**
118		* Field _xpos.
119		*/
120		private int _xpos;
121
122		/**
123		* keeps track of state for field: _xpos
124		*/
125		private boolean _has_xpos;
126
127		/**
128		* Field _ypos.
129		*/
130		private int _ypos;
131
132		/**
133		* keeps track of state for field: _ypos
134		*/
135		private boolean _has_ypos;
136
137		// ----------------/
138		// - Constructors -/
139		// ----------------/
140
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
141	140	public StructureState()...
142		{
143	140	super();
144	140	setContent("");
145		}
146
147		// -----------/
148		// - Methods -/
149		// -----------/
150
151		/**
152		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
153	0	public void deleteAlignwithAlignPanel()...
154		{
155	0	this._has_alignwithAlignPanel = false;
156		}
157
158		/**
159		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
160	0	public void deleteColourByJmol()...
161		{
162	0	this._has_colourByJmol = false;
163		}
164
165		/**
166		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
167	0	public void deleteColourwithAlignPanel()...
168		{
169	0	this._has_colourwithAlignPanel = false;
170		}
171
172		/**
173		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
174	0	public void deleteHeight()...
175		{
176	0	this._has_height = false;
177		}
178
179		/**
180		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
181	0	public void deleteVisible()...
182		{
183	0	this._has_visible = false;
184		}
185
186		/**
187		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
188	0	public void deleteWidth()...
189		{
190	0	this._has_width = false;
191		}
192
193		/**
194		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
195	0	public void deleteXpos()...
196		{
197	0	this._has_xpos = false;
198		}
199
200		/**
201		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
202	0	public void deleteYpos()...
203		{
204	0	this._has_ypos = false;
205		}
206
207		/**
208		* Returns the value of field 'alignwithAlignPanel'. The field
209		* 'alignwithAlignPanel' has the following description: Flag set if the
210		* alignment panel containing this JSeq should be included in those used to
211		* perform a structure superposition (since Jalview 2.7).
212		*
213		*
214		* @return the value of field 'AlignwithAlignPanel'.
215		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
216	160	public boolean getAlignwithAlignPanel()...
217		{
218	160	return this._alignwithAlignPanel;
219		}
220
221		/**
222		* Returns the value of field 'colourByJmol'. The field 'colourByJmol' has the
223		* following description: Flag set if the structure display is coloured by the
224		* Jmol state, rather than by one or more linked alignment views.
225		*
226		*
227		* @return the value of field 'ColourByJmol'.
228		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
229	160	public boolean getColourByJmol()...
230		{
231	160	return this._colourByJmol;
232		}
233
234		/**
235		* Returns the value of field 'colourwithAlignPanel'. The field
236		* 'colourwithAlignPanel' has the following description: Flag set if the
237		* alignment panel containing this JSeq should be included in those used to
238		* colour its associated sequences in this structureState(since Jalview 2.7).
239		*
240		*
241		* @return the value of field 'ColourwithAlignPanel'.
242		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
243	160	public boolean getColourwithAlignPanel()...
244		{
245	160	return this._colourwithAlignPanel;
246		}
247
248		/**
249		* Returns the value of field 'content'. The field 'content' has the following
250		* description: internal content storage
251		*
252		* @return the value of field 'Content'.
253		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
254	210	public java.lang.String getContent()...
255		{
256	210	return this._content;
257		}
258
259		/**
260		* Returns the value of field 'height'.
261		*
262		* @return the value of field 'Height'.
263		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
264	160	public int getHeight()...
265		{
266	160	return this._height;
267		}
268
269		/**
270		* Returns the value of field 'type'. The field 'type' has the following
271		* description: An identifier for the viewer type, currently either JMOL or
272		* CHIMERA
273		*
274		*
275		* @return the value of field 'Type'.
276		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
277	100	public java.lang.String getType()...
278		{
279	100	return this._type;
280		}
281
282		/**
283		* Returns the value of field 'viewId'. The field 'viewId' has the following
284		* description: additional identifier which properly disambiguates the
285		* structure view from any other view with the same attributes. This is not an
286		* ID, because it is possible to have many references to the same physical
287		* structure view from different sequences in an alignment. A structureState
288		* element citing the same viewId will appear for each instance.
289		*
290		*
291		* @return the value of field 'ViewId'.
292		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
293	340	public java.lang.String getViewId()...
294		{
295	340	return this._viewId;
296		}
297
298		/**
299		* Returns the value of field 'visible'.
300		*
301		* @return the value of field 'Visible'.
302		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
303	40	public boolean getVisible()...
304		{
305	40	return this._visible;
306		}
307
308		/**
309		* Returns the value of field 'width'.
310		*
311		* @return the value of field 'Width'.
312		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
313	160	public int getWidth()...
314		{
315	160	return this._width;
316		}
317
318		/**
319		* Returns the value of field 'xpos'.
320		*
321		* @return the value of field 'Xpos'.
322		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
323	160	public int getXpos()...
324		{
325	160	return this._xpos;
326		}
327
328		/**
329		* Returns the value of field 'ypos'.
330		*
331		* @return the value of field 'Ypos'.
332		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
333	160	public int getYpos()...
334		{
335	160	return this._ypos;
336		}
337
338		/**
339		* Method hasAlignwithAlignPanel.
340		*
341		* @return true if at least one AlignwithAlignPanel has been added
342		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
343	160	public boolean hasAlignwithAlignPanel()...
344		{
345	160	return this._has_alignwithAlignPanel;
346		}
347
348		/**
349		* Method hasColourByJmol.
350		*
351		* @return true if at least one ColourByJmol has been added
352		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
353	160	public boolean hasColourByJmol()...
354		{
355	160	return this._has_colourByJmol;
356		}
357
358		/**
359		* Method hasColourwithAlignPanel.
360		*
361		* @return true if at least one ColourwithAlignPanel has been added
362		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
363	160	public boolean hasColourwithAlignPanel()...
364		{
365	160	return this._has_colourwithAlignPanel;
366		}
367
368		/**
369		* Method hasHeight.
370		*
371		* @return true if at least one Height has been added
372		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
373	40	public boolean hasHeight()...
374		{
375	40	return this._has_height;
376		}
377
378		/**
379		* Method hasVisible.
380		*
381		* @return true if at least one Visible has been added
382		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
383	40	public boolean hasVisible()...
384		{
385	40	return this._has_visible;
386		}
387
388		/**
389		* Method hasWidth.
390		*
391		* @return true if at least one Width has been added
392		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
393	40	public boolean hasWidth()...
394		{
395	40	return this._has_width;
396		}
397
398		/**
399		* Method hasXpos.
400		*
401		* @return true if at least one Xpos has been added
402		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
403	40	public boolean hasXpos()...
404		{
405	40	return this._has_xpos;
406		}
407
408		/**
409		* Method hasYpos.
410		*
411		* @return true if at least one Ypos has been added
412		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
413	40	public boolean hasYpos()...
414		{
415	40	return this._has_ypos;
416		}
417
418		/**
419		* Returns the value of field 'alignwithAlignPanel'. The field
420		* 'alignwithAlignPanel' has the following description: Flag set if the
421		* alignment panel containing this JSeq should be included in those used to
422		* perform a structure superposition (since Jalview 2.7).
423		*
424		*
425		* @return the value of field 'AlignwithAlignPanel'.
426		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
427	0	public boolean isAlignwithAlignPanel()...
428		{
429	0	return this._alignwithAlignPanel;
430		}
431
432		/**
433		* Returns the value of field 'colourByJmol'. The field 'colourByJmol' has the
434		* following description: Flag set if the structure display is coloured by the
435		* Jmol state, rather than by one or more linked alignment views.
436		*
437		*
438		* @return the value of field 'ColourByJmol'.
439		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
440	0	public boolean isColourByJmol()...
441		{
442	0	return this._colourByJmol;
443		}
444
445		/**
446		* Returns the value of field 'colourwithAlignPanel'. The field
447		* 'colourwithAlignPanel' has the following description: Flag set if the
448		* alignment panel containing this JSeq should be included in those used to
449		* colour its associated sequences in this structureState(since Jalview 2.7).
450		*
451		*
452		* @return the value of field 'ColourwithAlignPanel'.
453		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
454	0	public boolean isColourwithAlignPanel()...
455		{
456	0	return this._colourwithAlignPanel;
457		}
458
459		/**
460		* Method isValid.
461		*
462		* @return true if this object is valid according to the schema
463		*/
		0% Uncovered Elements: 4 (4) Complexity: 2 Complexity Density: 0.5
464	0	public boolean isValid()...
465		{
466	0	try
467		{
468	0	validate();
469		} catch (org.exolab.castor.xml.ValidationException vex)
470		{
471	0	return false;
472		}
473	0	return true;
474		}
475
476		/**
477		* Returns the value of field 'visible'.
478		*
479		* @return the value of field 'Visible'.
480		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
481	0	public boolean isVisible()...
482		{
483	0	return this._visible;
484		}
485
486		/**
487		*
488		*
489		* @param out
490		* @throws org.exolab.castor.xml.MarshalException
491		* if object is null or if any SAXException is thrown during
492		* marshaling
493		* @throws org.exolab.castor.xml.ValidationException
494		* if this object is an invalid instance according to the schema
495		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
496	0	public void marshal(final java.io.Writer out)...
497		throws org.exolab.castor.xml.MarshalException,
498		org.exolab.castor.xml.ValidationException
499		{
500	0	Marshaller.marshal(this, out);
501		}
502
503		/**
504		*
505		*
506		* @param handler
507		* @throws java.io.IOException
508		* if an IOException occurs during marshaling
509		* @throws org.exolab.castor.xml.ValidationException
510		* if this object is an invalid instance according to the schema
511		* @throws org.exolab.castor.xml.MarshalException
512		* if object is null or if any SAXException is thrown during
513		* marshaling
514		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
515	0	public void marshal(final org.xml.sax.ContentHandler handler)...
516		throws java.io.IOException,
517		org.exolab.castor.xml.MarshalException,
518		org.exolab.castor.xml.ValidationException
519		{
520	0	Marshaller.marshal(this, handler);
521		}
522
523		/**
524		* Sets the value of field 'alignwithAlignPanel'. The field
525		* 'alignwithAlignPanel' has the following description: Flag set if the
526		* alignment panel containing this JSeq should be included in those used to
527		* perform a structure superposition (since Jalview 2.7).
528		*
529		*
530		* @param alignwithAlignPanel
531		* the value of field 'alignwithAlignPanel'.
532		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
533	140	public void setAlignwithAlignPanel(final boolean alignwithAlignPanel)...
534		{
535	140	this._alignwithAlignPanel = alignwithAlignPanel;
536	140	this._has_alignwithAlignPanel = true;
537		}
538
539		/**
540		* Sets the value of field 'colourByJmol'. The field 'colourByJmol' has the
541		* following description: Flag set if the structure display is coloured by the
542		* Jmol state, rather than by one or more linked alignment views.
543		*
544		*
545		* @param colourByJmol
546		* the value of field 'colourByJmol'.
547		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
548	140	public void setColourByJmol(final boolean colourByJmol)...
549		{
550	140	this._colourByJmol = colourByJmol;
551	140	this._has_colourByJmol = true;
552		}
553
554		/**
555		* Sets the value of field 'colourwithAlignPanel'. The field
556		* 'colourwithAlignPanel' has the following description: Flag set if the
557		* alignment panel containing this JSeq should be included in those used to
558		* colour its associated sequences in this structureState(since Jalview 2.7).
559		*
560		*
561		* @param colourwithAlignPanel
562		* the value of field 'colourwithAlignPanel'.
563		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
564	140	public void setColourwithAlignPanel(final boolean colourwithAlignPanel)...
565		{
566	140	this._colourwithAlignPanel = colourwithAlignPanel;
567	140	this._has_colourwithAlignPanel = true;
568		}
569
570		/**
571		* Sets the value of field 'content'. The field 'content' has the following
572		* description: internal content storage
573		*
574		* @param content
575		* the value of field 'content'.
576		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
577	240	public void setContent(final java.lang.String content)...
578		{
579	240	this._content = content;
580		}
581
582		/**
583		* Sets the value of field 'height'.
584		*
585		* @param height
586		* the value of field 'height'.
587		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
588	140	public void setHeight(final int height)...
589		{
590	140	this._height = height;
591	140	this._has_height = true;
592		}
593
594		/**
595		* Sets the value of field 'type'. The field 'type' has the following
596		* description: An identifier for the viewer type, currently either JMOL or
597		* CHIMERA
598		*
599		*
600		* @param type
601		* the value of field 'type'.
602		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
603	40	public void setType(final java.lang.String type)...
604		{
605	40	this._type = type;
606		}
607
608		/**
609		* Sets the value of field 'viewId'. The field 'viewId' has the following
610		* description: additional identifier which properly disambiguates the
611		* structure view from any other view with the same attributes. This is not an
612		* ID, because it is possible to have many references to the same physical
613		* structure view from different sequences in an alignment. A structureState
614		* element citing the same viewId will appear for each instance.
615		*
616		*
617		* @param viewId
618		* the value of field 'viewId'.
619		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
620	140	public void setViewId(final java.lang.String viewId)...
621		{
622	140	this._viewId = viewId;
623		}
624
625		/**
626		* Sets the value of field 'visible'.
627		*
628		* @param visible
629		* the value of field 'visible'.
630		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
631	140	public void setVisible(final boolean visible)...
632		{
633	140	this._visible = visible;
634	140	this._has_visible = true;
635		}
636
637		/**
638		* Sets the value of field 'width'.
639		*
640		* @param width
641		* the value of field 'width'.
642		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
643	140	public void setWidth(final int width)...
644		{
645	140	this._width = width;
646	140	this._has_width = true;
647		}
648
649		/**
650		* Sets the value of field 'xpos'.
651		*
652		* @param xpos
653		* the value of field 'xpos'.
654		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
655	140	public void setXpos(final int xpos)...
656		{
657	140	this._xpos = xpos;
658	140	this._has_xpos = true;
659		}
660
661		/**
662		* Sets the value of field 'ypos'.
663		*
664		* @param ypos
665		* the value of field 'ypos'.
666		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
667	140	public void setYpos(final int ypos)...
668		{
669	140	this._ypos = ypos;
670	140	this._has_ypos = true;
671		}
672
673		/**
674		* Method unmarshal.
675		*
676		* @param reader
677		* @throws org.exolab.castor.xml.MarshalException
678		* if object is null or if any SAXException is thrown during
679		* marshaling
680		* @throws org.exolab.castor.xml.ValidationException
681		* if this object is an invalid instance according to the schema
682		* @return the unmarshaled jalview.schemabinding.version2.StructureState
683		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
684	0	public static jalview.schemabinding.version2.StructureState unmarshal(...
685		final java.io.Reader reader)
686		throws org.exolab.castor.xml.MarshalException,
687		org.exolab.castor.xml.ValidationException
688		{
689	0	return (jalview.schemabinding.version2.StructureState) Unmarshaller
690		.unmarshal(jalview.schemabinding.version2.StructureState.class,
691		reader);
692		}
693
694		/**
695		*
696		*
697		* @throws org.exolab.castor.xml.ValidationException
698		* if this object is an invalid instance according to the schema
699		*/
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
700	0	public void validate() throws org.exolab.castor.xml.ValidationException...
701		{
702	0	org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
703	0	validator.validate(this);
704		}
705
706		}