Classes

Class	Line #	Total Statements	Complexity	Uncovered Elements	TOTAL Coverage	Actions
SecondaryStructure	22	22	18	39	0.00%	Show methods

Class SecondaryStructure

Class SecondaryStructure	Line # 22	Total Statements 22	Complexity 18	Uncovered Elements 39	TOTAL Coverage 0.00%
SecondaryStructure()   SecondaryStructure()	6363	1.01	1.01	1.01	0.0 0.00%
deleteGapped() : void   deleteGapped() : void	7474	1.01	1.01	1.01	0.0 0.00%
getAnnotationId() : java.lang.String   getAnnotationId() : java.lang.String	8787	1.01	1.01	1.01	0.0 0.00%
getGapped() : boolean   getGapped() : boolean	9999	1.01	1.01	1.01	0.0 0.00%
getTitle() : java.lang.String   getTitle() : java.lang.String	109109	1.01	1.01	1.01	0.0 0.00%
getViewerState() : java.lang.String   getViewerState() : java.lang.String	122122	1.01	1.01	1.01	0.0 0.00%
hasGapped() : boolean   hasGapped() : boolean	132132	1.01	1.01	1.01	0.0 0.00%
isGapped() : boolean   isGapped() : boolean	144144	1.01	1.01	1.01	0.0 0.00%
isValid() : boolean   isValid() : boolean	154154	4.04	2.02	4.04	0.0 0.00%
marshal(java.io.Writer) : void   marshal(java.io.Writer) : void	176176	1.01	1.01	1.01	0.0 0.00%
marshal(org.xml.sax.ContentHandler) : void   marshal(org.xml.sax.ContentHandler) : void	195195	1.01	1.01	1.01	0.0 0.00%
setAnnotationId(java.lang.String) : void   setAnnotationId(java.lang.String) : void	212212	1.01	1.01	1.01	0.0 0.00%
setGapped(boolean) : void   setGapped(boolean) : void	225225	2.02	1.01	2.02	0.0 0.00%
setTitle(java.lang.String) : void   setTitle(java.lang.String) : void	237237	1.01	1.01	1.01	0.0 0.00%
setViewerState(java.lang.String) : void   setViewerState(java.lang.String) : void	251251	1.01	1.01	1.01	0.0 0.00%
unmarshal(java.io.Reader) : jalview.schemabinding.version2.SecondaryStructure   unmarshal(java.io.Reader) : jalview.schemabinding.version2.SecondaryStructure	267267	1.01	1.01	1.01	0.0 0.00%
validate() : void   validate() : void	284284	2.02	1.01	2.02	0.0 0.00%

 

Contributing tests

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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 SecondaryStructure.
19		*
20		* @version $Revision$ $Date$
21		*/
		0% Uncovered Elements: 39 (39) Complexity: 18 Complexity Density: 0.82
22		public class SecondaryStructure implements java.io.Serializable
23		{
24
25		// --------------------------/
26		// - Class/Member Variables -/
27		// --------------------------/
28
29		/**
30		* Field _title.
31		*/
32		private java.lang.String _title;
33
34		/**
35		* id attribute of Annotation in vamsasModel for the secondary structure
36		* annotation shown in the viewer
37		*
38		*/
39		private java.lang.String _annotationId;
40
41		/**
42		* if true the RNA structure is shown with gaps, if false without
43		*
44		*/
45		private boolean _gapped;
46
47		/**
48		* keeps track of state for field: _gapped
49		*/
50		private boolean _has_gapped;
51
52		/**
53		* name of the project jar entry that holds the VARNA viewer state for the
54		* structure
55		*
56		*/
57		private java.lang.String _viewerState;
58
59		// ----------------/
60		// - Constructors -/
61		// ----------------/
62
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
63	0	public SecondaryStructure()...
64		{
65	0	super();
66		}
67
68		// -----------/
69		// - Methods -/
70		// -----------/
71
72		/**
73		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
74	0	public void deleteGapped()...
75		{
76	0	this._has_gapped = false;
77		}
78
79		/**
80		* Returns the value of field 'annotationId'. The field 'annotationId' has the
81		* following description: id attribute of Annotation in vamsasModel for the
82		* secondary structure annotation shown in the viewer
83		*
84		*
85		* @return the value of field 'AnnotationId'.
86		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
87	0	public java.lang.String getAnnotationId()...
88		{
89	0	return this._annotationId;
90		}
91
92		/**
93		* Returns the value of field 'gapped'. The field 'gapped' has the following
94		* description: if true the RNA structure is shown with gaps, if false without
95		*
96		*
97		* @return the value of field 'Gapped'.
98		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
99	0	public boolean getGapped()...
100		{
101	0	return this._gapped;
102		}
103
104		/**
105		* Returns the value of field 'title'.
106		*
107		* @return the value of field 'Title'.
108		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
109	0	public java.lang.String getTitle()...
110		{
111	0	return this._title;
112		}
113
114		/**
115		* Returns the value of field 'viewerState'. The field 'viewerState' has the
116		* following description: name of the project jar entry that holds the VARNA
117		* viewer state for the structure
118		*
119		*
120		* @return the value of field 'ViewerState'.
121		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
122	0	public java.lang.String getViewerState()...
123		{
124	0	return this._viewerState;
125		}
126
127		/**
128		* Method hasGapped.
129		*
130		* @return true if at least one Gapped has been added
131		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
132	0	public boolean hasGapped()...
133		{
134	0	return this._has_gapped;
135		}
136
137		/**
138		* Returns the value of field 'gapped'. The field 'gapped' has the following
139		* description: if true the RNA structure is shown with gaps, if false without
140		*
141		*
142		* @return the value of field 'Gapped'.
143		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
144	0	public boolean isGapped()...
145		{
146	0	return this._gapped;
147		}
148
149		/**
150		* Method isValid.
151		*
152		* @return true if this object is valid according to the schema
153		*/
		0% Uncovered Elements: 4 (4) Complexity: 2 Complexity Density: 0.5
154	0	public boolean isValid()...
155		{
156	0	try
157		{
158	0	validate();
159		} catch (org.exolab.castor.xml.ValidationException vex)
160		{
161	0	return false;
162		}
163	0	return true;
164		}
165
166		/**
167		*
168		*
169		* @param out
170		* @throws org.exolab.castor.xml.MarshalException
171		* if object is null or if any SAXException is thrown during
172		* marshaling
173		* @throws org.exolab.castor.xml.ValidationException
174		* if this object is an invalid instance according to the schema
175		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
176	0	public void marshal(final java.io.Writer out)...
177		throws org.exolab.castor.xml.MarshalException,
178		org.exolab.castor.xml.ValidationException
179		{
180	0	Marshaller.marshal(this, out);
181		}
182
183		/**
184		*
185		*
186		* @param handler
187		* @throws java.io.IOException
188		* if an IOException occurs during marshaling
189		* @throws org.exolab.castor.xml.ValidationException
190		* if this object is an invalid instance according to the schema
191		* @throws org.exolab.castor.xml.MarshalException
192		* if object is null or if any SAXException is thrown during
193		* marshaling
194		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
195	0	public void marshal(final org.xml.sax.ContentHandler handler)...
196		throws java.io.IOException,
197		org.exolab.castor.xml.MarshalException,
198		org.exolab.castor.xml.ValidationException
199		{
200	0	Marshaller.marshal(this, handler);
201		}
202
203		/**
204		* Sets the value of field 'annotationId'. The field 'annotationId' has the
205		* following description: id attribute of Annotation in vamsasModel for the
206		* secondary structure annotation shown in the viewer
207		*
208		*
209		* @param annotationId
210		* the value of field 'annotationId'.
211		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
212	0	public void setAnnotationId(final java.lang.String annotationId)...
213		{
214	0	this._annotationId = annotationId;
215		}
216
217		/**
218		* Sets the value of field 'gapped'. The field 'gapped' has the following
219		* description: if true the RNA structure is shown with gaps, if false without
220		*
221		*
222		* @param gapped
223		* the value of field 'gapped'.
224		*/
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
225	0	public void setGapped(final boolean gapped)...
226		{
227	0	this._gapped = gapped;
228	0	this._has_gapped = true;
229		}
230
231		/**
232		* Sets the value of field 'title'.
233		*
234		* @param title
235		* the value of field 'title'.
236		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
237	0	public void setTitle(final java.lang.String title)...
238		{
239	0	this._title = title;
240		}
241
242		/**
243		* Sets the value of field 'viewerState'. The field 'viewerState' has the
244		* following description: name of the project jar entry that holds the VARNA
245		* viewer state for the structure
246		*
247		*
248		* @param viewerState
249		* the value of field 'viewerState'.
250		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
251	0	public void setViewerState(final java.lang.String viewerState)...
252		{
253	0	this._viewerState = viewerState;
254		}
255
256		/**
257		* Method unmarshal.
258		*
259		* @param reader
260		* @throws org.exolab.castor.xml.MarshalException
261		* if object is null or if any SAXException is thrown during
262		* marshaling
263		* @throws org.exolab.castor.xml.ValidationException
264		* if this object is an invalid instance according to the schema
265		* @return the unmarshaled jalview.schemabinding.version2.SecondaryStructure
266		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
267	0	public static jalview.schemabinding.version2.SecondaryStructure unmarshal(...
268		final java.io.Reader reader)
269		throws org.exolab.castor.xml.MarshalException,
270		org.exolab.castor.xml.ValidationException
271		{
272	0	return (jalview.schemabinding.version2.SecondaryStructure) Unmarshaller
273		.unmarshal(
274		jalview.schemabinding.version2.SecondaryStructure.class,
275		reader);
276		}
277
278		/**
279		*
280		*
281		* @throws org.exolab.castor.xml.ValidationException
282		* if this object is an invalid instance according to the schema
283		*/
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
284	0	public void validate() throws org.exolab.castor.xml.ValidationException...
285		{
286	0	org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
287	0	validator.validate(this);
288		}
289
290		}