Classes

Class	Line #	Total Statements	Complexity	Uncovered Elements	TOTAL Coverage	Actions
JGroup	22	127	103	80	0.6521739465.2%	Show methods

Class JGroup

Class JGroup	Line # 22	Total Statements 127	Complexity 103	Uncovered Elements 80	TOTAL Coverage 0.6521739465.2%
JGroup()   JGroup()	219219	2.02	1.01	0.00	1.0 1.0100%
addSeq(java.lang.String) : void   addSeq(java.lang.String) : void	236236	1.01	1.01	0.00	1.0 1.0100%
addSeq(int,java.lang.String) : void   addSeq(int,java.lang.String) : void	250250	1.01	1.01	1.01	0.0 0.00%
deleteColourText() : void   deleteColourText() : void	258258	1.01	1.01	1.01	0.0 0.00%
deleteConsThreshold() : void   deleteConsThreshold() : void	265265	1.01	1.01	1.01	0.0 0.00%
deleteDisplayBoxes() : void   deleteDisplayBoxes() : void	272272	1.01	1.01	1.01	0.0 0.00%
deleteDisplayText() : void   deleteDisplayText() : void	279279	1.01	1.01	1.01	0.0 0.00%
deleteEnd() : void   deleteEnd() : void	286286	1.01	1.01	1.01	0.0 0.00%
deleteIgnoreGapsinConsensus() : void   deleteIgnoreGapsinConsensus() : void	293293	1.01	1.01	1.01	0.0 0.00%
deleteNormaliseSequenceLogo() : void   deleteNormaliseSequenceLogo() : void	300300	1.01	1.01	1.01	0.0 0.00%
deleteOutlineColour() : void   deleteOutlineColour() : void	307307	1.01	1.01	1.01	0.0 0.00%
deletePidThreshold() : void   deletePidThreshold() : void	314314	1.01	1.01	1.01	0.0 0.00%
deleteShowConsensusHistogram() : void   deleteShowConsensusHistogram() : void	321321	1.01	1.01	1.01	0.0 0.00%
deleteShowSequenceLogo() : void   deleteShowSequenceLogo() : void	328328	1.01	1.01	1.01	0.0 0.00%
deleteShowUnconserved() : void   deleteShowUnconserved() : void	335335	1.01	1.01	1.01	0.0 0.00%
deleteStart() : void   deleteStart() : void	342342	1.01	1.01	1.01	0.0 0.00%
deleteTextCol1() : void   deleteTextCol1() : void	349349	1.01	1.01	1.01	0.0 0.00%
deleteTextCol2() : void   deleteTextCol2() : void	356356	1.01	1.01	1.01	0.0 0.00%
deleteTextColThreshold() : void   deleteTextColThreshold() : void	363363	1.01	1.01	1.01	0.0 0.00%
enumerateSeq() : java.util.Enumeration   enumerateSeq() : java.util.Enumeration	373373	1.01	1.01	1.01	0.0 0.00%
getAnnotationColours() : jalview.schemabinding.version2.AnnotationColours   getAnnotationColours() : jalview.schemabinding.version2.AnnotationColours	383383	1.01	1.01	0.00	1.0 1.0100%
getColour() : java.lang.String   getColour() : java.lang.String	393393	1.01	1.01	0.00	1.0 1.0100%
getColourText() : boolean   getColourText() : boolean	403403	1.01	1.01	0.00	1.0 1.0100%
getConsThreshold() : int   getConsThreshold() : int	413413	1.01	1.01	0.00	1.0 1.0100%
getDisplayBoxes() : boolean   getDisplayBoxes() : boolean	423423	1.01	1.01	0.00	1.0 1.0100%
getDisplayText() : boolean   getDisplayText() : boolean	433433	1.01	1.01	0.00	1.0 1.0100%
getEnd() : int   getEnd() : int	443443	1.01	1.01	0.00	1.0 1.0100%
getId() : java.lang.String   getId() : java.lang.String	456456	1.01	1.01	0.00	1.0 1.0100%
getIgnoreGapsinConsensus() : boolean   getIgnoreGapsinConsensus() : boolean	466466	1.01	1.01	0.00	1.0 1.0100%
getName() : java.lang.String   getName() : java.lang.String	476476	1.01	1.01	0.00	1.0 1.0100%
getNormaliseSequenceLogo() : boolean   getNormaliseSequenceLogo() : boolean	486486	1.01	1.01	0.00	1.0 1.0100%
getOutlineColour() : int   getOutlineColour() : int	496496	1.01	1.01	0.00	1.0 1.0100%
getPidThreshold() : int   getPidThreshold() : int	506506	1.01	1.01	0.00	1.0 1.0100%
getSeq(int) : java.lang.String   getSeq(int) : java.lang.String	519519	3.03	3.03	2.02	0.6 0.660%
getSeq() : java.lang.String[]   getSeq() : java.lang.String[]	541541	2.02	1.01	0.00	1.0 1.0100%
getSeqCount() : int   getSeqCount() : int	552552	1.01	1.01	0.00	1.0 1.0100%
getShowConsensusHistogram() : boolean   getShowConsensusHistogram() : boolean	562562	1.01	1.01	0.00	1.0 1.0100%
getShowSequenceLogo() : boolean   getShowSequenceLogo() : boolean	572572	1.01	1.01	0.00	1.0 1.0100%
getShowUnconserved() : boolean   getShowUnconserved() : boolean	582582	1.01	1.01	0.00	1.0 1.0100%
getStart() : int   getStart() : int	592592	1.01	1.01	0.00	1.0 1.0100%
getTextCol1() : int   getTextCol1() : int	602602	1.01	1.01	0.00	1.0 1.0100%
getTextCol2() : int   getTextCol2() : int	612612	1.01	1.01	0.00	1.0 1.0100%
getTextColThreshold() : int   getTextColThreshold() : int	622622	1.01	1.01	0.00	1.0 1.0100%
hasColourText() : boolean   hasColourText() : boolean	632632	1.01	1.01	0.00	1.0 1.0100%
hasConsThreshold() : boolean   hasConsThreshold() : boolean	642642	1.01	1.01	0.00	1.0 1.0100%
hasDisplayBoxes() : boolean   hasDisplayBoxes() : boolean	652652	1.01	1.01	0.00	1.0 1.0100%
hasDisplayText() : boolean   hasDisplayText() : boolean	662662	1.01	1.01	0.00	1.0 1.0100%
hasEnd() : boolean   hasEnd() : boolean	672672	1.01	1.01	0.00	1.0 1.0100%
hasIgnoreGapsinConsensus() : boolean   hasIgnoreGapsinConsensus() : boolean	682682	1.01	1.01	0.00	1.0 1.0100%
hasNormaliseSequenceLogo() : boolean   hasNormaliseSequenceLogo() : boolean	692692	1.01	1.01	0.00	1.0 1.0100%
hasOutlineColour() : boolean   hasOutlineColour() : boolean	702702	1.01	1.01	0.00	1.0 1.0100%
hasPidThreshold() : boolean   hasPidThreshold() : boolean	712712	1.01	1.01	0.00	1.0 1.0100%
hasShowConsensusHistogram() : boolean   hasShowConsensusHistogram() : boolean	722722	1.01	1.01	0.00	1.0 1.0100%
hasShowSequenceLogo() : boolean   hasShowSequenceLogo() : boolean	732732	1.01	1.01	0.00	1.0 1.0100%
hasShowUnconserved() : boolean   hasShowUnconserved() : boolean	742742	1.01	1.01	0.00	1.0 1.0100%
hasStart() : boolean   hasStart() : boolean	752752	1.01	1.01	0.00	1.0 1.0100%
hasTextCol1() : boolean   hasTextCol1() : boolean	762762	1.01	1.01	0.00	1.0 1.0100%
hasTextCol2() : boolean   hasTextCol2() : boolean	772772	1.01	1.01	0.00	1.0 1.0100%
hasTextColThreshold() : boolean   hasTextColThreshold() : boolean	782782	1.01	1.01	0.00	1.0 1.0100%
isColourText() : boolean   isColourText() : boolean	792792	1.01	1.01	1.01	0.0 0.00%
isDisplayBoxes() : boolean   isDisplayBoxes() : boolean	802802	1.01	1.01	1.01	0.0 0.00%
isDisplayText() : boolean   isDisplayText() : boolean	812812	1.01	1.01	1.01	0.0 0.00%
isIgnoreGapsinConsensus() : boolean   isIgnoreGapsinConsensus() : boolean	822822	1.01	1.01	1.01	0.0 0.00%
isNormaliseSequenceLogo() : boolean   isNormaliseSequenceLogo() : boolean	832832	1.01	1.01	0.00	1.0 1.0100%
isShowConsensusHistogram() : boolean   isShowConsensusHistogram() : boolean	842842	1.01	1.01	0.00	1.0 1.0100%
isShowSequenceLogo() : boolean   isShowSequenceLogo() : boolean	852852	1.01	1.01	0.00	1.0 1.0100%
isShowUnconserved() : boolean   isShowUnconserved() : boolean	862862	1.01	1.01	0.00	1.0 1.0100%
isValid() : boolean   isValid() : boolean	872872	4.04	2.02	4.04	0.0 0.00%
marshal(java.io.Writer) : void   marshal(java.io.Writer) : void	894894	1.01	1.01	1.01	0.0 0.00%
marshal(org.xml.sax.ContentHandler) : void   marshal(org.xml.sax.ContentHandler) : void	913913	1.01	1.01	1.01	0.0 0.00%
removeAllSeq() : void   removeAllSeq() : void	923923	1.01	1.01	1.01	0.0 0.00%
removeSeq(java.lang.String) : boolean   removeSeq(java.lang.String) : boolean	934934	2.02	1.01	2.02	0.0 0.00%
removeSeqAt(int) : java.lang.String   removeSeqAt(int) : java.lang.String	946946	2.02	1.01	2.02	0.0 0.00%
setAnnotationColours(jalview.schemabinding.version2.AnnotationColours) : void   setAnnotationColours(jalview.schemabinding.version2.AnnotationColours) : void	958958	1.01	1.01	0.00	1.0 1.0100%
setColour(java.lang.String) : void   setColour(java.lang.String) : void	970970	1.01	1.01	0.00	1.0 1.0100%
setColourText(boolean) : void   setColourText(boolean) : void	981981	2.02	1.01	0.00	1.0 1.0100%
setConsThreshold(int) : void   setConsThreshold(int) : void	993993	2.02	1.01	0.00	1.0 1.0100%
setDisplayBoxes(boolean) : void   setDisplayBoxes(boolean) : void	10051005	2.02	1.01	0.00	1.0 1.0100%
setDisplayText(boolean) : void   setDisplayText(boolean) : void	10171017	2.02	1.01	0.00	1.0 1.0100%
setEnd(int) : void   setEnd(int) : void	10291029	2.02	1.01	0.00	1.0 1.0100%
setId(java.lang.String) : void   setId(java.lang.String) : void	10431043	1.01	1.01	0.00	1.0 1.0100%
setIgnoreGapsinConsensus(boolean) : void   setIgnoreGapsinConsensus(boolean) : void	10541054	2.02	1.01	0.00	1.0 1.0100%
setName(java.lang.String) : void   setName(java.lang.String) : void	10661066	1.01	1.01	0.00	1.0 1.0100%
setNormaliseSequenceLogo(boolean) : void   setNormaliseSequenceLogo(boolean) : void	10771077	2.02	1.01	0.00	1.0 1.0100%
setOutlineColour(int) : void   setOutlineColour(int) : void	10891089	2.02	1.01	0.00	1.0 1.0100%
setPidThreshold(int) : void   setPidThreshold(int) : void	11011101	2.02	1.01	0.00	1.0 1.0100%
setSeq(int,java.lang.String) : void   setSeq(int,java.lang.String) : void	11151115	3.03	3.03	5.05	0.0 0.00%
setSeq(java.lang.String[]) : void   setSeq(java.lang.String[]) : void	11331133	3.03	2.02	5.05	0.0 0.00%
setShowConsensusHistogram(boolean) : void   setShowConsensusHistogram(boolean) : void	11501150	2.02	1.01	0.00	1.0 1.0100%
setShowSequenceLogo(boolean) : void   setShowSequenceLogo(boolean) : void	11621162	2.02	1.01	0.00	1.0 1.0100%
setShowUnconserved(boolean) : void   setShowUnconserved(boolean) : void	11741174	2.02	1.01	0.00	1.0 1.0100%
setStart(int) : void   setStart(int) : void	11861186	2.02	1.01	0.00	1.0 1.0100%
setTextCol1(int) : void   setTextCol1(int) : void	11981198	2.02	1.01	0.00	1.0 1.0100%
setTextCol2(int) : void   setTextCol2(int) : void	12101210	2.02	1.01	0.00	1.0 1.0100%
setTextColThreshold(int) : void   setTextColThreshold(int) : void	12221222	2.02	1.01	0.00	1.0 1.0100%
unmarshal(java.io.Reader) : jalview.schemabinding.version2.JGroup   unmarshal(java.io.Reader) : jalview.schemabinding.version2.JGroup	12391239	1.01	1.01	1.01	0.0 0.00%
validate() : void   validate() : void	12541254	2.02	1.01	2.02	0.0 0.00%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.6347826	jalview.io.Jalview2xmlTests.testStoreAndRecoverColourThresholdsjalview.io.Jalview2xmlTests.testStoreAndRecoverColourThresholds	1PASS
	0.6304348	jalview.io.Jalview2xmlTests.testStoreAndRecoverExpandedviewsjalview.io.Jalview2xmlTests.testStoreAndRecoverExpandedviews	1PASS
	0.6304348	jalview.io.Jalview2xmlTests.testStoreAndRecoverReferenceSeqSettingsjalview.io.Jalview2xmlTests.testStoreAndRecoverReferenceSeqSettings	1PASS
	0.6304348	jalview.io.Jalview2xmlTests.testColourByAnnotScoresjalview.io.Jalview2xmlTests.testColourByAnnotScores	1PASS
	0.4826087	jalview.gui.AlignFrameTest.testNewView_colourThresholdsjalview.gui.AlignFrameTest.testNewView_colourThresholds	1PASS
	0.45652175	jalview.io.Jalview2xmlTests.gatherViewsHerejalview.io.Jalview2xmlTests.gatherViewsHere	1PASS
	0.45652175	jalview.io.Jalview2xmlTests.viewRefPdbAnnotationjalview.io.Jalview2xmlTests.viewRefPdbAnnotation	1PASS
	0.45652175	jalview.io.Jalview2xmlTests.testCopyViewSettingsjalview.io.Jalview2xmlTests.testCopyViewSettings	1PASS
	0.45652175	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 JGroup.
19		*
20		* @version $Revision$ $Date$
21		*/
		65.2% Uncovered Elements: 80 (230) Complexity: 103 Complexity Density: 0.81
22		public class JGroup implements java.io.Serializable
23		{
24
25		// --------------------------/
26		// - Class/Member Variables -/
27		// --------------------------/
28
29		/**
30		* Field _start.
31		*/
32		private int _start;
33
34		/**
35		* keeps track of state for field: _start
36		*/
37		private boolean _has_start;
38
39		/**
40		* Field _end.
41		*/
42		private int _end;
43
44		/**
45		* keeps track of state for field: _end
46		*/
47		private boolean _has_end;
48
49		/**
50		* Field _name.
51		*/
52		private java.lang.String _name;
53
54		/**
55		* Field _colour.
56		*/
57		private java.lang.String _colour;
58
59		/**
60		* Field _consThreshold.
61		*/
62		private int _consThreshold;
63
64		/**
65		* keeps track of state for field: _consThreshold
66		*/
67		private boolean _has_consThreshold;
68
69		/**
70		* Field _pidThreshold.
71		*/
72		private int _pidThreshold;
73
74		/**
75		* keeps track of state for field: _pidThreshold
76		*/
77		private boolean _has_pidThreshold;
78
79		/**
80		* Field _outlineColour.
81		*/
82		private int _outlineColour;
83
84		/**
85		* keeps track of state for field: _outlineColour
86		*/
87		private boolean _has_outlineColour;
88
89		/**
90		* Field _displayBoxes.
91		*/
92		private boolean _displayBoxes;
93
94		/**
95		* keeps track of state for field: _displayBoxes
96		*/
97		private boolean _has_displayBoxes;
98
99		/**
100		* Field _displayText.
101		*/
102		private boolean _displayText;
103
104		/**
105		* keeps track of state for field: _displayText
106		*/
107		private boolean _has_displayText;
108
109		/**
110		* Field _colourText.
111		*/
112		private boolean _colourText;
113
114		/**
115		* keeps track of state for field: _colourText
116		*/
117		private boolean _has_colourText;
118
119		/**
120		* Field _textCol1.
121		*/
122		private int _textCol1;
123
124		/**
125		* keeps track of state for field: _textCol1
126		*/
127		private boolean _has_textCol1;
128
129		/**
130		* Field _textCol2.
131		*/
132		private int _textCol2;
133
134		/**
135		* keeps track of state for field: _textCol2
136		*/
137		private boolean _has_textCol2;
138
139		/**
140		* Field _textColThreshold.
141		*/
142		private int _textColThreshold;
143
144		/**
145		* keeps track of state for field: _textColThreshold
146		*/
147		private boolean _has_textColThreshold;
148
149		/**
150		* Field _showUnconserved.
151		*/
152		private boolean _showUnconserved;
153
154		/**
155		* keeps track of state for field: _showUnconserved
156		*/
157		private boolean _has_showUnconserved;
158
159		/**
160		* Field _ignoreGapsinConsensus.
161		*/
162		private boolean _ignoreGapsinConsensus = true;
163
164		/**
165		* keeps track of state for field: _ignoreGapsinConsensus
166		*/
167		private boolean _has_ignoreGapsinConsensus;
168
169		/**
170		* Field _showConsensusHistogram.
171		*/
172		private boolean _showConsensusHistogram = true;
173
174		/**
175		* keeps track of state for field: _showConsensusHistogram
176		*/
177		private boolean _has_showConsensusHistogram;
178
179		/**
180		* Field _showSequenceLogo.
181		*/
182		private boolean _showSequenceLogo = false;
183
184		/**
185		* keeps track of state for field: _showSequenceLogo
186		*/
187		private boolean _has_showSequenceLogo;
188
189		/**
190		* Field _normaliseSequenceLogo.
191		*/
192		private boolean _normaliseSequenceLogo = false;
193
194		/**
195		* keeps track of state for field: _normaliseSequenceLogo
196		*/
197		private boolean _has_normaliseSequenceLogo;
198
199		/**
200		* Optional sequence group ID (only needs to be unique for this alignment)
201		*
202		*/
203		private java.lang.String _id;
204
205		/**
206		* Field _seqList.
207		*/
208		private java.util.Vector _seqList;
209
210		/**
211		* Field _annotationColours.
212		*/
213		private jalview.schemabinding.version2.AnnotationColours _annotationColours;
214
215		// ----------------/
216		// - Constructors -/
217		// ----------------/
218
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
219	75	public JGroup()...
220		{
221	75	super();
222	75	this._seqList = new java.util.Vector();
223		}
224
225		// -----------/
226		// - Methods -/
227		// -----------/
228
229		/**
230		*
231		*
232		* @param vSeq
233		* @throws java.lang.IndexOutOfBoundsException
234		* if the index given is outside the bounds of the collection
235		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
236	567	public void addSeq(final java.lang.String vSeq)...
237		throws java.lang.IndexOutOfBoundsException
238		{
239	567	this._seqList.addElement(vSeq);
240		}
241
242		/**
243		*
244		*
245		* @param index
246		* @param vSeq
247		* @throws java.lang.IndexOutOfBoundsException
248		* if the index given is outside the bounds of the collection
249		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
250	0	public void addSeq(final int index, final java.lang.String vSeq)...
251		throws java.lang.IndexOutOfBoundsException
252		{
253	0	this._seqList.add(index, vSeq);
254		}
255
256		/**
257		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
258	0	public void deleteColourText()...
259		{
260	0	this._has_colourText = false;
261		}
262
263		/**
264		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
265	0	public void deleteConsThreshold()...
266		{
267	0	this._has_consThreshold = false;
268		}
269
270		/**
271		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
272	0	public void deleteDisplayBoxes()...
273		{
274	0	this._has_displayBoxes = false;
275		}
276
277		/**
278		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
279	0	public void deleteDisplayText()...
280		{
281	0	this._has_displayText = false;
282		}
283
284		/**
285		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
286	0	public void deleteEnd()...
287		{
288	0	this._has_end = false;
289		}
290
291		/**
292		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
293	0	public void deleteIgnoreGapsinConsensus()...
294		{
295	0	this._has_ignoreGapsinConsensus = false;
296		}
297
298		/**
299		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
300	0	public void deleteNormaliseSequenceLogo()...
301		{
302	0	this._has_normaliseSequenceLogo = false;
303		}
304
305		/**
306		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
307	0	public void deleteOutlineColour()...
308		{
309	0	this._has_outlineColour = false;
310		}
311
312		/**
313		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
314	0	public void deletePidThreshold()...
315		{
316	0	this._has_pidThreshold = false;
317		}
318
319		/**
320		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
321	0	public void deleteShowConsensusHistogram()...
322		{
323	0	this._has_showConsensusHistogram = false;
324		}
325
326		/**
327		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
328	0	public void deleteShowSequenceLogo()...
329		{
330	0	this._has_showSequenceLogo = false;
331		}
332
333		/**
334		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
335	0	public void deleteShowUnconserved()...
336		{
337	0	this._has_showUnconserved = false;
338		}
339
340		/**
341		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
342	0	public void deleteStart()...
343		{
344	0	this._has_start = false;
345		}
346
347		/**
348		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
349	0	public void deleteTextCol1()...
350		{
351	0	this._has_textCol1 = false;
352		}
353
354		/**
355		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
356	0	public void deleteTextCol2()...
357		{
358	0	this._has_textCol2 = false;
359		}
360
361		/**
362		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
363	0	public void deleteTextColThreshold()...
364		{
365	0	this._has_textColThreshold = false;
366		}
367
368		/**
369		* Method enumerateSeq.
370		*
371		* @return an Enumeration over all java.lang.String elements
372		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
373	0	public java.util.Enumeration enumerateSeq()...
374		{
375	0	return this._seqList.elements();
376		}
377
378		/**
379		* Returns the value of field 'annotationColours'.
380		*
381		* @return the value of field 'AnnotationColours'.
382		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
383	26	public jalview.schemabinding.version2.AnnotationColours getAnnotationColours()...
384		{
385	26	return this._annotationColours;
386		}
387
388		/**
389		* Returns the value of field 'colour'.
390		*
391		* @return the value of field 'Colour'.
392		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
393	167	public java.lang.String getColour()...
394		{
395	167	return this._colour;
396		}
397
398		/**
399		* Returns the value of field 'colourText'.
400		*
401		* @return the value of field 'ColourText'.
402		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
403	87	public boolean getColourText()...
404		{
405	87	return this._colourText;
406		}
407
408		/**
409		* Returns the value of field 'consThreshold'.
410		*
411		* @return the value of field 'ConsThreshold'.
412		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
413	128	public int getConsThreshold()...
414		{
415	128	return this._consThreshold;
416		}
417
418		/**
419		* Returns the value of field 'displayBoxes'.
420		*
421		* @return the value of field 'DisplayBoxes'.
422		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
423	87	public boolean getDisplayBoxes()...
424		{
425	87	return this._displayBoxes;
426		}
427
428		/**
429		* Returns the value of field 'displayText'.
430		*
431		* @return the value of field 'DisplayText'.
432		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
433	87	public boolean getDisplayText()...
434		{
435	87	return this._displayText;
436		}
437
438		/**
439		* Returns the value of field 'end'.
440		*
441		* @return the value of field 'End'.
442		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
443	87	public int getEnd()...
444		{
445	87	return this._end;
446		}
447
448		/**
449		* Returns the value of field 'id'. The field 'id' has the following
450		* description: Optional sequence group ID (only needs to be unique for this
451		* alignment)
452		*
453		*
454		* @return the value of field 'Id'.
455		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
456	123	public java.lang.String getId()...
457		{
458	123	return this._id;
459		}
460
461		/**
462		* Returns the value of field 'ignoreGapsinConsensus'.
463		*
464		* @return the value of field 'IgnoreGapsinConsensus'.
465		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
466	87	public boolean getIgnoreGapsinConsensus()...
467		{
468	87	return this._ignoreGapsinConsensus;
469		}
470
471		/**
472		* Returns the value of field 'name'.
473		*
474		* @return the value of field 'Name'.
475		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
476	87	public java.lang.String getName()...
477		{
478	87	return this._name;
479		}
480
481		/**
482		* Returns the value of field 'normaliseSequenceLogo'.
483		*
484		* @return the value of field 'NormaliseSequenceLogo'.
485		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
486	24	public boolean getNormaliseSequenceLogo()...
487		{
488	24	return this._normaliseSequenceLogo;
489		}
490
491		/**
492		* Returns the value of field 'outlineColour'.
493		*
494		* @return the value of field 'OutlineColour'.
495		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
496	87	public int getOutlineColour()...
497		{
498	87	return this._outlineColour;
499		}
500
501		/**
502		* Returns the value of field 'pidThreshold'.
503		*
504		* @return the value of field 'PidThreshold'.
505		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
506	75	public int getPidThreshold()...
507		{
508	75	return this._pidThreshold;
509		}
510
511		/**
512		* Method getSeq.
513		*
514		* @param index
515		* @throws java.lang.IndexOutOfBoundsException
516		* if the index given is outside the bounds of the collection
517		* @return the value of the java.lang.String at the given index
518		*/
		60% Uncovered Elements: 2 (5) Complexity: 3 Complexity Density: 1
519	484	public java.lang.String getSeq(final int index)...
520		throws java.lang.IndexOutOfBoundsException
521		{
522		// check bounds for index
523	484	if (index < 0 || index >= this._seqList.size())
524		{
525	0	throw new IndexOutOfBoundsException("getSeq: Index value '" + index
526		+ "' not in range [0.." + (this._seqList.size() - 1) + "]");
527		}
528
529	484	return (java.lang.String) _seqList.get(index);
530		}
531
532		/**
533		* Method getSeq.Returns the contents of the collection in an Array.
534		* <p>
535		* Note: Just in case the collection contents are changing in another thread,
536		* we pass a 0-length Array of the correct type into the API call. This way we
537		* <i>know</i> that the Array returned is of exactly the correct length.
538		*
539		* @return this collection as an Array
540		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
541	24	public java.lang.String[] getSeq()...
542		{
543	24	java.lang.String[] array = new java.lang.String[0];
544	24	return (java.lang.String[]) this._seqList.toArray(array);
545		}
546
547		/**
548		* Method getSeqCount.
549		*
550		* @return the size of this collection
551		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
552	547	public int getSeqCount()...
553		{
554	547	return this._seqList.size();
555		}
556
557		/**
558		* Returns the value of field 'showConsensusHistogram'.
559		*
560		* @return the value of field 'ShowConsensusHistogram'.
561		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
562	24	public boolean getShowConsensusHistogram()...
563		{
564	24	return this._showConsensusHistogram;
565		}
566
567		/**
568		* Returns the value of field 'showSequenceLogo'.
569		*
570		* @return the value of field 'ShowSequenceLogo'.
571		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
572	24	public boolean getShowSequenceLogo()...
573		{
574	24	return this._showSequenceLogo;
575		}
576
577		/**
578		* Returns the value of field 'showUnconserved'.
579		*
580		* @return the value of field 'ShowUnconserved'.
581		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
582	24	public boolean getShowUnconserved()...
583		{
584	24	return this._showUnconserved;
585		}
586
587		/**
588		* Returns the value of field 'start'.
589		*
590		* @return the value of field 'Start'.
591		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
592	87	public int getStart()...
593		{
594	87	return this._start;
595		}
596
597		/**
598		* Returns the value of field 'textCol1'.
599		*
600		* @return the value of field 'TextCol1'.
601		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
602	87	public int getTextCol1()...
603		{
604	87	return this._textCol1;
605		}
606
607		/**
608		* Returns the value of field 'textCol2'.
609		*
610		* @return the value of field 'TextCol2'.
611		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
612	87	public int getTextCol2()...
613		{
614	87	return this._textCol2;
615		}
616
617		/**
618		* Returns the value of field 'textColThreshold'.
619		*
620		* @return the value of field 'TextColThreshold'.
621		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
622	87	public int getTextColThreshold()...
623		{
624	87	return this._textColThreshold;
625		}
626
627		/**
628		* Method hasColourText.
629		*
630		* @return true if at least one ColourText has been added
631		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
632	24	public boolean hasColourText()...
633		{
634	24	return this._has_colourText;
635		}
636
637		/**
638		* Method hasConsThreshold.
639		*
640		* @return true if at least one ConsThreshold has been added
641		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
642	24	public boolean hasConsThreshold()...
643		{
644	24	return this._has_consThreshold;
645		}
646
647		/**
648		* Method hasDisplayBoxes.
649		*
650		* @return true if at least one DisplayBoxes has been added
651		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
652	24	public boolean hasDisplayBoxes()...
653		{
654	24	return this._has_displayBoxes;
655		}
656
657		/**
658		* Method hasDisplayText.
659		*
660		* @return true if at least one DisplayText has been added
661		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
662	24	public boolean hasDisplayText()...
663		{
664	24	return this._has_displayText;
665		}
666
667		/**
668		* Method hasEnd.
669		*
670		* @return true if at least one End has been added
671		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
672	24	public boolean hasEnd()...
673		{
674	24	return this._has_end;
675		}
676
677		/**
678		* Method hasIgnoreGapsinConsensus.
679		*
680		* @return true if at least one IgnoreGapsinConsensus has been added
681		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
682	87	public boolean hasIgnoreGapsinConsensus()...
683		{
684	87	return this._has_ignoreGapsinConsensus;
685		}
686
687		/**
688		* Method hasNormaliseSequenceLogo.
689		*
690		* @return true if at least one NormaliseSequenceLogo has been added
691		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
692	87	public boolean hasNormaliseSequenceLogo()...
693		{
694	87	return this._has_normaliseSequenceLogo;
695		}
696
697		/**
698		* Method hasOutlineColour.
699		*
700		* @return true if at least one OutlineColour has been added
701		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
702	24	public boolean hasOutlineColour()...
703		{
704	24	return this._has_outlineColour;
705		}
706
707		/**
708		* Method hasPidThreshold.
709		*
710		* @return true if at least one PidThreshold has been added
711		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
712	24	public boolean hasPidThreshold()...
713		{
714	24	return this._has_pidThreshold;
715		}
716
717		/**
718		* Method hasShowConsensusHistogram.
719		*
720		* @return true if at least one ShowConsensusHistogram has been added
721		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
722	87	public boolean hasShowConsensusHistogram()...
723		{
724	87	return this._has_showConsensusHistogram;
725		}
726
727		/**
728		* Method hasShowSequenceLogo.
729		*
730		* @return true if at least one ShowSequenceLogo has been added
731		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
732	87	public boolean hasShowSequenceLogo()...
733		{
734	87	return this._has_showSequenceLogo;
735		}
736
737		/**
738		* Method hasShowUnconserved.
739		*
740		* @return true if at least one ShowUnconserved has been added
741		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
742	87	public boolean hasShowUnconserved()...
743		{
744	87	return this._has_showUnconserved;
745		}
746
747		/**
748		* Method hasStart.
749		*
750		* @return true if at least one Start has been added
751		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
752	24	public boolean hasStart()...
753		{
754	24	return this._has_start;
755		}
756
757		/**
758		* Method hasTextCol1.
759		*
760		* @return true if at least one TextCol1 has been added
761		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
762	24	public boolean hasTextCol1()...
763		{
764	24	return this._has_textCol1;
765		}
766
767		/**
768		* Method hasTextCol2.
769		*
770		* @return true if at least one TextCol2 has been added
771		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
772	24	public boolean hasTextCol2()...
773		{
774	24	return this._has_textCol2;
775		}
776
777		/**
778		* Method hasTextColThreshold.
779		*
780		* @return true if at least one TextColThreshold has been added
781		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
782	24	public boolean hasTextColThreshold()...
783		{
784	24	return this._has_textColThreshold;
785		}
786
787		/**
788		* Returns the value of field 'colourText'.
789		*
790		* @return the value of field 'ColourText'.
791		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
792	0	public boolean isColourText()...
793		{
794	0	return this._colourText;
795		}
796
797		/**
798		* Returns the value of field 'displayBoxes'.
799		*
800		* @return the value of field 'DisplayBoxes'.
801		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
802	0	public boolean isDisplayBoxes()...
803		{
804	0	return this._displayBoxes;
805		}
806
807		/**
808		* Returns the value of field 'displayText'.
809		*
810		* @return the value of field 'DisplayText'.
811		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
812	0	public boolean isDisplayText()...
813		{
814	0	return this._displayText;
815		}
816
817		/**
818		* Returns the value of field 'ignoreGapsinConsensus'.
819		*
820		* @return the value of field 'IgnoreGapsinConsensus'.
821		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
822	0	public boolean isIgnoreGapsinConsensus()...
823		{
824	0	return this._ignoreGapsinConsensus;
825		}
826
827		/**
828		* Returns the value of field 'normaliseSequenceLogo'.
829		*
830		* @return the value of field 'NormaliseSequenceLogo'.
831		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
832	13	public boolean isNormaliseSequenceLogo()...
833		{
834	13	return this._normaliseSequenceLogo;
835		}
836
837		/**
838		* Returns the value of field 'showConsensusHistogram'.
839		*
840		* @return the value of field 'ShowConsensusHistogram'.
841		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
842	63	public boolean isShowConsensusHistogram()...
843		{
844	63	return this._showConsensusHistogram;
845		}
846
847		/**
848		* Returns the value of field 'showSequenceLogo'.
849		*
850		* @return the value of field 'ShowSequenceLogo'.
851		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
852	63	public boolean isShowSequenceLogo()...
853		{
854	63	return this._showSequenceLogo;
855		}
856
857		/**
858		* Returns the value of field 'showUnconserved'.
859		*
860		* @return the value of field 'ShowUnconserved'.
861		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
862	63	public boolean isShowUnconserved()...
863		{
864	63	return this._showUnconserved;
865		}
866
867		/**
868		* Method isValid.
869		*
870		* @return true if this object is valid according to the schema
871		*/
		0% Uncovered Elements: 4 (4) Complexity: 2 Complexity Density: 0.5
872	0	public boolean isValid()...
873		{
874	0	try
875		{
876	0	validate();
877		} catch (org.exolab.castor.xml.ValidationException vex)
878		{
879	0	return false;
880		}
881	0	return true;
882		}
883
884		/**
885		*
886		*
887		* @param out
888		* @throws org.exolab.castor.xml.MarshalException
889		* if object is null or if any SAXException is thrown during
890		* marshaling
891		* @throws org.exolab.castor.xml.ValidationException
892		* if this object is an invalid instance according to the schema
893		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
894	0	public void marshal(final java.io.Writer out)...
895		throws org.exolab.castor.xml.MarshalException,
896		org.exolab.castor.xml.ValidationException
897		{
898	0	Marshaller.marshal(this, out);
899		}
900
901		/**
902		*
903		*
904		* @param handler
905		* @throws java.io.IOException
906		* if an IOException occurs during marshaling
907		* @throws org.exolab.castor.xml.ValidationException
908		* if this object is an invalid instance according to the schema
909		* @throws org.exolab.castor.xml.MarshalException
910		* if object is null or if any SAXException is thrown during
911		* marshaling
912		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
913	0	public void marshal(final org.xml.sax.ContentHandler handler)...
914		throws java.io.IOException,
915		org.exolab.castor.xml.MarshalException,
916		org.exolab.castor.xml.ValidationException
917		{
918	0	Marshaller.marshal(this, handler);
919		}
920
921		/**
922		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
923	0	public void removeAllSeq()...
924		{
925	0	this._seqList.clear();
926		}
927
928		/**
929		* Method removeSeq.
930		*
931		* @param vSeq
932		* @return true if the object was removed from the collection.
933		*/
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
934	0	public boolean removeSeq(final java.lang.String vSeq)...
935		{
936	0	boolean removed = _seqList.remove(vSeq);
937	0	return removed;
938		}
939
940		/**
941		* Method removeSeqAt.
942		*
943		* @param index
944		* @return the element removed from the collection
945		*/
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
946	0	public java.lang.String removeSeqAt(final int index)...
947		{
948	0	java.lang.Object obj = this._seqList.remove(index);
949	0	return (java.lang.String) obj;
950		}
951
952		/**
953		* Sets the value of field 'annotationColours'.
954		*
955		* @param annotationColours
956		* the value of field 'annotationColours'.
957		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
958	2	public void setAnnotationColours(...
959		final jalview.schemabinding.version2.AnnotationColours annotationColours)
960		{
961	2	this._annotationColours = annotationColours;
962		}
963
964		/**
965		* Sets the value of field 'colour'.
966		*
967		* @param colour
968		* the value of field 'colour'.
969		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
970	33	public void setColour(final java.lang.String colour)...
971		{
972	33	this._colour = colour;
973		}
974
975		/**
976		* Sets the value of field 'colourText'.
977		*
978		* @param colourText
979		* the value of field 'colourText'.
980		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
981	75	public void setColourText(final boolean colourText)...
982		{
983	75	this._colourText = colourText;
984	75	this._has_colourText = true;
985		}
986
987		/**
988		* Sets the value of field 'consThreshold'.
989		*
990		* @param consThreshold
991		* the value of field 'consThreshold'.
992		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
993	3	public void setConsThreshold(final int consThreshold)...
994		{
995	3	this._consThreshold = consThreshold;
996	3	this._has_consThreshold = true;
997		}
998
999		/**
1000		* Sets the value of field 'displayBoxes'.
1001		*
1002		* @param displayBoxes
1003		* the value of field 'displayBoxes'.
1004		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
1005	75	public void setDisplayBoxes(final boolean displayBoxes)...
1006		{
1007	75	this._displayBoxes = displayBoxes;
1008	75	this._has_displayBoxes = true;
1009		}
1010
1011		/**
1012		* Sets the value of field 'displayText'.
1013		*
1014		* @param displayText
1015		* the value of field 'displayText'.
1016		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
1017	75	public void setDisplayText(final boolean displayText)...
1018		{
1019	75	this._displayText = displayText;
1020	75	this._has_displayText = true;
1021		}
1022
1023		/**
1024		* Sets the value of field 'end'.
1025		*
1026		* @param end
1027		* the value of field 'end'.
1028		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
1029	75	public void setEnd(final int end)...
1030		{
1031	75	this._end = end;
1032	75	this._has_end = true;
1033		}
1034
1035		/**
1036		* Sets the value of field 'id'. The field 'id' has the following description:
1037		* Optional sequence group ID (only needs to be unique for this alignment)
1038		*
1039		*
1040		* @param id
1041		* the value of field 'id'.
1042		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1043	42	public void setId(final java.lang.String id)...
1044		{
1045	42	this._id = id;
1046		}
1047
1048		/**
1049		* Sets the value of field 'ignoreGapsinConsensus'.
1050		*
1051		* @param ignoreGapsinConsensus
1052		* the value of field 'ignoreGapsinConsensus'.
1053		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
1054	75	public void setIgnoreGapsinConsensus(final boolean ignoreGapsinConsensus)...
1055		{
1056	75	this._ignoreGapsinConsensus = ignoreGapsinConsensus;
1057	75	this._has_ignoreGapsinConsensus = true;
1058		}
1059
1060		/**
1061		* Sets the value of field 'name'.
1062		*
1063		* @param name
1064		* the value of field 'name'.
1065		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1066	75	public void setName(final java.lang.String name)...
1067		{
1068	75	this._name = name;
1069		}
1070
1071		/**
1072		* Sets the value of field 'normaliseSequenceLogo'.
1073		*
1074		* @param normaliseSequenceLogo
1075		* the value of field 'normaliseSequenceLogo'.
1076		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
1077	25	public void setNormaliseSequenceLogo(final boolean normaliseSequenceLogo)...
1078		{
1079	25	this._normaliseSequenceLogo = normaliseSequenceLogo;
1080	25	this._has_normaliseSequenceLogo = true;
1081		}
1082
1083		/**
1084		* Sets the value of field 'outlineColour'.
1085		*
1086		* @param outlineColour
1087		* the value of field 'outlineColour'.
1088		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
1089	75	public void setOutlineColour(final int outlineColour)...
1090		{
1091	75	this._outlineColour = outlineColour;
1092	75	this._has_outlineColour = true;
1093		}
1094
1095		/**
1096		* Sets the value of field 'pidThreshold'.
1097		*
1098		* @param pidThreshold
1099		* the value of field 'pidThreshold'.
1100		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
1101	33	public void setPidThreshold(final int pidThreshold)...
1102		{
1103	33	this._pidThreshold = pidThreshold;
1104	33	this._has_pidThreshold = true;
1105		}
1106
1107		/**
1108		*
1109		*
1110		* @param index
1111		* @param vSeq
1112		* @throws java.lang.IndexOutOfBoundsException
1113		* if the index given is outside the bounds of the collection
1114		*/
		0% Uncovered Elements: 5 (5) Complexity: 3 Complexity Density: 1
1115	0	public void setSeq(final int index, final java.lang.String vSeq)...
1116		throws java.lang.IndexOutOfBoundsException
1117		{
1118		// check bounds for index
1119	0	if (index < 0 || index >= this._seqList.size())
1120		{
1121	0	throw new IndexOutOfBoundsException("setSeq: Index value '" + index
1122		+ "' not in range [0.." + (this._seqList.size() - 1) + "]");
1123		}
1124
1125	0	this._seqList.set(index, vSeq);
1126		}
1127
1128		/**
1129		*
1130		*
1131		* @param vSeqArray
1132		*/
		0% Uncovered Elements: 5 (5) Complexity: 2 Complexity Density: 0.67
1133	0	public void setSeq(final java.lang.String[] vSeqArray)...
1134		{
1135		// -- copy array
1136	0	_seqList.clear();
1137
1138	0	for (int i = 0; i < vSeqArray.length; i++)
1139		{
1140	0	this._seqList.add(vSeqArray[i]);
1141		}
1142		}
1143
1144		/**
1145		* Sets the value of field 'showConsensusHistogram'.
1146		*
1147		* @param showConsensusHistogram
1148		* the value of field 'showConsensusHistogram'.
1149		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
1150	75	public void setShowConsensusHistogram(final boolean showConsensusHistogram)...
1151		{
1152	75	this._showConsensusHistogram = showConsensusHistogram;
1153	75	this._has_showConsensusHistogram = true;
1154		}
1155
1156		/**
1157		* Sets the value of field 'showSequenceLogo'.
1158		*
1159		* @param showSequenceLogo
1160		* the value of field 'showSequenceLogo'
1161		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
1162	75	public void setShowSequenceLogo(final boolean showSequenceLogo)...
1163		{
1164	75	this._showSequenceLogo = showSequenceLogo;
1165	75	this._has_showSequenceLogo = true;
1166		}
1167
1168		/**
1169		* Sets the value of field 'showUnconserved'.
1170		*
1171		* @param showUnconserved
1172		* the value of field 'showUnconserved'.
1173		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
1174	75	public void setShowUnconserved(final boolean showUnconserved)...
1175		{
1176	75	this._showUnconserved = showUnconserved;
1177	75	this._has_showUnconserved = true;
1178		}
1179
1180		/**
1181		* Sets the value of field 'start'.
1182		*
1183		* @param start
1184		* the value of field 'start'.
1185		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
1186	75	public void setStart(final int start)...
1187		{
1188	75	this._start = start;
1189	75	this._has_start = true;
1190		}
1191
1192		/**
1193		* Sets the value of field 'textCol1'.
1194		*
1195		* @param textCol1
1196		* the value of field 'textCol1'.
1197		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
1198	75	public void setTextCol1(final int textCol1)...
1199		{
1200	75	this._textCol1 = textCol1;
1201	75	this._has_textCol1 = true;
1202		}
1203
1204		/**
1205		* Sets the value of field 'textCol2'.
1206		*
1207		* @param textCol2
1208		* the value of field 'textCol2'.
1209		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
1210	75	public void setTextCol2(final int textCol2)...
1211		{
1212	75	this._textCol2 = textCol2;
1213	75	this._has_textCol2 = true;
1214		}
1215
1216		/**
1217		* Sets the value of field 'textColThreshold'.
1218		*
1219		* @param textColThreshold
1220		* the value of field 'textColThreshold'
1221		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
1222	75	public void setTextColThreshold(final int textColThreshold)...
1223		{
1224	75	this._textColThreshold = textColThreshold;
1225	75	this._has_textColThreshold = true;
1226		}
1227
1228		/**
1229		* Method unmarshal.
1230		*
1231		* @param reader
1232		* @throws org.exolab.castor.xml.MarshalException
1233		* if object is null or if any SAXException is thrown during
1234		* marshaling
1235		* @throws org.exolab.castor.xml.ValidationException
1236		* if this object is an invalid instance according to the schema
1237		* @return the unmarshaled jalview.schemabinding.version2.JGroup
1238		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
1239	0	public static jalview.schemabinding.version2.JGroup unmarshal(...
1240		final java.io.Reader reader)
1241		throws org.exolab.castor.xml.MarshalException,
1242		org.exolab.castor.xml.ValidationException
1243		{
1244	0	return (jalview.schemabinding.version2.JGroup) Unmarshaller.unmarshal(
1245		jalview.schemabinding.version2.JGroup.class, reader);
1246		}
1247
1248		/**
1249		*
1250		*
1251		* @throws org.exolab.castor.xml.ValidationException
1252		* if this object is an invalid instance according to the schema
1253		*/
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
1254	0	public void validate() throws org.exolab.castor.xml.ValidationException...
1255		{
1256	0	org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
1257	0	validator.validate(this);
1258		}
1259
1260		}