Classes

Class	Line #	Total Statements	Complexity	Uncovered Elements	TOTAL Coverage	Actions
Setting	22	95	74	70	0.590643359.1%	Show methods

Class Setting

Class Setting	Line # 22	Total Statements 95	Complexity 74	Uncovered Elements 70	TOTAL Coverage 0.590643359.1%
Setting()   Setting()	157157	3.03	1.01	0.00	1.0 1.0100%
addAttributeName(java.lang.String) : void   addAttributeName(java.lang.String) : void	176176	3.03	2.02	2.02	0.6 0.660%
addAttributeName(int,java.lang.String) : void   addAttributeName(int,java.lang.String) : void	197197	3.03	2.02	5.05	0.0 0.00%
deleteAutoScale() : void   deleteAutoScale() : void	213213	1.01	1.01	1.01	0.0 0.00%
deleteColour() : void   deleteColour() : void	220220	1.01	1.01	1.01	0.0 0.00%
deleteColourByLabel() : void   deleteColourByLabel() : void	227227	1.01	1.01	1.01	0.0 0.00%
deleteDisplay() : void   deleteDisplay() : void	234234	1.01	1.01	1.01	0.0 0.00%
deleteMax() : void   deleteMax() : void	241241	1.01	1.01	1.01	0.0 0.00%
deleteMin() : void   deleteMin() : void	248248	1.01	1.01	1.01	0.0 0.00%
deleteMincolour() : void   deleteMincolour() : void	255255	1.01	1.01	1.01	0.0 0.00%
deleteOrder() : void   deleteOrder() : void	262262	1.01	1.01	1.01	0.0 0.00%
deleteThreshold() : void   deleteThreshold() : void	269269	1.01	1.01	1.01	0.0 0.00%
deleteThreshstate() : void   deleteThreshstate() : void	276276	1.01	1.01	1.01	0.0 0.00%
enumerateAttributeName() : java.util.Enumeration   enumerateAttributeName() : java.util.Enumeration	286286	1.01	1.01	1.01	0.0 0.00%
getAttributeName(int) : java.lang.String   getAttributeName(int) : java.lang.String	299299	3.03	3.03	5.05	0.0 0.00%
getAttributeName() : java.lang.String[]   getAttributeName() : java.lang.String[]	322322	2.02	1.01	0.00	1.0 1.0100%
getAttributeNameCount() : int   getAttributeNameCount() : int	333333	1.01	1.01	0.00	1.0 1.0100%
getAutoScale() : boolean   getAutoScale() : boolean	343343	1.01	1.01	0.00	1.0 1.0100%
getColour() : int   getColour() : int	353353	1.01	1.01	0.00	1.0 1.0100%
getColourByLabel() : boolean   getColourByLabel() : boolean	363363	1.01	1.01	0.00	1.0 1.0100%
getDisplay() : boolean   getDisplay() : boolean	373373	1.01	1.01	0.00	1.0 1.0100%
getMatcherSet() : jalview.schemabinding.version2.MatcherSet   getMatcherSet() : jalview.schemabinding.version2.MatcherSet	384384	1.01	1.01	0.00	1.0 1.0100%
getMax() : float   getMax() : float	394394	1.01	1.01	0.00	1.0 1.0100%
getMin() : float   getMin() : float	404404	1.01	1.01	0.00	1.0 1.0100%
getMincolour() : int   getMincolour() : int	416416	1.01	1.01	0.00	1.0 1.0100%
getNoValueColour() : jalview.schemabinding.version2.types.NoValueColour   getNoValueColour() : jalview.schemabinding.version2.types.NoValueColour	426426	1.01	1.01	0.00	1.0 1.0100%
getOrder() : float   getOrder() : float	436436	1.01	1.01	0.00	1.0 1.0100%
getThreshold() : float   getThreshold() : float	448448	1.01	1.01	0.00	1.0 1.0100%
getThreshstate() : int   getThreshstate() : int	460460	1.01	1.01	0.00	1.0 1.0100%
getType() : java.lang.String   getType() : java.lang.String	470470	1.01	1.01	0.00	1.0 1.0100%
hasAutoScale() : boolean   hasAutoScale() : boolean	480480	1.01	1.01	0.00	1.0 1.0100%
hasColour() : boolean   hasColour() : boolean	490490	1.01	1.01	0.00	1.0 1.0100%
hasColourByLabel() : boolean   hasColourByLabel() : boolean	500500	1.01	1.01	0.00	1.0 1.0100%
hasDisplay() : boolean   hasDisplay() : boolean	510510	1.01	1.01	0.00	1.0 1.0100%
hasMax() : boolean   hasMax() : boolean	520520	1.01	1.01	0.00	1.0 1.0100%
hasMin() : boolean   hasMin() : boolean	530530	1.01	1.01	0.00	1.0 1.0100%
hasMincolour() : boolean   hasMincolour() : boolean	540540	1.01	1.01	0.00	1.0 1.0100%
hasOrder() : boolean   hasOrder() : boolean	550550	1.01	1.01	0.00	1.0 1.0100%
hasThreshold() : boolean   hasThreshold() : boolean	560560	1.01	1.01	0.00	1.0 1.0100%
hasThreshstate() : boolean   hasThreshstate() : boolean	570570	1.01	1.01	0.00	1.0 1.0100%
isAutoScale() : boolean   isAutoScale() : boolean	580580	1.01	1.01	1.01	0.0 0.00%
isColourByLabel() : boolean   isColourByLabel() : boolean	590590	1.01	1.01	1.01	0.0 0.00%
isDisplay() : boolean   isDisplay() : boolean	600600	1.01	1.01	1.01	0.0 0.00%
isValid() : boolean   isValid() : boolean	610610	4.04	2.02	4.04	0.0 0.00%
marshal(java.io.Writer) : void   marshal(java.io.Writer) : void	632632	1.01	1.01	1.01	0.0 0.00%
marshal(org.xml.sax.ContentHandler) : void   marshal(org.xml.sax.ContentHandler) : void	651651	1.01	1.01	1.01	0.0 0.00%
removeAllAttributeName() : void   removeAllAttributeName() : void	661661	1.01	1.01	1.01	0.0 0.00%
removeAttributeName(java.lang.String) : boolean   removeAttributeName(java.lang.String) : boolean	672672	2.02	1.01	2.02	0.0 0.00%
removeAttributeNameAt(int) : java.lang.String   removeAttributeNameAt(int) : java.lang.String	684684	2.02	1.01	2.02	0.0 0.00%
setAttributeName(int,java.lang.String) : void   setAttributeName(int,java.lang.String) : void	698698	3.03	3.03	5.05	0.0 0.00%
setAttributeName(java.lang.String[]) : void   setAttributeName(java.lang.String[]) : void	718718	3.03	2.02	0.00	1.0 1.0100%
setAutoScale(boolean) : void   setAutoScale(boolean) : void	735735	2.02	1.01	0.00	1.0 1.0100%
setColour(int) : void   setColour(int) : void	747747	2.02	1.01	0.00	1.0 1.0100%
setColourByLabel(boolean) : void   setColourByLabel(boolean) : void	759759	2.02	1.01	0.00	1.0 1.0100%
setDisplay(boolean) : void   setDisplay(boolean) : void	771771	2.02	1.01	0.00	1.0 1.0100%
setMatcherSet(jalview.schemabinding.version2.MatcherSet) : void   setMatcherSet(jalview.schemabinding.version2.MatcherSet) : void	784784	1.01	1.01	0.00	1.0 1.0100%
setMax(float) : void   setMax(float) : void	796796	2.02	1.01	0.00	1.0 1.0100%
setMin(float) : void   setMin(float) : void	808808	2.02	1.01	0.00	1.0 1.0100%
setMincolour(int) : void   setMincolour(int) : void	822822	2.02	1.01	0.00	1.0 1.0100%
setNoValueColour(jalview.schemabinding.version2.types.NoValueColour) : void   setNoValueColour(jalview.schemabinding.version2.types.NoValueColour) : void	834834	1.01	1.01	0.00	1.0 1.0100%
setOrder(float) : void   setOrder(float) : void	846846	2.02	1.01	0.00	1.0 1.0100%
setThreshold(float) : void   setThreshold(float) : void	860860	2.02	1.01	0.00	1.0 1.0100%
setThreshstate(int) : void   setThreshstate(int) : void	874874	2.02	1.01	0.00	1.0 1.0100%
setType(java.lang.String) : void   setType(java.lang.String) : void	886886	1.01	1.01	0.00	1.0 1.0100%
unmarshal(java.io.Reader) : jalview.schemabinding.version2.Setting   unmarshal(java.io.Reader) : jalview.schemabinding.version2.Setting	902902	1.01	1.01	1.01	0.0 0.00%
validate() : void   validate() : void	917917	2.02	1.01	2.02	0.0 0.00%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.5906433	jalview.io.Jalview2xmlTests.testSaveLoadFeatureColoursAndFiltersjalview.io.Jalview2xmlTests.testSaveLoadFeatureColoursAndFilters	1PASS
	0.30409357	jalview.io.Jalview2xmlTests.testStoreAndRecoverPDBEntryjalview.io.Jalview2xmlTests.testStoreAndRecoverPDBEntry	1PASS
	0.30409357	jalview.io.AnnotatedPDBFileInputTest.testJalviewProjectRelocationAnnotationjalview.io.AnnotatedPDBFileInputTest.testJalviewProjectRelocationAnnotation	1PASS
	0.30409357	jalview.io.Jalview2xmlTests.testStoreAndRecoverExpandedviewsjalview.io.Jalview2xmlTests.testStoreAndRecoverExpandedviews	1PASS
	0.30409357	jalview.io.Jalview2xmlTests.testStoreAndRecoverReferenceSeqSettingsjalview.io.Jalview2xmlTests.testStoreAndRecoverReferenceSeqSettings	1PASS
	0.18128654	jalview.io.Jalview2xmlTests.gatherViewsHerejalview.io.Jalview2xmlTests.gatherViewsHere	1PASS
	0.18128654	jalview.io.Jalview2xmlTests.viewRefPdbAnnotationjalview.io.Jalview2xmlTests.viewRefPdbAnnotation	1PASS
	0.18128654	jalview.io.Jalview2xmlTests.testCopyViewSettingsjalview.io.Jalview2xmlTests.testCopyViewSettings	1PASS
	0.18128654	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 Setting.
19		*
20		* @version $Revision$ $Date$
21		*/
		59.1% Uncovered Elements: 70 (171) Complexity: 74 Complexity Density: 0.78
22		public class Setting implements java.io.Serializable
23		{
24
25		// --------------------------/
26		// - Class/Member Variables -/
27		// --------------------------/
28
29		/**
30		* Field _type.
31		*/
32		private java.lang.String _type;
33
34		/**
35		* Field _colour.
36		*/
37		private int _colour;
38
39		/**
40		* keeps track of state for field: _colour
41		*/
42		private boolean _has_colour;
43
44		/**
45		* Field _display.
46		*/
47		private boolean _display;
48
49		/**
50		* keeps track of state for field: _display
51		*/
52		private boolean _has_display;
53
54		/**
55		* Field _order.
56		*/
57		private float _order;
58
59		/**
60		* keeps track of state for field: _order
61		*/
62		private boolean _has_order;
63
64		/**
65		* Optional minimum colour for graduated feature colour
66		*
67		*/
68		private int _mincolour;
69
70		/**
71		* keeps track of state for field: _mincolour
72		*/
73		private boolean _has_mincolour;
74
75		/**
76		* Field _noValueColour.
77		*/
78		private jalview.schemabinding.version2.types.NoValueColour _noValueColour = jalview.schemabinding.version2.types.NoValueColour
79		.valueOf("Min");
80
81		/**
82		* threshold value for graduated feature colour
83		*
84		*/
85		private float _threshold;
86
87		/**
88		* keeps track of state for field: _threshold
89		*/
90		private boolean _has_threshold;
91
92		/**
93		* threshold type for graduated feature colour
94		*
95		*/
96		private int _threshstate;
97
98		/**
99		* keeps track of state for field: _threshstate
100		*/
101		private boolean _has_threshstate;
102
103		/**
104		* Field _max.
105		*/
106		private float _max;
107
108		/**
109		* keeps track of state for field: _max
110		*/
111		private boolean _has_max;
112
113		/**
114		* Field _min.
115		*/
116		private float _min;
117
118		/**
119		* keeps track of state for field: _min
120		*/
121		private boolean _has_min;
122
123		/**
124		* Field _colourByLabel.
125		*/
126		private boolean _colourByLabel;
127
128		/**
129		* keeps track of state for field: _colourByLabel
130		*/
131		private boolean _has_colourByLabel;
132
133		/**
134		* Field _autoScale.
135		*/
136		private boolean _autoScale;
137
138		/**
139		* keeps track of state for field: _autoScale
140		*/
141		private boolean _has_autoScale;
142
143		/**
144		* name of feature attribute to colour by, or attribute and sub-attribute
145		*/
146		private java.util.Vector _attributeNameList;
147
148		/**
149		* optional filter(s) applied to the feature type
150		*/
151		private jalview.schemabinding.version2.MatcherSet _matcherSet;
152
153		// ----------------/
154		// - Constructors -/
155		// ----------------/
156
		100% Uncovered Elements: 0 (3) Complexity: 1 Complexity Density: 0.33
157	1456	public Setting()...
158		{
159	1456	super();
160	1456	setNoValueColour(jalview.schemabinding.version2.types.NoValueColour
161		.valueOf("Min"));
162	1456	this._attributeNameList = new java.util.Vector();
163		}
164
165		// -----------/
166		// - Methods -/
167		// -----------/
168
169		/**
170		*
171		*
172		* @param vAttributeName
173		* @throws java.lang.IndexOutOfBoundsException
174		* if the index given is outside the bounds of the collection
175		*/
		60% Uncovered Elements: 2 (5) Complexity: 2 Complexity Density: 0.67
176	3	public void addAttributeName(final java.lang.String vAttributeName)...
177		throws java.lang.IndexOutOfBoundsException
178		{
179		// check for the maximum size
180	3	if (this._attributeNameList.size() >= 2)
181		{
182	0	throw new IndexOutOfBoundsException(
183		"addAttributeName has a maximum of 2");
184		}
185
186	3	this._attributeNameList.addElement(vAttributeName);
187		}
188
189		/**
190		*
191		*
192		* @param index
193		* @param vAttributeName
194		* @throws java.lang.IndexOutOfBoundsException
195		* if the index given is outside the bounds of the collection
196		*/
		0% Uncovered Elements: 5 (5) Complexity: 2 Complexity Density: 0.67
197	0	public void addAttributeName(final int index,...
198		final java.lang.String vAttributeName)
199		throws java.lang.IndexOutOfBoundsException
200		{
201		// check for the maximum size
202	0	if (this._attributeNameList.size() >= 2)
203		{
204	0	throw new IndexOutOfBoundsException(
205		"addAttributeName has a maximum of 2");
206		}
207
208	0	this._attributeNameList.add(index, vAttributeName);
209		}
210
211		/**
212		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
213	0	public void deleteAutoScale()...
214		{
215	0	this._has_autoScale = false;
216		}
217
218		/**
219		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
220	0	public void deleteColour()...
221		{
222	0	this._has_colour = false;
223		}
224
225		/**
226		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
227	0	public void deleteColourByLabel()...
228		{
229	0	this._has_colourByLabel = false;
230		}
231
232		/**
233		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
234	0	public void deleteDisplay()...
235		{
236	0	this._has_display = false;
237		}
238
239		/**
240		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
241	0	public void deleteMax()...
242		{
243	0	this._has_max = false;
244		}
245
246		/**
247		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
248	0	public void deleteMin()...
249		{
250	0	this._has_min = false;
251		}
252
253		/**
254		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
255	0	public void deleteMincolour()...
256		{
257	0	this._has_mincolour = false;
258		}
259
260		/**
261		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
262	0	public void deleteOrder()...
263		{
264	0	this._has_order = false;
265		}
266
267		/**
268		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
269	0	public void deleteThreshold()...
270		{
271	0	this._has_threshold = false;
272		}
273
274		/**
275		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
276	0	public void deleteThreshstate()...
277		{
278	0	this._has_threshstate = false;
279		}
280
281		/**
282		* Method enumerateAttributeName.
283		*
284		* @return an Enumeration over all java.lang.String elements
285		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
286	0	public java.util.Enumeration enumerateAttributeName()...
287		{
288	0	return this._attributeNameList.elements();
289		}
290
291		/**
292		* Method getAttributeName.
293		*
294		* @param index
295		* @throws java.lang.IndexOutOfBoundsException
296		* if the index given is outside the bounds of the collection
297		* @return the value of the java.lang.String at the given index
298		*/
		0% Uncovered Elements: 5 (5) Complexity: 3 Complexity Density: 1
299	0	public java.lang.String getAttributeName(final int index)...
300		throws java.lang.IndexOutOfBoundsException
301		{
302		// check bounds for index
303	0	if (index < 0 || index >= this._attributeNameList.size())
304		{
305	0	throw new IndexOutOfBoundsException("getAttributeName: Index value '"
306		+ index + "' not in range [0.."
307		+ (this._attributeNameList.size() - 1) + "]");
308		}
309
310	0	return (java.lang.String) _attributeNameList.get(index);
311		}
312
313		/**
314		* Method getAttributeName.Returns the contents of the collection in an Array.
315		* <p>
316		* Note: Just in case the collection contents are changing in another thread,
317		* we pass a 0-length Array of the correct type into the API call. This way we
318		* <i>know</i> that the Array returned is of exactly the correct length.
319		*
320		* @return this collection as an Array
321		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
322	428	public java.lang.String[] getAttributeName()...
323		{
324	428	java.lang.String[] array = new java.lang.String[0];
325	428	return (java.lang.String[]) this._attributeNameList.toArray(array);
326		}
327
328		/**
329		* Method getAttributeNameCount.
330		*
331		* @return the size of this collection
332		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
333	4	public int getAttributeNameCount()...
334		{
335	4	return this._attributeNameList.size();
336		}
337
338		/**
339		* Returns the value of field 'autoScale'.
340		*
341		* @return the value of field 'AutoScale'.
342		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
343	12	public boolean getAutoScale()...
344		{
345	12	return this._autoScale;
346		}
347
348		/**
349		* Returns the value of field 'colour'.
350		*
351		* @return the value of field 'Colour'.
352		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
353	1669	public int getColour()...
354		{
355	1669	return this._colour;
356		}
357
358		/**
359		* Returns the value of field 'colourByLabel'.
360		*
361		* @return the value of field 'ColourByLabel'.
362		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
363	12	public boolean getColourByLabel()...
364		{
365	12	return this._colourByLabel;
366		}
367
368		/**
369		* Returns the value of field 'display'.
370		*
371		* @return the value of field 'Display'.
372		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
373	1669	public boolean getDisplay()...
374		{
375	1669	return this._display;
376		}
377
378		/**
379		* Returns the value of field 'matcherSet'. The field 'matcherSet' has the
380		* following description: optional filter(s) applied to the feature type
381		*
382		* @return the value of field 'MatcherSet'.
383		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
384	1669	public jalview.schemabinding.version2.MatcherSet getMatcherSet()...
385		{
386	1669	return this._matcherSet;
387		}
388
389		/**
390		* Returns the value of field 'max'.
391		*
392		* @return the value of field 'Max'.
393		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
394	12	public float getMax()...
395		{
396	12	return this._max;
397		}
398
399		/**
400		* Returns the value of field 'min'.
401		*
402		* @return the value of field 'Min'.
403		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
404	12	public float getMin()...
405		{
406	12	return this._min;
407		}
408
409		/**
410		* Returns the value of field 'mincolour'. The field 'mincolour' has the
411		* following description: Optional minimum colour for graduated feature colour
412		*
413		*
414		* @return the value of field 'Mincolour'.
415		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
416	12	public int getMincolour()...
417		{
418	12	return this._mincolour;
419		}
420
421		/**
422		* Returns the value of field 'noValueColour'.
423		*
424		* @return the value of field 'NoValueColour'.
425		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
426	430	public jalview.schemabinding.version2.types.NoValueColour getNoValueColour()...
427		{
428	430	return this._noValueColour;
429		}
430
431		/**
432		* Returns the value of field 'order'.
433		*
434		* @return the value of field 'Order'.
435		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
436	1669	public float getOrder()...
437		{
438	1669	return this._order;
439		}
440
441		/**
442		* Returns the value of field 'threshold'. The field 'threshold' has the
443		* following description: threshold value for graduated feature colour
444		*
445		*
446		* @return the value of field 'Threshold'.
447		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
448	12	public float getThreshold()...
449		{
450	12	return this._threshold;
451		}
452
453		/**
454		* Returns the value of field 'threshstate'. The field 'threshstate' has the
455		* following description: threshold type for graduated feature colour
456		*
457		*
458		* @return the value of field 'Threshstate'.
459		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
460	12	public int getThreshstate()...
461		{
462	12	return this._threshstate;
463		}
464
465		/**
466		* Returns the value of field 'type'.
467		*
468		* @return the value of field 'Type'.
469		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
470	1669	public java.lang.String getType()...
471		{
472	1669	return this._type;
473		}
474
475		/**
476		* Method hasAutoScale.
477		*
478		* @return true if at least one AutoScale has been added
479		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
480	430	public boolean hasAutoScale()...
481		{
482	430	return this._has_autoScale;
483		}
484
485		/**
486		* Method hasColour.
487		*
488		* @return true if at least one Colour has been added
489		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
490	426	public boolean hasColour()...
491		{
492	426	return this._has_colour;
493		}
494
495		/**
496		* Method hasColourByLabel.
497		*
498		* @return true if at least one ColourByLabel has been added
499		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
500	430	public boolean hasColourByLabel()...
501		{
502	430	return this._has_colourByLabel;
503		}
504
505		/**
506		* Method hasDisplay.
507		*
508		* @return true if at least one Display has been added
509		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
510	426	public boolean hasDisplay()...
511		{
512	426	return this._has_display;
513		}
514
515		/**
516		* Method hasMax.
517		*
518		* @return true if at least one Max has been added
519		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
520	426	public boolean hasMax()...
521		{
522	426	return this._has_max;
523		}
524
525		/**
526		* Method hasMin.
527		*
528		* @return true if at least one Min has been added
529		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
530	434	public boolean hasMin()...
531		{
532	434	return this._has_min;
533		}
534
535		/**
536		* Method hasMincolour.
537		*
538		* @return true if at least one Mincolour has been added
539		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
540	1669	public boolean hasMincolour()...
541		{
542	1669	return this._has_mincolour;
543		}
544
545		/**
546		* Method hasOrder.
547		*
548		* @return true if at least one Order has been added
549		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
550	1669	public boolean hasOrder()...
551		{
552	1669	return this._has_order;
553		}
554
555		/**
556		* Method hasThreshold.
557		*
558		* @return true if at least one Threshold has been added
559		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
560	430	public boolean hasThreshold()...
561		{
562	430	return this._has_threshold;
563		}
564
565		/**
566		* Method hasThreshstate.
567		*
568		* @return true if at least one Threshstate has been added
569		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
570	426	public boolean hasThreshstate()...
571		{
572	426	return this._has_threshstate;
573		}
574
575		/**
576		* Returns the value of field 'autoScale'.
577		*
578		* @return the value of field 'AutoScale'.
579		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
580	0	public boolean isAutoScale()...
581		{
582	0	return this._autoScale;
583		}
584
585		/**
586		* Returns the value of field 'colourByLabel'.
587		*
588		* @return the value of field 'ColourByLabel'.
589		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
590	0	public boolean isColourByLabel()...
591		{
592	0	return this._colourByLabel;
593		}
594
595		/**
596		* Returns the value of field 'display'.
597		*
598		* @return the value of field 'Display'.
599		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
600	0	public boolean isDisplay()...
601		{
602	0	return this._display;
603		}
604
605		/**
606		* Method isValid.
607		*
608		* @return true if this object is valid according to the schema
609		*/
		0% Uncovered Elements: 4 (4) Complexity: 2 Complexity Density: 0.5
610	0	public boolean isValid()...
611		{
612	0	try
613		{
614	0	validate();
615		} catch (org.exolab.castor.xml.ValidationException vex)
616		{
617	0	return false;
618		}
619	0	return true;
620		}
621
622		/**
623		*
624		*
625		* @param out
626		* @throws org.exolab.castor.xml.MarshalException
627		* if object is null or if any SAXException is thrown during
628		* marshaling
629		* @throws org.exolab.castor.xml.ValidationException
630		* if this object is an invalid instance according to the schema
631		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
632	0	public void marshal(final java.io.Writer out)...
633		throws org.exolab.castor.xml.MarshalException,
634		org.exolab.castor.xml.ValidationException
635		{
636	0	Marshaller.marshal(this, out);
637		}
638
639		/**
640		*
641		*
642		* @param handler
643		* @throws java.io.IOException
644		* if an IOException occurs during marshaling
645		* @throws org.exolab.castor.xml.ValidationException
646		* if this object is an invalid instance according to the schema
647		* @throws org.exolab.castor.xml.MarshalException
648		* if object is null or if any SAXException is thrown during
649		* marshaling
650		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
651	0	public void marshal(final org.xml.sax.ContentHandler handler)...
652		throws java.io.IOException,
653		org.exolab.castor.xml.MarshalException,
654		org.exolab.castor.xml.ValidationException
655		{
656	0	Marshaller.marshal(this, handler);
657		}
658
659		/**
660		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
661	0	public void removeAllAttributeName()...
662		{
663	0	this._attributeNameList.clear();
664		}
665
666		/**
667		* Method removeAttributeName.
668		*
669		* @param vAttributeName
670		* @return true if the object was removed from the collection.
671		*/
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
672	0	public boolean removeAttributeName(final java.lang.String vAttributeName)...
673		{
674	0	boolean removed = _attributeNameList.remove(vAttributeName);
675	0	return removed;
676		}
677
678		/**
679		* Method removeAttributeNameAt.
680		*
681		* @param index
682		* @return the element removed from the collection
683		*/
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
684	0	public java.lang.String removeAttributeNameAt(final int index)...
685		{
686	0	java.lang.Object obj = this._attributeNameList.remove(index);
687	0	return (java.lang.String) obj;
688		}
689
690		/**
691		*
692		*
693		* @param index
694		* @param vAttributeName
695		* @throws java.lang.IndexOutOfBoundsException
696		* if the index given is outside the bounds of the collection
697		*/
		0% Uncovered Elements: 5 (5) Complexity: 3 Complexity Density: 1
698	0	public void setAttributeName(final int index,...
699		final java.lang.String vAttributeName)
700		throws java.lang.IndexOutOfBoundsException
701		{
702		// check bounds for index
703	0	if (index < 0 || index >= this._attributeNameList.size())
704		{
705	0	throw new IndexOutOfBoundsException("setAttributeName: Index value '"
706		+ index + "' not in range [0.."
707		+ (this._attributeNameList.size() - 1) + "]");
708		}
709
710	0	this._attributeNameList.set(index, vAttributeName);
711		}
712
713		/**
714		*
715		*
716		* @param vAttributeNameArray
717		*/
		100% Uncovered Elements: 0 (5) Complexity: 2 Complexity Density: 0.67
718	2	public void setAttributeName(final java.lang.String[] vAttributeNameArray)...
719		{
720		// -- copy array
721	2	_attributeNameList.clear();
722
723	5	for (int i = 0; i < vAttributeNameArray.length; i++)
724		{
725	3	this._attributeNameList.add(vAttributeNameArray[i]);
726		}
727		}
728
729		/**
730		* Sets the value of field 'autoScale'.
731		*
732		* @param autoScale
733		* the value of field 'autoScale'.
734		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
735	8	public void setAutoScale(final boolean autoScale)...
736		{
737	8	this._autoScale = autoScale;
738	8	this._has_autoScale = true;
739		}
740
741		/**
742		* Sets the value of field 'colour'.
743		*
744		* @param colour
745		* the value of field 'colour'.
746		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
747	1456	public void setColour(final int colour)...
748		{
749	1456	this._colour = colour;
750	1456	this._has_colour = true;
751		}
752
753		/**
754		* Sets the value of field 'colourByLabel'.
755		*
756		* @param colourByLabel
757		* the value of field 'colourByLabel'.
758		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
759	8	public void setColourByLabel(final boolean colourByLabel)...
760		{
761	8	this._colourByLabel = colourByLabel;
762	8	this._has_colourByLabel = true;
763		}
764
765		/**
766		* Sets the value of field 'display'.
767		*
768		* @param display
769		* the value of field 'display'.
770		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
771	1456	public void setDisplay(final boolean display)...
772		{
773	1456	this._display = display;
774	1456	this._has_display = true;
775		}
776
777		/**
778		* Sets the value of field 'matcherSet'. The field 'matcherSet' has the
779		* following description: optional filter(s) applied to the feature type
780		*
781		* @param matcherSet
782		* the value of field 'matcherSet'.
783		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
784	6	public void setMatcherSet(...
785		final jalview.schemabinding.version2.MatcherSet matcherSet)
786		{
787	6	this._matcherSet = matcherSet;
788		}
789
790		/**
791		* Sets the value of field 'max'.
792		*
793		* @param max
794		* the value of field 'max'.
795		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
796	8	public void setMax(final float max)...
797		{
798	8	this._max = max;
799	8	this._has_max = true;
800		}
801
802		/**
803		* Sets the value of field 'min'.
804		*
805		* @param min
806		* the value of field 'min'.
807		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
808	8	public void setMin(final float min)...
809		{
810	8	this._min = min;
811	8	this._has_min = true;
812		}
813
814		/**
815		* Sets the value of field 'mincolour'. The field 'mincolour' has the
816		* following description: Optional minimum colour for graduated feature colour
817		*
818		*
819		* @param mincolour
820		* the value of field 'mincolour'.
821		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
822	8	public void setMincolour(final int mincolour)...
823		{
824	8	this._mincolour = mincolour;
825	8	this._has_mincolour = true;
826		}
827
828		/**
829		* Sets the value of field 'noValueColour'.
830		*
831		* @param noValueColour
832		* the value of field 'noValueColour'.
833		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
834	1673	public void setNoValueColour(...
835		final jalview.schemabinding.version2.types.NoValueColour noValueColour)
836		{
837	1673	this._noValueColour = noValueColour;
838		}
839
840		/**
841		* Sets the value of field 'order'.
842		*
843		* @param order
844		* the value of field 'order'.
845		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
846	1456	public void setOrder(final float order)...
847		{
848	1456	this._order = order;
849	1456	this._has_order = true;
850		}
851
852		/**
853		* Sets the value of field 'threshold'. The field 'threshold' has the
854		* following description: threshold value for graduated feature colour
855		*
856		*
857		* @param threshold
858		* the value of field 'threshold'.
859		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
860	8	public void setThreshold(final float threshold)...
861		{
862	8	this._threshold = threshold;
863	8	this._has_threshold = true;
864		}
865
866		/**
867		* Sets the value of field 'threshstate'. The field 'threshstate' has the
868		* following description: threshold type for graduated feature colour
869		*
870		*
871		* @param threshstate
872		* the value of field 'threshstate'.
873		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
874	8	public void setThreshstate(final int threshstate)...
875		{
876	8	this._threshstate = threshstate;
877	8	this._has_threshstate = true;
878		}
879
880		/**
881		* Sets the value of field 'type'.
882		*
883		* @param type
884		* the value of field 'type'.
885		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
886	1456	public void setType(final java.lang.String type)...
887		{
888	1456	this._type = type;
889		}
890
891		/**
892		* Method unmarshal.
893		*
894		* @param reader
895		* @throws org.exolab.castor.xml.MarshalException
896		* if object is null or if any SAXException is thrown during
897		* marshaling
898		* @throws org.exolab.castor.xml.ValidationException
899		* if this object is an invalid instance according to the schema
900		* @return the unmarshaled jalview.schemabinding.version2.Settin
901		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
902	0	public static jalview.schemabinding.version2.Setting unmarshal(...
903		final java.io.Reader reader)
904		throws org.exolab.castor.xml.MarshalException,
905		org.exolab.castor.xml.ValidationException
906		{
907	0	return (jalview.schemabinding.version2.Setting) Unmarshaller.unmarshal(
908		jalview.schemabinding.version2.Setting.class, reader);
909		}
910
911		/**
912		*
913		*
914		* @throws org.exolab.castor.xml.ValidationException
915		* if this object is an invalid instance according to the schema
916		*/
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
917	0	public void validate() throws org.exolab.castor.xml.ValidationException...
918		{
919	0	org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
920	0	validator.validate(this);
921		}
922
923		}