Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
ViewStyle	38	175	101	1.0100%	Show methods

Class ViewStyle

Class ViewStyle	Line # 38	Total Statements 175	Complexity 101	TOTAL Coverage 1.0100%
ViewStyle(ViewStyleI)   ViewStyle(ViewStyleI)	188188	47.047	1.01	1.0 1.0100%
ViewStyle()   ViewStyle()	242242	0.00	1.01	-1.0 -1.0 -
equals(Object) : boolean   equals(Object) : boolean	249249	8.08	3.03	1.0 1.0100%
hashCode() : int   hashCode() : int	327327	25.025	1.01	1.0 1.0100%
isUpperCasebold() : boolean   isUpperCasebold() : boolean	364364	1.01	1.01	1.0 1.0100%
setUpperCasebold(boolean) : void   setUpperCasebold(boolean) : void	374374	1.01	1.01	1.0 1.0100%
getAbovePIDThreshold() : boolean   getAbovePIDThreshold() : boolean	408408	1.01	1.01	1.0 1.0100%
getByConsensusSecondaryStructureSelected() : boolean   getByConsensusSecondaryStructureSelected() : boolean	414414	1.01	1.01	1.0 1.0100%
getCharHeight() : int   getCharHeight() : int	425425	1.01	1.01	1.0 1.0100%
getCharWidth() : int   getCharWidth() : int	436436	1.01	1.01	1.0 1.0100%
getColourAppliesToAllGroups() : boolean   getColourAppliesToAllGroups() : boolean	447447	1.01	1.01	1.0 1.0100%
getColourText() : boolean   getColourText() : boolean	458458	1.01	1.01	1.0 1.0100%
getConservationSelected() : boolean   getConservationSelected() : boolean	469469	1.01	1.01	1.0 1.0100%
getIncrement() : int   getIncrement() : int	480480	1.01	1.01	1.0 1.0100%
getScaleAboveWrapped() : boolean   getScaleAboveWrapped() : boolean	491491	1.01	1.01	1.0 1.0100%
getScaleLeftWrapped() : boolean   getScaleLeftWrapped() : boolean	502502	1.01	1.01	1.0 1.0100%
getScaleRightWrapped() : boolean   getScaleRightWrapped() : boolean	513513	1.01	1.01	1.0 1.0100%
getShowBoxes() : boolean   getShowBoxes() : boolean	524524	1.01	1.01	1.0 1.0100%
getShowHiddenMarkers() : boolean   getShowHiddenMarkers() : boolean	530530	1.01	1.01	1.0 1.0100%
getShowJVSuffix() : boolean   getShowJVSuffix() : boolean	541541	1.01	1.01	1.0 1.0100%
getShowText() : boolean   getShowText() : boolean	552552	1.01	1.01	1.0 1.0100%
getShowUnconserved() : boolean   getShowUnconserved() : boolean	558558	1.01	1.01	1.0 1.0100%
getTextColour() : Color   getTextColour() : Color	567567	1.01	1.01	1.0 1.0100%
getTextColour2() : Color   getTextColour2() : Color	576576	1.01	1.01	1.0 1.0100%
getThreshold() : int   getThreshold() : int	587587	1.01	1.01	1.0 1.0100%
getConsensusSecondaryStructureThreshold() : int   getConsensusSecondaryStructureThreshold() : int	593593	1.01	1.01	1.0 1.0100%
getThresholdTextColour() : int   getThresholdTextColour() : int	602602	1.01	1.01	1.0 1.0100%
getWrapAlignment() : boolean   getWrapAlignment() : boolean	613613	1.01	1.01	1.0 1.0100%
getWrappedWidth() : int   getWrappedWidth() : int	624624	1.01	1.01	1.0 1.0100%
isColourByReferenceSeq() : boolean   isColourByReferenceSeq() : boolean	630630	1.01	1.01	1.0 1.0100%
isConservationColourSelected() : boolean   isConservationColourSelected() : boolean	639639	1.01	1.01	1.0 1.0100%
isDisplayReferenceSeq() : boolean   isDisplayReferenceSeq() : boolean	645645	1.01	1.01	1.0 1.0100%
isRenderGaps() : boolean   isRenderGaps() : boolean	654654	1.01	1.01	1.0 1.0100%
isRightAlignIds() : boolean   isRightAlignIds() : boolean	660660	1.01	1.01	1.0 1.0100%
isSeqNameItalics() : boolean   isSeqNameItalics() : boolean	669669	1.01	1.01	1.0 1.0100%
isShowAnnotation() : boolean   isShowAnnotation() : boolean	675675	1.01	1.01	1.0 1.0100%
isShowColourText() : boolean   isShowColourText() : boolean	684684	1.01	1.01	1.0 1.0100%
isShowSequenceFeaturesHeight() : boolean   isShowSequenceFeaturesHeight() : boolean	693693	1.01	1.01	1.0 1.0100%
isShowSequenceFeatures() : boolean   isShowSequenceFeatures() : boolean	699699	1.01	1.01	1.0 1.0100%
setAbovePIDThreshold(boolean) : void   setAbovePIDThreshold(boolean) : void	712712	1.01	1.01	1.0 1.0100%
setByConsensusSecondaryStructureSelected(boolean) : void   setByConsensusSecondaryStructureSelected(boolean) : void	718718	1.01	1.01	1.0 1.0100%
setCharHeight(int) : void   setCharHeight(int) : void	730730	1.01	1.01	1.0 1.0100%
setCharWidth(int) : void   setCharWidth(int) : void	742742	1.01	1.01	1.0 1.0100%
setColourAppliesToAllGroups(boolean) : void   setColourAppliesToAllGroups(boolean) : void	753753	1.01	1.01	1.0 1.0100%
setColourByReferenceSeq(boolean) : void   setColourByReferenceSeq(boolean) : void	759759	1.01	1.01	1.0 1.0100%
setColourText(boolean) : void   setColourText(boolean) : void	771771	1.01	1.01	1.0 1.0100%
setConservationColourSelected(boolean) : void   setConservationColourSelected(boolean) : void	781781	1.01	1.01	1.0 1.0100%
setConservationSelected(boolean) : void   setConservationSelected(boolean) : void	794794	1.01	1.01	1.0 1.0100%
setDisplayReferenceSeq(boolean) : void   setDisplayReferenceSeq(boolean) : void	800800	1.01	1.01	1.0 1.0100%
setIncrement(int) : void   setIncrement(int) : void	812812	1.01	1.01	1.0 1.0100%
setConsensusSecondaryStructureThreshold(int) : void   setConsensusSecondaryStructureThreshold(int) : void	824824	1.01	1.01	1.0 1.0100%
setRenderGaps(boolean) : void   setRenderGaps(boolean) : void	836836	1.01	1.01	1.0 1.0100%
setRightAlignIds(boolean) : void   setRightAlignIds(boolean) : void	842842	1.01	1.01	1.0 1.0100%
setScaleAboveWrapped(boolean) : void   setScaleAboveWrapped(boolean) : void	854854	1.01	1.01	1.0 1.0100%
setScaleLeftWrapped(boolean) : void   setScaleLeftWrapped(boolean) : void	866866	1.01	1.01	1.0 1.0100%
setScaleRightWrapped(boolean) : void   setScaleRightWrapped(boolean) : void	879879	1.01	1.01	1.0 1.0100%
setSeqNameItalics(boolean) : void   setSeqNameItalics(boolean) : void	885885	1.01	1.01	1.0 1.0100%
setShowAnnotation(boolean) : void   setShowAnnotation(boolean) : void	891891	1.01	1.01	1.0 1.0100%
setShowBoxes(boolean) : void   setShowBoxes(boolean) : void	903903	1.01	1.01	1.0 1.0100%
setShowColourText(boolean) : void   setShowColourText(boolean) : void	913913	1.01	1.01	1.0 1.0100%
setShowHiddenMarkers(boolean) : void   setShowHiddenMarkers(boolean) : void	919919	1.01	1.01	1.0 1.0100%
setShowJVSuffix(boolean) : void   setShowJVSuffix(boolean) : void	931931	1.01	1.01	1.0 1.0100%
setShowSequenceFeaturesHeight(boolean) : void   setShowSequenceFeaturesHeight(boolean) : void	937937	1.01	1.01	1.0 1.0100%
setShowSequenceFeatures(boolean) : void   setShowSequenceFeatures(boolean) : void	950950	1.01	1.01	1.0 1.0100%
setShowText(boolean) : void   setShowText(boolean) : void	962962	1.01	1.01	1.0 1.0100%
setShowUnconserved(boolean) : void   setShowUnconserved(boolean) : void	968968	1.01	1.01	1.0 1.0100%
setTextColour(Color) : void   setTextColour(Color) : void	978978	1.01	1.01	1.0 1.0100%
setTextColour2(Color) : void   setTextColour2(Color) : void	988988	1.01	1.01	1.0 1.0100%
setThreshold(int) : void   setThreshold(int) : void	10001000	1.01	1.01	1.0 1.0100%
setThresholdTextColour(int) : void   setThresholdTextColour(int) : void	10101010	1.01	1.01	1.0 1.0100%
setWrapAlignment(boolean) : void   setWrapAlignment(boolean) : void	10221022	1.01	1.01	1.0 1.0100%
setWrappedWidth(int) : void   setWrappedWidth(int) : void	10341034	1.01	1.01	1.0 1.0100%
sameStyle(ViewStyleI) : boolean   sameStyle(ViewStyleI) : boolean	10401040	1.01	1.01	1.0 1.0100%
getFontName() : String   getFontName() : String	10461046	1.01	1.01	1.0 1.0100%
getFontSize() : int   getFontSize() : int	10521052	1.01	1.01	1.0 1.0100%
getFontStyle() : int   getFontStyle() : int	10581058	1.01	1.01	1.0 1.0100%
setFontName(String) : void   setFontName(String) : void	10641064	1.01	1.01	1.0 1.0100%
setFontSize(int) : void   setFontSize(int) : void	10701070	1.01	1.01	1.0 1.0100%
setFontStyle(int) : void   setFontStyle(int) : void	10771077	1.01	1.01	1.0 1.0100%
getIdWidth() : int   getIdWidth() : int	10831083	1.01	1.01	1.0 1.0100%
setIdWidth(int) : void   setIdWidth(int) : void	10931093	1.01	1.01	1.0 1.0100%
isCentreColumnLabels() : boolean   isCentreColumnLabels() : boolean	11021102	1.01	1.01	1.0 1.0100%
setCentreColumnLabels(boolean) : void   setCentreColumnLabels(boolean) : void	11121112	1.01	1.01	1.0 1.0100%
isShowDBRefs() : boolean   isShowDBRefs() : boolean	11211121	1.01	1.01	1.0 1.0100%
setShowDBRefs(boolean) : void   setShowDBRefs(boolean) : void	11311131	1.01	1.01	1.0 1.0100%
isShowNPFeats() : boolean   isShowNPFeats() : boolean	11401140	1.01	1.01	1.0 1.0100%
setShowNPFeats(boolean) : void   setShowNPFeats(boolean) : void	11501150	1.01	1.01	1.0 1.0100%
isScaleProteinAsCdna() : boolean   isScaleProteinAsCdna() : boolean	11561156	1.01	1.01	1.0 1.0100%
setScaleProteinAsCdna(boolean) : void   setScaleProteinAsCdna(boolean) : void	11621162	1.01	1.01	1.0 1.0100%
isProteinFontAsCdna() : boolean   isProteinFontAsCdna() : boolean	11681168	1.01	1.01	1.0 1.0100%
setProteinFontAsCdna(boolean) : void   setProteinFontAsCdna(boolean) : void	11741174	1.01	1.01	1.0 1.0100%
setShowComplementFeatures(boolean) : void   setShowComplementFeatures(boolean) : void	11801180	1.01	1.01	1.0 1.0100%
isShowComplementFeatures() : boolean   isShowComplementFeatures() : boolean	11861186	1.01	1.01	1.0 1.0100%
setShowComplementFeaturesOnTop(boolean) : void   setShowComplementFeaturesOnTop(boolean) : void	11921192	1.01	1.01	1.0 1.0100%
isShowComplementFeaturesOnTop() : boolean   isShowComplementFeaturesOnTop() : boolean	11981198	1.01	1.01	1.0 1.0100%
getSecondaryStructureSources() : List<String>   getSecondaryStructureSources() : List<String>	12041204	1.01	1.01	1.0 1.0100%
setSecondaryStructureSources(List<String>) : void   setSecondaryStructureSources(List<String>) : void	12101210	1.01	1.01	1.0 1.0100%
setShowStructureProvider(boolean) : void   setShowStructureProvider(boolean) : void	12171217	1.01	1.01	1.0 1.0100%
isShowStructureProvider() : boolean   isShowStructureProvider() : boolean	12231223	1.01	1.01	1.0 1.0100%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.8586956	jalview.gui.AlignmentPanelTest.testSetOverviewTitlejalview.gui.AlignmentPanelTest.testSetOverviewTitle	1PASS
	0.8586956	jalview.project.Jalview2xmlTests.testStoreAndRecoverOverviewjalview.project.Jalview2xmlTests.testStoreAndRecoverOverview	1PASS

 

Source view

1		/*
2		* Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3		* Copyright (C) $$Year-Rel$$ The Jalview Authors
4		*
5		* This file is part of Jalview.
6		*
7		* Jalview is free software: you can redistribute it and/or
8		* modify it under the terms of the GNU General Public License
9		* as published by the Free Software Foundation, either version 3
10		* of the License, or (at your option) any later version.
11		*
12		* Jalview is distributed in the hope that it will be useful, but
13		* WITHOUT ANY WARRANTY; without even the implied warranty
14		* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15		* PURPOSE. See the GNU General Public License for more details.
16		*
17		* You should have received a copy of the GNU General Public License
18		* along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19		* The Jalview Authors are detailed in the 'AUTHORS' file.
20		*/
21		package jalview.viewmodel.styles;
22
23		import java.awt.Color;
24		import java.util.Arrays;
25		import java.util.List;
26
27		import jalview.api.ViewStyleI;
28
29		/**
30		* A container for holding alignment view properties. View properties are
31		* data-independent, which means they can be safely copied between views
32		* involving different alignment data without causing exceptions in the
33		* rendering system.
34		*
35		* @author jprocter
36		*
37		*/
		100% Uncovered Elements: 0 (276) Complexity: 101 Complexity Density: 0.58
38		public class ViewStyle implements ViewStyleI
39		{
40		private boolean abovePIDThreshold = false;
41
42		int charHeight;
43
44		int charWidth;
45
46		int idWidth = -1;
47
48		/**
49		* gui state - changes to colour scheme propagated to all groups
50		*/
51		private boolean colourAppliesToAllGroups;
52
53		/**
54		* centre columnar annotation labels in displayed alignment annotation
55		*/
56		boolean centreColumnLabels = false;
57
58		private boolean showdbrefs;
59
60		private boolean shownpfeats;
61
62		// --------END Structure Conservation
63
64		/**
65		* colour according to the reference sequence defined on the alignment
66		*/
67		private boolean colourByReferenceSeq = false;
68
69		boolean conservationColourSelected = false;
70
71		boolean byConsensusSecondaryStructureSelected = false;
72
73		/**
74		* show the reference sequence in the alignment view
75		*/
76		private boolean displayReferenceSeq = false;
77
78		private int increment;
79
80		private int consensusSecondaryStructureThreshold;
81
82		/**
83		* display gap characters
84		*/
85		boolean renderGaps = true;
86
87		private boolean rightAlignIds = false;
88
89		boolean scaleAboveWrapped = false;
90
91		boolean scaleLeftWrapped = true;
92
93		boolean scaleRightWrapped = true;
94
95		boolean seqNameItalics;
96
97		/**
98		* show annotation tracks on the alignment
99		*/
100		private boolean showAnnotation = true;
101
102		/**
103		* render each residue in a coloured box
104		*/
105		boolean showBoxes = true;
106
107		/**
108		* Colour sequence text
109		*/
110		boolean showColourText = false;
111
112		/**
113		* show blue triangles
114		*/
115		boolean showHiddenMarkers = true;
116
117		/**
118		* show /start-end in ID panel
119		*/
120		boolean showJVSuffix = true;
121
122		/**
123		* scale features height according to score
124		*/
125		boolean showSeqFeaturesHeight;
126
127		/**
128		* display setting for showing/hiding sequence features on alignment view
129		*/
130		boolean showSequenceFeatures = false;
131
132		/**
133		* display sequence symbols
134		*/
135		boolean showText = true;
136
137		/**
138		* show non-conserved residues only
139		*/
140		protected boolean showUnconserved = false;
141
142		Color textColour = Color.black;
143
144		Color textColour2 = Color.white;
145
146		/**
147		* PID or consensus threshold
148		*/
149		int threshold;
150
151		/**
152		* threshold for switching between textColour & textColour2
153		*/
154		int thresholdTextColour = 0;
155
156		/**
157		* upper case characters in sequence are shown in bold
158		*/
159		boolean upperCasebold = false;
160
161		/**
162		* name of base font for view
163		*/
164		private String fontName;
165
166		/**
167		* size for base font
168		*/
169		private int fontSize;
170
171		/*
172		* If true, scale protein residues to 3 times width of cDNA bases (in
173		* SplitFrame views only)
174		*/
175		private boolean scaleProteinAsCdna = true;
176
177		/*
178		* if true, font changes to protein or cDNA are applied to both
179		* sides of a split screen
180		*/
181		private boolean proteinFontAsCdna = true;
182
183		/**
184		* Copy constructor
185		*
186		* @param vs
187		*/
		100% Uncovered Elements: 0 (47) Complexity: 1 Complexity Density: 0.02
188	242	public ViewStyle(ViewStyleI vs)...
189		{
190	242	setAbovePIDThreshold(vs.getAbovePIDThreshold());
191	242	setCentreColumnLabels(vs.isCentreColumnLabels());
192	242	setCharHeight(vs.getCharHeight());
193	242	setCharWidth(vs.getCharWidth());
194	242	setColourAppliesToAllGroups(vs.getColourAppliesToAllGroups());
195	242	setColourByReferenceSeq(vs.isColourByReferenceSeq());
196	242	setColourText(vs.getColourText());
197	242	setByConsensusSecondaryStructureSelected(
198		vs.getByConsensusSecondaryStructureSelected());
199	242	setConsensusSecondaryStructureThreshold(
200		vs.getConsensusSecondaryStructureThreshold());
201	242	setConservationColourSelected(vs.isConservationColourSelected());
202	242	setConservationSelected(vs.getConservationSelected());
203	242	setDisplayReferenceSeq(vs.isDisplayReferenceSeq());
204	242	setFontName(vs.getFontName());
205	242	setFontSize(vs.getFontSize());
206	242	setFontStyle(vs.getFontStyle());
207	242	setIdWidth(vs.getIdWidth());
208	242	setIncrement(vs.getIncrement());
209	242	setRenderGaps(vs.isRenderGaps());
210	242	setRightAlignIds(vs.isRightAlignIds());
211	242	setScaleAboveWrapped(vs.getScaleAboveWrapped());
212	242	setScaleLeftWrapped(vs.getScaleLeftWrapped());
213	242	setScaleProteinAsCdna(vs.isScaleProteinAsCdna());
214	242	setProteinFontAsCdna(vs.isProteinFontAsCdna());
215	242	setScaleRightWrapped(vs.getScaleRightWrapped());
216	242	setSeqNameItalics(vs.isSeqNameItalics());
217	242	setShowAnnotation(vs.isShowAnnotation());
218	242	setShowBoxes(vs.getShowBoxes());
219	242	setShowColourText(vs.isShowColourText());
220	242	setShowDBRefs(vs.isShowDBRefs());
221	242	setShowHiddenMarkers(vs.getShowHiddenMarkers());
222	242	setShowJVSuffix(vs.getShowJVSuffix());
223	242	setShowNPFeats(vs.isShowNPFeats());
224	242	setShowSequenceFeaturesHeight(vs.isShowSequenceFeaturesHeight());
225	242	setShowSequenceFeatures(vs.isShowSequenceFeatures());
226	242	setShowComplementFeatures(vs.isShowComplementFeatures());
227	242	setShowComplementFeaturesOnTop(vs.isShowComplementFeaturesOnTop());
228	242	setShowText(vs.getShowText());
229	242	setShowUnconserved(vs.getShowUnconserved());
230	242	setTextColour(vs.getTextColour());
231	242	setTextColour2(vs.getTextColour2());
232	242	setThreshold(vs.getThreshold());
233	242	setThresholdTextColour(vs.getThresholdTextColour());
234	242	setUpperCasebold(vs.isUpperCasebold());
235	242	setWrapAlignment(vs.getWrapAlignment());
236	242	setWrappedWidth(vs.getWrappedWidth());
237	242	setSecondaryStructureSources(vs.getSecondaryStructureSources());
238	242	setShowStructureProvider(vs.isShowStructureProvider());
239		// ViewStyle.configureFrom(this, viewStyle);
240		}
241
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
242	534	public ViewStyle()...
243		{
244		}
245
246		/**
247		* Returns true if all attributes of the ViewStyles have the same value
248		*/
		100% Uncovered Elements: 0 (10) Complexity: 3 Complexity Density: 0.38
249	52	@Override...
250		public boolean equals(Object other)
251		{
252	52	if (other == null || !(other instanceof ViewStyle))
253		{
254	2	return false;
255		}
256	50	ViewStyle vs = (ViewStyle) other;
257
258	50	boolean match = (getAbovePIDThreshold() == vs.getAbovePIDThreshold()
259		&& isCentreColumnLabels() == vs.isCentreColumnLabels()
260		&& getCharHeight() == vs.getCharHeight()
261		&& getCharWidth() == vs.getCharWidth()
262		&& getColourAppliesToAllGroups() == vs
263		.getColourAppliesToAllGroups()
264		&& isColourByReferenceSeq() == vs.isColourByReferenceSeq()
265		&& getColourText() == vs.getColourText()
266		&& isConservationColourSelected() == vs
267		.isConservationColourSelected()
268		&& getByConsensusSecondaryStructureSelected() == vs
269		.getByConsensusSecondaryStructureSelected()
270		&& getConservationSelected() == vs.getConservationSelected()
271		&& isDisplayReferenceSeq() == vs.isDisplayReferenceSeq()
272		&& getFontSize() == vs.getFontSize()
273		&& getFontStyle() == vs.getFontStyle()
274		&& getIdWidth() == vs.getIdWidth()
275		&& getIncrement() == vs.getIncrement()
276		&& getConsensusSecondaryStructureThreshold() == vs
277		.getConsensusSecondaryStructureThreshold()
278		&& isRenderGaps() == vs.isRenderGaps()
279		&& isRightAlignIds() == vs.isRightAlignIds()
280		&& getScaleAboveWrapped() == vs.getScaleAboveWrapped()
281		&& getScaleLeftWrapped() == vs.getScaleLeftWrapped()
282		&& isScaleProteinAsCdna() == vs.isScaleProteinAsCdna()
283		&& isProteinFontAsCdna() == vs.isProteinFontAsCdna()
284		&& getScaleRightWrapped() == vs.getScaleRightWrapped()
285		&& isSeqNameItalics() == vs.isSeqNameItalics()
286		&& isShowAnnotation() == vs.isShowAnnotation()
287		&& getShowBoxes() == vs.getShowBoxes()
288		&& isShowColourText() == vs.isShowColourText()
289		&& isShowDBRefs() == vs.isShowDBRefs()
290		&& getShowHiddenMarkers() == vs.getShowHiddenMarkers()
291		&& getShowJVSuffix() == vs.getShowJVSuffix()
292		&& isShowNPFeats() == vs.isShowNPFeats()
293		&& isShowSequenceFeaturesHeight() == vs
294		.isShowSequenceFeaturesHeight()
295		&& isShowSequenceFeatures() == vs.isShowSequenceFeatures()
296		&& isShowComplementFeatures() == vs.isShowComplementFeatures()
297		&& isShowComplementFeaturesOnTop() == vs
298		.isShowComplementFeaturesOnTop()
299		&& getShowText() == vs.getShowText()
300		&& getShowUnconserved() == vs.getShowUnconserved()
301		&& getThreshold() == vs.getThreshold()
302		&& getThresholdTextColour() == vs.getThresholdTextColour()
303		&& isUpperCasebold() == vs.isUpperCasebold()
304		&& getWrapAlignment() == vs.getWrapAlignment()
305		&& getWrappedWidth() == vs.getWrappedWidth()
306		&& getSecondaryStructureSources() == vs
307		.getSecondaryStructureSources()
308		&& isShowStructureProvider() == vs.isShowStructureProvider());
309		/*
310		* and compare non-primitive types; syntax below will match null with null
311		* values
312		*/
313	50	match = match && String.valueOf(getFontName())
314		.equals(String.valueOf(vs.getFontName()));
315	50	match = match && String.valueOf(getTextColour())
316		.equals(String.valueOf(vs.getTextColour()));
317	50	match = match && String.valueOf(getTextColour2())
318		.equals(String.valueOf(vs.getTextColour2()));
319	50	return match;
320		// return equivalent(this, (ViewStyle) other);
321		}
322
323		/**
324		* Overridden to ensure that whenever vs1.equals(vs2) then vs1.hashCode() ==
325		* vs2.hashCode()
326		*/
		100% Uncovered Elements: 0 (25) Complexity: 1 Complexity Density: 0.04
327	92	@Override...
328		public int hashCode()
329		{
330		/*
331		* No need to include all properties, just a selection...
332		*/
333	92	int hash = 0;
334	92	int m = 1;
335		// Boolean.hashCode returns 1231 or 1237
336	92	hash += m++ * Boolean.valueOf(this.abovePIDThreshold).hashCode();
337	92	hash += m++ * Boolean.valueOf(this.centreColumnLabels).hashCode();
338	92	hash += m++ * Boolean.valueOf(this.colourAppliesToAllGroups).hashCode();
339	92	hash += m++ * Boolean.valueOf(this.displayReferenceSeq).hashCode();
340	92	hash += m++ * Boolean.valueOf(this.renderGaps).hashCode();
341	92	hash += m++ * Boolean.valueOf(this.rightAlignIds).hashCode();
342	92	hash += m++ * Boolean.valueOf(this.scaleProteinAsCdna).hashCode();
343	92	hash += m++ * Boolean.valueOf(this.scaleRightWrapped).hashCode();
344	92	hash += m++ * Boolean.valueOf(this.seqNameItalics).hashCode();
345	92	hash += m++ * Boolean.valueOf(this.showAnnotation).hashCode();
346	92	hash += m++ * Boolean.valueOf(this.showBoxes).hashCode();
347	92	hash += m++ * Boolean.valueOf(this.showdbrefs).hashCode();
348	92	hash += m++ * Boolean.valueOf(this.showJVSuffix).hashCode();
349	92	hash += m++ * Boolean.valueOf(this.showSequenceFeatures).hashCode();
350	92	hash += m++ * Boolean.valueOf(this.showUnconserved).hashCode();
351	92	hash += m++ * Boolean.valueOf(this.wrapAlignment).hashCode();
352	92	hash += m++ * this.charHeight;
353	92	hash += m++ * this.charWidth;
354	92	hash += m++ * fontSize;
355	92	hash += m++ * fontStyle;
356	92	hash += m++ * idWidth;
357	92	hash += String.valueOf(this.fontName).hashCode();
358	92	return hash;
359		}
360
361		/**
362		* @return the upperCasebold
363		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
364	264	@Override...
365		public boolean isUpperCasebold()
366		{
367	264	return upperCasebold;
368		}
369
370		/**
371		* @param upperCasebold
372		* the upperCasebold to set
373		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
374	242	@Override...
375		public void setUpperCasebold(boolean upperCasebold)
376		{
377	242	this.upperCasebold = upperCasebold;
378		}
379
380		/**
381		* flag for wrapping
382		*/
383		boolean wrapAlignment = false;
384
385		/**
386		* number columns in wrapped alignment
387		*/
388		int wrappedWidth;
389
390		private int fontStyle;
391
392		private boolean showComplementFeatures;
393
394		private boolean showComplementFeaturesOnTop;
395
396		/**
397		* secondary structure annotation rows shown in the view
398		*/
399		private List<String> secondaryStructureSources = Arrays.asList(new String[0]);
400
401		private boolean showStructureProvider;
402
403		/**
404		* GUI state
405		*
406		* @return true if percent identity threshold is applied to shading
407		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
408	1253	@Override...
409		public boolean getAbovePIDThreshold()
410		{
411	1253	return abovePIDThreshold;
412		}
413
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
414	1233	@Override...
415		public boolean getByConsensusSecondaryStructureSelected()
416		{
417	1233	return byConsensusSecondaryStructureSelected;
418		}
419
420		/**
421		* DOCUMENT ME!
422		*
423		* @return DOCUMENT ME!
424		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
425	114548	@Override...
426		public int getCharHeight()
427		{
428	114548	return charHeight;
429		}
430
431		/**
432		* DOCUMENT ME!
433		*
434		* @return DOCUMENT ME!
435		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
436	1530020	@Override...
437		public int getCharWidth()
438		{
439	1530023	return charWidth;
440		}
441
442		/**
443		*
444		*
445		* @return flag indicating if colourchanges propagated to all groups
446		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
447	1334	@Override...
448		public boolean getColourAppliesToAllGroups()
449		{
450	1334	return colourAppliesToAllGroups;
451		}
452
453		/**
454		* DOCUMENT ME!
455		*
456		* @return DOCUMENT ME!
457		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
458	480500	@Override...
459		public boolean getColourText()
460		{
461	480502	return showColourText;
462		}
463
464		/**
465		* GUI state
466		*
467		* @return true if conservation based shading is enabled
468		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
469	1407	@Override...
470		public boolean getConservationSelected()
471		{
472	1407	return conservationColourSelected;
473		}
474
475		/**
476		* GUI State
477		*
478		* @return get scalar for bleaching colourschemes by conservation
479		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
480	312	@Override...
481		public int getIncrement()
482		{
483	312	return increment;
484		}
485
486		/**
487		* DOCUMENT ME!
488		*
489		* @return DOCUMENT ME!
490		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
491	1256	@Override...
492		public boolean getScaleAboveWrapped()
493		{
494	1256	return scaleAboveWrapped;
495		}
496
497		/**
498		* DOCUMENT ME!
499		*
500		* @return DOCUMENT ME!
501		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
502	1664	@Override...
503		public boolean getScaleLeftWrapped()
504		{
505	1664	return scaleLeftWrapped;
506		}
507
508		/**
509		* DOCUMENT ME!
510		*
511		* @return DOCUMENT ME!
512		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
513	2515	@Override...
514		public boolean getScaleRightWrapped()
515		{
516	2515	return scaleRightWrapped;
517		}
518
519		/**
520		* DOCUMENT ME!
521		*
522		* @return DOCUMENT ME!
523		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
524	553882	@Override...
525		public boolean getShowBoxes()
526		{
527	553883	return showBoxes;
528		}
529
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
530	6367	@Override...
531		public boolean getShowHiddenMarkers()
532		{
533	6367	return showHiddenMarkers;
534		}
535
536		/**
537		* DOCUMENT ME!
538		*
539		* @return DOCUMENT ME!
540		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
541	47631	@Override...
542		public boolean getShowJVSuffix()
543		{
544	47631	return showJVSuffix;
545		}
546
547		/**
548		* DOCUMENT ME!
549		*
550		* @return DOCUMENT ME!
551		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
552	481149	@Override...
553		public boolean getShowText()
554		{
555	481149	return showText;
556		}
557
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
558	478003	@Override...
559		public boolean getShowUnconserved()
560		{
561	478000	return showUnconserved;
562		}
563
564		/**
565		* @return the textColour
566		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
567	739243	@Override...
568		public Color getTextColour()
569		{
570	739245	return textColour;
571		}
572
573		/**
574		* @return the textColour2
575		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
576	298	@Override...
577		public Color getTextColour2()
578		{
579	298	return textColour2;
580		}
581
582		/**
583		* DOCUMENT ME!
584		*
585		* @return DOCUMENT ME!
586		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
587	268	@Override...
588		public int getThreshold()
589		{
590	268	return threshold;
591		}
592
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
593	310	@Override...
594		public int getConsensusSecondaryStructureThreshold()
595		{
596	310	return consensusSecondaryStructureThreshold;
597		}
598
599		/**
600		* @return the thresholdTextColour
601		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
602	480442	@Override...
603		public int getThresholdTextColour()
604		{
605	480444	return thresholdTextColour;
606		}
607
608		/**
609		* DOCUMENT ME!
610		*
611		* @return DOCUMENT ME!
612		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
613	32575	@Override...
614		public boolean getWrapAlignment()
615		{
616	32575	return wrapAlignment;
617		}
618
619		/**
620		* DOCUMENT ME!
621		*
622		* @return DOCUMENT ME!
623		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
624	262	@Override...
625		public int getWrappedWidth()
626		{
627	262	return wrappedWidth;
628		}
629
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
630	333	@Override...
631		public boolean isColourByReferenceSeq()
632		{
633	333	return colourByReferenceSeq;
634		}
635
636		/**
637		* @return the conservationColourSelected
638		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
639	414	@Override...
640		public boolean isConservationColourSelected()
641		{
642	414	return conservationColourSelected;
643		}
644
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
645	966	@Override...
646		public boolean isDisplayReferenceSeq()
647		{
648	966	return displayReferenceSeq;
649		}
650
651		/**
652		* @return the renderGaps
653		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
654	3951	@Override...
655		public boolean isRenderGaps()
656		{
657	3951	return renderGaps;
658		}
659
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
660	15213	@Override...
661		public boolean isRightAlignIds()
662		{
663	15213	return rightAlignIds;
664		}
665
666		/**
667		* @return the seqNameItalics
668		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
669	3408	@Override...
670		public boolean isSeqNameItalics()
671		{
672	3408	return seqNameItalics;
673		}
674
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
675	4746	@Override...
676		public boolean isShowAnnotation()
677		{
678	4746	return showAnnotation;
679		}
680
681		/**
682		* @return the showColourText
683		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
684	991	@Override...
685		public boolean isShowColourText()
686		{
687	991	return showColourText;
688		}
689
690		/**
691		* @return the showSeqFeaturesHeight
692		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
693	280	@Override...
694		public boolean isShowSequenceFeaturesHeight()
695		{
696	280	return showSeqFeaturesHeight;
697		}
698
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
699	463094	@Override...
700		public boolean isShowSequenceFeatures()
701		{
702	463155	return showSequenceFeatures;
703		}
704
705		/**
706		* GUI state
707		*
708		*
709		* @param b
710		* indicate if percent identity threshold is applied to shading
711		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
712	340	@Override...
713		public void setAbovePIDThreshold(boolean b)
714		{
715	340	abovePIDThreshold = b;
716		}
717
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
718	331	@Override...
719		public void setByConsensusSecondaryStructureSelected(boolean b)
720		{
721	331	byConsensusSecondaryStructureSelected = b;
722		}
723
724		/**
725		* DOCUMENT ME!
726		*
727		* @param h
728		* DOCUMENT ME!
729		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
730	866	@Override...
731		public void setCharHeight(int h)
732		{
733	866	this.charHeight = h;
734		}
735
736		/**
737		* DOCUMENT ME!
738		*
739		* @param w
740		* DOCUMENT ME!
741		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
742	869	@Override...
743		public void setCharWidth(int w)
744		{
745	869	this.charWidth = w;
746		}
747
748		/**
749		* @param value
750		* indicating if subsequent colourscheme changes will be propagated
751		* to all groups
752		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
753	967	@Override...
754		public void setColourAppliesToAllGroups(boolean b)
755		{
756	967	colourAppliesToAllGroups = b;
757		}
758
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
759	252	@Override...
760		public void setColourByReferenceSeq(boolean colourByReferenceSeq)
761		{
762	252	this.colourByReferenceSeq = colourByReferenceSeq;
763		}
764
765		/**
766		* DOCUMENT ME!
767		*
768		* @param state
769		* DOCUMENT ME!
770		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
771	331	@Override...
772		public void setColourText(boolean state)
773		{
774	331	showColourText = state;
775		}
776
777		/**
778		* @param conservationColourSelected
779		* the conservationColourSelected to set
780		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
781	242	@Override...
782		public void setConservationColourSelected(
783		boolean conservationColourSelected)
784		{
785	242	this.conservationColourSelected = conservationColourSelected;
786		}
787
788		/**
789		* GUI state
790		*
791		* @param b
792		* enable conservation based shading
793		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
794	339	@Override...
795		public void setConservationSelected(boolean b)
796		{
797	339	conservationColourSelected = b;
798		}
799
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
800	252	@Override...
801		public void setDisplayReferenceSeq(boolean displayReferenceSeq)
802		{
803	252	this.displayReferenceSeq = displayReferenceSeq;
804		}
805
806		/**
807		*
808		* @param inc
809		* set the scalar for bleaching colourschemes according to degree of
810		* conservation
811		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
812	331	@Override...
813		public void setIncrement(int inc)
814		{
815	331	increment = inc;
816		}
817
818		/**
819		*
820		* @param val
821		* set the scalar for bleaching colourschemes according to degree of
822		* secondary structure conservation
823		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
824	331	@Override...
825		public void setConsensusSecondaryStructureThreshold(int val)
826		{
827	331	consensusSecondaryStructureThreshold = val;
828		}
829
830		/**
831		* DOCUMENT ME!
832		*
833		* @param state
834		* DOCUMENT ME!
835		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
836	331	@Override...
837		public void setRenderGaps(boolean state)
838		{
839	331	renderGaps = state;
840		}
841
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
842	863	@Override...
843		public void setRightAlignIds(boolean rightAlignIds)
844		{
845	863	this.rightAlignIds = rightAlignIds;
846		}
847
848		/**
849		* DOCUMENT ME!
850		*
851		* @param b
852		* DOCUMENT ME!
853		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
854	251	@Override...
855		public void setScaleAboveWrapped(boolean b)
856		{
857	251	scaleAboveWrapped = b;
858		}
859
860		/**
861		* DOCUMENT ME!
862		*
863		* @param b
864		* DOCUMENT ME!
865		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
866	253	@Override...
867		public void setScaleLeftWrapped(boolean b)
868		{
869	253	scaleLeftWrapped = b;
870		}
871
872		/**
873		*
874		*
875		* @param scaleRightWrapped
876		* - true or false
877		*/
878
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
879	251	@Override...
880		public void setScaleRightWrapped(boolean b)
881		{
882	251	scaleRightWrapped = b;
883		}
884
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
885	774	@Override...
886		public void setSeqNameItalics(boolean italics)
887		{
888	774	seqNameItalics = italics;
889		}
890
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
891	954	@Override...
892		public void setShowAnnotation(boolean b)
893		{
894	954	showAnnotation = b;
895		}
896
897		/**
898		* DOCUMENT ME!
899		*
900		* @param state
901		* DOCUMENT ME!
902		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
903	331	@Override...
904		public void setShowBoxes(boolean state)
905		{
906	331	showBoxes = state;
907		}
908
909		/**
910		* @param showColourText
911		* the showColourText to set
912		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
913	242	@Override...
914		public void setShowColourText(boolean showColourText)
915		{
916	242	this.showColourText = showColourText;
917		}
918
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
919	242	@Override...
920		public void setShowHiddenMarkers(boolean show)
921		{
922	242	showHiddenMarkers = show;
923		}
924
925		/**
926		* DOCUMENT ME!
927		*
928		* @param b
929		* DOCUMENT ME!
930		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
931	864	@Override...
932		public void setShowJVSuffix(boolean b)
933		{
934	864	showJVSuffix = b;
935		}
936
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
937	242	@Override...
938		public void setShowSequenceFeaturesHeight(boolean selected)
939		{
940	242	showSeqFeaturesHeight = selected;
941
942		}
943
944		/**
945		* set the flag
946		*
947		* @param b
948		* features are displayed if true
949		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
950	391	@Override...
951		public void setShowSequenceFeatures(boolean b)
952		{
953	391	showSequenceFeatures = b;
954		}
955
956		/**
957		* DOCUMENT ME!
958		*
959		* @param state
960		* DOCUMENT ME!
961		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
962	331	@Override...
963		public void setShowText(boolean state)
964		{
965	331	showText = state;
966		}
967
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
968	863	@Override...
969		public void setShowUnconserved(boolean showunconserved)
970		{
971	863	showUnconserved = showunconserved;
972		}
973
974		/**
975		* @param textColour
976		* the textColour to set
977		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
978	331	@Override...
979		public void setTextColour(Color textColour)
980		{
981	331	this.textColour = textColour;
982		}
983
984		/**
985		* @param textColour2
986		* the textColour2 to set
987		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
988	331	@Override...
989		public void setTextColour2(Color textColour2)
990		{
991	331	this.textColour2 = textColour2;
992		}
993
994		/**
995		* DOCUMENT ME!
996		*
997		* @param thresh
998		* DOCUMENT ME!
999		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1000	352	@Override...
1001		public void setThreshold(int thresh)
1002		{
1003	352	threshold = thresh;
1004		}
1005
1006		/**
1007		* @param thresholdTextColour
1008		* the thresholdTextColour to set
1009		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1010	331	@Override...
1011		public void setThresholdTextColour(int thresholdTextColour)
1012		{
1013	331	this.thresholdTextColour = thresholdTextColour;
1014		}
1015
1016		/**
1017		* DOCUMENT ME!
1018		*
1019		* @param state
1020		* DOCUMENT ME!
1021		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1022	875	@Override...
1023		public void setWrapAlignment(boolean state)
1024		{
1025	875	wrapAlignment = state;
1026		}
1027
1028		/**
1029		* DOCUMENT ME!
1030		*
1031		* @param w
1032		* DOCUMENT ME!
1033		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1034	1123	@Override...
1035		public void setWrappedWidth(int w)
1036		{
1037	1123	this.wrappedWidth = w;
1038		}
1039
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1040	3	@Override...
1041		public boolean sameStyle(ViewStyleI that)
1042		{
1043	3	return this.equals(that);
1044		}
1045
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1046	344	@Override...
1047		public String getFontName()
1048		{
1049	344	return fontName;
1050		}
1051
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1052	408	@Override...
1053		public int getFontSize()
1054		{
1055	408	return fontSize;
1056		}
1057
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1058	406	@Override...
1059		public int getFontStyle()
1060		{
1061	406	return fontStyle;
1062		}
1063
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1064	956	@Override...
1065		public void setFontName(String name)
1066		{
1067	956	fontName = name;
1068		}
1069
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1070	956	@Override...
1071		public void setFontSize(int size)
1072		{
1073	956	fontSize = size;
1074
1075		}
1076
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1077	956	@Override...
1078		public void setFontStyle(int style)
1079		{
1080	956	fontStyle = style;
1081		}
1082
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1083	7202	@Override...
1084		public int getIdWidth()
1085		{
1086	7202	return idWidth;
1087		}
1088
1089		/**
1090		* @param idWidth
1091		* the idWidth to set
1092		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1093	943	@Override...
1094		public void setIdWidth(int idWidth)
1095		{
1096	943	this.idWidth = idWidth;
1097		}
1098
1099		/**
1100		* @return the centreColumnLabels
1101		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1102	1043	@Override...
1103		public boolean isCentreColumnLabels()
1104		{
1105	1043	return centreColumnLabels;
1106		}
1107
1108		/**
1109		* @param centreColumnLabels
1110		* the centreColumnLabels to set
1111		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1112	863	@Override...
1113		public void setCentreColumnLabels(boolean centreColumnLabels)
1114		{
1115	863	this.centreColumnLabels = centreColumnLabels;
1116		}
1117
1118		/**
1119		* @return the showdbrefs
1120		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1121	1039	@Override...
1122		public boolean isShowDBRefs()
1123		{
1124	1039	return showdbrefs;
1125		}
1126
1127		/**
1128		* @param showdbrefs
1129		* the showdbrefs to set
1130		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1131	863	@Override...
1132		public void setShowDBRefs(boolean showdbrefs)
1133		{
1134	863	this.showdbrefs = showdbrefs;
1135		}
1136
1137		/**
1138		* @return the shownpfeats
1139		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1140	1033	@Override...
1141		public boolean isShowNPFeats()
1142		{
1143	1033	return shownpfeats;
1144		}
1145
1146		/**
1147		* @param shownpfeats
1148		* the shownpfeats to set
1149		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1150	863	@Override...
1151		public void setShowNPFeats(boolean shownpfeats)
1152		{
1153	863	this.shownpfeats = shownpfeats;
1154		}
1155
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1156	351	@Override...
1157		public boolean isScaleProteinAsCdna()
1158		{
1159	351	return this.scaleProteinAsCdna;
1160		}
1161
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1162	863	@Override...
1163		public void setScaleProteinAsCdna(boolean b)
1164		{
1165	863	this.scaleProteinAsCdna = b;
1166		}
1167
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1168	298	@Override...
1169		public boolean isProteinFontAsCdna()
1170		{
1171	298	return proteinFontAsCdna;
1172		}
1173
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1174	242	@Override...
1175		public void setProteinFontAsCdna(boolean b)
1176		{
1177	242	proteinFontAsCdna = b;
1178		}
1179
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1180	331	@Override...
1181		public void setShowComplementFeatures(boolean b)
1182		{
1183	331	showComplementFeatures = b;
1184		}
1185
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1186	463546	@Override...
1187		public boolean isShowComplementFeatures()
1188		{
1189	463602	return showComplementFeatures;
1190		}
1191
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1192	331	@Override...
1193		public void setShowComplementFeaturesOnTop(boolean b)
1194		{
1195	331	showComplementFeaturesOnTop = b;
1196		}
1197
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1198	323	@Override...
1199		public boolean isShowComplementFeaturesOnTop()
1200		{
1201	323	return showComplementFeaturesOnTop;
1202		}
1203
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1204	3534	@Override...
1205		public List<String> getSecondaryStructureSources()
1206		{
1207	3534	return secondaryStructureSources;
1208		}
1209
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1210	2060	@Override...
1211		public void setSecondaryStructureSources(
1212		List<String> secondaryStructureSources)
1213		{
1214	2060	this.secondaryStructureSources = secondaryStructureSources;
1215		}
1216
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1217	863	@Override...
1218		public void setShowStructureProvider(boolean showStructureProvider)
1219		{
1220	863	this.showStructureProvider = showStructureProvider;
1221		}
1222
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1223	6827	@Override...
1224		public boolean isShowStructureProvider()
1225		{
1226	6827	return showStructureProvider;
1227		}
1228		}