Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
ViewStyle	37	175	101	1.0100%	Show methods

Class ViewStyle

Class ViewStyle	Line # 37	Total Statements 175	Complexity 101	TOTAL Coverage 1.0100%
ViewStyle(ViewStyleI)   ViewStyle(ViewStyleI)	187187	47.047	1.01	1.0 1.0100%
ViewStyle()   ViewStyle()	241241	0.00	1.01	-1.0 -1.0 -
equals(Object) : boolean   equals(Object) : boolean	248248	8.08	3.03	1.0 1.0100%
hashCode() : int   hashCode() : int	326326	25.025	1.01	1.0 1.0100%
isUpperCasebold() : boolean   isUpperCasebold() : boolean	363363	1.01	1.01	1.0 1.0100%
setUpperCasebold(boolean) : void   setUpperCasebold(boolean) : void	373373	1.01	1.01	1.0 1.0100%
getAbovePIDThreshold() : boolean   getAbovePIDThreshold() : boolean	407407	1.01	1.01	1.0 1.0100%
getByConsensusSecondaryStructureSelected() : boolean   getByConsensusSecondaryStructureSelected() : boolean	413413	1.01	1.01	1.0 1.0100%
getCharHeight() : int   getCharHeight() : int	424424	1.01	1.01	1.0 1.0100%
getCharWidth() : int   getCharWidth() : int	435435	1.01	1.01	1.0 1.0100%
getColourAppliesToAllGroups() : boolean   getColourAppliesToAllGroups() : boolean	446446	1.01	1.01	1.0 1.0100%
getColourText() : boolean   getColourText() : boolean	457457	1.01	1.01	1.0 1.0100%
getConservationSelected() : boolean   getConservationSelected() : boolean	468468	1.01	1.01	1.0 1.0100%
getIncrement() : int   getIncrement() : int	479479	1.01	1.01	1.0 1.0100%
getScaleAboveWrapped() : boolean   getScaleAboveWrapped() : boolean	490490	1.01	1.01	1.0 1.0100%
getScaleLeftWrapped() : boolean   getScaleLeftWrapped() : boolean	501501	1.01	1.01	1.0 1.0100%
getScaleRightWrapped() : boolean   getScaleRightWrapped() : boolean	512512	1.01	1.01	1.0 1.0100%
getShowBoxes() : boolean   getShowBoxes() : boolean	523523	1.01	1.01	1.0 1.0100%
getShowHiddenMarkers() : boolean   getShowHiddenMarkers() : boolean	529529	1.01	1.01	1.0 1.0100%
getShowJVSuffix() : boolean   getShowJVSuffix() : boolean	540540	1.01	1.01	1.0 1.0100%
getShowText() : boolean   getShowText() : boolean	551551	1.01	1.01	1.0 1.0100%
getShowUnconserved() : boolean   getShowUnconserved() : boolean	557557	1.01	1.01	1.0 1.0100%
getTextColour() : Color   getTextColour() : Color	566566	1.01	1.01	1.0 1.0100%
getTextColour2() : Color   getTextColour2() : Color	575575	1.01	1.01	1.0 1.0100%
getThreshold() : int   getThreshold() : int	586586	1.01	1.01	1.0 1.0100%
getConsensusSecondaryStructureThreshold() : int   getConsensusSecondaryStructureThreshold() : int	592592	1.01	1.01	1.0 1.0100%
getThresholdTextColour() : int   getThresholdTextColour() : int	601601	1.01	1.01	1.0 1.0100%
getWrapAlignment() : boolean   getWrapAlignment() : boolean	612612	1.01	1.01	1.0 1.0100%
getWrappedWidth() : int   getWrappedWidth() : int	623623	1.01	1.01	1.0 1.0100%
isColourByReferenceSeq() : boolean   isColourByReferenceSeq() : boolean	629629	1.01	1.01	1.0 1.0100%
isConservationColourSelected() : boolean   isConservationColourSelected() : boolean	638638	1.01	1.01	1.0 1.0100%
isDisplayReferenceSeq() : boolean   isDisplayReferenceSeq() : boolean	644644	1.01	1.01	1.0 1.0100%
isRenderGaps() : boolean   isRenderGaps() : boolean	653653	1.01	1.01	1.0 1.0100%
isRightAlignIds() : boolean   isRightAlignIds() : boolean	659659	1.01	1.01	1.0 1.0100%
isSeqNameItalics() : boolean   isSeqNameItalics() : boolean	668668	1.01	1.01	1.0 1.0100%
isShowAnnotation() : boolean   isShowAnnotation() : boolean	674674	1.01	1.01	1.0 1.0100%
isShowColourText() : boolean   isShowColourText() : boolean	683683	1.01	1.01	1.0 1.0100%
isShowSequenceFeaturesHeight() : boolean   isShowSequenceFeaturesHeight() : boolean	692692	1.01	1.01	1.0 1.0100%
isShowSequenceFeatures() : boolean   isShowSequenceFeatures() : boolean	698698	1.01	1.01	1.0 1.0100%
setAbovePIDThreshold(boolean) : void   setAbovePIDThreshold(boolean) : void	711711	1.01	1.01	1.0 1.0100%
setByConsensusSecondaryStructureSelected(boolean) : void   setByConsensusSecondaryStructureSelected(boolean) : void	717717	1.01	1.01	1.0 1.0100%
setCharHeight(int) : void   setCharHeight(int) : void	729729	1.01	1.01	1.0 1.0100%
setCharWidth(int) : void   setCharWidth(int) : void	741741	1.01	1.01	1.0 1.0100%
setColourAppliesToAllGroups(boolean) : void   setColourAppliesToAllGroups(boolean) : void	752752	1.01	1.01	1.0 1.0100%
setColourByReferenceSeq(boolean) : void   setColourByReferenceSeq(boolean) : void	758758	1.01	1.01	1.0 1.0100%
setColourText(boolean) : void   setColourText(boolean) : void	770770	1.01	1.01	1.0 1.0100%
setConservationColourSelected(boolean) : void   setConservationColourSelected(boolean) : void	780780	1.01	1.01	1.0 1.0100%
setConservationSelected(boolean) : void   setConservationSelected(boolean) : void	793793	1.01	1.01	1.0 1.0100%
setDisplayReferenceSeq(boolean) : void   setDisplayReferenceSeq(boolean) : void	799799	1.01	1.01	1.0 1.0100%
setIncrement(int) : void   setIncrement(int) : void	811811	1.01	1.01	1.0 1.0100%
setConsensusSecondaryStructureThreshold(int) : void   setConsensusSecondaryStructureThreshold(int) : void	823823	1.01	1.01	1.0 1.0100%
setRenderGaps(boolean) : void   setRenderGaps(boolean) : void	835835	1.01	1.01	1.0 1.0100%
setRightAlignIds(boolean) : void   setRightAlignIds(boolean) : void	841841	1.01	1.01	1.0 1.0100%
setScaleAboveWrapped(boolean) : void   setScaleAboveWrapped(boolean) : void	853853	1.01	1.01	1.0 1.0100%
setScaleLeftWrapped(boolean) : void   setScaleLeftWrapped(boolean) : void	865865	1.01	1.01	1.0 1.0100%
setScaleRightWrapped(boolean) : void   setScaleRightWrapped(boolean) : void	878878	1.01	1.01	1.0 1.0100%
setSeqNameItalics(boolean) : void   setSeqNameItalics(boolean) : void	884884	1.01	1.01	1.0 1.0100%
setShowAnnotation(boolean) : void   setShowAnnotation(boolean) : void	890890	1.01	1.01	1.0 1.0100%
setShowBoxes(boolean) : void   setShowBoxes(boolean) : void	902902	1.01	1.01	1.0 1.0100%
setShowColourText(boolean) : void   setShowColourText(boolean) : void	912912	1.01	1.01	1.0 1.0100%
setShowHiddenMarkers(boolean) : void   setShowHiddenMarkers(boolean) : void	918918	1.01	1.01	1.0 1.0100%
setShowJVSuffix(boolean) : void   setShowJVSuffix(boolean) : void	930930	1.01	1.01	1.0 1.0100%
setShowSequenceFeaturesHeight(boolean) : void   setShowSequenceFeaturesHeight(boolean) : void	936936	1.01	1.01	1.0 1.0100%
setShowSequenceFeatures(boolean) : void   setShowSequenceFeatures(boolean) : void	949949	1.01	1.01	1.0 1.0100%
setShowText(boolean) : void   setShowText(boolean) : void	961961	1.01	1.01	1.0 1.0100%
setShowUnconserved(boolean) : void   setShowUnconserved(boolean) : void	967967	1.01	1.01	1.0 1.0100%
setTextColour(Color) : void   setTextColour(Color) : void	977977	1.01	1.01	1.0 1.0100%
setTextColour2(Color) : void   setTextColour2(Color) : void	987987	1.01	1.01	1.0 1.0100%
setThreshold(int) : void   setThreshold(int) : void	999999	1.01	1.01	1.0 1.0100%
setThresholdTextColour(int) : void   setThresholdTextColour(int) : void	10091009	1.01	1.01	1.0 1.0100%
setWrapAlignment(boolean) : void   setWrapAlignment(boolean) : void	10211021	1.01	1.01	1.0 1.0100%
setWrappedWidth(int) : void   setWrappedWidth(int) : void	10331033	1.01	1.01	1.0 1.0100%
sameStyle(ViewStyleI) : boolean   sameStyle(ViewStyleI) : boolean	10391039	1.01	1.01	1.0 1.0100%
getFontName() : String   getFontName() : String	10451045	1.01	1.01	1.0 1.0100%
getFontSize() : int   getFontSize() : int	10511051	1.01	1.01	1.0 1.0100%
getFontStyle() : int   getFontStyle() : int	10571057	1.01	1.01	1.0 1.0100%
setFontName(String) : void   setFontName(String) : void	10631063	1.01	1.01	1.0 1.0100%
setFontSize(int) : void   setFontSize(int) : void	10691069	1.01	1.01	1.0 1.0100%
setFontStyle(int) : void   setFontStyle(int) : void	10761076	1.01	1.01	1.0 1.0100%
getIdWidth() : int   getIdWidth() : int	10821082	1.01	1.01	1.0 1.0100%
setIdWidth(int) : void   setIdWidth(int) : void	10921092	1.01	1.01	1.0 1.0100%
isCentreColumnLabels() : boolean   isCentreColumnLabels() : boolean	11011101	1.01	1.01	1.0 1.0100%
setCentreColumnLabels(boolean) : void   setCentreColumnLabels(boolean) : void	11111111	1.01	1.01	1.0 1.0100%
isShowDBRefs() : boolean   isShowDBRefs() : boolean	11201120	1.01	1.01	1.0 1.0100%
setShowDBRefs(boolean) : void   setShowDBRefs(boolean) : void	11301130	1.01	1.01	1.0 1.0100%
isShowNPFeats() : boolean   isShowNPFeats() : boolean	11391139	1.01	1.01	1.0 1.0100%
setShowNPFeats(boolean) : void   setShowNPFeats(boolean) : void	11491149	1.01	1.01	1.0 1.0100%
isScaleProteinAsCdna() : boolean   isScaleProteinAsCdna() : boolean	11551155	1.01	1.01	1.0 1.0100%
setScaleProteinAsCdna(boolean) : void   setScaleProteinAsCdna(boolean) : void	11611161	1.01	1.01	1.0 1.0100%
isProteinFontAsCdna() : boolean   isProteinFontAsCdna() : boolean	11671167	1.01	1.01	1.0 1.0100%
setProteinFontAsCdna(boolean) : void   setProteinFontAsCdna(boolean) : void	11731173	1.01	1.01	1.0 1.0100%
setShowComplementFeatures(boolean) : void   setShowComplementFeatures(boolean) : void	11791179	1.01	1.01	1.0 1.0100%
isShowComplementFeatures() : boolean   isShowComplementFeatures() : boolean	11851185	1.01	1.01	1.0 1.0100%
setShowComplementFeaturesOnTop(boolean) : void   setShowComplementFeaturesOnTop(boolean) : void	11911191	1.01	1.01	1.0 1.0100%
isShowComplementFeaturesOnTop() : boolean   isShowComplementFeaturesOnTop() : boolean	11971197	1.01	1.01	1.0 1.0100%
getSecondaryStructureSources() : List<String>   getSecondaryStructureSources() : List<String>	12031203	1.01	1.01	1.0 1.0100%
setSecondaryStructureSources(List<String>) : void   setSecondaryStructureSources(List<String>) : void	12091209	1.01	1.01	1.0 1.0100%
setShowStructureProvider(boolean) : void   setShowStructureProvider(boolean) : void	12161216	1.01	1.01	1.0 1.0100%
isShowStructureProvider() : boolean   isShowStructureProvider() : boolean	12221222	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.List;
25
26		import jalview.api.ViewStyleI;
27
28		/**
29		* A container for holding alignment view properties. View properties are
30		* data-independent, which means they can be safely copied between views
31		* involving different alignment data without causing exceptions in the
32		* rendering system.
33		*
34		* @author jprocter
35		*
36		*/
		100% Uncovered Elements: 0 (276) Complexity: 101 Complexity Density: 0.58
37		public class ViewStyle implements ViewStyleI
38		{
39		private boolean abovePIDThreshold = false;
40
41		int charHeight;
42
43		int charWidth;
44
45		int idWidth = -1;
46
47		/**
48		* gui state - changes to colour scheme propagated to all groups
49		*/
50		private boolean colourAppliesToAllGroups;
51
52		/**
53		* centre columnar annotation labels in displayed alignment annotation
54		*/
55		boolean centreColumnLabels = false;
56
57		private boolean showdbrefs;
58
59		private boolean shownpfeats;
60
61		// --------END Structure Conservation
62
63		/**
64		* colour according to the reference sequence defined on the alignment
65		*/
66		private boolean colourByReferenceSeq = false;
67
68		boolean conservationColourSelected = false;
69
70		boolean byConsensusSecondaryStructureSelected = false;
71
72		/**
73		* show the reference sequence in the alignment view
74		*/
75		private boolean displayReferenceSeq = false;
76
77		private int increment;
78
79		private int consensusSecondaryStructureThreshold;
80
81		/**
82		* display gap characters
83		*/
84		boolean renderGaps = true;
85
86		private boolean rightAlignIds = false;
87
88		boolean scaleAboveWrapped = false;
89
90		boolean scaleLeftWrapped = true;
91
92		boolean scaleRightWrapped = true;
93
94		boolean seqNameItalics;
95
96		/**
97		* show annotation tracks on the alignment
98		*/
99		private boolean showAnnotation = true;
100
101		/**
102		* render each residue in a coloured box
103		*/
104		boolean showBoxes = true;
105
106		/**
107		* Colour sequence text
108		*/
109		boolean showColourText = false;
110
111		/**
112		* show blue triangles
113		*/
114		boolean showHiddenMarkers = true;
115
116		/**
117		* show /start-end in ID panel
118		*/
119		boolean showJVSuffix = true;
120
121		/**
122		* scale features height according to score
123		*/
124		boolean showSeqFeaturesHeight;
125
126		/**
127		* display setting for showing/hiding sequence features on alignment view
128		*/
129		boolean showSequenceFeatures = false;
130
131		/**
132		* display sequence symbols
133		*/
134		boolean showText = true;
135
136		/**
137		* show non-conserved residues only
138		*/
139		protected boolean showUnconserved = false;
140
141		Color textColour = Color.black;
142
143		Color textColour2 = Color.white;
144
145		/**
146		* PID or consensus threshold
147		*/
148		int threshold;
149
150		/**
151		* threshold for switching between textColour & textColour2
152		*/
153		int thresholdTextColour = 0;
154
155		/**
156		* upper case characters in sequence are shown in bold
157		*/
158		boolean upperCasebold = false;
159
160		/**
161		* name of base font for view
162		*/
163		private String fontName;
164
165		/**
166		* size for base font
167		*/
168		private int fontSize;
169
170		/*
171		* If true, scale protein residues to 3 times width of cDNA bases (in
172		* SplitFrame views only)
173		*/
174		private boolean scaleProteinAsCdna = true;
175
176		/*
177		* if true, font changes to protein or cDNA are applied to both
178		* sides of a split screen
179		*/
180		private boolean proteinFontAsCdna = true;
181
182		/**
183		* Copy constructor
184		*
185		* @param vs
186		*/
		100% Uncovered Elements: 0 (47) Complexity: 1 Complexity Density: 0.02
187	232	public ViewStyle(ViewStyleI vs)...
188		{
189	232	setAbovePIDThreshold(vs.getAbovePIDThreshold());
190	232	setCentreColumnLabels(vs.isCentreColumnLabels());
191	232	setCharHeight(vs.getCharHeight());
192	232	setCharWidth(vs.getCharWidth());
193	232	setColourAppliesToAllGroups(vs.getColourAppliesToAllGroups());
194	232	setColourByReferenceSeq(vs.isColourByReferenceSeq());
195	232	setColourText(vs.getColourText());
196	232	setByConsensusSecondaryStructureSelected(
197		vs.getByConsensusSecondaryStructureSelected());
198	232	setConsensusSecondaryStructureThreshold(
199		vs.getConsensusSecondaryStructureThreshold());
200	232	setConservationColourSelected(vs.isConservationColourSelected());
201	232	setConservationSelected(vs.getConservationSelected());
202	232	setDisplayReferenceSeq(vs.isDisplayReferenceSeq());
203	232	setFontName(vs.getFontName());
204	232	setFontSize(vs.getFontSize());
205	232	setFontStyle(vs.getFontStyle());
206	232	setIdWidth(vs.getIdWidth());
207	232	setIncrement(vs.getIncrement());
208	232	setRenderGaps(vs.isRenderGaps());
209	232	setRightAlignIds(vs.isRightAlignIds());
210	232	setScaleAboveWrapped(vs.getScaleAboveWrapped());
211	232	setScaleLeftWrapped(vs.getScaleLeftWrapped());
212	232	setScaleProteinAsCdna(vs.isScaleProteinAsCdna());
213	232	setProteinFontAsCdna(vs.isProteinFontAsCdna());
214	232	setScaleRightWrapped(vs.getScaleRightWrapped());
215	232	setSeqNameItalics(vs.isSeqNameItalics());
216	232	setShowAnnotation(vs.isShowAnnotation());
217	232	setShowBoxes(vs.getShowBoxes());
218	232	setShowColourText(vs.isShowColourText());
219	232	setShowDBRefs(vs.isShowDBRefs());
220	232	setShowHiddenMarkers(vs.getShowHiddenMarkers());
221	232	setShowJVSuffix(vs.getShowJVSuffix());
222	232	setShowNPFeats(vs.isShowNPFeats());
223	232	setShowSequenceFeaturesHeight(vs.isShowSequenceFeaturesHeight());
224	232	setShowSequenceFeatures(vs.isShowSequenceFeatures());
225	232	setShowComplementFeatures(vs.isShowComplementFeatures());
226	232	setShowComplementFeaturesOnTop(vs.isShowComplementFeaturesOnTop());
227	232	setShowText(vs.getShowText());
228	232	setShowUnconserved(vs.getShowUnconserved());
229	232	setTextColour(vs.getTextColour());
230	232	setTextColour2(vs.getTextColour2());
231	232	setThreshold(vs.getThreshold());
232	232	setThresholdTextColour(vs.getThresholdTextColour());
233	232	setUpperCasebold(vs.isUpperCasebold());
234	232	setWrapAlignment(vs.getWrapAlignment());
235	232	setWrappedWidth(vs.getWrappedWidth());
236	232	setSecondaryStructureSources(vs.getSecondaryStructureSources());
237	232	setShowStructureProvider(vs.isShowStructureProvider());
238		// ViewStyle.configureFrom(this, viewStyle);
239		}
240
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
241	510	public ViewStyle()...
242		{
243		}
244
245		/**
246		* Returns true if all attributes of the ViewStyles have the same value
247		*/
		100% Uncovered Elements: 0 (10) Complexity: 3 Complexity Density: 0.38
248	52	@Override...
249		public boolean equals(Object other)
250		{
251	52	if (other == null || !(other instanceof ViewStyle))
252		{
253	2	return false;
254		}
255	50	ViewStyle vs = (ViewStyle) other;
256
257	50	boolean match = (getAbovePIDThreshold() == vs.getAbovePIDThreshold()
258		&& isCentreColumnLabels() == vs.isCentreColumnLabels()
259		&& getCharHeight() == vs.getCharHeight()
260		&& getCharWidth() == vs.getCharWidth()
261		&& getColourAppliesToAllGroups() == vs
262		.getColourAppliesToAllGroups()
263		&& isColourByReferenceSeq() == vs.isColourByReferenceSeq()
264		&& getColourText() == vs.getColourText()
265		&& isConservationColourSelected() == vs
266		.isConservationColourSelected()
267		&& getByConsensusSecondaryStructureSelected() == vs
268		.getByConsensusSecondaryStructureSelected()
269		&& getConservationSelected() == vs.getConservationSelected()
270		&& isDisplayReferenceSeq() == vs.isDisplayReferenceSeq()
271		&& getFontSize() == vs.getFontSize()
272		&& getFontStyle() == vs.getFontStyle()
273		&& getIdWidth() == vs.getIdWidth()
274		&& getIncrement() == vs.getIncrement()
275		&& getConsensusSecondaryStructureThreshold() == vs
276		.getConsensusSecondaryStructureThreshold()
277		&& isRenderGaps() == vs.isRenderGaps()
278		&& isRightAlignIds() == vs.isRightAlignIds()
279		&& getScaleAboveWrapped() == vs.getScaleAboveWrapped()
280		&& getScaleLeftWrapped() == vs.getScaleLeftWrapped()
281		&& isScaleProteinAsCdna() == vs.isScaleProteinAsCdna()
282		&& isProteinFontAsCdna() == vs.isProteinFontAsCdna()
283		&& getScaleRightWrapped() == vs.getScaleRightWrapped()
284		&& isSeqNameItalics() == vs.isSeqNameItalics()
285		&& isShowAnnotation() == vs.isShowAnnotation()
286		&& getShowBoxes() == vs.getShowBoxes()
287		&& isShowColourText() == vs.isShowColourText()
288		&& isShowDBRefs() == vs.isShowDBRefs()
289		&& getShowHiddenMarkers() == vs.getShowHiddenMarkers()
290		&& getShowJVSuffix() == vs.getShowJVSuffix()
291		&& isShowNPFeats() == vs.isShowNPFeats()
292		&& isShowSequenceFeaturesHeight() == vs
293		.isShowSequenceFeaturesHeight()
294		&& isShowSequenceFeatures() == vs.isShowSequenceFeatures()
295		&& isShowComplementFeatures() == vs.isShowComplementFeatures()
296		&& isShowComplementFeaturesOnTop() == vs
297		.isShowComplementFeaturesOnTop()
298		&& getShowText() == vs.getShowText()
299		&& getShowUnconserved() == vs.getShowUnconserved()
300		&& getThreshold() == vs.getThreshold()
301		&& getThresholdTextColour() == vs.getThresholdTextColour()
302		&& isUpperCasebold() == vs.isUpperCasebold()
303		&& getWrapAlignment() == vs.getWrapAlignment()
304		&& getWrappedWidth() == vs.getWrappedWidth()
305		&& getSecondaryStructureSources() == vs
306		.getSecondaryStructureSources()
307		&& isShowStructureProvider() == vs.isShowStructureProvider());
308		/*
309		* and compare non-primitive types; syntax below will match null with null
310		* values
311		*/
312	50	match = match && String.valueOf(getFontName())
313		.equals(String.valueOf(vs.getFontName()));
314	50	match = match && String.valueOf(getTextColour())
315		.equals(String.valueOf(vs.getTextColour()));
316	50	match = match && String.valueOf(getTextColour2())
317		.equals(String.valueOf(vs.getTextColour2()));
318	50	return match;
319		// return equivalent(this, (ViewStyle) other);
320		}
321
322		/**
323		* Overridden to ensure that whenever vs1.equals(vs2) then vs1.hashCode() ==
324		* vs2.hashCode()
325		*/
		100% Uncovered Elements: 0 (25) Complexity: 1 Complexity Density: 0.04
326	92	@Override...
327		public int hashCode()
328		{
329		/*
330		* No need to include all properties, just a selection...
331		*/
332	92	int hash = 0;
333	92	int m = 1;
334		// Boolean.hashCode returns 1231 or 1237
335	92	hash += m++ * Boolean.valueOf(this.abovePIDThreshold).hashCode();
336	92	hash += m++ * Boolean.valueOf(this.centreColumnLabels).hashCode();
337	92	hash += m++ * Boolean.valueOf(this.colourAppliesToAllGroups).hashCode();
338	92	hash += m++ * Boolean.valueOf(this.displayReferenceSeq).hashCode();
339	92	hash += m++ * Boolean.valueOf(this.renderGaps).hashCode();
340	92	hash += m++ * Boolean.valueOf(this.rightAlignIds).hashCode();
341	92	hash += m++ * Boolean.valueOf(this.scaleProteinAsCdna).hashCode();
342	92	hash += m++ * Boolean.valueOf(this.scaleRightWrapped).hashCode();
343	92	hash += m++ * Boolean.valueOf(this.seqNameItalics).hashCode();
344	92	hash += m++ * Boolean.valueOf(this.showAnnotation).hashCode();
345	92	hash += m++ * Boolean.valueOf(this.showBoxes).hashCode();
346	92	hash += m++ * Boolean.valueOf(this.showdbrefs).hashCode();
347	92	hash += m++ * Boolean.valueOf(this.showJVSuffix).hashCode();
348	92	hash += m++ * Boolean.valueOf(this.showSequenceFeatures).hashCode();
349	92	hash += m++ * Boolean.valueOf(this.showUnconserved).hashCode();
350	92	hash += m++ * Boolean.valueOf(this.wrapAlignment).hashCode();
351	92	hash += m++ * this.charHeight;
352	92	hash += m++ * this.charWidth;
353	92	hash += m++ * fontSize;
354	92	hash += m++ * fontStyle;
355	92	hash += m++ * idWidth;
356	92	hash += String.valueOf(this.fontName).hashCode();
357	92	return hash;
358		}
359
360		/**
361		* @return the upperCasebold
362		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
363	254	@Override...
364		public boolean isUpperCasebold()
365		{
366	254	return upperCasebold;
367		}
368
369		/**
370		* @param upperCasebold
371		* the upperCasebold to set
372		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
373	232	@Override...
374		public void setUpperCasebold(boolean upperCasebold)
375		{
376	232	this.upperCasebold = upperCasebold;
377		}
378
379		/**
380		* flag for wrapping
381		*/
382		boolean wrapAlignment = false;
383
384		/**
385		* number columns in wrapped alignment
386		*/
387		int wrappedWidth;
388
389		private int fontStyle;
390
391		private boolean showComplementFeatures;
392
393		private boolean showComplementFeaturesOnTop;
394
395		/**
396		* secondary structure annotation rows shown in the view
397		*/
398		private List<String> secondaryStructureSources = List.of(new String[0]);
399
400		private boolean showStructureProvider;
401
402		/**
403		* GUI state
404		*
405		* @return true if percent identity threshold is applied to shading
406		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
407	1210	@Override...
408		public boolean getAbovePIDThreshold()
409		{
410	1210	return abovePIDThreshold;
411		}
412
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
413	1190	@Override...
414		public boolean getByConsensusSecondaryStructureSelected()
415		{
416	1190	return byConsensusSecondaryStructureSelected;
417		}
418
419		/**
420		* DOCUMENT ME!
421		*
422		* @return DOCUMENT ME!
423		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
424	115575	@Override...
425		public int getCharHeight()
426		{
427	115575	return charHeight;
428		}
429
430		/**
431		* DOCUMENT ME!
432		*
433		* @return DOCUMENT ME!
434		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
435	1521435	@Override...
436		public int getCharWidth()
437		{
438	1521435	return charWidth;
439		}
440
441		/**
442		*
443		*
444		* @return flag indicating if colourchanges propagated to all groups
445		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
446	1282	@Override...
447		public boolean getColourAppliesToAllGroups()
448		{
449	1282	return colourAppliesToAllGroups;
450		}
451
452		/**
453		* DOCUMENT ME!
454		*
455		* @return DOCUMENT ME!
456		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
457	433100	@Override...
458		public boolean getColourText()
459		{
460	433100	return showColourText;
461		}
462
463		/**
464		* GUI state
465		*
466		* @return true if conservation based shading is enabled
467		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
468	1350	@Override...
469		public boolean getConservationSelected()
470		{
471	1350	return conservationColourSelected;
472		}
473
474		/**
475		* GUI State
476		*
477		* @return get scalar for bleaching colourschemes by conservation
478		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
479	302	@Override...
480		public int getIncrement()
481		{
482	302	return increment;
483		}
484
485		/**
486		* DOCUMENT ME!
487		*
488		* @return DOCUMENT ME!
489		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
490	1207	@Override...
491		public boolean getScaleAboveWrapped()
492		{
493	1207	return scaleAboveWrapped;
494		}
495
496		/**
497		* DOCUMENT ME!
498		*
499		* @return DOCUMENT ME!
500		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
501	1600	@Override...
502		public boolean getScaleLeftWrapped()
503		{
504	1600	return scaleLeftWrapped;
505		}
506
507		/**
508		* DOCUMENT ME!
509		*
510		* @return DOCUMENT ME!
511		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
512	2408	@Override...
513		public boolean getScaleRightWrapped()
514		{
515	2408	return scaleRightWrapped;
516		}
517
518		/**
519		* DOCUMENT ME!
520		*
521		* @return DOCUMENT ME!
522		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
523	471546	@Override...
524		public boolean getShowBoxes()
525		{
526	471546	return showBoxes;
527		}
528
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
529	7366	@Override...
530		public boolean getShowHiddenMarkers()
531		{
532	7366	return showHiddenMarkers;
533		}
534
535		/**
536		* DOCUMENT ME!
537		*
538		* @return DOCUMENT ME!
539		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
540	49117	@Override...
541		public boolean getShowJVSuffix()
542		{
543	49117	return showJVSuffix;
544		}
545
546		/**
547		* DOCUMENT ME!
548		*
549		* @return DOCUMENT ME!
550		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
551	433718	@Override...
552		public boolean getShowText()
553		{
554	433718	return showText;
555		}
556
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
557	431226	@Override...
558		public boolean getShowUnconserved()
559		{
560	431226	return showUnconserved;
561		}
562
563		/**
564		* @return the textColour
565		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
566	737024	@Override...
567		public Color getTextColour()
568		{
569	737024	return textColour;
570		}
571
572		/**
573		* @return the textColour2
574		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
575	286	@Override...
576		public Color getTextColour2()
577		{
578	286	return textColour2;
579		}
580
581		/**
582		* DOCUMENT ME!
583		*
584		* @return DOCUMENT ME!
585		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
586	258	@Override...
587		public int getThreshold()
588		{
589	258	return threshold;
590		}
591
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
592	300	@Override...
593		public int getConsensusSecondaryStructureThreshold()
594		{
595	300	return consensusSecondaryStructureThreshold;
596		}
597
598		/**
599		* @return the thresholdTextColour
600		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
601	433040	@Override...
602		public int getThresholdTextColour()
603		{
604	433040	return thresholdTextColour;
605		}
606
607		/**
608		* DOCUMENT ME!
609		*
610		* @return DOCUMENT ME!
611		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
612	30884	@Override...
613		public boolean getWrapAlignment()
614		{
615	30884	return wrapAlignment;
616		}
617
618		/**
619		* DOCUMENT ME!
620		*
621		* @return DOCUMENT ME!
622		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
623	252	@Override...
624		public int getWrappedWidth()
625		{
626	252	return wrappedWidth;
627		}
628
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
629	323	@Override...
630		public boolean isColourByReferenceSeq()
631		{
632	323	return colourByReferenceSeq;
633		}
634
635		/**
636		* @return the conservationColourSelected
637		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
638	400	@Override...
639		public boolean isConservationColourSelected()
640		{
641	400	return conservationColourSelected;
642		}
643
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
644	961	@Override...
645		public boolean isDisplayReferenceSeq()
646		{
647	961	return displayReferenceSeq;
648		}
649
650		/**
651		* @return the renderGaps
652		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
653	3731	@Override...
654		public boolean isRenderGaps()
655		{
656	3731	return renderGaps;
657		}
658
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
659	19564	@Override...
660		public boolean isRightAlignIds()
661		{
662	19564	return rightAlignIds;
663		}
664
665		/**
666		* @return the seqNameItalics
667		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
668	3471	@Override...
669		public boolean isSeqNameItalics()
670		{
671	3471	return seqNameItalics;
672		}
673
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
674	5196	@Override...
675		public boolean isShowAnnotation()
676		{
677	5196	return showAnnotation;
678		}
679
680		/**
681		* @return the showColourText
682		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
683	950	@Override...
684		public boolean isShowColourText()
685		{
686	950	return showColourText;
687		}
688
689		/**
690		* @return the showSeqFeaturesHeight
691		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
692	270	@Override...
693		public boolean isShowSequenceFeaturesHeight()
694		{
695	270	return showSeqFeaturesHeight;
696		}
697
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
698	459590	@Override...
699		public boolean isShowSequenceFeatures()
700		{
701	459621	return showSequenceFeatures;
702		}
703
704		/**
705		* GUI state
706		*
707		*
708		* @param b
709		* indicate if percent identity threshold is applied to shading
710		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
711	326	@Override...
712		public void setAbovePIDThreshold(boolean b)
713		{
714	326	abovePIDThreshold = b;
715		}
716
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
717	317	@Override...
718		public void setByConsensusSecondaryStructureSelected(boolean b)
719		{
720	317	byConsensusSecondaryStructureSelected = b;
721		}
722
723		/**
724		* DOCUMENT ME!
725		*
726		* @param h
727		* DOCUMENT ME!
728		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
729	828	@Override...
730		public void setCharHeight(int h)
731		{
732	828	this.charHeight = h;
733		}
734
735		/**
736		* DOCUMENT ME!
737		*
738		* @param w
739		* DOCUMENT ME!
740		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
741	831	@Override...
742		public void setCharWidth(int w)
743		{
744	831	this.charWidth = w;
745		}
746
747		/**
748		* @param value
749		* indicating if subsequent colourscheme changes will be propagated
750		* to all groups
751		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
752	925	@Override...
753		public void setColourAppliesToAllGroups(boolean b)
754		{
755	925	colourAppliesToAllGroups = b;
756		}
757
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
758	242	@Override...
759		public void setColourByReferenceSeq(boolean colourByReferenceSeq)
760		{
761	242	this.colourByReferenceSeq = colourByReferenceSeq;
762		}
763
764		/**
765		* DOCUMENT ME!
766		*
767		* @param state
768		* DOCUMENT ME!
769		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
770	317	@Override...
771		public void setColourText(boolean state)
772		{
773	317	showColourText = state;
774		}
775
776		/**
777		* @param conservationColourSelected
778		* the conservationColourSelected to set
779		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
780	232	@Override...
781		public void setConservationColourSelected(
782		boolean conservationColourSelected)
783		{
784	232	this.conservationColourSelected = conservationColourSelected;
785		}
786
787		/**
788		* GUI state
789		*
790		* @param b
791		* enable conservation based shading
792		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
793	325	@Override...
794		public void setConservationSelected(boolean b)
795		{
796	325	conservationColourSelected = b;
797		}
798
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
799	242	@Override...
800		public void setDisplayReferenceSeq(boolean displayReferenceSeq)
801		{
802	242	this.displayReferenceSeq = displayReferenceSeq;
803		}
804
805		/**
806		*
807		* @param inc
808		* set the scalar for bleaching colourschemes according to degree of
809		* conservation
810		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
811	317	@Override...
812		public void setIncrement(int inc)
813		{
814	317	increment = inc;
815		}
816
817		/**
818		*
819		* @param val
820		* set the scalar for bleaching colourschemes according to degree of
821		* secondary structure conservation
822		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
823	317	@Override...
824		public void setConsensusSecondaryStructureThreshold(int val)
825		{
826	317	consensusSecondaryStructureThreshold = val;
827		}
828
829		/**
830		* DOCUMENT ME!
831		*
832		* @param state
833		* DOCUMENT ME!
834		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
835	317	@Override...
836		public void setRenderGaps(boolean state)
837		{
838	317	renderGaps = state;
839		}
840
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
841	825	@Override...
842		public void setRightAlignIds(boolean rightAlignIds)
843		{
844	825	this.rightAlignIds = rightAlignIds;
845		}
846
847		/**
848		* DOCUMENT ME!
849		*
850		* @param b
851		* DOCUMENT ME!
852		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
853	241	@Override...
854		public void setScaleAboveWrapped(boolean b)
855		{
856	241	scaleAboveWrapped = b;
857		}
858
859		/**
860		* DOCUMENT ME!
861		*
862		* @param b
863		* DOCUMENT ME!
864		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
865	243	@Override...
866		public void setScaleLeftWrapped(boolean b)
867		{
868	243	scaleLeftWrapped = b;
869		}
870
871		/**
872		*
873		*
874		* @param scaleRightWrapped
875		* - true or false
876		*/
877
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
878	241	@Override...
879		public void setScaleRightWrapped(boolean b)
880		{
881	241	scaleRightWrapped = b;
882		}
883
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
884	740	@Override...
885		public void setSeqNameItalics(boolean italics)
886		{
887	740	seqNameItalics = italics;
888		}
889
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
890	912	@Override...
891		public void setShowAnnotation(boolean b)
892		{
893	912	showAnnotation = b;
894		}
895
896		/**
897		* DOCUMENT ME!
898		*
899		* @param state
900		* DOCUMENT ME!
901		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
902	317	@Override...
903		public void setShowBoxes(boolean state)
904		{
905	317	showBoxes = state;
906		}
907
908		/**
909		* @param showColourText
910		* the showColourText to set
911		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
912	232	@Override...
913		public void setShowColourText(boolean showColourText)
914		{
915	232	this.showColourText = showColourText;
916		}
917
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
918	232	@Override...
919		public void setShowHiddenMarkers(boolean show)
920		{
921	232	showHiddenMarkers = show;
922		}
923
924		/**
925		* DOCUMENT ME!
926		*
927		* @param b
928		* DOCUMENT ME!
929		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
930	826	@Override...
931		public void setShowJVSuffix(boolean b)
932		{
933	826	showJVSuffix = b;
934		}
935
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
936	232	@Override...
937		public void setShowSequenceFeaturesHeight(boolean selected)
938		{
939	232	showSeqFeaturesHeight = selected;
940
941		}
942
943		/**
944		* set the flag
945		*
946		* @param b
947		* features are displayed if true
948		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
949	373	@Override...
950		public void setShowSequenceFeatures(boolean b)
951		{
952	373	showSequenceFeatures = b;
953		}
954
955		/**
956		* DOCUMENT ME!
957		*
958		* @param state
959		* DOCUMENT ME!
960		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
961	317	@Override...
962		public void setShowText(boolean state)
963		{
964	317	showText = state;
965		}
966
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
967	825	@Override...
968		public void setShowUnconserved(boolean showunconserved)
969		{
970	825	showUnconserved = showunconserved;
971		}
972
973		/**
974		* @param textColour
975		* the textColour to set
976		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
977	317	@Override...
978		public void setTextColour(Color textColour)
979		{
980	317	this.textColour = textColour;
981		}
982
983		/**
984		* @param textColour2
985		* the textColour2 to set
986		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
987	317	@Override...
988		public void setTextColour2(Color textColour2)
989		{
990	317	this.textColour2 = textColour2;
991		}
992
993		/**
994		* DOCUMENT ME!
995		*
996		* @param thresh
997		* DOCUMENT ME!
998		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
999	338	@Override...
1000		public void setThreshold(int thresh)
1001		{
1002	338	threshold = thresh;
1003		}
1004
1005		/**
1006		* @param thresholdTextColour
1007		* the thresholdTextColour to set
1008		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1009	317	@Override...
1010		public void setThresholdTextColour(int thresholdTextColour)
1011		{
1012	317	this.thresholdTextColour = thresholdTextColour;
1013		}
1014
1015		/**
1016		* DOCUMENT ME!
1017		*
1018		* @param state
1019		* DOCUMENT ME!
1020		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1021	837	@Override...
1022		public void setWrapAlignment(boolean state)
1023		{
1024	837	wrapAlignment = state;
1025		}
1026
1027		/**
1028		* DOCUMENT ME!
1029		*
1030		* @param w
1031		* DOCUMENT ME!
1032		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1033	1074	@Override...
1034		public void setWrappedWidth(int w)
1035		{
1036	1074	this.wrappedWidth = w;
1037		}
1038
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1039	3	@Override...
1040		public boolean sameStyle(ViewStyleI that)
1041		{
1042	3	return this.equals(that);
1043		}
1044
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1045	330	@Override...
1046		public String getFontName()
1047		{
1048	330	return fontName;
1049		}
1050
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1051	394	@Override...
1052		public int getFontSize()
1053		{
1054	394	return fontSize;
1055		}
1056
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1057	392	@Override...
1058		public int getFontStyle()
1059		{
1060	392	return fontStyle;
1061		}
1062
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1063	914	@Override...
1064		public void setFontName(String name)
1065		{
1066	914	fontName = name;
1067		}
1068
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1069	914	@Override...
1070		public void setFontSize(int size)
1071		{
1072	914	fontSize = size;
1073
1074		}
1075
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1076	914	@Override...
1077		public void setFontStyle(int style)
1078		{
1079	914	fontStyle = style;
1080		}
1081
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1082	6605	@Override...
1083		public int getIdWidth()
1084		{
1085	6605	return idWidth;
1086		}
1087
1088		/**
1089		* @param idWidth
1090		* the idWidth to set
1091		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1092	1202	@Override...
1093		public void setIdWidth(int idWidth)
1094		{
1095	1202	this.idWidth = idWidth;
1096		}
1097
1098		/**
1099		* @return the centreColumnLabels
1100		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1101	1002	@Override...
1102		public boolean isCentreColumnLabels()
1103		{
1104	1002	return centreColumnLabels;
1105		}
1106
1107		/**
1108		* @param centreColumnLabels
1109		* the centreColumnLabels to set
1110		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1111	825	@Override...
1112		public void setCentreColumnLabels(boolean centreColumnLabels)
1113		{
1114	825	this.centreColumnLabels = centreColumnLabels;
1115		}
1116
1117		/**
1118		* @return the showdbrefs
1119		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1120	996	@Override...
1121		public boolean isShowDBRefs()
1122		{
1123	996	return showdbrefs;
1124		}
1125
1126		/**
1127		* @param showdbrefs
1128		* the showdbrefs to set
1129		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1130	825	@Override...
1131		public void setShowDBRefs(boolean showdbrefs)
1132		{
1133	825	this.showdbrefs = showdbrefs;
1134		}
1135
1136		/**
1137		* @return the shownpfeats
1138		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1139	990	@Override...
1140		public boolean isShowNPFeats()
1141		{
1142	990	return shownpfeats;
1143		}
1144
1145		/**
1146		* @param shownpfeats
1147		* the shownpfeats to set
1148		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1149	825	@Override...
1150		public void setShowNPFeats(boolean shownpfeats)
1151		{
1152	825	this.shownpfeats = shownpfeats;
1153		}
1154
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1155	339	@Override...
1156		public boolean isScaleProteinAsCdna()
1157		{
1158	339	return this.scaleProteinAsCdna;
1159		}
1160
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1161	825	@Override...
1162		public void setScaleProteinAsCdna(boolean b)
1163		{
1164	825	this.scaleProteinAsCdna = b;
1165		}
1166
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1167	288	@Override...
1168		public boolean isProteinFontAsCdna()
1169		{
1170	288	return proteinFontAsCdna;
1171		}
1172
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1173	232	@Override...
1174		public void setProteinFontAsCdna(boolean b)
1175		{
1176	232	proteinFontAsCdna = b;
1177		}
1178
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1179	317	@Override...
1180		public void setShowComplementFeatures(boolean b)
1181		{
1182	317	showComplementFeatures = b;
1183		}
1184
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1185	460976	@Override...
1186		public boolean isShowComplementFeatures()
1187		{
1188	460987	return showComplementFeatures;
1189		}
1190
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1191	317	@Override...
1192		public void setShowComplementFeaturesOnTop(boolean b)
1193		{
1194	317	showComplementFeaturesOnTop = b;
1195		}
1196
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1197	311	@Override...
1198		public boolean isShowComplementFeaturesOnTop()
1199		{
1200	311	return showComplementFeaturesOnTop;
1201		}
1202
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1203	2726	@Override...
1204		public List<String> getSecondaryStructureSources()
1205		{
1206	2726	return secondaryStructureSources;
1207		}
1208
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1209	1609	@Override...
1210		public void setSecondaryStructureSources(
1211		List<String> secondaryStructureSources)
1212		{
1213	1609	this.secondaryStructureSources = secondaryStructureSources;
1214		}
1215
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1216	825	@Override...
1217		public void setShowStructureProvider(boolean showStructureProvider)
1218		{
1219	825	this.showStructureProvider = showStructureProvider;
1220		}
1221
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
1222	6971	@Override...
1223		public boolean isShowStructureProvider()
1224		{
1225	6971	return showStructureProvider;
1226		}
1227		}