Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
ViewStyleI	26	0	0	-1.0 -	Show methods

Class ViewStyleI

Class ViewStyleI	Line # 26	Total Statements 0	Complexity 0	TOTAL Coverage -1.0 -

 

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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.api;
22
23		import java.awt.Color;
24		import java.util.List;
25
		- Uncovered Elements: 0 (0) Complexity: 0 Complexity Density: -
26		public interface ViewStyleI
27		{
28		void setShowComplementFeatures(boolean b);
29
30		boolean isShowComplementFeatures();
31
32		void setShowComplementFeaturesOnTop(boolean b);
33
34		boolean isShowComplementFeaturesOnTop();
35
36		void setColourAppliesToAllGroups(boolean b);
37
38		boolean getColourAppliesToAllGroups();
39
40		boolean getAbovePIDThreshold();
41
42		boolean getByConsensusSecondaryStructureSelected();
43
44		void setIncrement(int inc);
45
46		int getIncrement();
47
48		boolean getConservationSelected();
49
50		void setConservationSelected(boolean b);
51
52		void setShowHiddenMarkers(boolean show);
53
54		boolean getShowHiddenMarkers();
55
56		void setScaleRightWrapped(boolean b);
57
58		void setScaleLeftWrapped(boolean b);
59
60		void setScaleAboveWrapped(boolean b);
61
62		boolean getScaleLeftWrapped();
63
64		boolean getScaleAboveWrapped();
65
66		boolean getScaleRightWrapped();
67
68		void setAbovePIDThreshold(boolean b);
69
70		void setByConsensusSecondaryStructureSelected(boolean b);
71
72		void setShowStructureProvider(boolean b);
73
74		boolean isShowStructureProvider();
75
76		void setThreshold(int thresh);
77
78		int getThreshold();
79
80		boolean getShowJVSuffix();
81
82		void setShowJVSuffix(boolean b);
83
84		void setWrapAlignment(boolean state);
85
86		void setShowText(boolean state);
87
88		void setRenderGaps(boolean state);
89
90		boolean getColourText();
91
92		void setColourText(boolean state);
93
94		void setShowBoxes(boolean state);
95
96		boolean getWrapAlignment();
97
98		boolean getShowText();
99
100		int getWrappedWidth();
101
102		void setWrappedWidth(int w);
103
104		int getCharHeight();
105
106		void setCharHeight(int h);
107
108		int getCharWidth();
109
110		void setCharWidth(int w);
111
112		boolean getShowBoxes();
113
114		boolean getShowUnconserved();
115
116		void setShowUnconserved(boolean showunconserved);
117
118		/**
119		* @return true if a reference sequence is set and should be displayed
120		*/
121		boolean isDisplayReferenceSeq();
122
123		/**
124		* @return set the flag for displaying reference sequences when they are
125		* available
126		*/
127		void setDisplayReferenceSeq(boolean displayReferenceSeq);
128
129		/**
130		* @return true if colourschemes should render according to reference sequence
131		* rather than consensus if available
132		*/
133		boolean isColourByReferenceSeq();
134
135		void setSeqNameItalics(boolean default1);
136
137		void setShowSequenceFeatures(boolean b);
138
139		boolean isShowSequenceFeatures();
140
141		boolean isRightAlignIds();
142
143		void setRightAlignIds(boolean rightAlignIds);
144
145		/**
146		* Returns true if annotation panel should be shown below alignment
147		*
148		* @return
149		*/
150		boolean isShowAnnotation();
151
152		/**
153		* Set flag for whether annotation panel should be shown below alignment
154		*
155		* @param b
156		*/
157		void setShowAnnotation(boolean b);
158
159		void setShowSequenceFeaturesHeight(boolean selected);
160
161		/**
162		* @return true set flag for deciding if colourschemes should render according
163		* to reference sequence rather than consensus if available
164		*/
165		void setColourByReferenceSeq(boolean colourByReferenceSeq);
166
167		Color getTextColour();
168
169		Color getTextColour2();
170
171		int getThresholdTextColour();
172
173		boolean isConservationColourSelected();
174
175		boolean isRenderGaps();
176
177		boolean isShowColourText();
178
179		boolean isShowSequenceFeaturesHeight();
180
181		void setConservationColourSelected(boolean conservationColourSelected);
182
183		void setShowColourText(boolean showColourText);
184
185		void setTextColour(Color textColour);
186
187		void setThresholdTextColour(int thresholdTextColour);
188
189		void setTextColour2(Color textColour2);
190
191		boolean isSeqNameItalics();
192
193		void setUpperCasebold(boolean upperCasebold);
194
195		boolean isUpperCasebold();
196
197		boolean sameStyle(ViewStyleI them);
198
199		void setFontName(String name);
200
201		void setFontStyle(int style);
202
203		void setFontSize(int size);
204
205		int getFontStyle();
206
207		String getFontName();
208
209		int getFontSize();
210
211		/**
212		* @return width of Sequence and Annotation ID margin. If less than zero, then
213		* width will be autocalculated
214		*/
215		int getIdWidth();
216
217		/**
218		* Set width if
219		*
220		* @param i
221		*/
222
223		void setIdWidth(int i);
224
225		/**
226		* centre columnar annotation labels in displayed alignment annotation
227		*/
228		boolean isCentreColumnLabels();
229
230		/**
231		* centre columnar annotation labels in displayed alignment annotation
232		*/
233		void setCentreColumnLabels(boolean centreColumnLabels);
234
235		/**
236		* enable or disable the display of Database Cross References in the sequence
237		* ID tooltip
238		*/
239		void setShowDBRefs(boolean showdbrefs);
240
241		/**
242		*
243		* @return true if Database References are to be displayed on tooltips.
244		*/
245		boolean isShowDBRefs();
246
247		/**
248		*
249		* @return true if Non-positional features are to be displayed on tooltips.
250		*/
251		boolean isShowNPFeats();
252
253		/**
254		* enable or disable the display of Non-Positional sequence features in the
255		* sequence ID tooltip
256		*
257		* @param show
258		*/
259		void setShowNPFeats(boolean shownpfeats);
260
261		/**
262		* Get flag to scale protein residues 3 times the width of cDNA bases (only
263		* applicable in SplitFrame views)
264		*
265		* @return
266		*/
267		boolean isScaleProteinAsCdna();
268
269		/**
270		* Set flag to scale protein residues 3 times the width of cDNA bases (only
271		* applicable in SplitFrame views)
272		*
273		* @return
274		*/
275		void setScaleProteinAsCdna(boolean b);
276
277		/**
278		* Answers true if split screen protein and cDNA use the same font
279		*
280		* @return
281		*/
282		boolean isProteinFontAsCdna();
283
284		/**
285		* Set the flag for whether split screen protein and cDNA use the same font
286		*
287		* @return
288		*/
289		void setProteinFontAsCdna(boolean b);
290
291		void setSecondaryStructureSources(List<String> secondaryStructureSources);
292
293		List<String> getSecondaryStructureSources();
294
295		int getConsensusSecondaryStructureThreshold();
296
297		/**
298		*
299		* @param val
300		* set the scalar for bleaching colourschemes according to degree of
301		* secondary structure conservation
302		*/
303		void setConsensusSecondaryStructureThreshold(int val);
304		}