1. Project Clover database Fri Dec 6 2024 13:47:14 GMT
  2. Package jalview.api

File ViewStyleI.java

 

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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   
 
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    }