2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
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.
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.
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.
23 import jalview.datamodel.SequenceFeature;
24 import jalview.datamodel.SequenceI;
26 import java.awt.Color;
27 import java.awt.Graphics;
28 import java.util.List;
32 * Abstract feature renderer interface
37 public interface FeatureRenderer
41 * Returns the combined feature colour for a given sequence and column
42 * position, taking into account feature colour schemes, ordering, feature and
43 * feature group visibility, and transparency. Returns null if there is no
44 * visible feature at the position.
46 * The Graphics argument is optional and may be null if no transparency is
47 * applied. With feature transparency, visible features are written to the
48 * graphics context and the composite colour can be read off.
50 * This is provided for use by Structure Viewers and the Overview Window to
51 * get the feature colour of the rendered sequence.
58 Color findFeatureColour(SequenceI sequence, int column, Graphics g);
61 * trigger the feature discovery process for a newly created feature renderer.
68 * @return display style for a feature
70 FeatureColourI getFeatureStyle(String ft);
73 * update the feature style for a particular feature
78 void setColour(String ft, FeatureColourI ggc);
80 AlignViewportI getViewport();
84 * @return container managing list of feature types and their visibility
86 FeaturesDisplayedI getFeaturesDisplayed();
89 * get display style for all features types - visible or invisible
93 Map<String, FeatureColourI> getFeatureColours();
96 * query the alignment view to find all features
98 * @param newMadeVisible
99 * - when true, automatically make newly discovered types visible
101 void findAllFeatures(boolean newMadeVisible);
104 * get display style for all features types currently visible
108 Map<String, FeatureColourI> getDisplayedFeatureCols();
111 * get all registered groups
115 List<String> getFeatureGroups();
118 * get groups that are visible/invisible
123 List<String> getGroups(boolean visible);
126 * change visibility for a range of groups
131 void setGroupVisibility(List<String> toset, boolean visible);
134 * change visibiilty of given group
139 void setGroupVisibility(String group, boolean visible);
142 * Returns features at the specified position on the given sequence.
143 * Non-positional features are not included.
149 List<SequenceFeature> findFeaturesAtRes(SequenceI sequence, int res);
152 * get current displayed types, in ordering of rendering (on top last)
154 * @return a (possibly empty) list of feature types
157 List<String> getDisplayedFeatureTypes();
160 * get current displayed groups
162 * @return a (possibly empty) list of feature groups
164 List<String> getDisplayedFeatureGroups();
167 * display all features of these types
169 * @param featureTypes
171 void setAllVisible(List<String> featureTypes);
174 * display featureType
178 void setVisible(String featureType);
181 * Sets the transparency value, between 0 (full transparency) and 1 (no
186 void setTransparency(float value);
189 * Returns the transparency value, between 0 (full transparency) and 1 (no
194 float getTransparency();