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.
21 package jalview.schemes;
23 import jalview.datamodel.AnnotatedCollectionI;
24 import jalview.datamodel.SequenceCollectionI;
25 import jalview.datamodel.SequenceI;
27 import java.awt.Color;
30 public interface ColourSchemeI
35 * @return the colour for the given character
37 public Color findColour(char c);
42 * - sequence symbol or gap
46 * - sequence being coloured
47 * @return context dependent colour for the given symbol at the position in
50 public Color findColour(char c, int j, SequenceI seq);
53 * assign the given consensus profile for the colourscheme
55 public void setConsensus(java.util.Hashtable[] h);
58 * assign the given conservation to the colourscheme
62 public void setConservation(jalview.analysis.Conservation c);
65 * enable or disable conservation shading for this colourscheme
67 * @param conservationApplied
69 public void setConservationApplied(boolean conservationApplied);
73 * @return true if conservation shading is enabled for this colourscheme
75 public boolean conservationApplied();
78 * set scale factor for bleaching of colour in unconserved regions
82 public void setConservationInc(int i);
86 * @return scale factor for bleaching colour in unconserved regions
88 public int getConservationInc();
92 * @return percentage identity threshold for applying colourscheme
94 public int getThreshold();
97 * set percentage identity threshold and type of %age identity calculation for
101 * 0..100 percentage identity for applying this colourscheme
103 * when true, calculate PID without including gapped positions
105 public void setThreshold(int ct, boolean ignoreGaps);
108 * recalculate dependent data using the given sequence collection, taking
109 * account of hidden rows
114 public void alignmentChanged(AnnotatedCollectionI alignment,
115 Map<SequenceI, SequenceCollectionI> hiddenReps);
118 * create a new instance of the colourscheme configured to colour the given
122 * @param hiddenRepSequences
123 * @return copy of current scheme with any inherited settings transfered
125 public ColourSchemeI applyTo(AnnotatedCollectionI sg,
126 Map<SequenceI, SequenceCollectionI> hiddenRepSequences);