2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
3 * Copyright (C) 2014 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 of the License, or (at your option) any later version.
11 * Jalview is distributed in the hope that it will be useful, but
12 * WITHOUT ANY WARRANTY; without even the implied warranty
13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
14 * PURPOSE. See the GNU General Public License for more details.
16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
17 * The Jalview Authors are detailed in the 'AUTHORS' file.
19 package jalview.schemes;
21 import java.awt.Color;
24 import jalview.datamodel.AlignmentI;
25 import jalview.datamodel.AnnotatedCollectionI;
26 import jalview.datamodel.SequenceCollectionI;
27 import jalview.datamodel.SequenceGroup;
28 import jalview.datamodel.SequenceI;
30 public interface ColourSchemeI
35 * @return the colour for the given character
37 public Color findColour(char c);
41 * @param c - sequence symbol or gap
42 * @param j - position in seq
43 * @param seq - sequence being coloured
44 * @return context dependent colour for the given symbol at the position in the given sequence
46 public Color findColour(char c, int j, SequenceI seq);
49 * assign the given consensus profile for the colourscheme
51 public void setConsensus(java.util.Hashtable[] h);
54 * assign the given conservation to the colourscheme
57 public void setConservation(jalview.analysis.Conservation c);
60 * enable or disable conservation shading for this colourscheme
61 * @param conservationApplied
63 public void setConservationApplied(boolean conservationApplied);
66 * @return true if conservation shading is enabled for this colourscheme
68 public boolean conservationApplied();
71 * set scale factor for bleaching of colour in unconserved regions
74 public void setConservationInc(int i);
78 * @return scale factor for bleaching colour in unconserved regions
80 public int getConservationInc();
84 * @return percentage identity threshold for applying colourscheme
86 public int getThreshold();
89 * set percentage identity threshold and type of %age identity calculation for shading
90 * @param ct 0..100 percentage identity for applying this colourscheme
91 * @param ignoreGaps when true, calculate PID without including gapped positions
93 public void setThreshold(int ct, boolean ignoreGaps);
96 * recalculate dependent data using the given sequence collection, taking account of hidden rows
100 public void alignmentChanged(AnnotatedCollectionI alignment,
101 Map<SequenceI, SequenceCollectionI> hiddenReps);
104 * create a new instance of the colourscheme configured to colour the given connection
106 * @param hiddenRepSequences
107 * @return copy of current scheme with any inherited settings transfered
109 public ColourSchemeI applyTo(AnnotatedCollectionI sg,
110 Map<SequenceI, SequenceCollectionI> hiddenRepSequences);