2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
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
32 public Color findColour(char c);
34 public Color findColour(char c, int j, SequenceI seq);
36 public void setConsensus(java.util.Hashtable[] h);
38 public void setConservation(jalview.analysis.Conservation c);
40 public boolean conservationApplied();
42 public void setConservationInc(int i);
44 public int getConservationInc();
46 public int getThreshold();
48 public void setThreshold(int ct, boolean ignoreGaps);
50 public void alignmentChanged(AnnotatedCollectionI alignment,
51 Map<SequenceI, SequenceCollectionI> hiddenReps);