2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
3 * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
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/>.
18 package jalview.schemes;
20 import java.awt.Color;
22 import jalview.datamodel.AnnotatedCollectionI;
23 import jalview.datamodel.SequenceI;
25 public interface ColourSchemeI
27 public Color findColour(char c);
29 public Color findColour(char c, int j, SequenceI seq);
31 public void setConsensus(java.util.Hashtable[] h);
33 public void setConservation(jalview.analysis.Conservation c);
35 public boolean conservationApplied();
37 public void setConservationInc(int i);
39 public int getConservationInc();
41 public int getThreshold();
43 public void setThreshold(int ct, boolean ignoreGaps);
45 public void alignmentChanged(AnnotatedCollectionI alignment);