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.api.AlignViewportI;
24 import jalview.datamodel.AnnotatedCollectionI;
25 import jalview.datamodel.SequenceCollectionI;
26 import jalview.datamodel.SequenceGroup;
27 import jalview.datamodel.SequenceI;
28 import jalview.util.Comparison;
30 import java.awt.Color;
33 public class PIDColourScheme extends ResidueColourScheme
35 private static final Color[] pidColours = { new Color(100, 100, 255),
36 new Color(153, 153, 255), new Color(204, 204, 255), };
38 private static final float[] thresholds = { 80, 60, 40, };
42 public PIDColourScheme()
47 public Color findColour(char c, int j, SequenceI seq,
48 String consensusResidue, float pid)
51 * compare as upper case; note consensusResidue is
52 * always computed as uppercase
54 if ('a' <= c && c <= 'z')
59 if (consensusResidue == null || Comparison.isGap(c))
64 Color colour = Color.white;
67 * test whether this is the consensus (or joint consensus) residue
69 boolean matchesConsensus = consensusResidue.contains(String.valueOf(c));
72 for (int i = 0; i < thresholds.length; i++)
74 if (pid > thresholds[i])
76 colour = pidColours[i];
86 public String getSchemeName()
88 return JalviewColourScheme.PID.toString();
92 * Returns a new instance of this colour scheme with which the given data may
96 public ColourSchemeI getInstance(AlignViewportI view,
97 AnnotatedCollectionI coll,
98 Map<SequenceI, SequenceCollectionI> hrs)
100 return new PIDColourScheme();
104 public boolean isSimple()