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.SequenceGroup;
26 import jalview.datamodel.SequenceI;
27 import jalview.util.Comparison;
29 import java.awt.Color;
32 public class PIDColourScheme extends ResidueColourScheme
34 public Color[] pidColours;
36 public float[] thresholds;
40 public PIDColourScheme()
42 this.pidColours = ResidueProperties.pidColours;
43 this.thresholds = ResidueProperties.pidThresholds;
47 public Color findColour(char c, int j, SequenceI seq,
48 String consensusResidue, float pid)
51 * make everything uppercase; note this does nothing (fast)
52 * if consensusResidue is already uppercase
54 consensusResidue = consensusResidue.toUpperCase();
55 if ('a' <= c && c <= 'z')
60 if (consensusResidue == null || Comparison.isGap(c))
65 Color colour = Color.white;
68 * test whether this is the consensus (or joint consensus) residue
70 boolean matchesConsensus = consensusResidue.contains(
74 for (int i = 0; i < thresholds.length; i++)
76 if (pid > thresholds[i])
78 colour = pidColours[i];
88 public String getSchemeName()
90 return JalviewColourScheme.PID.toString();
94 * Returns a new instance of this colour scheme with which the given data may
98 public ColourSchemeI getInstance(AnnotatedCollectionI coll,
99 Map<SequenceI, SequenceCollectionI> hrs)
101 return new PIDColourScheme();
105 public boolean isSimple()