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.SequenceGroup;
24 import jalview.datamodel.SequenceI;
25 import jalview.util.Comparison;
27 import java.awt.Color;
29 public class PIDColourScheme extends ResidueColourScheme
31 public Color[] pidColours;
33 public float[] thresholds;
37 public PIDColourScheme()
39 this.pidColours = ResidueProperties.pidColours;
40 this.thresholds = ResidueProperties.pidThresholds;
44 public Color findColour(char c, int j, SequenceI seq)
46 if ('a' <= c && c <= 'z')
51 if (consensus == null || j >= consensus.length || consensus[j] == null)
56 if ((threshold != 0) && !aboveThreshold(c, j))
61 Color currentColour = Color.white;
65 if (consensus.length <= j)
71 * test whether this is the consensus (or joint consensus) residue
73 boolean matchesConsensus = consensus[j].getModalResidue().contains(
77 sc = consensus[j].getPercentageIdentity(ignoreGaps);
79 if (!Comparison.isGap(c))
81 for (int i = 0; i < thresholds.length; i++)
83 if (sc > thresholds[i])
85 currentColour = pidColours[i];
92 if (conservationColouring)
94 currentColour = applyConservation(currentColour, j);