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.ProfileI;
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 public Color[] pidColours;
37 public float[] thresholds;
41 public PIDColourScheme()
43 this.pidColours = ResidueProperties.pidColours;
44 this.thresholds = ResidueProperties.pidThresholds;
48 public Color findColour(char c, int j, SequenceI seq)
50 if ('a' <= c && c <= 'z')
55 if (consensus == null || consensus.get(j) == null)
60 if ((threshold != 0) && !aboveThreshold(c, j))
65 Color currentColour = Color.white;
71 * test whether this is the consensus (or joint consensus) residue
73 ProfileI profile = consensus.get(j);
74 boolean matchesConsensus = profile.getModalResidue().contains(
78 sc = profile.getPercentageIdentity(ignoreGaps);
80 if (!Comparison.isGap(c))
82 for (int i = 0; i < thresholds.length; i++)
84 if (sc > thresholds[i])
86 currentColour = pidColours[i];
93 if (conservationColouring)
95 currentColour = applyConservation(currentColour, j);
102 public String getSchemeName()
104 return JalviewColourScheme.PID.toString();
108 * Returns a new instance of this colour scheme with which the given data may
112 public ColourSchemeI getInstance(AnnotatedCollectionI coll,
113 Map<SequenceI, SequenceCollectionI> hrs)
115 return new PIDColourScheme();