2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
3 * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, 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 jalview.datamodel.SequenceI;
22 import java.awt.Color;
30 public class ScoreColourScheme extends ResidueColourScheme
39 public double[] scores;
42 * Creates a new ScoreColourScheme object.
51 public ScoreColourScheme(int symbolIndex[], double[] scores, double min,
60 // Make colours in constructor
61 // Why wasn't this done earlier?
62 int i, iSize = scores.length;
63 colors = new Color[scores.length];
64 for (i = 0; i < iSize; i++)
66 float red = (float) (scores[i] - (float) min) / (float) (max - min);
77 colors[i] = makeColour(red);
89 * @return DOCUMENT ME!
92 public Color findColour(char c, int j, SequenceI seq)
96 if (!aboveThreshold(c, j))
102 if (jalview.util.Comparison.isGap(c))
107 Color currentColour = colors[ResidueProperties.aaIndex[c]];
109 if (conservationColouring)
111 currentColour = applyConservation(currentColour, j);
114 return currentColour;
123 * @return DOCUMENT ME!
125 public Color makeColour(float c)
127 return new Color(c, (float) 0.0, (float) 1.0 - c);