2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
3 * Copyright (C) 2014 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 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/>.
17 * The Jalview Authors are detailed in the 'AUTHORS' file.
19 package jalview.schemes;
21 import jalview.datamodel.SequenceI;
23 import java.awt.Color;
31 public class ScoreColourScheme extends ResidueColourScheme
40 public double[] scores;
43 * Creates a new ScoreColourScheme object.
52 public ScoreColourScheme(int symbolIndex[], double[] scores, double min,
61 // Make colours in constructor
62 // Why wasn't this done earlier?
63 int i, iSize = scores.length;
64 colors = new Color[scores.length];
65 for (i = 0; i < iSize; i++)
67 float red = (float) (scores[i] - (float) min) / (float) (max - min);
78 colors[i] = makeColour(red);
90 * @return DOCUMENT ME!
93 public Color findColour(char c, int j, SequenceI seq)
97 if (!aboveThreshold(c, j))
103 if (jalview.util.Comparison.isGap(c))
108 Color currentColour = colors[ResidueProperties.aaIndex[c]];
110 if (conservationColouring)
112 currentColour = applyConservation(currentColour, j);
115 return currentColour;
124 * @return DOCUMENT ME!
126 public Color makeColour(float c)
128 return new Color(c, (float) 0.0, (float) 1.0 - c);