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.SequenceI;
24 import jalview.util.Comparison;
26 import java.awt.Color;
34 public class ScoreColourScheme extends ResidueColourScheme
43 public double[] scores;
46 * Creates a new ScoreColourScheme object.
55 public ScoreColourScheme(int symbolIndex[], double[] scores, double min,
64 // Make colours in constructor
65 // Why wasn't this done earlier?
66 int i, iSize = scores.length;
67 colors = new Color[scores.length];
68 for (i = 0; i < iSize; i++)
70 float red = (float) (scores[i] - (float) min) / (float) (max - min);
81 colors[i] = makeColour(red);
93 * @return DOCUMENT ME!
96 public Color findColour(char c, int j, SequenceI seq)
100 if (!aboveThreshold(c, j))
106 if (Comparison.isGap(c))
111 Color currentColour = colors[ResidueProperties.aaIndex[c]];
113 if (conservationColouring)
115 currentColour = applyConservation(currentColour, j);
118 return currentColour;
127 * @return DOCUMENT ME!
129 public Color makeColour(float c)
131 return new Color(c, (float) 0.0, (float) 1.0 - c);