-/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
-package jalview.schemes;\r
-\r
-import java.awt.*;\r
-\r
-\r
-public class ScoreColourScheme extends ResidueColourScheme {\r
- public double min;\r
- public double max;\r
- public double[] scores;\r
-\r
- public ScoreColourScheme(double[] scores, double min, double max) {\r
- super();\r
-\r
- this.scores = scores;\r
- this.min = min;\r
- this.max = max;\r
- }\r
-\r
- public Color findColour(String s, int j) {\r
- if (threshold > 0) {\r
- if (!aboveThreshold(s, j)) {\r
- return Color.white;\r
- }\r
- }\r
-\r
- float red = (float) (scores[((Integer) ResidueProperties.aaHash.get(s)).intValue()] -\r
- (float) min) / (float) (max - min);\r
-\r
- if (red > 1.0f) {\r
- red = 1.0f;\r
- }\r
-\r
- if (red < 0.0f) {\r
- red = 0.0f;\r
- }\r
-\r
- char c = s.charAt(0);\r
-\r
- if (jalview.util.Comparison.isGap((c))) {\r
- return Color.white;\r
- }\r
-\r
- // This isn';t great - pool of colours in here?\r
- return makeColour(red);\r
- }\r
-\r
- public Color makeColour(float c) {\r
- return new Color(c, (float) 0.0, (float) 1.0 - c);\r
- }\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.schemes;
+
+import jalview.api.AlignViewportI;
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.SequenceI;
+import jalview.util.Comparison;
+
+import java.awt.Color;
+
+/**
+ * A base class for colour schemes which define a graduated colour range based
+ * on
+ * <ul>
+ * <li>a minimum colour</li>
+ * <li>a maximum colour</li>
+ * <li>a score assigned to each residue</li>
+ * </ul>
+ */
+public class ScoreColourScheme extends ResidueColourScheme
+{
+ String schemeName;
+
+ double min;
+
+ double max;
+
+ Color minColour;
+
+ Color maxColour;
+
+ double[] scores;
+
+ /**
+ * Constructor
+ *
+ * @param symbolIndex
+ * a lookup where the index is a char e.g. 'R' or 'r', and the value
+ * is its position in the colour table lookup
+ * @param scores
+ * per residue, with indices corresponding to those for colour lookup
+ */
+ public ScoreColourScheme(String name, int[] symbolIndex, double[] scores,
+ Color minColour, Color maxColour)
+ {
+ super(symbolIndex);
+ this.schemeName = name;
+ this.minColour = minColour;
+ this.maxColour = maxColour;
+
+ setMinMax(scores);
+ this.scores = scores;
+
+ int iSize = scores.length;
+ colors = new Color[scores.length];
+ for (int i = 0; i < iSize; i++)
+ {
+ colors[i] = getScoreColour(scores[i]);
+ }
+ }
+
+ /**
+ * Computes a colour for a score by
+ * <ul>
+ * <li>first scaling the score linearly from 0 (minScore) to 1 (maxScore)</li>
+ * <li>then interpolating rgb values from minColour to maxColour</li>
+ * </ul>
+ * This method is used to make colours for residue scores, but may also be
+ * called to generate a colour for an intermediate score value (for example, a
+ * column average).
+ */
+ public Color getScoreColour(double rawScore)
+ {
+ float score = (float) (rawScore - (float) min) / (float) (max - min);
+ score = Math.max(score, 0f);
+ score = Math.min(score, 1f);
+
+ int r = minColour.getRed()
+ + Math.round((maxColour.getRed() - minColour.getRed()) * score);
+ int g = minColour.getGreen()
+ + Math.round(
+ (maxColour.getGreen() - minColour.getGreen()) * score);
+ int b = minColour.getBlue()
+ + Math.round(
+ (maxColour.getBlue() - minColour.getBlue()) * score);
+
+ Color c = new Color(r, g, b);
+ return c;
+ }
+
+ /**
+ * Inspects score values and saves the minimum and maximum
+ *
+ * @param vals
+ */
+ void setMinMax(double[] vals)
+ {
+ double dMin = Double.MAX_VALUE;
+ double dMax = -Double.MAX_VALUE;
+
+ for (int i = 0; i < vals.length - 1; i++)
+ {
+ dMin = Math.min(dMin, vals[i]);
+ dMax = Math.max(dMax, vals[i]);
+ }
+
+ this.min = vals.length == 0 ? 0d : dMin;
+ this.max = vals.length == 0 ? 0d : dMax;
+ }
+
+ @Override
+ public Color findColour(char c, int j, SequenceI seq)
+ {
+ if (Comparison.isGap(c))
+ {
+ return Color.white;
+ }
+ return super.findColour(c);
+ }
+
+ @Override
+ public String getSchemeName()
+ {
+ return schemeName;
+ }
+
+ /**
+ * Returns a new instance of this colour scheme with which the given data may
+ * be coloured
+ */
+ @Override
+ public ColourSchemeI getInstance(AlignViewportI view,
+ AnnotatedCollectionI coll)
+ {
+ return new ScoreColourScheme(schemeName, symbolIndex, scores, minColour,
+ maxColour);
+ }
+}
git://source.jalview.org / jalview.git / blobdiff