-/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2006 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
-/**\r
- * DOCUMENT ME!\r
- *\r
- * @author $author$\r
- * @version $Revision$\r
- */\r
-public class ScoreColourScheme extends ResidueColourScheme\r
-{\r
- /** DOCUMENT ME!! */\r
- public double min;\r
-\r
- /** DOCUMENT ME!! */\r
- public double max;\r
-\r
- /** DOCUMENT ME!! */\r
- public double[] scores;\r
-\r
- /**\r
- * Creates a new ScoreColourScheme object.\r
- *\r
- * @param scores DOCUMENT ME!\r
- * @param min DOCUMENT ME!\r
- * @param max DOCUMENT ME!\r
- */\r
- public ScoreColourScheme(double[] scores, double min, double max)\r
- {\r
- super();\r
-\r
- this.scores = scores;\r
- this.min = min;\r
- this.max = max;\r
-\r
- // Make colours in constructor\r
- // Why wasn't this done earlier?\r
- int i, iSize=scores.length;\r
- colors = new Color[scores.length];\r
- for (i = 0; i < iSize; i++)\r
- {\r
- float red = (float) (scores[i] - (float) min) / (float) (max - min);\r
-\r
- if (red > 1.0f)\r
- {\r
- red = 1.0f;\r
- }\r
-\r
- if (red < 0.0f)\r
- {\r
- red = 0.0f;\r
- }\r
- colors[i] = makeColour(red);\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param s DOCUMENT ME!\r
- * @param j DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public Color findColour(String s, int j)\r
- {\r
- if (threshold > 0)\r
- {\r
- if (!aboveThreshold(s, j))\r
- {\r
- return Color.white;\r
- }\r
- }\r
-\r
- char c = s.charAt(0);\r
-\r
- if (jalview.util.Comparison.isGap((c)))\r
- {\r
- return Color.white;\r
- }\r
-\r
- currentColour = colors[((Integer) ResidueProperties.aaHash.get(s)).intValue()];\r
-\r
- if(conservationColouring)\r
- applyConservation(j);\r
-\r
- return currentColour;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param c DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public Color makeColour(float c)\r
- {\r
- return new Color(c, (float) 0.0, (float) 1.0 - c);\r
- }\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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.datamodel.SequenceI;
+
+import java.awt.Color;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class ScoreColourScheme extends ResidueColourScheme
+{
+ /** DOCUMENT ME!! */
+ public double min;
+
+ /** DOCUMENT ME!! */
+ public double max;
+
+ /** DOCUMENT ME!! */
+ public double[] scores;
+
+ /**
+ * Creates a new ScoreColourScheme object.
+ *
+ * @param scores
+ * DOCUMENT ME!
+ * @param min
+ * DOCUMENT ME!
+ * @param max
+ * DOCUMENT ME!
+ */
+ public ScoreColourScheme(int symbolIndex[], double[] scores, double min,
+ double max)
+ {
+ super(symbolIndex);
+
+ this.scores = scores;
+ this.min = min;
+ this.max = max;
+
+ // Make colours in constructor
+ // Why wasn't this done earlier?
+ int i, iSize = scores.length;
+ colors = new Color[scores.length];
+ for (i = 0; i < iSize; i++)
+ {
+ float red = (float) (scores[i] - (float) min) / (float) (max - min);
+
+ if (red > 1.0f)
+ {
+ red = 1.0f;
+ }
+
+ if (red < 0.0f)
+ {
+ red = 0.0f;
+ }
+ colors[i] = makeColour(red);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param s
+ * DOCUMENT ME!
+ * @param j
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ @Override
+ public Color findColour(char c, int j, SequenceI seq)
+ {
+ if (threshold > 0)
+ {
+ if (!aboveThreshold(c, j))
+ {
+ return Color.white;
+ }
+ }
+
+ if (jalview.util.Comparison.isGap(c))
+ {
+ return Color.white;
+ }
+
+ Color currentColour = colors[ResidueProperties.aaIndex[c]];
+
+ if (conservationColouring)
+ {
+ currentColour = applyConservation(currentColour, j);
+ }
+
+ return currentColour;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param c
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Color makeColour(float c)
+ {
+ return new Color(c, (float) 0.0, (float) 1.0 - c);
+ }
+}
git://source.jalview.org / jalview.git / blobdiff