/*\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
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2007 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
+public class ScoreColourScheme\r
+ 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
+ /** 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
- 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
+ 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
- * 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
+\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(char c, int j)\r
+ {\r
+ if (threshold > 0)\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
+ if (!aboveThreshold(c, j))\r
+ {\r
+ return Color.white;\r
+ }\r
+ }\r
\r
- return currentColour;\r
+ if (jalview.util.Comparison.isGap(c))\r
+ {\r
+ return Color.white;\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
+ Color currentColour = colors[ResidueProperties.aaIndex[c]];\r
+\r
+ if (conservationColouring)\r
{\r
- return new Color(c, (float) 0.0, (float) 1.0 - c);\r
+ currentColour = applyConservation(currentColour, j);\r
}\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
git://source.jalview.org / jalview.git / blobdiff