+/*\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 jalview.datamodel.*;\r
-import jalview.jbgui.*;\r
-\r
-import java.util.*;\r
import java.awt.*;\r
\r
-public class ScoreColourScheme extends ResidueColourScheme {\r
+/**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @author $author$\r
+ * @version $Revision$\r
+ */\r
+public class ScoreColourScheme\r
+ extends ResidueColourScheme\r
+{\r
+ /** DOCUMENT ME!! */\r
public double min;\r
+\r
+ /** DOCUMENT ME!! */\r
public double max;\r
- public double[] scores;\r
\r
- public ScoreColourScheme( double[] scores,\r
- double min,\r
- double max) {\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
-\r
\r
- public Color findColour(String s,int j,Vector aa)\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 (threshold > 0)\r
+ if (red > 1.0f)\r
{\r
- if (!aboveThreshold(aa,s,j))\r
- return Color.white;\r
+ red = 1.0f;\r
}\r
\r
- float red = (float)(scores[((Integer)ResidueProperties.aaHash.get(s)).intValue()]\r
- - (float)min)/(float)(max - min);\r
- if (red > 1.0f)\r
- red = 1.0f;\r
-\r
- if (red < 0.0f)\r
- red = 0.0f;\r
-\r
- char c = s.charAt(0);\r
+ if (red < 0.0f)\r
+ {\r
+ red = 0.0f;\r
+ }\r
+ colors[i] = makeColour(red);\r
+ }\r
+ }\r
\r
- if(jalview.util.Comparison.isGap((c)))\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 (!aboveThreshold(c, j))\r
+ {\r
return Color.white;\r
+ }\r
+ }\r
\r
- // This isn';t great - pool of colours in here?\r
- return makeColour(red);\r
+ if (jalview.util.Comparison.isGap(c))\r
+ {\r
+ return Color.white;\r
}\r
- public Color makeColour(float c) {\r
- return new Color(c,(float)0.0,(float)1.0-c);\r
+\r
+ Color currentColour = colors[ResidueProperties.aaIndex[c]];\r
+\r
+ if (conservationColouring)\r
+ {\r
+ currentColour = applyConservation(currentColour, j);\r
}\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