import java.awt.*;\r
\r
\r
-public class ScoreColourScheme extends ResidueColourScheme {\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
- public ScoreColourScheme(double[] scores, double min, double max) {\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
- 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
+ // 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
+ if (red > 1.0f)\r
+ {\r
red = 1.0f;\r
- }\r
+ }\r
\r
- if (red < 0.0f) {\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
+ if (jalview.util.Comparison.isGap((c)))\r
+ {\r
return Color.white;\r
}\r
\r
- // This isn';t great - pool of colours in here?\r
- return makeColour(red);\r
+ currentColour = colors[((Integer) ResidueProperties.aaHash.get(s)).intValue()];\r
+\r
+ if(conservationColouring)\r
+ applyConservation(j);\r
+\r
+ return currentColour;\r
}\r
\r
- public Color makeColour(float c) {\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