\r
package jalview.schemes;\r
import java.awt.*;\r
-import jalview.gui.*;\r
-import jalview.datamodel.*;\r
import jalview.analysis.*;\r
+import java.util.Vector;\r
\r
public class ConservationColourScheme extends ResidueColourScheme {\r
public Conservation conserve;\r
- boolean byResidue = true;\r
public ColourSchemeI cs;\r
public int inc = 30;\r
- int colourThreshold = 7;\r
\r
public ConservationColourScheme(Conservation cons, ColourSchemeI oldcs)\r
{\r
super();\r
conserve = cons;\r
cs = oldcs;\r
-\r
}\r
\r
+ public void setConsensus(Vector consensus)\r
+ {\r
+ this.consensus = consensus;\r
+ if(cs!=null)\r
+ cs.setConsensus(consensus);\r
+ }\r
\r
- public Color findColour(String s, int i, java.util.Vector whatever)\r
+ public Color findColour(String s, int i)\r
{\r
- Color c = null;\r
- if (colourThreshold > 0 && conserve.getConsSequence() != null)\r
- {\r
- if (conserve.getConsSequence().getSequence().charAt(i)=='*'\r
- || conserve.getConsSequence().getSequence().charAt(i)=='+')\r
- {\r
- if (byResidue)\r
- c = findColour(s, i);\r
- else\r
- c = Color.red;\r
- }\r
- else\r
- {\r
- if (byResidue)\r
- {\r
+ Color c = Color.white;\r
+ if (cs == null)\r
+ return c;\r
\r
- int tmp = 10;\r
- int t = 0;\r
- if (!jalview.util.Comparison.isGap(conserve.getConsSequence().\r
- getSequence().charAt(i)))\r
- t = Integer.parseInt(conserve.getConsSequence().getSequence().\r
- substring(i, i + 1));\r
+ char ch = conserve.getConsSequence().getSequence().charAt(i);\r
+ if (ch == '*' || ch == '+')\r
+ {\r
+ c = cs.findColour(s, i);\r
+ }\r
+ else\r
+ {\r
+ int tmp = 10;\r
+ int t = 0;\r
+ if (!jalview.util.Comparison.isGap(ch))\r
+ t = Integer.parseInt(ch + "");\r
\r
- c = findColour(s, i);\r
+ c = cs.findColour(s, i);\r
\r
- while (tmp >= t)\r
- {\r
- // c = c.darker();\r
- c = lighter(c, inc);\r
- tmp--;\r
- }\r
- }\r
- else\r
- c = Color.yellow;\r
+ while (tmp >= t)\r
+ {\r
+ c = lighter(c, inc);\r
+ tmp--;\r
}\r
- }\r
- return c;\r
- }\r
\r
- public Color findColour(String s, int j) {\r
- if(cs!=null)\r
- return cs.findColour( s, j, null);\r
- else\r
- return Color.white;\r
- }\r
+ }\r
\r
+ return c;\r
+ }\r
\r
\r
public Color lighter(Color c, int inc) {\r