/*\r
* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\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
\r
}\r
\r
+\r
+ public String getAnnotation()\r
+ {\r
+ return annotation.label;\r
+ }\r
+\r
+ public int getAboveThreshold()\r
+ {\r
+ return aboveAnnotationThreshold;\r
+ }\r
+\r
+ public float getAnnotationThreshold()\r
+ {\r
+ if(annotationThreshold==null)\r
+ return 0;\r
+ else\r
+ return annotationThreshold.value;\r
+ }\r
+\r
+ public ColourSchemeI getBaseColour()\r
+ {\r
+ return colourScheme;\r
+ }\r
+\r
public Color getMinColour()\r
{\r
return new Color( (int) r1, (int) g1, (int) b1);\r
*\r
* @return DOCUMENT ME!\r
*/\r
- public Color findColour(String n)\r
+ public Color findColour(char c)\r
{\r
return Color.red;\r
}\r
*\r
* @return DOCUMENT ME!\r
*/\r
- public Color findColour(String n, int j)\r
+ public Color findColour(char c, int j)\r
{\r
- currentColour = Color.white;\r
+ Color currentColour = Color.white;\r
\r
- if ((threshold == 0) || aboveThreshold(n, j))\r
+ if ((threshold == 0) || aboveThreshold(c, j))\r
{\r
if( j<annotation.annotations.length\r
&& annotation.annotations[j]!=null\r
- && !jalview.util.Comparison.isGap(n.charAt(0)))\r
+ && !jalview.util.Comparison.isGap(c))\r
{\r
if( aboveAnnotationThreshold==NO_THRESHOLD\r
|| (annotationThreshold!=null && aboveAnnotationThreshold==ABOVE_THRESHOLD && annotation.annotations[j].value>=annotationThreshold.value)\r
{\r
if(colourScheme!=null)\r
{\r
- currentColour = colourScheme.findColour(n, j);\r
+ currentColour = colourScheme.findColour(c, j);\r
}\r
else if(range!=0)\r
{\r
}\r
\r
if(conservationColouring)\r
- applyConservation(j);\r
+ currentColour = applyConservation(currentColour, j);\r
\r
return currentColour;\r
}\r