/*\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
public Color findColour(String n, int j)\r
{\r
+ currentColour = Color.white;\r
+\r
if ((threshold == 0) || aboveThreshold(n, j))\r
{\r
- if( j+1>annotation.annotations.length || annotation.annotations[j]==null)\r
- currentColour = Color.white;\r
- else\r
+ if( j<annotation.annotations.length\r
+ && annotation.annotations[j]!=null\r
+ && !jalview.util.Comparison.isGap(n.charAt(0)))\r
{\r
if( aboveAnnotationThreshold==NO_THRESHOLD\r
|| (annotationThreshold!=null && aboveAnnotationThreshold==ABOVE_THRESHOLD && annotation.annotations[j].value>=annotationThreshold.value)\r
\r
currentColour = new Color( (int) dr, (int) dg, (int) db);\r
}\r
- else\r
- currentColour = Color.white;\r
}\r
- else\r
- currentColour = Color.white;\r
}\r
}\r
- else\r
- {\r
- return Color.white;\r
- }\r
\r
if(conservationColouring)\r
applyConservation(j);\r