/** DOCUMENT ME!! */\r
int inc = 30;\r
\r
- /**\r
- * The colour to be calculated, manipulated and returned\r
- */\r
- Color currentColour = null;\r
-\r
-\r
\r
/**\r
* Creates a new ResidueColourScheme object.\r
/**\r
* Find a colour without an index in a sequence\r
*/\r
- public Color findColour(String aa)\r
+ public Color findColour(char c)\r
{\r
- return colors[ResidueProperties.aaIndex[aa.charAt(0)]];\r
+ return colors[ResidueProperties.aaIndex[c]];\r
}\r
\r
\r
\r
- public Color findColour(String s, int j)\r
+ public Color findColour(char c, int j)\r
{\r
+ Color currentColour;\r
\r
- int index = ResidueProperties.aaIndex[s.charAt(0)];\r
-\r
- if ((threshold == 0) || aboveThreshold(ResidueProperties.aa[index], j))\r
+ if ((threshold == 0) || aboveThreshold(c, j))\r
{\r
- currentColour = colors[index];\r
+ currentColour = colors[ResidueProperties.aaIndex[c]];\r
}\r
else\r
{\r
}\r
\r
if(conservationColouring)\r
- applyConservation(j);\r
+ currentColour = applyConservation(currentColour, j);\r
\r
\r
return currentColour;\r
*\r
* @return DOCUMENT ME!\r
*/\r
- public boolean aboveThreshold(String s, int j)\r
+ public boolean aboveThreshold(char c, int j)\r
{\r
- char c = s.charAt(0);\r
if ('a' <= c && c <= 'z')\r
{\r
// TO UPPERCASE !!!\r
//Faster than toUpperCase\r
c -= ('a' - 'A');\r
- s = String.valueOf(c);\r
}\r
\r
if (consensus == null || consensus[j] == null)\r
return false;\r
\r
if ( ( ( (Integer) consensus[j].get(AAFrequency.MAXCOUNT)).intValue() != -1) &&\r
- consensus[j].contains(s))\r
+ consensus[j].contains(String.valueOf(c)))\r
{\r
if ( ( (Float) consensus[j].get(ignoreGaps)).floatValue() >= threshold)\r
{\r
* @return DOCUMENT ME!\r
*/\r
\r
- void applyConservation(int i)\r
+ Color applyConservation(Color currentColour, int i)\r
{\r
\r
if ((conservation[i] != '*') && (conservation[i] != '+'))\r
float t = 11 - (conservation[i] - '0');\r
if(t==0)\r
{\r
- currentColour = Color.white;\r
- return;\r
+ return Color.white;\r
}\r
\r
int red = currentColour.getRed();\r
currentColour = new Color(red, green, blue);\r
}\r
}\r
+ return currentColour;\r
}\r
\r
\r