String seq;\r
while(j < seqs.size())\r
{\r
- seq = ( (SequenceI) seqs.get(j)).getSequence();\r
- for (i = start; i <= end; i++)\r
+ seq = ( (SequenceI) seqs.elementAt(j)).getSequence();\r
+ int end_j = seq.length()-1;\r
+ for (i = start; i <= end_j; i++)\r
{\r
if(seq.length()-1<i)\r
res = 23;\r
size = i;\r
}\r
\r
- public Color findColour(String s, int j, Vector seqs)\r
+ public Color findColour(String s, int j)\r
{\r
int i = ((Integer)ResidueProperties.aaHash.get(s)).intValue();\r
\r
Color c = Color.white;\r
\r
- if(i>20)\r
+ if(i>19)\r
return c;\r
\r
for (int k=0; k < ResidueColour[i].conses.length ; k++)\r
\r
}\r
\r
+ public void setConsensus(Vector consensus)\r
+ {\r
+ // Clustal colouring cannot be coloured by PID\r
+ }\r
\r
public boolean canThreshold()\r
{\r