SequenceI [] seqs = new SequenceI[iSize];\r
SequenceI [] inorder = getSequencesInOrder(align);\r
\r
+\r
for (int i = 0; i < iSize; i++)\r
{\r
SequenceI seq = inorder[i];\r
*/\r
public void addSequence(SequenceI s, boolean recalc)\r
{\r
- if (!sequences.contains(s))\r
+ if (s!=null && !sequences.contains(s))\r
{\r
sequences.addElement(s);\r
}\r
\r
try\r
{\r
- cs.setConsensus(AAFrequency.calculate(sequences, 0, getWidth()));\r
+ cs.setConsensus(AAFrequency.calculate(sequences, startRes, endRes+1));\r
\r
if (cs instanceof ClustalxColourScheme)\r
{\r
{\r
Conservation c = new Conservation(groupName,\r
ResidueProperties.propHash, 3, sequences,\r
- 0, getWidth());\r
+ startRes, endRes+1);\r
c.calculate();\r
c.verdict(false, 25);\r
\r