for(int j=0; j<uprefs.length; j++)\r
{\r
addSeqId(sequence, uprefs[j].getAccessionId());\r
- queryString.append(uprefs[i].getAccessionId()+";");\r
+ queryString.append(uprefs[j].getAccessionId()+";");\r
}\r
}\r
else\r
System.out.println("Adding dbref to " + sequence.getName() + " : " +\r
entry.getAccession().elementAt(0).toString());\r
\r
- String nonGapped = AlignSeq.extractGaps("-. ", sequence.getSequence()).\r
+ String nonGapped = AlignSeq.extractGaps("-. ",\r
+ sequence.getSequenceAsString()).\r
toUpperCase();\r
\r
int absStart = entry.getUniprotSequence().getContent().indexOf(\r