mappingDetails.append(String.valueOf(maxAlignseq.seq2start)).append(
" ");
mappingDetails.append(String.valueOf(maxAlignseq.seq2end));
-
mappingDetails.append(NEWLINE).append("SEQ start/end ");
+ // TODO JAL-1887 should be fixed from here
mappingDetails.append(
String.valueOf(maxAlignseq.seq1start + seq.getStart() - 1))
.append(" ");
resNum = tmp.resNumber;
if (tmp.alignmentMapping >= -1)
{
- // TODO (JAL-1836) address root cause: negative residue no in PDB file
+ // TODO (JAL-1836) address root cause: negative residue no in PDB
+ // file
mapping[tmp.alignmentMapping + 1][0] = tmp.resNumber;
mapping[tmp.alignmentMapping + 1][1] = tmp.atomIndex;
}
{
results = MappingUtils.buildSearchResults(seq, index,
seqmappings);
- }
+ }
if (handlingVamsasMo)
{
results.addResult(seq, index, index);