- * @return aligned column for residue (0 if residue is upstream from alignment, -1 if residue is downstream from alignment)
- * note. Sequence object returns sequence.getEnd() for positions upstream currently. TODO: change sequence for assert(findIndex(seq.getEnd()+1)==-1) and fix incremental bugs
+ * @return aligned column for residue (0 if residue is upstream from
+ * alignment, -1 if residue is downstream from alignment) note.
+ * Sequence object returns sequence.getEnd() for positions upstream
+ * currently. TODO: change sequence for
+ * assert(findIndex(seq.getEnd()+1)==-1) and fix incremental bugs