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root/gclib/gclib/GAlnExtend.cpp
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# Line 463 | Line 463
463          if (edit_block == NULL) {
464             // if no traceback is specified, the next row of
465             //   last_seq2_off can reuse previously allocated memory
466 <           //TODO FIXME The following assumes two arrays of
466 >           //WARNING The following assumes two arrays of
467             //  at least max_dist+4 int's have already been allocated
468              last_seq2_off[d + 1] = last_seq2_off[d - 1];
469              }
# Line 472 | Line 472
472              // so a new row must be allocated
473              last_seq2_off[d + 1] = (int*)mem_pool->getByteSpace((diag_upper - diag_lower + 7)*sizeof(int));
474              // move the origin for this row backwards
475 <            //TODO FIXME: dubious pointer arithmetic ?!
475 >            // dubious pointer arithmetic ?!
476              //last_seq2_off[d + 1] = last_seq2_off[d + 1] - diag_lower + 2;
477              }
478      }   // end loop over distinct distances
# Line 893 | Line 893
893      if (editscript)
894         ed_script_rev->Append(ed_script_fwd); //combine the two extensions
895    }
896
896    if (retscore>=MIN_GREEDY_SCORE) {
897      alninfo=new GXAlnInfo(q_seq, q_alnstart+1-q_ext_l, q_alnstart+q_ext_r, s_seq, s_alnstart+1-s_ext_l, s_alnstart+s_ext_r);
898      int hsp_length = GMIN(q_ext_l+q_ext_r, s_ext_l+s_ext_r);

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