Example #1
0
static void AddBioSourceToSeqEntry (SeqEntryPtr sep)
{
  BioseqPtr    bsp;
  ValNodePtr   descorp;
  BioSourcePtr biop;
  OrgNamePtr   onp;
  OrgRefPtr    orp;

  if (sep == NULL)
    return;
  if ((bsp = sep->data.ptrvalue) == NULL)
    return;

  descorp = ValNodeNew (bsp->descr);
  descorp->choice = Seq_descr_source;
  biop = BioSourceNew ();
  descorp->data.ptrvalue = biop;
  orp = OrgRefNew ();
  biop->org = orp;
  onp = OrgNameNew ();
  orp->orgname = onp;
  biop->genome = 1;
  onp->gcode = 1;
  onp->mgcode = 1;

  if (bsp->descr == NULL)
    bsp->descr = descorp;

  return;
}
Example #2
0
static BioSourcePtr OldParseTitleIntoBioSource (
  SqnTagPtr stp,
  BioseqPtr bsp,
  CharPtr organism
)

{
  BioSourcePtr  biop = NULL;
  ValNodePtr    db;
  DbtagPtr      dbt;
  Int2          idx;
  ObjectIdPtr   oip;
  OrgModPtr     omp;
  OrgNamePtr    onp;
  OrgRefPtr     orp;
  SubSourcePtr  ssp;
  CharPtr       str;
  int           val;

  if (stp == NULL && StringHasNoText (organism)) return NULL;

  str = SqnTagFind (stp, "top");
  if (str != NULL && bsp != NULL) {
    if (StringICmp (str, "linear") == 0) {
      bsp->topology = TOPOLOGY_LINEAR;
    } else if (StringICmp (str, "circular") == 0) {
      bsp->topology = TOPOLOGY_CIRCULAR;
    }
  }
  str = SqnTagFind (stp, "org");
  if (str == NULL) {
    str = organism;
  }
  if (StringHasNoText (str)) return NULL;
   biop = BioSourceNew ();
  if (biop == NULL) return NULL;
  orp = OrgRefNew ();
  if (orp == NULL) return NULL;
  biop->org = orp;
  onp = OrgNameNew ();
  if (onp == NULL) return NULL;
  orp->orgname = onp;
  orp->taxname = StringSave (str);

  /* look for entry of organisms in commonOrgStuff table */

  for (idx = 0; commonOrgStuff [idx].taxname != NULL; idx++) {
    if (StringICmp (orp->taxname, commonOrgStuff [idx].taxname) == 0) {
      onp->gcode = commonOrgStuff [idx].gcode;
      onp->mgcode = commonOrgStuff [idx].mgcode;
      onp->div = StringSave (commonOrgStuff [idx].division);
      onp->lineage = StringSave (commonOrgStuff [idx].lineage);
      db = ValNodeNew (NULL);
      if (db != NULL) {
        dbt = DbtagNew ();
        if (dbt != NULL) {
          oip = ObjectIdNew ();
          if (oip != NULL) {
            oip->id = commonOrgStuff [idx].taxID;
            dbt->db = StringSave ("taxon");
            dbt->tag = oip;
            db->data.ptrvalue = (Pointer) dbt;
            orp->db = db;
          }
        }
      }
    }
  }

  /* otherwise can get genetic codes from FASTA defline */

  str = SqnTagFind (stp, "gcode");
  if (str != NULL && sscanf (str, "%d", &val) == 1) {
    onp->gcode = (Uint1) val; /* cytoplasmic */
  }

  str = SqnTagFind (stp, "mgcode");
  if (str != NULL && sscanf (str, "%d", &val) == 1) {
    onp->mgcode = (Uint1) val; /* mitochondrial */
  }

  str = SqnTagFind (stp, "location");
  if (str != NULL && StringICmp (str, "mitochondrion") == 0) {
    biop->genome = GENOME_mitochondrion;
  } else {
    biop->genome = GENOME_genomic;
  }

  str = SqnTagFind (stp, "strain");
  if (str != NULL) {
    omp = OrgModNew ();
    if (omp != NULL) {
      omp->subtype = ORGMOD_strain;
      omp->subname = StringSave (str);
      onp->mod = omp;
    }
  }

  str = SqnTagFind (stp, "chromosome");
  if (str != NULL) {
    ssp = SubSourceNew ();
    if (ssp != NULL) {
      ssp->subtype = SUBSRC_chromosome;
      ssp->name = StringSave (str);
      biop->subtype = ssp;
    }
  }

  return biop;
}
Example #3
0
static Int2 Main_old (void)
 
{
   AsnIoPtr aip, xml_aip = NULL;
   BioseqPtr query_bsp, PNTR query_bsp_array;
   BioSourcePtr source;
   BLAST_MatrixPtr matrix;
   BLAST_OptionsBlkPtr options;
   BLAST_KarlinBlkPtr ka_params=NULL, ka_params_gap=NULL;
   BlastPruneSapStructPtr prune;
   Boolean db_is_na, query_is_na, show_gi, believe_query=FALSE;
   Boolean html=FALSE;
   CharPtr params_buffer=NULL;
   Int4 number_of_descriptions, number_of_alignments;
   SeqAlignPtr  seqalign, PNTR seqalign_array;
   SeqAnnotPtr seqannot;
   SeqEntryPtr PNTR sepp;
   TxDfDbInfoPtr dbinfo=NULL, dbinfo_head;
   Uint1 align_type, align_view, out_type;
   Uint4 align_options, print_options;
   ValNodePtr mask_loc, mask_loc_start, next_mask_loc;
   ValNodePtr vnp, other_returns, error_returns;
   
   CharPtr blast_program, blast_database, blast_inputfile, blast_outputfile;
   FILE *infp, *outfp, *mqfp=NULL;
   Int4 index, num_bsps, total_length, total_processed = 0;
   Int2 ctr = 1;
   Char prefix[2];
   SeqLocPtr last_mask, mask_slp;
   Boolean done, hits_found;
   Boolean lcase_masking;
   MBXmlPtr mbxp = NULL;
   Boolean traditional_formatting;

    blast_program = "blastn";
    blast_database = myargs [ARG_DB].strvalue;
    blast_inputfile = myargs [ARG_QUERY].strvalue;
    blast_outputfile = myargs [ARG_OUT].strvalue;
    if (myargs[ARG_HTML].intvalue)
        html = TRUE;

    if ((infp = FileOpen(blast_inputfile, "r")) == NULL) {
       ErrPostEx(SEV_FATAL, 1, 0, "mgblast: Unable to open input file %s\n", blast_inputfile);
       return (1);
    }

    align_view = (Int1) myargs[ARG_FORMAT].intvalue;
    /* Geo mod: 
      -- replaced myargs[ARG_OUTTYPE].intvalue with out_type from now on
    */
    out_type=(Int1) myargs[ARG_OUTTYPE].intvalue;
    if (out_type==MGBLAST_FLTHITS || out_type==MGBLAST_HITGAPS) {
      align_view = 12 + (out_type-MGBLAST_FLTHITS ); 
      out_type=MBLAST_ALIGNMENTS;
      //Attention: 12 MUST be the -m mgblast tab option for MGBLAST_FLTHITS format
      // and MGBLAST_HITGAPS = MGBLAST_FLTHITS+1
       if (align_view>12) { // this is MGBLAST_HITGAPS output
            gap_Info=TRUE;
            if (dbgaps_buf==NULL)
                  dbgaps_buf=(CharPtr) Malloc(dbgaps_bufsize + 1);
            if (qgaps_buf==NULL) 
                qgaps_buf=(CharPtr) Malloc(qgaps_bufsize + 1);
            }
      }

    outfp = NULL;

    traditional_formatting = 
        (out_type == MBLAST_ALIGNMENTS ||
         out_type == MBLAST_DELAYED_TRACEBACK);

    if ((!traditional_formatting ||
            (align_view != 7 && align_view != 10 && align_view != 11)) && 
            blast_outputfile != NULL) {
       if ((outfp = FileOpen(blast_outputfile, "w")) == NULL) {
          ErrPostEx(SEV_FATAL, 1, 0, "blast: Unable to open output file %s\n", blast_outputfile);
          return (1);
       }
    }

    //align_type = BlastGetTypes(blast_program, &query_is_na, &db_is_na);
    align_type = BlastGetTypes(blast_program, &query_is_na, &db_is_na);
    /*
    if (!traditional_formatting)
        believe_query = TRUE;
    else
        believe_query = (Boolean) myargs[ARG_BELIEVEQUERY].intvalue;
    */
    //Geo mod: 
    believe_query=FALSE;
    //If ASN.1 output is requested and believe_query is not set to TRUE,
    //   exit with an error.    
    if (!believe_query && (myargs[ARG_ASNOUT].strvalue ||
                           align_view == 10 || align_view == 11)) {
        ErrPostEx(SEV_FATAL, 1, 0, 
                  "-J option must be TRUE to produce ASN.1 output; before "
                  "changing -J to TRUE please also ensure that all query "
                  "sequence identifiers are unique");
        return -1;
    }
        
    options = BLASTOptionNewEx(blast_program, TRUE, TRUE);
    if (options == NULL)
        return 3;

    options->do_sum_stats = FALSE;
    options->is_neighboring = FALSE;
        options->expect_value  = (Nlm_FloatHi) myargs [ARG_EVALUE].floatvalue;
    number_of_descriptions = myargs[ARG_DESCRIPTIONS].intvalue;    
    number_of_alignments = myargs[ARG_ALIGNMENTS].intvalue;    
    options->hitlist_size = MAX(number_of_descriptions, number_of_alignments);

    if (myargs[ARG_XDROP].intvalue != 0)
           options->gap_x_dropoff = myargs[ARG_XDROP].intvalue;
    if (myargs[ARG_XDROP_UNGAPPED].intvalue != 0)
           options->dropoff_2nd_pass = myargs[ARG_XDROP_UNGAPPED].intvalue;
        if (myargs[ARG_XDROP_FINAL].intvalue != 0)
           options->gap_x_dropoff_final = myargs[ARG_XDROP_FINAL].intvalue;

    if (StringICmp(myargs[ARG_FILTER].strvalue, "T") == 0)
       options->filter_string = StringSave("D");
    else
       options->filter_string = StringSave(myargs[ARG_FILTER].strvalue);
    
    show_gi = (Boolean) myargs[ARG_SHOWGIS].intvalue;
    options->penalty = myargs[ARG_MISMATCH].intvalue;
    options->reward = myargs[ARG_MATCH].intvalue;
        if (myargs[ARG_GAPOPEN].intvalue >= 0)
        options->gap_open = myargs[ARG_GAPOPEN].intvalue;
        if (myargs[ARG_GAPEXT].intvalue >= 0)
        options->gap_extend = myargs[ARG_GAPEXT].intvalue;

    if (options->gap_open == 0 && options->reward % 2 == 0 && 
        options->gap_extend == options->reward / 2 - options->penalty)
       /* This is the default value */
    options->gap_extend = 0;

    options->genetic_code = 1;
    options->db_genetic_code = 1; /* Default; it's not needed here anyway */
    options->number_of_cpus = myargs[ARG_THREADS].intvalue;
    if (myargs[ARG_WORDSIZE].intvalue != 0)
           options->wordsize = myargs[ARG_WORDSIZE].intvalue;
        if (myargs[ARG_MINSCORE].intvalue == 0)
           options->cutoff_s2 = options->wordsize*options->reward;
        else 
           options->cutoff_s2 = myargs[ARG_MINSCORE].intvalue;

        options->db_length = (Int8) myargs[ARG_DBSIZE].floatvalue;
        options->searchsp_eff = (Nlm_FloatHi) myargs[ARG_SEARCHSP].floatvalue;

    options->perform_culling = FALSE;
    /* Kludge */
    options->block_width  = myargs[ARG_MAXPOS].intvalue;

    options->strand_option = myargs[ARG_STRAND].intvalue;
        options->window_size = myargs[ARG_WINDOW].intvalue;
#ifdef DO_NOT_SUPPRESS_BLAST_OP        
        options->mb_template_length = myargs[ARG_TEMPL_LEN].intvalue;
        if (myargs[ARG_TEMPL_LEN].intvalue != 0)
            options->mb_one_base_step = (Boolean) myargs[ARG_EVERYBASE].intvalue;
        options->mb_disc_type = myargs[ARG_TEMPL_TYPE].intvalue;
#endif
        lcase_masking = (Boolean) myargs[ARG_LCASE].intvalue;
        /* Allow dynamic programming gapped extension only with affine 
           gap scores */
        if (options->gap_open != 0 || options->gap_extend != 0)
           options->mb_use_dyn_prog = (Boolean) myargs[ARG_DYNAMIC].intvalue;

        print_options = 0;
        align_options = 0;
        align_options += TXALIGN_COMPRESS;
        align_options += TXALIGN_END_NUM;
        if (show_gi) {
       align_options += TXALIGN_SHOW_GI;
       print_options += TXALIGN_SHOW_GI;
        }
            
        if (align_view) {
       align_options += TXALIGN_MASTER;
       if (align_view == 1 || align_view == 3)
          align_options += TXALIGN_MISMATCH;
       if (align_view == 3 || align_view == 4 || align_view == 6)
          align_options += TXALIGN_FLAT_INS;
       if (align_view == 5 || align_view == 6)
          align_options += TXALIGN_BLUNT_END;
        } else {
       align_options += TXALIGN_MATRIX_VAL;
       align_options += TXALIGN_SHOW_QS;
    }

    if (html) {
       align_options += TXALIGN_HTML;
       print_options += TXALIGN_HTML;
    }

    if (myargs[ARG_GILIST].strvalue)
       options->gifile = StringSave(myargs[ARG_GILIST].strvalue);
   
    if (out_type == MBLAST_ENDPOINTS)
      options->no_traceback = 1;
   else if (out_type == MBLAST_DELAYED_TRACEBACK)
       options->no_traceback = 2;
    else
       options->no_traceback = 0;

    options->megablast_full_deflines = (Boolean) myargs[ARG_FULLID].intvalue;
    options->perc_identity = (FloatLo) myargs[ARG_PERC_IDENT].floatvalue;
    options->hsp_num_max = myargs[ARG_MAXHSP].intvalue;

    if (!believe_query)
           options->megablast_full_deflines = TRUE;
        /*if (options->megablast_full_deflines)
          believe_query = FALSE;*/

    query_bsp_array = (BioseqPtr PNTR) MemNew((MAX_NUM_QUERIES+1)*sizeof(BioseqPtr));
    sepp = (SeqEntryPtr PNTR) MemNew(MAX_NUM_QUERIES*sizeof(SeqEntryPtr));

    StrCpy(prefix, "");

    global_fp = outfp;
        options->output = outfp;

    if (traditional_formatting) {
       if (align_view < 7) {
              if (html) {
                 fprintf(outfp, "<HTML>\n<TITLE>MEGABLAST Search Results</TITLE>\n");
                 fprintf(outfp, "<BODY BGCOLOR=\"#FFFFFF\" LINK=\"#0000FF\" "
                         "VLINK=\"#660099\" ALINK=\"#660099\">\n");
                 fprintf(outfp, "<PRE>\n");
              }
              init_buff_ex(90);
              BlastPrintVersionInfo("mgblast", html, outfp);
              fprintf(outfp, "\n");
              MegaBlastPrintReference(html, 90, outfp);
              fprintf(outfp, "\n");
              
              if(!PrintDbInformation(blast_database, !db_is_na, 70, outfp, html))
                 return 1;
              
              free_buff();
    
#ifdef OS_UNIX
              fprintf(global_fp, "%s", "Searching");
#endif
           }
    }
    
        aip = NULL;
        if (myargs[ARG_ASNOUT].strvalue != NULL) {
           if ((aip = AsnIoOpen (myargs[ARG_ASNOUT].strvalue,"w")) == NULL) {
              ErrPostEx(SEV_FATAL, 1, 0, "blast: Unable to open output file %s\n", myargs[ARG_ASNOUT].strvalue);
              return 1;
           }
        }
        else if (align_view == 10 || align_view == 11)
        {
            const char* mode = (align_view == 10) ? "w" : "wb";
            if ((aip = AsnIoOpen (blast_outputfile, (char*) mode)) == NULL) {
                    ErrPostEx(SEV_FATAL, 1, 0, "blast: Unable to open output file %s\n", blast_outputfile);
                    return 1;
            }
        }


        if (align_view == 7) {
           xml_aip = AsnIoOpen(blast_outputfile, "wx");
        }

        if (myargs[ARG_QUERYLOC].strvalue) {       
            Int4 start, end;
            Megablast_GetLoc(myargs[ARG_QUERYLOC].strvalue, &start, &end);
            options->required_start = start - 1;
            options->required_end = end -1;
        }

    done = FALSE;
    while (!done) {
       num_bsps = 0;
       total_length = 0;
       done = TRUE;
       SeqMgrHoldIndexing(TRUE);
       mask_slp = last_mask = NULL;
   
       while ((sepp[num_bsps]=FastaToSeqEntryForDb(infp, query_is_na, NULL,
                               believe_query, prefix, &ctr, 
                               &mask_slp)) != NULL) {
              if (!lcase_masking) /* Lower case ignored */
                 mask_slp = SeqLocFree(mask_slp);
         if (mask_slp) {
           if (!last_mask)
              options->query_lcase_mask = last_mask = mask_slp;
           else {
              last_mask->next = mask_slp;
              last_mask = last_mask->next;
              }
           mask_slp = NULL;
           }
          query_bsp = NULL;
         SeqEntryExplore(sepp[num_bsps], &query_bsp, FindNuc);
         //debug:
         /*
         char query_buffer[255];
         SeqIdWrite(query_bsp->id, query_buffer, PRINTID_FASTA_LONG, BUFFER_LENGTH);
         fprintf(stderr, "===> query_buf=%s\n", query_buffer);
         */
         if (query_bsp == NULL) {
           ErrPostEx(SEV_FATAL, 1, 0, "Unable to obtain bioseq\n");
           return 2;
          }
          
          source = BioSourceNew();
          source->org = OrgRefNew();
          source->org->orgname = OrgNameNew();
          source->org->orgname->gcode = options->genetic_code;
          ValNodeAddPointer(&(query_bsp->descr), Seq_descr_source, source);
          
          query_bsp_array[num_bsps++] = query_bsp;
          
          total_length += query_bsp->length;
          if (total_length > myargs[ARG_MAXQUERY].intvalue || 
          num_bsps >= MAX_NUM_QUERIES) {
         done = FALSE;
         break;
          }
       }

           if (num_bsps == 0)
               break;

       SeqMgrHoldIndexing(FALSE);
       other_returns = NULL;
       error_returns = NULL;
       
       if (out_type==MBLAST_ENDPOINTS) 
          seqalign_array = BioseqMegaBlastEngine(query_bsp_array, blast_program,
                             blast_database, options,
                             &other_returns, &error_returns,
                             dummy_callback, NULL, NULL, 0, 
                             MegaBlastPrintEndpoints);
       else if (out_type==MBLAST_SEGMENTS) 
          seqalign_array = BioseqMegaBlastEngine(query_bsp_array, blast_program,
                             blast_database, options,
                             &other_returns, &error_returns,
                             dummy_callback, NULL, NULL, 0,
                             MegaBlastPrintSegments);
       else if (out_type==MBLAST_ALIGN_INFO) {
              /* -- Geo mod: do not print header
              PrintTabularOutputHeader(blast_database, 
                                       (num_bsps==1) ? query_bsp_array[0] : NULL,
                                       NULL, "megablast", 0, believe_query,
                                       global_fp);*/
          seqalign_array = BioseqMegaBlastEngine(query_bsp_array, blast_program,
                             blast_database, options,
                             &other_returns, &error_returns,
                             dummy_callback, NULL, NULL, 0,
                                MegaBlastPrintAlignInfo);
       } else if (out_type==MBLAST_ALIGNMENTS) {
          seqalign_array = BioseqMegaBlastEngine(query_bsp_array, blast_program,
                  blast_database, options, &other_returns, 
                                  &error_returns, align_view < 7 ? tick_callback : NULL,
                                  NULL, NULL, 0, NULL);
          }
       
#ifdef OS_UNIX
       fflush(global_fp);
#endif

       if (error_returns) {
             BlastErrorPrint(error_returns);
              for (vnp = error_returns; vnp; vnp = vnp->next) {
                 BlastDestroyErrorMessage((BlastErrorMsgPtr)vnp->data.ptrvalue);
              }
              ValNodeFree(error_returns);
           }
              
              
       if (traditional_formatting) {
          dbinfo = NULL;
          ka_params = NULL;
          ka_params_gap = NULL;
          params_buffer = NULL;
          mask_loc = NULL;
          matrix = NULL;
          for (vnp=other_returns; vnp; vnp = vnp->next) {
           switch (vnp->choice) {
           case TXDBINFO:
              dbinfo = vnp->data.ptrvalue;
              break;
           case TXKABLK_NOGAP:
              ka_params = vnp->data.ptrvalue;
              break;
           case TXKABLK_GAP:
              ka_params_gap = vnp->data.ptrvalue;
              break;
           case TXPARAMETERS:
              params_buffer = vnp->data.ptrvalue;
              break;
           case TXMATRIX:
              matrix = vnp->data.ptrvalue;
              break;
           case SEQLOC_MASKING_NOTSET:
           case SEQLOC_MASKING_PLUS1:
           case SEQLOC_MASKING_PLUS2:
           case SEQLOC_MASKING_PLUS3:
           case SEQLOC_MASKING_MINUS1:
           case SEQLOC_MASKING_MINUS2:
           case SEQLOC_MASKING_MINUS3:
              ValNodeAddPointer(&mask_loc, vnp->choice, vnp->data.ptrvalue);
              break;
           default:
              break;
           }
          }    
          
#ifdef OS_UNIX
        if(align_view < 7) {
                 fprintf(global_fp, "%s\n", " done");
              }
#endif
          
        if (myargs[ARG_MASKEDQUERY].strvalue) {
                 if ((mqfp = FileOpen(myargs[ARG_MASKEDQUERY].strvalue, "w")) == NULL)
                    ErrPostEx(SEV_WARNING, 1, 0, "Unable to open file %s for masked query\n",
                              myargs[ARG_MASKEDQUERY].strvalue);
              }

        hits_found = FALSE;

        mask_loc_start = next_mask_loc = mask_loc;
        mask_loc = NULL;

        if (align_view == 7) {
           mbxp = PSIXmlInit(xml_aip, "megablast", blast_database, 
                             options, query_bsp_array[0], 0);
           }

        if (seqalign_array) { //results returned back for processing
             ReadDBBioseqFetchEnable ("megablast", blast_database, db_is_na, TRUE);
             for (index=0; index<num_bsps; index++) {
                    seqalign = seqalign_array[index];
                    if (next_mask_loc && 
                        SeqIdComp(SeqLocId((SeqLocPtr)next_mask_loc->data.ptrvalue), 
                                  query_bsp_array[index]->id) == SIC_YES) {
                       mask_loc = (SeqLocPtr) 
                       MemDup(next_mask_loc, sizeof(SeqLoc));
                       next_mask_loc = next_mask_loc->next;
                       mask_loc->next = NULL;
                    }
                    if (mqfp) {
                       /* convert mask locations from all sources into
                          a single seqloc */
                       mask_slp = NULL;
                       if (mask_loc) 
                          mask_slp = blastMergeFilterLocs(mask_slp, 
                              (SeqLocPtr)mask_loc->data.ptrvalue,
                              FALSE, 0, 0);
                       PrintMaskedSequence(query_bsp_array[index], mask_slp,
                                           mqfp, 50, lcase_masking);
                       SeqLocSetFree(mask_slp);
                       }
                    if (seqalign==NULL) {
                       mask_loc = MemFree(mask_loc);
                       continue;
                    }
                    hits_found = TRUE;
                    if (align_view < 7) {
                       init_buff_ex(70);
                       AcknowledgeBlastQuery(query_bsp_array[index], 70, outfp, 
                                             believe_query, html);
                       free_buff();
                       }
                    if (align_view == 8 || align_view == 9) {
                       if (align_view == 9)
                          PrintTabularOutputHeader(blast_database, 
                             query_bsp_array[index], NULL, blast_program, 0,
                             believe_query, global_fp);
                       /* debug:
                       char qbuf[512];
                       strcpy(qbuf, BioseqGetTitle(query_bsp_array[index]));
                       fprintf(stderr, "---> Here: query title=%s\n", qbuf);
                       */
                       BlastPrintTabulatedResults(seqalign, 
                           query_bsp_array[index], NULL, number_of_alignments,
                            blast_program, !options->gapped_calculation, 
                            believe_query, 0, 0, 
                            global_fp, (align_view == 9));
                            

                       ObjMgrFreeCache(0);

                       SeqAlignSetFree(seqalign);
                       mask_loc = MemFree(mask_loc);
                       continue;
                    } 
                       //Geo mod:   
                   else if (align_view>=12)  {
                        MGBlastPrintTab(seqalign, 
                            query_bsp_array[index], number_of_alignments,
                            !options->gapped_calculation, 
                            global_fp);
                        ObjMgrFreeCache(0);

                        SeqAlignSetFree(seqalign);
                        mask_loc = MemFree(mask_loc);
                        continue;
                        }
                    else if(align_view == 7) {
                       IterationPtr iterp;

                       iterp = BXMLBuildOneQueryIteration(seqalign, 
                                  NULL, FALSE, 
                                  !options->gapped_calculation, index, 
                                  NULL, query_bsp_array[index], mask_loc);
                       IterationAsnWrite(iterp, mbxp->aip, mbxp->atp);
                       AsnIoFlush(mbxp->aip);
                       IterationFree(iterp);
                       SeqAlignSetFree(seqalign);
                       mask_loc = MemFree(mask_loc);
                       continue;
                    }
                    seqannot = SeqAnnotNew();
                    seqannot->type = 2;
                    AddAlignInfoToSeqAnnot(seqannot, align_type);
                    seqannot->data = seqalign;
                    if (aip) {
                       SeqAnnotAsnWrite((SeqAnnotPtr) seqannot, aip, NULL);
                       AsnIoReset(aip);
                    }
                    if (outfp) { /* Uncacheing causes problems with ordinal nos. vs. gi's. */
                       prune = BlastPruneHitsFromSeqAlign(seqalign, number_of_descriptions, NULL);
                       ObjMgrSetHold();
                       init_buff_ex(85);
                       PrintDefLinesFromSeqAlign(prune->sap, 80,
                                                 outfp, print_options, FIRST_PASS, NULL);
                       free_buff();
                       
                       prune = BlastPruneHitsFromSeqAlign(seqalign, number_of_alignments, prune);
                       seqannot->data = prune->sap;
                       if (align_view != 0)
                          ShowTextAlignFromAnnot(seqannot, 60, outfp, NULL,
                                                 NULL, align_options, NULL, 
                                                 mask_loc, NULL);
                       else
                          ShowTextAlignFromAnnot(seqannot, 60, outfp, NULL, NULL, align_options, NULL, mask_loc, FormatScoreFunc);
                       seqannot->data = seqalign;
                       prune = BlastPruneSapStructDestruct(prune);
                       ObjMgrClearHold();
                       ObjMgrFreeCache(0);
                    }
                    seqannot = SeqAnnotFree(seqannot);
                    mask_loc = MemFree(mask_loc);
                 } /* End loop on seqaligns for different queries */
                 ReadDBBioseqFetchDisable();
              } 

              if (mbxp != NULL) {
                 MBXmlClose(mbxp, other_returns, !options->gapped_calculation);
              }

              if (mqfp)
                 FileClose(mqfp);

              if (!hits_found && align_view < 7)
                 fprintf(outfp, "\n\n ***** No hits found ******\n\n");

              matrix = BLAST_MatrixDestruct(matrix);
          
              if(html) 
                 fprintf(outfp, "<PRE>\n");
              init_buff_ex(85);
              dbinfo_head = dbinfo;
              if(align_view < 7) {
                 while (dbinfo) {
                    PrintDbReport(dbinfo, 70, outfp);
                    dbinfo = dbinfo->next;
                 }
              }
              dbinfo_head = TxDfDbInfoDestruct(dbinfo_head);
              
              if (ka_params) {
                 if(align_view < 7)
                    PrintKAParameters(ka_params->Lambda, ka_params->K, ka_params->H, 70, outfp, FALSE);
                 MemFree(ka_params);
              }
              if (ka_params_gap) {
                 if(align_view < 7)
                    PrintKAParameters(ka_params_gap->Lambda, ka_params_gap->K, ka_params_gap->H, 70, outfp, TRUE);
                 MemFree(ka_params_gap);
              }
              if(align_view < 7)
                 PrintTildeSepLines(params_buffer, 70, outfp);
              MemFree(params_buffer);
              free_buff();
              mask_loc = mask_loc_start;
              while (mask_loc) {
                 SeqLocSetFree(mask_loc->data.ptrvalue);
                 mask_loc = mask_loc->next;
              }
              ValNodeFree(mask_loc_start);
       } else { //not traditional formatting
          /* Just destruct all other_returns parts */
          for (vnp=other_returns; vnp; vnp = vnp->next) {
         switch (vnp->choice) {
         case TXDBINFO:
            TxDfDbInfoDestruct(vnp->data.ptrvalue);
            break;
         case TXKABLK_NOGAP:
         case TXKABLK_GAP:
         case TXPARAMETERS:
            MemFree(vnp->data.ptrvalue);
            break;
         case TXMATRIX:
            BLAST_MatrixDestruct(vnp->data.ptrvalue);
            break;
         case SEQLOC_MASKING_NOTSET:
         case SEQLOC_MASKING_PLUS1:
         case SEQLOC_MASKING_PLUS2:
         case SEQLOC_MASKING_PLUS3:
         case SEQLOC_MASKING_MINUS1:
         case SEQLOC_MASKING_MINUS2:
         case SEQLOC_MASKING_MINUS3:
                    mask_loc = vnp->data.ptrvalue;
                    SeqLocSetFree(mask_loc);
         default:
            break;
         }
          }
       }
       other_returns = ValNodeFree(other_returns);
       MemFree(seqalign_array);
           options->query_lcase_mask = 
              SeqLocSetFree(options->query_lcase_mask);

       /* Freeing SeqEntries can be very expensive, do this only if 
          this is not the last iteration of search */
       if (!done) { 
          for (index=0; index<num_bsps; index++) {
         sepp[index] = SeqEntryFree(sepp[index]);
         query_bsp_array[index] = NULL;
          }       
           }
           total_processed += num_bsps;
    } /* End of loop on complete searches */
        
        aip = AsnIoClose(aip);

        /*if (align_view == 7)
          xml_aip = AsnIoClose(xml_aip);*/

        if (align_view < 7 && html) 
           fprintf(outfp, "</PRE>\n</BODY>\n</HTML>\n");
        if (align_view < 7 && myargs[ARG_LOGINFO].intvalue)
           fprintf(outfp, "Mega BLAST run finished, processed %d queries\n",
                   total_processed);
    MemFree(query_bsp_array);
    MemFree(sepp);
    MemFree(qgaps_buf);
    MemFree(dbgaps_buf);
    options = BLASTOptionDelete(options);
    FileClose(infp);
        FileClose(outfp);
    
    return 0;
}