/* $Id: wwwblast.c,v 6.29 2000/11/29 16:11:31 dondosha Exp $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
* National Center for Biotechnology Information
*
* This software/database is a "United States Government Work" under the
* terms of the United States Copyright Act. It was written as part of
* the author's official duties as a United States Government employee and
* thus cannot be copyrighted. This software/database is freely available
* to the public for use. The National Library of Medicine and the U.S.
* Government have not placed any restriction on its use or reproduction.
*
* Although all reasonable efforts have been taken to ensure the accuracy
* and reliability of the software and data, the NLM and the U.S.
* Government do not and cannot warrant the performance or results that
* may be obtained by using this software or data. The NLM and the U.S.
* Government disclaim all warranties, express or implied, including
* warranties of performance, merchantability or fitness for any particular
* purpose.
*
* Please cite the author in any work or product based on this material.
*
* ===========================================================================
*
* File Name: $RCSfile: wwwblast.c,v $
*
* Author: Sergei Shavirin
*
* Initial Creation Date: 03/15/2000
*
* $Revision: 6.29 $
*
* File Description:
* Standalone WWW Blast CGI program.
*
* $Log: wwwblast.c,v $
* Revision 6.29 2000/11/29 16:11:31 dondosha
* If multiple queries, send proper lower case mask to the search engine
*
* Revision 6.28 2000/11/17 14:40:04 dondosha
* Changed MegaBlastResultsNew call to MemNew
*
* Revision 6.27 2000/11/16 22:37:07 dondosha
* Added endpoint Mega BLAST results handling
*
* Revision 6.26 2000/10/31 20:18:52 shavirin
* Added printing of correct XML output when no hits found
* Added printing progeress messages to avoid browser timeout.
*
* Revision 6.25 2000/10/23 20:19:57 dondosha
* Open and close AsnIo outside calls to BXMLPrintOutput function
*
* Revision 6.24 2000/10/18 20:19:31 shavirin
* Added title for OOF Blastx.
*
* Revision 6.23 2000/10/16 22:18:17 shavirin
* Added possibility to perform OOF blastx
*
* Revision 6.22 2000/10/16 20:27:03 shavirin
* Added possibility to run RPS Blast.
*
* Revision 6.21 2000/09/28 16:48:20 dondosha
* Changed MegaBlast related code to get a single SeqAlignPtr from server
*
* Revision 6.20 2000/09/28 15:16:55 shavirin
* Added message if request was limited to results of Entrez query.
*
* Revision 6.19 2000/09/27 22:17:04 shavirin
* Added possibility to limit search to results of entrez query.
*
* Revision 6.18 2000/09/13 22:28:10 dondosha
* Removed extra that is now printed in PrintDefLinesFromSeqAlign
*
* Revision 6.17 2000/09/13 20:47:51 dondosha
* Small cleanup with closures of html blocks
*
* Revision 6.16 2000/09/12 21:57:28 dondosha
* Pass the correct scoring matrix to ShowTextAlignFromAnnot
*
* Revision 6.15 2000/09/11 17:51:07 shavirin
* Removed redundant tag.
*
* Revision 6.14 2000/09/08 20:18:12 dondosha
* Print the title, background and GIF image before creating options
*
* Revision 6.13 2000/09/08 14:49:28 dondosha
* Allow graphical overview with multiple queries
*
* Revision 6.12 2000/09/07 18:01:38 dondosha
* Pass a callback to the server from TraditionalBlastReportEngineWithImage; allow multiple queries for all BLAST searches
*
* Revision 6.11 2000/09/05 18:00:25 dondosha
* Added query acknowledgement for each query in WWWBlastDoSearch for megablast
*
* Revision 6.10 2000/09/01 17:55:14 dondosha
* Call SeqEntryLoad at the beginning; corrections for megablast page
*
* Revision 6.9 2000/08/30 22:22:35 dondosha
* Enhance function WWWBlastDoSearch to handle megablast search
*
* Revision 6.8 2000/08/28 20:20:59 dondosha
* Added functionality for megablast web page
*
* Revision 6.7 2000/08/09 20:30:30 shavirin
* Added possibility to print XML output.
*
* Revision 6.6 2000/07/31 20:44:12 shavirin
* Minor change (initialized variable) from Haruna Cofer (haruna@detroit.sgi.com)
*
* Revision 6.5 2000/05/17 15:50:51 shavirin
* Moved many functions to the wwwbutl.c file.
*
* Revision 6.4 2000/04/21 18:10:59 shavirin
* Added possibility to print Patrick's alignment.
*
* Revision 6.3 2000/03/28 14:44:20 shavirin
* Changed function ctime_r to ctime() for compatibility.
*
* Revision 6.2 2000/03/24 16:05:37 shavirin
* Added option to be used as NCBI client/server.
*
* Revision 6.1 2000/03/20 19:01:00 shavirin
* Initial revision.
*
*
* ==========================================================================
*/
#include
static int LIBCALLBACK WWWTickCallback(Int4 sequence_number,
Int4 number_of_positive_hits)
{
if(!TestSTDOut()) {
return -1;
}
/* fprintf(stdout, "."); */
printf("\n",
sequence_number, number_of_positive_hits);
fflush(stdout);
return 1;
}
static Int4 get_number_alignment(SeqAlignPtr align)
{
Int4 num = 0;
while(align)
{
++num;
align = align->next;
}
return num;
}
static void
PrintMotd(CharPtr string, FILE *fp, Boolean html_format)
{
Char buffer[100];
CharPtr ptr;
if (string == NULL)
return;
buffer[0] = NULLB;
ptr = buffer;
if (html_format) {
fprintf(fp, "\n");
}
while (*string != NULLB) {
if (*string == '~') {
*ptr = NULLB;
fprintf(fp, "%s\n", buffer);
buffer[0] = NULLB;
ptr = buffer;
string++;
if (*string == NULLB)
break;
} else {
*ptr=*string;
ptr++; string++;
}
}
*ptr = NULLB;
fprintf(fp, "%s\n", buffer);
if (html_format) {
fprintf(fp, "\n");
}
fflush(fp);
return;
}
#ifdef NCBI_CLIENT_SERVER
static Boolean LIBCALLBACK
callback (BlastResponsePtr brp, Boolean PNTR cancel)
{
fprintf(stdout, "
\n");
return TRUE;
}
static Boolean
TraditionalBlastReportEngineWithImage(SeqLocPtr slp, BioseqPtr bsp, BlastNet3Hptr bl3hp, WWWBlastInfoPtr theInfo)
{
BlastDbinfoPtr dbinfo;
BlastKABlkPtr ka_params=NULL, ka_params_gap=NULL;
BlastPruneSapStructPtr prune;
BLAST_MatrixPtr matrix;
Int4Ptr PNTR txmatrix;
Boolean query_is_na, db_is_na;
Boolean status;
CharPtr params_buffer=NULL;
Int4 number_of_hits_private=0, length;
SeqAlignPtr seqalign = NULL, sap, next_seqalign;
SeqAnnotPtr seqannot=NULL;
TxDfDbInfoPtr tx_dbinfo=NULL, tx_dbinfo_head;
ValNodePtr mask_loc, mask_loc_start, other_returns, error_returns, vnp, vnp1=NULL;
Uint1 align_type;
Uint1 f_order[FEATDEF_ANY], g_order[FEATDEF_ANY];
/* Variables for multiple query output */
SeqLocPtr tmp_slp;
Boolean done = TRUE;
BLAST_OptionsBlkPtr options = theInfo->options;
CharPtr program = theInfo->program, database = theInfo->database;
Uint4 align_options = theInfo->align_options;
DenseSegPtr dsp, next_dsp;
AsnIoPtr xml_aip;
MegaBlastResultsPtr mb_results = NULL;
MemSet((Pointer)(g_order), 0, (size_t)(FEATDEF_ANY* sizeof(Uint1)));
MemSet((Pointer)(f_order), 0, (size_t)(FEATDEF_ANY* sizeof(Uint1)));
if (bsp == NULL && slp == NULL)
return FALSE;
if (bl3hp == NULL || program == NULL || database == NULL)
return FALSE;
align_type = BlastGetTypes(program, &query_is_na, &db_is_na);
init_buff_ex(85);
dbinfo = BlastRequestDbInfo(bl3hp, database, !db_is_na);
if (dbinfo && !(options->is_megablast_search && options->no_traceback))
PrintDbInformationBasic(database, !db_is_na, 70, dbinfo->definition, dbinfo->number_seqs, dbinfo->total_length, stdout, TRUE);
dbinfo = BlastDbinfoFree(dbinfo);
free_buff();
if (bsp)
seqalign = BlastBioseqNetCore(bl3hp, bsp, program, database, options, &other_returns, &error_returns, callback, NULL, &status);
else if (options->is_megablast_search) {
seqalign = MegaBlastSeqLocNetCore(bl3hp, slp, program, database, options, &other_returns, &error_returns, callback, &status);
} else
seqalign = BlastSeqLocNetCore(bl3hp, slp, program, database, options, &other_returns, &error_returns, callback, NULL, &status);
BlastErrorPrintExtra(error_returns, TRUE, stdout);
mask_loc = NULL;
matrix = NULL;
txmatrix = NULL;
for (vnp=other_returns; vnp; vnp = vnp->next) {
switch (vnp->choice) {
case BlastResponse_mbalign:
mb_results = (MegaBlastResultsPtr) vnp->data.ptrvalue;
break;
case TXDBINFO:
tx_dbinfo = (TxDfDbInfoPtr) vnp->data.ptrvalue;
break;
case TXKABLK_NOGAP:
ka_params = (BlastKABlkPtr) vnp->data.ptrvalue;
break;
case TXKABLK_GAP:
ka_params_gap = (BlastKABlkPtr) vnp->data.ptrvalue;
break;
case TXPARAMETERS:
params_buffer = (CharPtr) vnp->data.ptrvalue;
break;
case TXMATRIX:
matrix = (BLAST_MatrixPtr) vnp->data.ptrvalue;
if (matrix)
txmatrix = BlastMatrixToTxMatrix(matrix);
/*BLAST_MatrixDestruct(matrix);*/
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:
if (!options->is_megablast_search)
ValNodeAddPointer(&mask_loc, vnp->choice, vnp->data.ptrvalue);
break;
default:
break;
}
}
/* If results come as alignment endpoints only from Mega BLAST */
if (mb_results) {
MegaBlastHitPtr mb_hit = mb_results->mbhits, next_hit;
while (mb_hit) {
fprintf(stdout, "%s\t%s\t%d\t%d\t%d\t%d\t%d\n", mb_hit->id1,
mb_hit->id2, mb_hit->query_offset, mb_hit->subject_offset,
mb_hit->query_end, mb_hit->subject_end, mb_hit->score);
mb_hit = mb_hit->next;
}
MegaBlastResultsFree(mb_results);
} else if (!seqalign)
done = FALSE;
ReadDBBioseqFetchEnable ("blastall", database, db_is_na, TRUE);
tmp_slp = slp;
if(theInfo->xml_output)
xml_aip = AsnIoOpen("stdout", "wx");
while (seqalign) {
if (!options->is_megablast_search)
next_seqalign = NULL;
else {
sap = seqalign;
while (sap != NULL) {
if (sap->next != NULL) {
dsp = (DenseSegPtr) (sap->segs);
next_dsp = (DenseSegPtr) (sap->next->segs);
if (SeqIdComp(dsp->ids, next_dsp->ids) != SIC_YES) {
next_seqalign = sap->next;
sap->next = NULL;
}
} else
next_seqalign = NULL;
sap = sap->next;
}
dsp = (DenseSegPtr) (seqalign->segs);
while (tmp_slp && SeqIdComp(dsp->ids, SeqLocId(tmp_slp)) != SIC_YES)
tmp_slp = tmp_slp->next;
if (tmp_slp == NULL) /* Should never happen */
break;
bsp = BioseqLockById(SeqLocId(tmp_slp));
init_buff_ex(85);
fprintf(stdout, "
");
AcknowledgeBlastQuery(bsp, 70, stdout, FALSE, TRUE);
free_buff();
BioseqUnlock(bsp);
}
if(theInfo->xml_output) {
printf("");
BXMLPrintOutput(xml_aip, seqalign, options,
program, database,
bsp, other_returns, 0, 0, NULL);
AsnIoReset(xml_aip);
printf("");
} else {
seqannot = SeqAnnotNew();
seqannot->type = 2;
AddAlignInfoToSeqAnnot(seqannot, align_type);
seqannot->data = seqalign;
if(theInfo->show_overview) {
Char f_name[64], title[1024], href[64];
Int4 align_num;
sprintf(f_name, "%ld%ld.gif", (long)random(), (long)getpid());
sprintf(href, "nph-viewgif.cgi?");
align_num = get_number_alignment(seqalign);
sprintf(title,
"\n", (long)align_num);
/* Open HTML form */
fprintf(stdout, "