blast_setup_cxx.cpp

ncbi源码

    if (CFile(full_path).Exists()) {
        retval = full_path;
        retval.erase(retval.size() - mtx.size());
        return retval;
    }

    // Try using local "data" directory
    full_path = "data";
    full_path += CFile::AddTrailingPathSeparator(full_path);
    full_path += mtx;
    if (CFile(full_path).Exists()) {
        retval = full_path;
        retval.erase(retval.size() - mtx.size());
        return retval;
    }

    CNcbiApplication* app = CNcbiApplication::Instance();
    if (!app)
        return retval;

    const string& blastmat_env = app->GetEnvironment().Get("BLASTMAT");
    if (CFile(blastmat_env).Exists()) {
        full_path = blastmat_env;
        full_path += CFile::AddTrailingPathSeparator(full_path);
        full_path += is_prot ? "aa" : "nt";
        full_path += CFile::AddTrailingPathSeparator(full_path);
        full_path += mtx;
        if (CFile(full_path).Exists()) {
            retval = full_path;
            retval.erase(retval.size() - mtx.size());
            return retval;
        }
    }

#ifdef OS_UNIX
    full_path = BLASTMAT_DIR;
    full_path += CFile::AddTrailingPathSeparator(full_path);
    full_path += is_prot ? "aa" : "nt";
    full_path += CFile::AddTrailingPathSeparator(full_path);
    full_path += mtx;
    if (CFile(full_path).Exists()) {
        retval = full_path;
        retval.erase(retval.size() - mtx.size());
        return retval;
    }
#endif

    // Try again without the "aa" or "nt"
    if (CFile(blastmat_env).Exists()) {
        full_path = blastmat_env;
        full_path += CFile::AddTrailingPathSeparator(full_path);
        full_path += mtx;
        if (CFile(full_path).Exists()) {
            retval = full_path;
            retval.erase(retval.size() - mtx.size());
            return retval;
        }
    }

#ifdef OS_UNIX
    full_path = BLASTMAT_DIR;
    full_path += CFile::AddTrailingPathSeparator(full_path);
    full_path += mtx;
    if (CFile(full_path).Exists()) {
        retval = full_path;
        retval.erase(retval.size() - mtx.size());
        return retval;
    }
#endif

    return retval;
}

/// Checks if a BLAST database exists at a given file path: looks for 
/// an alias file first, then for an index file
static bool BlastDbFileExists(string& path, bool is_prot)
{
    // Check for alias file first
    string full_path = path + (is_prot ? ".pal" : ".nal");
    if (CFile(full_path).Exists())
        return true;
    // Check for an index file
    full_path = path + (is_prot ? ".pin" : ".nin");
    if (CFile(full_path).Exists())
        return true;
    return false;
}

string
FindBlastDbPath(const char* dbname, bool is_prot)
{
    string retval;
    string full_path;       // full path to matrix file

    if (!dbname)
        return retval;

    string database(dbname);

    // Look for matrix file in local directory
    full_path = database;
    if (BlastDbFileExists(full_path, is_prot)) {
        return retval;
    }

    CNcbiApplication* app = CNcbiApplication::Instance();
    if (app) {
        const string& blastdb_env = app->GetEnvironment().Get("BLASTDB");
        if (CFile(blastdb_env).Exists()) {
            full_path = blastdb_env;
            full_path += CFile::AddTrailingPathSeparator(full_path);
            full_path += database;
            if (BlastDbFileExists(full_path, is_prot)) {
                retval = full_path;
                retval.erase(retval.size() - database.size());
                return retval;
            }
        }
    }

    // Obtain the matrix path from the ncbi configuration file
    CMetaRegistry::SEntry sentry;
    sentry = CMetaRegistry::Load("ncbi", CMetaRegistry::eName_RcOrIni);
    string path = 
        sentry.registry ? sentry.registry->Get("BLAST", "BLASTDB") : "";

    full_path = CFile::MakePath(path, database);
    if (BlastDbFileExists(full_path, is_prot)) {
        retval = full_path;
        retval.erase(retval.size() - database.size());
        return retval;
    }

    return retval;
}

unsigned int
GetNumberOfFrames(EProgram p)
{
    unsigned int retval = 0;

    switch (p) {
    case eBlastn:
        retval = 2;
        break;
    case eBlastp:
    case eRPSBlast:
    case eTblastn: 
    case eRPSTblastn: 
        retval = 1;
        break;
    case eBlastx:
    case eTblastx:
        retval = 6;
        break;
    default:
        NCBI_THROW(CBlastException, eBadParameter, 
                   "Cannot get number of frames for invalid program type");
    }

    return retval;
}
END_SCOPE(blast)
END_NCBI_SCOPE

/* @} */

/*
* ===========================================================================
*
* $Log: blast_setup_cxx.cpp,v $
* Revision 1000.7  2004/06/01 18:05:58  gouriano
* PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.68
*
* Revision 1.68  2004/05/21 21:41:02  gorelenk
* Added PCH ncbi_pch.hpp
*
* Revision 1.67  2004/04/19 19:52:02  papadopo
* correct off-by-one error in sequence size computation
*
* Revision 1.66  2004/04/16 14:28:49  papadopo
* add use of eRPSBlast and eRPSTblastn programs
*
* Revision 1.65  2004/04/07 03:06:15  camacho
* Added blast_encoding.[hc], refactoring blast_stat.[hc]
*
* Revision 1.64  2004/04/06 20:45:28  dondosha
* Added function FindBlastDbPath: should be moved to seqdb library
*
* Revision 1.63  2004/03/24 19:14:48  dondosha
* Fixed memory leaks
*
* Revision 1.62  2004/03/19 19:22:55  camacho
* Move to doxygen group AlgoBlast, add missing CVS logs at EOF
*
* Revision 1.61  2004/03/15 19:57:52  dondosha
* SetupSubjects takes just program argument instead of CBlastOptions*
*
* Revision 1.60  2004/03/11 17:26:46  dicuccio
* Use NStr::ToUpper() instead of transform
*
* Revision 1.59  2004/03/09 18:53:25  dondosha
* Do not set db length and number of sequences options to real values - these are calculated and assigned to parameters structure fields
*
* Revision 1.58  2004/03/06 00:39:47  camacho
* Some refactorings, changed boolen parameter to enum in GetSequence
*
* Revision 1.57  2004/02/24 18:14:56  dondosha
* Set the maximal length in the set of queries, when filling BlastQueryInfo structure
*
* Revision 1.56  2004/02/18 15:16:28  camacho
* Consolidated ncbi2na mask definition
*
* Revision 1.55  2004/01/07 17:39:27  vasilche
* Fixed include path to genbank loader.
*
* Revision 1.54  2003/12/29 17:00:57  camacho
* Update comment
*
* Revision 1.53  2003/12/15 19:55:14  camacho
* Minor fix to ensure exception safety
*
* Revision 1.52  2003/12/03 16:43:47  dondosha
* Renamed BlastMask to BlastMaskLoc, BlastResults to BlastHSPResults
*
* Revision 1.51  2003/11/26 18:36:45  camacho
* Renaming blast_option*pp -> blast_options*pp
*
* Revision 1.50  2003/11/26 18:24:00  camacho
* +Blast Option Handle classes
*
* Revision 1.49  2003/11/24 17:12:44  dondosha
* Query info structure does not have a total_length member any more; use last context offset
*
* Revision 1.48  2003/11/06 21:25:37  camacho
* Revert previous change, add assertions
*
* Revision 1.47  2003/11/04 17:14:22  dondosha
* Length in subject sequence block C structure should not include sentinels
*
* Revision 1.46  2003/10/31 19:45:03  camacho
* Fix setting of subject sequence length
*
* Revision 1.45  2003/10/31 16:53:32  dondosha
* Set length in query sequence block correctly
*
* Revision 1.44  2003/10/29 04:46:16  camacho
* Use fixed AutoPtr for GetSequence return value
*
* Revision 1.43  2003/10/27 21:27:36  camacho
* Remove extra argument to GetSequenceView, minor refactorings
*
* Revision 1.42  2003/10/22 14:21:55  camacho
* Added sanity checking assertions
*
* Revision 1.41  2003/10/21 13:04:54  camacho
* Fix bug in SetupSubjects, use sequence blk set functions
*
* Revision 1.40  2003/10/16 13:38:54  coulouri
* use anonymous exceptions to fix unreferenced variable compiler warning
*
* Revision 1.39  2003/10/15 18:18:00  camacho
* Fix to setup query info structure for proteins
*
* Revision 1.38  2003/10/15 15:09:32  camacho
* Changes from Mike DiCuccio to use GetSequenceView to retrieve sequences.
*
* Revision 1.37  2003/10/08 15:13:56  dondosha
* Test if subject mask is not NULL before converting to a C structure
*
* Revision 1.36  2003/10/08 15:05:47  dondosha
* Test if mask is not NULL before converting to a C structure
*
* Revision 1.35  2003/10/07 17:34:05  dondosha
* Add lower case masks to SSeqLocs forming the vector of sequence locations
*
* Revision 1.34  2003/10/03 16:12:18  dondosha
* Fix in previous change for plus strand search
*
* Revision 1.33  2003/10/02 22:10:46  dondosha
* Corrections for one-strand translated searches
*
* Revision 1.32  2003/09/30 03:23:18  camacho
* Fixes to FindMatrixPath
*
* Revision 1.31  2003/09/29 21:38:29  camacho
* Assign retval only when successfully found path to matrix
*
* Revision 1.30  2003/09/29 20:35:03  camacho
* Replace abort() with exception in GetNumberOfFrames
*
* Revision 1.29  2003/09/16 16:48:13  dondosha
* Use BLAST_PackDNA and BlastSetUp_SeqBlkNew from the core blast library for setting up subject sequences
*
* Revision 1.28  2003/09/12 17:52:42  camacho
* Stop using pair<> as return value from GetSequence
*
* Revision 1.27  2003/09/11 20:55:01  camacho
* Temporary fix for AutoPtr return value
*
* Revision 1.26  2003/09/11 17:45:03  camacho
* Changed CBlastOption -> CBlastOptions
*
* Revision 1.25  2003/09/10 04:27:43  camacho
* 1) Minor change to return type of GetSequence
* 2) Fix to previous revision
*
* Revision 1.24  2003/09/09 22:15:02  dondosha
* Added cast in return statement in GetSequence method, fixing compiler error
*
* Revision 1.23  2003/09/09 15:57:23  camacho
* Fix indentation
*
* Revision 1.22  2003/09/09 14:21:39  coulouri
* change blastkar.h to blast_stat.h
*
* Revision 1.21  2003/09/09 12:57:15  camacho
* + internal setup functions, use smart pointers to handle memory mgmt
*
* Revision 1.20  2003/09/05 19:06:31  camacho
* Use regular new to allocate genetic code string
*
* Revision 1.19  2003/09/03 19:36:27  camacho
* Fix include path for blast_setup.hpp
*
* Revision 1.18  2003/08/28 22:42:54  camacho
* Change BLASTGetSequence signature
*
* Revision 1.17  2003/08/28 15:49:02  madden
* Fix for packing DNA as well as correct buflen
*
* Revision 1.16  2003/08/25 16:24:14  camacho
* Updated BLASTGetMatrixPath
*
* Revision 1.15  2003/08/19 17:39:07  camacho
* Minor fix to use of metaregistry class
*
* Revision 1.14  2003/08/18 20:58:57  camacho
* Added blast namespace, removed *__.hpp includes
*
* Revision 1.13  2003/08/14 13:51:24  camacho
* Use CMetaRegistry class to load the ncbi config file
*
* Revision 1.12  2003/08/11 15:17:39  dondosha
* Added algo/blast/core to all #included headers
*
* Revision 1.11  2003/08/11 14:00:41  dicuccio
* Indenting changes.  Fixed use of C++ namespaces (USING_SCOPE(objects) inside of
* BEGIN_NCBI_SCOPE block)
*
* Revision 1.10  2003/08/08 19:43:07  dicuccio
* Compilation fixes: #include file rearrangement; fixed use of 'list' and
* 'vector' as variable names; fixed missing ostrea<< for __int64
*
* Revision 1.9  2003/08/04 15:18:23  camacho
* Minor fixes
*
* Revision 1.8  2003/08/01 22:35:02  camacho
* Added function to get matrix path (fixme)
*
* Revision 1.7  2003/08/01 17:40:56  dondosha
* Use renamed functions and structures from local blastkar.h
*
* Revision 1.6  2003/07/31 19:45:33  camacho
* Eliminate Ptr notation
*
* Revision 1.5  2003/07/30 15:00:01  camacho
* Do not use Malloc/MemNew/MemFree
*
* Revision 1.4  2003/07/25 13:55:58  camacho
* Removed unnecessary #includes
*
* Revision 1.3  2003/07/24 18:22:50  camacho
* #include blastkar.h
*
* Revision 1.2  2003/07/23 21:29:06  camacho
* Update BLASTFindGeneticCode to get genetic code string with C++ toolkit
*
* Revision 1.1  2003/07/10 18:34:19  camacho
* Initial revision
*
*
* ===========================================================================
*/