genetic_code_table.cpp

ncbi源码

    
    int weight = 0;
    int index = 0;
    int mul = 16;
    for ( int i = 0; i < 3; ++i ) {
        switch ( toupper(codon[i]) ) {
        case 'A' :
            weight = 2;
            break;
        case 'C' :
            weight = 1;
            break;
        case 'G' :
            weight = 3;
            break;
        case 'T' :
        case 'U' :
            weight = 0;
            break;
        }

        index += mul * weight;
        mul /= 4;
    }

    return index;
}



// constructor
CGen_code_table_imp::CGen_code_table_imp(void)
{
    // initialize common CTrans_table tables
    CTrans_table::x_InitFsaTable ();

    // Compose a long-long string
    string str;
    for (size_t i = 0;  sm_GenCodeTblMemStr [i];  i++) {
        str += sm_GenCodeTblMemStr [i];
    }

    // create an in memory stream on sm_GenCodeTblMemStr
    CNcbiIstrstream is(str.c_str(), str.length());
    auto_ptr<CObjectIStream>
        asn_codes_in(CObjectIStream::Open(eSerial_AsnText, is));

    // read single copy of genetic-code table
    m_GcTable = new CGenetic_code_table;
    *asn_codes_in >> *m_GcTable;
}

// destructor
CGen_code_table_imp::~CGen_code_table_imp(void)
{
}

// constructor
CTrans_table::CTrans_table(const CGenetic_code& gc)
{
    const string * ncbieaa  = 0;
    const string * sncbieaa = 0;

    // find amino acid and orf start strings given genetic code instance
    ITERATE (CGenetic_code::Tdata, gcd, gc.Get ()) {
        switch ((*gcd)->Which ()) {
            case CGenetic_code::C_E::e_Ncbieaa :
                ncbieaa = & (*gcd)->GetNcbieaa ();
                break;
            case CGenetic_code::C_E::e_Sncbieaa :
                sncbieaa = & (*gcd)->GetSncbieaa ();
                break;
            default:
                break;
        }
    }

    // throw exception if unable to find ncbieaa and sncbieaa strings
    if (ncbieaa == 0 || sncbieaa == 0) {
        NCBI_THROW (CException, eUnknown,
                    "Could not find ncbieaa and sncbieaa");
    }

    // initialize translation table for this genetic code instance
    x_InitFsaTransl (ncbieaa, sncbieaa);
}

const CTrans_table& CGen_code_table_imp::GetTransTable (int id)
{
    _ASSERT(id >= 0);

    // look for already created translation table
    if ( size_t(id) < m_TransTablesById.size ()) {
        CRef< CTrans_table> tbl = m_TransTablesById [id];
        if (tbl != 0) {
        	// already in list, already initialized, so return
            return *tbl;
        }
    }

    // this mutex is automatically freed when the function exits
    DEFINE_STATIC_FAST_MUTEX(mtx);
    CFastMutexGuard   LOCK (mtx);

    // test again within mutex lock to see if another thread was just adding it
    if ( size_t(id) < m_TransTablesById.size ()) {
        CRef< CTrans_table> tbl = m_TransTablesById [id];
        if (tbl != 0) {
        	// already in list, already initialized, so return
            return *tbl;
        }
    }

    // now look for the genetic code and initialize the translation table
    ITERATE (CGenetic_code_table::Tdata, gcl, m_GcTable->Get ()) {
        ITERATE (CGenetic_code::Tdata, gcd, (*gcl)->Get ()) {
            if ((*gcd)->IsId ()  &&  (*gcd)->GetId () == id) {

        	    // found proper genetic code, so create new trans table
        	    CRef< CTrans_table> tbl(new CTrans_table (**gcl));

        	    // extend size of translation table list, if necessary
        	    if ( size_t(id) >= m_TransTablesById.size ()) {
        	        m_TransTablesById.resize (id + 1);
        	    }

        	    // add new table to list of translation tables
        	    m_TransTablesById [id] = tbl;

        	    return *tbl;
            }
        }
    }

    // throw exception if failure
    NCBI_THROW (CException, eUnknown,
                "Unable to find genetic code number " +
                NStr::IntToString (id));
}

const CTrans_table& CGen_code_table_imp::GetTransTable (const CGenetic_code& gc)
{
    const string * ncbieaa  = 0;
    const string * sncbieaa = 0;

    ITERATE (CGenetic_code::Tdata, gcd, gc.Get ()) {
        switch ((*gcd)->Which ()) {
            case CGenetic_code::C_E::e_Id :
            {
                // lookup table by ID
                int id = (*gcd)->GetId ();
                return GetTransTable (id);
            }
            case CGenetic_code::C_E::e_Ncbieaa :
                ncbieaa = & (*gcd)->GetNcbieaa ();
                break;
            case CGenetic_code::C_E::e_Sncbieaa :
                sncbieaa = & (*gcd)->GetSncbieaa ();
                break;
            default:
                break;
        }
    }

    if (ncbieaa != 0  &&  sncbieaa != 0) {
      // return * new CTrans_table (gc);

      NCBI_THROW (CException, eUnknown,
                  "GetTransTable without ID not yet supported");
    }

    NCBI_THROW (CException, eUnknown,
                "GetTransTable does not have sufficient information");
}

const CGenetic_code_table & CGen_code_table_imp::GetCodeTable (void)
{
    return *m_GcTable;
}


const string& CGen_code_table_imp::GetNcbieaa(int id) const
{
    ITERATE (CGenetic_code_table::Tdata, gcl, m_GcTable->Get ()) {
        if ( (*gcl)->GetId() == id ) {
            return (*gcl)->GetNcbieaa();
        }
    }
    return CNcbiEmptyString::Get();
}


const string& CGen_code_table_imp::GetNcbieaa(const CGenetic_code& gc) const
{
    return gc.GetNcbieaa();
}


const string& CGen_code_table_imp::GetSncbieaa(int id) const
{
    ITERATE (CGenetic_code_table::Tdata, gcl, m_GcTable->Get ()) {
        if ( (*gcl)->GetId() == id ) {
            return (*gcl)->GetSncbieaa();
        }
    }
    
    return CNcbiEmptyString::Get();
}


const string& CGen_code_table_imp::GetSncbieaa(const CGenetic_code& gc) const
{
    return gc.GetSncbieaa();
}


// standard genetic code
//
// ncbieaa  "FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG"
// sncbieaa "---M---------------M---------------M----------------------------"
//
// -- Base1  TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
// -- Base2  TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
// -- Base3  TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG

/*
                         Second Position
First      T             C             A             G      Third
-----------------------------------------------------------------
  T   TTT Phe [F]   TCT Ser [S]   TAT Tyr [Y]   TGT Cys [C]   T
      TTC Phe [F]   TCC Ser [S]   TAC Tyr [Y]   TGC Cys [C]   C
      TTA Leu [L]   TCA Ser [S]   TAA Ter [*]   TGA Ter [*]   A
      TTG Leu [L]   TCG Ser [S]   TAG Ter [*]   TGG Trp [W]   G
-----------------------------------------------------------------
  C   CTT Leu [L]   CCT Pro [P]   CAT His [H]   CGT Arg [R]   T
      CTC Leu [L]   CCC Pro [P]   CAC His [H]   CGC Arg [R]   C
      CTA Leu [L]   CCA Pro [P]   CAA Gln [Q]   CGA Arg [R]   A
      CTG Leu [L]   CCG Pro [P]   CAG Gln [Q]   CGG Arg [R]   G
-----------------------------------------------------------------
  A   ATT Ile [I]   ACT Thr [T]   AAT Asn [N]   AGT Ser [S]   T
      ATC Ile [I]   ACC Thr [T]   AAC Asn [N]   AGC Ser [S]   C
      ATA Ile [I]   ACA Thr [T]   AAA Lys [K]   AGA Arg [R]   A
      ATG Met [M]   ACG Thr [T]   AAG Lys [K]   AGG Arg [R]   G
-----------------------------------------------------------------
  G   GTT Val [V]   GCT Ala [A]   GAT Asp [D]   GGT Gly [G]   T
      GTC Val [V]   GCC Ala [A]   GAC Asp [D]   GGC Gly [G]   C
      GTA Val [V]   GCA Ala [A]   GAA Glu [E]   GGA Gly [G]   A
      GTG Val [V]   GCG Ala [A]   GAG Glu [E]   GGG Gly [G]   G
-----------------------------------------------------------------
*/

// local copy of gc.prt genetic code table ASN.1
const char * CGen_code_table_imp::sm_GenCodeTblMemStr [] =
{
    "Genetic-code-table ::= {\n",
    "{ name \"Standard\" , name \"SGC0\" , id 1 ,\n",
    "ncbieaa  \"FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG\",\n",
    "sncbieaa \"---M---------------M---------------M----------------------------\" } ,\n",
    "{ name \"Vertebrate Mitochondrial\" , name \"SGC1\" , id 2 ,\n",
    "ncbieaa  \"FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSS**VVVVAAAADDEEGGGG\",\n",
    "sncbieaa \"--------------------------------MMMM---------------M------------\" } ,\n",
    "{ name \"Yeast Mitochondrial\" , name \"SGC2\" , id 3 ,\n",
    "ncbieaa  \"FFLLSSSSYY**CCWWTTTTPPPPHHQQRRRRIIMMTTTTNNKKSSRRVVVVAAAADDEEGGGG\",\n",
    "sncbieaa \"----------------------------------MM----------------------------\" } ,\n",
    "{ name \"Mold Mitochondrial; Protozoan Mitochondrial; Coelenterate\n",
    "Mitochondrial; Mycoplasma; Spiroplasma\" ,\n",
    "name \"SGC3\" , id 4 ,\n",
    "ncbieaa  \"FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG\",\n",
    "sncbieaa \"--MM---------------M------------MMMM---------------M------------\" } ,\n",
    "{ name \"Invertebrate Mitochondrial\" , name \"SGC4\" , id 5 ,\n",
    "ncbieaa  \"FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSVVVVAAAADDEEGGGG\",\n",
    "sncbieaa \"---M----------------------------MMMM---------------M------------\" } ,\n",
    "{ name \"Ciliate Nuclear; Dasycladacean Nuclear; Hexamita Nuclear\" ,\n",
    "name \"SGC5\" , id 6 ,\n",
    "ncbieaa  \"FFLLSSSSYYQQCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG\",\n",
    "sncbieaa \"-----------------------------------M----------------------------\" } ,\n",
    "{ name \"Echinoderm Mitochondrial; Flatworm Mitochondrial\" , name \"SGC8\" , id 9 ,\n",
    "ncbieaa  \"FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG\",\n",
    "sncbieaa \"-----------------------------------M---------------M------------\" } ,\n",
    "{ name \"Euplotid Nuclear\" , name \"SGC9\" , id 10 ,\n",
    "ncbieaa  \"FFLLSSSSYY**CCCWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG\",\n",
    "sncbieaa \"-----------------------------------M----------------------------\" } ,\n",
    "{ name \"Bacterial and Plant Plastid\" , id 11 ,\n",
    "ncbieaa  \"FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG\",\n",
    "sncbieaa \"---M---------------M------------MMMM---------------M------------\" } ,\n",
    "{ name \"Alternative Yeast Nuclear\" , id 12 ,\n",
    "ncbieaa  \"FFLLSSSSYY**CC*WLLLSPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG\",\n",
    "sncbieaa \"-------------------M---------------M----------------------------\" } ,\n",
    "{ name \"Ascidian Mitochondrial\" , id 13 ,\n",
    "ncbieaa  \"FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSGGVVVVAAAADDEEGGGG\",\n",
    "sncbieaa \"-----------------------------------M----------------------------\" } ,\n",
    "{ name \"Alternative Flatworm Mitochondrial\" , id 14 ,\n",
    "ncbieaa  \"FFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG\",\n",
    "sncbieaa \"-----------------------------------M----------------------------\" } ,\n",
    "{ name \"Blepharisma Macronuclear\" , id 15 ,\n",
    "ncbieaa  \"FFLLSSSSYY*QCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG\",\n",
    "sncbieaa \"-----------------------------------M----------------------------\" } ,\n",
    "{ name \"Chlorophycean Mitochondrial\" , id 16 ,\n",
    "ncbieaa  \"FFLLSSSSYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG\",\n",
    "sncbieaa \"-----------------------------------M----------------------------\" } ,\n",
    "{ name \"Trematode Mitochondrial\" , id 21 ,\n",
    "ncbieaa  \"FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNNKSSSSVVVVAAAADDEEGGGG\",\n",
    "sncbieaa \"-----------------------------------M---------------M------------\" } ,\n",
    "{ name \"Scenedesmus obliquus mitochondrial\" , id 22 ,\n",
    "ncbieaa  \"FFLLSS*SYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG\",\n",
    "sncbieaa \"-----------------------------------M----------------------------\" } ,\n",
    "{ name \"Thraustochytrium mitochondrial code\" , id 23 ,\n",
    "ncbieaa  \"FF*LSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG\",\n",
    "sncbieaa \"--------------------------------M--M---------------M------------\" } };\n",
    0  // to indicate that there is no more data
};


END_objects_SCOPE // namespace ncbi::objects::

END_NCBI_SCOPE


/*
* ===========================================================================
*
* $Log: Genetic_code_table.cpp,v $
* Revision 1000.2  2004/06/01 19:33:54  gouriano
* PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R6.17
*
* Revision 6.17  2004/05/19 17:26:04  gorelenk
* Added include of PCH - ncbi_pch.hpp
*
* Revision 6.16  2004/03/24 13:58:59  friedman
* Fixed mutex comments
*
* Revision 6.15  2004/03/23 20:08:10  friedman
* Replaced 'static CFastMutex' with DEFINE_STATIC_FAST_MUTEX
*
* Revision 6.14  2003/08/19 19:23:00  kans
* s_ValidCodon test should use && instead of || (AU)
*
* Revision 6.13  2003/04/29 22:12:35  tolstoy
* Comments for two previous commit from Tolstoy : 2 bugs fixed in function IndexToCodon
* 1) incorrect order of letters in the table na - was TCGA
* 2) incorrect operation for bit counting - was total % div
* cofirmation from Johnatan Kans
*
* Revision 6.12  2003/04/29 14:35:16  tolstoy
* *** empty log message ***
*
* Revision 6.11  2003/04/28 20:05:22  tolstoy
* *** empty log message ***
*
* Revision 6.10  2003/04/18 19:40:38  kans
* changed iterate to ITERATE
*
* Revision 6.9  2003/02/24 18:52:57  vasilche
* Added optional mapped locations arguments to feature comparison.
*
* Revision 6.8  2002/11/26 18:50:31  shomrat
* Add GetGenCode
*
* Revision 6.7  2002/11/04 21:29:16  grichenk
* Fixed usage of const CRef<> and CRef<> constructor
*
* Revision 6.6  2002/09/19 18:07:05  kans
* code 9 is echinoderm and flatworm mito, code 14 is alternative flatworm mito
*
* Revision 6.5  2002/09/13 18:33:57  kans
* sm_GenCodeTblMemStr returned to an array of strings for consistency with sm_StrAsnData in sequence.cpp
*
* Revision 6.4  2002/09/12 19:59:12  kans
* CGen_code_table_imp instantiated after type info system (diccucio)
*
* Revision 6.3  2002/09/10 15:19:55  kans
* added GetCodeTable method, moved sm_GenCodeTblMemStr into implementation class
*
* Revision 6.2  2002/09/09 21:12:05  ucko
* Add braces around e_Id case to avoid scoping error.
* Add default cases to make GCC happy.
* Make sure id >= 0.
*
* Revision 6.1  2002/09/09 20:58:21  kans
* added CTrans_table and CGen_code_table classes
*
*
* ===========================================================================
*/
/* Original file checksum: lines: 64, chars: 1914, CRC32: 6d579336 */