test_pin.cpp

来自「ncbi源码」· C++ 代码 · 共 1,309 行 · 第 1/3 页

                    }
                    
                    cout << dec << "\n";

                    nt.RetSequence(& buf);
                }
                
                if (1) {
                    int length = nt.GetAmbigSeq(oid, & buf, kSeqDBNuclNcbiNA8);
                    
                    int y = (length > 16) ? 16 : length;
                
                    for(int x = 0; x < y; x++) {
                        if ((x & 3) == 0)
                            cout << " ";
                    
                        if (unsigned(buf[x]) < 0x10)
                            cout << "0";
                    
                        cout << hex << (unsigned(buf[x]) & 0xFF) << " ";
                    }
                    
                    cout << dec << "\n";
                    
                    nt.RetSequence(& buf);
                }
                
                if (1) {
                    int length = nt.GetAmbigSeq(oid, & buf, kSeqDBNuclBlastNA8);
                
                    int y = (length > 16) ? 16 : length;
                
                    for(int x = 0; x < y; x++) {
                        if ((x & 3) == 0)
                            cout << " ";
                    
                        if (unsigned(buf[x]) < 0x10)
                            cout << "0";
                    
                        cout << hex << (unsigned(buf[x]) & 0xFF) << " ";
                    }
                    
                    cout << dec << "\n\n";
                    
                    nt.RetSequence(& buf);
                }
                
                oid++;
            }
            
            return 0;
        } else desc += " [-memtest]";
        
        if (s == "-getambig") {
            CSeqDB nt(/*dbpath,*/ "nt", 'n', 0, 0, false);
            
            Uint4 oid = 0;
            
            for(int i = 0; i<100; i++) {
                const char * buf(0);
                
                if (! nt.CheckOrFindOID(oid))
                    break;
                
                cout << "-----------------" << endl;
                
                {
                    int length = nt.GetSequence(oid, & buf);
                    
                    cout << "NT OID = " << oid << ", length is " << length << endl;
                    
                    int y = (length > 16) ? 16 : length;
                    
                    for(int x = 0; x < y; x++) {
                        if ((x & 3) == 0)
                            cout << " ";
                        
                        if (unsigned(buf[x]) < 0x10)
                            cout << "0";
                        
                        cout << hex << (unsigned(buf[x]) & 0xFF) << " ";
                    }
                    
                    cout << dec << "\n";

                    nt.RetSequence(& buf);
                }
                
                {
                    int length = nt.GetAmbigSeq(oid, & buf, kSeqDBNuclNcbiNA8);
                
                    int y = (length > 16) ? 16 : length;
                
                    for(int x = 0; x < y; x++) {
                        if ((x & 3) == 0)
                            cout << " ";
                    
                        if (unsigned(buf[x]) < 0x10)
                            cout << "0";
                    
                        cout << hex << (unsigned(buf[x]) & 0xFF) << " ";
                    }
                    
                    cout << dec << "\n";
                    
                    nt.RetSequence(& buf);
                }
                
                {
                    int length = nt.GetAmbigSeq(oid, & buf, kSeqDBNuclBlastNA8);
                
                    int y = (length > 16) ? 16 : length;
                
                    for(int x = 0; x < y; x++) {
                        if ((x & 3) == 0)
                            cout << " ";
                    
                        if (unsigned(buf[x]) < 0x10)
                            cout << "0";
                    
                        cout << hex << (unsigned(buf[x]) & 0xFF) << " ";
                    }
                    
                    cout << dec << "\n\n";
                    
                    nt.RetSequence(& buf);
                }
                
                oid++;
            }
            
            return 0;
        } else desc += " [-getambig]";
        
        if (s == "-iter2") {
            {
                CSeqDB phil(/*dbpath,*/ "swissprot pataa", 'p');
            
                {
                    CSeqDBIter skywalk = phil.Begin();

                    for(int i = 0; i<20; i++) {
                        cout << "### Seq [" << skywalk.GetOID() << "] length = " << skywalk.GetLength() << endl;
                        ++skywalk;
                    }
                }
            
                {
                    CSeqDBIter skywalk = phil.Begin();

                    for(int i = 0; i<20; i++) {
                        cout << "### Seq [" << skywalk.GetOID() << "] length = " << skywalk.GetLength() << endl;
                        CRef<CBioseq> bioseq = phil.GetBioseq(skywalk.GetOID());
                        auto_ptr<CObjectOStream> outpstr(CObjectOStream::Open(eSerial_AsnText, cout));
                        *outpstr << *bioseq;
                        ++skywalk;
                    }
                }
            }
            {
                CSeqDB phil(/*dbpath,*/ "pataa swissprot", 'p');
            
                {
                    CSeqDBIter skywalk = phil.Begin();

                    for(int i = 0; i<20; i++) {
                        cout << "### Seq [" << skywalk.GetOID() << "] length = " << skywalk.GetLength() << endl;
                        ++skywalk;
                    }
                }
            
                {
                    CSeqDBIter skywalk = phil.Begin();

                    for(int i = 0; i<20; i++) {
                        cout << "### Seq [" << skywalk.GetOID() << "] length = " << skywalk.GetLength() << endl;
                        CRef<CBioseq> bioseq = phil.GetBioseq(skywalk.GetOID());
                        auto_ptr<CObjectOStream> outpstr(CObjectOStream::Open(eSerial_AsnText, cout));
                        *outpstr << *bioseq;
                        ++skywalk;
                    }
                }
            }
            
            return 0;
        } else desc += " [-iter2]";
        
        if (s == "-iter") {
            CSeqDB phil(/*dbpath,*/ "swissprot pdb", 'p');
            
            {
                CSeqDBIter skywalk = phil.Begin();

                for(int i = 0; i<200; i++) {
                    cout << "### Seq [" << skywalk.GetOID() << "] length = " << skywalk.GetLength() << endl;
                    ++skywalk;
                }
            }
            
            if (0) {
                for(int i = 0; i<200; i++) {
                    cout << "\n### Seq [" << i << "] length = " << phil.GetSeqLength(i) << "\n" << endl;
                    CRef<CBioseq> bioseq = phil.GetBioseq(i);

                    auto_ptr<CObjectOStream> outpstr(CObjectOStream::Open(eSerial_AsnText, cout));
                    *outpstr << *bioseq;
                }
            }
            
            {
                CSeqDBIter skywalk = phil.Begin();

                for(int i = 0; i<200; i++) {
                    cout << "### Seq [" << skywalk.GetOID() << "] length = " << skywalk.GetLength() << endl;
                    CRef<CBioseq> bioseq = phil.GetBioseq(skywalk.GetOID());
                    auto_ptr<CObjectOStream> outpstr(CObjectOStream::Open(eSerial_AsnText, cout));
                    *outpstr << *bioseq;
                    ++skywalk;
                }
            }
            
            if (0) {
                for(int i = 0; i<200; i++) {
                    cout << "\n### Seq [" << i << "] length = " << phil.GetSeqLength(i) << "\n" << endl;
                }
            }
            
            return 0;
        } else desc += " [-iter]";
        
        if (s == "-iterpdb") {
            CSeqDB phil(/*dbpath,*/ "pdb", 'p');
            
            {
                CSeqDBIter skywalk = phil.Begin();

                for(int i = 0; i<200; i++) {
                    cout << "### Seq [" << skywalk.GetOID() << "] length = " << skywalk.GetLength() << endl;
                    ++skywalk;
                }
            }
            
            if (0) {
                for(int i = 0; i<100; i++) {
                    cout << "\n### Seq [" << i << "] length = " << phil.GetSeqLength(i) << "\n" << endl;
                    CRef<CBioseq> bioseq = phil.GetBioseq(i);

                    auto_ptr<CObjectOStream> outpstr(CObjectOStream::Open(eSerial_AsnText, cout));
                    *outpstr << *bioseq;
                }
            }
            
            return 0;
        } else desc += " [-iterpdb]";
        
        if (s == "-itersp") {
            CSeqDB phil(/*dbpath,*/ "swissprot", 'p');
            
            {
                CSeqDBIter skywalk = phil.Begin();

                for(int i = 0; i<200; i++) {
                    cout << "### Seq [" << skywalk.GetOID() << "] length = " << skywalk.GetLength() << endl;
                    ++skywalk;
                }
            }
            
            if (0) {
                for(int i = 0; i<100; i++) {
                    cout << "\n### Seq [" << i << "] length = " << phil.GetSeqLength(i) << "\n" << endl;
                    CRef<CBioseq> bioseq = phil.GetBioseq(i);

                    auto_ptr<CObjectOStream> outpstr(CObjectOStream::Open(eSerial_AsnText, cout));
                    *outpstr << *bioseq;
                }
            }
            
            return 0;
        } else desc += " [-itersp]";
        
        if (s == "-spcount") {
            CSeqDB phil(/*dbpath,*/ "swissprot", 'p');
            
            double besht = 100.0;
            double woist = 0.0;
            double totul = 0.0;
            
            for(int i = 0; i<10; i++) {
                CSeqDBIter skywalk = phil.Begin();
                
                double spt1 = dbl_time();
                Uint8 mylen = 0;
                
                while(skywalk) {
                    int this_oid = 0;
                    //int this_len = 0;
                    
                    //mylen += (this_len = phil.GetSeqLength( this_oid = skywalk.GetOID() ));
                    this_oid = skywalk.GetOID();
                    ++ skywalk;
                    mylen ++;
                    
                    //cout << this_oid << " is length " << this_len << endl;
                }
                
                double spt2  = dbl_time();
                double rezzy = spt2 - spt1;
                
                cout << "mylen " << mylen
                     << " spt2 - spt1 = " << rezzy << endl;
                
                if (rezzy > woist)
                    woist = rezzy;
                if (rezzy < besht)
                    besht = rezzy;
                
                totul += rezzy;
            }
            
            totul -= (besht + woist);
            
            cout << "Average = " << (totul/8.0) << endl;
            
            return 0;
        } else desc += " [-spcount]";
        
        if (s == "-swiss") {
            CSeqDB phil(/*dbpath,*/ "swissprot", 'p');
             
            {
                Uint8 tlen = 0;
                Uint4 numb = 0;
                
                CSeqDBIter skywalk = phil.Begin();
                
                {
                    int i = 276;
                    cout << "this_oid = " << i << " length = " << 0 << endl;
                    cout << "\n### Seq [" << i << "] length = " << phil.GetSeqLength(i) << "\n" << endl;
                    CRef<CBioseq> bioseq = phil.GetBioseq(i);
                    
                    auto_ptr<CObjectOStream> outpstr(CObjectOStream::Open(eSerial_AsnText, cout));
                    *outpstr << *bioseq;
                }

                while(skywalk) {
                    int this_oid = 0;
                    int this_len = 0;
                    
                    numb ++;
                    tlen += (this_len = phil.GetSeqLength( this_oid = skywalk.GetOID() ));
                    ++ skywalk;
                    
                    cout << this_oid << endl;
                    
                    if (numb > 145680) {
                        int i = this_oid;
                        cout << "this_oid = " << this_oid << " length = " << this_len << endl;
                        cout << "\n### Seq [" << i << "] length = " << phil.GetSeqLength(i) << "\n" << endl;
                        CRef<CBioseq> bioseq = phil.GetBioseq(i);

                        auto_ptr<CObjectOStream> outpstr(CObjectOStream::Open(eSerial_AsnText, cout));
                        *outpstr << *bioseq;
                    }
                }
                
                cout << "\n### Total swissprot length [" << tlen << "] numb = " << numb << "\n" << endl;
            }
             
            return 0;
        } else desc += " [-swiss]";
        
        
        if (s == "-lib") {
            CSeqDB phil(/*dbpath,*/ "nt nt month est", 'n');
            phil.GetSeqLength(123);
            phil.GetSeqLengthApprox(123);
            phil.GetHdr(123);
            phil.GetBioseq(123);
            
            const char * buffer = 0;
            phil.GetSequence(123, & buffer);
            phil.RetSequence(& buffer);

            cout << "\nSeq type:    " << phil.GetSeqType();
            cout << "\nTitle:       " << phil.GetTitle();
            cout << "\nDate:        " << phil.GetDate();
            cout << "\nNumSeqs:     " << phil.GetNumSeqs();
            cout << "\nTotalLength: " << phil.GetTotalLength();
            cout << "\nMax Length:  " << phil.GetMaxLength() << endl;
            cout << endl;
            
            return 0;
        } else desc += " [-lib]";
        
        if (s == "-summary") {
            CSeqDB phil(/*dbpath,*/ "month", 'n');
            cout << "dbpath: " << dbpath            << endl;
            cout << "title:  " << phil.GetTitle()   << endl;
            cout << "nseqs:  " << phil.GetNumSeqs() << endl;
            cout << "tleng:  " << phil.GetTotalLength() << endl;
            return 0;
        } else desc += " [-summary]";
        
//         if (s == "-alias") {
//             string dbname = "pdb";
            
//             if (! args.empty()) {
//                 dbname = args.front();
//                 args.pop_front(); 
//             }

//             string ending = "pal";
//             if (! args.empty()) {
//                 ending = args.front();
//                 args.pop_front(); 
//             }
            
//             ncbi::CSeqDBAliasNode phil(/*dbpath,*/ dbname, ending[0]);
            
//             vector<string> vols;
            
//             phil.GetVolumeNames(vols);
            
//             for(Uint4 i = 0; i<vols.size(); i++) {
//                 cout << "[" << i << "] "
//                      << vols[i] << endl;
//             }
            
//             return 0;
//         } else desc += " [-alias]";
        
        if (s == "-len3") {
            string dbname1("nr");
            string dbname2("pataa");
            string dbname3(dbname1 + " " + dbname2);