source: tags/initial/ALIV3/a3.cxx

// -----------------------------------------------------------------------------
//      Include-Dateien
// -----------------------------------------------------------------------------

#include <iostream.h>
#include <fstream.h>
#include <stdio.h>
#include <stdlib.h>

#include "a3_arbdb.hxx"
#include "a3_bihelix.hxx"
#include "a3_ali.hxx"

// -----------------------------------------------------------------------------
        static void Usage ( void )
// -----------------------------------------------------------------------------
{
        cout << "\nAUFRUF: aliv3 <Datenbank> <Sequenz>\n";
        cout << "\n        <Datenbank> ::= Eine ARB-Datenbank (z.B.: 23sx.arb).";
        cout << "\n        <Sequenz>   ::= Name einer RNS-Sequenz (z.B.: ECOLI).\n";
        cout << "\nDarueberhinaus muss noch eine Datei matches.txt existieren, in der die Teilloesungen";
        cout << "\ndes Prealigners zeilenweise abgelegt sind. Innerhalb einer Zeile muessen die Positions-";
        cout << "\npaare der Loesung durch Kommata getrennt sein (z.B.: 5 10, 20 30, ...).\n\n";
}

// -----------------------------------------------------------------------------
        static DArray *ReadMatches ( str file )
// -----------------------------------------------------------------------------
{
        short     error = 0;
        DArray   *pre   = new DArray;
        ifstream  input(file);
                
        if (!pre || !input) error = 1;
        else
        {
                str line = NULL;
                
                pre->Free(DARRAY_NOFREE);
                pre->Null(DARRAY_NONULL);
                
                while (!error)
                {
//                      if              (!input.gets(&line) && !input.eof()) error = 2;
//                      else if (strlen(line))
                        {
                            PSolution *psol = new PSolution;

                                if (!psol) error = 3;
                                else
                                {
                                        str tmp = strtok(line,",");

                                        while (!error && tmp)
                                        {
                                                HMatch *m = new HMatch;

                                                if (!m) error = 4;
                                                else
                                                {
                                                        sscanf(tmp,"%d%d",&m->first,&m->last);

                                                        psol->match.Add(m);
                                                        psol->score += (m->last - m->first + 1);

                                                        tmp = strtok(NULL,",");
                                                }
                                        }

                                        if (!error)
                                        {
                                                psol->match.Sort(hmatchcmp);
                                                pre->Add(psol);
                                        }
                                }

                                delete line;
                        }

                        if (input.eof()) break;
                }
                
                if (!error) pre->Sort(psolcmp);
        }

        if (error) delete pre, pre = NULL;
        
        return pre;
}

// -----------------------------------------------------------------------------
        int main ( int   argc,
                           char *argv[] )
// -----------------------------------------------------------------------------
{
        int error = 0;
        
        if (argc != 3) Usage();
        else
        {
                A3Arbdb db;
                
                if (db.open(argv[1])) error = 1;
                else
                {
                    db.begin_transaction();
                    
                    str seq = db.get_sequence_string(argv[2]),
                        fam = db.get_sequence_string("EscCol19");

                    db.commit_transaction();
                        
                        if (!(seq && fam)) error = 2;
                        else
                        {
//                              DArray *pre = ReadMatches("matches.txt");

                                cout << "\n" << seq;
//                              cout << "\n" << fam << "\n";
                                
//                              if (!pre) error = 3;
//                              else
                                {
                                    A3_BI_Helix helix;
                                    str err = helix.init(db.gb_main);
                                    long pos = 0;

                                    if (err) cout << err << ", " << helix.size;

                                    while(pos < helix.size)
                                        {
                                            if (helix.entries[pos].pair_type != HELIX_PAIR) cout << ".";
                                            else
                                                {
                                                    if (helix.entries[pos].pair_pos < pos) cout << "]";
                                                    else cout << "[";
                                                }

                                            pos++;
                                        }

                                    cout << flush;

//                                      Aligner  ali(seq[2],seq[0],seq[1],*pre);
//                                      DArray  &tmp = ali.Align();

//                                      delete &tmp;
//                                      delete  pre;
                                }
                        }

                        if (seq) delete seq;
                        if (fam) delete fam;

                        db.close();
                }
        }

        if (error) cout << "\nALIV3: Fehler Nummer " << error << " ist aufgetreten!\n\n";
        
        return error;
}