mgaln.h

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#ifndef MGSALN_H
#define MGSALN_H

//file: mgsaln.h
#include <stdio.h>
#include "dynamicaln.h"

class mgsaln {
 private:
        struct SEQALN_SEQUENCE *seq1,*seq2; /* 1st & 2nd sequences to be compared. */
        struct SEQALN_CONSTANTS  *scoring;  /* Scoring constants. */
        struct SEQALN_RESULTS  *results;    /* Computation results. */
        struct SEQALN_IO *io;

 public:
        mgsaln(char* seq2name, char* seq1str, char* seq2name, char* seq2str);


        int i,j;
        int seq1status;
        extern char *newmem();

        seq1 = (struct SEQALN_SEQUENCE *)newmem(1, sizeof(struct SEQALN_SEQUENCE));
        seq2 = (struct SEQALN_SEQUENCE *)newmem(1, sizeof(struct SEQALN_SEQUENCE));
        scoring = (struct SEQALN_CONSTANTS *)newmem(1, sizeof(struct SEQALN_CONSTANTS));
        results = (struct SEQALN_RESULTS *)newmem(1, sizeof(struct SEQALN_RESULTS));
        io = (struct SEQALN_IO *)newmem(1, sizeof(struct SEQALN_IO));

        io->STDIN = stdin;
        io->STDOUT = stdout;
        io->STDERR = stderr;

        if (argc<7)
          {
            (void)fprintf(io->STDOUT,"Shortcut:\n\n   %s file1 file2 ", argv[0]);
            (void)fprintf(io->STDOUT,"matrix offset ");
            (void)fprintf(io->STDOUT,"alpha beta ");
            (void)fprintf(io->STDOUT,"[flags]\n\n");
          }
        scoring->ptype = GLOBAL;
        scoring->stype = MATRIX;
        scoring->mtype = SIMILARITY;
        scoring->btype = FULL;
        scoring->memuse = SQUARE;
        parseargs(seq1,seq2,scoring,results,io,argc,argv); /* Parse program arguments */
        results_init(seq1,seq2,scoring,results,io); /* Initialize results data struct */

        /*
          We have all the parameter information.  Now proceed w/computation.
        */
        seq1status = seq1->len;
        while (seq1status > 0) {  /* Stop at 0-length seq, or EOF (seq1status==-1) */
          globalS(seq1,seq2,scoring,results,io);
          if (scoring->memuse == LINEAR) {
            if (scoring->rptscore) {
              rpt_align(seq1,seq2,scoring,results,io);
            }
          }
          else {
            for (i=0; i<=scoring->rptboth; i++) {
        trace(seq1,seq2,scoring,results,io);
        if (scoring->rpttrace) {
          print_trace(scoring,results,io);
        }
        if (scoring->rptscore || scoring->rptalign) {
          gen_align(seq1,seq2,scoring,results,io); /* Generate the alignment */
          rpt_align(seq1,seq2,scoring,results,io); /* Print the alignment */
        }
        if (scoring->rptboth) {
          scoring->traceupper = !scoring->traceupper;
          (void)fprintf(io->STDOUT,"\n");
        }
            }
          }
          seq1status = load_seq(seq1,scoring,io);
          if (seq1status > 0) {
            results_init(seq1,seq2,scoring,results,io);
          }
        }  /* End of while seq1status . . . */
        
        exit(0);
}

#endif