jpayne@69: #include "translate.hh"
jpayne@69: 
jpayne@69: 
jpayne@69: long int Translate_DNA
jpayne@69:      (char * A, char * tA, int Frame)
jpayne@69: 
jpayne@69:      // function to translate dna sequence to aminoacid sequence
jpayne@69:      // uses esttrans' headers and algo
jpayne@69:      // A as read in from gene.h Read_String
jpayne@69:      // tA should be an empty string malloced to atleast (Len A / 3)
jpayne@69:      // frame is 1,2,3,4,5,6
jpayne@69:      // returns new (strlen(tA+1)) or -1 on error
jpayne@69: 
jpayne@69: {
jpayne@69:   int     dna_int;
jpayne@69:   int     dnaseq_len, aaseq_len;
jpayne@69:   int     aa_index;
jpayne@69:   char    *dna_seq, *dna_ptr, *dna_end, *aa_ptr;
jpayne@69: 
jpayne@69:   dnaseq_len = strlen ( A + 1 );
jpayne@69:   aa_ptr =  tA + 1;
jpayne@69:   dna_seq = A + 1;
jpayne@69:   dna_end = A + dnaseq_len;
jpayne@69: 
jpayne@69:   if ( Frame >= 1  &&  Frame <= 3 )
jpayne@69:     {
jpayne@69:       dna_end -= 2;
jpayne@69:       dna_ptr = dna_seq + Frame - 1;
jpayne@69:       for (; dna_ptr <= dna_end;)
jpayne@69: 	{
jpayne@69: 	  dna_int = transdna [ int(*dna_ptr++) ];
jpayne@69: 	  if ( dna_int == BAD_PEP_CHAR ) {
jpayne@69: 	    fprintf(stderr,"WARNING: Forcing unrecognized DNA char to N\n");
jpayne@69: 	    dna_int = DNA_XN;
jpayne@69: 	  }
jpayne@69: 	  aa_index = dna_int;
jpayne@69: 	  aa_index <<= 4;
jpayne@69: 	  
jpayne@69: 	  dna_int = transdna [ int(*dna_ptr++) ];
jpayne@69: 	  if ( dna_int == BAD_PEP_CHAR ) {
jpayne@69: 	    fprintf(stderr,"WARNING: Forcing unrecognized DNA char to N\n");
jpayne@69: 	    dna_int = DNA_XN;
jpayne@69: 	  }
jpayne@69: 	  aa_index += dna_int;
jpayne@69: 	  aa_index <<= 4;
jpayne@69: 	  
jpayne@69: 	  dna_int = transdna [ int(*dna_ptr++) ];
jpayne@69: 	  if ( dna_int == BAD_PEP_CHAR ) {
jpayne@69: 	    fprintf(stderr,"WARNING: Forcing unrecognized DNA char to N\n");
jpayne@69: 	    dna_int = DNA_XN;
jpayne@69: 	  }
jpayne@69: 	  aa_index += dna_int;
jpayne@69: 	  
jpayne@69: 	  *(aa_ptr++) = universal[aa_index];
jpayne@69: 	}
jpayne@69:       
jpayne@69:       *aa_ptr = '\0';
jpayne@69:       aaseq_len = strlen ( tA + 1 );
jpayne@69:     }
jpayne@69:   else if ( Frame >= 4  &&  Frame <= 6 )
jpayne@69:     {
jpayne@69:       Frame -= 3;
jpayne@69: 
jpayne@69:       dna_seq += 2;
jpayne@69:       dna_ptr = dna_end - Frame + 1;
jpayne@69:       for (; dna_ptr >= dna_seq;)
jpayne@69: 	{
jpayne@69: 	  dna_int = compdna [ transdna [ int(*dna_ptr--)] ];
jpayne@69: 	  if ( dna_int == BAD_PEP_CHAR ) {
jpayne@69: 	    fprintf(stderr,"WARNING: Forcing unrecognized DNA char to N\n");
jpayne@69: 	    dna_int = DNA_XN;
jpayne@69: 	  }
jpayne@69: 	  aa_index = dna_int;
jpayne@69: 	  aa_index <<= 4;
jpayne@69: 	  
jpayne@69: 	  dna_int = compdna [ transdna [ int(*dna_ptr--)] ];
jpayne@69: 	  if ( dna_int == BAD_PEP_CHAR ) {
jpayne@69: 	    fprintf(stderr,"WARNING: Forcing unrecognized DNA char to N\n");
jpayne@69: 	    dna_int = DNA_XN;
jpayne@69: 	  }
jpayne@69: 	  aa_index += dna_int;
jpayne@69: 	  aa_index <<= 4;
jpayne@69: 	  
jpayne@69: 	  dna_int = compdna [ transdna [ int(*dna_ptr--)] ];
jpayne@69: 	  if ( dna_int == BAD_PEP_CHAR ) {
jpayne@69: 	    fprintf(stderr,"WARNING: Forcing unrecognized DNA char to N\n");
jpayne@69: 	    dna_int = DNA_XN;
jpayne@69: 	  }
jpayne@69: 	  aa_index += dna_int;
jpayne@69: 	  
jpayne@69: 	  *(aa_ptr++) = universal[aa_index];
jpayne@69: 	}
jpayne@69:       
jpayne@69:       *aa_ptr = '\0';
jpayne@69:       aaseq_len = strlen ( tA + 1 );
jpayne@69:     }
jpayne@69:   else
jpayne@69:     aaseq_len = -1;
jpayne@69:      
jpayne@69: 
jpayne@69:   return aaseq_len;
jpayne@69: }
jpayne@69: