Stores information about one alignment. More...
#include <structs.h>
Public Attributes | |
int | db_len |
char * | hitseq |
char * | queryseq |
char * | hitname |
char * | queryname |
int | shift |
int | sStart |
int | sEnd |
int | length |
char | strand |
float | alnscore |
float | ntfalnscore |
double | evalue |
float | percID |
int | mismatches |
int | gapopening |
int | qStart |
int | qEnd |
Stores information about one alignment.
gotoh_aln contains all information about a single alignment. Alignment scores and positions in the database are computed during the forward recursion, while the alignment is obtained in the backward recursion. The E-value is calculated only after the complete set of database sequences has been scanned.
float gotoh_aln::alnscore |
Alignment score
Length of complete database sequence -> for maf output
double gotoh_aln::evalue |
E-value for alignment score
Number of gap opening events
char* gotoh_aln::hitname |
Name of database entry
char* gotoh_aln::hitseq |
Aligned database (hit) sequence (with gaps)
Length of alignment
Number of mismatching pairs of bases
float gotoh_aln::ntfalnscore |
Unshifted (real) alignment score
float gotoh_aln::percID |
Percent identity. Number of real matches vs. number of maximal possible matches
int gotoh_aln::qEnd |
End of alignment in query. Should always be sizeof(query) due to global alignment
Start of alignment in query. Should always be 0 due to global alignment
char* gotoh_aln::queryname |
Name of query sequence/pattern
char* gotoh_aln::queryseq |
Aligned query sequence/pattern (with gaps)
int gotoh_aln::sEnd |
End position in database entry
int gotoh_aln::shift |
Score to shift x-axis to zero
Start position in database entry
char gotoh_aln::strand |
Strand of hit in database