Holds the input 2-sided motif. More...
#include <structs.h>
Public Attributes | |
char * | comment |
char * | name |
int | nLeft |
int | nRight |
int | len |
float ** | stemL |
float ** | stemR |
float * | minL |
float * | maxL |
float * | infoL |
int * | maxCL |
char * | consL |
float * | minR |
float * | maxR |
float * | infoR |
int * | maxCR |
char * | consR |
int | n_bp |
int ** | basepairs |
float | scoreBP |
float | maxScore |
Holds the input 2-sided motif.
gotoh_motif holds the frequency matrices and the base pair table of a 2-sided motif. Additionally, it stores min, max, information content and consensus as well as maximal possible scores for sequence and structure.
int** gotoh_motif::basepairs |
Positions of paired bases in their stems and base pair type. 3 columns:
0
- i (left) 1
- j (right) 2
- type char* gotoh_motif::comment |
Comment for the motif, provided in input file.
char* gotoh_motif::consL |
Base at maxCL
- Consensus sequence of left stem.
char* gotoh_motif::consR |
Base at maxCR
- Consensus sequence of left stem.
float* gotoh_motif::infoL |
Information content of stemL
.
float* gotoh_motif::infoR |
Information content of stemR
.
int gotoh_motif::len |
Minimal length of motif. Default: nLeft
+ nRight
+ 3
int* gotoh_motif::maxCL |
Number of base at max value in stemL
. {0
,1,2,3,4} for {A
,C,G,U,-}.
int* gotoh_motif::maxCR |
Number of base at max value in stemR
. {0
,1,2,3,4} for {A
,C,G,U,-}.
float* gotoh_motif::maxL |
Maximal values of stemL
.
float* gotoh_motif::maxR |
Maximal values of stemR
.
float gotoh_motif::maxScore |
Complete score of consensus motif: sum((sum(maxL), sum(maxR), scoreBP))
float* gotoh_motif::minL |
Minimal values of stemL
.
float* gotoh_motif::minR |
Minimal values of stemR
.
Number of base pairs.
char* gotoh_motif::name |
Name of the motif. So far, same as comment.
The size of the left stem of a 2-sided motif.
The size of the right stem of a 2-sided motif.
float gotoh_motif::scoreBP |
Structure score consensus motif
float** gotoh_motif::stemL |
Frequency table of left stem.
float** gotoh_motif::stemR |
Frequency table of right stem.