Sequences are classed as redundant (0 in the array, i.e. they are possibly to be discarded later) if they exceed a threshold (%) level of sequence similarity to any other in the set (the shortest sequence of the current pair will be discarded).
The set output will always contain at least 1 sequence.
AjBool embXyzSeqsetNR (
const AjPList input,
AjPInt* keep,
ajint* nset,
const AjPMatrixf matrix,
float gapopen,
float gapextend,
float thresh
);
| input: | (Input) | List of ajPSeq's |
| matrix: | (Input) | Residue substitution matrix |
| gapopen: | (Input) | Gap insertion penalty |
| gapextend: | (Input) | Gap extension penalty |
| thresh: | (Input) | Threshold residue id. for "redundancy" |
| keep: | (Output) | 0: rejected (redundant) sequence, 1: the sequence was retained |
| nset: | (Output) | Number of sequences in nr set (no. of 1's in the keep array) |
| AjBool: | ajTrue on success |
Sequences are classed as redundant (0 in the array, i.e. they are possibly to be discarded later) if they exceed a threshold (%) level of sequence similarity to any other in the set (the shortest sequence of the current pair will be discarded).
The set output will always contain at least 1 sequence.
Sequences are classed as redundant (0 in the array, i.e. they are possibly to be discarded later) if they lie outside a range of threshold (%) sequence similarity to others in the set (the shortest sequence of the current pair will be discarded).
AjBool embXyzSeqsetNRRange (
const AjPList input,
AjPInt* keep,
ajint* nset,
const AjPMatrixf matrix,
float gapopen,
float gapextend,
float thresh1,
float thresh2
);
| input: | (Input) | List of ajPSeq's |
| matrix: | (Input) | Residue substitution matrix |
| gapopen: | (Input) | Gap insertion penalty |
| gapextend: | (Input) | Gap extension penalty |
| thresh1: | (Input) | Threshold lower limit |
| thresh2: | (Input) | Threshold upper limit |
| keep: | (Output) | 0: rejected (redundant) sequence, 1: the sequence was retained |
| nset: | (Output) | Number of sequences in nr set (no. of 1's in the keep array) |
| AjBool: | ajTrue on success |
Sequences are classed as redundant (0 in the array, i.e. they are possibly to be discarded later) if they lie outside a range of threshold (%) sequence similarity to others in the set (the shortest sequence of the current pair will be discarded).