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 );

Type | Name | Read/Write | Description |
---|---|---|---|

const AjPList | input | Input | List of ajPSeq's |

AjPInt* | keep | Output | 0: rejected (redundant) sequence, 1: the sequence was retained |

ajint* | nset | Output | Number of sequences in nr set (no. of 1's in the keep array) |

const AjPMatrixf | matrix | Input | Residue substitution matrix |

float | gapopen | Input | Gap insertion penalty |

float | gapextend | Input | Gap extension penalty |

float | thresh | Input | Threshold residue id. for "redundancy" |

AjBool | RETURN | ajTrue on success |

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 );

Type | Name | Read/Write | Description |
---|---|---|---|

const AjPList | input | Input | List of ajPSeq's |

AjPInt* | keep | Output | 0: rejected (redundant) sequence, 1: the sequence was retained |

ajint* | nset | Output | Number of sequences in nr set (no. of 1's in the keep array) |

const AjPMatrixf | matrix | Input | Residue substitution matrix |

float | gapopen | Input | Gap insertion penalty |

float | gapextend | Input | Gap extension penalty |

float | thresh1 | Input | Threshold lower limit |

float | thresh2 | Input | Threshold upper limit |

AjBool | RETURN | ajTrue on success |

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).