Class Specialization

ChainedSeed

Describes a seed with start and end position2 and diagonal upper and lower bounds. Additionaly diagonal segments
between start and end position2 are stored.

ChainedSeed |

Parameters

The type of number that schuld be used. Must have negative numbers (e.g. int/long). |

Specialization of

Member Functions

Constructor |

Functions

Adds a seed to an existing set. (Seed) | |

Adds diagonal to the seed. | |

Calculates a banded alignment around a Seed. (Seed) | |

Dimension of a seed. (Seed) | |

Returns the diagonal of the end point. (Seed) | |

Extends a seed. (Seed) | |

Extends a seed and increases the score. (Seed) | |

Constructs a alignment from a ChainedSeed. | |

Returns the most left diagonal of the seed (maximum diagonal value). (Seed) | |

Returns the first position of the seed in the query. (Seed) | |

Returns the first position of the seed in the database. (Seed) | |

The begin position of segment in a seed. (Seed) | |

Returns the most right diagonal of the seed (minimum diagonal value). (Seed) | |

Returns the last position of the seed in the query. (Seed) | |

Returns the last position of the seed in the database. (Seed) | |

The end position of segment in a seed. (Seed) | |

Calculates the score of a seed. | |

Sets a new value for the most left diagonal. (Seed) | |

Updates the start point of the seed. (Seed) | |

Updates the start point of the seed. (Seed) | |

Sets begin position of segment in a seed. (Seed) | |

Sets a new value for the most right diagonal. (Seed) | |

Updates the end point of the seed. (Seed) | |

Updates the end point of the seed. (Seed) | |

Sets end position of segment in a seed. (Seed) | |

Returns the diagonal of the start point. (Seed) |

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