9

ϕ
_{
i
}

Propagation direction of fragment i.

9

ϕ
_{
j
}

Propagation direction of fragment j.

9

D

The function that calculates the orientation difference between ϕ_{
i
} and the reverse direction of ϕ_{
j
}.

9

ϕ
_{
max
}

The maximum allowable difference between ϕ_{
i
} and the reverse direction of ϕ_{
j
}.

10

d
_{
i,j
}

The magnitude of the distance vector between i and j.

10

d
_{
max
}

The maximum allowable gap length.

11

φ
_{
i,j
}

The direction of the distance vector pointing from i to j.

11

ψ
_{
max
}

The maximum allowed direction mismatch between the fragment i and distance vector.

12

ϕ
^{a}_{
m
}

The propagation direction of the tip of bridging fragment m close to fragment i.

13

φ
^{a}_{
i,m
}

The distance vector between fragment i and the its closest tip of fragment m.

14

ϕ
^{b}_{
m
}

The propagation direction of the tip of bridging fragment m close to fragment j.

15

φ
^{b}_{
j,m
}

The distance vector between fragment j and the its closest tip of fragment m.

16

C
_{
i
}

Eligibility cost for connecting the base terminus and its ith partner tips.

16

C
_{
angle_weight
}

Weight for similarity criterion.

16

C
_{
gap_weight
}

Weight for continuity criterion.

16

Δ
θ
_{
i
}

Difference for similarity.

16

Δ
θ
_{
gapi
}

Difference for continuity.
