Table 1 Definition of geometric constraints parameters

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.