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Clone Mass | Clones in CloneSet | Parameter Count | Clone Similarity | Syntax Category [Sequence Length] |
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8 | 2 | 3 | 0.969 | block |
Clone Abstraction | Parameter Bindings |
Clone Instance (Click to see clone) | Line Count | Source Line | Source File |
---|---|---|---|
1 | 8 | 334 | Bio/pairwise2.py |
2 | 5 | 342 | Bio/pairwise2.py |
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# Align the first residue in sequenceB to the ith residue in # sequence A. This is like opening up i gaps at the beginning # of sequence B. score = match_fn(sequenceA[i],sequenceB[0]) if penalize_end_gaps: score+=gap_B_fn(0,i) score_matrix[i][0] = score |
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score = match_fn(sequenceA[0],sequenceB[i]) if penalize_end_gaps: score+=gap_A_fn(0,i) score_matrix[0][i] = score # Fill in the score matrix. Each position in the matrix # represents an alignment between a character from sequenceA to # one in sequence B. As I iterate through the matrix, find the # alignment by choose the best of: # 1) extending a previous alignment without gaps # 2) adding a gap in sequenceA # 3) adding a gap in sequenceB |
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# Align the first residue in sequenceB to the ith residue in # sequence A. This is like opening up i gaps at the beginning # of sequence B. score = match_fn(sequenceA[ [[#variable31a0da20]]],sequenceB[ [[#variable31a0d9c0]]]) if penalize_end_gaps: score+= [[#variable31a0d940]](0,i) score_matrix[ [[#variable31a0da20]]][ [[#variable31a0d9c0]]] = score # Fill in the score matrix. Each position in the matrix # represents an alignment between a character from sequenceA to # one in sequence B. As I iterate through the matrix, find the # alignment by choose the best of: # 1) extending a previous alignment without gaps # 2) adding a gap in sequenceA # 3) adding a gap in sequenceB |
CloneAbstraction |
Parameter Index | Clone Instance | Parameter Name | Value |
---|---|---|---|
1 | 1 | [[#31a0da20]] | i |
1 | 2 | [[#31a0da20]] | 0 |
2 | 1 | [[#31a0d9c0]] | 0 |
2 | 2 | [[#31a0d9c0]] | i |
3 | 1 | [[#31a0d940]] | gap_B_fn |
3 | 2 | [[#31a0d940]] | gap_A_fn |