full GA up and running that looks very promising for doing our contig
ordering!
This takes 15 seconds to run at home (600 MHz Pentium III) for 10000
generations. Order is perfect, except that 8 should be at the leftmost
end.
Scores are all the sulston exponents between each neighbour and the next.
This tries to minimize that quantity. It's very fast.
Cool, eh!
-----------------------------------------------------------------
Best = 0 Score = 581
499 446 426 399 385 374 311 292 251 224 195 190 162 139 124 94 61 31 8 958 920 892 841 633 626 617 596 562
Total Mutations = 7624 Good Mutations = 36
Total Crossovers = 3707 Good Crossovers = 6
Total SpanXovers = 3724 Good SpanXovers = 8
Total Fix Worst = 7537 Good Fix Worst = 212
Total BlockShift = 7408 Good BlockShift = 27
Total Mountain = 0 Good Mountain = 0
-----------------------------------------------------------------
shakti 107 [~/GDEV/contiger] %
The inital contig order was randomly shuffled 1000 times, giving clones
like below:
Gen = 1 best = 211 (4)
399 311 446 499 162 958 374 633 841 139 190 195 251 292 892 31 61 94 596 426 562 617 626 385 8 920 224 124
This was the best order at the start.
