Re: counting breakpoints

[Michael Brudno]

> Now that I'm thinking about it more, I'm not sure if I really understood the
> breakpoint counting.

> For example,
>
> 1 2 | 4 3 | -6 -5
>
> Would have 2 breakpoints where I drew the bars, right?  But is this only
> relative to 1 2 3 4 5 6?

Actually there is also a breakpont between 4 and 3.

>
> If the other sequence was 1 2 4 3 5 6, then would there only be one
> breakpoint at 1 2 4 3 | -6 -5 instead?

Yes, this is correct. Basically you can think of renumbering the
elements of the sequences so that they are in order on one, and then
counting breakpoints in the other. For example, the breakpoints
between

1 2 4 -6 -5 3 and -2 -1 3 4 -5 6 can be computed by renumbering the
first one A B C D E F. The second one becomes

-B -A F C E -D .

The breakpoint are between all pairs after the first one.

-Mike