interval set operations

[Brent Pedersen]

Is there anything in biogo for interval sets? For example, I'd like to
be able to have a set of intervals A and another set B and to get,
e.g. the union,intersection,subtraction, etc.

I didn't see this; would there be a place for this somewhere if I were
to implement? Perhaps as functions on feat.Range and feat.Set?

thanks,
-Brent

[Dan Kortschak]

When I want unordered sets (i.e. most of the time) I use
map[struct{chr, start, end int}]struct{} or map[struct{chr string;
start, end int}]. If I want an ordered set I use interval.IntTree[1].

[1]https://godoc.org/github.com/biogo/store/interval#IntTree

[Dan Kortschak]

Actually, the first is more likely to be map[struct{chr, start, end
int}]T or map[struct{chr string;> start, end int}]T where T is the type
storing the interval. It depends on whether I'm keeping coverage or I
actually need access to the actual value that is part of the set. With
the T payload, it becomes necessary to do insertion uniqueness
validation.

Also note that interval.IntTree will give you a multiset, not a true
set unless insertion uniqueness validation is performed.

[Brent Pedersen]

I mean a set where e.g. I can union (1, 9) and (7, 14) and it will
give (1, 14) and then I can subtract (5, 8) and get (1, 5), (9, 14)

[Dan Kortschak]

Ahh, OK. biogo/store/step will do that for you.

[Brent Pedersen]

Great! So, does this seem reasonable for Intersection of multiple *step.Vector

https://gist.github.com/brentp/4419f6711917096bce83e7eddb648c85 ?

Or is there a more efficient (in LOC or CPU) way?
If this is generally close, then having a Vector.Clone() method would
be convenient.

thanks,
-Brent

[Brent Pedersen]

I ended up with this: https://godoc.org/github.com/brentp/rangeset
embedding step.Vector

[Dan Kortschak]

Is there a reason to have the step vector embedded anonymously?

[Brent Pedersen]

You mean instead of naming it, like:

type RangeSet struct {
v *step.Vector
}

?
I guess originally, I was thinking the user might want to access some
of the public methods from the step.Vector.

On Mon, Feb 13, 2017 at 2:51 PM, Dan Kortschak

[Dan Kortschak]

You've made it type safe by providing the comparer, so you may as well go the whole way and stop people doing the wrong thing. If there are things that are worth exposing, expose them explicitly.

--
afk
Dan

From: Brent Pedersen
Sent: Tuesday, 14 February, 08:30
Subject: Re: [biogo-user] interval set operations
To: Dan Kortschak
Cc: biogo...@googlegroups.com

You mean instead of naming it, like: type RangeSet struct { v *step.Vector } ? I guess originally, I was thinking the user might want to access some of the public methods from the step.Vector. On Mon, Feb 13, 2017 at 2:51 PM, Dan Kortschak wrote: > Is there a reason to have the step vector embedded anonymously? > > On Mon, 2017-02-13 at 14:22 -0700, Brent Pedersen wrote: >> I ended up with this: https://godoc.org/github.com/brentp/rangeset >> embedding step.Vector >> >> On Mon, Feb 13, 2017 at 10:18 AM, Brent Pedersen >> wrote: >> > >> > Great! So, does this seem reasonable for Intersection of multiple >> > *step.Vector >> > >> > https://gist.github.com/brentp/4419f6711917096bce83e7eddb648c85 ? >> > >> > Or is there a more efficient (in LOC or CPU) way? >> > If this is generally close, then having a Vector.Clone() method >> > would >> > be convenient. >> > >> > thanks, >> > -Brent >> > >> > On Sat, Feb 11, 2017 at 9:18 PM, Dan Kortschak >> > wrote: >> > > >> > > Ahh, OK. biogo/store/step will do that for you. >> > > >> > > On Sat, 2017-02-11 at 21:11 -0700, Brent Pedersen wrote: >> > > > >> > > > I mean a set where e.g. I can union (1, 9) and (7, 14) and it >> > > > will >> > > > give (1, 14) and then I can subtract (5, 8) and get (1, 5), (9, >> > > > 14)

[Brent Pedersen]

Agreed.
I made the change.