[DAS2] Fwd: locations and writeback behavior

[Lincoln Stein]

---------- Forwarded message ----------
From: das2-owner at lists.open-bio.org <das2-owner at lists.open-bio.org>
Date: Aug 21, 2006 2:49 PM
Subject: Re: [DAS2] locations and writeback behavior
To: lincoln.stein at gmail.com

You are not allowed to post to this mailing list, and your message has
been automatically rejected.  If you think that your messages are
being rejected in error, contact the mailing list owner at
das2-owner at lists.open-bio.org.




---------- Forwarded message ----------
From: "Lincoln Stein" <lincoln.stein at gmail.com>
To: "Andrew Dalke" <dalke at dalkescientific.com>
Date: Mon, 21 Aug 2006 14:48:55 -0400
Subject: Re: [DAS2] locations and writeback behavior
I think that the server should accept the locations given for features
without checking that the children are contained within their parents'
coordinates. This is because there are genomic features that are
discontinuous.

Lincoln


On 8/19/06, Andrew Dalke <dalke at dalkescientific.com> wrote:
>
> Assume there is the requirement that parent node locations must
> cover children locations.  What does the server do on writeback
> for the following circumstances:
>
> Case #1. the parent feature has no locations
>
> Foo: -- no locations --
>    Bar: (10, 20)
>    Baz: (50, 60)
>
> Here are 6 possibilities:
>    1. reject the writeback
>    2. accept it and use an implicit location of (10, 60)
>         (implicit means the record is not modified and clients
>          downloading feature Foo will not get any locations for it
>          but the server will act as if it was present.)
>    3. accept it and use an implicit location of [(10, 20), (50, 60)]
>    4. accept it and insert the location (10, 60) (explict; clients
>          fetching feature Foo will see the server inserted locations)
>    5. accept it and explicitly insert the locations [(10, 20), (50, 60)]
>    6. accept it unchanged; range searches will always fail because
>        the root node has no locations
>
> Case #2. the parent feature has a location which does not overlap
>   all of the children
>
> Foo: (15, 85)
>    Bar: (10, 20)
>    Baz: (50, 60)
>
>
> Case #3: the parent has multiple locations; the parent's locations
>     overlap those of the children
>
> Foo: (10, 30), (40, 66), (543, 567)
>    Bar: (10, 20)
>    Baz: (50, 60)
>
>
> Case #4: the parent has a single location which is broader than
>    those of the children
>
> Foo: (10, 567)
>    Bar: (10, 20)
>    Baz: (50, 60)
>
>
> Case #5: the children contain multiple locations, the parent
>      covers them all
> Foo: (10, 100)
>    Bar: (10, 20), (22, 24)
>    Baz: (50, 60), (70, 80)
>
>
> The server already does some validation for cyclic detection.
> It can easily check for ranges as well.  As I understand things
> the answers should be:
>    Case #1: reject (parent must cover all children locations)
>    Case #2: reject (parent must cover all children locations)
>    Case #3: reject (parent can only have a single location per segment)
>    Case #4: accept, and use the broader range
>    Case #5: accept (leaves and leaves only may have multiple
>                        locations on the same segment)
>
> and the reasons for these answers are:
>    - it doesn't make sense to have location-less parents when
>        the children don't have locations
>    - it makes the search algorithm work correctly
>
>                                         Andrew
>                                         dalke at dalkescientific.com
>
> _______________________________________________
> DAS2 mailing list
> DAS2 at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/das2
>



--
Lincoln D. Stein
Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724
(516) 367-8380 (voice)
(516) 367-8389 (fax)
FOR URGENT MESSAGES & SCHEDULING,
PLEASE CONTACT MY ASSISTANT,
SANDRA MICHELSEN, AT michelse at cshl.edu




-- 
Lincoln D. Stein
Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724
(516) 367-8380 (voice)
(516) 367-8389 (fax)
FOR URGENT MESSAGES & SCHEDULING,
PLEASE CONTACT MY ASSISTANT,
SANDRA MICHELSEN, AT michelse at cshl.edu