pfaat-devel — Pfaat developers

[Pfaat-devel] RE: adding a standard sequence

[<Bar...@av...>]

Hi --

	I see that I can put the trans-membrane region and set of residue
positions information into already existing parts of the ruler data. The =
only
caveate for putting it there is that that info will be lost if the user =
needs
to temporarily mark those columns for other reasons and then wants them =
to be
redisplayed.=20

	I will take a look at putting the standard sequence name in a new
variable in the ruler.

Barry

>  -----Original Message-----
> From: 	Dancis, Barry PH/US/EXT =20
> Sent:	Monday, November 17, 2003 3:08 PM
> To:	Pfaat (E-mail)
> Subject:	adding a standard sequence
>=20
> Hi --
>=20
> 	I would like to have a sequence identified as the standard. For
> prototyping purposes, I hardwired the name of the sequence in class
> AlignmentFrame and created new classes, StandardSequence and
> Standardcomponent, handling the standard like a consensus display menu =
item
> but with a menu of its own. The standard gets displayed below the
> consensus.
>=20
> 	I would like to make the implementation more robust, storing the name
> of the standard in the pfam file and loading the name during the =
normal
> upload. I will also want to indicate the location of transmembrane =
regions
> (using a display similar to the bar graph for the consensus sequences) =
as
> well as calculations based on the relative distance from a set of =
given
> residues. Thus, the load process needs to be able to return data not
> currently in the alignment, namely
>=20
> Name of Standard Sequence
> Location of Regions for display as a bar graph
> Set of residue positions for use in calculations to appear in the =
Alignment
> info bar at the top
>=20
> 	The question then is how does this info get stored in the pfam file,
> returned to the caller of the load and afterwards, get provided by the
> caller of the alignmentsave.
>=20
> 	My inclination at the moment is a special standard class that
> contains position-specific information and that class would be stored =
in a
> private variable of the Alignment Class. By putting them all in the =
same
> class, it should nicely package that data and cause minimal changes to =
the
> Alignment Class.
>=20
> 	I am also thinking about displaying the standard sequence and the
> transmembrane regions above the ruler.
>=20
> 	Any thoughts?
>=20
> Thanks,
>=20
> Barry

[Pfaat-devel] adding a standard sequence

[<Bar...@av...>]

Hi --

	I would like to have a sequence identified as the standard. For
prototyping purposes, I hardwired the name of the sequence in class
AlignmentFrame and created new classes, StandardSequence and
Standardcomponent, handling the standard like a consensus display menu =
item
but with a menu of its own. The standard gets displayed below the =
consensus.

	I would like to make the implementation more robust, storing the name
of the standard in the pfam file and loading the name during the normal
upload. I will also want to indicate the location of transmembrane =
regions
(using a display similar to the bar graph for the consensus sequences) =
as
well as calculations based on the relative distance from a set of given
residues. Thus, the load process needs to be able to return data not
currently in the alignment, namely

Name of Standard Sequence
Location of Regions for display as a bar graph
Set of residue positions for use in calculations to appear in the =
Alignment
info bar at the top

	The question then is how does this info get stored in the pfam file,
returned to the caller of the load and afterwards, get provided by the =
caller
of the alignmentsave.

	My inclination at the moment is a special standard class that
contains position-specific information and that class would be stored in =
a
private variable of the Alignment Class. By putting them all in the same
class, it should nicely package that data and cause minimal changes to =
the
Alignment Class.

	I am also thinking about displaying the standard sequence and the
transmembrane regions above the ruler.

	Any thoughts?

Thanks,

Barry