[Biojava-l] Re: changed (improved) SequenceDB ...
Aaron Kitzmiller
AKitzmiller@genetics.com
Thu, 29 Jun 2000 13:14:03 -0400
Couple of things regarding this thread...
1. I ring in on the side that is against frequent changes to interfaces. We still haven't made the switch to SymbolList from ResidueList, simply because we have stretched resources.
2. Our experience with home-grown persistence wrappers has been very good. Our Broker classes combine the functionality of SequenceFactory and SequenceDB into a single persistence manager that encapsulates the persistence method (SQL in our case) which often has impact on both query and construction.
"Where's the code?" you might ask. As I mentioned, we're a little bit stretched at this point, but after a few name changes and other tweaks, I can at least send out the interfaces for review.
Aaron K.
Message: 1
Date: Thu, 29 Jun 2000 12:01:12 +0200
From: Gerald Loeffler <Gerald.Loeffler@vienna.at>
Reply-To: Gerald.Loeffler@vienna.at
To: biojava-l@biojava.org
boundary="------------667865E7FE51C44C7E5DB4AA"
Subject: [Biojava-l] changed (improved) SequenceDB and stuff
This is a multi-part message in MIME format.
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hi matthew!
I made the following slight changes to SequenceDB and related classes
and hope that you find them acceptable and hence check them into your
CVS repository:
o org.biojava.bio.seq.SequenceDB:
o added getName() method which returns the (possibly null) name of a
sequence db
o org.biojava.bio.seq.HashSequenceDB:
o HashSequenceDB() and HashSequenceDB(IDMaker idMaker) create a
SequenceDB with name null.
o added public constructor HashSequenceDB(IDMaker idMaker, String name)
o added protected constructor HashSequenceDB(String name)
o implemented getName() method
o org.biojava.bio.seq.AbstractAnnotator:
o changed (the now ambiguous) instantiation of a HashSequenceDB from
HashSequenceDB(null) to HashSequenceDB(null, null).
o org.acedb.seq.AceSequenceDB:
o implemented getName() to return the name of the node
(AceSet.getName()).
o org.biojava.bridge.Biocorba.Seqcore.SequenceDBAdapter:
o implemented getName() to return the name of the primary corba
sequence db (PrimarySeqDB.database_name()).
The changed files are attached to this mail.
Though minor in nature, the addition of the getName() method to
interface SequenceDB will result in all implementations (outside the
BioJava distribution) of this interface to break in the sense that they
will all have to add an implementation of the getName() method...
cheers,
gerald
--
Gerald.Loeffler@vienna.at _________________ Software Architect
http://www.imp.univie.ac.at ____ http://www.daemonstration.com
OOA&D, Java, J2EE, JSP, Servlets, JavaBeans, ODBMS, RDBMS, XML
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--__--__--
Message: 2
Date: Thu, 29 Jun 2000 15:07:29 +0100
From: Matthew Pocock <mrp@sanger.ac.uk>
Organization: The Sanger Center
To: Gerald.Loeffler@vienna.at
CC: biojava-l@biojava.org
Subject: Re: [Biojava-l] changed (improved) SequenceDB and stuff
Thanks Gerald.
I have merge these changes in to CVS now. In retrospect, naming seqDBs is probably a
good thing. The only tweaks I made were:
a) HashSequenceDB now has a range of constructors, including a no-args variant
b) HashSequenceDB is now Serializable
c) org.biojava.bridge.Bioorba.Seqcore - PrimarySeqDBImpl & SeqDBImpl now use the propper
getName semantics, rather than magicing names from thin air.
d) updated the demos to work (the two corba servers)
Let me know if you are interested in read/write CVS access.
Great work
Matthew
Gerald Loeffler wrote:
> I made the following slight changes to SequenceDB and related classes
> and hope that you find them acceptable and hence check them into your
> CVS repository:
>
> o org.biojava.bio.seq.SequenceDB:
> o added getName() method which returns the (possibly null) name of a
> sequence db
>
</snip>
> Though minor in nature, the addition of the getName() method to
> interface SequenceDB will result in all implementations (outside the
> BioJava distribution) of this interface to break in the sense that they
> will all have to add an implementation of the getName() method...
>
> cheers,
> gerald
> --
> Gerald.Loeffler@vienna.at _________________ Software Architect
> http://www.imp.univie.ac.at ____ http://www.daemonstration.com
> OOA&D, Java, J2EE, JSP, Servlets, JavaBeans, ODBMS, RDBMS, XML
--__--__--
Message: 3
From: hilmar.lapp@pharma.Novartis.com
To: Matthew Pocock <mrp@sanger.ac.uk>, Gerald.Loeffler@vienna.at
cc: biojava-l@biojava.org
Date: Thu, 29 Jun 2000 16:34:53 +0100
Subject: Re: [Biojava-l] changed (improved) SequenceDB and stuff
> Though minor in nature, the addition of the getName() method to
> interface SequenceDB will result in all implementations (outside the
> BioJava distribution) of this interface to break in the sense that they
> will all have to add an implementation of the getName() method...
>
Yes indeed, and it does break for instance a lot of my code.
A comment from a practical point of view, and from someone working in an
industrial environment where it does really matter whether or not software
deliberately breaks once you upgrade your (class-)libraries, and the person
who coded it is currently not available. To this end, OO adds a significant
improvement, because essentially you DO NOT have to fiddle around in
library code, but instead you can derive your own things if you're
unsatisfied with what the library offers. Of course, that's theory, and
practice is different, but still, I think it's not a bad idea to at least
aim at it.
To make a long story short, what I wanted to suggest is, why not have an
interface NamedSequenceDB which inherits from SequenceDB, and everyone is
fine to have his SequenceDB implementation be a named one. There are a lot
of cases where you simply don't need a name, and the fact that it hasn't
been there until now at least doesn't disprove this.
What do you think?
Hilmar
--__--__--
Message: 4
Date: Thu, 29 Jun 2000 17:09:29 +0200
From: Gerald Loeffler <Gerald.Loeffler@vienna.at>
Reply-To: Gerald.Loeffler@vienna.at
To: hilmar.lapp@pharma.Novartis.com
CC: Matthew Pocock <mrp@sanger.ac.uk>, biojava-l@biojava.org
Subject: Re: [Biojava-l] changed (improved) SequenceDB and stuff
hilmar.lapp@pharma.Novartis.com wrote:
>
> > Though minor in nature, the addition of the getName() method to
> > interface SequenceDB will result in all implementations (outside the
> > BioJava distribution) of this interface to break in the sense that they
> > will all have to add an implementation of the getName() method...
> >
...
> To make a long story short, what I wanted to suggest is, why not have an
> interface NamedSequenceDB which inherits from SequenceDB, and everyone is
> fine to have his SequenceDB implementation be a named one. There are a lot
> of cases where you simply don't need a name, and the fact that it hasn't
> been there until now at least doesn't disprove this.
you're absolutely right - i thought about doing exactly this (even using
the same interface name) but dismissed it because i guessed (wrongly, it
seems) that directly implementing SequenceDB (as opposed to using one of
the supplied concrete implementations of SequenceDB) would not be too
common (although i'm doing this right now (-:).
Anyways, as much as i'd hate to see an incompatible change like this
happen in (lets say) one of the java.* packages, i'm not sure whether we
should be so strict about BioJava. Absolutely prohibiting incompatible
changes in BioJava is probably a bit premature because it hinders what
is still a bit of a work-in-progress (definitely no offence intended,
Matthew!).
A possible way to manage change to the BioJava API could be to introduce
versioning and restrict incomptible changes to the (rare) increases in
the major version number. The symbol/seq-part of BioJava could be
designated 1.0 right now, and future incompatible changes (like the
ambiguity change or this db-naming change) may only occur in one go when
moving to 2.0....
cheers,
gerald
>
> What do you think?
>
> Hilmar
--
Gerald.Loeffler@vienna.at _________________ Software Architect
http://www.imp.univie.ac.at ____ http://www.daemonstration.com
OOA&D, Java, J2EE, JSP, Servlets, JavaBeans, ODBMS, RDBMS, XML
--__--__--
Message: 5
Date: Thu, 29 Jun 2000 11:24:37 -0400 (EDT)
From: Jason Stajich <jason@chg.mc.duke.edu>
To: BioJava List <biojava-l@biojava.org>
cc: mrp@sanger.ac.uk
Subject: Re: [Biojava-l] changed (improved) SequenceDB and stuff
On Thu, 29 Jun 2000, Gerald Loeffler wrote:
> hilmar.lapp@pharma.Novartis.com wrote:
> >
> > > Though minor in nature, the addition of the getName() method to
> > > interface SequenceDB will result in all implementations (outside the
> > > BioJava distribution) of this interface to break in the sense that they
> > > will all have to add an implementation of the getName() method...
> > >
> ...
> > To make a long story short, what I wanted to suggest is, why not have an
> > interface NamedSequenceDB which inherits from SequenceDB, and everyone is
> > fine to have his SequenceDB implementation be a named one. There are a lot
> > of cases where you simply don't need a name, and the fact that it hasn't
> > been there until now at least doesn't disprove this.
>
> you're absolutely right - i thought about doing exactly this (even using
> the same interface name) but dismissed it because i guessed (wrongly, it
> seems) that directly implementing SequenceDB (as opposed to using one of
> the supplied concrete implementations of SequenceDB) would not be too
> common (although i'm doing this right now (-:).
>
> Anyways, as much as i'd hate to see an incompatible change like this
> happen in (lets say) one of the java.* packages, i'm not sure whether we
> should be so strict about BioJava. Absolutely prohibiting incompatible
> changes in BioJava is probably a bit premature because it hinders what
> is still a bit of a work-in-progress (definitely no offence intended,
> Matthew!).
While you're thinking about SequenceDBs - I'm working on a methodology
from the bioperl end to manage a MutableSeqDB - I want to be able to add /
update/ delete sequences from a 'real' database. This is going to require
a transactional db on the back end and/or careful code, but we a looking
to see if we can do it with the ensembl project's db first. This
would ideally something that would make its way into the biocorba idl as
well as implemented in the bio* project's code. More details to come as I
finalize the design proposal.
> A possible way to manage change to the BioJava API could be to introduce
> versioning and restrict incomptible changes to the (rare) increases in
> the major version number. The symbol/seq-part of BioJava could be
> designated 1.0 right now, and future incompatible changes (like the
> ambiguity change or this db-naming change) may only occur in one go when
moving to 2.0....
>
> cheers,
> gerald
>
> >
> > What do you think?
> >
> > Hilmar
>
> --
> Gerald.Loeffler@vienna.at _________________ Software Architect
> http://www.imp.univie.ac.at ____ http://www.daemonstration.com
> OOA&D, Java, J2EE, JSP, Servlets, JavaBeans, ODBMS, RDBMS, XML
> _______________________________________________
> Biojava-l mailing list - Biojava-l@biojava.org
> http://biojava.org/mailman/listinfo/biojava-l
>
Jason Stajich
Center for Human Genetics
Duke University Medical Center
jason@chg.mc.duke.edu
(919)684-1806 (office)
(919)684-2275 (fax)
http://wwwchg.mc.duke.edu/
--__--__--
Message: 6
Date: Thu, 29 Jun 2000 17:58:33 +0200
From: Gerald Loeffler <Gerald.Loeffler@vienna.at>
Reply-To: Gerald.Loeffler@vienna.at
To: Jason Stajich <jason@chg.mc.duke.edu>, Biojava-l@biojava.org
Subject: Re: [Biojava-l] changed (improved) SequenceDB and stuff
Jason Stajich wrote:
> While you're thinking about SequenceDBs - I'm working on a methodology
> from the bioperl end to manage a MutableSeqDB - I want to be able to add /
> update/ delete sequences from a 'real' database. This is going to require
> a transactional db on the back end and/or careful code, but we a looking
> to see if we can do it with the ensembl project's db first. This
> would ideally something that would make its way into the biocorba idl as
> well as implemented in the bio* project's code. More details to come as I
> finalize the design proposal.
sounds very interesting!
I'm currently thinking/working on an implementation of SequenceDB whose
getSequence() method goes (via JDBC) into a relational database, fetches
data associated with the requested sequence and instantiates a Sequence
object. The object of the SequenceDB-sub-class does not know anything
about the database content, it just passes on the request for a sequence
to the relational DB. Should be similary to what you are planning except
that mine is strictly read-only while yours is read/write/update.
Seems that the MutableSeqDB you mention should be a sub-interface of
SequenceDB with replaceSequence() and addSequence() methods...
good luck,
gerald
>
> > A possible way to manage change to the BioJava API could be to introduce
> > versioning and restrict incomptible changes to the (rare) increases in
> > the major version number. The symbol/seq-part of BioJava could be
> > designated 1.0 right now, and future incompatible changes (like the
> > ambiguity change or this db-naming change) may only occur in one go when
> moving to 2.0....
> >
> > cheers,
> > gerald
> >
> > >
> > > What do you think?
> > >
> > > Hilmar
> >
> > --
> > Gerald.Loeffler@vienna.at _________________ Software Architect
> > http://www.imp.univie.ac.at ____ http://www.daemonstration.com
> > OOA&D, Java, J2EE, JSP, Servlets, JavaBeans, ODBMS, RDBMS, XML
> > _______________________________________________
> > Biojava-l mailing list - Biojava-l@biojava.org
> > http://biojava.org/mailman/listinfo/biojava-l
> >
>
> Jason Stajich
> Center for Human Genetics
> Duke University Medical Center
> jason@chg.mc.duke.edu
> (919)684-1806 (office)
> (919)684-2275 (fax)
> http://wwwchg.mc.duke.edu/
>
> _______________________________________________
> Biojava-l mailing list - Biojava-l@biojava.org
> http://biojava.org/mailman/listinfo/biojava-l
--
Gerald.Loeffler@vienna.at _________________ Software Architect
http://www.imp.univie.ac.at ____ http://www.daemonstration.com
OOA&D, Java, J2EE, JSP, Servlets, JavaBeans, ODBMS, RDBMS, XML
--__--__--
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Aaron Kitzmiller
Manager Systems Development -Cambridge
Bioinformatics Department
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Phone: (617) 665-6831
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Email: akitzmiller@genetics.com