From holland at ebi.ac.uk  Mon Oct  1 07:57:44 2007
From: holland at ebi.ac.uk (Richard Holland)
Date: Mon, 01 Oct 2007 12:57:44 +0100
Subject: [Biojava-dev] BioJava 3 Proposal
Message-ID: <4700E0B8.6010409@ebi.ac.uk>

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Hash: SHA1

I see it's all gone a bit quiet this last week or two!

Here is the current proposal as it stands:

http://biojava.org/wiki/BioJava3_Proposal

(There's also quite a bit of discussion on the topic on the associated
'discussion' page).

Please make comments directly to the wiki page. The more comments we
get, the more likely it is we will proceed with a development plan which
suits the majority of our users.

I plan to make a summary of this page public to biojava-l sometime in
November. This summary page would then be put through the same feedback
and discussion process, and would be open for anyone to comment
(including, most importantly, our users). The final plan would be based
on the outcome of these public discussions.

cheers,
Richard
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From markjschreiber at gmail.com  Tue Oct  2 07:59:15 2007
From: markjschreiber at gmail.com (Mark Schreiber)
Date: Tue, 2 Oct 2007 19:59:15 +0800
Subject: [Biojava-dev] BioJava 3 Proposal
In-Reply-To: <4700E0B8.6010409@ebi.ac.uk>
References: <4700E0B8.6010409@ebi.ac.uk>
Message-ID: <93b45ca50710020459j7110f5b6u82ca6394b826d41b@mail.gmail.com>

Hi -

There was some talk of making biojava3 aware of plugins and service
provider interfaces (SPI). It is therefore timely that Sun have
released an article on how this can easily be achieved now that the
ServiceLoader API has been exposed in JSE6

http://java.sun.com/developer/technicalArticles/javase/extensible/

- Mark

On 10/1/07, Richard Holland <holland at ebi.ac.uk> wrote:
> -----BEGIN PGP SIGNED MESSAGE-----
> Hash: SHA1
>
> I see it's all gone a bit quiet this last week or two!
>
> Here is the current proposal as it stands:
>
> http://biojava.org/wiki/BioJava3_Proposal
>
> (There's also quite a bit of discussion on the topic on the associated
> 'discussion' page).
>
> Please make comments directly to the wiki page. The more comments we
> get, the more likely it is we will proceed with a development plan which
> suits the majority of our users.
>
> I plan to make a summary of this page public to biojava-l sometime in
> November. This summary page would then be put through the same feedback
> and discussion process, and would be open for anyone to comment
> (including, most importantly, our users). The final plan would be based
> on the outcome of these public discussions.
>
> cheers,
> Richard
> -----BEGIN PGP SIGNATURE-----
> Version: GnuPG v1.4.2.2 (GNU/Linux)
> Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org
>
> iD8DBQFHAOC34C5LeMEKA/QRAqQzAJoDxrSbqBcxZQZayKIzx0k5NJguNwCeO+c4
> 58Id2MR4Ql1+Cd474YaneqE=
> =XO63
> -----END PGP SIGNATURE-----
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>

From ayates at ebi.ac.uk  Tue Oct  2 08:17:00 2007
From: ayates at ebi.ac.uk (Andy Yates)
Date: Tue, 02 Oct 2007 13:17:00 +0100
Subject: [Biojava-dev] BioJava 3 Proposal
In-Reply-To: <93b45ca50710020459j7110f5b6u82ca6394b826d41b@mail.gmail.com>
References: <4700E0B8.6010409@ebi.ac.uk>
	<93b45ca50710020459j7110f5b6u82ca6394b826d41b@mail.gmail.com>
Message-ID: <470236BC.6030500@ebi.ac.uk>

This is quite a cool little feature really. Gets over that inital 
problem of how do you specify multiple implementations of something at 
runtime (something I've just done but this seems like a far better fit). 
Anyway looks good will report back on how easy it is to do & how well it 
works :)

Andy

Mark Schreiber wrote:
> Hi -
> 
> There was some talk of making biojava3 aware of plugins and service
> provider interfaces (SPI). It is therefore timely that Sun have
> released an article on how this can easily be achieved now that the
> ServiceLoader API has been exposed in JSE6
> 
> http://java.sun.com/developer/technicalArticles/javase/extensible/
> 
> - Mark
> 
> On 10/1/07, Richard Holland <holland at ebi.ac.uk> wrote:
>> -----BEGIN PGP SIGNED MESSAGE-----
>> Hash: SHA1
>>
>> I see it's all gone a bit quiet this last week or two!
>>
>> Here is the current proposal as it stands:
>>
>> http://biojava.org/wiki/BioJava3_Proposal
>>
>> (There's also quite a bit of discussion on the topic on the associated
>> 'discussion' page).
>>
>> Please make comments directly to the wiki page. The more comments we
>> get, the more likely it is we will proceed with a development plan which
>> suits the majority of our users.
>>
>> I plan to make a summary of this page public to biojava-l sometime in
>> November. This summary page would then be put through the same feedback
>> and discussion process, and would be open for anyone to comment
>> (including, most importantly, our users). The final plan would be based
>> on the outcome of these public discussions.
>>
>> cheers,
>> Richard
>> -----BEGIN PGP SIGNATURE-----
>> Version: GnuPG v1.4.2.2 (GNU/Linux)
>> Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org
>>
>> iD8DBQFHAOC34C5LeMEKA/QRAqQzAJoDxrSbqBcxZQZayKIzx0k5NJguNwCeO+c4
>> 58Id2MR4Ql1+Cd474YaneqE=
>> =XO63
>> -----END PGP SIGNATURE-----
>> _______________________________________________
>> biojava-dev mailing list
>> biojava-dev at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>>
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev

From holland at ebi.ac.uk  Wed Oct  3 03:42:50 2007
From: holland at ebi.ac.uk (Richard Holland)
Date: Wed, 03 Oct 2007 08:42:50 +0100
Subject: [Biojava-dev] BioJava 3 Proposal
In-Reply-To: <93b45ca50710020459j7110f5b6u82ca6394b826d41b@mail.gmail.com>
References: <4700E0B8.6010409@ebi.ac.uk>
	<93b45ca50710020459j7110f5b6u82ca6394b826d41b@mail.gmail.com>
Message-ID: <470347FA.2060201@ebi.ac.uk>

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

sounds good. could you add the link to the wiki?

Mark Schreiber wrote:
> Hi -
> 
> There was some talk of making biojava3 aware of plugins and service
> provider interfaces (SPI). It is therefore timely that Sun have
> released an article on how this can easily be achieved now that the
> ServiceLoader API has been exposed in JSE6
> 
> http://java.sun.com/developer/technicalArticles/javase/extensible/
> 
> - Mark
> 
> On 10/1/07, Richard Holland <holland at ebi.ac.uk> wrote:
> I see it's all gone a bit quiet this last week or two!
> 
> Here is the current proposal as it stands:
> 
> http://biojava.org/wiki/BioJava3_Proposal
> 
> (There's also quite a bit of discussion on the topic on the associated
> 'discussion' page).
> 
> Please make comments directly to the wiki page. The more comments we
> get, the more likely it is we will proceed with a development plan which
> suits the majority of our users.
> 
> I plan to make a summary of this page public to biojava-l sometime in
> November. This summary page would then be put through the same feedback
> and discussion process, and would be open for anyone to comment
> (including, most importantly, our users). The final plan would be based
> on the outcome of these public discussions.
> 
> cheers,
> Richard
_______________________________________________
biojava-dev mailing list
biojava-dev at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/biojava-dev
>>

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From gwaldon at geneinfinity.org  Fri Oct  5 13:24:34 2007
From: gwaldon at geneinfinity.org (george waldon)
Date: Fri, 05 Oct 2007 10:24:34 -0700
Subject: [Biojava-dev] BioJava 3 Proposal
Message-ID: <20071005172434.3365.qmail@mmm1924.dulles19-verio.com>

Would-it be helpful to implement SPI for manipulating sequence formats? 

For example, we could have:

RichSequenceFormat fasta = Lookup.getDefault().lookup(FastaFormat.class);

This would allow anyone to implement their own version of sequence format. The lookup would return the internal implementation by default or an external one is any is found.

- George


> -----Original Message-----
> From: biojava-dev-bounces at lists.open-bio.org [mailto:biojava-dev-
> bounces at lists.open-bio.org] On Behalf Of Mark Schreiber
> Sent: Tuesday, October 02, 2007 4:59 AM
> To: Richard Holland
> Cc: biojava-dev at biojava.org
> Subject: Re: [Biojava-dev] BioJava 3 Proposal
> 
> Hi -
> 
> There was some talk of making biojava3 aware of plugins and service
> provider interfaces (SPI). It is therefore timely that Sun have
> released an article on how this can easily be achieved now that the
> ServiceLoader API has been exposed in JSE6
> 
> http://java.sun.com/developer/technicalArticles/javase/extensible/
> 
> - Mark
> 
> On 10/1/07, Richard Holland <holland at ebi.ac.uk> wrote:
> > -----BEGIN PGP SIGNED MESSAGE-----
> > Hash: SHA1
> >
> > I see it's all gone a bit quiet this last week or two!
> >
> > Here is the current proposal as it stands:
> >
> > http://biojava.org/wiki/BioJava3_Proposal
> >
> > (There's also quite a bit of discussion on the topic on the associated
> > 'discussion' page).
> >
> > Please make comments directly to the wiki page. The more comments we
> > get, the more likely it is we will proceed with a development plan which
> > suits the majority of our users.
> >
> > I plan to make a summary of this page public to biojava-l sometime in
> > November. This summary page would then be put through the same feedback
> > and discussion process, and would be open for anyone to comment
> > (including, most importantly, our users). The final plan would be based
> > on the outcome of these public discussions.
> >
> > cheers,
> > Richard
> > -----BEGIN PGP SIGNATURE-----
> > Version: GnuPG v1.4.2.2 (GNU/Linux)
> > Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org
> >
> > iD8DBQFHAOC34C5LeMEKA/QRAqQzAJoDxrSbqBcxZQZayKIzx0k5NJguNwCeO+c4
> > 58Id2MR4Ql1+Cd474YaneqE=
> > =XO63
> > -----END PGP SIGNATURE-----
> > _______________________________________________
> > biojava-dev mailing list
> > biojava-dev at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/biojava-dev
> >
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev

From holland at ebi.ac.uk  Fri Oct  5 13:56:47 2007
From: holland at ebi.ac.uk (Richard Holland)
Date: Fri, 5 Oct 2007 18:56:47 +0100 (BST)
Subject: [Biojava-dev] BioJava 3 Proposal
In-Reply-To: <20071005172434.3365.qmail@mmm1924.dulles19-verio.com>
References: <20071005172434.3365.qmail@mmm1924.dulles19-verio.com>
Message-ID: <38114.80.42.44.56.1191607007.squirrel@webmail.ebi.ac.uk>

That sounds cool. Could you add your suggestion to the wiki?

cheers,
Richard

On Fri, October 5, 2007 6:24 pm, george waldon wrote:
> Would-it be helpful to implement SPI for manipulating sequence formats?
>
> For example, we could have:
>
> RichSequenceFormat fasta = Lookup.getDefault().lookup(FastaFormat.class);
>
> This would allow anyone to implement their own version of sequence format.
> The lookup would return the internal implementation by default or an
> external one is any is found.
>
> - George
>
>
>> -----Original Message-----
>> From: biojava-dev-bounces at lists.open-bio.org [mailto:biojava-dev-
>> bounces at lists.open-bio.org] On Behalf Of Mark Schreiber
>> Sent: Tuesday, October 02, 2007 4:59 AM
>> To: Richard Holland
>> Cc: biojava-dev at biojava.org
>> Subject: Re: [Biojava-dev] BioJava 3 Proposal
>>
>> Hi -
>>
>> There was some talk of making biojava3 aware of plugins and service
>> provider interfaces (SPI). It is therefore timely that Sun have
>> released an article on how this can easily be achieved now that the
>> ServiceLoader API has been exposed in JSE6
>>
>> http://java.sun.com/developer/technicalArticles/javase/extensible/
>>
>> - Mark
>>
>> On 10/1/07, Richard Holland <holland at ebi.ac.uk> wrote:
>> > -----BEGIN PGP SIGNED MESSAGE-----
>> > Hash: SHA1
>> >
>> > I see it's all gone a bit quiet this last week or two!
>> >
>> > Here is the current proposal as it stands:
>> >
>> > http://biojava.org/wiki/BioJava3_Proposal
>> >
>> > (There's also quite a bit of discussion on the topic on the associated
>> > 'discussion' page).
>> >
>> > Please make comments directly to the wiki page. The more comments we
>> > get, the more likely it is we will proceed with a development plan
>> which
>> > suits the majority of our users.
>> >
>> > I plan to make a summary of this page public to biojava-l sometime in
>> > November. This summary page would then be put through the same
>> feedback
>> > and discussion process, and would be open for anyone to comment
>> > (including, most importantly, our users). The final plan would be
>> based
>> > on the outcome of these public discussions.
>> >
>> > cheers,
>> > Richard
>> > -----BEGIN PGP SIGNATURE-----
>> > Version: GnuPG v1.4.2.2 (GNU/Linux)
>> > Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org
>> >
>> > iD8DBQFHAOC34C5LeMEKA/QRAqQzAJoDxrSbqBcxZQZayKIzx0k5NJguNwCeO+c4
>> > 58Id2MR4Ql1+Cd474YaneqE=
>> > =XO63
>> > -----END PGP SIGNATURE-----
>> > _______________________________________________
>> > biojava-dev mailing list
>> > biojava-dev at lists.open-bio.org
>> > http://lists.open-bio.org/mailman/listinfo/biojava-dev
>> >
>> _______________________________________________
>> biojava-dev mailing list
>> biojava-dev at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-dev
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>


-- 
Richard Holland
BioMart (http://www.biomart.org/)
EMBL-EBI
Hinxton, Cambridgeshire CB10 1SD, UK


From gwaldon at geneinfinity.org  Fri Oct  5 14:57:38 2007
From: gwaldon at geneinfinity.org (george waldon)
Date: Fri, 05 Oct 2007 11:57:38 -0700
Subject: [Biojava-dev] BioJava 3 Proposal
Message-ID: <20071005185738.76972.qmail@mmm1924.dulles19-verio.com>

I will.

Another thought. You could also have an SPI for lookup itself. LookupProviders could be declared in the manifest and provide dynamically all sorts of services at runtime. You could also have a way to register in the main lookup classes you don't want to show during the process, making possible to prevent conflicts (when several implementations are available and only one is desirable).

- George


> -----Original Message-----
> From: Richard Holland [mailto:holland at ebi.ac.uk]
> Sent: Friday, October 05, 2007 10:57 AM
> To: george waldon
> Cc: markjschreiber at gmail.com; biojava-dev at biojava.org
> Subject: Re: [Biojava-dev] BioJava 3 Proposal
> 
> That sounds cool. Could you add your suggestion to the wiki?
> 
> cheers,
> Richard
> 
> On Fri, October 5, 2007 6:24 pm, george waldon wrote:
> > Would-it be helpful to implement SPI for manipulating sequence formats?
> >
> > For example, we could have:
> >
> > RichSequenceFormat fasta =
> Lookup.getDefault().lookup(FastaFormat.class);
> >
> > This would allow anyone to implement their own version of sequence
> format.
> > The lookup would return the internal implementation by default or an
> > external one is any is found.
> >
> > - George
> >
> >
> >> -----Original Message-----
> >> From: biojava-dev-bounces at lists.open-bio.org [mailto:biojava-dev-
> >> bounces at lists.open-bio.org] On Behalf Of Mark Schreiber
> >> Sent: Tuesday, October 02, 2007 4:59 AM
> >> To: Richard Holland
> >> Cc: biojava-dev at biojava.org
> >> Subject: Re: [Biojava-dev] BioJava 3 Proposal
> >>
> >> Hi -
> >>
> >> There was some talk of making biojava3 aware of plugins and service
> >> provider interfaces (SPI). It is therefore timely that Sun have
> >> released an article on how this can easily be achieved now that the
> >> ServiceLoader API has been exposed in JSE6
> >>
> >> http://java.sun.com/developer/technicalArticles/javase/extensible/
> >>
> >> - Mark
> >>
> >> On 10/1/07, Richard Holland <holland at ebi.ac.uk> wrote:
> >> > -----BEGIN PGP SIGNED MESSAGE-----
> >> > Hash: SHA1
> >> >
> >> > I see it's all gone a bit quiet this last week or two!
> >> >
> >> > Here is the current proposal as it stands:
> >> >
> >> > http://biojava.org/wiki/BioJava3_Proposal
> >> >
> >> > (There's also quite a bit of discussion on the topic on the
> associated
> >> > 'discussion' page).
> >> >
> >> > Please make comments directly to the wiki page. The more comments we
> >> > get, the more likely it is we will proceed with a development plan
> >> which
> >> > suits the majority of our users.
> >> >
> >> > I plan to make a summary of this page public to biojava-l sometime in
> >> > November. This summary page would then be put through the same
> >> feedback
> >> > and discussion process, and would be open for anyone to comment
> >> > (including, most importantly, our users). The final plan would be
> >> based
> >> > on the outcome of these public discussions.
> >> >
> >> > cheers,
> >> > Richard
> >> > -----BEGIN PGP SIGNATURE-----
> >> > Version: GnuPG v1.4.2.2 (GNU/Linux)
> >> > Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org
> >> >
> >> > iD8DBQFHAOC34C5LeMEKA/QRAqQzAJoDxrSbqBcxZQZayKIzx0k5NJguNwCeO+c4
> >> > 58Id2MR4Ql1+Cd474YaneqE=
> >> > =XO63
> >> > -----END PGP SIGNATURE-----
> >> > _______________________________________________
> >> > biojava-dev mailing list
> >> > biojava-dev at lists.open-bio.org
> >> > http://lists.open-bio.org/mailman/listinfo/biojava-dev
> >> >
> >> _______________________________________________
> >> biojava-dev mailing list
> >> biojava-dev at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/biojava-dev
> > _______________________________________________
> > biojava-dev mailing list
> > biojava-dev at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/biojava-dev
> >
> 
> 
> --
> Richard Holland
> BioMart (http://www.biomart.org/)
> EMBL-EBI
> Hinxton, Cambridgeshire CB10 1SD, UK


From ayates at ebi.ac.uk  Mon Oct  8 04:05:26 2007
From: ayates at ebi.ac.uk (Andy Yates)
Date: Mon, 08 Oct 2007 09:05:26 +0100
Subject: [Biojava-dev] BioJava 3 Proposal
In-Reply-To: <20071005185738.76972.qmail@mmm1924.dulles19-verio.com>
References: <20071005185738.76972.qmail@mmm1924.dulles19-verio.com>
Message-ID: <4709E4C6.9020601@ebi.ac.uk>

It seems like this would be a good way of pushing out fixes/format 
changes to parsers in between official releases of the API. I just don't 
want to go down the route of "everything can be solved with this api" 
which I know I've been guilty of with other toolkits. Overall though the 
concept is sound :)

george waldon wrote:
> I will.
> 
> Another thought. You could also have an SPI for lookup itself. LookupProviders could be declared in the manifest and provide dynamically all sorts of services at runtime. You could also have a way to register in the main lookup classes you don't want to show during the process, making possible to prevent conflicts (when several implementations are available and only one is desirable).
> 
> - George
> 
> 
>> -----Original Message-----
>> From: Richard Holland [mailto:holland at ebi.ac.uk]
>> Sent: Friday, October 05, 2007 10:57 AM
>> To: george waldon
>> Cc: markjschreiber at gmail.com; biojava-dev at biojava.org
>> Subject: Re: [Biojava-dev] BioJava 3 Proposal
>>
>> That sounds cool. Could you add your suggestion to the wiki?
>>
>> cheers,
>> Richard
>>
>> On Fri, October 5, 2007 6:24 pm, george waldon wrote:
>>> Would-it be helpful to implement SPI for manipulating sequence formats?
>>>
>>> For example, we could have:
>>>
>>> RichSequenceFormat fasta =
>> Lookup.getDefault().lookup(FastaFormat.class);
>>> This would allow anyone to implement their own version of sequence
>> format.
>>> The lookup would return the internal implementation by default or an
>>> external one is any is found.
>>>
>>> - George
>>>
>>>
>>>> -----Original Message-----
>>>> From: biojava-dev-bounces at lists.open-bio.org [mailto:biojava-dev-
>>>> bounces at lists.open-bio.org] On Behalf Of Mark Schreiber
>>>> Sent: Tuesday, October 02, 2007 4:59 AM
>>>> To: Richard Holland
>>>> Cc: biojava-dev at biojava.org
>>>> Subject: Re: [Biojava-dev] BioJava 3 Proposal
>>>>
>>>> Hi -
>>>>
>>>> There was some talk of making biojava3 aware of plugins and service
>>>> provider interfaces (SPI). It is therefore timely that Sun have
>>>> released an article on how this can easily be achieved now that the
>>>> ServiceLoader API has been exposed in JSE6
>>>>
>>>> http://java.sun.com/developer/technicalArticles/javase/extensible/
>>>>
>>>> - Mark
>>>>
>>>> On 10/1/07, Richard Holland <holland at ebi.ac.uk> wrote:
>>>>> -----BEGIN PGP SIGNED MESSAGE-----
>>>>> Hash: SHA1
>>>>>
>>>>> I see it's all gone a bit quiet this last week or two!
>>>>>
>>>>> Here is the current proposal as it stands:
>>>>>
>>>>> http://biojava.org/wiki/BioJava3_Proposal
>>>>>
>>>>> (There's also quite a bit of discussion on the topic on the
>> associated
>>>>> 'discussion' page).
>>>>>
>>>>> Please make comments directly to the wiki page. The more comments we
>>>>> get, the more likely it is we will proceed with a development plan
>>>> which
>>>>> suits the majority of our users.
>>>>>
>>>>> I plan to make a summary of this page public to biojava-l sometime in
>>>>> November. This summary page would then be put through the same
>>>> feedback
>>>>> and discussion process, and would be open for anyone to comment
>>>>> (including, most importantly, our users). The final plan would be
>>>> based
>>>>> on the outcome of these public discussions.
>>>>>
>>>>> cheers,
>>>>> Richard
>>>>> -----BEGIN PGP SIGNATURE-----
>>>>> Version: GnuPG v1.4.2.2 (GNU/Linux)
>>>>> Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org
>>>>>
>>>>> iD8DBQFHAOC34C5LeMEKA/QRAqQzAJoDxrSbqBcxZQZayKIzx0k5NJguNwCeO+c4
>>>>> 58Id2MR4Ql1+Cd474YaneqE=
>>>>> =XO63
>>>>> -----END PGP SIGNATURE-----
>>>>> _______________________________________________
>>>>> biojava-dev mailing list
>>>>> biojava-dev at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>>>>>
>>>> _______________________________________________
>>>> biojava-dev mailing list
>>>> biojava-dev at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>>> _______________________________________________
>>> biojava-dev mailing list
>>> biojava-dev at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>>>
>>
>> --
>> Richard Holland
>> BioMart (http://www.biomart.org/)
>> EMBL-EBI
>> Hinxton, Cambridgeshire CB10 1SD, UK
> 
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev

From gwaldon at geneinfinity.org  Fri Oct 12 18:12:33 2007
From: gwaldon at geneinfinity.org (george waldon)
Date: Fri, 12 Oct 2007 15:12:33 -0700
Subject: [Biojava-dev] alternate tokenization
Message-ID: <20071012221233.68667.qmail@mmm1924.dulles19-verio.com>

Hello,

I would like to add alternate tokenizations in AlphabetManager.xml for the DNA alphabet and the PROTEIN-TERM alphabet. 

These tokenizations will be used for stringifying DNA sequences in capital letters, like in "ATCG", and proteins with a mix of capital and small letters, like in "SerGluPro".

Comments welcome,
George


From holland at ebi.ac.uk  Fri Oct 12 18:21:59 2007
From: holland at ebi.ac.uk (Richard Holland)
Date: Fri, 12 Oct 2007 23:21:59 +0100 (BST)
Subject: [Biojava-dev] alternate tokenization
In-Reply-To: <20071012221233.68667.qmail@mmm1924.dulles19-verio.com>
References: <20071012221233.68667.qmail@mmm1924.dulles19-verio.com>
Message-ID: <49886.80.42.44.56.1192227719.squirrel@webmail.ebi.ac.uk>

interesting idea. we kind of have this already but not really - the stuff
is all there but not wired up right.

best to add it to the wiki so we don't forget to finish the wiring. :)

cheers,
Richard

On Fri, October 12, 2007 11:12 pm, george waldon wrote:
> Hello,
>
> I would like to add alternate tokenizations in AlphabetManager.xml for the
> DNA alphabet and the PROTEIN-TERM alphabet.
>
> These tokenizations will be used for stringifying DNA sequences in capital
> letters, like in "ATCG", and proteins with a mix of capital and small
> letters, like in "SerGluPro".
>
> Comments welcome,
> George
>
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>


-- 
Richard Holland
BioMart (http://www.biomart.org/)
EMBL-EBI
Hinxton, Cambridgeshire CB10 1SD, UK


From prashantha.karunakar at gmail.com  Fri Oct  5 03:01:13 2007
From: prashantha.karunakar at gmail.com (prashantha bhat)
Date: Fri, 05 Oct 2007 07:01:13 -0000
Subject: [Biojava-dev] Biojava download for windows XP
Message-ID: <c115ce3f0710050001g2ad8644eg976033fe8b62c22b@mail.gmail.com>

Sir,
I am prashantha from Indgen life technologies,
we are planning to teach Biojava to the students of bioinformatics on
windows XP platform,
we are unable to download the Biojava software,
Please do cooperate in this isseu,
yours obediently,
prashantha

From steffen_moeller at gmx.de  Tue Oct  9 06:43:48 2007
From: steffen_moeller at gmx.de (Steffen Moeller)
Date: Tue, 09 Oct 2007 10:43:48 -0000
Subject: [Biojava-dev] LGPL information forgotten at
	BlastLikeDataSetCollection.dtd ?
Message-ID: <200710091221.13033.steffen_moeller@gmx.de>

Dear all,

I prepared a Debian package for biojava but a distribution with the main 
distribution was rejected because of missing copyright information here

	dtd/BlastLikeDataSetCollection.dtd
	(which just says 'all rights reserved')

and almost everywhere else

~/biojava-1.5$ grep -r LGPL src | wc -l
25
~/biojava-1.5$ find src -name "*.java" | wc -l
1342

Please consider to have the copyright information added to your sources. 

I am a bit uncertain about how to treat non-source files. In principle, a 
<!-- copyright statement as a comment --> would be required for these files, 
too. However, it should be acceptable to distribute them as they are, 
applying the copyright file that is distributed with the source, as long as 
no indication is given (as for dtd/BlastLikeDataSetCollection.dtd) that a 
redistribution would not be appreciated.

~/biojava-1.5$ grep -ri "all rights reserved" src | wc -l
41
~/biojava-1.5$ grep -ri "all rights reserved" . | wc -l
48

If there are files for which you cannot decide the license easily but that may 
not be required for an almost functional Debian package, then I would be 
prepared to remove those files from the package...hoping that it is not too 
many.

Many thanks for your help ... and for BioJava in the first place

Steffen

From holland at ebi.ac.uk  Wed Oct 24 05:56:13 2007
From: holland at ebi.ac.uk (Richard Holland)
Date: Wed, 24 Oct 2007 10:56:13 +0100
Subject: [Biojava-dev] [Fwd:  BioJava 3 Proposal]
Message-ID: <471F16BD.2040501@ebi.ac.uk>

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

Hi all. I'm planning on opening this wiki page to the general public
(ie. biojava-l) on Monday next week (Oct 29th). The email that will
accompany the public announcement is shown below.

If you'd like to review it and add any further comments or suggestions
before everyone else gets to see it, please make those changes before
this coming weekend is over!

The page will be made visible as-is, and will be left open for public
comment until January when I will distribute a summary of its contents
and start work on a plan of action.

cheers,
Richard

Here is the email that will be sent out on Monday:

- ----
Dear BioJava users,

The BioJava developers are considering options for the future
development of the BioJava toolkit. We consider that it needs
improvement in a few major areas to make it easier to use and
understand, and also faster and more scalable.

The options are to either rewrite large parts of the existing code,
working within the existing interfaces and paradigms, or to develop a
new set of BioJava packages from the ground up in order to take
advantage of lessons learned from the design patterns of the existing code.

The BioJava developers have spent the last couple of months discussing
ideas and proposals related to these options on a Wiki page, and would
now like to open this discussion to all users of BioJava and the
bioinformatics community in general. We would like to invite anyone who
has any ideas or suggestions to contribute these to the Wiki page,
and/or to comment on the ideas and suggestions that have already been
posted there.

Here is a link to the Wiki page, and also a link to the associated Talk
page where much of the discussion has taken place so far:

	http://biojava.org/wiki/BioJava3_Proposal
	http://biojava.org/wiki/Talk:BioJava3_Proposal

It is our intention to leave the discussion open until early January
2008 when we will summarise it and use it as the basis of a plan of
action. We will then distribute the summary and the action plan via the
BioJava website.

We look forward to hearing your comments and ideas. Please do remember
to make them directly to the Wiki page so that they are preserved in
context, making it easier for us to summarise them later!

cheers,
Richard
(on behalf of all BioJava developers)
- ----

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-------------- next part --------------
An embedded message was scrubbed...
From: Richard Holland <holland at ebi.ac.uk>
Subject: [Biojava-dev] BioJava 3 Proposal
Date: Mon, 01 Oct 2007 12:57:44 +0100
Size: 4031
Url: http://lists.open-bio.org/pipermail/biojava-dev/attachments/20071024/968e425a/attachment-0001.mht 

From holland at ebi.ac.uk  Wed Oct 31 10:51:51 2007
From: holland at ebi.ac.uk (Richard Holland)
Date: Wed, 31 Oct 2007 14:51:51 +0000
Subject: [Biojava-dev] Biojava download for windows XP
In-Reply-To: <c115ce3f0710050001g2ad8644eg976033fe8b62c22b@mail.gmail.com>
References: <c115ce3f0710050001g2ad8644eg976033fe8b62c22b@mail.gmail.com>
Message-ID: <47289687.2070109@ebi.ac.uk>

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

BioJava can be downloaded from this page:

http://biojava.org/wiki/BioJava:Download

If you are getting errors, please let us know what they are so that we
can try to fix them.

cheers,
Richard


prashantha bhat wrote:
> Sir,
> I am prashantha from Indgen life technologies,
> we are planning to teach Biojava to the students of bioinformatics on
> windows XP platform,
> we are unable to download the Biojava software,
> Please do cooperate in this isseu,
> yours obediently,
> prashantha
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
> 
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Version: GnuPG v1.4.2.2 (GNU/Linux)
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=6M0C
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From markjschreiber at gmail.com  Wed Oct 31 10:55:44 2007
From: markjschreiber at gmail.com (Mark Schreiber)
Date: Wed, 31 Oct 2007 22:55:44 +0800
Subject: [Biojava-dev] help (F1 F1) regarding biojava
In-Reply-To: <5c85b5bb0709270005m366227acx65ca6151e870ce79@mail.gmail.com>
References: <5c85b5bb0709270005m366227acx65ca6151e870ce79@mail.gmail.com>
Message-ID: <93b45ca50710310755n1826b1b7waa3506ec148bf5ea@mail.gmail.com>

Hi -

It's a little hard to see what you are trying to do but one likely error is
using FastaFormat to read something from NCBI or GenBank which is most
likely in Genbank format.

I would also strongly recommend using the equivalent classes from the
org.biojavax packages as many of the classes you are using are not actively
supported any more.

- Mark

On 9/27/07, pranav waila <pranav.waila at gmail.com> wrote:
>
> package org.biojava.bio.seq.db;
>
> import org.biojava.bio.seq.*;
> import org.biojava.bio.seq.io.*;
> import org.biojava.bio.*;
> import org.biojava.bio.seq.db.*;
> import org.biojava.bio.seq.io.*;
> import java.net.*;
> class test{
>     public static SequenceFormat sf;
>
>     public static void main(String args[]){
>
>         System.getProperties().put("proxySet","true");
>
>         System.getProperties().put("proxyPort","3128");
>         System.getProperties().put("proxyHost","172.16.0.6");
>
>         Sequence s;
>         sf=new FastaFormat();
>         //sf=new GenbankXmlFormat();
>                 NCBISequenceDB ncbi = new NCBISequenceDB(
> NCBISequenceDB.DB_PROTEIN,sf);//new FastaFormat());
> //        GenbankSequenceDB gdb=new GenbankSequenceDB();
>         //ncbi.setSequenceFormat(FASTA);
>     try{
>
>
>
> //        Sequence sequenceFromGenbank = ncbi.getSequence("P10659");
> //        System.out.println(sequenceFromGenbank.getName());
>
> // older code
>         s=ncbi.getSequence("P10659");
>
>         //s=gdb.getAddress();//getSequence("P10659");//3789789");
>         System.out.print("check");
>         System.out.println(ncbi.getSequence("190786"));
>
> //
>     }
>     catch(Exception e){
>         e.printStackTrace();
>         //System.out.println("protien name is : zinteminia");
>     }
>
>     }
> }
>
>
> This is my code for fetching the sequence from NCBI but it is giving
> somany
> exceptions. can u provide me some code to do so..
>
> the errors are as follows :
>
> Bio java exception could not read sequence
>
> CAN U PLEASE HELP ME.
>
> waiting for reply
>
> PRANAV WAILA
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>

From markjschreiber at gmail.com  Wed Oct 31 10:57:59 2007
From: markjschreiber at gmail.com (Mark Schreiber)
Date: Wed, 31 Oct 2007 22:57:59 +0800
Subject: [Biojava-dev] LGPL information forgotten at
	BlastLikeDataSetCollection.dtd ?
In-Reply-To: <200710091221.13033.steffen_moeller@gmx.de>
References: <200710091221.13033.steffen_moeller@gmx.de>
Message-ID: <93b45ca50710310757x5d3774f5n11a653b664c14e70@mail.gmail.com>

Hi -

Everything in Java should be LGPL. The only exceptions are jar files that
come from Apache and Jakarta projects (some of which may also be LGPL)

- Mark

On 10/9/07, Steffen Moeller <steffen_moeller at gmx.de> wrote:
>
> Dear all,
>
> I prepared a Debian package for biojava but a distribution with the main
> distribution was rejected because of missing copyright information here
>
>         dtd/BlastLikeDataSetCollection.dtd
>         (which just says 'all rights reserved')
>
> and almost everywhere else
>
> ~/biojava-1.5$ grep -r LGPL src | wc -l
> 25
> ~/biojava-1.5$ find src -name "*.java" | wc -l
> 1342
>
> Please consider to have the copyright information added to your sources.
>
> I am a bit uncertain about how to treat non-source files. In principle, a
> <!-- copyright statement as a comment --> would be required for these
> files,
> too. However, it should be acceptable to distribute them as they are,
> applying the copyright file that is distributed with the source, as long
> as
> no indication is given (as for dtd/BlastLikeDataSetCollection.dtd) that a
> redistribution would not be appreciated.
>
> ~/biojava-1.5$ grep -ri "all rights reserved" src | wc -l
> 41
> ~/biojava-1.5$ grep -ri "all rights reserved" . | wc -l
> 48
>
> If there are files for which you cannot decide the license easily but that
> may
> not be required for an almost functional Debian package, then I would be
> prepared to remove those files from the package...hoping that it is not
> too
> many.
>
> Many thanks for your help ... and for BioJava in the first place
>
> Steffen
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>

From markjschreiber at gmail.com  Wed Oct 31 10:58:27 2007
From: markjschreiber at gmail.com (Mark Schreiber)
Date: Wed, 31 Oct 2007 22:58:27 +0800
Subject: [Biojava-dev] LGPL information forgotten at
	BlastLikeDataSetCollection.dtd ?
In-Reply-To: <93b45ca50710310757x5d3774f5n11a653b664c14e70@mail.gmail.com>
References: <200710091221.13033.steffen_moeller@gmx.de>
	<93b45ca50710310757x5d3774f5n11a653b664c14e70@mail.gmail.com>
Message-ID: <93b45ca50710310758t72615e79p5c7e03b734e31277@mail.gmail.com>

Sorry, I mean everything in biojava (not java)

On 10/31/07, Mark Schreiber <markjschreiber at gmail.com> wrote:
>
> Hi -
>
> Everything in Java should be LGPL. The only exceptions are jar files that
> come from Apache and Jakarta projects (some of which may also be LGPL)
>
> - Mark
>
> On 10/9/07, Steffen Moeller <steffen_moeller at gmx.de> wrote:
> >
> > Dear all,
> >
> > I prepared a Debian package for biojava but a distribution with the main
> > distribution was rejected because of missing copyright information here
> >
> >         dtd/BlastLikeDataSetCollection.dtd
> >         (which just says 'all rights reserved')
> >
> > and almost everywhere else
> >
> > ~/biojava-1.5$ grep -r LGPL src | wc -l
> > 25
> > ~/biojava-1.5$ find src -name "*.java" | wc -l
> > 1342
> >
> > Please consider to have the copyright information added to your sources.
> >
> >
> > I am a bit uncertain about how to treat non-source files. In principle,
> > a
> > <!-- copyright statement as a comment --> would be required for these
> > files,
> > too. However, it should be acceptable to distribute them as they are,
> > applying the copyright file that is distributed with the source, as long
> > as
> > no indication is given (as for dtd/BlastLikeDataSetCollection.dtd) that
> > a
> > redistribution would not be appreciated.
> >
> > ~/biojava-1.5$ grep -ri "all rights reserved" src | wc -l
> > 41
> > ~/biojava-1.5$ grep -ri "all rights reserved" . | wc -l
> > 48
> >
> > If there are files for which you cannot decide the license easily but
> > that may
> > not be required for an almost functional Debian package, then I would be
> > prepared to remove those files from the package...hoping that it is not
> > too
> > many.
> >
> > Many thanks for your help ... and for BioJava in the first place
> >
> > Steffen
> > _______________________________________________
> > biojava-dev mailing list
> > biojava-dev at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/biojava-dev
> >
>
>

From holland at ebi.ac.uk  Wed Oct 31 10:58:20 2007
From: holland at ebi.ac.uk (Richard Holland)
Date: Wed, 31 Oct 2007 14:58:20 +0000
Subject: [Biojava-dev] LGPL information forgotten
 at	BlastLikeDataSetCollection.dtd ?
In-Reply-To: <200710091221.13033.steffen_moeller@gmx.de>
References: <200710091221.13033.steffen_moeller@gmx.de>
Message-ID: <4728980C.90307@ebi.ac.uk>

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

We've worked on the policy to date that the copyright notice file
included with the distribution applies to all files in that distribution.

If someone has the time to go through and apply the notices to all the
files, we'd greatly appreciate it, but right now I'm a bit busy with my
'real job' and can't do it myself.

The BlastLikeDataSetCollection DTD was created in 2000 by Simon
Brocklehurst, who describes it here:

http://portal.open-bio.org/pipermail/biojava-l/2000-August/000446.html

It might be an idea for you to contact him directly to see if he has any
problems with us changing it to LGPL.

Thanks for making the Debian package - I think it'll be really useful to
get it out to a wider audience.

cheers,
Richard

Steffen Moeller wrote:
> Dear all,
> 
> I prepared a Debian package for biojava but a distribution with the main 
> distribution was rejected because of missing copyright information here
> 
> 	dtd/BlastLikeDataSetCollection.dtd
> 	(which just says 'all rights reserved')
> 
> and almost everywhere else
> 
> ~/biojava-1.5$ grep -r LGPL src | wc -l
> 25
> ~/biojava-1.5$ find src -name "*.java" | wc -l
> 1342
> 
> Please consider to have the copyright information added to your sources. 
> 
> I am a bit uncertain about how to treat non-source files. In principle, a 
> <!-- copyright statement as a comment --> would be required for these files, 
> too. However, it should be acceptable to distribute them as they are, 
> applying the copyright file that is distributed with the source, as long as 
> no indication is given (as for dtd/BlastLikeDataSetCollection.dtd) that a 
> redistribution would not be appreciated.
> 
> ~/biojava-1.5$ grep -ri "all rights reserved" src | wc -l
> 41
> ~/biojava-1.5$ grep -ri "all rights reserved" . | wc -l
> 48
> 
> If there are files for which you cannot decide the license easily but that may 
> not be required for an almost functional Debian package, then I would be 
> prepared to remove those files from the package...hoping that it is not too 
> many.
> 
> Many thanks for your help ... and for BioJava in the first place
> 
> Steffen
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
> 
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From holland at ebi.ac.uk  Wed Oct 31 11:12:09 2007
From: holland at ebi.ac.uk (Richard Holland)
Date: Wed, 31 Oct 2007 15:12:09 +0000
Subject: [Biojava-dev] help (F1 F1) regarding biojava
In-Reply-To: <5c85b5bb0709270005m366227acx65ca6151e870ce79@mail.gmail.com>
References: <5c85b5bb0709270005m366227acx65ca6151e870ce79@mail.gmail.com>
Message-ID: <47289B49.1090309@ebi.ac.uk>

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

Hello.

First thing you need to do is provide the full stack trace, not just the
last message. This will help us to pinpoint the problem.

Secondly, I notice you are using NCBISequenceDB and GenbankSequenceDB.
These are deprecated and have been replaced with GenbankRichSequenceDB:

http://www.biojava.org/docs/api15/org/biojavax/bio/db/ncbi/GenbankRichSequenceDB.html

Thirdly, I notice you are trying to set proxy settings. BioJava does not
currently support proxies for either GenbankRichSequenceDB or the
deprecated NCBISequenceDB/GenbankSequenceDB (internally it is making
direct connections to the server using Socket and not using
HttpURLConnection which knows about proxies). If you need this to be
changed, please do raise a bug report requesting it at
http://bugzilla.open-bio.org/ and we will do our best to come up with a
patch to fix it.

cheers,
Richard

pranav waila wrote:
> package org.biojava.bio.seq.db;
> 
> import org.biojava.bio.seq.*;
> import org.biojava.bio.seq.io.*;
> import org.biojava.bio.*;
> import org.biojava.bio.seq.db.*;
> import org.biojava.bio.seq.io.*;
> import java.net.*;
> class test{
>     public static SequenceFormat sf;
> 
>     public static void main(String args[]){
> 
>         System.getProperties().put("proxySet","true");
> 
>         System.getProperties().put("proxyPort","3128");
>         System.getProperties().put("proxyHost","172.16.0.6");
> 
>         Sequence s;
>         sf=new FastaFormat();
>         //sf=new GenbankXmlFormat();
>                 NCBISequenceDB ncbi = new NCBISequenceDB(
> NCBISequenceDB.DB_PROTEIN,sf);//new FastaFormat());
> //        GenbankSequenceDB gdb=new GenbankSequenceDB();
>         //ncbi.setSequenceFormat(FASTA);
>     try{
> 
> 
> 
> //        Sequence sequenceFromGenbank = ncbi.getSequence("P10659");
> //        System.out.println(sequenceFromGenbank.getName());
> 
> // older code
>         s=ncbi.getSequence("P10659");
> 
>         //s=gdb.getAddress();//getSequence("P10659");//3789789");
>         System.out.print("check");
>         System.out.println(ncbi.getSequence("190786"));
> 
> //
>     }
>     catch(Exception e){
>         e.printStackTrace();
>         //System.out.println("protien name is : zinteminia");
>     }
> 
>     }
> }
> 
> 
> This is my code for fetching the sequence from NCBI but it is giving somany
> exceptions. can u provide me some code to do so..
> 
> the errors are as follows :
> 
> Bio java exception could not read sequence
> 
> CAN U PLEASE HELP ME.
> 
> waiting for reply
> 
> PRANAV WAILA
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
> 
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From ap3 at sanger.ac.uk  Wed Oct 31 12:04:03 2007
From: ap3 at sanger.ac.uk (Andreas Prlic)
Date: Wed, 31 Oct 2007 16:04:03 +0000
Subject: [Biojava-dev] LGPL information forgotten at
	BlastLikeDataSetCollection.dtd ?
In-Reply-To: <200710091221.13033.steffen_moeller@gmx.de>
References: <200710091221.13033.steffen_moeller@gmx.de>
Message-ID: <91680D8F-0DC9-4C22-A2E3-A35A32C149A0@sanger.ac.uk>

Hi Steffen,

great to hear about your debian package!
would be good to advertise it also on the BioJava wiki pages.


> ~/biojava-1.5$ grep -ri "all rights reserved" . | wc -l
> 48

Many of the files that contain the text "all rights reserved" actually
are coming with the correct BioJava LGPL header on top of the file.  
The misleading text is only somewhere in the
  javadoc - strings. Therefore I would consider those files to be  
correctly under LGPL.

I can remove the misleading text from the javadoc tonight, if nobody  
objects.


> grep -r LGPL src | wc -l
> 25

The default BioJava header does not contain the text "LGPL" but
"GNU Lesser General Public License". Therefore this is better:

grep -r "gnu.org/copyleft/lesser.html" src | wc -l
1238

Andreas



On 9 Oct 2007, at 11:21, Steffen Moeller wrote:

> Dear all,
>
> I prepared a Debian package for biojava but a distribution with the  
> main
> distribution was rejected because of missing copyright information  
> here
>
> 	dtd/BlastLikeDataSetCollection.dtd
> 	(which just says 'all rights reserved')
>
> and almost everywhere else
>
> ~/biojava-1.5$ grep -r LGPL src | wc -l
> 25
> ~/biojava-1.5$ find src -name "*.java" | wc -l
> 1342
>
> Please consider to have the copyright information added to your  
> sources.
>
> I am a bit uncertain about how to treat non-source files. In  
> principle, a
> <!-- copyright statement as a comment --> would be required for  
> these files,
> too. However, it should be acceptable to distribute them as they are,
> applying the copyright file that is distributed with the source, as  
> long as
> no indication is given (as for dtd/BlastLikeDataSetCollection.dtd)  
> that a
> redistribution would not be appreciated.
>
> ~/biojava-1.5$ grep -ri "all rights reserved" src | wc -l
> 41
> ~/biojava-1.5$ grep -ri "all rights reserved" . | wc -l
> 48
>
> If there are files for which you cannot decide the license easily  
> but that may
> not be required for an almost functional Debian package, then I  
> would be
> prepared to remove those files from the package...hoping that it is  
> not too
> many.
>
> Many thanks for your help ... and for BioJava in the first place
>
> Steffen
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev

-----------------------------------------------------------------------

Andreas Prlic      Wellcome Trust Sanger Institute
                               Hinxton, Cambridge CB10 1SA, UK
			 +44 (0) 1223 49 6891

-----------------------------------------------------------------------



-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 

From heuermh at acm.org  Wed Oct 31 23:06:11 2007
From: heuermh at acm.org (Michael Heuer)
Date: Wed, 31 Oct 2007 22:06:11 -0500 (EST)
Subject: [Biojava-dev] LGPL information forgotten at
 BlastLikeDataSetCollection.dtd ?
In-Reply-To: <91680D8F-0DC9-4C22-A2E3-A35A32C149A0@sanger.ac.uk>
Message-ID: <Pine.GSO.4.44.0710312158390.2281-100000@shell3.shore.net>


A question for all the devs, what are our thoughts regarding version 3 of
the LGPL?

Our version of the LGPL license header does not contain an explicit
version nor does it contain the standard clause "or any later version.""

The LICENSE file at biojava/LICENSE contains the text of version 2.1 of
the LPGL.

We should make this explicit, by including "version 2.1", "version 2.1 or
any later version", "version 3", or "version 3 or any later version" in
the LICENSE file and all the license headers.

In the case of version 3 or version 3 or any later version, we should
include the files COPYING and COPYING.LESSER per

http://www.fsf.org/licensing/licenses/gpl-howto.html

   michael


On Wed, 31 Oct 2007, Andreas Prlic wrote:

> Hi Steffen,
>
> great to hear about your debian package!
> would be good to advertise it also on the BioJava wiki pages.
>
>
> > ~/biojava-1.5$ grep -ri "all rights reserved" . | wc -l
> > 48
>
> Many of the files that contain the text "all rights reserved" actually
> are coming with the correct BioJava LGPL header on top of the file.
> The misleading text is only somewhere in the
>   javadoc - strings. Therefore I would consider those files to be
> correctly under LGPL.
>
> I can remove the misleading text from the javadoc tonight, if nobody
> objects.
>
>
> > grep -r LGPL src | wc -l
> > 25
>
> The default BioJava header does not contain the text "LGPL" but
> "GNU Lesser General Public License". Therefore this is better:
>
> grep -r "gnu.org/copyleft/lesser.html" src | wc -l
> 1238
>
> Andreas
>
>
>
> On 9 Oct 2007, at 11:21, Steffen Moeller wrote:
>
> > Dear all,
> >
> > I prepared a Debian package for biojava but a distribution with the
> > main
> > distribution was rejected because of missing copyright information
> > here
> >
> > 	dtd/BlastLikeDataSetCollection.dtd
> > 	(which just says 'all rights reserved')
> >
> > and almost everywhere else
> >
> > ~/biojava-1.5$ grep -r LGPL src | wc -l
> > 25
> > ~/biojava-1.5$ find src -name "*.java" | wc -l
> > 1342
> >
> > Please consider to have the copyright information added to your
> > sources.
> >
> > I am a bit uncertain about how to treat non-source files. In
> > principle, a
> > <!-- copyright statement as a comment --> would be required for
> > these files,
> > too. However, it should be acceptable to distribute them as they are,
> > applying the copyright file that is distributed with the source, as
> > long as
> > no indication is given (as for dtd/BlastLikeDataSetCollection.dtd)
> > that a
> > redistribution would not be appreciated.
> >
> > ~/biojava-1.5$ grep -ri "all rights reserved" src | wc -l
> > 41
> > ~/biojava-1.5$ grep -ri "all rights reserved" . | wc -l
> > 48
> >
> > If there are files for which you cannot decide the license easily
> > but that may
> > not be required for an almost functional Debian package, then I
> > would be
> > prepared to remove those files from the package...hoping that it is
> > not too
> > many.
> >
> > Many thanks for your help ... and for BioJava in the first place
> >
> > Steffen
> > _______________________________________________
> > biojava-dev mailing list
> > biojava-dev at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/biojava-dev
>
> -----------------------------------------------------------------------
>
> Andreas Prlic      Wellcome Trust Sanger Institute
>                                Hinxton, Cambridge CB10 1SA, UK
> 			 +44 (0) 1223 49 6891
>
> -----------------------------------------------------------------------
>
>
>
> --
>  The Wellcome Trust Sanger Institute is operated by Genome Research
>  Limited, a charity registered in England with number 1021457 and a
>  company registered in England with number 2742969, whose registered
>  office is 215 Euston Road, London, NW1 2BE.
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>


From heuermh at acm.org  Wed Oct 31 23:35:38 2007
From: heuermh at acm.org (Michael Heuer)
Date: Wed, 31 Oct 2007 22:35:38 -0500 (EST)
Subject: [Biojava-dev] [Fwd:  BioJava 3 Proposal]
In-Reply-To: <471F16BD.2040501@ebi.ac.uk>
Message-ID: <Pine.GSO.4.44.0710312206250.2281-100000@shell3.shore.net>

Hello Richard,

I'm not sure if I want any of this up on the wiki, but here are a few
of my thoughts...

Immutable classes, not beans, are the safest and most efficient.

Statements like "We would adhere rigidly to a common coding style and
heavily comment the code." only work if there is a way to measure and
enforce it.  A better way to say this would be something like "All
committed code must have zero style errors as measured by Checkstyle with
our local checkstyle configuration, have zero coding errors as measured by
FindBugs with our local findbugs configuration, have 95% unit test
coverage as measured by Cobertura", and so on.

Sequence features aught to align with the Sequence Ontology (SO/SOFA).
The two top-level sequence feature types are Region (SO:0000001, "A
sequence_feature with an extent greater than zero.") and Junction
(SO:0000699, "A sequence_feature with an extent of zero.").

Is there a role for biojava in any of

Ontologies in OBO format
Ontologies in OWL format
BioPAX
MAGE-ML/SOFT/MINiML
FuGO/OBI
SMBL/CellML
Web services/BioMoby
etc.

or is each best handled by their respective projects/tools?

   michael


Richard Holland wrote:

> -----BEGIN PGP SIGNED MESSAGE-----
> Hash: SHA1
>
> Hi all. I'm planning on opening this wiki page to the general public
> (ie. biojava-l) on Monday next week (Oct 29th). The email that will
> accompany the public announcement is shown below.
>
> If you'd like to review it and add any further comments or suggestions
> before everyone else gets to see it, please make those changes before
> this coming weekend is over!
>
> The page will be made visible as-is, and will be left open for public
> comment until January when I will distribute a summary of its contents
> and start work on a plan of action.
>
> cheers,
> Richard
>
> Here is the email that will be sent out on Monday:
>
> - ----
> Dear BioJava users,
>
> The BioJava developers are considering options for the future
> development of the BioJava toolkit. We consider that it needs
> improvement in a few major areas to make it easier to use and
> understand, and also faster and more scalable.
>
> The options are to either rewrite large parts of the existing code,
> working within the existing interfaces and paradigms, or to develop a
> new set of BioJava packages from the ground up in order to take
> advantage of lessons learned from the design patterns of the existing code.
>
> The BioJava developers have spent the last couple of months discussing
> ideas and proposals related to these options on a Wiki page, and would
> now like to open this discussion to all users of BioJava and the
> bioinformatics community in general. We would like to invite anyone who
> has any ideas or suggestions to contribute these to the Wiki page,
> and/or to comment on the ideas and suggestions that have already been
> posted there.
>
> Here is a link to the Wiki page, and also a link to the associated Talk
> page where much of the discussion has taken place so far:
>
> 	http://biojava.org/wiki/BioJava3_Proposal
> 	http://biojava.org/wiki/Talk:BioJava3_Proposal
>
> It is our intention to leave the discussion open until early January
> 2008 when we will summarise it and use it as the basis of a plan of
> action. We will then distribute the summary and the action plan via the
> BioJava website.
>
> We look forward to hearing your comments and ideas. Please do remember
> to make them directly to the Wiki page so that they are preserved in
> context, making it easier for us to summarise them later!
>
> cheers,
> Richard
> (on behalf of all BioJava developers)
> - ----
>
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