[Biojava-l] Restriction digest progess

I've had some free time to get started on this. Here's a summary of what is currently checked in: org.biojava.bio.symbol.MotifTools This is another support class which contains static methods (well, just one right now). String createRegex(SymbolList motif) will create a regular expression Strin

LGPL (was RE: [Biojava-l] Restriction digest progress)

Hi, Since I am not why you are asking (i.e. did you want to make your own software to market, or is someone like a boss concerned about you contributing) you should read it yourself rather than rely on anyone else's' interpretation, just to be on the safe side? http://www.gnu.org/licenses/licens

RE: [Biojava-l] Restriction digest progess

To Biojava, I see the following on the first page of the Biojava Web site: BioJava is distributed under LGPL. This means that you can use the libraries without your software being forced under either the LGPL or GPL. Can someone tell me what this means? Thanks again, Brian O. -Original

RE: LGPL (was RE: [Biojava-l] Restriction digest progress)

Mat, I did read the licenses themselves, I believe I understand them, somewhat. What I don't understand is the idea that Biojava is distributed under the LGPL so that it's not under the LGPL. Is this what the Biojava authors actually want to say? It looks like a typo. Is there a third kind of GPL

RE: LGPL (was RE: [Biojava-l] Restriction digest progress)

Hi, Then this should apply, from a long ago conversation I had with by Simon Brocklehust, It depends what you mean by 'free'. Biojava *itself* _is_ free under the LGPL in the following senses: o The source code of biojava is available without charge to anyone who wants it. o Having made cha

Re: [Biojava-l] Restriction digest progess

Brian Osborne wrote: >To Biojava, > >I see the following on the first page of the Biojava Web site: > >BioJava is distributed under LGPL. This means that you can use the libraries >without your software being forced under either the LGPL or GPL. > >Can someone tell me what this means? > >Thanks a

Re: LGPL (was RE: [Biojava-l] Restriction digest progress)

> > >Mat, > >I did read the licenses themselves, I believe I understand them, somewhat. >What I don't understand is the idea that Biojava is distributed under the >LGPL so that it's not under the LGPL. Is this what the Biojava authors >actually want to say? It looks like a typo. Is there a third k

Re: LGPL (was RE: [Biojava-l] Restriction digest progress)

> "Brian" == Brian Osborne <[EMAIL PROTECTED]> writes: Brian> Mat, I did read the licenses themselves, I believe I Brian> understand them, somewhat. What I don't understand is the Brian> idea that Biojava is distributed under the LGPL so that Brian> it's not under the LGPL. I

[Biojava-l] Retrieve Genbank file

Could you suggest how can I retrieve Genbank files given the Accession Number. Thanks a lot. __ Do You Yahoo!? Sign up for SBC Yahoo! Dial - First Month Free http://sbc.yahoo.com ___ Biojava-l mailing l

Re: LGPL (was RE: [Biojava-l] Restriction digest progress)

Brian Osborne wrote: >Mat, > >I did read the licenses themselves, I believe I understand them, somewhat. >What I don't understand is the idea that Biojava is distributed under the >LGPL so that it's not under the LGPL. Is this what the Biojava authors >actually want to say? It looks like a typo.

Re: [Biojava-l] SortedFeatureHolder (by location)

>The simple and dirty solution here, is to just have your Sequence class >have a constructor that takes an object of type Sequence. >The constructor just copies the data from the Sequence class ( that you get >from SeqIOTools.readEMBL(br) ) into your own >class. It will be about 20 lines of cod

RE: LGPL (was RE: [Biojava-l] Restriction digest progress)

Kalle, Keith, and Mat, Thanks very much, your comments have been very helpful. Brian O. -Original Message- From: Kalle Naslund [mailto:[EMAIL PROTECTED]] Sent: Tuesday, July 02, 2002 12:46 PM To: Brian Osborne Cc: [EMAIL PROTECTED] Subject: Re: LGPL (was RE: [Biojava-l] Restriction dig

Re: [Biojava-l] SortedFeatureHolder (by location)

> "pootle" == pootle monster <[EMAIL PROTECTED]> writes: [...] pootle> I have made my own OrderedSequence Object constructed thus Cool. pootle> that is all fine but I now can not see how to add features pootle> to it I would like to do somthing like this: pootle> Iterator

[Biojava-l] Variable Modifications

I have added support for variable modifications to the Proteomics.MassCalc class. This will allow calculations of any hypothetical peptides that might arise from a modification. For example if a peptide has two Methionines and the user tells it to look for the Met-Ox for as well as the Native Met

RE: [Biojava-l] Parsing SwissProt flat file through BioJava

Hi - Possibly this info has ended up in the Annotation object of the sequence. Does anyone else have an explanation for this? - Mark > -Original Message- > From: Santosh Kumar [mailto:[EMAIL PROTECTED]] > Sent: Wednesday, 3 July 2002 4:31 p.m. > To: Schreiber, Mark > Subject: RE: [Bio