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 license?
But to answer your answer one of your questions, we here at Cognia have contributed to Biojava and we're all happy to do so, including the business people (and I help with Bioperl myself). What's not as clear is the reverse case, meaning what happens if we incorporate Biojava code into our products. Thanks again, Brian O. -----Original Message----- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]]On Behalf Of Wiepert, Mathieu Sent: Tuesday, July 02, 2002 8:45 AM To: 'Brian Osborne'; BioJava List Subject: 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/licenses.html http://www.gnu.org/licenses/licenses.html#LGPL -Mat -----Original Message----- From: Brian Osborne [mailto:[EMAIL PROTECTED]] Sent: Tuesday, July 02, 2002 7:37 AM To: BioJava List Subject: 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 Message----- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]]On Behalf Of Keith James Sent: Tuesday, July 02, 2002 5:18 AM To: BioJava List Subject: [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 String from a SymbolList, including ambiguities: e.g. AANNNTGG returns A{2}[ACTG]{3}TG{2} This should work for all finite alphabets. This class is used by RestrictionEnzyme (see below) to create regex Strings for the forward and reverse strand recognition sites. There is a new package molbio alongside the proteomics package. org.biojava.bio.molbio.RestrictionEnzyme This class specifies restriction enzyme properties (recognition site, cut site(s), type of end produced) and also returns regex Strings suitable for finding forward and reverse strand recognition sites. The constructors are public so that you can create custom enzymes, but the main way to get instances is through the RestrictionEnzymeManager. org.biojava.bio.molbio.RestrictionEnzymeManager This class is allows you to get an enzyme by name, get all isoschizomers of an enzyme by name, get all n-cutters and get a pair of java.util.regex.Patterns for the forward and reverse strand sites. There is a properties file (RestrictionEnzymeManager.properties) which is loaded as a ResourceBundle and tells the class where to find a REBASE file (withrefm.### format, same format as used by EMBOSS program rebaseextract - see REBASE site). I have not checked in a fallback copy of REBASE - it's quite big and I wanted to get some feedback first. Do we want the whole of a specific version of REBASE, or just a subset of common enzymes? Anyone can override this by using their own copy of REBASE and putting a new properties file in their CLASSPATH. The part which is only partly implemented is searching. You can now do searches using org.biojava.bio.seq.io.SymbolListCharSequence This class is an implementation of the Java 1.4 interface CharSequence. It wraps a SymbolList and allows full regex seaching of any SymbolList whose Symbols can be tokenized to chars. It appears that the regex Matcher does not call the subSequence or toString methods, only charAt (which translates directly to symbolAt) so no extra copies of a big sequence get made. You need to use the regex engine in Java 1.4 Finally there's stuff to do: org.biojava.bio.molbio.RestrictionDigest Is not written. This will do the convenience stuff of spitting out SymbolList products etc. It should probably be threaded to search multiple enzymes (or at least both strands for one enzyme) simultaneously. One thing I'm not clear on. Do we want "biologically correct" cutting. That is, if my sequence has two different enzyme sites which overlap and I do sequential digests, does the second fail to cut because its site is now partly single-stranded, even though the regex still matches on one strand? It seems the right way to me, but it may not to to everyone. In summary, you can currently do full ambiguity searches on both strands with a bit of work. 1. Get a copy of REBASE format #31 2. Edit the RestrictionEnzymeManager.properties file to point to it Do something like this: RestrictionEnzyme ecoRI = RestrictionEnzymeManager.getEnzyme("EcoRI"); Pattern [] pat = RestrictionEnzymeManager.getPatterns(ecoRI); CharSequence charSeq = new SymbolListCharSequence(mySymbolList); Matcher forward = pat[0].matcher(charSeq); Matcher reverse = pat[1].matcher(charSeq); Then proceed to use the Matcher as normal. Right now the coordinate you get back will be the start of the recognition site and you will have to calculate the actual cut(s). There are methods in RestrictionEnzyme which return the position(s) of the cut site in the coordinate space of the recognition site SymbolList (there are some freaky enzymes which cut both sides of their recognition site). Please report bugs (or better still, add a test case which fails because of the bug). Enjoy. Keith -- -= Keith James - [EMAIL PROTECTED] - http://www.sanger.ac.uk/Users/kdj =- Pathogen Sequencing Unit, Wellcome Trust Sanger Institute, Cambridge, UK _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
