From mark.schreiber at novartis.com Fri Sep 2 01:36:45 2005 From: mark.schreiber at novartis.com (mark.schreiber@novartis.com) Date: Fri Sep 2 01:33:32 2005 Subject: [Biojava-l] [offtopic] biojava developers in the UK Message-ID: Hi Everyone - Slightly off topic but... I'm going to be in the UK next week and have some free time to kill. I would be keen to meet up with any biojava developers who are in the Cambridge or London areas who want to discuss the project/ bioinformatics. Dates are roughly the 7th of Sept to the 15th of Sept. Please post replies directly to my gmail address (markjschreiber {at} gmail.com). I will not frequently monitor my work mail or this list so this will be the best way to contact me. - Mark Mark Schreiber Principal Scientist (Bioinformatics) Novartis Institute for Tropical Diseases (NITD) 10 Biopolis Road #05-01 Chromos Singapore 138670 www.nitd.novartis.com phone +65 6722 2973 fax +65 6722 2910 From mark.schreiber at novartis.com Sun Sep 4 11:07:46 2005 From: mark.schreiber at novartis.com (mark.schreiber@novartis.com) Date: Sun Sep 4 21:54:59 2005 Subject: [Biojava-l] Global Sequence Alignment Message-ID: An HTML attachment was scrubbed... URL: http://portal.open-bio.org/pipermail/biojava-l/attachments/20050904/c26e5a8c/attachment.htm From mountainswhim at gmail.com Wed Sep 7 10:14:19 2005 From: mountainswhim at gmail.com (Eric Buckley) Date: Wed Sep 7 11:58:49 2005 Subject: [Biojava-l] is valid character Message-ID: <6ab8906c050907071469d8cab5@mail.gmail.com> I was wondering if there is a way to check if a character is valid within an alphabet. For example I want to do some preprocessing on a string before I convert the string to a SymbolList using DNATools. However if an invalid character exists in the string an Exception will be thrown, so I would first like to remove (or replace) all of the invalid characters. Eric Buckley From hollandr at gis.a-star.edu.sg Wed Sep 7 22:45:04 2005 From: hollandr at gis.a-star.edu.sg (Richard HOLLAND) Date: Wed Sep 7 22:48:01 2005 Subject: [Biojava-l] is valid character Message-ID: <6D9E9B9DF347EF4385F6271C64FB8D56021E4915@BIONIC.biopolis.one-north.com> Hi Eric, You can do something like this to check if a particular letter (token) is in an alphabet: Alphabet myAlphabet = ... ; // get your alphabet from somewhere SymbolTokenization st = myAlphabet.getTokenization("token"); String token = "X"; // the token to check for boolean alphaContainsToken = true; try { st.parseToken("X"); // see if your alphabet contains the letter X } catch (IllegalSymbolException e) { alphaContainsToken = false; } if (alphaContainsToken) System.out.println("Alphabet DOES contain token "+token); else System.out.println("Alphabet DOES NOT contain token "+token); cheers, Richard Richard Holland Bioinformatics Specialist GIS extension 8199 --------------------------------------------- This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not copy or use it for any purpose, or disclose its content to any other person. Thank you. --------------------------------------------- > -----Original Message----- > From: biojava-l-bounces@portal.open-bio.org > [mailto:biojava-l-bounces@portal.open-bio.org] On Behalf Of > Eric Buckley > Sent: Wednesday, September 07, 2005 10:14 PM > To: biojava-l@biojava.org > Subject: [Biojava-l] is valid character > > > I was wondering if there is a way to check if a character is > valid within an > alphabet. For example I want to do some preprocessing on a > string before I > convert the string to a SymbolList using DNATools. However if > an invalid > character exists in the string an Exception will be thrown, > so I would first > like to remove (or replace) all of the invalid characters. > > Eric Buckley > > _______________________________________________ > Biojava-l mailing list - Biojava-l@biojava.org > http://biojava.org/mailman/listinfo/biojava-l > From duze at gmx.de Tue Sep 13 07:10:26 2005 From: duze at gmx.de (=?ISO-8859-1?Q?=22Andreas_Dr=E4ger=22?=) Date: Tue Sep 13 07:07:45 2005 Subject: [Biojava-l] 3 questions and problems Message-ID: <31203.1126609826@www2.gmx.net> Hello, I would like to ask three questions or to mention problems, respectively. 1. Trying to write a protein-sequence in a GenPept file resulted in the following error message: ClassCastException in GenpeptFileFormer line 361. What does this mean and how can I write my sequences? 2. There is a problem with BioSQL. The attribute alphabet in the table biosequence has the type VARCHAR(10). The BioJava alphabet PROTEIN-TERM has 12 characters. I always got an error message, when I tryed to get a protein sequence with this alphabet from the database. A simple select statement showed that the alphabet in the table is abbrevated to PROTEIN-TE, which is not equal to the BioJava name and causes trouble. I solved this problem by altering the table declaration to VARCHAR(12). Now it works fine. Is there another solution for this or should this be the only one? 3. I also experimented with the HMM for pair wise sequence alignments, which was proposed in the cookbook. Has anybody an idea how one could combine this HMM with the SubstitutionMatrix from the alignment package? I don't see how we can produce a senseful distribution including a substitution matrix in the match state. This might especially be hard to realize because we can't exclude that there are some ambigious symbols in the sequences to be aligned, which are not in the substitution matrix at all. I am thankfull for any good ideas. Sincerely Andreas Dr?ger -- Lust, ein paar Euro nebenbei zu verdienen? Ohne Kosten, ohne Risiko! Satte Provisionen f?r GMX Partner: http://www.gmx.net/de/go/partner From mark.schreiber at novartis.com Sun Sep 18 23:36:57 2005 From: mark.schreiber at novartis.com (mark.schreiber@novartis.com) Date: Sun Sep 18 23:43:46 2005 Subject: [Biojava-l] 3 questions and problems Message-ID: >Hello, > >I would like to ask three questions or to mention problems, respectively. > >1. Trying to write a protein-sequence in a GenPept file resulted in the >following error message: ClassCastException in GenpeptFileFormer line 361. >What does this mean and how can I write my sequences? The class is trying to cast an object called value to a List without checking it's type. Aparently in the case you have value is not an instance of a List. Try changing the code to this and let me know if it fixes the problem. If it does I'll commit it to CVS. ub.append("ACCESSION "); List l; if(value instanceof List){ l = (List)value; }else{ l = new ArrayList(); l.add(value); } for (Iterator ai = l.iterator(); ai.hasNext();) { ub.append((String) ai.next()); } acb = new StringBuffer(ub.toString()); >2. There is a problem with BioSQL. The attribute alphabet in the table >biosequence has the type VARCHAR(10). The BioJava alphabet PROTEIN-TERM has >12 characters. I always got an error message, when I tryed to get a protein >sequence with this alphabet from the database. A simple select statement >showed that the alphabet in the table is abbrevated to PROTEIN-TE, which is >not equal to the BioJava name and causes trouble. I solved this problem by >altering the table declaration to VARCHAR(12). Now it works fine. Is there >another solution for this or should this be the only one? This is probably the best fix for now. Ideally it would be good for biosql to standardise some alphabet names but this might not happen for a while. Might be worth suggesting to the biosql list that the size of the alphabet name field be increased. >3. I also experimented with the HMM for pair wise sequence alignments, which >was proposed in the cookbook. Has anybody an idea how one could combine this >HMM with the SubstitutionMatrix from the alignment package? I don't see how >we can produce a senseful distribution including a substitution matrix in >the match state. This might especially be hard to realize because we can't >exclude that there are some ambigious symbols in the sequences to be >aligned, which are not in the substitution matrix at all. I am thankfull for >any good ideas. It is possible in theory to make a Distribution from a similarity matrix providing you know how it was made. Typically similarity matrices are log odds scores that are mutliplied by a constant and then rounded to an integer. The value of the constant is probably irrelevant (it's a constant) so you could convert back again as long as you can normalize to 1.0. This is not perfect as you get some rounding errors but it should be close enough. By the way, it seems your alignment classes have not been checked in. Are you going to do this soon? - Mark Sincerely Andreas Dr?ger -- Lust, ein paar Euro nebenbei zu verdienen? Ohne Kosten, ohne Risiko! Satte Provisionen f?r GMX Partner: http://www.gmx.net/de/go/partner _______________________________________________ Biojava-l mailing list - Biojava-l@biojava.org http://biojava.org/mailman/listinfo/biojava-l From hollandr at gis.a-star.edu.sg Tue Sep 20 01:59:23 2005 From: hollandr at gis.a-star.edu.sg (Richard HOLLAND) Date: Tue Sep 20 02:12:33 2005 Subject: [Biojava-l] 3 questions and problems Message-ID: <6D9E9B9DF347EF4385F6271C64FB8D56021E4E8D@BIONIC.biopolis.one-north.com> Here's my 2P: 1. Don't know what's causing it, but does not occur when using the new BioJavaX Genbank file former - still undergoing testing+documentation at present but if you're feeling like risking the cutting edge it's in CVS under biojava-live - org.biojavax.bio.seq.io.SeqIOTools behaves almost identically to the one you mention below. It reads/writes instances of org.biojavax.bio.seq.RichSequence - if you pass it a plain old Sequence it'll do its best but you'll probably lose detail. At the moment, GenPept format = GenBank format, unless anyone can tell me the exact difference beyond the symbol frequency line. 2. Protein-Term is a weird BioJava specific thing - I asked Hilmar about this before and he says there is no concept of it in BioPerl, and he would not alter BioSQL to allow for it. I'm not even sure what it's for myself. Is using just Protein a viable alternative? 3. Dunno, that's a question that sounds like something Mark might be able to answer. cheers, Richard Richard Holland Bioinformatics Specialist GIS extension 8199 --------------------------------------------- This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not copy or use it for any purpose, or disclose its content to any other person. Thank you. --------------------------------------------- > -----Original Message----- > From: biojava-l-bounces@portal.open-bio.org > [mailto:biojava-l-bounces@portal.open-bio.org] On Behalf Of > "Andreas Dr?ger" > Sent: Tuesday, September 13, 2005 7:10 PM > To: biojava-l@biojava.org > Subject: [Biojava-l] 3 questions and problems > > > Hello, > > I would like to ask three questions or to mention problems, > respectively. > > 1. Trying to write a protein-sequence in a GenPept file > resulted in the > following error message: ClassCastException in > GenpeptFileFormer line 361. > What does this mean and how can I write my sequences? > > 2. There is a problem with BioSQL. The attribute alphabet in the table > biosequence has the type VARCHAR(10). The BioJava alphabet > PROTEIN-TERM has > 12 characters. I always got an error message, when I tryed to > get a protein > sequence with this alphabet from the database. A simple > select statement > showed that the alphabet in the table is abbrevated to > PROTEIN-TE, which is > not equal to the BioJava name and causes trouble. I solved > this problem by > altering the table declaration to VARCHAR(12). Now it works > fine. Is there > another solution for this or should this be the only one? > > 3. I also experimented with the HMM for pair wise sequence > alignments, which > was proposed in the cookbook. Has anybody an idea how one > could combine this > HMM with the SubstitutionMatrix from the alignment package? I > don't see how > we can produce a senseful distribution including a > substitution matrix in > the match state. This might especially be hard to realize > because we can't > exclude that there are some ambigious symbols in the sequences to be > aligned, which are not in the substitution matrix at all. I > am thankfull for > any good ideas. > > > Sincerely > Andreas Dr?ger > > -- > Lust, ein paar Euro nebenbei zu verdienen? Ohne Kosten, ohne Risiko! > Satte Provisionen f?r GMX Partner: http://www.gmx.net/de/go/partner > _______________________________________________ > Biojava-l mailing list - Biojava-l@biojava.org > http://biojava.org/mailman/listinfo/biojava-l > From mark.schreiber at novartis.com Tue Sep 20 05:08:26 2005 From: mark.schreiber at novartis.com (mark.schreiber@novartis.com) Date: Tue Sep 20 05:09:05 2005 Subject: [Biojava-l] 3 questions and problems Message-ID: Protein-Term is an Alphabet that includes the * symbol (for termination codon). It is useful when doing a six frame translation and you want to include the possiblity of having a *. Protein-Term completely contains Protein and due to some wizardry I'm not even going to try and explain it thinks all protein symbols are also members of Protein-Term. The best solution might be to change biojava such that the name Protein is stored in the database and that biojava will know that the best option to read this back in is Protein-Term. My other suggestion would be that it is highly unlikely anyone would want to store a sequence with * in it so all biojava protein sequences could be stored and read as protein. Having said that I'm sure someone somewhere will try it : ) - Mark "Richard HOLLAND" Sent by: biojava-l-bounces@portal.open-bio.org 09/20/2005 01:59 PM To: "Andreas Dr?ger" , cc: (bcc: Mark Schreiber/GP/Novartis) Subject: RE: [Biojava-l] 3 questions and problems Here's my 2P: 1. Don't know what's causing it, but does not occur when using the new BioJavaX Genbank file former - still undergoing testing+documentation at present but if you're feeling like risking the cutting edge it's in CVS under biojava-live - org.biojavax.bio.seq.io.SeqIOTools behaves almost identically to the one you mention below. It reads/writes instances of org.biojavax.bio.seq.RichSequence - if you pass it a plain old Sequence it'll do its best but you'll probably lose detail. At the moment, GenPept format = GenBank format, unless anyone can tell me the exact difference beyond the symbol frequency line. 2. Protein-Term is a weird BioJava specific thing - I asked Hilmar about this before and he says there is no concept of it in BioPerl, and he would not alter BioSQL to allow for it. I'm not even sure what it's for myself. Is using just Protein a viable alternative? 3. Dunno, that's a question that sounds like something Mark might be able to answer. cheers, Richard Richard Holland Bioinformatics Specialist GIS extension 8199 --------------------------------------------- This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not copy or use it for any purpose, or disclose its content to any other person. Thank you. --------------------------------------------- > -----Original Message----- > From: biojava-l-bounces@portal.open-bio.org > [mailto:biojava-l-bounces@portal.open-bio.org] On Behalf Of > "Andreas Dr?ger" > Sent: Tuesday, September 13, 2005 7:10 PM > To: biojava-l@biojava.org > Subject: [Biojava-l] 3 questions and problems > > > Hello, > > I would like to ask three questions or to mention problems, > respectively. > > 1. Trying to write a protein-sequence in a GenPept file > resulted in the > following error message: ClassCastException in > GenpeptFileFormer line 361. > What does this mean and how can I write my sequences? > > 2. There is a problem with BioSQL. The attribute alphabet in the table > biosequence has the type VARCHAR(10). The BioJava alphabet > PROTEIN-TERM has > 12 characters. I always got an error message, when I tryed to > get a protein > sequence with this alphabet from the database. A simple > select statement > showed that the alphabet in the table is abbrevated to > PROTEIN-TE, which is > not equal to the BioJava name and causes trouble. I solved > this problem by > altering the table declaration to VARCHAR(12). Now it works > fine. Is there > another solution for this or should this be the only one? > > 3. I also experimented with the HMM for pair wise sequence > alignments, which > was proposed in the cookbook. Has anybody an idea how one > could combine this > HMM with the SubstitutionMatrix from the alignment package? I > don't see how > we can produce a senseful distribution including a > substitution matrix in > the match state. This might especially be hard to realize > because we can't > exclude that there are some ambigious symbols in the sequences to be > aligned, which are not in the substitution matrix at all. I > am thankfull for > any good ideas. > > > Sincerely > Andreas Dr?ger > > -- > Lust, ein paar Euro nebenbei zu verdienen? Ohne Kosten, ohne Risiko! > Satte Provisionen f?r GMX Partner: http://www.gmx.net/de/go/partner > _______________________________________________ > Biojava-l mailing list - Biojava-l@biojava.org > http://biojava.org/mailman/listinfo/biojava-l > _______________________________________________ Biojava-l mailing list - Biojava-l@biojava.org http://biojava.org/mailman/listinfo/biojava-l From reneehalbrook74 at yahoo.com Tue Sep 20 06:54:53 2005 From: reneehalbrook74 at yahoo.com (Renee Halbrook) Date: Tue Sep 20 07:03:35 2005 Subject: [Biojava-l] Newbie Question: Blast Results Visualization Message-ID: <20050920105453.12998.qmail@web40502.mail.yahoo.com> Hi, I was wondering if there are any pre-written Blast Visualization packages.( To display a picture of Blast Hits, similar to results in NCBI) I know there is one in BioPerl, ( I think it is Bio::SearchIO) but my web-application is written in Java/ jsp. Any feedback/ pointers on how to approach this would be greatly appreciated. Thanks in advance for any help. Renee Halbrook __________________________________ Yahoo! Mail - PC Magazine Editors' Choice 2005 http://mail.yahoo.com From mark.schreiber at novartis.com Tue Sep 20 21:46:08 2005 From: mark.schreiber at novartis.com (mark.schreiber@novartis.com) Date: Tue Sep 20 21:53:13 2005 Subject: [Biojava-l] Newbie Question: Blast Results Visualization Message-ID: There is nothing in the biojava packages. However I know that there are people who have written such things in Java/JSP making use of biojava. Anyone want to volunteer some code? - Mark Renee Halbrook Sent by: biojava-l-bounces@portal.open-bio.org 09/20/2005 06:54 PM To: biojava-l@biojava.org cc: (bcc: Mark Schreiber/GP/Novartis) Subject: [Biojava-l] Newbie Question: Blast Results Visualization Hi, I was wondering if there are any pre-written Blast Visualization packages.( To display a picture of Blast Hits, similar to results in NCBI) I know there is one in BioPerl, ( I think it is Bio::SearchIO) but my web-application is written in Java/ jsp. Any feedback/ pointers on how to approach this would be greatly appreciated. Thanks in advance for any help. Renee Halbrook __________________________________ Yahoo! Mail - PC Magazine Editors' Choice 2005 http://mail.yahoo.com _______________________________________________ Biojava-l mailing list - Biojava-l@biojava.org http://biojava.org/mailman/listinfo/biojava-l From m.caron at umontreal.ca Wed Sep 21 23:24:17 2005 From: m.caron at umontreal.ca (Maxime Caron) Date: Thu Sep 22 01:11:35 2005 Subject: [Biojava-l] classpath Message-ID: <1127359457.433223e1c1ea0@www.courrier.umontreal.ca> Hi, I?m sorry if this has been asked before. I added the .jar files to my $CLASSPATH under linux and I still can?t compile my code; it doesn?t find the classes. The path syntax is correct and the files are properly downloaded. Any ideas? Thank you. From mark.schreiber at novartis.com Thu Sep 22 01:22:52 2005 From: mark.schreiber at novartis.com (mark.schreiber@novartis.com) Date: Thu Sep 22 01:23:05 2005 Subject: [Biojava-l] classpath Message-ID: For advice on setting your classpath for biojava take a look at http://www.biojava.org/started.html Try typing echo $CLASSPATH to make sure your classpath is actually getting set. If everything looks ok and it still won't compile then send an email to the list with your javac error statement. - Mark Mark Schreiber Principal Scientist (Bioinformatics) Novartis Institute for Tropical Diseases (NITD) 10 Biopolis Road #05-01 Chromos Singapore 138670 www.nitd.novartis.com phone +65 6722 2973 fax +65 6722 2910 Maxime Caron Sent by: biojava-l-bounces@portal.open-bio.org 09/22/2005 11:24 AM To: biojava-l@biojava.org cc: (bcc: Mark Schreiber/GP/Novartis) Subject: [Biojava-l] classpath Hi, I'm sorry if this has been asked before. I added the .jar files to my $CLASSPATH under linux and I still can't compile my code; it doesn't find the classes. The path syntax is correct and the files are properly downloaded. Any ideas? Thank you. _______________________________________________ Biojava-l mailing list - Biojava-l@biojava.org http://biojava.org/mailman/listinfo/biojava-l From hollandr at gis.a-star.edu.sg Thu Sep 22 01:24:56 2005 From: hollandr at gis.a-star.edu.sg (Richard HOLLAND) Date: Thu Sep 22 01:25:22 2005 Subject: [Biojava-l] classpath Message-ID: <6D9E9B9DF347EF4385F6271C64FB8D5602428428@BIONIC.biopolis.one-north.com> Sounds like you might have done this: set CLASSPATH=/path/to/biojava.jar javac myprogram.java java myprogram What you need to do is this: set CLASSPATH=/path/to/biojava.jar javac -cp $CLASSPATH myprogram.java java -cp $CLASSPATH myprogram Also, check that your classpath only contains one reference to the jar file, not two or more, as having multiple references to copies in different locations has the same effect as not including it at all. cheers, Richard Richard Holland Bioinformatics Specialist GIS extension 8199 --------------------------------------------- This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not copy or use it for any purpose, or disclose its content to any other person. Thank you. --------------------------------------------- > -----Original Message----- > From: biojava-l-bounces@portal.open-bio.org > [mailto:biojava-l-bounces@portal.open-bio.org] On Behalf Of > Maxime Caron > Sent: Thursday, September 22, 2005 11:24 AM > To: biojava-l@biojava.org > Subject: [Biojava-l] classpath > > > Hi, > > I'm sorry if this has been asked before. I added the .jar > files to my $CLASSPATH > under linux and I still can't compile my code; it doesn't > find the classes. The > path syntax is correct and the files are properly downloaded. > > Any ideas? > > Thank you. > > > _______________________________________________ > Biojava-l mailing list - Biojava-l@biojava.org > http://biojava.org/mailman/listinfo/biojava-l > From Martin.Szugat at GMX.net Fri Sep 23 07:36:49 2005 From: Martin.Szugat at GMX.net (Martin Szugat) Date: Fri Sep 23 07:44:09 2005 Subject: [Biojava-l] Apache License vs. (L)GPL Message-ID: <200509231143.j8NBhNnq021556@portal.open-bio.org> Hi! I'm using BioJava with my BioWeka project (www.bioweka.org). I'd like to create a distribution with BioWeka (GPL), BioJava (LGPL) and the Apache Commons libraries (Apache license) which are required by BioJava. However there seems to be an incompatibility between the GPL/LGPL and the Apache license: http://apache.slashdot.org/article.pl?sid=04/02/18/215242&tid=117&tid=185&ti d=17&tid=2 But the Apache foundation says the licenses are compatible: http://www.apache.org/foundation/licence-FAQ.html#GPL So I'm a little bit confused if I'm allowed to package all libraries in the same distribution. Maybe someone can clarify that. I already contacted the Apache foundation but didn't get an answer, yet. Best regards Martin From ragibb at ucalgary.ca Fri Sep 23 11:35:16 2005 From: ragibb at ucalgary.ca (Ross Gibb) Date: Fri Sep 23 12:01:16 2005 Subject: [Biojava-l] Apache License vs. (L)GPL In-Reply-To: <200509231143.j8NBhNnq021556@portal.open-bio.org> References: <200509231143.j8NBhNnq021556@portal.open-bio.org> Message-ID: <433420B4.8020500@ucalgary.ca> Now you're into the murky realm of software licensing. The best advice is to ask a lawyer who understands this stuff. I am NOT a lawyer, so if you listen to what I say you do so at your own risk. I guess the first question is what do you want to do with the code? If you are writing an in house application, or something you are not going to distribute, you can do what you want with the code. The GNU license in particular gives you freedom as in free speech. Meaning, you can do whatever you want with it as long as you don't distribute it. As soon as you distribute it then there are certain conditions under the GPL that you have to adhere to. Now for the case where you want to distribute it. This is my opinion, do with it what you like. Of the GPL, LGPL and the Apache license, the GPL is the most restrictive so that's the one you are going to be restricted by. Obviously anything you distribute is going to have to be open source. I am going to assume that you are just using the software that you mentioned and have not changed any of it. In a text file I would state what pieces are covered under what license. For example, list the jar files and what license they are covered by and include the text of the license(s). Now the tricky part, what kind of license does your project get as a whole? I would say the GPL. The Apache license is very flexible, much more so than the GPL, and the Apache site believes they are compatible with the GPL, so I think it is safe to place the project as a whole under the GPL. You are not changing the Apache license because someone could look at your documentation see what piece of Apache you used and go and download it independently from Apache. The real answer is that none of these licenses have been throughly tested in court (precedence) and it really depends on what you want to do with it. Therefore, any advice you get is going to be at some level speculation. Your best bet is to follow what other reputable software is doing. Ross Martin Szugat wrote: >Hi! > >I'm using BioJava with my BioWeka project (www.bioweka.org). I'd like to >create a distribution with BioWeka (GPL), BioJava (LGPL) and the Apache >Commons libraries (Apache license) which are required by BioJava. However >there seems to be an incompatibility between the GPL/LGPL and the Apache >license: > >http://apache.slashdot.org/article.pl?sid=04/02/18/215242&tid=117&tid=185&ti >d=17&tid=2 > >But the Apache foundation says the licenses are compatible: > >http://www.apache.org/foundation/licence-FAQ.html#GPL > >So I'm a little bit confused if I'm allowed to package all libraries in the >same distribution. Maybe someone can clarify that. I already contacted the >Apache foundation but didn't get an answer, yet. > >Best regards > >Martin > > >_______________________________________________ >Biojava-l mailing list - Biojava-l@biojava.org >http://biojava.org/mailman/listinfo/biojava-l > > > From Martin.Szugat at GMX.net Fri Sep 23 12:22:18 2005 From: Martin.Szugat at GMX.net (Martin Szugat) Date: Fri Sep 23 12:25:54 2005 Subject: [Biojava-l] Apache License vs. (L)GPL In-Reply-To: Message-ID: <200509231622.j8NGMEnq027406@portal.open-bio.org> Hi Michael, First thanks for your reply! > I think the concern is only in the opposite direction, when an > Apache-licensed library wishes to include a GPL-licensed library as a > dependency. That's also my opinion. > > As long as you adhere to the conditions of the LGPL for BioJava (include > the text of the LGPL in your distribution) and of the Apache license for > the commons libraries (include the text of the Apache licence and a > NOTICE.txt file in the distribution or a section in your README.txt with > the text "This product includes software developed by The Apache Software > Foundation (http://www.apache.org/).") then you are fine. I've done that already so I hope I'm on the safe side :) Best regards Martin > > michael > > > On Fri, 23 Sep 2005, Martin Szugat wrote: > > > Hi! > > > > I'm using BioJava with my BioWeka project (www.bioweka.org). I'd like to > > create a distribution with BioWeka (GPL), BioJava (LGPL) and the Apache > > Commons libraries (Apache license) which are required by BioJava. > However > > there seems to be an incompatibility between the GPL/LGPL and the Apache > > license: > > > > > http://apache.slashdot.org/article.pl?sid=04/02/18/215242&tid=117&tid=185& > ti > > d=17&tid=2 > > > > But the Apache foundation says the licenses are compatible: > > > > http://www.apache.org/foundation/licence-FAQ.html#GPL > > > > So I'm a little bit confused if I'm allowed to package all libraries in > the > > same distribution. Maybe someone can clarify that. I already contacted > the > > Apache foundation but didn't get an answer, yet. > > > > Best regards > > > > Martin > > > > > > _______________________________________________ > > Biojava-l mailing list - Biojava-l@biojava.org > > http://biojava.org/mailman/listinfo/biojava-l > > From Martin.Szugat at GMX.net Fri Sep 23 12:31:31 2005 From: Martin.Szugat at GMX.net (Martin Szugat) Date: Fri Sep 23 12:31:30 2005 Subject: [Biojava-l] Apache License vs. (L)GPL In-Reply-To: <433420B4.8020500@ucalgary.ca> Message-ID: <200509231631.j8NGVInq027704@portal.open-bio.org> Hi Ross, Thanks for your reply! I think the point is that is allowed to include the Apache libraries in a GPL licensed project but not in the other direction. But I'm not sure :( Nevertheless it helps me in my decision when other people like you share the same opinion. So thanks again for your detailed answer! Best regards Martin > -----Original Message----- > From: biojava-l-bounces@portal.open-bio.org [mailto:biojava-l- > bounces@portal.open-bio.org] On Behalf Of Ross Gibb > Sent: Friday, September 23, 2005 5:35 PM > To: biojava-l@biojava.org > Subject: Re: [Biojava-l] Apache License vs. (L)GPL > > Now you're into the murky realm of software licensing. The best advice > is to ask a lawyer who understands this stuff. I am NOT a lawyer, so > if you listen to what I say you do so at your own risk. I guess the > first question is what do you want to do with the code? If you are > writing an in house application, or something you are not going to > distribute, you can do what you want with the code. The GNU license in > particular gives you freedom as in free speech. Meaning, you can do > whatever you want with it as long as you don't distribute it. As soon > as you distribute it then there are certain conditions under the GPL > that you have to adhere to. > > Now for the case where you want to distribute it. This is my opinion, > do with it what you like. Of the GPL, LGPL and the Apache license, the > GPL is the most restrictive so that's the one you are going to be > restricted by. Obviously anything you distribute is going to have to be > open source. I am going to assume that you are just using the software > that you mentioned and have not changed any of it. In a text file I > would state what pieces are covered under what license. For example, > list the jar files and what license they are covered by and include the > text of the license(s). Now the tricky part, what kind of license does > your project get as a whole? I would say the GPL. The Apache license > is very flexible, much more so than the GPL, and the Apache site > believes they are compatible with the GPL, so I think it is safe to > place the project as a whole under the GPL. You are not changing the > Apache license because someone could look at your documentation see what > piece of Apache you used and go and download it independently from Apache. > > The real answer is that none of these licenses have been throughly > tested in court (precedence) and it really depends on what you want to > do with it. Therefore, any advice you get is going to be at some level > speculation. Your best bet is to follow what other reputable software > is doing. > > Ross > > Martin Szugat wrote: > > >Hi! > > > >I'm using BioJava with my BioWeka project (www.bioweka.org). I'd like to > >create a distribution with BioWeka (GPL), BioJava (LGPL) and the Apache > >Commons libraries (Apache license) which are required by BioJava. However > >there seems to be an incompatibility between the GPL/LGPL and the Apache > >license: > > > >http://apache.slashdot.org/article.pl?sid=04/02/18/215242&tid=117&tid=185 > &ti > >d=17&tid=2 > > > >But the Apache foundation says the licenses are compatible: > > > >http://www.apache.org/foundation/licence-FAQ.html#GPL > > > >So I'm a little bit confused if I'm allowed to package all libraries in > the > >same distribution. Maybe someone can clarify that. I already contacted > the > >Apache foundation but didn't get an answer, yet. > > > >Best regards > > > >Martin > > > > > >_______________________________________________ > >Biojava-l mailing list - Biojava-l@biojava.org > >http://biojava.org/mailman/listinfo/biojava-l > > > > > > > _______________________________________________ > Biojava-l mailing list - Biojava-l@biojava.org > http://biojava.org/mailman/listinfo/biojava-l From heuermh at acm.org Fri Sep 23 12:12:30 2005 From: heuermh at acm.org (Michael Heuer) Date: Fri Sep 23 12:32:41 2005 Subject: [Biojava-l] Apache License vs. (L)GPL In-Reply-To: <200509231143.j8NBhNnq021556@portal.open-bio.org> Message-ID: Hello Martin, I think the concern is only in the opposite direction, when an Apache-licensed library wishes to include a GPL-licensed library as a dependency. As long as you adhere to the conditions of the LGPL for BioJava (include the text of the LGPL in your distribution) and of the Apache license for the commons libraries (include the text of the Apache licence and a NOTICE.txt file in the distribution or a section in your README.txt with the text "This product includes software developed by The Apache Software Foundation (http://www.apache.org/).") then you are fine. michael On Fri, 23 Sep 2005, Martin Szugat wrote: > Hi! > > I'm using BioJava with my BioWeka project (www.bioweka.org). I'd like to > create a distribution with BioWeka (GPL), BioJava (LGPL) and the Apache > Commons libraries (Apache license) which are required by BioJava. However > there seems to be an incompatibility between the GPL/LGPL and the Apache > license: > > http://apache.slashdot.org/article.pl?sid=04/02/18/215242&tid=117&tid=185&ti > d=17&tid=2 > > But the Apache foundation says the licenses are compatible: > > http://www.apache.org/foundation/licence-FAQ.html#GPL > > So I'm a little bit confused if I'm allowed to package all libraries in the > same distribution. Maybe someone can clarify that. I already contacted the > Apache foundation but didn't get an answer, yet. > > Best regards > > Martin > > > _______________________________________________ > Biojava-l mailing list - Biojava-l@biojava.org > http://biojava.org/mailman/listinfo/biojava-l > From mark.schreiber at novartis.com Sun Sep 25 21:42:51 2005 From: mark.schreiber at novartis.com (mark.schreiber@novartis.com) Date: Sun Sep 25 21:42:48 2005 Subject: [Biojava-l] Apache License vs. (L)GPL Message-ID: In Biojava the main code is LGPL and some of our dependencies are Apache license. This doesn't seem to cause any problem. In your distribution you can release the biojava jars as LGPL, the dependencies as Apache and BioWeka as GPL. The only thorny part is code that you write which has dependency on Weka. This probably needs to be released as GPL under my understanding of the GPL. Under my understanding of IP law (I'm not a lawyer) 99% of licensing is enforcability. If you release code under reasonable terms how likely is it that the Weka group will sue you? The remaining 1% is always negotiable. Why not ask the Weka group how they think it should be distributed? If you get a letter from them to say you can put an LGPL or Apache license on your code then your covered. They seem like reasonable people, they're from New Zealand. It's a small and reasonable nation : ) My pseudo-legal advice would be to negotiate this directly with the Weka group. Then everyone is happy. - Mark Mark Schreiber Principal Scientist (Bioinformatics) Novartis Institute for Tropical Diseases (NITD) 10 Biopolis Road #05-01 Chromos Singapore 138670 www.nitd.novartis.com phone +65 6722 2973 fax +65 6722 2910 Michael Heuer Sent by: biojava-l-bounces@portal.open-bio.org 09/24/2005 12:12 AM To: Martin Szugat cc: biojava-l@biojava.org, (bcc: Mark Schreiber/GP/Novartis) Subject: Re: [Biojava-l] Apache License vs. (L)GPL Hello Martin, I think the concern is only in the opposite direction, when an Apache-licensed library wishes to include a GPL-licensed library as a dependency. As long as you adhere to the conditions of the LGPL for BioJava (include the text of the LGPL in your distribution) and of the Apache license for the commons libraries (include the text of the Apache licence and a NOTICE.txt file in the distribution or a section in your README.txt with the text "This product includes software developed by The Apache Software Foundation (http://www.apache.org/).") then you are fine. michael On Fri, 23 Sep 2005, Martin Szugat wrote: > Hi! > > I'm using BioJava with my BioWeka project (www.bioweka.org). I'd like to > create a distribution with BioWeka (GPL), BioJava (LGPL) and the Apache > Commons libraries (Apache license) which are required by BioJava. However > there seems to be an incompatibility between the GPL/LGPL and the Apache > license: > > http://apache.slashdot.org/article.pl?sid=04/02/18/215242&tid=117&tid=185&ti > d=17&tid=2 > > But the Apache foundation says the licenses are compatible: > > http://www.apache.org/foundation/licence-FAQ.html#GPL > > So I'm a little bit confused if I'm allowed to package all libraries in the > same distribution. Maybe someone can clarify that. I already contacted the > Apache foundation but didn't get an answer, yet. > > Best regards > > Martin > > > _______________________________________________ > Biojava-l mailing list - Biojava-l@biojava.org > http://biojava.org/mailman/listinfo/biojava-l > _______________________________________________ Biojava-l mailing list - Biojava-l@biojava.org http://biojava.org/mailman/listinfo/biojava-l From Martin.Szugat at GMX.net Mon Sep 26 05:52:57 2005 From: Martin.Szugat at GMX.net (Martin Szugat) Date: Mon Sep 26 05:54:07 2005 Subject: [Biojava-l] Apache License vs. (L)GPL In-Reply-To: Message-ID: <200509260952.j8Q9qdnq029778@portal.open-bio.org> Hi Mark, Asking the Weka people is a good idea! I didn't think about this because the distribution does not contain the Weka library however you are right my library is based on Weka and so I have to clarify that. Thanks for the advice! Martin > -----Original Message----- > From: mark.schreiber@novartis.com [mailto:mark.schreiber@novartis.com] > Sent: Monday, September 26, 2005 3:43 AM > To: Michael Heuer > Cc: biojava-l@biojava.org; biojava-l-bounces@portal.open-bio.org; Martin > Szugat > Subject: Re: [Biojava-l] Apache License vs. (L)GPL > > In Biojava the main code is LGPL and some of our dependencies are Apache > license. This doesn't seem to cause any problem. In your distribution you > can release the biojava jars as LGPL, the dependencies as Apache and > BioWeka as GPL. The only thorny part is code that you write which has > dependency on Weka. This probably needs to be released as GPL under my > understanding of the GPL. > > Under my understanding of IP law (I'm not a lawyer) 99% of licensing is > enforcability. If you release code under reasonable terms how likely is it > that the Weka group will sue you? The remaining 1% is always negotiable. > Why not ask the Weka group how they think it should be distributed? If you > get a letter from them to say you can put an LGPL or Apache license on > your code then your covered. They seem like reasonable people, they're > from New Zealand. It's a small and reasonable nation : ) > > My pseudo-legal advice would be to negotiate this directly with the Weka > group. Then everyone is happy. > > - Mark > > Mark Schreiber > Principal Scientist (Bioinformatics) > > Novartis Institute for Tropical Diseases (NITD) > 10 Biopolis Road > #05-01 Chromos > Singapore 138670 > www.nitd.novartis.com > > phone +65 6722 2973 > fax +65 6722 2910 > > > > > > Michael Heuer > Sent by: biojava-l-bounces@portal.open-bio.org > 09/24/2005 12:12 AM > > > To: Martin Szugat > cc: biojava-l@biojava.org, (bcc: Mark Schreiber/GP/Novartis) > Subject: Re: [Biojava-l] Apache License vs. (L)GPL > > > Hello Martin, > > I think the concern is only in the opposite direction, when an > Apache-licensed library wishes to include a GPL-licensed library as a > dependency. > > As long as you adhere to the conditions of the LGPL for BioJava (include > the text of the LGPL in your distribution) and of the Apache license for > the commons libraries (include the text of the Apache licence and a > NOTICE.txt file in the distribution or a section in your README.txt with > the text "This product includes software developed by The Apache Software > Foundation (http://www.apache.org/).") then you are fine. > > michael > > > On Fri, 23 Sep 2005, Martin Szugat wrote: > > > Hi! > > > > I'm using BioJava with my BioWeka project (www.bioweka.org). I'd like to > > create a distribution with BioWeka (GPL), BioJava (LGPL) and the Apache > > Commons libraries (Apache license) which are required by BioJava. > However > > there seems to be an incompatibility between the GPL/LGPL and the Apache > > license: > > > > > http://apache.slashdot.org/article.pl?sid=04/02/18/215242&tid=117&tid=185& > ti > > d=17&tid=2 > > > > But the Apache foundation says the licenses are compatible: > > > > http://www.apache.org/foundation/licence-FAQ.html#GPL > > > > So I'm a little bit confused if I'm allowed to package all libraries in > the > > same distribution. Maybe someone can clarify that. I already contacted > the > > Apache foundation but didn't get an answer, yet. > > > > Best regards > > > > Martin > > > > > > _______________________________________________ > > Biojava-l mailing list - Biojava-l@biojava.org > > http://biojava.org/mailman/listinfo/biojava-l > > > > > _______________________________________________ > Biojava-l mailing list - Biojava-l@biojava.org > http://biojava.org/mailman/listinfo/biojava-l > From felipe.albrecht at gmail.com Fri Sep 30 09:33:24 2005 From: felipe.albrecht at gmail.com (Felipe Albrecht) Date: Fri Sep 30 09:36:17 2005 Subject: [Biojava-l] Asn.1 Parser Message-ID: Hello, Im needing read some Asn.1 Files, for this, I searched in the web by java asn.1 parses, but I dont found anyone. Because this, I think to write my parser using Javacc and do as one biojava extension. My questions are: * Really, dont exist a Asn.1 Java parser? * If not, how is the best aproach? Do like Dom parser, that generate class representing the elements or do like Sax, that occour actions when enter in the elements? * Uses javacc? The code gerate by javacc is bigger, but is more easy to write and to keep the code. Or do "by hand" the read? Thanks Felipe Albrecht From heuermh at acm.org Fri Sep 30 16:11:30 2005 From: heuermh at acm.org (Michael Heuer) Date: Fri Sep 30 16:28:45 2005 Subject: [Biojava-l] Asn.1 Parser In-Reply-To: Message-ID: Hello Felipe, You should be able to find support for ASN.1 in the ncbi toolkit, e.g. > http://www.ncbi.nlm.nih.gov/Web/Newsltr/V14N1/toolkit.html And google turned this up for me: > http://directory.apache.org/subprojects/asn1/index.html "The Apache ASN.1 runtime is a high performance non-blocking replacement for the Snacc4J runtime and eventually its Java stub compiler for ASN.1. It is designed from the ground up to work with NIO constructs like Channels and ByteBuffers." michael On Fri, 30 Sep 2005, Felipe Albrecht wrote: > Hello, > > Im needing read some Asn.1 Files, > for this, I searched in the web by java asn.1 parses, but I dont found anyone. > > Because this, I think to write my parser using Javacc and do as one > biojava extension. > > My questions are: > * Really, dont exist a Asn.1 Java parser? > > * If not, how is the best aproach? > Do like Dom parser, that generate class representing the elements > or do like Sax, that occour actions when enter in the elements? > * Uses javacc? The code gerate by javacc is bigger, but is more easy > to write and to keep the code. Or do "by hand" the read? > > Thanks > > Felipe Albrecht > > _______________________________________________ > Biojava-l mailing list - Biojava-l@biojava.org > http://biojava.org/mailman/listinfo/biojava-l >