From ngsbioinformatics at gmail.com Tue Dec 11 12:18:27 2012 From: ngsbioinformatics at gmail.com (Ryan Golhar) Date: Tue, 11 Dec 2012 12:18:27 -0500 Subject: [Biojava-l] bj 3.0.5 vs 3.0.4 Message-ID: Hi - I just noticed 3.0.5 FeatureList class is missing sortByGenomicStart function. Why was this removed? From ngsbioinformatics at gmail.com Tue Dec 11 13:03:03 2012 From: ngsbioinformatics at gmail.com (Ryan Golhar) Date: Tue, 11 Dec 2012 13:03:03 -0500 Subject: [Biojava-l] bj 3.0.5 vs 3.0.4 In-Reply-To: References: Message-ID: I just realized this may be something I implemented myself as I don't see it in SVN on biojava 3.0.4. I'd like to submit this is a feature to sort feature based on genomic start position. On Tue, Dec 11, 2012 at 12:18 PM, Ryan Golhar wrote: > Hi - I just noticed 3.0.5 FeatureList class is missing sortByGenomicStart > function. Why was this removed? From interlichtspielhaus at gmail.com Tue Dec 25 16:52:07 2012 From: interlichtspielhaus at gmail.com (INTERLICHTSPIELHAUS) Date: Tue, 25 Dec 2012 22:52:07 +0100 Subject: [Biojava-l] download biojava3-aa-prop3.0.5-sources.jar : 404 Message-ID: hi the sources jar biojava3-aa-prop3.0.5-sources.jar doesn't seem to be in the right spot: http://biojava.org/wiki/BioJava:Download The requested URL /download/maven/org/biojava/biojava3-aa-prop/3.0.5/biojava3-aa-prop3.0.5-sources.jar was not found on this server. regards inS From andreas at sdsc.edu Sat Dec 1 00:57:55 2012 From: andreas at sdsc.edu (Andreas Prlic) Date: Fri, 30 Nov 2012 16:57:55 -0800 Subject: [Biojava-l] biojava 3.0.5 released Message-ID: BioJava 3.0.5 has been released and is available from http://www.biojava.org/wiki/BioJava:Download as well as from the BioJava maven repository at http://www.biojava.org/download/maven/ . New Features: - New parser for CATH classification - New parser for Stockholm file format - Significantly improved representation of biological assemblies of protein structures. Now can re-create biological assembly from asymmetric unit - Several bug fixes Thanks to Daniel Asarnow for contributing the CATH parser and Amr Al Hossary and Marco Vaz for their contributions to the Stockholm parser. Happy BioJava-ing, Andreas From ngsbioinformatics at gmail.com Tue Dec 11 17:18:27 2012 From: ngsbioinformatics at gmail.com (Ryan Golhar) Date: Tue, 11 Dec 2012 12:18:27 -0500 Subject: [Biojava-l] bj 3.0.5 vs 3.0.4 Message-ID: Hi - I just noticed 3.0.5 FeatureList class is missing sortByGenomicStart function. Why was this removed? From ngsbioinformatics at gmail.com Tue Dec 11 18:03:03 2012 From: ngsbioinformatics at gmail.com (Ryan Golhar) Date: Tue, 11 Dec 2012 13:03:03 -0500 Subject: [Biojava-l] bj 3.0.5 vs 3.0.4 In-Reply-To: References: Message-ID: I just realized this may be something I implemented myself as I don't see it in SVN on biojava 3.0.4. I'd like to submit this is a feature to sort feature based on genomic start position. On Tue, Dec 11, 2012 at 12:18 PM, Ryan Golhar wrote: > Hi - I just noticed 3.0.5 FeatureList class is missing sortByGenomicStart > function. Why was this removed? From interlichtspielhaus at gmail.com Tue Dec 25 21:52:07 2012 From: interlichtspielhaus at gmail.com (INTERLICHTSPIELHAUS) Date: Tue, 25 Dec 2012 22:52:07 +0100 Subject: [Biojava-l] download biojava3-aa-prop3.0.5-sources.jar : 404 Message-ID: hi the sources jar biojava3-aa-prop3.0.5-sources.jar doesn't seem to be in the right spot: http://biojava.org/wiki/BioJava:Download The requested URL /download/maven/org/biojava/biojava3-aa-prop/3.0.5/biojava3-aa-prop3.0.5-sources.jar was not found on this server. regards inS