The biojava3-genome library leverages the sequence relationships in biojava3- core to read(gtf,gff2,gff3) files and write gff3 files. The file formats for gtf, gff2, gff3 . Collection of quick ‘recipes’ for common BioJava tasks – biojava/biojava- cookbook. Contribute to biojava/biojava-tutorial development by creating an account on Please check the BioJava Cookbook for a more comprehensive collection of.

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Both, the nucleotide sequence and the peptide sequence are contained in the same StrapProtein object. Both provide comprehensive collections of methods for protein sequences.

Even single amino acids or nucleotides are object references. Henk van den Toorn 6 4. Also is there any proper documentation for Biojava?

Both can read and write many sequence file formats.

The BIOJAVA interface in STRAP

Multiple positions are given by boolean arrays. Another disadvantage is that no checks are performed in STRAP whether the characters cookhook sequences are valid with respect to an underlying alphabet. The other class creates a StrapProtein object from a GappedSequence object.

Sign up using Facebook. I’ve done a lot of searching and found that the actual culprit is slf4j, that’s used throughout BioJava. By clicking “Post Your Answer”, you acknowledge that you have read our updated terms of serviceprivacy policy and cookie policyand that your continued use of the website is subject to these policies. I’m trying to test this example from the Biojava legacy cookbook, but it gives me the foll Powered by Biostar version 2. Biojava requires slf4j which does have osgi headers.


Whenever I try to instantiate some object of a class from BioJava, the application freezes and I have to kill it using the Windows task manager. Stack Overflow works best with JavaScript enabled. Does it make sense or do you think b This way people can help if they happen to have experience. Please log in to add an answer. Thanks for responding, I’ll have a look.

You can also clone a specific tag say 4. BioJava is well designed in terms of type safety, ontology and object design. BioJava is applicable to nucleotide and peptide sequences and can be vookbook for entire genomes. I have been using biojava and was able to load fasta files. Cokobook using biojava classes and modules over Eclipse IDE.

Both are used by Java programmers for coding Bioinformatics algorithms. That’s a great idea, Jaap, you’re right. One makes an GappedSequence object from a Bijoava instance. Hi Henk, you should post some of the code your using, try to get a minimal example which has the bug.

I have a difficult experiment and I need some advice on how to proceed. There is a biojava vookbook at. For the class StrapProtein however, single residue positions ccookbook indicated by integer numbers between 0 and countResidues The wrapper should then be used in the BioJava dependent modules, but it bkojava work for other modules depending on slf4j as well.

Besides speed the low memory consumption is an important advantage of basic data types. I suggest you can manage biojava dependencies via Maven to resolve those inconsistencies, check out these links: I am working with large fastq file. However locking of the app is weird, if there was something wrong with the runtime dependencies Cookbbook would have expected an early ‘unsatisfied dependencies’ error.


A StrapProtein can hold both biojvaa the same time if a coding nucleotide sequence was read and translated into protein. I don’t know why it freezes the platform application, but I’m able to cause my module to not install by creating a slf4j logger in it. Here’s the wrapper’s pom file: Hi people, I have got a Java question for you: Two classes are provided to convert objects between both tool-kits: I’ve done a lot of tracing, and found the program freezes when running the constructor or, as I went through reflection to debug it, inside the ConstructorAccessor when the Constructor.

java – Can’t get biojava to work in a Maven Netbeans application – Stack Overflow

To enhance speed, STRAP avoids frequent object instantiations and invocation of non-final object-methods to enhance speed. The advantages are that the entire sequence does not necessarily reside in memory and that programs are less susceptible to programming errors. I’m still very confused about this I’m sorry I can’t help you, I don’t know a lot about maven, netbeans or biojava Classes in Strap expose internal data.

Thank you, I’ll give that a go. The sequence position specific features contained in the classes are also transformed. Post as a guest Name. Looks like the differences are because of some mess with versions, to get more details you need to check biouava version of biojava and the source code of imported classes.