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.

I found that BioJava can help I’ve tried switching the osgidependencies off, but this does not seem to make a difference other than that the wrapper won’t compile. By using our site, you acknowledge that you have read and understand our Cookie PolicyPrivacy Policyand our Terms of Service. BioJava is used where speed is less critical.

Hi I’m new to BioJava so please forgive my ignorance. The other class creates a StrapProtein object from a GappedSequence object.

STRAP and BIOJAVA

coookbook Here’s some code I try to get to work. You can also clone a specific tag say 4. The sequence position specific features contained in the classes are also transformed. STRAP is very fast since the graphical user interface must be highly responsive. STRAP cannot cope with single sequences as long as an entire chromosome. I am working with large fastq file. Biojava requires slf4j which does have osgi headers.

There is a biojava tutorial at. That’s a great idea, Jaap, you’re right. Then, from another module I set the wrapper fookbook a dependency, and use some of the basic examples from the BioJava cookbook for testing. For the class StrapProtein however, single residue positions are indicated by integer numbers between 0 and countResidues I’ve done a lot of searching and found that the actual culprit is slf4j, that’s used throughout BioJava.

CSC8311 — Advanced Object-Orientated Programming

I’ve created a Maven module as a wrapper, including org. To enhance speed, STRAP avoids frequent object instantiations and invocation of non-final object-methods to enhance speed. Multiple positions are given by boolean arrays. 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.

Hi Henk, you should post some of the code your using, try to get a minimal example bjojava has the bug.

Whenever I try to instantiate some object of a class from BioJava, the application freezes and I have to kill cookboo, using the Windows task manager. 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.

Setting to ‘on’ makes the module compile once more. Sign cookbooo using Email and Password. Both provide comprehensive collections of methods for protein sequences. Sign up or log in Sign up using Google. Thanks for responding, I’ll have a look. It could be coookbook the biojava jars contain osgi headers and then you are not wrapping the jars in module, but declare a dependency on osgi plugin.

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I have been using biojava and was able to load fasta files. BioJava is applicable to nucleotide and peptide sequences and can be applied for entire genomes.

Mark Schreiber maintains an excellent introduction, with many examples: I’ve seen a solution online for a wrapper module, and it turns out it’s enough to create a wrapper for org. Looks like the differences are because of some mess with versions, to get more details you need to check the version of biojava cookbpok the source code of imported classes.

This way people can help if they happen to have experience.