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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I’ve seen a solution online for a wrapper module, and it turns out it’s enough to create a wrapper for org.

Both provide comprehensive collections of methods for protein sequences. Both are open source projects. True at a given index means selected whereas false means not selected. I’ve tried switching the osgidependencies off, but this does not seem to make a difference other than that the wrapper won’t compile.

The sequence position specific features contained in the classes are also transformed. Both, the nucleotide sequence and the peptide sequence are contained in the same StrapProtein object.

A StrapProtein can hold both at the same time if a coding nucleotide sequence was read and translated into protein.


I’m trying to use the There is biojaav biojava tutorial at. BioJava is applicable to nucleotide and peptide sequences and can be applied for entire genomes.

Mark Schreiber maintains an excellent introduction, with many examples: Therefore programmers might commit programming errors like manipulating byte arrays directly instead of using the setter methods. In the menu Plugins of the toolbar is a menu item Start standard plugin Hi I’m new to BioJava so please forgive my ignorance.

I’ve created a Maven module as a wrapper, including org. The symbols can be retrieved one after the other with an iterator or sub-sequences can be obtained. Both can read and write many sequence file formats. In BioJava sequence positions are realized by the class Location.

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I’m sorry I can’t help you, I don’t know a lot about maven, netbeans or biojava STRAP is designed for protein sequences but can read coding nucleotide files, which are then translated to peptide sequences. The other class creates a StrapProtein object from a GappedSequence object.

Please log in to add an answer. BioJava is used where speed is less critical. It could be that the biojava jars contain osgi headers and then you are not wrapping the jars in module, but declare a dependency on osgi plugin. In the Netbeans IDE, the classes are found and used in autocompletion, and the project builds successfully, in each case indicating that principally the dependencies are set up correctly.


That’s a great idea, Jaap, you’re right.


Thanks for responding, I’ll have a coikbook. I’m using biojava classes and modules over Eclipse IDE. Here’s the wrapper’s pom file: You can also clone a specific tag say 4.

The difference in imports is due to the package name change in Biojava version 4.

CSC8311 — Advanced Object-Orientated Programming

Unfortunately, I’m not completely clear on when to use a module as osgi or just as a jar. Here’s some code I try to get to work. Input and output are just text fields. When debugging, it seems everything locks up when I try to instantiate an object.