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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To enhance speed, STRAP avoids frequent object instantiations and invocation of non-final object-methods to enhance speed. Sign up using Email and Password. The sequence position specific features contained in the classes are also transformed.

Sign up or log in Sign up using Google. I am working with large fastq file. Then, from another module I set the cookbook as a dependency, and use some of the basic examples from the BioJava cookbook for testing. I have a difficult experiment and I need some advice on how to proceed. The wrapper should then be used in the BioJava dependent modules, but it should work for other modules depending on slf4j as well.

CSC8311 — Advanced Object-Orientated Programming

I searched for possible solutions but did not find anything helpful. 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. BioJava is well designed in terms of type safety, ontology and object design. Thanks for responding, I’ll have a look. The other class creates a StrapProtein object from a GappedSequence object.

In BioJava peptide sequences and nucleotide sequences are lists of symbols. That’s a great idea, Jaap, you’re right. The difference in imports is due to the package name change in Bipjava version 4.


Now all packages are starting with org. Both provide comprehensive collections of methods for protein sequences. Both are used by Java programmers for coding Bioinformatics algorithms. There you can select the BioJava example. A StrapProtein can hold both at the same time if a coding cookboo, sequence was read and translated into protein. I found that BioJava can help 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.

STRAP is designed for protein sequences but can read coding nucleotide files, which are then translated to peptide sequences.

The BIOJAVA interface in STRAP

Sign up using Facebook. I’ve tried to perform the same code in a regular swing app, and it works indeed locking the gui but in a regular time frame. Two classes are provided biojavq convert objects between both tool-kits: STRAP is very fast since the graphical user interface must be highly responsive. I’ve created a Maven module as a wrapper, including org. Input and output are just text fields. Therefore programmers might commit programming biojxva like manipulating byte arrays directly instead of using the setter methods.

BioJava throws exceptions when methods are invoked with invalid parameters. Does it make sense or do you think b Both are open source projects.

When debugging, it seems everything locks up when I try to instantiate an object. In the menu Plugins of the toolbar is a menu item Start standard plugin 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.

Sorry for my lazyness. The advantages are that the entire sequence does not necessarily reside in memory and coookbook programs are less susceptible to programming errors. By using our site, you acknowledge that you have read and understand our Cookie PolicyPrivacy Policyand our Terms of Service.


I’ve seen a solution online for a wrapper module, and it coolbook out it’s enough to create a wrapper for org. Hi I’m new to BioJava so please forgive my ignorance. Unfortunately, I’m not completely clear on when to use a module as osgi or just as a jar. Discontiguous Location objects are composed of several contiguous RangeLocation objects or PointLocation objects.

I’ve tried switching the osgidependencies off, but cookbookk does not seem biojaba make a difference other than that the wrapper won’t compile. In BioJava sequence positions are realized by the class Location.

I’m using biojava classes and modules over Eclipse IDE. Powered by Biostar version 2. Hi Henk, you should post some of the code your using, try to get a minimal example which has the bug.

BioJava in Anger

Post Your Answer Discard 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. Classes in Strap cookbpok internal data. Can’t get biojava to work in a Maven Netbeans application Ask Question. 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.

Thank you, I’ll give that a go. Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

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