biojava
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biojava
:book::microscope::coffee: BioJava is an open-source project dedicated to providing a Java library for processing biological data.
Hi, The code only keeps one alt_id for a term since it stores it as a value for [alt_id](https://github.com/biojava/biojava/blob/master/biojava-ontology/src/main/java/org/biojava/nbio/ontology/obo/OboFileHandler.java#L170) key in annotation. Would it be possible for you to fix...
Since we are releasing a new version of biojava that introduces a number of **API** changes, I would like to suggest a review of some of the command line (**CLI**)...
It would be great to be able to create sequence aligner objects without specifying target and query sequences, so that the parameters (or options), like gap penalty, alignment type and...
see this thread on the mailing list http://lists.open-bio.org/pipermail/biojava-l/2016-July/011489.html A test file is here https://github.com/biopython/biopython/blob/master/Tests/Abi/3730.ab1
Creating a new `contact.ResidueIdentifier` (not to be confused with `ResidueNumber`) requires that the Group have a valid alignedResIndex in the corresponding `Compound`. Is there a reasonable way to handle missing...
We don't have an easy way of serializing/deserializing a collection of sequences. This does not work: http://mailman.open-bio.org/pipermail/biojava-l/2015-February/011357.html Alternative workarounds could be: - Tweak Kryo for some nonstandard InstantiatorStrategy - Use...
Hi guys, it might be an issue with the code on my end, but although my BasePairParameters class works to serialize my data, it still doesn't correctly serialize the Structure...
When trying to display a structure in **Jmol**, for example from the `MultipleAlignmentGUI`, the following error gets thrown and the JmolPanel remains empty: java.lang.ArithmeticException: / by zero at org.jmol.adapter.readers.cif.MessagePackReader.getInts(MessagePackReader.java:406) at...
When an alignment is performed in the `AlignmentGUI`, the resulting Jmol panel does show the first structure and the ligand of the second structure, but it does not show any...
AbstractSequence always gets very first occurrence of source:db_xref and uses it as a taxon ID. [line 133](https://github.com/biojava/biojava/blob/master/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/AbstractSequence.java#L133) Here is the example of NCBI entry it fails to parse https://www.ncbi.nlm.nih.gov/protein/AAK76245.1 Taxonomy...
