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.
Maven allows you to run the compiler as a separate process by setting `true`. This feature can lead to much less garbage collection and make Maven build faster. This project...
This addresses #1019 and was developed in parallel with @josemduarte's fix #1020. It has been rebased to remove duplicated effort, and now consists mostly of additional tests for the bug.
D-AminoAcids (https://proteopedia.org/wiki/index.php/Amino_Acids) are optical isomers or enantiomers (mirror images) of naturally occuring L-AminoAcids. They have the same structure but with opposite chirality. When I parse structures that contain D-AminoAcids, they...
I think `Profile` was indended to be general enough to represent multiple sequence alignments. However `SimpleProfile` is the only current implementation and it only supports pairwise alignments. There is also...
Hello, I am software developer (new to biojava) currently using the Biojava API [biojava-core - 4.0.0 , alignment -1.9.3] for an application. We are trying to accomplish Alignment render of...
Given a transcript sequence derived from a GeneSequence defined on reverse strand of a chromosomal sequence, the method getCodingSequence doesn't return the reverse complement, but just the reverse. This seems...
Hi, Been looking at the ontology module as it might be useful in my day job. I tried parsing the latest GO flatfile at http://geneontology.org/docs/download-ontology/#go_basic and the parser handles it...
Support of D-AminoAcids (to be recognized as AminoAcids instead of HetAtomGroups). Other modoficatiosn may follow to support bigger ChemComp names. Related to #993
Test coverage is little low - covering more code would enable - more confident refactoring. In a code-base with contributions over a long period of time there are cases where...
What's the intended meaning of `PDBHeader.getDescription`? It is populated in mmCIF with the `_struct_keywords.pdbx_keywords` field, the same as `getClassification()` (e.g. lyase, oxidase, etc). It seems to be unused in PDB...