biojava
biojava copied to clipboard
biojava
:book::microscope::coffee: BioJava is an open-source project dedicated to providing a Java library for processing biological data.
This feature calculates the aromaticity value of a protein according to Lobry, 1994. It is simply the relative frequency of Phe+Trp+Tyr.
Using a local alignment with linear gap penalty resulted in the failure trace below. Setting pointers to dimension (ye+1,1) fixed the error. Added a test "testLinearAlignmentLocal()" in TestDNAAlignment.java to verify...
I'd like to propose that we make our first Java 11 release and call it 6.1.0. That will mean that BioJava won't be possible to use under a JRE 8...
I am using BioJava through Maven, using biojava 6.0.5 and biojava-ws 6.0.4 (because trying to use 6.0.5 produces errors): ``` org.biojava biojava 6.0.5 pom org.biojava biojava-ws 6.0.4 ``` I'm trying...
A discussion came up in PR #774 regarding the correct behavior when parsing an mmCif file without `auth_seq_id`. BioJava 4.2.11 requires the `auth_seq_id` column. This is a problem because it...
...while setting all the metadata consistently and handling ligands intuitively (i.e. keeping the adjacent/bound ligands in). The closest approximation of this functionality can be done via `new StructureName("4hhb.A").reduce(structure)`, but: 1....
When a file is being downloaded, two metadata files are created for size and hash (as possible). I applied this validation framework to the files I know (structure files, SCOP...
The following functions in [PDBStatus](https://github.com/biojava/biojava/blob/master/biojava-structure/src/main/java/org/biojava/nbio/structure/PDBStatus.java) are called from [PDBStatusTest.java:](https://github.com/biojava/biojava/blob/master/biojava-structure/src/test/java/org/biojava/nbio/structure/PDBStatusTest.java) 1.public static Status **getStatus**(String pdbId) throws IOException 2.public static Status[] **getStatus**(String[] pdbIds) throws IOException 3.public static String getCurrent(String oldPdbId) throws IOException...
Adds junit-4 extension, saflate, which provides a rule to skip network flaky tests on network related exceptions during test execution.
- It is quite often when a file is being downloaded that it downloads incomplete or corrupted; which could lead to unexpected potential problems. - I propose to create one...