Aleix Lafita

Hi @tulay, thank you for reporting the issue! Can you be more specific to what Class should be modified in order to adapt the API? I mean the method you...

I checked the specification of the OBO file format and there can be multiple number of `alt_id`. ftp://ftp.geneontology.org/go/www/GO.format.obo-1_2.shtml ``` alt_id Defines an alternate id for this term. A term may...

This is not a bug in **biojava**, but a _feature_ or _characteristic_ of the dynamic programming algorithms for sequence alignment. The solution would involve changing the design of the DP...

Hi @stefanharjes, I was actually arguing to close the issue (without any further modification), because DP algorithms for sequence alignment have the underlying model of AA substitution. My point is...

@stefanharjes I think you confused this issue with #288 (about sub-optimal results). I will answer to your comment in that issue instead of here. This issue is about consecutive gaps,...

Errors 2 and 3 seem to be minor and I guess what we can do is to provide better logging when they occur. Error 1 seems to be the most...

We discussed the need for a **Fast** (and accurate enough) structural alignment algorithm. Another project that could be interesting in addition to the **Non-Sequential** algorithm. I propose as a research...

The structures that superseded them do not throw any `Exception` for parsing, which means the problem was solved when they were obsoleted. However, it seems a common error, since it...

If I remember correctly the input to the `CESymm` method is actually the `Atom` array extracted from the `Structure` object. I wonder if this could be a bigger problem related...

It seems that this field is quite general in use. I propose to create a new method `getKeywords()` to store the data on `_struct_keywords.pdbx_keywords` and leave the `getDescription()` method to...