Remove seq data - Githubissues

cmbi / kmad

Knowledge based multiple sequence alignment for intrinsically disordered proteins

http://www.cmbi.ru.nl/kmad

GNU General Public License v3.0

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Remove seq data #37

Closed joannalange closed 8 years ago

joannalange commented 8 years ago

Remove the seq_data namespace and move all its functionality to the fasta namespace; use the FastaData struct instead of SequenceData struct.

@jonblack, any comments?

jonblack commented 8 years ago

The functions moved from seq_data.h/.cpp (get_conf_data, remove_gaps, assign_feature_by_pattern, find_real_pos, make_feature_list) aren't involved in parsing the "fasta" file so should be somewhere else. I suspect for now f_config.h/.cpp is the best place (when we refactor the config stuff we can improve upon this);
I've created some issues for the config parsing and put them in #38 for later.

jonblack commented 8 years ago

Are you still working on the other comments I made?

joannalange commented 8 years ago

Slowly, didn't have much time last week, but I hope to get it done in the next couple of days

joannalange commented 8 years ago

I've moved the functions to f_config, do you think I can merge it now, @jonblack?

jonblack commented 8 years ago

:+1: Looks good. Make sure you merge + squash in GitHub so we don't have a long list of commits in the history :smile:

joannalange commented 8 years ago

Huh... I don't get it, I squashed all commits from the remove-seq-data branch but still all of them are in history... I guess I'm doing something wrong

@jonblack, should I have done sth else apart from just rebasing it and clicking the 'merge pull request' button? Should I do it from the cmd line or sth like that?

jonblack commented 8 years ago

When you merge in GitHub there is a drop down with the option to squash. That's the easiest way.

joannalange commented 8 years ago

ahhhh alright, will know the next time