smith-chem-wisc / PrivateNeo

OLD. SEE https://github.com/zrolfs/MetaMorpheus/tree/Neo-Fusion for current code. Downstream analysis for MetaMorpheus to identify novel spliced peptides
0 stars 0 forks source link

Rough reorganization #2

Closed acesnik closed 7 years ago

acesnik commented 7 years ago

Hey Zach,

Here's a rough start on reorganizing the Neo code. More work to be done.

Namely, we generally place working logic in a separate project, which makes the dependency of the GUI on the working logic clearer. It also makes it easier to move over to mzLib should we want to do that.

I also created a testing project.

Are you interested in having this type of organization? If so, feel free to merge and work off of this.

Yet to be done: MassCalculator is interwoven with MessageBox.Show() methods, which should be removed. You could throw exceptions instead, or return strings to display in the GUI. Then, you can move it to the internal logic project to satisfy the dependencies of other classes on that one.

AC

acesnik commented 7 years ago

I'd recommend you check it out through here: https://github.com/acesnik/PrivateNeo, since the diff is pretty busy.

zrolfs commented 7 years ago

I was planning on doing most of the changes that you made, so I appreciate the help. I'm fine merging the first two commits, but why were the dictionary's deleted in the 3rd?

acesnik commented 7 years ago

Those are generated on the fly when you build and run the program. They're in the debug folder.

acesnik commented 7 years ago

If any of those aren't generated on the fly, they should be included in your project folders, so be sure to check on that before merging.

zrolfs commented 7 years ago

The dictionaries can take hours to produce on the fly. There's a check to pull a dictionary from the bin if it already exists

acesnik commented 7 years ago

Okay, would you like them in one of the project folders instead?

zrolfs commented 7 years ago

Yes please.

acesnik commented 7 years ago

It can be copied to the bin from the project.

acesnik commented 7 years ago

Sounds good.

acesnik commented 7 years ago

Should be set, now.

zrolfs commented 7 years ago

Hi Anthony, It's looking good so far. I'm changing the error messages to only show if there's a message, but otherwise I like the changes. There are several methods that are no longer used, so I'll delete a couple of those and commit the edits into this pull request. I'm just running some manual tests before accepting the pull request.

acesnik commented 7 years ago

🎉