Quantifiable interfaces for results reading in FlashLFQ #793
Conversation
…gional IQuantifiable in FlashLFQ
…g full file paths
…gger file name additions and wrote tests
…bilty v peptideprophetprobability)
Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## master #793 +/- ##
==========================================
+ Coverage 75.48% 75.52% +0.04%
==========================================
Files 201 202 +1
Lines 30857 30945 +88
Branches 3112 3129 +17
==========================================
+ Hits 23292 23371 +79
- Misses 7039 7040 +1
- Partials 526 534 +8
|
There was a problem hiding this comment.
An excellent display of object oriented programming. Best first time PR that I have seen to date.
I have a few suggestions, but nothing major. Comments were main stylistic and simple things to improve readability and usability.
Excess white space can be removed at the end of many files.
| string proteinAccessions; | ||
| string geneName; | ||
| string organism; | ||
|
|
There was a problem hiding this comment.
Specifically, you should mention that what happens here is also done in UsefulProteomicsDatabases/ProteinDatabaseLoader. i.e., you're parsing a fasta header. What you have is fine for now, but ideally, a future refactor would create a method for parsing fasta headers that is shared by Readers and UsefulProteomicsDatabases
|
There should be more comments at the level of whole classes/interfaces. Like, the descriptions you have in the summary comment for this PR are great. If you just copy and paste those into the top of their respective interfaces/classes, that would be perfect |
| using System.Text; | ||
| using System.Threading.Tasks; | ||
|
|
||
| namespace FlashLFQ.ResultsReading |
There was a problem hiding this comment.
Change the namespace to just FlashLFQ
mzLib/Readers/ExternalResults/BaseClasses/IQuantifiableRecord.cs
Outdated
Show resolved
Hide resolved
| /// <summary> | ||
| /// MsFragger v22.0 output renames the header "PeptideProphet Probability" as just "Probability". | ||
| /// Headers are mutually exclusive, will not both occur in the same file. | ||
| /// As such, both instances need to be accounted for seperately as optional fields. |
There was a problem hiding this comment.
You should delete this line (100)
Overall: created interfaces that enable external result files to be usable by FlashLFQ through the IdentificationAdapter
Interfaces
Implementation
Classes