Miriam annotation #1266
Miriam annotation #1266
Conversation
Codecov Report
@@ Coverage Diff @@
## develop #1266 +/- ##
==========================================
Coverage ? 43.09%
==========================================
Files ? 869
Lines ? 63541
Branches ? 0
==========================================
Hits ? 27380
Misses ? 36161
Partials ? 0
Continue to review full report at Codecov.
|
|
merge |
| % invertSelection: Invert the qualifierSelection i.e. use | ||
| % only those specified (default: false); | ||
| % | ||
| % OUTPUT: |
| arrayDim2Pos = arrayDim2Pos + 1; | ||
| end | ||
|
|
||
| %Now, build a struct out of this cell array. |
There was a problem hiding this comment.
May you format all comments as % now, ... (space and lowercase) ?
| % only a single element is annotated, or a cell array of | ||
| % chars if multiple elements are annotated. | ||
| % | ||
| % OPTIONAL INPUT |
|
|
||
| %Get the defined databases | ||
| try | ||
| dbs = getRegisteredDatabases(); |
There was a problem hiding this comment.
Can this error be thrown inside of getRegisteredDatabases?
| databases = repmat({databases},numel(ids),1); | ||
| end | ||
|
|
||
|
|
There was a problem hiding this comment.
May you add here a few more comments?
| annotationQualifier = columnVector(annotationQualifier); | ||
|
|
||
|
|
||
|
|
There was a problem hiding this comment.
Also here, a few more comments would be nice.
| annotationQualifiers = unique(annotationQualifier); | ||
| udatabases = unique(databases); | ||
|
|
||
|
|
There was a problem hiding this comment.
Any more comments that you could add?
|
|
||
|
|
||
| %Now, we have to go through all base Fields | ||
| for field = 1 : numel(usedFields) |
There was a problem hiding this comment.
Maybe add more comments here to make this part more readable.
| assert(all(strcmp(modelWithID.rxnisbrendaID(2:end),''))); | ||
| assert(strcmp(modelWithID.rxnisbrendaID{1},validBrendaID)); | ||
| additionalIDs = {validBrendaID, '2.3.4.5', '5.6.7.8'}; | ||
| %Add multiple additional IDs (we need the ID 3 times. |
There was a problem hiding this comment.
May you add a blank line before each comment to improve readability?
| assert(strcmp(annotations.cvterms(1).qualifierType,'bioQualifier')) | ||
| %It contains all those IDs. | ||
| assert(isempty(setxor({annotations.cvterms(1).ressources(:).id},additionalIDs))); | ||
| %And its the brenda database |
There was a problem hiding this comment.
The format of the comments is not consistent (see my comments above).
|
Thanks @tpfau 👍 |
This pr adds functionality to add MIRIAM annotations to the model.
I hereby confirm that I have:
developas a target branch (top left drop-down menu)(Note: You may replace [ ] with [X] to check the box)