Using the branch new_feature_model, update packages/jbrowse-plugin-apollo/src/util/loadAssemblyIntoClient.ts to use the new annotation feature format. The new feature format has been imported in that file, so it will need to be adjusted so the the "feature" created and eventually passed to ref.addFeature(feature) matches the new feature format.
You can compare the new and current feature formats, they are in packages/apollo-mst/src/AnnotationFeature.ts (current) and packages/apollo-mst/src/AnnotationFeatureModel.ts (new), but a few things I'll point out:
min and max instead of start and end
CDS features are collapsed so that a feature in multiple positions becomes a single feature (no more "discontinuoutLocations", just take the min of the first CDS and the max of the last CDS)
No more phase (we will calculate it when needed)
"score", if defined, should be added to attributes
You can test this out with the Apollo -> open Local GFF3 file menu. You can use this GFF3:
Using the branch new_feature_model, update
packages/jbrowse-plugin-apollo/src/util/loadAssemblyIntoClient.tsto use the new annotation feature format. The new feature format has been imported in that file, so it will need to be adjusted so the the "feature" created and eventually passed toref.addFeature(feature)matches the new feature format.You can compare the new and current feature formats, they are in
packages/apollo-mst/src/AnnotationFeature.ts(current) andpackages/apollo-mst/src/AnnotationFeatureModel.ts(new), but a few things I'll point out:minandmaxinstead ofstartandendYou can test this out with the
Apollo -> open Local GFF3 filemenu. You can use this GFF3:volvox_canonical_gene.gff3.gz