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Add evidence for protein viewer modifications
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kimrutherford committed Sep 19, 2024

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1 parent b964f52 commit a85ba3b
Showing 2 changed files with 10 additions and 0 deletions.
7 changes: 7 additions & 0 deletions src/pombase/bio/protein_view.rs
Original file line number Diff line number Diff line change
@@ -146,6 +146,7 @@ fn feature_from_allele(allele_details: &AlleleDetails, seq_length: usize)
feature_group: None,
display_extension: BTreeSet::new(),
assigned_by: None,
evidence: None,
positions,
})
} else {
@@ -175,6 +176,7 @@ fn make_mutant_summary(mutants_track: &ProteinViewTrack) -> ProteinViewTrack {
feature_group: None,
display_extension: BTreeSet::new(),
assigned_by: None,
evidence: None,
positions: vec![(residue_and_pos, pos, pos)],
}
})
@@ -391,6 +393,7 @@ fn make_modification_track(gene_details: &GeneDetails,
.unwrap_or_else(|| panic!("can't find annotation {}", annotation_id));

let assigned_by = &annotation_detail.assigned_by;
let evidence = &annotation_detail.evidence;

let mut annotation_residues = vec![];

@@ -456,6 +459,7 @@ fn make_modification_track(gene_details: &GeneDetails,
feature_group,
display_extension: BTreeSet::new(),
assigned_by: assigned_by.clone(),
evidence: evidence.clone(),
positions: vec![(description, residue_pos, residue_pos)],
}
});
@@ -508,6 +512,7 @@ fn make_pfam_track(gene_details: &GeneDetails) -> ProteinViewTrack {
annotated_terms: BTreeSet::new(),
feature_group: None,
assigned_by: Some(flex_str!["InterPro"]),
evidence: None,
display_extension: BTreeSet::new(),

positions,
@@ -546,6 +551,7 @@ fn make_generic_track(track_name: FlexStr, feature_coords: &Vec<(usize, usize)>,
feature_group: None,
display_extension: BTreeSet::new(),
assigned_by: None,
evidence: None,
positions,
}
})
@@ -574,6 +580,7 @@ fn make_binding_sites_track(gene_details: &GeneDetails) -> ProteinViewTrack {
feature_group: None,
display_extension: BTreeSet::new(),
assigned_by: None,
evidence: None,
positions: vec![(feature_name.clone(), start, end)],
}
})
3 changes: 3 additions & 0 deletions src/pombase/data_types.rs
Original file line number Diff line number Diff line change
@@ -2448,6 +2448,9 @@ pub struct ProteinViewFeature {
#[serde(skip_serializing_if="Option::is_none")]
pub assigned_by: Option<AssignedBy>,

#[serde(skip_serializing_if="Option::is_none")]
pub evidence: Option<Evidence>,

// start, end pairs:
pub positions: Vec<ProteinViewFeaturePos>,
}

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