gramene-search 2.27.0 → 2.29.0

package/dist/index.js

@@ -11549,6 +11549,46 @@ function $31284fcdc45a1688$export$3a249e9030170bda(ensemblRest) {
 }
 
 
+/**
+ * Reference sequence for the primer designer's CAPS annotation.
+ *
+ * A variant listing from `/primers` carries coordinates and alleles but no
+ * bases, and restriction sites cannot be found without them, so the designer
+ * takes sequence from its host. Ensembl REST's `sequence/region` returns the
+ * plus strand of a window as `{molecule, seq, id, query}`.
+ *
+ * Read from `config.ensemblRest`, which must be the same Ensembl release the
+ * primers API reads variants from (release 115 for sorghum_v11). This matters
+ * more here than it does for the gene track: a gene model from the wrong
+ * release is visibly out of place, whereas sequence from the wrong release
+ * produces a confident and wrong enzyme call. The designer checks every window
+ * against the reference alleles the API reports and shows nothing if they
+ * disagree, but the right release is still the actual fix.
+ */ /**
+ * Beyond this the annotation is not worth the transfer; the variant listing is
+ * already capped well below it, so this only guards against a stray query.
+ */ const $f49aa8a0cf25aef4$var$MAX_SPAN = 200000;
+function $f49aa8a0cf25aef4$export$30e3f6c97d3f3a29(ensemblRest) {
+    if (!ensemblRest) return undefined;
+    return async ({ system_name: system_name, region: region, start: start, end: end }, options)=>{
+        if (!system_name || !region || start < 1 || end < start || end - start + 1 > $f49aa8a0cf25aef4$var$MAX_SPAN) return null;
+        const signal = options && options.signal;
+        const url = `${ensemblRest}/sequence/region/${encodeURIComponent(system_name)}/${encodeURIComponent(region)}:${start}-${end}` + `?content-type=application/json`;
+        const res = await fetch(url, {
+            headers: {
+                Accept: 'application/json'
+            },
+            signal: signal
+        });
+        if (!res.ok) throw new Error(`HTTP ${res.status}`);
+        const body = await res.json();
+        // A short or absent read would be indexed with genomic offsets and give
+        // wrong answers quietly; the designer discards it, and so does this.
+        return body && typeof body.seq === 'string' ? body.seq.toUpperCase() : null;
+    };
+}
+
+
 // Primers detail: PCR/qPCR primer design, genome specificity and pan-genome
 // coverage checks (gramene-primers <PrimerDesigner>, backed by the
 // gramene-swagger /primers endpoints).
@@ -11589,6 +11629,9 @@ const $88d24ae9beb83d5d$var$Primers = (props)=>{
     const genesInRegion = (0, $gXNCa$react.useMemo)(()=>(0, $31284fcdc45a1688$export$3a249e9030170bda)(ensemblRest), [
         ensemblRest
     ]);
+    const sequenceForRegion = (0, $gXNCa$react.useMemo)(()=>(0, $f49aa8a0cf25aef4$export$30e3f6c97d3f3a29)(ensemblRest), [
+        ensemblRest
+    ]);
     const byGene = props.uiViewState && props.uiViewState.byGene && props.uiViewState.byGene[geneId];
     const saved = byGene && byGene.primers;
     const { doSetPrimersState: doSetPrimersState } = props;
@@ -11610,6 +11653,7 @@ const $88d24ae9beb83d5d$var$Primers = (props)=>{
         systemName: gene.system_name,
         modes: $88d24ae9beb83d5d$var$MODES,
         genesInRegion: genesInRegion,
+        sequenceForRegion: sequenceForRegion,
         defaultMode: "gene",
         // an empty slice (never visited, or a snapshot without primers) leaves
         // the designer uncontrolled until its first change is stored