XXX FIXME: strand

nextstrain · May 11, 2023 · 0da0966 · 0da0966
1 parent 4568d58
commit 0da0966
Show file tree

Hide file tree

Showing 3 changed files with 8 additions and 0 deletions.
diff --git a/src/components/entropy/entropyD3.js b/src/components/entropy/entropyD3.js
@@ -104,6 +104,7 @@ EntropyChart.prototype.update = function update({
 
 /* convert amino acid X in gene Y to a nucleotide number */
 EntropyChart.prototype._aaToNtCoord = function _aaToNtCoord(gene, aaPos) {
+  // XXX FIXME: strand
   if (this.geneMap[gene].strand === "-") {
     return this.geneMap[gene].end - aaPos * 3 + 1;
   }
@@ -177,9 +178,12 @@ EntropyChart.prototype._drawZoomGenes = function _drawZoomGenes(annotations) {
   const strokeCol = posInSequence < 1e6 ? "white" : "black"; /* black for large because otherwise disappear against background */
   /* check if we've got 2 reading frames (genes on both the "+" & "-" strands) and if so then modify
   the offset accordingly. If not, plot them all in the middle to save space */
+  // XXX FIXME: strand
+  // XXX FIXME: does this assume there are always strand==="+" annotations? I think so.
   const genesOnBothStrands = !!annotations.filter((a) => a.strand === "-").length;
   const readingFrameOffset = (strand) => {
     if (genesOnBothStrands) {
+      // XXX FIXME: strand
       return strand === "-" ? 20 : 0;
     }
     return 10;

diff --git a/src/components/entropy/infoPanel.js b/src/components/entropy/infoPanel.js
@@ -45,8 +45,10 @@ const InfoPanel = ({hovered, width, height, mutType, showCounts, geneMap, t}) =>
     styles.container.bottom = height - pos.y;
   }
 
+  // XXX FIXME: strand
   const isNegStrand = hovered.d.prot ? geneMap[hovered.d.prot].strand === "-" : null;
 
+  // XXX FIXME: strand
   const nucPos = hovered.d.prot ?
     mutType === "aa" ?
       isNegStrand ? geneMap[hovered.d.prot].end - hovered.d.codon * 3 + 3 :
@@ -72,6 +74,7 @@ const InfoPanel = ({hovered, width, height, mutType, showCounts, geneMap, t}) =>
         </div>
         <p/>
         <div>
+          // XXX FIXME: strand
           {isNegStrand === null ? `` : isNegStrand ? t("Negative strand") : t("Positive strand")}
         </div>
         <p/>

diff --git a/src/util/entropyCreateStateFromJsons.js b/src/util/entropyCreateStateFromJsons.js
@@ -19,6 +19,7 @@ const getAnnotations = (jsonData) => {
         prot: prot,
         start: jsonData[prot].start - 1, // see above
         end: jsonData[prot].end,
+        // XXX FIXME: strand?
         strand: jsonData[prot].strand,
         fill: genotypeColors[aaCount % 10]
       });