jbrowse-plugin-mafviewer 1.4.0 → 1.4.2

package/dist/out.js

@@ -28526,7 +28526,7 @@ var JBrowsePluginMafViewer = (() => {
   var import_Plugin = __toESM(require_Plugin());
 
   // package.json
-  var version = "1.4.0";
+  var version = "1.4.2";
 
   // src/BigMafAdapter/index.ts
   var import_pluggableElementTypes = __toESM(require_pluggableElementTypes());
@@ -31055,7 +31055,7 @@ ${r}`).join("\n");
   }
 
   // src/LinearMafRenderer/rendering/matches.ts
-  function renderMatches(context2, alignment, seq, leftPx, rowTop, sampleId, _featureId, alignmentStart, chr) {
+  function renderMatches(context2, alignment, seq, leftPx, rowTop, sampleId, alignmentStart, chr) {
     if (context2.showAllLetters) {
       return;
     }
@@ -31089,7 +31089,7 @@ ${r}`).join("\n");
   }
 
   // src/LinearMafRenderer/rendering/mismatches.ts
-  function renderMismatches(context2, alignment, seq, leftPx, rowTop, sampleId, _featureId, alignmentStart, chr) {
+  function renderMismatches(context2, alignment, seq, leftPx, rowTop, sampleId, alignmentStart, chr) {
     const {
       ctx,
       scale,
@@ -31125,7 +31125,7 @@ ${r}`).join("\n");
                   pos: genomicOffset + alignmentStart,
                   chr,
                   base: currentChar,
-                  sampleId: i
+                  sampleId
                 }
               );
             }
@@ -31165,7 +31165,7 @@ ${r}`).join("\n");
   function getLetter(a, showAsUpperCase) {
     return showAsUpperCase ? a.toUpperCase() : a;
   }
-  function renderText(context2, alignment, origAlignment, seq, leftPx, rowTop, _sampleId, _featureId) {
+  function renderText(context2, alignment, origAlignment, seq, leftPx, rowTop) {
     const {
       ctx,
       scale,
@@ -31201,7 +31201,7 @@ ${r}`).join("\n");
 
   // src/LinearMafRenderer/rendering/insertions.ts
   var import_util18 = __toESM(require_util());
-  function renderInsertions(context2, alignment, seq, leftPx, rowTop, bpPerPx, sampleId, _featureId, alignmentStart, chr) {
+  function renderInsertions(context2, alignment, seq, leftPx, rowTop, bpPerPx, sampleId, alignmentStart, chr) {
     const { ctx, scale, h, canvasWidth, rowHeight } = context2;
     const { charHeight } = getCharWidthHeight();
     for (let i = 0, genomicOffset = 0, seqLength = alignment.length; i < seqLength; i++) {
@@ -31312,7 +31312,6 @@ ${r}`).join("\n");
     const [leftPx] = (0, import_util20.featureSpanPx)(feature, region, bpPerPx);
     const alignments2 = feature.get("alignments");
     const referenceSeq = feature.get("seq").toLowerCase();
-    const featureId = feature.id() || `feature_${feature.get("start")}_${feature.get("end")}`;
     for (const [sampleId, alignmentData] of Object.entries(alignments2)) {
       const row = sampleToRowMap.get(sampleId);
       if (row === void 0) {
@@ -31329,7 +31328,6 @@ ${r}`).join("\n");
         leftPx,
         rowTop,
         row,
-        featureId,
         alignmentData.start,
         alignmentData.chr
       );
@@ -31340,7 +31338,6 @@ ${r}`).join("\n");
         leftPx,
         rowTop,
         row,
-        featureId,
         alignmentData.start,
         alignmentData.chr
       );
@@ -31350,9 +31347,7 @@ ${r}`).join("\n");
         originalAlignment,
         referenceSeq,
         leftPx,
-        rowTop,
-        sampleId,
-        featureId
+        rowTop
       );
     }
   }
@@ -31360,7 +31355,6 @@ ${r}`).join("\n");
     const [leftPx] = (0, import_util20.featureSpanPx)(feature, region, bpPerPx);
     const alignments2 = feature.get("alignments");
     const referenceSeq = feature.get("seq").toLowerCase();
-    const featureId = feature.id() || `feature_${feature.get("start")}_${feature.get("end")}`;
     for (const [sampleId, alignmentData] of Object.entries(alignments2)) {
       const row = sampleToRowMap.get(sampleId);
       if (row === void 0) {
@@ -31376,7 +31370,6 @@ ${r}`).join("\n");
         rowTop,
         bpPerPx,
         row,
-        featureId,
         alignmentData.start,
         alignmentData.chr
       );
@@ -31537,8 +31530,8 @@ ${r}`).join("\n");
       }
       const x = rbush2.search(offsetX, offsetY, offsetX + 1, offsetY + 1);
       if (x.length) {
-        const elt = x.findIndex((idx) => items[idx]?.isInsertion);
-        const r = elt !== -1 ? items[elt] : items[x[0]];
+        const elt = x.find((idx) => items[idx]?.isInsertion);
+        const r = elt !== void 0 ? items[elt] : items[x[0]];
         const s = samples[r.sampleId];
         return {
           ...r,