jbrowse-plugin-msaview 3.4.0 → 3.5.0

package/dist/MsaViewPanel/util.js

@@ -15,6 +15,50 @@
 export function hasQueryRow(model) {
     return model.rows.some(r => r[0] === model.querySeqName);
 }
+/**
+ * Read the transcript's fields whichever shape it arrived in: a caller inside
+ * the session may still hand over a live Feature.
+ */
+export function transcriptFields(transcript) {
+    if (!transcript) {
+        return {};
+    }
+    return typeof transcript.toJSON === 'function'
+        ? transcript.toJSON()
+        : transcript;
+}
+function str(val) {
+    return typeof val === 'string' ? val : undefined;
+}
+/** what a transcript is called, preferring its name over its id */
+export function transcriptName(transcript) {
+    const fields = transcriptFields(transcript);
+    return str(fields.name) ?? str(fields.id);
+}
+/**
+ * The visible column showing residue `proteinPos` (0-based) of the transcript,
+ * or undefined when the query row does not carry that residue or react-msaview
+ * is hiding its column.
+ *
+ * Two things separate the transcript from the row. `querySeqOffset` is the
+ * trimming — a pasted BLAST alignment carries the aligned region, not the whole
+ * protein. And the row can simply stop short: react-msaview answers one column
+ * past the end for a position it does not have, which would light the last
+ * column for every residue beyond the row, so the round trip back through
+ * visibleColToSeqPos is what rejects those.
+ */
+export function transcriptPosToVisibleCol(model, proteinPos) {
+    const { querySeqName, querySeqOffset } = model;
+    const seqPos = proteinPos - querySeqOffset;
+    if (seqPos < 0) {
+        return undefined;
+    }
+    const col = model.seqPosToVisibleCol(querySeqName, seqPos);
+    return col !== undefined &&
+        model.visibleColToSeqPos(querySeqName, col) === seqPos
+        ? col
+        : undefined;
+}
 export function hasHoverPosition(hovered) {
     return (!!hovered &&
         typeof hovered === 'object' &&