jbrowse-plugin-msaview 2.7.4 → 2.8.0

package/dist/utils/ncbiOrthologs.d.ts

@@ -1,6 +1,18 @@
 export declare const COMMON_SPECIES: readonly [{
     readonly label: "Human";
     readonly taxId: 9606;
+}, {
+    readonly label: "Chimpanzee";
+    readonly taxId: 9598;
+}, {
+    readonly label: "Gorilla";
+    readonly taxId: 9595;
+}, {
+    readonly label: "Rhesus macaque";
+    readonly taxId: 9544;
+}, {
+    readonly label: "Marmoset";
+    readonly taxId: 9483;
 }, {
     readonly label: "Mouse";
     readonly taxId: 10090;
@@ -8,14 +20,32 @@ export declare const COMMON_SPECIES: readonly [{
     readonly label: "Rat";
     readonly taxId: 10116;
 }, {
-    readonly label: "Cow";
-    readonly taxId: 9913;
+    readonly label: "Guinea pig";
+    readonly taxId: 10141;
 }, {
-    readonly label: "Pig";
-    readonly taxId: 9823;
+    readonly label: "Rabbit";
+    readonly taxId: 9986;
+}, {
+    readonly label: "Cat";
+    readonly taxId: 9685;
 }, {
     readonly label: "Dog";
     readonly taxId: 9615;
+}, {
+    readonly label: "Horse";
+    readonly taxId: 9796;
+}, {
+    readonly label: "Pig";
+    readonly taxId: 9823;
+}, {
+    readonly label: "Cow";
+    readonly taxId: 9913;
+}, {
+    readonly label: "Sheep";
+    readonly taxId: 9940;
+}, {
+    readonly label: "Opossum";
+    readonly taxId: 13616;
 }, {
     readonly label: "Chicken";
     readonly taxId: 9031;

package/dist/utils/ncbiOrthologs.js

@@ -23,14 +23,44 @@ const DATASETS = 'https://api.ncbi.nlm.nih.gov/datasets/v2';
 const EUTILS = 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils';
 // The species panel offered in the launch dialog, ordered from the reference
 // outward so a run that finds only close relatives still reads as a ladder.
-// Orthologs absent for a given gene are skipped rather than erroring.
+// Orthologs absent for a given gene are skipped rather than erroring, and the
+// index order here is the ROW order of the alignment (COMMON_TAX_RANK below).
+//
+// THE MAMMALS EARN THEIR PLACE, and the reason is measured rather than aesthetic.
+// The thirteen this list used to hold were one per major clade, which reads well
+// on a gene conserved to yeast and produces almost nothing on a gene that is not:
+// NCBI publishes 165 orthologs for human NLRP1 and every one of them is a mammal,
+// so of the old thirteen only Human, Mouse, Cow, Pig and Dog returned a row --
+// five, and Rat not among them, since NLRP1 is absent in Rattus norvegicus. The
+// same query against this list returns twelve. An inflammasome gene is not an
+// unusual case; anything immune, reproductive or lineage-specific behaves the
+// same way, and those are the genes a person opens an ortholog alignment on.
+//
+// Cat, rabbit and opossum are here despite contributing nothing to that gene.
+// They are the three that most often separate "absent in this clade" from
+// "absent in this species", which is the question a gap in the alignment raises.
+//
+// The cost is the run, and it is roughly linear: one NCBI protein fetch per
+// species and a Clustal Omega job over what comes back, so ~23 rows is about
+// twice the ~13-row wait. Still seconds rather than the minutes BLAST takes,
+// which is the comparison the panel's own text makes.
 export const COMMON_SPECIES = [
     { label: 'Human', taxId: 9606 },
+    { label: 'Chimpanzee', taxId: 9598 },
+    { label: 'Gorilla', taxId: 9595 },
+    { label: 'Rhesus macaque', taxId: 9544 },
+    { label: 'Marmoset', taxId: 9483 },
     { label: 'Mouse', taxId: 10090 },
     { label: 'Rat', taxId: 10116 },
-    { label: 'Cow', taxId: 9913 },
-    { label: 'Pig', taxId: 9823 },
+    { label: 'Guinea pig', taxId: 10141 },
+    { label: 'Rabbit', taxId: 9986 },
+    { label: 'Cat', taxId: 9685 },
     { label: 'Dog', taxId: 9615 },
+    { label: 'Horse', taxId: 9796 },
+    { label: 'Pig', taxId: 9823 },
+    { label: 'Cow', taxId: 9913 },
+    { label: 'Sheep', taxId: 9940 },
+    { label: 'Opossum', taxId: 13616 },
     { label: 'Chicken', taxId: 9031 },
     { label: 'Frog', taxId: 8364 },
     { label: 'Zebrafish', taxId: 7955 },

package/dist/version.d.ts

@@ -1 +1 @@
-export declare const version = "2.7.4";
+export declare const version = "2.8.0";

package/dist/version.js

@@ -1 +1 @@
-export const version = '2.7.4';
+export const version = '2.8.0';

package/package.json

@@ -1,5 +1,5 @@
 {
-  "version": "2.7.4",
+  "version": "2.8.0",
   "license": "MIT",
   "name": "jbrowse-plugin-msaview",
   "repository": {

package/src/LaunchMsaView/components/OrthologQuery/OrthologPanel.tsx

@@ -26,18 +26,22 @@ const useStyles = makeStyles()({
   selectField: {
     width: 180,
   },
+  // A GRID, not a wrapping flex row of fixed-width items. The old form was three
+  // 160px columns inside a 560px box, which is five rows for thirteen species and
+  // eight for twenty-three -- and the checkbox list is the tallest thing in the
+  // dialog, so those rows are the dialog's height. Five auto-fitted columns is
+  // five rows for twenty-three, i.e. more species in less space, and it reflows
+  // rather than being pinned to a width the dialog may not have.
   speciesBox: {
-    display: 'flex',
-    flexWrap: 'wrap',
-    maxWidth: 560,
-    marginTop: 12,
+    display: 'grid',
+    gridTemplateColumns: 'repeat(auto-fit, minmax(130px, 1fr))',
+    maxWidth: 700,
+    marginTop: 4,
   },
+  // The label carries the row height; the default control padding is what makes
+  // 23 rows of it tall.
   species: {
-    width: 160,
-  },
-  infoText: {
-    marginTop: 20,
-    maxWidth: 620,
+    marginRight: 0,
   },
 })
 
@@ -69,13 +73,14 @@ const OrthologPanel = observer(function ({
   return (
     <>
       <LaunchPanelContent error={e}>
-        <Typography>
-          Builds the alignment from NCBI&apos;s precomputed orthologs — one gene
-          per species — instead of searching. There is no job to wait on: the
-          NCBI lookups take about a second, and only the multiple alignment at
-          EBI costs real time (~10s), against 10+ minutes for BLAST. Rows come
-          out labelled by species rather than by accession, and NCBI&apos;s CDD
-          domains are overlaid automatically.
+        {/* One line rather than seven. What a reader needs here is which tab
+            to pick, and that is the seconds-against-minutes comparison; the
+            rest (species labels, CDD overlay, the query row being the selected
+            transcript) is visible in the result or documented, and as prose it
+            was most of the dialog's height. */}
+        <Typography variant="body2">
+          NCBI&apos;s precomputed orthologs, one gene per species, aligned at EBI
+          in seconds rather than the 10+ minutes BLAST takes.
         </Typography>
 
         <div>
@@ -104,7 +109,7 @@ const OrthologPanel = observer(function ({
           />
         </div>
 
-        <Typography variant="subtitle2" style={{ marginTop: 12 }}>
+        <Typography variant="subtitle2" style={{ marginTop: 8 }}>
           Species to include (those without an ortholog are skipped)
         </Typography>
         <div className={classes.speciesBox}>
@@ -131,11 +136,6 @@ const OrthologPanel = observer(function ({
 
         <TranscriptSelector feature={feature} {...transcriptSelection} />
 
-        <Typography className={classes.infoText} variant="body2">
-          The query row is the transcript selected above, not NCBI&apos;s
-          representative protein, so the alignment stays linked to the genome
-          view at codon resolution.
-        </Typography>
       </LaunchPanelContent>
       <SubmitCancelActions
         submitDisabled={!proteinSequence || taxa.length < 2}

package/src/LaunchMsaView/components/TranscriptSelector.tsx

@@ -53,6 +53,12 @@ export default function TranscriptSelector({
         <TextField
           variant="outlined"
           label={`Choose isoform of ${getGeneDisplayName(feature)}`}
+          // The query row is this transcript rather than NCBI's representative
+          // protein, which is what keeps the alignment linked to the genome view
+          // at codon resolution. It used to be a paragraph under the panel; as
+          // helper text it says the same thing where the choice is made and
+          // costs no height of its own.
+          helperText="the query row, so the alignment stays linked to the genome view"
           select
           className={classes.minWidth}
           value={selectedId}

package/src/utils/ncbiOrthologs.ts

@@ -26,14 +26,44 @@ const EUTILS = 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils'
 
 // The species panel offered in the launch dialog, ordered from the reference
 // outward so a run that finds only close relatives still reads as a ladder.
-// Orthologs absent for a given gene are skipped rather than erroring.
+// Orthologs absent for a given gene are skipped rather than erroring, and the
+// index order here is the ROW order of the alignment (COMMON_TAX_RANK below).
+//
+// THE MAMMALS EARN THEIR PLACE, and the reason is measured rather than aesthetic.
+// The thirteen this list used to hold were one per major clade, which reads well
+// on a gene conserved to yeast and produces almost nothing on a gene that is not:
+// NCBI publishes 165 orthologs for human NLRP1 and every one of them is a mammal,
+// so of the old thirteen only Human, Mouse, Cow, Pig and Dog returned a row --
+// five, and Rat not among them, since NLRP1 is absent in Rattus norvegicus. The
+// same query against this list returns twelve. An inflammasome gene is not an
+// unusual case; anything immune, reproductive or lineage-specific behaves the
+// same way, and those are the genes a person opens an ortholog alignment on.
+//
+// Cat, rabbit and opossum are here despite contributing nothing to that gene.
+// They are the three that most often separate "absent in this clade" from
+// "absent in this species", which is the question a gap in the alignment raises.
+//
+// The cost is the run, and it is roughly linear: one NCBI protein fetch per
+// species and a Clustal Omega job over what comes back, so ~23 rows is about
+// twice the ~13-row wait. Still seconds rather than the minutes BLAST takes,
+// which is the comparison the panel's own text makes.
 export const COMMON_SPECIES = [
   { label: 'Human', taxId: 9606 },
+  { label: 'Chimpanzee', taxId: 9598 },
+  { label: 'Gorilla', taxId: 9595 },
+  { label: 'Rhesus macaque', taxId: 9544 },
+  { label: 'Marmoset', taxId: 9483 },
   { label: 'Mouse', taxId: 10090 },
   { label: 'Rat', taxId: 10116 },
-  { label: 'Cow', taxId: 9913 },
-  { label: 'Pig', taxId: 9823 },
+  { label: 'Guinea pig', taxId: 10141 },
+  { label: 'Rabbit', taxId: 9986 },
+  { label: 'Cat', taxId: 9685 },
   { label: 'Dog', taxId: 9615 },
+  { label: 'Horse', taxId: 9796 },
+  { label: 'Pig', taxId: 9823 },
+  { label: 'Cow', taxId: 9913 },
+  { label: 'Sheep', taxId: 9940 },
+  { label: 'Opossum', taxId: 13616 },
   { label: 'Chicken', taxId: 9031 },
   { label: 'Frog', taxId: 8364 },
   { label: 'Zebrafish', taxId: 7955 },

package/src/version.ts

@@ -1 +1 @@
-export const version = '2.7.4'
+export const version = '2.8.0'