jbrowse-plugin-msaview 3.7.0 → 3.8.0

package/README.md

@@ -1,25 +1,26 @@
 # jbrowse-plugin-msaview
 
-This plugin packages https://github.com/gmod/react-msaview for usage inside of
-JBrowse 2
-
-See the docs for the react-msaview for more info
-https://github.com/GMOD/react-msaview/blob/main/docs/user_guide.md
+A multiple sequence alignment and phylogenetic tree viewer for JBrowse 2, linked
+column by column to the genome. It packages
+[react-msaview](https://github.com/GMOD/react-msaview), whose
+[user guide](https://github.com/GMOD/react-msaview/blob/main/docs/user_guide.md)
+covers the viewer itself.
 
 ## Gallery
 
 ![](img/1.png)
 
-MSAView plugin running in JBrowse 2
+The [demo](#demo) below: TP53 in the genome view beside a vertebrate p53
+alignment carrying per-residue variant tracks. Each release recaptures it with
+`pnpm readme-figure`.
 
 ## Demo
 
-[p53 across vertebrates, linked to the genome and the structure](https://jbrowse.org/code/jb2/main/?config=https://jbrowse.org/ucsc/hg38/config.json&session=spec-{%22views%22:[{%22type%22:%22LinearGenomeView%22,%22id%22:%22lgv1%22,%22assembly%22:%22hg38%22,%22loc%22:%22chr17:7,661,779-7,687,538%22,%22tracks%22:[%22hg38-ncbiRefSeqSelect%22,%22hg38-clinvarMain%22]},{%22type%22:%22MsaView%22,%22displayName%22:%22p53%20across%20vertebrates%22,%22msaFileLocation%22:{%22uri%22:%22https://gmod.org/JBrowseMSA/demo/data/p53/p53-vertebrates.afa%22},%22treeFileLocation%22:{%22uri%22:%22https://gmod.org/JBrowseMSA/demo/data/p53/p53-vertebrates.nh%22},%22querySeqName%22:%22Human%22,%22relativeTo%22:%22Human%22,%22connectedViewId%22:%22lgv1%22,%22connectedTranscript%22:%22NM_000546.6%22,%22placement%22:%22splitRight%22,%22colorSchemeName%22:%22clustalx_protein_dynamic%22,%22highlights%22:[{%22row%22:%22Human%22,%22start%22:102,%22end%22:292,%22label%22:%22DNA-binding%22,%22color%22:%22rgba%28255,140,0,0.15%29%22},{%22row%22:%22Human%22,%22start%22:175,%22end%22:175,%22label%22:%22R175%22},{%22row%22:%22Human%22,%22start%22:245,%22end%22:245,%22label%22:%22G245%22},{%22row%22:%22Human%22,%22start%22:248,%22end%22:248,%22label%22:%22R248%22},{%22row%22:%22Human%22,%22start%22:249,%22end%22:249,%22label%22:%22R249%22},{%22row%22:%22Human%22,%22start%22:273,%22end%22:273,%22label%22:%22R273%22},{%22row%22:%22Human%22,%22start%22:282,%22end%22:282,%22label%22:%22R282%22}],%22columnTracks%22:[{%22id%22:%22clinvar%22,%22name%22:%22ClinVar%20pathogenic%20missense%22,%22kind%22:%22bar%22,%22row%22:%22Human%22,%22color%22:%22%23c0392b%22,%22height%22:60,%22max%22:8,%22values%22:[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2,1,0,0,2,4,3,0,6,0,0,0,0,0,0,0,0,0,0,1,2,1,5,0,0,2,2,3,1,1,4,0,0,2,0,0,2,0,3,0,0,0,1,0,0,0,6,2,0,0,1,1,3,6,2,0,1,0,2,1,1,0,0,2,0,0,2,1,3,0,3,3,1,3,5,1,3,0,0,0,0,0,0,0,0,1,0,0,4,3,1,1,1,0,1,0,0,0,0,0,3,0,0,0,0,0,0,0,3,2,1,1,0,1,0,3,0,0,0,0,0,0,0,0,0,0,0,3,0,4,0,2,4,6,2,3,5,2,0,4,5,4,1,6,2,1,2,0,1,3,0,0,0,2,1,0,0,0,0,0,2,3,3,0,1,4,1,3,6,0,2,1,1,3,0,3,8,3,1,0,2,2,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,1,0,1,0,0,5,0,0,0,1,1,0,2,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0]},{%22id%22:%22alphamissense%22,%22name%22:%22AlphaMissense%20mean%20%28x100%29%22,%22kind%22:%22bar%22,%22row%22:%22Human%22,%22color%22:%22%231565c0%22,%22height%22:60,%22max%22:100,%22values%22:[49,27,19,11,12,14,18,10,12,14,28,17,40,57,73,65,65,68,95,29,30,72,95,21,24,60,39,21,18,17,18,16,17,12,11,13,14,13,14,21,22,20,17,20,16,16,15,14,17,17,15,13,37,29,11,19,16,11,11,12,14,20,14,12,11,20,13,19,15,14,12,13,15,17,14,17,15,19,20,17,15,15,22,22,19,22,20,24,17,23,67,41,46,66,63,37,90,98,63,35,36,20,76,15,99,13,58,48,98,26,81,57,97,43,17,64,87,68,90,98,96,92,73,81,98,91,95,23,13,81,56,97,84,97,98,87,86,81,91,84,94,93,89,66,81,57,77,26,20,13,90,69,17,52,70,49,91,98,87,88,94,87,95,89,48,54,52,76,76,68,92,87,98,78,99,100,98,97,100,96,85,50,38,52,32,74,52,32,83,87,71,47,99,95,89,95,91,96,95,81,20,25,69,48,98,24,64,93,17,23,84,56,99,92,91,93,70,89,76,91,77,27,92,87,57,92,58,35,54,68,75,87,85,87,74,93,96,100,95,98,99,100,94,100,100,98,97,100,99,93,93,59,91,91,87,92,93,99,87,22,21,94,24,76,83,99,98,36,61,97,93,93,99,95,100,97,100,100,99,100,100,97,84,60,98,96,47,62,13,18,56,34,17,17,11,9,9,16,11,15,13,18,20,17,81,75,26,26,23,13,12,14,16,18,18,14,15,15,47,54,46,19,13,34,24,50,56,88,36,87,48,93,63,98,73,40,89,90,45,60,88,51,36,81,77,55,79,75,87,31,54,67,23,18,17,16,25,22,13,15,15,16,20,18,15,20,25,13,15,56,21,47,45,21,16,16,15,21,16,20,66,47,13,26,19,66,13,28,18,16,47,54,66]},{%22id%22:%22mavedb%22,%22name%22:%22MaveDB%20nutlin-3,%20p53WT%22,%22kind%22:%22bar%22,%22row%22:%22Human%22,%22color%22:%22%232e7d32%22,%22height%22:60,%22max%22:2,%22values%22:[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.6,0,0.1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.1,0,0,0.2,0.4,0,0,0,0,0.1,0,0.8,0,0.7,0.3,1.6,0.1,1.4,0.1,1.3,0,0,0,0.1,0,0.1,0.5,0.2,0.4,0.4,0.8,0.8,1.4,1.5,0.1,0.1,1.2,1,1.7,1.1,1.4,1.3,0.8,0.5,0.5,0.8,0.4,1.2,0.4,1.4,0.7,1.2,0.6,1.1,0.5,0.4,0.6,1.5,1.3,0,0.7,1.3,0.3,1.4,1,1.4,0.8,1.4,0.8,1.8,0.8,0.3,0,0.2,0.8,0.4,0,0.6,0.7,1.7,1,1.2,2,1.1,0.6,2,0.8,0.7,0.3,0.1,0.4,0.2,0.3,0.1,0.1,0.5,0.8,0.1,0.1,1.4,1.6,1.4,0.7,1.3,0.1,0.1,0,0,0,0.9,0.3,1.8,0,0,1,0,0.1,0.9,0.7,1.2,1.1,1.5,1.4,0.6,1.3,0.5,1.5,0.4,0.3,0.6,0.3,0.1,0.4,0.3,0.2,0.7,0.5,0.6,1.4,0.5,1.4,0.6,1.7,1.1,1.9,0.8,1.3,1.3,1.7,0.9,1.7,2.2,2,0.9,1.5,2.1,1,1.4,0.3,1.3,1.2,1.4,0.8,1.4,1.4,0.9,0.5,0.5,0.7,0.5,0.5,0.8,1.6,1,0.9,0.8,1.5,1.3,1.5,1.5,1.7,1.8,0.5,0.4,2,0,0.9,0.6,1,0,0,1,1.8,0,0.1,0.2,0.1,0.2,0,0.1,0.4,0.4,0.3,0.4,0.6,0.4,0.6,0.5,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0]}],%22region%22:{%22row%22:%22Human%22,%22start%22:170,%22end%22:290}},{%22type%22:%22ProteinView%22,%22uniprotId%22:%22P04637%22,%22transcriptId%22:%22NM_000546.6%22,%22connectedViewId%22:%22lgv1%22,%22connectedView%22:{%22assembly%22:%22hg38%22,%22loc%22:%22chr17:7,661,779-7,687,538%22,%22tracks%22:[%22hg38-ncbiRefSeqSelect%22]}}]}):
-TP53 in hg38 with ClinVar, a vertebrate p53 alignment carrying ClinVar,
-AlphaMissense and MaveDB per-residue tracks, and the AlphaFold model of P04637.
-Hovering a codon, a column or a residue lights the other two views. See
-[DEVELOPERS.md](DEVELOPERS.md#demo-p53-variant-evidence) for how the link is
-built.
+[p53 across vertebrates, linked to the genome and the structure](https://jbrowse.org/code/jb2/main/?config=https://jbrowse.org/ucsc/hg38/config.json&session=spec-{%22views%22:[{%22type%22:%22LinearGenomeView%22,%22id%22:%22lgv1%22,%22assembly%22:%22hg38%22,%22loc%22:%22chr17:7,661,779-7,687,538%22,%22tracks%22:[%22hg38-ncbiRefSeqSelect%22]},{%22type%22:%22MsaView%22,%22displayName%22:%22p53%20across%20vertebrates%22,%22msa%22:%22https://gmod.org/JBrowseMSA/demo/data/p53/p53-vertebrates.afa%22,%22tree%22:%22https://gmod.org/JBrowseMSA/demo/data/p53/p53-vertebrates.nh%22,%22query%22:%22Human%22,%22connectedViewId%22:%22lgv1%22,%22connectedTranscript%22:%22NM_000546.6%22,%22placement%22:%22splitRight%22,%22colorSchemeName%22:%22clustalx_protein_dynamic%22,%22highlights%22:[{%22start%22:102,%22end%22:292,%22label%22:%22DNA-binding%22,%22color%22:%22rgba%28255,140,0,0.15%29%22},175,245,248,249,273,282],%22region%22:%22170-290%22,%22columnTracks%22:[{%22name%22:%22ClinVar%20pathogenic%20missense%22,%22color%22:%22%23c0392b%22,%22max%22:8,%22start%22:105,%22values%22:[2,1,0,0,2,4,3,0,6,0,0,0,0,0,0,0,0,0,0,1,2,1,5,0,0,2,2,3,1,1,4,0,0,2,0,0,2,0,3,0,0,0,1,0,0,0,6,2,0,0,1,1,3,6,2,0,1,0,2,1,1,0,0,2,0,0,2,1,3,0,3,3,1,3,5,1,3,0,0,0,0,0,0,0,0,1,0,0,4,3,1,1,1,0,1,0,0,0,0,0,3,0,0,0,0,0,0,0,3,2,1,1,0,1,0,3,0,0,0,0,0,0,0,0,0,0,0,3,0,4,0,2,4,6,2,3,5,2,0,4,5,4,1,6,2,1,2,0,1,3,0,0,0,2,1,0,0,0,0,0,2,3,3,0,1,4,1,3,6,0,2,1,1,3,0,3,8,3,1,0,2,2,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,1,0,1,0,0,5,0,0,0,1,1,0,2,0,0,1]},{%22name%22:%22AlphaMissense%20mean%20%28x100%29%22,%22color%22:%22%231565c0%22,%22max%22:100,%22values%22:[49,27,19,11,12,14,18,10,12,14,28,17,40,57,73,65,65,68,95,29,30,72,95,21,24,60,39,21,18,17,18,16,17,12,11,13,14,13,14,21,22,20,17,20,16,16,15,14,17,17,15,13,37,29,11,19,16,11,11,12,14,20,14,12,11,20,13,19,15,14,12,13,15,17,14,17,15,19,20,17,15,15,22,22,19,22,20,24,17,23,67,41,46,66,63,37,90,98,63,35,36,20,76,15,99,13,58,48,98,26,81,57,97,43,17,64,87,68,90,98,96,92,73,81,98,91,95,23,13,81,56,97,84,97,98,87,86,81,91,84,94,93,89,66,81,57,77,26,20,13,90,69,17,52,70,49,91,98,87,88,94,87,95,89,48,54,52,76,76,68,92,87,98,78,99,100,98,97,100,96,85,50,38,52,32,74,52,32,83,87,71,47,99,95,89,95,91,96,95,81,20,25,69,48,98,24,64,93,17,23,84,56,99,92,91,93,70,89,76,91,77,27,92,87,57,92,58,35,54,68,75,87,85,87,74,93,96,100,95,98,99,100,94,100,100,98,97,100,99,93,93,59,91,91,87,92,93,99,87,22,21,94,24,76,83,99,98,36,61,97,93,93,99,95,100,97,100,100,99,100,100,97,84,60,98,96,47,62,13,18,56,34,17,17,11,9,9,16,11,15,13,18,20,17,81,75,26,26,23,13,12,14,16,18,18,14,15,15,47,54,46,19,13,34,24,50,56,88,36,87,48,93,63,98,73,40,89,90,45,60,88,51,36,81,77,55,79,75,87,31,54,67,23,18,17,16,25,22,13,15,15,16,20,18,15,20,25,13,15,56,21,47,45,21,16,16,15,21,16,20,66,47,13,26,19,66,13,28,18,16,47,54,66]},{%22name%22:%22MaveDB%20nutlin-3,%20p53WT%22,%22color%22:%22%232e7d32%22,%22max%22:2,%22start%22:27,%22values%22:[0.6,0,0.1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.1,0,0,0.2,0.4,0,0,0,0,0.1,0,0.8,0,0.7,0.3,1.6,0.1,1.4,0.1,1.3,0,0,0,0.1,0,0.1,0.5,0.2,0.4,0.4,0.8,0.8,1.4,1.5,0.1,0.1,1.2,1,1.7,1.1,1.4,1.3,0.8,0.5,0.5,0.8,0.4,1.2,0.4,1.4,0.7,1.2,0.6,1.1,0.5,0.4,0.6,1.5,1.3,0,0.7,1.3,0.3,1.4,1,1.4,0.8,1.4,0.8,1.8,0.8,0.3,0,0.2,0.8,0.4,0,0.6,0.7,1.7,1,1.2,2,1.1,0.6,2,0.8,0.7,0.3,0.1,0.4,0.2,0.3,0.1,0.1,0.5,0.8,0.1,0.1,1.4,1.6,1.4,0.7,1.3,0.1,0.1,0,0,0,0.9,0.3,1.8,0,0,1,0,0.1,0.9,0.7,1.2,1.1,1.5,1.4,0.6,1.3,0.5,1.5,0.4,0.3,0.6,0.3,0.1,0.4,0.3,0.2,0.7,0.5,0.6,1.4,0.5,1.4,0.6,1.7,1.1,1.9,0.8,1.3,1.3,1.7,0.9,1.7,2.2,2,0.9,1.5,2.1,1,1.4,0.3,1.3,1.2,1.4,0.8,1.4,1.4,0.9,0.5,0.5,0.7,0.5,0.5,0.8,1.6,1,0.9,0.8,1.5,1.3,1.5,1.5,1.7,1.8,0.5,0.4,2,0,0.9,0.6,1,0,0,1,1.8,0,0.1,0.2,0.1,0.2,0,0.1,0.4,0.4,0.3,0.4,0.6,0.4,0.6,0.5]}]},{%22type%22:%22ProteinView%22,%22uniprotId%22:%22P04637%22,%22transcriptId%22:%22NM_000546.6%22,%22connectedViewId%22:%22lgv1%22,%22connectedView%22:{%22assembly%22:%22hg38%22,%22loc%22:%22chr17:7,661,779-7,687,538%22,%22tracks%22:[%22hg38-ncbiRefSeqSelect%22]}}]}):
+TP53 in hg38, a vertebrate p53 alignment carrying ClinVar, AlphaMissense and
+MaveDB per-residue tracks, and the AlphaFold model of P04637. Hovering a codon,
+a column or a residue lights the other two views.
+[Launching](docs/launching.md#the-readme-demo-taken-apart) takes the link apart.
 
 An older shared session:
 https://jbrowse.org/code/jb2/main/index.html?config=https://unpkg.com/jbrowse-plugin-msaview/dist/config.json&session=share-BVmmEYAoAv&password=SuQaN
@@ -43,7 +44,7 @@ https://jbrowse.org/code/jb2/main/index.html?config=https://unpkg.com/jbrowse-pl
 - Aligns and builds trees in the browser, so a UniRef launch needs no job at any
   external service; EBI's aligners remain an option
 - Every launch is also a session-spec URL (`orthologParams`, `searchParams`,
-  `connectedTranscript`), see [DEVELOPERS.md](DEVELOPERS.md)
+  `connectedTranscript`), see [launching](docs/launching.md)
 
 ## File format supports
 
@@ -54,30 +55,43 @@ https://jbrowse.org/code/jb2/main/index.html?config=https://unpkg.com/jbrowse-pl
 - Clustal files (e.g. .aln file, uses clustal-js parser)
 - Newick (tree can be loaded separately as a .nh file)
 
-## Publication
+## Availability
 
-If you find this tool useful please cite our work
+This plugin is installed by default on https://genomes.jbrowse.org so you can
+use it on any species there
 
-Diesh, C., Stevens, G., Bridge, C., Hogue, G., Buels, R., Cain, S., Stein, L., &
-Holmes, I. (2026). Proteins in the Genome Browser: Integration of Phylogenies,
-Alignments, and Structures With Nucleotide-level Evidence in JBrowse 2. Journal
-of Molecular Biology, 169645. https://doi.org/10.1016/j.jmb.2026.169645
+## Documentation
 
-See also https://github.com/GMOD/proteinbrowser for overview
+Using the plugin:
 
-## Availability
+- [Alignments from a gene](docs/alignments-from-a-gene.md): the launch dialog's
+  sources — NCBI, PANTHER and UniRef orthologs, EBI searches — and aligning in
+  the browser.
+- [Your own alignments](docs/your-own-alignments.md): opening an alignment you
+  made, from a file, a link, or a per-gene dataset a site configures.
+- [BLAST](docs/blast.md): why searches run at EBI rather than NCBI, and the
+  manual route to NCBI's `nr`.
 
-This plugin is installed by default on https://genomes.jbrowse.org so you can
-use it on any species there
+Linking and embedding:
+
+- [Launching from a URL or code](docs/launching.md): worked session-spec links,
+  the genome connection, highlights, opening on a residue, and placement.
+- [Launch parameters](docs/launch-parameters.md): every argument and field.
+- [Linked views](docs/linked-views.md): how a column reaches its codon and a
+  protein3d structure.
 
-## Programmatic usage
+Working on the plugin:
 
-See [DEVELOPERS.md](DEVELOPERS.md)
+- [DEVELOPERS.md](DEVELOPERS.md): running it locally, the checks, the README
+  figure and publishing.
 
-## Publishing
+## Publication
 
-just push a new tag using e.g.
+If you find this tool useful please cite our work
 
-```
-pnpm version minor
-```
+Diesh, C., Stevens, G., Bridge, C., Hogue, G., Buels, R., Cain, S., Stein, L., &
+Holmes, I. (2026). Proteins in the Genome Browser: Integration of Phylogenies,
+Alignments, and Structures With Nucleotide-level Evidence in JBrowse 2. Journal
+of Molecular Biology, 169645. https://doi.org/10.1016/j.jmb.2026.169645
+
+See also https://github.com/GMOD/proteinbrowser for overview

package/dist/LaunchMsaView/launchTarget.d.ts

@@ -6,6 +6,9 @@ export interface ContextMenuInfo {
         featureId: string;
         type?: string;
     };
+    subfeature?: {
+        featureId: string;
+    };
     displayedRegionIndex: number;
 }
 export interface DisplayModel {

package/dist/LaunchMsaView/launchTarget.js

@@ -38,6 +38,7 @@ export function launchTarget(self) {
         return isGeneLikeType(info.item.type)
             ? {
                 fetchFeature: () => fetchFullFeature(info.item.featureId, info.displayedRegionIndex),
+                preferredTranscriptId: info.subfeature?.featureId,
             }
             : undefined;
     }

package/dist/LaunchMsaView/launchTarget.test.js

@@ -108,6 +108,19 @@ describe('launchTarget', () => {
         // the choice is ever stated
         expect(target?.preferredTranscriptId).toBe(mrna.id());
     });
+    // the canvas host names the clicked isoform beside the gene it fetches, as
+    // its own Collapse introns dialog reads it
+    test('carries the isoform a canvas click landed on', () => {
+        const host = modernHost('gene');
+        const target = launchTarget({
+            ...host,
+            contextMenuInfo: {
+                ...host.contextMenuInfo,
+                subfeature: { featureId: 'mrna-2' },
+            },
+        });
+        expect(target?.preferredTranscriptId).toBe('mrna-2');
+    });
     // a host that has both shapes must not fall through to the legacy branch and
     // launch on a stale feature when the click was not on a gene
     test('a non-gene click on a host carrying both shapes offers nothing', () => {

package/dist/LaunchMsaViewExtensionPoint/index.js

@@ -1,7 +1,30 @@
+import { expandSpec } from 'react-msaview';
 import { launchMsaView } from '../utils/launchMsaView';
+/**
+ * `msa` and `tree` onto the plugin's own sources, so a url still goes through
+ * `init.msaUrl` and its format sniffing, and `query` onto `querySeqName`
+ */
+function withLongSources({ msa, tree, ...args }) {
+    const inlineMsa = msa?.includes('\n') ? msa : undefined;
+    const inlineTree = tree?.trimStart().startsWith('(') ? tree : undefined;
+    const data = inlineMsa || inlineTree
+        ? {
+            ...args.data,
+            ...(inlineMsa ? { msa: inlineMsa } : {}),
+            ...(inlineTree ? { tree: inlineTree } : {}),
+        }
+        : args.data;
+    return {
+        ...args,
+        data: data,
+        ...(msa && !inlineMsa ? { msaFileLocation: { uri: msa } } : {}),
+        ...(tree && !inlineTree ? { treeFileLocation: { uri: tree } } : {}),
+        querySeqName: args.querySeqName ?? args.query,
+    };
+}
 export default function LaunchMsaViewExtensionPointF(pluginManager) {
     pluginManager.addToExtensionPoint('LaunchView-MsaView', (args) => {
-        const { session, data, msaFileLocation, msaIndexedLocation, msaName, treeFileLocation, querySeqName, searchParams, ...rest } = args;
+        const { session, query, data, msaFileLocation, msaIndexedLocation, msaName, treeFileLocation, querySeqName, searchParams, ...rest } = withLongSources(args);
         // `orthologParams` and `searchParams` name no alignment at all — the
         // view builds one at launch, which is the dialog's Orthologs and BLAST
         // tabs reached declaratively.
@@ -27,7 +50,7 @@ export default function LaunchMsaViewExtensionPointF(pluginManager) {
             querySeqName,
         };
         launchMsaView(session, {
-            ...rest,
+            ...expandSpec({ ...rest, query }),
             ...(searchParams ? { blastParams: searchParams } : {}),
             data,
             ...(treeFileLocation

package/dist/LaunchMsaViewExtensionPoint/index.test.js

@@ -77,3 +77,48 @@ test('one field set is enough to need init', () => {
         querySeqName: 'QUERY',
     });
 });
+test('msa and tree urls reach the plugin sources, query the query row', () => {
+    const snapshot = launch({
+        msa: 'https://example.com/p53.afa',
+        tree: 'https://example.com/p53.nh',
+        query: 'Human',
+    });
+    expect(snapshot.init).toMatchObject({
+        msaUrl: 'https://example.com/p53.afa',
+        querySeqName: 'Human',
+    });
+    expect(snapshot.treeFilehandle).toEqual({
+        uri: 'https://example.com/p53.nh',
+        locationType: 'UriLocation',
+    });
+    expect(snapshot.relativeTo).toBe('Human');
+    expect('msa' in snapshot || 'query' in snapshot).toBe(false);
+});
+test('inline msa and newick text become inline data', () => {
+    const snapshot = launch({ msa: '>a\nMEEP\n>b\nMEEP', tree: '(a,b);' });
+    expect(snapshot.data).toEqual({ msa: '>a\nMEEP\n>b\nMEEP', tree: '(a,b);' });
+    expect('init' in snapshot).toBe(false);
+});
+test('highlights, region and column tracks expand onto the query row', () => {
+    const snapshot = launch({
+        msa: 'https://example.com/p53.afa',
+        query: 'Human',
+        highlights: ['102-292 DNA-binding', 175],
+        region: '170-290',
+        columnTracks: [{ name: 'ClinVar', start: 3, values: [2, 1] }],
+    });
+    expect(snapshot.highlights).toEqual([
+        { row: 'Human', start: 102, end: 292, label: 'DNA-binding' },
+        { row: 'Human', start: 175, end: 175, label: '{residue}{position}' },
+    ]);
+    expect(snapshot.region).toEqual({ row: 'Human', start: 170, end: 290 });
+    expect(snapshot.columnTracks).toEqual([
+        {
+            id: 'clinvar',
+            name: 'ClinVar',
+            kind: 'bar',
+            row: 'Human',
+            values: [0, 0, 2, 1],
+        },
+    ]);
+});

package/dist/MsaViewPanel/model.d.ts

@@ -7,7 +7,6 @@ import type { TranscriptRef } from './util';
 import type { MenuItem } from '@jbrowse/core/ui';
 import type { Instance } from '@jbrowse/mobx-state-tree';
 import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
-import type { Region } from 'react-msaview';
 type LGV = LinearGenomeViewModel;
 type MaybeLGV = LGV | undefined;
 export interface IRegion {
@@ -112,7 +111,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
     displayName: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
     minimized: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
-}, "id" | "type" | "autoTreeAreaWidth" | "drawLabels" | "drawNodeBubbles" | "drawNodeLabels" | "drawTree" | "labelsAlignRight" | "overviewHeight" | "showBranchLen" | "showTreeOverview" | "treeAreaWidth" | "treeWidth" | "bgColor" | "colorSchemeName" | "msaFormat" | "showColumnStats" | "allowedGappyness" | "clades" | "colWidth" | "collapsed" | "columnTracks" | "currentAlignment" | "data" | "drawMsaLetters" | "encodings" | "gffFilehandle" | "height" | "hideGaps" | "highlightColumns" | "highlights" | "msaFilehandle" | "relativeTo" | "residueMappings" | "rowHeight" | "rowPanels" | "scrollX" | "scrollY" | "scrollZoom" | "scrollZoomAxis" | "showDomainLegend" | "showDomains" | "showOnly" | "subFeatureRows" | "trackHeights" | "treeFilehandle" | "treeMetadataFilehandle" | "turnedOffFeatures" | "turnedOffTracks"> & Omit<Omit<Omit<{}, "autoTreeAreaWidth" | "drawLabels" | "drawNodeBubbles" | "drawNodeLabels" | "drawTree" | "labelsAlignRight" | "overviewHeight" | "showBranchLen" | "showTreeOverview" | "treeAreaWidth" | "treeWidth"> & {
+}, "id" | "type" | "autoTreeAreaWidth" | "drawLabels" | "drawNodeBubbles" | "drawNodeLabels" | "drawTree" | "labelsAlignRight" | "overviewHeight" | "showBranchLen" | "showTreeOverview" | "treeAreaWidth" | "treeWidth" | "bgColor" | "colorSchemeName" | "msaFormat" | "showColumnStats" | "allowedGappyness" | "clades" | "colWidth" | "collapsed" | "columnTracks" | "currentAlignment" | "data" | "drawMsaLetters" | "encodings" | "gffFilehandle" | "height" | "hideGaps" | "highlightColumns" | "highlights" | "msaFilehandle" | "region" | "relativeTo" | "residueMappings" | "rowHeight" | "rowPanels" | "scrollX" | "scrollY" | "scrollZoom" | "scrollZoomAxis" | "showDomainLegend" | "showDomains" | "showOnly" | "subFeatureRows" | "trackHeights" | "treeFilehandle" | "treeMetadataFilehandle" | "turnedOffFeatures" | "turnedOffTracks"> & Omit<Omit<Omit<{}, "autoTreeAreaWidth" | "drawLabels" | "drawNodeBubbles" | "drawNodeLabels" | "drawTree" | "labelsAlignRight" | "overviewHeight" | "showBranchLen" | "showTreeOverview" | "treeAreaWidth" | "treeWidth"> & {
     drawLabels: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     labelsAlignRight: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     treeAreaWidth: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
@@ -129,7 +128,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     colorSchemeName: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
     showColumnStats: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     msaFormat: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<import("msa-parsers").MSAFormat>>;
-}, "id" | "type" | "allowedGappyness" | "clades" | "colWidth" | "collapsed" | "columnTracks" | "currentAlignment" | "data" | "drawMsaLetters" | "encodings" | "gffFilehandle" | "height" | "hideGaps" | "highlightColumns" | "highlights" | "msaFilehandle" | "relativeTo" | "residueMappings" | "rowHeight" | "rowPanels" | "scrollX" | "scrollY" | "scrollZoom" | "scrollZoomAxis" | "showDomainLegend" | "showDomains" | "showOnly" | "subFeatureRows" | "trackHeights" | "treeFilehandle" | "treeMetadataFilehandle" | "turnedOffFeatures" | "turnedOffTracks"> & {
+}, "id" | "type" | "allowedGappyness" | "clades" | "colWidth" | "collapsed" | "columnTracks" | "currentAlignment" | "data" | "drawMsaLetters" | "encodings" | "gffFilehandle" | "height" | "hideGaps" | "highlightColumns" | "highlights" | "msaFilehandle" | "region" | "relativeTo" | "residueMappings" | "rowHeight" | "rowPanels" | "scrollX" | "scrollY" | "scrollZoom" | "scrollZoomAxis" | "showDomainLegend" | "showDomains" | "showOnly" | "subFeatureRows" | "trackHeights" | "treeFilehandle" | "treeMetadataFilehandle" | "turnedOffFeatures" | "turnedOffTracks"> & {
     id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
     showDomains: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     showDomainLegend: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
@@ -545,10 +544,11 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     relativeTo: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
     highlightColumns: import("@jbrowse/mobx-state-tree").IType<number[] | undefined, number[] | undefined, number[] | undefined>;
     highlights: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<import("react-msaview").Highlight, import("react-msaview").Highlight, import("react-msaview").Highlight>>, [undefined]>;
+    region: import("@jbrowse/mobx-state-tree").IType<import("react-msaview").Region | undefined, import("react-msaview").Region | undefined, import("react-msaview").Region | undefined>;
     clades: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<import("react-msaview").Clade, import("react-msaview").Clade, import("react-msaview").Clade>>, [undefined]>;
     encodings: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<import("react-msaview").Encoding, import("react-msaview").Encoding, import("react-msaview").Encoding>>, [undefined]>;
     rowPanels: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<import("react-msaview").RowPanelSpec, import("react-msaview").RowPanelSpec, import("react-msaview").RowPanelSpec>>, [undefined]>;
-}, "init" | "querySeqName" | "querySeqOffset" | "zoomToBaseLevel" | "launchCompleted" | "connectedViewId" | "connectedFeature" | "connectedTranscript" | "blastParams" | "orthologParams" | "uniprotId" | "dataStoreId" | "mafRegion" | "region"> & {
+}, "init" | "querySeqName" | "querySeqOffset" | "zoomToBaseLevel" | "launchCompleted" | "connectedViewId" | "connectedFeature" | "connectedTranscript" | "blastParams" | "orthologParams" | "uniprotId" | "dataStoreId" | "mafRegion"> & {
     connectedViewId: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
     connectedFeature: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
     connectedTranscript: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
@@ -562,7 +562,6 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     dataStoreId: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
     launchCompleted: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     mafRegion: import("@jbrowse/mobx-state-tree").IType<MafRegion | undefined, MafRegion | undefined, MafRegion | undefined>;
-    region: import("@jbrowse/mobx-state-tree").IType<Region | undefined, Region | undefined, Region | undefined>;
 }, {
     width: number;
     bodyMounted: boolean;
@@ -646,6 +645,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     setHostCarriesData(arg: boolean): void;
     setMousePos(col?: number, row?: number): void;
     setHighlightedColumns(columns?: number[]): void;
+    setRegion(region?: import("react-msaview").Region): void;
     setHighlights(highlights: import("react-msaview").Highlight[]): void;
     setClades(clades: import("react-msaview").Clade[]): void;
     applyHighlight(owner: string, highlights: import("react-msaview").Highlight[]): void;
@@ -798,7 +798,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     visibleColToGlobalCol(visibleCol: number): number;
     seqPosToGlobalCol(rowName: string, seqPos: number): number | undefined;
     seqPosToVisibleCol(rowName: string, seqPos: number): number | undefined;
-    visibleSpan({ row, start: rawStart, end: rawEnd }: Region): {
+    visibleSpan({ row, start: rawStart, end: rawEnd }: import("react-msaview").Region): {
         startCol: number;
         endCol: number;
     } | undefined;
@@ -897,6 +897,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
         start: number;
         end: number;
     }[];
+    fillHighlightLabel(label: string, row?: string, start?: number): string;
     readonly resolvedHighlights: import("react-msaview").ResolvedHighlight[];
     columnStatsAt(col: number): import("react-msaview").ColumnStats | undefined;
     getRowData(name: string): {
@@ -923,7 +924,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     setFilter(accession: string, shown: boolean): void;
     fit(): void;
     fitVertically(): void;
-    zoomToRegion(region: Region): void;
+    zoomToRegion(region: import("react-msaview").Region): void;
     fitHorizontally(): void;
     afterCreate(): void;
 } & {
@@ -1015,10 +1016,6 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
      * #action
      */
     setQuerySeqName(arg: string): void;
-    /**
-     * #action
-     */
-    setQuerySeqOffset(arg: number): void;
     /**
      * #action
      */
@@ -1031,14 +1028,6 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
      * #action
      */
     setLaunchCompleted(arg: boolean): void;
-    /**
-     * #action
-     */
-    setMafRegion(arg?: MafRegion): void;
-    /**
-     * #action
-     */
-    setRegion(arg?: Region): void;
     /**
      * #action
      */
@@ -1233,6 +1222,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     relativeTo: string | undefined;
     highlightColumns: number[] | undefined;
     highlights: import("react-msaview").Highlight[];
+    region: import("react-msaview").Region | undefined;
     clades: import("react-msaview").Clade[];
     encodings: import("react-msaview").Encoding[];
     rowPanels: import("react-msaview").RowPanelSpec[];
@@ -1364,6 +1354,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     relativeTo: string | undefined;
     highlightColumns: number[] | undefined;
     highlights: import("react-msaview").Highlight[];
+    region: import("react-msaview").Region | undefined;
     clades: import("react-msaview").Clade[];
     encodings: import("react-msaview").Encoding[];
     rowPanels: import("react-msaview").RowPanelSpec[];

package/dist/MsaViewPanel/model.js

@@ -5,7 +5,6 @@ import { genomeToTranscriptSeqMapping } from 'g2p_mapper';
 import { autorun } from 'mobx';
 import { MSAModelF } from 'react-msaview';
 import { autoLoadProteinDomains, launchBlastIfNeeded, launchOrthologsIfNeeded, loadStoredData, observeProteinHighlights, processInit, runCleanup, storeDataToIndexedDB, syncGenomeHoverToMsaColumn, } from './afterCreateAutoruns';
-import { applyRegion } from './applyRegion';
 import { msaCoordToGenomeCoord, msaCoordToGenomeRegions, } from './msaCoordToGenomeCoord';
 import { deleteMsaData } from './msaDataStore';
 import { resolveConnectedTranscriptIfNeeded } from './resolveConnectedTranscript';
@@ -108,13 +107,6 @@ export default function stateModelFactory() {
          * #property
          */
         mafRegion: types.frozen(),
-        /**
-         * #property
-         * where the view opens: 1-based residues of `row`, or alignment
-         * columns without one. Zoomed onto once and then cleared, so a
-         * reloaded session keeps the reader's own scroll.
-         */
-        region: types.frozen(),
     }))
         .volatile(() => ({
         /**
@@ -277,12 +269,6 @@ export default function stateModelFactory() {
         setQuerySeqName(arg) {
             self.querySeqName = arg;
         },
-        /**
-         * #action
-         */
-        setQuerySeqOffset(arg) {
-            self.querySeqOffset = arg;
-        },
         /**
          * #action
          */
@@ -301,18 +287,6 @@ export default function stateModelFactory() {
         setLaunchCompleted(arg) {
             self.launchCompleted = arg;
         },
-        /**
-         * #action
-         */
-        setMafRegion(arg) {
-            self.mafRegion = arg;
-        },
-        /**
-         * #action
-         */
-        setRegion(arg) {
-            self.region = arg;
-        },
         /**
          * #action
          */
@@ -507,9 +481,6 @@ export default function stateModelFactory() {
             // so they're factories returning the autorun body rather than plain fns
             addDisposer(self, autorun(syncGenomeHoverToMsaColumn(self)));
             addDisposer(self, autorun(observeProteinHighlights(self)));
-            addDisposer(self, autorun(() => {
-                applyRegion(self);
-            }));
         },
     }));
 }