Open a view at a searchable feature's location in a plugin?

[john-portwood]

Hello! Quick question here -- is it possible to specify a searchable feature instead of a region in the 'loc' parameter when opening a new view? I have this button here that attempts to do so:

React.createElement(
            'button',
            {
              id: 'buttonMarker',
              onClick: async event => {
                console.log('markerName button click = ', markerName)
                pluginManager.rootModel.session.addView('LinearGenomeView', {
                  type: 'LinearGenomeView',
                  init: {
                    loc: markerName,
                    tracks: [shortGenomeName+'_pangenome_markers'],
                    assembly: genomeName,
                  },
                })
              },
            },
            'GO!'
          ),

However I get this error:

Error: Unknown reference sequence "pg_1681152"
../../../packages/core/util/index.ts:390:11 (at R ()
../../../packages/core/util/index.ts:502:18 (at D ()
../../../plugins/linear-genome-view/src/LinearGenomeView/util.ts:158:22 (at)
    at Array.map (<anonymous>)
../../../plugins/linear-genome-view/src/LinearGenomeView/util.ts:157:19 (at s ()
../../../plugins/linear-genome-view/src/LinearGenomeView/model.ts:1483:27 (at Object.navToLocString ()
JBrowse 3.2.0

The feature pg_1681152 is searchable and can be queried when it's passed as a URL param:
http://jbrowse2.maizegdb.org/?config=config.json&loc=pg_1681152&assembly=Zm-B97-REFERENCE-NAM-1.0&tracks=B97_pangenome_markers

I'm currently using the JBrowse1TextSearchAdapter though. Could that be an issue?

[cmdcolin]

is it possible to specify a searchable feature instead of a region in the 'loc' parameter when opening a new view

currently no, regardless of text search adapter type. it could be a feature we could consider though

[john-portwood]

Sounds good, thanks Colin! I've just learned about the navToSearchString() function and can implement the functionality I want by hard-coding a region when the view opens initially, and then calling this function to immediately change the region to the location of the feature:

React.createElement(
           'button',
           {
             id: 'buttonMarker',
             onClick: event => {
               const view = pluginManager.rootModel.session.addView('LinearGenomeView', {
                 type: 'LinearGenomeView',
                 init: {
                   loc: "chr1:1-5,000",
                   tracks: [shortGenomeName+'_pangenome_markers'],
                   assembly: genomeName
                 },
               });
               view.navToSearchString({ 
                 input: markerName, 
                 assembly: genomeObj
               });
             }
           },
           'GO!'
         ),

[cmdcolin]

Excellent. I might be able to consider swapping or otherwise adding navToSearchString to the "init" processing so that becomes less needed, but that looks like a good workaround

The code for the init processing is here

jbrowse-components/plugins/linear-genome-view/src/LinearGenomeView/model.ts

Lines 1781 to 1785 in 8db0ad7

	self
	.navToLocString(init.loc, init.assembly)
	.catch((e: unknown) => {
	getSession(self).notifyError(`${e}`, e)
	})

It just calls navToLocString instead of navToSearchString (navtoSearchString essentially looks to see if something 'looks like a locstring, and navigates to it if so, otherwise calls search')