@jbrowse/plugin-linear-comparative-view 2.6.1

package/esm/LGVSyntenyDisplay/model.js

@@ -0,0 +1,152 @@
+import { ConfigurationReference, } from '@jbrowse/core/configuration';
+import { getSession, getContainingTrack, getContainingView, } from '@jbrowse/core/util';
+import { MismatchParser, linearPileupDisplayStateModelFactory, } from '@jbrowse/plugin-alignments';
+import { types } from 'mobx-state-tree';
+import { when } from 'mobx';
+const { parseCigar } = MismatchParser;
+function findPosInCigar(cigar, startX) {
+    let featX = 0;
+    let mateX = 0;
+    for (let i = 0; i < cigar.length; i++) {
+        const len = +cigar[i];
+        const op = cigar[i + 1];
+        const min = Math.min(len, startX - featX);
+        if (featX >= startX) {
+            break;
+        }
+        else if (op === 'I') {
+            mateX += len;
+        }
+        else if (op === 'D') {
+            featX += min;
+        }
+        else if (op === 'M') {
+            mateX += min;
+            featX += min;
+        }
+    }
+    return [featX, mateX];
+}
+async function navToSynteny(feature, self) {
+    const session = getSession(self);
+    const track = getContainingTrack(self);
+    const view = getContainingView(self);
+    const reg = view.dynamicBlocks.contentBlocks[0];
+    const cigar = feature.get('CIGAR');
+    const strand = feature.get('strand');
+    const regStart = reg.start;
+    const regEnd = reg.end;
+    const featStart = feature.get('start');
+    const featEnd = feature.get('end');
+    const mate = feature.get('mate');
+    const mateStart = mate.start;
+    const mateEnd = mate.end;
+    const mateAsm = mate.assemblyName;
+    const mateRef = mate.refName;
+    const featAsm = reg.assemblyName;
+    const featRef = reg.refName;
+    let rMateStart;
+    let rMateEnd;
+    let rFeatStart;
+    let rFeatEnd;
+    if (cigar) {
+        const p = parseCigar(cigar);
+        const [fStartX, mStartX] = findPosInCigar(p, regStart - featStart);
+        const [fEndX, mEndX] = findPosInCigar(p, regEnd - featStart);
+        // avoid multiply by 0 with strand undefined
+        const flipper = strand === -1 ? -1 : 1;
+        rFeatStart = featStart + fStartX;
+        rFeatEnd = featStart + fEndX;
+        rMateStart = (strand === -1 ? mateEnd : mateStart) + mStartX * flipper;
+        rMateEnd = (strand === -1 ? mateEnd : mateStart) + mEndX * flipper;
+    }
+    else {
+        rFeatStart = featStart;
+        rFeatEnd = featEnd;
+        rMateStart = mateStart;
+        rMateEnd = mateEnd;
+    }
+    const trackId = track.configuration.trackId;
+    const view2 = session.addView('LinearSyntenyView', {
+        type: 'LinearSyntenyView',
+        views: [
+            {
+                id: `${Math.random()}`,
+                type: 'LinearGenomeView',
+                hideHeader: true,
+            },
+            {
+                id: `${Math.random()}`,
+                type: 'LinearGenomeView',
+                hideHeader: true,
+            },
+        ],
+        tracks: [
+            {
+                configuration: trackId,
+                type: 'SyntenyTrack',
+                displays: [
+                    {
+                        type: 'LinearSyntenyDisplay',
+                        configuration: `${trackId}-LinearSyntenyDisplay`,
+                    },
+                ],
+            },
+        ],
+    });
+    const f = (n) => Math.floor(n);
+    const l1 = `${featRef}:${f(rFeatStart)}-${f(rFeatEnd)}`;
+    const m1 = Math.min(rMateStart, rMateEnd);
+    const m2 = Math.max(rMateStart, rMateEnd);
+    const l2 = `${mateRef}:${f(m1)}-${f(m2)}${strand === -1 ? '[rev]' : ''}`;
+    await when(() => view2.width !== undefined);
+    await Promise.all([
+        view2.views[0].navToLocString(l1, featAsm),
+        view2.views[1].navToLocString(l2, mateAsm),
+    ]);
+}
+/**
+ * #stateModel LGVSyntenyDisplay
+ * extends `LinearPileupDisplay`, displays location of "synteny" feature in a
+ * plain LGV, allowing linking out to external synteny views
+ */
+function stateModelFactory(schema) {
+    return types
+        .compose('LGVSyntenyDisplay', linearPileupDisplayStateModelFactory(schema), types.model({
+        /**
+         * #property
+         */
+        type: types.literal('LGVSyntenyDisplay'),
+        /**
+         * #property
+         */
+        configuration: ConfigurationReference(schema),
+    }))
+        .views(self => {
+        const superContextMenuItems = self.contextMenuItems;
+        return {
+            contextMenuItems() {
+                const feature = self.contextMenuFeature;
+                return [
+                    ...superContextMenuItems(),
+                    ...(feature
+                        ? [
+                            {
+                                label: 'Open synteny view for this position',
+                                onClick: () => navToSynteny(feature, self),
+                            },
+                        ]
+                        : []),
+                ];
+            },
+        };
+    })
+        .actions(self => ({
+        afterCreate() {
+            // use color by strand to help indicate inversions better
+            self.setColorScheme({ type: 'strand' });
+        },
+    }));
+}
+export default stateModelFactory;
+//# sourceMappingURL=model.js.map

package/esm/LGVSyntenyDisplay/model.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"model.js","sourceRoot":"","sources":["../../src/LGVSyntenyDisplay/model.ts"],"names":[],"mappings":"AAAA,OAAO,EACL,sBAAsB,GAEvB,MAAM,6BAA6B,CAAA;AACpC,OAAO,EACL,UAAU,EACV,kBAAkB,EAClB,iBAAiB,GAElB,MAAM,oBAAoB,CAAA;AAC3B,OAAO,EACL,cAAc,EACd,oCAAoC,GACrC,MAAM,4BAA4B,CAAA;AACnC,OAAO,EAAqB,KAAK,EAAE,MAAM,iBAAiB,CAAA;AAC1D,OAAO,EAAE,IAAI,EAAE,MAAM,MAAM,CAAA;AAO3B,MAAM,EAAE,UAAU,EAAE,GAAG,cAAc,CAAA;AAErC,SAAS,cAAc,CAAC,KAAe,EAAE,MAAc;IACrD,IAAI,KAAK,GAAG,CAAC,CAAA;IACb,IAAI,KAAK,GAAG,CAAC,CAAA;IACb,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,KAAK,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;QACrC,MAAM,GAAG,GAAG,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;QACrB,MAAM,EAAE,GAAG,KAAK,CAAC,CAAC,GAAG,CAAC,CAAC,CAAA;QACvB,MAAM,GAAG,GAAG,IAAI,CAAC,GAAG,CAAC,GAAG,EAAE,MAAM,GAAG,KAAK,CAAC,CAAA;QAEzC,IAAI,KAAK,IAAI,MAAM,EAAE;YACnB,MAAK;SACN;aAAM,IAAI,EAAE,KAAK,GAAG,EAAE;YACrB,KAAK,IAAI,GAAG,CAAA;SACb;aAAM,IAAI,EAAE,KAAK,GAAG,EAAE;YACrB,KAAK,IAAI,GAAG,CAAA;SACb;aAAM,IAAI,EAAE,KAAK,GAAG,EAAE;YACrB,KAAK,IAAI,GAAG,CAAA;YACZ,KAAK,IAAI,GAAG,CAAA;SACb;KACF;IACD,OAAO,CAAC,KAAK,EAAE,KAAK,CAAC,CAAA;AACvB,CAAC;AAED,KAAK,UAAU,YAAY,CAAC,OAAgB,EAAE,IAAuB;IACnE,MAAM,OAAO,GAAG,UAAU,CAAC,IAAI,CAAC,CAAA;IAChC,MAAM,KAAK,GAAG,kBAAkB,CAAC,IAAI,CAAC,CAAA;IACtC,MAAM,IAAI,GAAG,iBAAiB,CAAC,IAAI,CAAC,CAAA;IACpC,MAAM,GAAG,GAAG,IAAI,CAAC,aAAa,CAAC,aAAa,CAAC,CAAC,CAAC,CAAA;IAC/C,MAAM,KAAK,GAAG,OAAO,CAAC,GAAG,CAAC,OAAO,CAAC,CAAA;IAClC,MAAM,MAAM,GAAG,OAAO,CAAC,GAAG,CAAC,QAAQ,CAAC,CAAA;IACpC,MAAM,QAAQ,GAAG,GAAG,CAAC,KAAK,CAAA;IAC1B,MAAM,MAAM,GAAG,GAAG,CAAC,GAAG,CAAA;IACtB,MAAM,SAAS,GAAG,OAAO,CAAC,GAAG,CAAC,OAAO,CAAC,CAAA;IACtC,MAAM,OAAO,GAAG,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,CAAA;IAClC,MAAM,IAAI,GAAG,OAAO,CAAC,GAAG,CAAC,MAAM,CAAC,CAAA;IAChC,MAAM,SAAS,GAAG,IAAI,CAAC,KAAK,CAAA;IAC5B,MAAM,OAAO,GAAG,IAAI,CAAC,GAAG,CAAA;IACxB,MAAM,OAAO,GAAG,IAAI,CAAC,YAAY,CAAA;IACjC,MAAM,OAAO,GAAG,IAAI,CAAC,OAAO,CAAA;IAC5B,MAAM,OAAO,GAAG,GAAG,CAAC,YAAY,CAAA;IAChC,MAAM,OAAO,GAAG,GAAG,CAAC,OAAO,CAAA;IAE3B,IAAI,UAAkB,CAAA;IACtB,IAAI,QAAgB,CAAA;IACpB,IAAI,UAAkB,CAAA;IACtB,IAAI,QAAgB,CAAA;IAEpB,IAAI,KAAK,EAAE;QACT,MAAM,CAAC,GAAG,UAAU,CAAC,KAAK,CAAC,CAAA;QAC3B,MAAM,CAAC,OAAO,EAAE,OAAO,CAAC,GAAG,cAAc,CAAC,CAAC,EAAE,QAAQ,GAAG,SAAS,CAAC,CAAA;QAClE,MAAM,CAAC,KAAK,EAAE,KAAK,CAAC,GAAG,cAAc,CAAC,CAAC,EAAE,MAAM,GAAG,SAAS,CAAC,CAAA;QAE5D,4CAA4C;QAC5C,MAAM,OAAO,GAAG,MAAM,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;QACtC,UAAU,GAAG,SAAS,GAAG,OAAO,CAAA;QAChC,QAAQ,GAAG,SAAS,GAAG,KAAK,CAAA;QAC5B,UAAU,GAAG,CAAC,MAAM,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,SAAS,CAAC,GAAG,OAAO,GAAG,OAAO,CAAA;QACtE,QAAQ,GAAG,CAAC,MAAM,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,SAAS,CAAC,GAAG,KAAK,GAAG,OAAO,CAAA;KACnE;SAAM;QACL,UAAU,GAAG,SAAS,CAAA;QACtB,QAAQ,GAAG,OAAO,CAAA;QAClB,UAAU,GAAG,SAAS,CAAA;QACtB,QAAQ,GAAG,OAAO,CAAA;KACnB;IACD,MAAM,OAAO,GAAG,KAAK,CAAC,aAAa,CAAC,OAAO,CAAA;IAE3C,MAAM,KAAK,GAAG,OAAO,CAAC,OAAO,CAAC,mBAAmB,EAAE;QACjD,IAAI,EAAE,mBAAmB;QACzB,KAAK,EAAE;YACL;gBACE,EAAE,EAAE,GAAG,IAAI,CAAC,MAAM,EAAE,EAAE;gBACtB,IAAI,EAAE,kBAAkB;gBACxB,UAAU,EAAE,IAAI;aACjB;YACD;gBACE,EAAE,EAAE,GAAG,IAAI,CAAC,MAAM,EAAE,EAAE;gBACtB,IAAI,EAAE,kBAAkB;gBACxB,UAAU,EAAE,IAAI;aACjB;SACF;QACD,MAAM,EAAE;YACN;gBACE,aAAa,EAAE,OAAO;gBACtB,IAAI,EAAE,cAAc;gBACpB,QAAQ,EAAE;oBACR;wBACE,IAAI,EAAE,sBAAsB;wBAC5B,aAAa,EAAE,GAAG,OAAO,uBAAuB;qBACjD;iBACF;aACF;SACF;KACF,CAAQ,CAAA;IACT,MAAM,CAAC,GAAG,CAAC,CAAS,EAAE,EAAE,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;IACtC,MAAM,EAAE,GAAG,GAAG,OAAO,IAAI,CAAC,CAAC,UAAU,CAAC,IAAI,CAAC,CAAC,QAAQ,CAAC,EAAE,CAAA;IACvD,MAAM,EAAE,GAAG,IAAI,CAAC,GAAG,CAAC,UAAU,EAAE,QAAQ,CAAC,CAAA;IACzC,MAAM,EAAE,GAAG,IAAI,CAAC,GAAG,CAAC,UAAU,EAAE,QAAQ,CAAC,CAAA;IACzC,MAAM,EAAE,GAAG,GAAG,OAAO,IAAI,CAAC,CAAC,EAAE,CAAC,IAAI,CAAC,CAAC,EAAE,CAAC,GAAG,MAAM,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,EAAE,EAAE,CAAA;IACxE,MAAM,IAAI,CAAC,GAAG,EAAE,CAAC,KAAK,CAAC,KAAK,KAAK,SAAS,CAAC,CAAA;IAC3C,MAAM,OAAO,CAAC,GAAG,CAAC;QAChB,KAAK,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,cAAc,CAAC,EAAE,EAAE,OAAO,CAAC;QAC1C,KAAK,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,cAAc,CAAC,EAAE,EAAE,OAAO,CAAC;KAC3C,CAAC,CAAA;AACJ,CAAC;AAED;;;;GAIG;AACH,SAAS,iBAAiB,CAAC,MAAkC;IAC3D,OAAO,KAAK;SACT,OAAO,CACN,mBAAmB,EACnB,oCAAoC,CAAC,MAAM,CAAC,EAC5C,KAAK,CAAC,KAAK,CAAC;QACV;;WAEG;QACH,IAAI,EAAE,KAAK,CAAC,OAAO,CAAC,mBAAmB,CAAC;QACxC;;WAEG;QACH,aAAa,EAAE,sBAAsB,CAAC,MAAM,CAAC;KAC9C,CAAC,CACH;SACA,KAAK,CAAC,IAAI,CAAC,EAAE;QACZ,MAAM,qBAAqB,GAAG,IAAI,CAAC,gBAAgB,CAAA;QACnD,OAAO;YACL,gBAAgB;gBACd,MAAM,OAAO,GAAG,IAAI,CAAC,kBAAkB,CAAA;gBACvC,OAAO;oBACL,GAAG,qBAAqB,EAAE;oBAC1B,GAAG,CAAC,OAAO;wBACT,CAAC,CAAC;4BACE;gCACE,KAAK,EAAE,qCAAqC;gCAC5C,OAAO,EAAE,GAAG,EAAE,CAAC,YAAY,CAAC,OAAO,EAAE,IAAI,CAAC;6BAC3C;yBACF;wBACH,CAAC,CAAC,EAAE,CAAC;iBACR,CAAA;YACH,CAAC;SACF,CAAA;IACH,CAAC,CAAC;SACD,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAChB,WAAW;YACT,yDAAyD;YACzD,IAAI,CAAC,cAAc,CAAC,EAAE,IAAI,EAAE,QAAQ,EAAE,CAAC,CAAA;QACzC,CAAC;KACF,CAAC,CAAC,CAAA;AACP,CAAC;AAED,eAAe,iBAAiB,CAAA"}

package/esm/LaunchLinearSyntenyView.d.ts

@@ -0,0 +1,2 @@
+import PluginManager from '@jbrowse/core/PluginManager';
+export default function LaunchLinearSyntenyView(pluginManager: PluginManager): void;

package/esm/LaunchLinearSyntenyView.js

@@ -0,0 +1,55 @@
+import { when } from 'mobx';
+export default function LaunchLinearSyntenyView(pluginManager) {
+    pluginManager.addToExtensionPoint('LaunchView-LinearSyntenyView', 
+    // @ts-expect-error
+    async ({ session, views, tracks = [], }) => {
+        try {
+            const { assemblyManager } = session;
+            const model = session.addView('LinearSyntenyView', {});
+            await when(() => !!model.width);
+            model.setViews(await Promise.all(views.map(async (view) => {
+                const asm = await assemblyManager.waitForAssembly(view.assembly);
+                if (!asm) {
+                    throw new Error(`Assembly ${view.assembly} failed to load`);
+                }
+                return {
+                    type: 'LinearGenomeView',
+                    bpPerPx: 1,
+                    offsetPx: 0,
+                    hideHeader: true,
+                    displayedRegions: asm.regions,
+                };
+            })));
+            await Promise.all(model.views.map(view => when(() => view.initialized)));
+            const idsNotFound = [];
+            await Promise.all(views.map(async (data, idx) => {
+                const view = model.views[idx];
+                const { loc, tracks = [] } = data;
+                await view.navToLocString(loc);
+                tracks.forEach(track => tryTrack(view, track, idsNotFound));
+            }));
+            tracks.forEach(track => tryTrack(model, track, idsNotFound));
+            if (idsNotFound.length) {
+                throw new Error(`Could not resolve identifiers: ${idsNotFound.join(',')}`);
+            }
+        }
+        catch (e) {
+            session.notify(`${e}`, 'error');
+            throw e;
+        }
+    });
+}
+function tryTrack(model, trackId, idsNotFound) {
+    try {
+        model.showTrack(trackId);
+    }
+    catch (e) {
+        if (`${e}`.match('Could not resolve identifier')) {
+            idsNotFound.push(trackId);
+        }
+        else {
+            throw e;
+        }
+    }
+}
+//# sourceMappingURL=LaunchLinearSyntenyView.js.map

package/esm/LaunchLinearSyntenyView.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"LaunchLinearSyntenyView.js","sourceRoot":"","sources":["../src/LaunchLinearSyntenyView.ts"],"names":[],"mappings":"AAGA,OAAO,EAAE,IAAI,EAAE,MAAM,MAAM,CAAA;AAI3B,MAAM,CAAC,OAAO,UAAU,uBAAuB,CAAC,aAA4B;IAC1E,aAAa,CAAC,mBAAmB,CAC/B,8BAA8B;IAC9B,mBAAmB;IACnB,KAAK,EAAE,EACL,OAAO,EACP,KAAK,EACL,MAAM,GAAG,EAAE,GAKZ,EAAE,EAAE;QACH,IAAI;YACF,MAAM,EAAE,eAAe,EAAE,GAAG,OAAO,CAAA;YACnC,MAAM,KAAK,GAAG,OAAO,CAAC,OAAO,CAAC,mBAAmB,EAAE,EAAE,CAAQ,CAAA;YAE7D,MAAM,IAAI,CAAC,GAAG,EAAE,CAAC,CAAC,CAAC,KAAK,CAAC,KAAK,CAAC,CAAA;YAE/B,KAAK,CAAC,QAAQ,CACZ,MAAM,OAAO,CAAC,GAAG,CACf,KAAK,CAAC,GAAG,CAAC,KAAK,EAAC,IAAI,EAAC,EAAE;gBACrB,MAAM,GAAG,GAAG,MAAM,eAAe,CAAC,eAAe,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAA;gBAChE,IAAI,CAAC,GAAG,EAAE;oBACR,MAAM,IAAI,KAAK,CAAC,YAAY,IAAI,CAAC,QAAQ,iBAAiB,CAAC,CAAA;iBAC5D;gBACD,OAAO;oBACL,IAAI,EAAE,kBAA2B;oBACjC,OAAO,EAAE,CAAC;oBACV,QAAQ,EAAE,CAAC;oBACX,UAAU,EAAE,IAAI;oBAChB,gBAAgB,EAAE,GAAG,CAAC,OAAO;iBAC9B,CAAA;YACH,CAAC,CAAC,CACH,CACF,CAAA;YAED,MAAM,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,KAAK,CAAC,GAAG,CAAC,IAAI,CAAC,EAAE,CAAC,IAAI,CAAC,GAAG,EAAE,CAAC,IAAI,CAAC,WAAW,CAAC,CAAC,CAAC,CAAA;YAExE,MAAM,WAAW,GAAG,EAAc,CAAA;YAClC,MAAM,OAAO,CAAC,GAAG,CACf,KAAK,CAAC,GAAG,CAAC,KAAK,EAAE,IAAI,EAAE,GAAG,EAAE,EAAE;gBAC5B,MAAM,IAAI,GAAG,KAAK,CAAC,KAAK,CAAC,GAAG,CAAC,CAAA;gBAC7B,MAAM,EAAE,GAAG,EAAE,MAAM,GAAG,EAAE,EAAE,GAAG,IAAI,CAAA;gBACjC,MAAM,IAAI,CAAC,cAAc,CAAC,GAAG,CAAC,CAAA;gBAC9B,MAAM,CAAC,OAAO,CAAC,KAAK,CAAC,EAAE,CAAC,QAAQ,CAAC,IAAI,EAAE,KAAK,EAAE,WAAW,CAAC,CAAC,CAAA;YAC7D,CAAC,CAAC,CACH,CAAA;YAED,MAAM,CAAC,OAAO,CAAC,KAAK,CAAC,EAAE,CAAC,QAAQ,CAAC,KAAK,EAAE,KAAK,EAAE,WAAW,CAAC,CAAC,CAAA;YAE5D,IAAI,WAAW,CAAC,MAAM,EAAE;gBACtB,MAAM,IAAI,KAAK,CACb,kCAAkC,WAAW,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAC1D,CAAA;aACF;SACF;QAAC,OAAO,CAAC,EAAE;YACV,OAAO,CAAC,MAAM,CAAC,GAAG,CAAC,EAAE,EAAE,OAAO,CAAC,CAAA;YAC/B,MAAM,CAAC,CAAA;SACR;IACH,CAAC,CACF,CAAA;AACH,CAAC;AAED,SAAS,QAAQ,CACf,KAA2C,EAC3C,OAAe,EACf,WAAqB;IAErB,IAAI;QACF,KAAK,CAAC,SAAS,CAAC,OAAO,CAAC,CAAA;KACzB;IAAC,OAAO,CAAC,EAAE;QACV,IAAI,GAAG,CAAC,EAAE,CAAC,KAAK,CAAC,8BAA8B,CAAC,EAAE;YAChD,WAAW,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;SAC1B;aAAM;YACL,MAAM,CAAC,CAAA;SACR;KACF;AACH,CAAC"}

package/esm/LinearComparativeDisplay/configSchemaF.d.ts

@@ -0,0 +1,5 @@
+/**
+ * #config LinearComparativeDisplay
+ */
+declare function configSchemaFactory(pluginManager: any): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
+export default configSchemaFactory;

package/esm/LinearComparativeDisplay/configSchemaF.js

@@ -0,0 +1,16 @@
+/* eslint-disable @typescript-eslint/no-explicit-any */
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
+/**
+ * #config LinearComparativeDisplay
+ */
+function configSchemaFactory(pluginManager) {
+    return ConfigurationSchema('LinearComparativeDisplay', {}, {
+        explicitlyTyped: true,
+        /**
+         * #identifier
+         */
+        explicitIdentifier: 'displayId',
+    });
+}
+export default configSchemaFactory;
+//# sourceMappingURL=configSchemaF.js.map

package/esm/LinearComparativeDisplay/configSchemaF.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"configSchemaF.js","sourceRoot":"","sources":["../../src/LinearComparativeDisplay/configSchemaF.ts"],"names":[],"mappings":"AAAA,uDAAuD;AACvD,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AAEjE;;GAEG;AACH,SAAS,mBAAmB,CAAC,aAAkB;IAC7C,OAAO,mBAAmB,CACxB,0BAA0B,EAC1B,EAAE,EACF;QACE,eAAe,EAAE,IAAI;QAErB;;WAEG;QACH,kBAAkB,EAAE,WAAW;KAChC,CACF,CAAA;AACH,CAAC;AAED,eAAe,mBAAmB,CAAA"}

package/esm/LinearComparativeDisplay/index.d.ts

@@ -0,0 +1,3 @@
+import PluginManager from '@jbrowse/core/PluginManager';
+declare const _default: (pluginManager: PluginManager) => void;
+export default _default;

package/esm/LinearComparativeDisplay/index.js

@@ -0,0 +1,19 @@
+import DisplayType from '@jbrowse/core/pluggableElementTypes/DisplayType';
+import configSchemaFactory from './configSchemaF';
+import stateModelFactory from './stateModelFactory';
+export default (pluginManager) => {
+    pluginManager.addDisplayType(() => {
+        const configSchema = configSchemaFactory(pluginManager);
+        return new DisplayType({
+            name: 'LinearComparativeDisplay',
+            configSchema,
+            stateModel: stateModelFactory(configSchema),
+            trackType: 'SyntenyTrack',
+            viewType: 'LinearComparativeView',
+            ReactComponent: () => {
+                return null;
+            },
+        });
+    });
+};
+//# sourceMappingURL=index.js.map

package/esm/LinearComparativeDisplay/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/LinearComparativeDisplay/index.ts"],"names":[],"mappings":"AAAA,OAAO,WAAW,MAAM,iDAAiD,CAAA;AAGzE,OAAO,mBAAmB,MAAM,iBAAiB,CAAA;AACjD,OAAO,iBAAiB,MAAM,qBAAqB,CAAA;AAEnD,eAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,cAAc,CAAC,GAAG,EAAE;QAChC,MAAM,YAAY,GAAG,mBAAmB,CAAC,aAAa,CAAC,CAAA;QACvD,OAAO,IAAI,WAAW,CAAC;YACrB,IAAI,EAAE,0BAA0B;YAChC,YAAY;YACZ,UAAU,EAAE,iBAAiB,CAAC,YAAY,CAAC;YAC3C,SAAS,EAAE,cAAc;YACzB,QAAQ,EAAE,uBAAuB;YACjC,cAAc,EAAE,GAAG,EAAE;gBACnB,OAAO,IAAI,CAAA;YACb,CAAC;SACF,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC,CAAA"}

package/esm/LinearComparativeDisplay/stateModelFactory.d.ts

@@ -0,0 +1,275 @@
+/// <reference types="react" />
+import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
+import { Instance } from 'mobx-state-tree';
+import { Feature } from '@jbrowse/core/util';
+/**
+ * #stateModel LinearComparativeDisplay
+ */
+declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): import("mobx-state-tree").IModelType<{
+    id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
+    type: import("mobx-state-tree").ISimpleType<string>;
+    rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+} & {
+    type: import("mobx-state-tree").ISimpleType<"LinearComparativeDisplay">;
+    configuration: AnyConfigurationSchemaType;
+    height: import("mobx-state-tree").IType<number | undefined, number, number>;
+}, {
+    rendererTypeName: string;
+    error: unknown;
+    message: string | undefined;
+} & {
+    readonly RenderingComponent: import("react").FC<{
+        model: {
+            id: string;
+            type: string;
+            rpcDriverName: string | undefined;
+        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+            rendererTypeName: string;
+            error: unknown;
+            message: string | undefined;
+        } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
+            id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
+            type: import("mobx-state-tree").ISimpleType<string>;
+            rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>; /**
+             * #action
+             * controlled by a reaction
+             */
+        }, {
+            rendererTypeName: string;
+            error: unknown;
+            message: string | undefined;
+        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+        onHorizontalScroll?: Function | undefined;
+        blockState?: Record<string, any> | undefined;
+    }>;
+    readonly DisplayBlurb: import("react").FC<{
+        model: {
+            id: string;
+            type: string;
+            rpcDriverName: string | undefined;
+        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+            rendererTypeName: string; /**
+             * #action
+             * controlled by a reaction
+             */
+            error: unknown;
+            message: string | undefined;
+        } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
+            id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
+            type: import("mobx-state-tree").ISimpleType<string>;
+            rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+        }, {
+            rendererTypeName: string;
+            error: unknown;
+            message: string | undefined;
+        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+    }> | null;
+    readonly adapterConfig: any;
+    readonly parentTrack: any;
+    renderProps(): any;
+    readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
+    readonly DisplayMessageComponent: import("react").FC<any> | undefined;
+    trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
+    readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
+    regionCannotBeRendered(): null;
+} & {
+    setMessage(arg?: string | undefined): void;
+    setError(error?: unknown): void;
+    setRpcDriverName(rpcDriverName: string): void;
+    reload(): void;
+} & {
+    renderInProgress: AbortController | undefined;
+    features: Feature[] | undefined;
+    message: string | undefined;
+} & {
+    /**
+     * #getter
+     */
+    renderProps(): {
+        rpcDriverName: string | undefined;
+        displayModel: {
+            id: string;
+            type: "LinearComparativeDisplay";
+            rpcDriverName: string | undefined;
+            configuration: {
+                [x: string]: any;
+            } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+                setSubschema(slotName: string, data: unknown): any;
+            } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>;
+            height: number;
+        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+            rendererTypeName: string;
+            error: unknown;
+            message: string | undefined;
+        } & {
+            readonly RenderingComponent: import("react").FC<{
+                model: {
+                    id: string;
+                    type: string;
+                    rpcDriverName: string | undefined;
+                } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+                    rendererTypeName: string;
+                    error: unknown;
+                    message: string | undefined;
+                } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
+                    id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
+                    type: import("mobx-state-tree").ISimpleType<string>;
+                    rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>; /**
+                     * #action
+                     * controlled by a reaction
+                     */
+                }, {
+                    rendererTypeName: string;
+                    error: unknown;
+                    message: string | undefined;
+                }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+                onHorizontalScroll?: Function | undefined;
+                blockState?: Record<string, any> | undefined;
+            }>;
+            readonly DisplayBlurb: import("react").FC<{
+                model: {
+                    id: string;
+                    type: string;
+                    rpcDriverName: string | undefined;
+                } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+                    rendererTypeName: string; /**
+                     * #action
+                     * controlled by a reaction
+                     */
+                    error: unknown;
+                    message: string | undefined;
+                } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
+                    id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
+                    type: import("mobx-state-tree").ISimpleType<string>;
+                    rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+                }, {
+                    rendererTypeName: string;
+                    error: unknown;
+                    message: string | undefined;
+                }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+            }> | null;
+            readonly adapterConfig: any;
+            readonly parentTrack: any;
+            renderProps(): any;
+            readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
+            readonly DisplayMessageComponent: import("react").FC<any> | undefined;
+            trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
+            readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
+            regionCannotBeRendered(): null;
+        } & {
+            setMessage(arg?: string | undefined): void;
+            setError(error?: unknown): void;
+            setRpcDriverName(rpcDriverName: string): void;
+            reload(): void;
+        } & {
+            renderInProgress: AbortController | undefined;
+            features: Feature[] | undefined;
+            message: string | undefined;
+        } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
+            id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
+            type: import("mobx-state-tree").ISimpleType<string>;
+            rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+        } & {
+            type: import("mobx-state-tree").ISimpleType<"LinearComparativeDisplay">;
+            configuration: AnyConfigurationSchemaType;
+            height: import("mobx-state-tree").IType<number | undefined, number, number>;
+        }, {
+            rendererTypeName: string;
+            error: unknown;
+            message: string | undefined;
+        } & {
+            readonly RenderingComponent: import("react").FC<{
+                model: {
+                    id: string;
+                    type: string;
+                    rpcDriverName: string | undefined;
+                } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+                    rendererTypeName: string;
+                    error: unknown;
+                    message: string | undefined;
+                } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
+                    id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
+                    type: import("mobx-state-tree").ISimpleType<string>;
+                    rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>; /**
+                     * #action
+                     * controlled by a reaction
+                     */
+                }, {
+                    rendererTypeName: string;
+                    error: unknown;
+                    message: string | undefined;
+                }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+                onHorizontalScroll?: Function | undefined;
+                blockState?: Record<string, any> | undefined;
+            }>;
+            readonly DisplayBlurb: import("react").FC<{
+                model: {
+                    id: string;
+                    type: string;
+                    rpcDriverName: string | undefined;
+                } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+                    rendererTypeName: string; /**
+                     * #action
+                     * controlled by a reaction
+                     */
+                    error: unknown;
+                    message: string | undefined;
+                } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
+                    id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
+                    type: import("mobx-state-tree").ISimpleType<string>;
+                    rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+                }, {
+                    rendererTypeName: string;
+                    error: unknown;
+                    message: string | undefined;
+                }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+            }> | null;
+            readonly adapterConfig: any;
+            readonly parentTrack: any;
+            renderProps(): any;
+            readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
+            readonly DisplayMessageComponent: import("react").FC<any> | undefined;
+            trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
+            readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
+            regionCannotBeRendered(): null;
+        } & {
+            setMessage(arg?: string | undefined): void;
+            setError(error?: unknown): void;
+            setRpcDriverName(rpcDriverName: string): void;
+            reload(): void;
+        } & {
+            renderInProgress: AbortController | undefined;
+            features: Feature[] | undefined;
+            message: string | undefined;
+        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+        highResolutionScaling: number;
+    };
+} & {
+    /**
+     * #action
+     * controlled by a reaction
+     */
+    setLoading(abortController: AbortController): void;
+    /**
+     * #action
+     * controlled by a reaction
+     */
+    setMessage(messageText: string): void;
+    /**
+     * #action
+     * controlled by a reaction
+     */
+    setRendered(args?: {
+        features: Feature[];
+    }): void;
+    /**
+     * #action
+     * controlled by a reaction
+     */
+    setError(error: unknown): void;
+} & {
+    afterAttach(): void;
+}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
+export default stateModelFactory;
+export type LinearComparativeDisplayModel = ReturnType<typeof stateModelFactory>;
+export type LinearComparativeDisplay = Instance<LinearComparativeDisplayModel>;