@jbrowse/plugin-linear-genome-view 2.3.3 → 2.4.0

package/dist/LinearGenomeView/util.js

@@ -51,7 +51,7 @@ function makeTicks(start, end, bpPerPx, emitMajor = true, emitMinor = true) {
     const iterPitch = gridPitch.minorPitch || gridPitch.majorPitch;
     let index = 0;
     const ticks = [];
-    for (let base = Math.ceil(minBase / iterPitch) * iterPitch; base < maxBase; base += iterPitch) {
+    for (let base = Math.floor(minBase / iterPitch) * iterPitch; base < Math.ceil(maxBase / iterPitch) * iterPitch + 1; base += iterPitch) {
         if (emitMinor && base % (gridPitch.majorPitch * 2)) {
             ticks.push({ type: 'minor', base: base - 1, index });
             index += 1;

package/dist/LinearGenomeView/util.js.map

@@ -1 +1 @@
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+{"version":3,"file":"util.js","sourceRoot":"","sources":["../../src/LinearGenomeView/util.ts"],"names":[],"mappings":";;;AAAA;;;;GAIG;AACH,SAAgB,eAAe,CAC7B,KAAa,EACb,eAAuB,EACvB,eAAuB;IAEvB,KAAK,GAAG,IAAI,CAAC,GAAG,CAAC,KAAK,CAAC,CAAA;IACvB,MAAM,eAAe,GAAG,eAAe,GAAG,KAAK,CAAA;IAC/C,MAAM,cAAc,GAAG,QAAQ,CAC7B,MAAM,CAAC,eAAe,CAAC,CAAC,aAAa,EAAE,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,EACtD,EAAE,CACH,CAAA;IAED,IAAI,UAAU,GAAG,EAAE,IAAI,cAAc,CAAA;IACrC,OAAO,UAAU,GAAG,eAAe,EAAE;QACnC,UAAU,IAAI,CAAC,CAAA;QACf,IAAI,UAAU,IAAI,eAAe,EAAE;YACjC,MAAK;SACN;QACD,UAAU,IAAI,GAAG,CAAA;KAClB;IAED,UAAU,GAAG,IAAI,CAAC,GAAG,CAAC,UAAU,EAAE,CAAC,CAAC,CAAA;IAEpC,MAAM,YAAY,GAAG,UAAU,GAAG,KAAK,CAAA;IAEvC,IAAI,UAAU,GAAG,CAAC,CAAA;IAClB,IAAI,CAAC,CAAC,UAAU,GAAG,EAAE,CAAC,IAAI,YAAY,GAAG,EAAE,IAAI,eAAe,EAAE;QAC9D,UAAU,GAAG,UAAU,GAAG,EAAE,CAAA;KAC7B;SAAM,IAAI,CAAC,CAAC,UAAU,GAAG,CAAC,CAAC,IAAI,YAAY,GAAG,CAAC,IAAI,eAAe,EAAE;QACnE,UAAU,GAAG,UAAU,GAAG,CAAC,CAAA;KAC5B;SAAM,IAAI,CAAC,CAAC,UAAU,GAAG,CAAC,CAAC,IAAI,YAAY,GAAG,CAAC,IAAI,eAAe,EAAE;QACnE,UAAU,GAAG,UAAU,GAAG,CAAC,CAAA;KAC5B;IAED,OAAO,EAAE,UAAU,EAAE,UAAU,EAAE,CAAA;AACnC,CAAC;AAnCD,0CAmCC;AAED,SAAgB,SAAS,CACvB,KAAa,EACb,GAAW,EACX,OAAe,EACf,SAAS,GAAG,IAAI,EAChB,SAAS,GAAG,IAAI;IAEhB,MAAM,SAAS,GAAG,eAAe,CAAC,OAAO,EAAE,EAAE,EAAE,EAAE,CAAC,CAAA;IAElD,IAAI,OAAO,GAAG,KAAK,CAAA;IACnB,IAAI,OAAO,GAAG,GAAG,CAAA;IACjB,IAAI,OAAO,KAAK,IAAI,IAAI,OAAO,KAAK,IAAI,EAAE;QACxC,OAAO,EAAE,CAAA;KACV;IAED,IAAI,OAAO,GAAG,CAAC,EAAE;QACf,CAAC;QAAA,CAAC,OAAO,EAAE,OAAO,CAAC,GAAG,CAAC,OAAO,EAAE,OAAO,CAAC,CAAA;KACzC;IAED,yEAAyE;IACzE,iDAAiD;IACjD,OAAO,IAAI,IAAI,CAAC,GAAG,CAAC,EAAE,GAAG,OAAO,CAAC,GAAG,CAAC,CAAA;IACrC,OAAO,IAAI,IAAI,CAAC,GAAG,CAAC,EAAE,GAAG,OAAO,CAAC,GAAG,CAAC,CAAA;IAErC,MAAM,SAAS,GAAG,SAAS,CAAC,UAAU,IAAI,SAAS,CAAC,UAAU,CAAA;IAC9D,IAAI,KAAK,GAAG,CAAC,CAAA;IACb,MAAM,KAAK,GAAG,EAAE,CAAA;IAChB,KACE,IAAI,IAAI,GAAG,IAAI,CAAC,KAAK,CAAC,OAAO,GAAG,SAAS,CAAC,GAAG,SAAS,EACtD,IAAI,GAAG,IAAI,CAAC,IAAI,CAAC,OAAO,GAAG,SAAS,CAAC,GAAG,SAAS,GAAG,CAAC,EACrD,IAAI,IAAI,SAAS,EACjB;QACA,IAAI,SAAS,IAAI,IAAI,GAAG,CAAC,SAAS,CAAC,UAAU,GAAG,CAAC,CAAC,EAAE;YAClD,KAAK,CAAC,IAAI,CAAC,EAAE,IAAI,EAAE,OAAO,EAAE,IAAI,EAAE,IAAI,GAAG,CAAC,EAAE,KAAK,EAAE,CAAC,CAAA;YACpD,KAAK,IAAI,CAAC,CAAA;SACX;aAAM,IAAI,SAAS,IAAI,CAAC,CAAC,IAAI,GAAG,CAAC,SAAS,CAAC,UAAU,GAAG,CAAC,CAAC,CAAC,EAAE;YAC5D,KAAK,CAAC,IAAI,CAAC,EAAE,IAAI,EAAE,OAAO,EAAE,IAAI,EAAE,IAAI,GAAG,CAAC,EAAE,KAAK,EAAE,CAAC,CAAA;YACpD,KAAK,IAAI,CAAC,CAAA;SACX;KACF;IACD,OAAO,KAAK,CAAA;AACd,CAAC;AAzCD,8BAyCC"}

package/dist/index.d.ts

@@ -3,7 +3,8 @@ import Plugin from '@jbrowse/core/Plugin';
 import PluginManager from '@jbrowse/core/PluginManager';
 import { BaseLinearDisplay, BaseLinearDisplayComponent, BlockModel, BlockMsg, baseLinearDisplayConfigSchema } from './BaseLinearDisplay';
 import { configSchemaFactory as linearBareDisplayConfigSchemaFactory } from './LinearBareDisplay';
-import { renderToSvg, LinearGenomeViewModel, LinearGenomeViewStateModel, RefNameAutocomplete, SearchBox } from './LinearGenomeView';
+import { LinearGenomeViewModel, LinearGenomeViewStateModel, RefNameAutocomplete, SearchBox } from './LinearGenomeView';
+import { renderToSvg, totalHeight, SVGTracks, SVGRuler } from './LinearGenomeView/svgcomponents/SVGLinearGenomeView';
 import { configSchema as linearBasicDisplayConfigSchemaFactory, modelFactory as linearBasicDisplayModelFactory } from './LinearBasicDisplay';
 export default class LinearGenomeViewPlugin extends Plugin {
     name: string;
@@ -13,7 +14,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 id: string;
                 type: string;
                 rpcDriverName: string | undefined;
-                height: number;
+                heightPreConfig: number | undefined;
                 blockState: import("mobx-state-tree").IMSTMap<import("mobx-state-tree").IModelType<{
                     key: import("mobx-state-tree").ISimpleType<string>;
                     region: import("mobx-state-tree").IModelType<{
@@ -168,6 +169,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 estimatedRegionStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined;
                 estimatedRegionStats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined;
             } & {
+                readonly height: any;
                 readonly blockType: "dynamicBlocks" | "staticBlocks";
                 readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
             } & {
@@ -197,7 +199,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 setRegionStatsP(p?: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined): void;
                 setRegionStats(estimatedRegionStats?: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined): void;
                 clearRegionStats(): void;
-                setHeight(displayHeight: number): number;
+                setHeight(displayHeight: number): any;
                 resizeHeight(distance: number): number;
                 setScrollTop(scrollTop: number): void;
                 updateStatsLimit(stats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats): void;
@@ -230,13 +232,14 @@ export default class LinearGenomeViewPlugin extends Plugin {
             } & {
                 renderSvg(opts: import("./LinearGenomeView").ExportSvgOptions & {
                     overrideHeight: number;
+                    theme: import("@mui/material").ThemeOptions;
                 }): Promise<JSX.Element>;
             } & 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>>;
             } & {
-                height: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
+                heightPreConfig: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
                 blockState: import("mobx-state-tree").IMapType<import("mobx-state-tree").IModelType<{
                     key: import("mobx-state-tree").ISimpleType<string>;
                     region: import("mobx-state-tree").IModelType<{
@@ -346,6 +349,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 estimatedRegionStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined;
                 estimatedRegionStats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined;
             } & {
+                readonly height: any;
                 readonly blockType: "dynamicBlocks" | "staticBlocks";
                 readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
             } & {
@@ -375,7 +379,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 setRegionStatsP(p?: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined): void;
                 setRegionStats(estimatedRegionStats?: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined): void;
                 clearRegionStats(): void;
-                setHeight(displayHeight: number): number;
+                setHeight(displayHeight: number): any;
                 resizeHeight(distance: number): number;
                 setScrollTop(scrollTop: number): void;
                 updateStatsLimit(stats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats): void;
@@ -408,12 +412,67 @@ export default class LinearGenomeViewPlugin extends Plugin {
             } & {
                 renderSvg(opts: import("./LinearGenomeView").ExportSvgOptions & {
                     overrideHeight: number;
+                    theme: import("@mui/material").ThemeOptions;
                 }): Promise<JSX.Element>;
-            }, import("mobx-state-tree")._NotCustomized, {
+            }, import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
+                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>>;
+            } & {
+                heightPreConfig: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+                blockState: import("mobx-state-tree").IMapType<import("mobx-state-tree").IModelType<{
+                    key: import("mobx-state-tree").ISimpleType<string>;
+                    region: import("mobx-state-tree").IModelType<{
+                        refName: import("mobx-state-tree").ISimpleType<string>;
+                        start: import("mobx-state-tree").ISimpleType<number>;
+                        end: import("mobx-state-tree").ISimpleType<number>;
+                        reversed: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+                    } & {
+                        assemblyName: import("mobx-state-tree").ISimpleType<string>;
+                    }, {
+                        setRefName(newRefName: string): void;
+                    }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
+                    reloadFlag: import("mobx-state-tree").IType<number | undefined, number, number>;
+                    isLeftEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+                    isRightEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+                }, {
+                    renderInProgress: AbortController | undefined;
+                    filled: boolean;
+                    reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
+                    features: Map<string, import("@jbrowse/core/util").Feature> | undefined;
+                    layout: any;
+                    status: string;
+                    error: unknown;
+                    message: string | undefined;
+                    maxHeightReached: boolean;
+                    ReactComponent: ({ model, }: {
+                        model: any;
+                    }) => any;
+                    renderProps: any;
+                } & {
+                    doReload(): void;
+                    afterAttach(): void;
+                    setStatus(message: string): void;
+                    setLoading(abortController: AbortController): void;
+                    setMessage(messageText: string): void;
+                    setRendered(props: {
+                        reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>>;
+                        features: Map<string, import("@jbrowse/core/util").Feature>;
+                        layout: any;
+                        maxHeightReached: boolean;
+                        renderProps: any;
+                    } | undefined): void;
+                    setError(error: unknown): void;
+                    reload(): void;
+                    beforeDestroy(): void;
+                }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+                userBpPerPxLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+                userByteSizeLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+            }>>, {
                 type: string;
-                height: number;
                 id: string;
                 rpcDriverName: string | undefined;
+                heightPreConfig: number | undefined;
                 userBpPerPxLimit: number | undefined;
                 userByteSizeLimit: number | undefined;
             }>>;
@@ -424,7 +483,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
             type: import("mobx-state-tree").ISimpleType<string>;
             rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
         } & {
-            height: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
+            heightPreConfig: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
             blockState: import("mobx-state-tree").IMapType<import("mobx-state-tree").IModelType<{
                 key: import("mobx-state-tree").ISimpleType<string>;
                 region: import("mobx-state-tree").IModelType<{
@@ -534,6 +593,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
             estimatedRegionStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined;
             estimatedRegionStats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined;
         } & {
+            readonly height: any;
             readonly blockType: "dynamicBlocks" | "staticBlocks";
             readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
         } & {
@@ -563,7 +623,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
             setRegionStatsP(p?: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined): void;
             setRegionStats(estimatedRegionStats?: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined): void;
             clearRegionStats(): void;
-            setHeight(displayHeight: number): number;
+            setHeight(displayHeight: number): any;
             resizeHeight(distance: number): number;
             setScrollTop(scrollTop: number): void;
             updateStatsLimit(stats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats): void;
@@ -596,12 +656,67 @@ export default class LinearGenomeViewPlugin extends Plugin {
         } & {
             renderSvg(opts: import("./LinearGenomeView").ExportSvgOptions & {
                 overrideHeight: number;
+                theme: import("@mui/material").ThemeOptions;
             }): Promise<JSX.Element>;
-        }, import("mobx-state-tree")._NotCustomized, {
+        }, import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
+            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>>;
+        } & {
+            heightPreConfig: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+            blockState: import("mobx-state-tree").IMapType<import("mobx-state-tree").IModelType<{
+                key: import("mobx-state-tree").ISimpleType<string>;
+                region: import("mobx-state-tree").IModelType<{
+                    refName: import("mobx-state-tree").ISimpleType<string>;
+                    start: import("mobx-state-tree").ISimpleType<number>;
+                    end: import("mobx-state-tree").ISimpleType<number>;
+                    reversed: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+                } & {
+                    assemblyName: import("mobx-state-tree").ISimpleType<string>;
+                }, {
+                    setRefName(newRefName: string): void;
+                }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
+                reloadFlag: import("mobx-state-tree").IType<number | undefined, number, number>;
+                isLeftEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+                isRightEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+            }, {
+                renderInProgress: AbortController | undefined;
+                filled: boolean;
+                reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
+                features: Map<string, import("@jbrowse/core/util").Feature> | undefined;
+                layout: any;
+                status: string;
+                error: unknown;
+                message: string | undefined;
+                maxHeightReached: boolean;
+                ReactComponent: ({ model, }: {
+                    model: any;
+                }) => any;
+                renderProps: any;
+            } & {
+                doReload(): void;
+                afterAttach(): void;
+                setStatus(message: string): void;
+                setLoading(abortController: AbortController): void;
+                setMessage(messageText: string): void;
+                setRendered(props: {
+                    reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>>;
+                    features: Map<string, import("@jbrowse/core/util").Feature>;
+                    layout: any;
+                    maxHeightReached: boolean;
+                    renderProps: any;
+                } | undefined): void;
+                setError(error: unknown): void;
+                reload(): void;
+                beforeDestroy(): void;
+            }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+            userBpPerPxLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+            userByteSizeLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+        }>>, {
             type: string;
-            height: number;
             id: string;
             rpcDriverName: string | undefined;
+            heightPreConfig: number | undefined;
             userBpPerPxLimit: number | undefined;
             userByteSizeLimit: number | undefined;
         }>;
@@ -723,7 +838,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 moveTrack(movingId: string, targetId: string): void;
                 closeView(): void;
                 toggleTrack(trackId: string): void;
-                setTrackLabels(setting: "offset" | "hidden" | "overlapping"): void;
+                setTrackLabels(setting: "overlapping" | "offset" | "hidden"): void;
                 toggleCenterLine(): void;
                 setDisplayedRegions(regions: import("@jbrowse/core/util").Region[]): void;
                 activateTrackSelector(): import("@jbrowse/core/util").Widget;
@@ -915,7 +1030,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 moveTrack(movingId: string, targetId: string): void;
                 closeView(): void;
                 toggleTrack(trackId: string): void;
-                setTrackLabels(setting: "offset" | "hidden" | "overlapping"): void;
+                setTrackLabels(setting: "overlapping" | "offset" | "hidden"): void;
                 toggleCenterLine(): void;
                 setDisplayedRegions(regions: import("@jbrowse/core/util").Region[]): void;
                 activateTrackSelector(): import("@jbrowse/core/util").Widget;
@@ -1117,7 +1232,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 moveTrack(movingId: string, targetId: string): void;
                 closeView(): void;
                 toggleTrack(trackId: string): void;
-                setTrackLabels(setting: "offset" | "hidden" | "overlapping"): void;
+                setTrackLabels(setting: "overlapping" | "offset" | "hidden"): void;
                 toggleCenterLine(): void;
                 setDisplayedRegions(regions: import("@jbrowse/core/util").Region[]): void;
                 activateTrackSelector(): import("@jbrowse/core/util").Widget;
@@ -1309,7 +1424,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 moveTrack(movingId: string, targetId: string): void;
                 closeView(): void;
                 toggleTrack(trackId: string): void;
-                setTrackLabels(setting: "offset" | "hidden" | "overlapping"): void;
+                setTrackLabels(setting: "overlapping" | "offset" | "hidden"): void;
                 toggleCenterLine(): void;
                 setDisplayedRegions(regions: import("@jbrowse/core/util").Region[]): void;
                 activateTrackSelector(): import("@jbrowse/core/util").Widget;
@@ -1511,7 +1626,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 moveTrack(movingId: string, targetId: string): void;
                 closeView(): void;
                 toggleTrack(trackId: string): void;
-                setTrackLabels(setting: "offset" | "hidden" | "overlapping"): void;
+                setTrackLabels(setting: "overlapping" | "offset" | "hidden"): void;
                 toggleCenterLine(): void;
                 setDisplayedRegions(regions: import("@jbrowse/core/util").Region[]): void;
                 activateTrackSelector(): import("@jbrowse/core/util").Widget;
@@ -1703,7 +1818,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 moveTrack(movingId: string, targetId: string): void;
                 closeView(): void;
                 toggleTrack(trackId: string): void;
-                setTrackLabels(setting: "offset" | "hidden" | "overlapping"): void;
+                setTrackLabels(setting: "overlapping" | "offset" | "hidden"): void;
                 toggleCenterLine(): void;
                 setDisplayedRegions(regions: import("@jbrowse/core/util").Region[]): void;
                 activateTrackSelector(): import("@jbrowse/core/util").Widget;
@@ -1793,6 +1908,6 @@ export default class LinearGenomeViewPlugin extends Plugin {
     install(pluginManager: PluginManager): void;
     configure(pluginManager: PluginManager): void;
 }
-export { baseLinearDisplayConfigSchema, linearBareDisplayConfigSchemaFactory, linearBasicDisplayConfigSchemaFactory, linearBasicDisplayModelFactory, renderToSvg, BaseLinearDisplayComponent, BaseLinearDisplay, RefNameAutocomplete, SearchBox, BlockMsg, };
+export { baseLinearDisplayConfigSchema, linearBareDisplayConfigSchemaFactory, linearBasicDisplayConfigSchemaFactory, linearBasicDisplayModelFactory, renderToSvg, totalHeight, SVGTracks, SVGRuler, BaseLinearDisplayComponent, BaseLinearDisplay, RefNameAutocomplete, SearchBox, BlockMsg, };
 export type { LinearGenomeViewModel, LinearGenomeViewStateModel, BlockModel };
 export type { BaseLinearDisplayModel } from './BaseLinearDisplay';

package/dist/index.js

@@ -26,7 +26,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.BlockMsg = exports.SearchBox = exports.RefNameAutocomplete = exports.BaseLinearDisplay = exports.BaseLinearDisplayComponent = exports.renderToSvg = exports.linearBasicDisplayModelFactory = exports.linearBasicDisplayConfigSchemaFactory = exports.linearBareDisplayConfigSchemaFactory = exports.baseLinearDisplayConfigSchema = void 0;
+exports.BlockMsg = exports.SearchBox = exports.RefNameAutocomplete = exports.BaseLinearDisplay = exports.BaseLinearDisplayComponent = exports.SVGRuler = exports.SVGTracks = exports.totalHeight = exports.renderToSvg = exports.linearBasicDisplayModelFactory = exports.linearBasicDisplayConfigSchemaFactory = exports.linearBareDisplayConfigSchemaFactory = exports.baseLinearDisplayConfigSchema = void 0;
 const Plugin_1 = __importDefault(require("@jbrowse/core/Plugin"));
 const util_1 = require("@jbrowse/core/util");
 // icons
@@ -40,9 +40,13 @@ Object.defineProperty(exports, "baseLinearDisplayConfigSchema", { enumerable: tr
 const LinearBareDisplay_1 = __importStar(require("./LinearBareDisplay"));
 Object.defineProperty(exports, "linearBareDisplayConfigSchemaFactory", { enumerable: true, get: function () { return LinearBareDisplay_1.configSchemaFactory; } });
 const LinearGenomeView_1 = __importStar(require("./LinearGenomeView"));
-Object.defineProperty(exports, "renderToSvg", { enumerable: true, get: function () { return LinearGenomeView_1.renderToSvg; } });
 Object.defineProperty(exports, "RefNameAutocomplete", { enumerable: true, get: function () { return LinearGenomeView_1.RefNameAutocomplete; } });
 Object.defineProperty(exports, "SearchBox", { enumerable: true, get: function () { return LinearGenomeView_1.SearchBox; } });
+const SVGLinearGenomeView_1 = require("./LinearGenomeView/svgcomponents/SVGLinearGenomeView");
+Object.defineProperty(exports, "renderToSvg", { enumerable: true, get: function () { return SVGLinearGenomeView_1.renderToSvg; } });
+Object.defineProperty(exports, "totalHeight", { enumerable: true, get: function () { return SVGLinearGenomeView_1.totalHeight; } });
+Object.defineProperty(exports, "SVGTracks", { enumerable: true, get: function () { return SVGLinearGenomeView_1.SVGTracks; } });
+Object.defineProperty(exports, "SVGRuler", { enumerable: true, get: function () { return SVGLinearGenomeView_1.SVGRuler; } });
 const LinearBasicDisplay_1 = __importStar(require("./LinearBasicDisplay"));
 Object.defineProperty(exports, "linearBasicDisplayConfigSchemaFactory", { enumerable: true, get: function () { return LinearBasicDisplay_1.configSchema; } });
 Object.defineProperty(exports, "linearBasicDisplayModelFactory", { enumerable: true, get: function () { return LinearBasicDisplay_1.modelFactory; } });

package/dist/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,kEAAyC;AAEzC,6CAAgF;AAEhF,QAAQ;AACR,8EAAyD;AAEzD,SAAS;AACT,2DAM4B;AAwE1B,kGA7EA,qCAAiB,OA6EA;AADjB,2GA3EA,8CAA0B,OA2EA;AAI1B,yFA7EA,4BAAQ,OA6EA;AAZR,8GAhEA,iDAA6B,OAgEA;AA9D/B,yEAE4B;AA6D1B,qHA9DuB,uCAAoC,OA8DvB;AA5DtC,uEAO2B;AA8DzB,oGAlEA,sCAAmB,OAkEA;AACnB,0FAlEA,4BAAS,OAkEA;AA7DX,8FAK6D;AAiD3D,4FArDA,iCAAW,OAqDA;AACX,4FArDA,iCAAW,OAqDA;AACX,0FArDA,+BAAS,OAqDA;AACT,yFArDA,8BAAQ,OAqDA;AAnDV,2EAG6B;AA2C3B,sHA7CgB,iCAAqC,OA6ChB;AACrC,+GA7CgB,iCAA8B,OA6ChB;AA1ChC,kEAA0C;AAC1C,8DAAsC;AACtC,sFAA8D;AAE9D,MAAqB,sBAAuB,SAAQ,gBAAM;IAA1D;;QACE,SAAI,GAAG,wBAAwB,CAAA;QAE/B,YAAO,GAAG;YACR,0BAA0B,EAA1B,8CAA0B;YAC1B,iBAAiB,EAAjB,qCAAiB;YACjB,6BAA6B,EAA7B,iDAA6B;YAC7B,SAAS,EAAT,4BAAS;YACT,YAAY,EAAZ,+BAAY;YACZ,gBAAgB,EAAhB,mCAAgB;SACjB,CAAA;IAsBH,CAAC;IApBC,OAAO,CAAC,aAA4B;QAClC,IAAA,sBAAa,EAAC,aAAa,CAAC,CAAA;QAC5B,IAAA,oBAAW,EAAC,aAAa,CAAC,CAAA;QAC1B,IAAA,4BAAmB,EAAC,aAAa,CAAC,CAAA;QAClC,IAAA,0BAAiB,EAAC,aAAa,CAAC,CAAA;QAChC,IAAA,2BAAkB,EAAC,aAAa,CAAC,CAAA;QACjC,IAAA,gCAAuB,EAAC,aAAa,CAAC,CAAA;IACxC,CAAC;IAED,SAAS,CAAC,aAA4B;QACpC,IAAI,IAAA,4BAAqB,EAAC,aAAa,CAAC,SAAS,CAAC,EAAE;YAClD,aAAa,CAAC,SAAS,CAAC,eAAe,CAAC,CAAC,KAAK,CAAC,EAAE;gBAC/C,KAAK,EAAE,oBAAoB;gBAC3B,IAAI,EAAE,mBAAa;gBACnB,OAAO,EAAE,CAAC,OAA6B,EAAE,EAAE;oBACzC,OAAO,CAAC,OAAO,CAAC,kBAAkB,EAAE,EAAE,CAAC,CAAA;gBACzC,CAAC;aACF,CAAC,CAAA;SACH;IACH,CAAC;CACF;AAhCD,yCAgCC"}

package/esm/BaseLinearDisplay/components/Block.js

@@ -17,7 +17,7 @@ const useStyles = makeStyles()(theme => ({
     },
     interRegionPaddingBlock: {
         minHeight: '100%',
-        backgroundColor: theme.palette.text.primary,
+        backgroundColor: theme.palette.text.disabled,
     },
     boundaryPaddingBlock: {
         minHeight: '100%',

package/esm/BaseLinearDisplay/components/Block.js.map

@@ -1 +1 @@
-{"version":3,"file":"Block.js","sourceRoot":"","sources":["../../../src/BaseLinearDisplay/components/Block.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAC1C,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;IACvC,YAAY,EAAE;QACZ,QAAQ,EAAE,UAAU;QACpB,SAAS,EAAE,MAAM;QACjB,SAAS,EAAE,YAAY;QACvB,UAAU,EAAE,QAAQ;QACpB,QAAQ,EAAE,QAAQ;KACnB;IACD,WAAW,EAAE;QACX,SAAS,EAAE,MAAM;QACjB,SAAS,EAAE,YAAY;QACvB,eAAe,EAAE,MAAM;QACvB,eAAe,EACb,oHAAoH;KACvH;IACD,uBAAuB,EAAE;QACvB,SAAS,EAAE,MAAM;QACjB,eAAe,EAAE,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,OAAO;KAC5C;IACD,oBAAoB,EAAE;QACpB,SAAS,EAAE,MAAM;QACjB,eAAe,EAAE,KAAK,CAAC,OAAO,CAAC,MAAM,CAAC,kBAAkB;KACzD;CACF,CAAC,CAAC,CAAA;AAEH,MAAM,YAAY,GAAG,QAAQ,CAAC,UAAU,EACtC,KAAK,EACL,QAAQ,GAIT;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,EAAE,OAAO,EAAE,GAAG,KAAK,CAAA;IACzB,OAAO,CACL,6BAAK,KAAK,EAAE,EAAE,KAAK,EAAE,OAAO,EAAE,EAAE,SAAS,EAAE,OAAO,CAAC,YAAY,IAC5D,QAAQ,CACL,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,SAAS,WAAW,CAAC,EAAE,KAAK,EAAqB;IAC/C,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,OAAO,6BAAK,SAAS,EAAE,OAAO,CAAC,WAAW,EAAE,KAAK,EAAE,EAAE,KAAK,EAAE,GAAI,CAAA;AAClE,CAAC;AAED,SAAS,uBAAuB,CAAC,EAC/B,QAAQ,EACR,KAAK,EACL,KAAK,GAAG,EAAE,GAKX;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,OAAO,CACL,6BACE,KAAK,EAAE;YACL,GAAG,KAAK;YACR,KAAK;SACN,EACD,SAAS,EACP,QAAQ;YACN,CAAC,CAAC,OAAO,CAAC,oBAAoB;YAC9B,CAAC,CAAC,OAAO,CAAC,uBAAuB,GAErC,CACH,CAAA;AACH,CAAC;AAED,OAAO,EAAE,YAAY,EAAE,WAAW,EAAE,uBAAuB,EAAE,CAAA"}
+{"version":3,"file":"Block.js","sourceRoot":"","sources":["../../../src/BaseLinearDisplay/components/Block.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAC1C,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;IACvC,YAAY,EAAE;QACZ,QAAQ,EAAE,UAAU;QACpB,SAAS,EAAE,MAAM;QACjB,SAAS,EAAE,YAAY;QACvB,UAAU,EAAE,QAAQ;QACpB,QAAQ,EAAE,QAAQ;KACnB;IACD,WAAW,EAAE;QACX,SAAS,EAAE,MAAM;QACjB,SAAS,EAAE,YAAY;QACvB,eAAe,EAAE,MAAM;QACvB,eAAe,EACb,oHAAoH;KACvH;IACD,uBAAuB,EAAE;QACvB,SAAS,EAAE,MAAM;QACjB,eAAe,EAAE,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,QAAQ;KAC7C;IACD,oBAAoB,EAAE;QACpB,SAAS,EAAE,MAAM;QACjB,eAAe,EAAE,KAAK,CAAC,OAAO,CAAC,MAAM,CAAC,kBAAkB;KACzD;CACF,CAAC,CAAC,CAAA;AAEH,MAAM,YAAY,GAAG,QAAQ,CAAC,UAAU,EACtC,KAAK,EACL,QAAQ,GAIT;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,EAAE,OAAO,EAAE,GAAG,KAAK,CAAA;IACzB,OAAO,CACL,6BAAK,KAAK,EAAE,EAAE,KAAK,EAAE,OAAO,EAAE,EAAE,SAAS,EAAE,OAAO,CAAC,YAAY,IAC5D,QAAQ,CACL,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,SAAS,WAAW,CAAC,EAAE,KAAK,EAAqB;IAC/C,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,OAAO,6BAAK,SAAS,EAAE,OAAO,CAAC,WAAW,EAAE,KAAK,EAAE,EAAE,KAAK,EAAE,GAAI,CAAA;AAClE,CAAC;AAED,SAAS,uBAAuB,CAAC,EAC/B,QAAQ,EACR,KAAK,EACL,KAAK,GAAG,EAAE,GAKX;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,OAAO,CACL,6BACE,KAAK,EAAE;YACL,GAAG,KAAK;YACR,KAAK;SACN,EACD,SAAS,EACP,QAAQ;YACN,CAAC,CAAC,OAAO,CAAC,oBAAoB;YAC9B,CAAC,CAAC,OAAO,CAAC,uBAAuB,GAErC,CACH,CAAA;AACH,CAAC;AAED,OAAO,EAAE,YAAY,EAAE,WAAW,EAAE,uBAAuB,EAAE,CAAA"}

package/esm/BaseLinearDisplay/components/ServerSideRenderedBlockContent.js

@@ -7,17 +7,17 @@ import { LoadingEllipses } from '@jbrowse/core/ui';
 import RefreshIcon from '@mui/icons-material/Refresh';
 // locals
 import BlockMsg from './BlockMsg';
-const useStyles = makeStyles()(theme => ({
-    loading: {
-        paddingLeft: '0.6em',
-        backgroundColor: theme.palette.action.disabledBackground,
-        backgroundImage: 'repeating-linear-gradient(45deg, transparent, transparent 5px, rgba(255,255,255,.5) 5px, rgba(255,255,255,.5) 10px)',
-        height: '100%',
-        width: '100%',
-        pointerEvents: 'none',
-        textAlign: 'center',
-    },
-}));
+const useStyles = makeStyles()(theme => {
+    const bg = theme.palette.action.disabledBackground;
+    return {
+        loading: {
+            paddingLeft: '0.6em',
+            backgroundColor: theme.palette.background.default,
+            backgroundImage: `repeating-linear-gradient(45deg, transparent, transparent 5px, ${bg} 5px, ${bg} 10px)`,
+            textAlign: 'center',
+        },
+    };
+});
 // eslint-disable-next-line @typescript-eslint/no-explicit-any
 const LoadingMessage = observer(({ model }) => {
     // only show the loading message after 300ms to prevent excessive flickering

package/esm/BaseLinearDisplay/components/ServerSideRenderedBlockContent.js.map

@@ -1 +1 @@
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package/esm/BaseLinearDisplay/models/BaseLinearDisplayModel.d.ts

@@ -7,6 +7,7 @@ import { Region } from '@jbrowse/core/util/types';
 import CompositeMap from '@jbrowse/core/util/compositeMap';
 import { Instance } from 'mobx-state-tree';
 import { ExportSvgOptions } from '../../LinearGenomeView';
+import { ThemeOptions } from '@mui/material';
 export interface Layout {
     minX: number;
     minY: number;
@@ -23,7 +24,7 @@ export declare const BaseLinearDisplay: import("mobx-state-tree").IModelType<{
     /**
      * #property
      */
-    height: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
+    heightPreConfig: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
     /**
      * #property
      * updated via autorun
@@ -145,6 +146,7 @@ export declare const BaseLinearDisplay: import("mobx-state-tree").IModelType<{
     estimatedRegionStatsP: Promise<Stats> | undefined;
     estimatedRegionStats: Stats | undefined;
 } & {
+    readonly height: any;
     /**
      * #getter
      */
@@ -248,7 +250,7 @@ export declare const BaseLinearDisplay: import("mobx-state-tree").IModelType<{
     /**
      * #action
      */
-    setHeight(displayHeight: number): number;
+    setHeight(displayHeight: number): any;
     /**
      * #action
      */
@@ -352,12 +354,80 @@ export declare const BaseLinearDisplay: import("mobx-state-tree").IModelType<{
      */
     renderSvg(opts: ExportSvgOptions & {
         overrideHeight: number;
+        theme: ThemeOptions;
     }): Promise<JSX.Element>;
-}, import("mobx-state-tree")._NotCustomized, {
+}, import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
+    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>>;
+} & {
+    /**
+     * #property
+     */
+    heightPreConfig: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+    /**
+     * #property
+     * updated via autorun
+     */
+    blockState: import("mobx-state-tree").IMapType<import("mobx-state-tree").IModelType<{
+        key: import("mobx-state-tree").ISimpleType<string>;
+        region: import("mobx-state-tree").IModelType<{
+            refName: import("mobx-state-tree").ISimpleType<string>;
+            start: import("mobx-state-tree").ISimpleType<number>;
+            end: import("mobx-state-tree").ISimpleType<number>;
+            reversed: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+        } & {
+            assemblyName: import("mobx-state-tree").ISimpleType<string>;
+        }, {
+            setRefName(newRefName: string): void;
+        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
+        reloadFlag: import("mobx-state-tree").IType<number | undefined, number, number>;
+        isLeftEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+        isRightEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    }, {
+        renderInProgress: AbortController | undefined;
+        filled: boolean;
+        reactElement: React.ReactElement<any, string | React.JSXElementConstructor<any>> | undefined;
+        features: Map<string, Feature> | undefined;
+        layout: any;
+        status: string;
+        error: unknown;
+        message: string | undefined;
+        maxHeightReached: boolean;
+        ReactComponent: ({ model, }: {
+            model: any;
+        }) => any;
+        renderProps: any;
+    } & {
+        doReload(): void;
+        afterAttach(): void;
+        setStatus(message: string): void;
+        setLoading(abortController: AbortController): void;
+        setMessage(messageText: string): void;
+        setRendered(props: {
+            reactElement: React.ReactElement<any, string | React.JSXElementConstructor<any>>;
+            features: Map<string, Feature>;
+            layout: any;
+            maxHeightReached: boolean;
+            renderProps: any;
+        } | undefined): void;
+        setError(error: unknown): void;
+        reload(): void;
+        beforeDestroy(): void;
+    }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+    /**
+     * #property
+     */
+    userBpPerPxLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+    /**
+     * #property
+     */
+    userByteSizeLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+}>>, {
     type: string;
-    height: number;
     id: string;
     rpcDriverName: string | undefined;
+    heightPreConfig: number | undefined;
     userBpPerPxLimit: number | undefined;
     userByteSizeLimit: number | undefined;
 }>;