@jbrowse/plugin-alignments 2.4.2 → 2.6.0

package/esm/SNPCoverageRenderer/SNPCoverageRenderer.js.map

@@ -1 +1 @@
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+{"version":3,"file":"SNPCoverageRenderer.js","sourceRoot":"","sources":["../../src/SNPCoverageRenderer/SNPCoverageRenderer.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,kBAAkB,EAAE,MAAM,kBAAkB,CAAA;AACrD,OAAO,EAAE,aAAa,EAAE,QAAQ,EAAW,MAAM,oBAAoB,CAAA;AACrE,OAAO,EAAE,cAAc,EAAE,MAAM,6BAA6B,CAAA;AAE5D,OAAO,EACL,SAAS,EACT,QAAQ,EAER,kBAAkB,EAClB,sBAAsB,GACvB,MAAM,wBAAwB,CAAA;AA2B/B,MAAM,WAAW,GAAG,GAAG,CAAA;AAEvB,MAAM,CAAC,OAAO,OAAO,mBAAoB,SAAQ,kBAAkB;IACjE,4EAA4E;IAC5E,kDAAkD;IAClD,KAAK,CAAC,IAAI,CACR,GAA6B,EAC7B,KAAyC;QAEzC,MAAM,EACJ,QAAQ,EACR,OAAO,EACP,OAAO,EACP,mBAAmB,EACnB,kBAAkB,GAAG,EAAE,EACvB,SAAS,EACT,MAAM,EAAE,gBAAgB,EACxB,KAAK,EAAE,WAAW,EAClB,MAAM,EAAE,GAAG,EACX,KAAK,GACN,GAAG,KAAK,CAAA;QACT,MAAM,KAAK,GAAG,kBAAkB,CAAC,WAAW,CAAC,CAAA;QAC7C,MAAM,CAAC,MAAM,CAAC,GAAG,OAAO,CAAA;QACxB,MAAM,KAAK,GAAG,CAAC,MAAM,CAAC,GAAG,GAAG,MAAM,CAAC,KAAK,CAAC,GAAG,OAAO,CAAA;QAEnD,yEAAyE;QACzE,oEAAoE;QACpE,iDAAiD;QACjD,MAAM,MAAM,GAAG,sBAAsB,CAAA;QACrC,MAAM,MAAM,GAAG,gBAAgB,GAAG,MAAM,GAAG,CAAC,CAAA;QAE5C,MAAM,EAAE,MAAM,EAAE,GAAG,SAAS,CAAA;QAC5B,IAAI,CAAC,MAAM,EAAE;YACX,OAAM;SACP;QACD,MAAM,IAAI,GAAG,EAAE,GAAG,SAAS,EAAE,KAAK,EAAE,CAAC,CAAC,EAAE,MAAM,CAAC,EAAE,CAAA;QACjD,MAAM,SAAS,GAAG,QAAQ,CAAC,IAAI,CAAC,CAAA;QAEhC,mEAAmE;QACnE,MAAM,kBAAkB,GAAG,QAAQ,CAAC;YAClC,GAAG,IAAI;YACP,KAAK,EAAE,CAAC,CAAC,EAAE,MAAM,GAAG,CAAC,CAAC;YACtB,SAAS,EAAE,QAAQ;SACpB,CAAC,CAAA;QACF,MAAM,OAAO,GAAG,SAAS,CAAC,SAAS,CAAC,SAAS,CAAC,CAAA;QAC9C,MAAM,YAAY,GAAG,SAAS,CAAC,QAAQ,CAAC,CAAA;QAExC,MAAM,kBAAkB,GAAG,cAAc,CAAC,GAAG,EAAE,oBAAoB,CAAC,CAAA;QACpE,MAAM,mBAAmB,GAAG,cAAc,CAAC,GAAG,EAAE,qBAAqB,CAAC,CAAA;QACtE,MAAM,QAAQ,GAAG,cAAc,CAAC,GAAG,EAAE,UAAU,CAAC,CAAA;QAChD,MAAM,cAAc,GAAG,cAAc,CAAC,GAAG,EAAE,gBAAgB,CAAC,CAAA;QAE5D,sEAAsE;QACtE,MAAM,GAAG,GAAG,CAAC,CAAS,EAAE,EAAE,CAAC,MAAM,GAAG,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,MAAM,CAAA;QAChE,MAAM,QAAQ,GAAG,CAAC,CAAS,EAAE,EAAE,CAAC,GAAG,CAAC,OAAO,CAAC,GAAG,GAAG,CAAC,CAAC,CAAC,CAAA;QACrD,kCAAkC;QAClC,MAAM,IAAI,GAAG,CAAC,CAAS,EAAE,EAAE,CAAC,MAAM,GAAG,CAAC,kBAAkB,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,MAAM,CAAA;QAC1E,MAAM,SAAS,GAAG,CAAC,CAAS,EAAE,EAAE,CAAC,IAAI,CAAC,YAAY,CAAC,GAAG,IAAI,CAAC,CAAC,CAAC,CAAA;QAE7D,MAAM,EAAE,KAAK,EAAE,GAAG,KAAK,CAAC,OAAO,CAAA;QAC/B,MAAM,YAAY,GAA8B;YAC9C,CAAC,EAAE,KAAK,CAAC,CAAC,CAAC,IAAI;YACf,CAAC,EAAE,KAAK,CAAC,CAAC,CAAC,IAAI;YACf,CAAC,EAAE,KAAK,CAAC,CAAC,CAAC,IAAI;YACf,CAAC,EAAE,KAAK,CAAC,CAAC,CAAC,IAAI;YACf,SAAS,EAAE,QAAQ;YACnB,QAAQ,EAAE,MAAM;YAChB,QAAQ,EAAE,KAAK;YACf,KAAK,EAAE,cAAc,CAAC,GAAG,EAAE,OAAO,CAAC;YACnC,IAAI,EAAE,KAAK;YACX,MAAM,EAAE,MAAM;SACf,CAAA;QAED,MAAM,KAAK,GAAG,CAAC,GAAG,QAAQ,CAAC,MAAM,EAAE,CAAC,CAAA;QACpC,MAAM,QAAQ,GAAG,KAAK,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,GAAG,CAAC,MAAM,CAAC,KAAK,MAAM,CAAC,CAAA;QAC5D,MAAM,KAAK,GAAG,KAAK,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,GAAG,CAAC,MAAM,CAAC,KAAK,MAAM,CAAC,CAAA;QAEzD,wEAAwE;QACxE,+CAA+C;QAC/C,GAAG,CAAC,SAAS,GAAG,YAAY,CAAC,KAAK,CAAA;QAClC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;YACxC,MAAM,OAAO,GAAG,QAAQ,CAAC,CAAC,CAAC,CAAA;YAC3B,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG,aAAa,CAAC,OAAO,EAAE,MAAM,EAAE,OAAO,CAAC,CAAA;YACjE,MAAM,CAAC,GAAG,OAAO,GAAG,MAAM,GAAG,WAAW,CAAA;YACxC,MAAM,KAAK,GAAG,OAAO,CAAC,GAAG,CAAC,OAAO,CAAW,CAAA;YAC5C,GAAG,CAAC,QAAQ,CAAC,MAAM,EAAE,GAAG,CAAC,KAAK,CAAC,EAAE,CAAC,EAAE,QAAQ,CAAC,KAAK,CAAC,CAAC,CAAA;SACrD;QAED,0EAA0E;QAC1E,2EAA2E;QAC3E,0EAA0E;QAC1E,0EAA0E;QAC1E,wEAAwE;QACxE,IAAI,SAAS,GAAG,CAAC,CAAA;QAEjB,wEAAwE;QACxE,+DAA+D;QAC/D,MAAM,8BAA8B,GAAG,MAAM,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC,GAAG,OAAO,CAAC,CAAC,CAAC,CAAC,CAAA;QAExE,yEAAyE;QACzE,yEAAyE;QACzE,oCAAoC;QAEpC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;YACxC,MAAM,OAAO,GAAG,QAAQ,CAAC,CAAC,CAAC,CAAA;YAC3B,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG,aAAa,CAAC,OAAO,EAAE,MAAM,EAAE,OAAO,CAAC,CAAA;YAEjE,MAAM,KAAK,GAAG,OAAO,CAAC,GAAG,CAAC,OAAO,CAAW,CAAA;YAC5C,MAAM,OAAO,GAAG,OAAO,CAAC,GAAG,CAAC,SAAS,CAAY,CAAA;YACjD,MAAM,CAAC,GAAG,IAAI,CAAC,GAAG,CAAC,OAAO,GAAG,MAAM,EAAE,CAAC,CAAC,CAAA;YACvC,MAAM,UAAU,GAAG,OAAO,CAAC,KAAK,CAAA;YAChC,MAAM,IAAI,GAAG,MAAM,CAAC,IAAI,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC,IAAI,EAAE,CAAA;YAE5C,IAAI,IAAI,GAAG,CAAC,CAAA;YACZ,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,IAAI,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;gBACpC,MAAM,IAAI,GAAG,IAAI,CAAC,CAAC,CAAC,CAAA;gBACpB,MAAM,EAAE,KAAK,EAAE,GAAG,OAAO,CAAC,GAAG,CAAC,IAAI,CAAC,CAAA;gBACnC,GAAG,CAAC,SAAS;oBACX,YAAY,CAAC,IAAI,CAAC;wBAClB,kBAAkB,CAAC,IAAI,CAAC,OAAO,CAAC,MAAM,EAAE,EAAE,CAAC,CAAC;wBAC5C,OAAO,CAAA;gBAET,MAAM,MAAM,GAAG,QAAQ,CAAC,KAAK,CAAC,CAAA;gBAC9B,MAAM,MAAM,GAAG,GAAG,CAAC,KAAK,CAAC,GAAG,MAAM,CAAA;gBAClC,GAAG,CAAC,QAAQ,CACV,IAAI,CAAC,KAAK,CAAC,MAAM,CAAC,EAClB,MAAM,GAAG,CAAC,CAAC,KAAK,GAAG,IAAI,CAAC,GAAG,KAAK,CAAC,GAAG,MAAM,EAC1C,CAAC,EACD,CAAC,KAAK,GAAG,KAAK,CAAC,GAAG,MAAM,CACzB,CAAA;gBACD,IAAI,IAAI,KAAK,CAAA;aACd;YAED,MAAM,eAAe,GAAG,MAAM,CAAC,IAAI,CAAC,OAAO,CAAC,MAAM,CAAC,CAAA;YACnD,MAAM,eAAe,GAAG,GAAG,CAAA;YAC3B,IAAI,mBAAmB,EAAE;gBACvB,IAAI,IAAI,GAAG,CAAC,CAAA;gBACZ,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,eAAe,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;oBAC/C,MA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package/esm/SNPCoverageRenderer/configSchema.d.ts

@@ -1,2 +1,48 @@
-declare const SNPCoverageRenderer: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+declare const SNPCoverageRenderer: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    /**
+     * #slot
+     */
+    clipColor: {
+        type: string;
+        description: string;
+        defaultValue: string;
+    };
+    /**
+     * #slot
+     */
+    indicatorThreshold: {
+        type: string;
+        description: string;
+        defaultValue: number;
+    };
+    /**
+     * #slot
+     */
+    drawArcs: {
+        type: string;
+        description: string;
+        defaultValue: boolean;
+    };
+    /**
+     * #slot
+     */
+    drawInterbaseCounts: {
+        type: string;
+        description: string;
+        defaultValue: boolean;
+    };
+    /**
+     * #slot
+     */
+    drawIndicators: {
+        type: string;
+        description: string;
+        defaultValue: boolean;
+    };
+    color: {
+        type: string;
+        description: string;
+        defaultValue: string;
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 export default SNPCoverageRenderer;

package/esm/SNPCoverageRenderer/configSchema.js

@@ -44,6 +44,11 @@ const SNPCoverageRenderer = ConfigurationSchema('SNPCoverageRenderer', {
         description: 'draw a triangular indicator where an event has been detected',
         defaultValue: true,
     },
+    color: {
+        type: 'color',
+        description: 'Background color for the SNPCoverage renderer',
+        defaultValue: '#d3d3d3',
+    },
 }, { explicitlyTyped: true });
 export default SNPCoverageRenderer;
 //# sourceMappingURL=configSchema.js.map

package/esm/SNPCoverageRenderer/configSchema.js.map

@@ -1 +1 @@
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+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/SNPCoverageRenderer/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AAEjE;;GAEG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,mBAAmB,GAAG,mBAAmB,CAC7C,qBAAqB,EACrB;IACE;;OAEG;IACH,SAAS,EAAE;QACT,IAAI,EAAE,OAAO;QACb,WAAW,EAAE,kCAAkC;QAC/C,YAAY,EAAE,KAAK;KACpB;IACD;;OAEG;IACH,kBAAkB,EAAE;QAClB,IAAI,EAAE,QAAQ;QACd,WAAW,EACT,+DAA+D;QACjE,YAAY,EAAE,GAAG;KAClB;IACD;;OAEG;IACH,QAAQ,EAAE;QACR,IAAI,EAAE,SAAS;QACf,WAAW,EAAE,6CAA6C;QAC1D,YAAY,EAAE,IAAI;KACnB;IACD;;OAEG;IACH,mBAAmB,EAAE;QACnB,IAAI,EAAE,SAAS;QACf,WAAW,EACT,iJAAiJ;QACnJ,YAAY,EAAE,IAAI;KACnB;IACD;;OAEG;IACH,cAAc,EAAE;QACd,IAAI,EAAE,SAAS;QACf,WAAW,EACT,8DAA8D;QAChE,YAAY,EAAE,IAAI;KACnB;IAED,KAAK,EAAE;QACL,IAAI,EAAE,OAAO;QACb,WAAW,EAAE,+CAA+C;QAC5D,YAAY,EAAE,SAAS;KACxB;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA;AAED,eAAe,mBAAmB,CAAA"}

package/esm/shared/BaseDisplayComponent.d.ts

@@ -0,0 +1,8 @@
+import React from 'react';
+import { LinearReadCloudDisplayModel } from '../LinearReadCloudDisplay/model';
+import { LinearReadArcsDisplayModel } from '../LinearReadArcsDisplay/model';
+declare const _default: ({ model, children, }: {
+    model: LinearReadArcsDisplayModel | LinearReadCloudDisplayModel;
+    children?: React.ReactNode;
+}) => React.JSX.Element | null;
+export default _default;

package/esm/shared/BaseDisplayComponent.js

@@ -0,0 +1,44 @@
+import React from 'react';
+import { LoadingEllipses } from '@jbrowse/core/ui';
+import { BlockMsg } from '@jbrowse/plugin-linear-genome-view';
+import { makeStyles } from 'tss-react/mui';
+import { observer } from 'mobx-react';
+import { getContainingView } from '@jbrowse/core/util';
+const useStyles = makeStyles()(theme => {
+    const bg = theme.palette.action.disabledBackground;
+    return {
+        loading: {
+            backgroundColor: theme.palette.background.default,
+            backgroundImage: `repeating-linear-gradient(45deg, transparent, transparent 5px, ${bg} 5px, ${bg} 10px)`,
+            position: 'absolute',
+            bottom: 0,
+            height: 50,
+            width: 300,
+            right: 0,
+            pointerEvents: 'none',
+            textAlign: 'center',
+        },
+    };
+});
+export default observer(function ({ model, children, }) {
+    const { error, regionTooLarge } = model;
+    return error ? (React.createElement(BlockMsg, { message: `${error}`, severity: "error", buttonText: "Reload", action: model.reload })) : regionTooLarge ? (model.regionCannotBeRendered()) : (React.createElement(DataDisplay, { model: model }, children));
+});
+const DataDisplay = observer(function ({ model, children, }) {
+    const { drawn, loading } = model;
+    const view = getContainingView(model);
+    const left = (model.lastDrawnOffsetPx || 0) - view.offsetPx;
+    return (
+    // this data-testid is located here because changing props on the canvas
+    // itself is very sensitive to triggering ref invalidation
+    React.createElement("div", { "data-testid": `drawn-${drawn}` },
+        React.createElement("div", { style: { position: 'absolute', left } }, children),
+        left !== 0 || loading ? React.createElement(LoadingBar, { model: model }) : null));
+});
+const LoadingBar = observer(function ({ model, }) {
+    const { classes } = useStyles();
+    const { message } = model;
+    return (React.createElement("div", { className: classes.loading },
+        React.createElement(LoadingEllipses, { message: message })));
+});
+//# sourceMappingURL=BaseDisplayComponent.js.map

package/esm/shared/BaseDisplayComponent.js.map

@@ -0,0 +1 @@
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package/esm/shared/FilterByTag.d.ts

@@ -1,18 +1,19 @@
-/// <reference types="react" />
+import React from 'react';
+interface FilterBy {
+    flagExclude: number;
+    flagInclude: number;
+    readName?: string;
+    tagFilter?: {
+        tag: string;
+        value: string;
+    };
+}
 declare function FilterByTagDlg(props: {
     model: {
-        filterBy?: {
-            flagExclude: number;
-            flagInclude: number;
-            readName?: string;
-            tagFilter?: {
-                tag: string;
-                value: string;
-            };
-        };
-        setFilterBy: Function;
+        filterBy: FilterBy;
+        setFilterBy: (arg: FilterBy) => void;
     };
     handleClose: () => void;
-}): JSX.Element;
+}): React.JSX.Element;
 declare const _default: typeof FilterByTagDlg;
 export default _default;

package/esm/shared/FilterByTag.js

@@ -50,11 +50,11 @@ function FilterByTagDlg(props) {
     const { model, handleClose } = props;
     const { classes } = useStyles();
     const { filterBy } = model;
-    const [flagInclude, setFlagInclude] = useState(filterBy === null || filterBy === void 0 ? void 0 : filterBy.flagInclude);
-    const [flagExclude, setFlagExclude] = useState(filterBy === null || filterBy === void 0 ? void 0 : filterBy.flagExclude);
-    const [tag, setTag] = useState(((_a = filterBy === null || filterBy === void 0 ? void 0 : filterBy.tagFilter) === null || _a === void 0 ? void 0 : _a.tag) || '');
-    const [tagValue, setTagValue] = useState(((_b = filterBy === null || filterBy === void 0 ? void 0 : filterBy.tagFilter) === null || _b === void 0 ? void 0 : _b.value) || '');
-    const [readName, setReadName] = useState((filterBy === null || filterBy === void 0 ? void 0 : filterBy.readName) || '');
+    const [flagInclude, setFlagInclude] = useState(filterBy.flagInclude);
+    const [flagExclude, setFlagExclude] = useState(filterBy.flagExclude);
+    const [tag, setTag] = useState(((_a = filterBy.tagFilter) === null || _a === void 0 ? void 0 : _a.tag) || '');
+    const [tagValue, setTagValue] = useState(((_b = filterBy.tagFilter) === null || _b === void 0 ? void 0 : _b.value) || '');
+    const [readName, setReadName] = useState(filterBy.readName || '');
     const validTag = tag.match(/^[A-Za-z][A-Za-z0-9]$/);
     const site = 'https://broadinstitute.github.io/picard/explain-flags.html';
     return (React.createElement(Dialog, { open: true, onClose: handleClose, title: "Filter options" },
@@ -76,16 +76,11 @@ function FilterByTagDlg(props) {
                 React.createElement(Typography, null, "Filter by tag name and value. Use * in the value field to get all reads containing any value for that tag. Example: filter tag name SA with value * to get all split/supplementary reads. Other examples include HP for haplotype, or RG for read group"),
                 React.createElement(TextField, { className: classes.field, value: tag, onChange: event => setTag(event.target.value), placeholder: "Enter tag name", inputProps: {
                         maxLength: 2,
-                        'data-testid': 'color-tag-name-input',
-                    }, error: tag.length === 2 && !validTag, helperText: tag.length === 2 && !validTag ? 'Not a valid tag' : '', "data-testid": "color-tag-name" }),
-                React.createElement(TextField, { className: classes.field, value: tagValue, onChange: event => setTagValue(event.target.value), placeholder: "Enter tag value", inputProps: {
-                        'data-testid': 'color-tag-name-input',
-                    }, "data-testid": "color-tag-value" })),
+                    }, error: tag.length === 2 && !validTag, helperText: tag.length === 2 && !validTag ? 'Not a valid tag' : '' }),
+                React.createElement(TextField, { className: classes.field, value: tagValue, onChange: event => setTagValue(event.target.value), placeholder: "Enter tag value" })),
             React.createElement(Paper, { className: classes.paper, variant: "outlined" },
                 React.createElement(Typography, null, "Filter by read name"),
-                React.createElement(TextField, { className: classes.field, value: readName, onChange: event => setReadName(event.target.value), placeholder: "Enter read name", inputProps: {
-                        'data-testid': 'color-tag-readname-input',
-                    }, "data-testid": "color-tag-readname" })),
+                React.createElement(TextField, { className: classes.field, value: readName, onChange: event => setReadName(event.target.value), placeholder: "Enter read name" })),
             React.createElement(DialogActions, null,
                 React.createElement(Button, { variant: "contained", color: "primary", autoFocus: true, type: "submit", onClick: () => {
                         model.setFilterBy({

package/esm/shared/FilterByTag.js.map

@@ -1 +1 @@
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package/esm/shared/afterAttach.d.ts

@@ -0,0 +1,2 @@
+import { IAnyStateTreeNode } from 'mobx-state-tree';
+export declare function doAfterAttach<T extends IAnyStateTreeNode>(self: T, cb: (self: T, ctx: CanvasRenderingContext2D, width: number, height: number) => void): void;

package/esm/shared/afterAttach.js

@@ -0,0 +1,40 @@
+import { getContainingView } from '@jbrowse/core/util';
+import { createAutorun } from '../util';
+import { fetchChains } from './fetchChains';
+export function doAfterAttach(self, cb) {
+    createAutorun(self, async () => {
+        await fetchChains(self);
+    }, { delay: 1000 });
+    function draw(view) {
+        const canvas = self.ref;
+        if (!canvas) {
+            return;
+        }
+        const ctx = canvas.getContext('2d');
+        if (!ctx) {
+            return;
+        }
+        if (!self.chainData) {
+            return;
+        }
+        ctx.clearRect(0, 0, canvas.width, self.height * 2);
+        ctx.resetTransform();
+        ctx.scale(2, 2);
+        cb(self, ctx, canvas.width, self.height);
+        self.setLastDrawnOffsetPx(view.offsetPx);
+        self.setLastDrawnBpPerPx(view.bpPerPx);
+    }
+    // first autorun instantly draws if bpPerPx changes
+    createAutorun(self, async () => {
+        const view = getContainingView(self);
+        if (view.bpPerPx !== self.lastDrawnBpPerPx) {
+            draw(view);
+        }
+    });
+    // second autorun draws after delay 1000 e.g. if offsetPx changes
+    createAutorun(self, async () => {
+        const view = getContainingView(self);
+        draw(view);
+    }, { delay: 1000 });
+}
+//# sourceMappingURL=afterAttach.js.map

package/esm/shared/afterAttach.js.map

@@ -0,0 +1 @@
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package/esm/shared/color.d.ts

@@ -1,17 +1,55 @@
 import { ChainStats } from './fetchChains';
-export declare function getInsertSizeColor(f1: {
+export declare const fillColor: {
+    color_fwd_strand_not_proper: string;
+    color_rev_strand_not_proper: string;
+    color_fwd_strand: string;
+    color_rev_strand: string;
+    color_fwd_missing_mate: string;
+    color_rev_missing_mate: string;
+    color_fwd_diff_chr: string;
+    color_rev_diff_chr: string;
+    color_pair_lr: string;
+    color_pair_rr: string;
+    color_pair_rl: string;
+    color_pair_ll: string;
+    color_nostrand: string;
+    color_interchrom: string;
+    color_longinsert: string;
+    color_shortinsert: string;
+    color_unknown: string;
+};
+export declare const strokeColor: {
+    color_fwd_strand_not_proper: string;
+    color_rev_strand_not_proper: string;
+    color_fwd_strand: string;
+    color_rev_strand: string;
+    color_fwd_missing_mate: string;
+    color_rev_missing_mate: string;
+    color_fwd_diff_chr: string;
+    color_rev_diff_chr: string;
+    color_pair_lr: string;
+    color_pair_rr: string;
+    color_pair_rl: string;
+    color_pair_ll: string;
+    color_nostrand: string;
+    color_interchrom: string;
+    color_longinsert: string;
+    color_shortinsert: string;
+    color_unknown: string;
+};
+export declare function getPairedInsertSizeColor(f1: {
     refName: string;
     tlen?: number;
 }, f2: {
     refName: string;
-}, stats?: ChainStats): "" | "red" | "purple" | "#f0f";
-export declare function getInsertSizeAndOrientationColor(f1: {
+}, stats?: ChainStats): readonly [string, string] | undefined;
+export declare function getPairedInsertSizeAndOrientationColor(f1: {
     refName: string;
     pair_orientation?: string;
     tlen?: number;
 }, f2: {
     refName: string;
-}, stats?: ChainStats): string;
-export declare function getOrientationColor(f: {
+}, stats?: ChainStats): readonly [string, string];
+export declare function getPairedOrientationColor(f: {
     pair_orientation?: string;
-}): string;
+}): readonly [string, string];

package/esm/shared/color.js

@@ -1,37 +1,71 @@
-import { orientationTypes } from '../util';
-const alignmentColoring = {
+import { orientationTypes, pairMap } from '../util';
+export const fillColor = {
+    color_fwd_strand_not_proper: '#ECC8C8',
+    color_rev_strand_not_proper: '#BEBED8',
+    color_fwd_strand: '#EC8B8B',
+    color_rev_strand: '#8F8FD8',
+    color_fwd_missing_mate: '#D11919',
+    color_rev_missing_mate: '#1919D1',
+    color_fwd_diff_chr: '#000',
+    color_rev_diff_chr: '#969696',
     color_pair_lr: '#c8c8c8',
     color_pair_rr: 'navy',
     color_pair_rl: 'teal',
     color_pair_ll: 'green',
+    color_nostrand: '#c8c8c8',
+    color_interchrom: 'purple',
+    color_longinsert: 'red',
+    color_shortinsert: 'pink',
+    color_unknown: 'grey',
 };
-export function getInsertSizeColor(f1, f2, stats) {
+// manually calculated by running
+// const color = require('color')
+// Object.fromEntries(Object.entries(fillColor).map(([key,val])=>{
+//   return [key, color(val).darken('0.3').hex()]
+// }))
+// this avoids (expensive) use of Color module at runtime
+export const strokeColor = {
+    color_fwd_strand_not_proper: '#CA6767',
+    color_rev_strand_not_proper: '#7272AA',
+    color_fwd_strand: '#DC2A2A',
+    color_rev_strand: '#4141BA',
+    color_fwd_missing_mate: '#921111',
+    color_rev_missing_mate: '#111192',
+    color_fwd_diff_chr: '#000000',
+    color_rev_diff_chr: '#696969',
+    color_pair_lr: '#8C8C8C',
+    color_pair_rr: '#00005A',
+    color_pair_rl: '#005A5A',
+    color_pair_ll: '#005A00',
+    color_nostrand: '#8C8C8C',
+    color_interchrom: '#5A005A',
+    color_longinsert: '#B30000',
+    color_shortinsert: '#FF3A5C',
+    color_unknown: 'grey',
+};
+export function getPairedInsertSizeColor(f1, f2, stats) {
     const sameRef = f1.refName === f2.refName;
     const tlen = Math.abs(f1.tlen || 0);
     if (sameRef && tlen > ((stats === null || stats === void 0 ? void 0 : stats.upper) || 0)) {
-        return 'red';
+        return [fillColor.color_longinsert, strokeColor.color_longinsert];
     }
     else if (sameRef && tlen < ((stats === null || stats === void 0 ? void 0 : stats.lower) || 0)) {
-        return '#f0f';
+        return [fillColor.color_shortinsert, strokeColor.color_shortinsert];
     }
     else if (!sameRef) {
-        return 'purple';
+        return [fillColor.color_interchrom, strokeColor.color_interchrom];
     }
-    return '';
+    return undefined;
 }
-export function getInsertSizeAndOrientationColor(f1, f2, stats) {
-    return getInsertSizeColor(f1, f2, stats) || getOrientationColor(f1);
+export function getPairedInsertSizeAndOrientationColor(f1, f2, stats) {
+    return (getPairedInsertSizeColor(f1, f2, stats) || getPairedOrientationColor(f1));
 }
-export function getOrientationColor(f) {
-    const type = orientationTypes['fr'];
-    const orientation = type[f.pair_orientation || ''];
-    const map = {
-        LR: 'color_pair_lr',
-        RR: 'color_pair_rr',
-        RL: 'color_pair_rl',
-        LL: 'color_pair_ll',
-    };
-    const val = map[orientation];
-    return alignmentColoring[val] || 'grey';
+export function getPairedOrientationColor(f) {
+    const type = orientationTypes.fr;
+    const type2 = pairMap[type[f.pair_orientation || '']];
+    return [
+        fillColor[type2] || fillColor.color_unknown,
+        strokeColor[type2] || strokeColor.color_unknown,
+    ];
 }
 //# sourceMappingURL=color.js.map

package/esm/shared/color.js.map

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package/esm/shared/fetchChains.d.ts

@@ -1,4 +1,5 @@
-import { IAnyStateTreeNode } from 'mobx-state-tree';
+import { LinearReadArcsDisplayModel } from '../LinearReadArcsDisplay/model';
+import { LinearReadCloudDisplayModel } from '../LinearReadCloudDisplay/model';
 export interface ReducedFeature {
     name: string;
     strand: number;
@@ -24,4 +25,4 @@ export interface ChainData {
     chains: ReducedFeature[][];
     stats?: ChainStats;
 }
-export declare function fetchChains(self: IAnyStateTreeNode): Promise<void>;
+export declare function fetchChains(self: LinearReadArcsDisplayModel | LinearReadCloudDisplayModel): Promise<void>;

package/esm/shared/fetchChains.js

@@ -1,26 +1,20 @@
 import { getContainingTrack, getContainingView, getSession, } from '@jbrowse/core/util';
 import { getSnapshot } from 'mobx-state-tree';
 export async function fetchChains(self) {
-    try {
-        const { rpcSessionId: sessionId } = getContainingTrack(self);
-        const { rpcManager } = getSession(self);
-        const view = getContainingView(self);
-        if (!view.initialized || self.error) {
-            return;
-        }
-        self.setLoading(true);
-        const ret = (await rpcManager.call(sessionId, 'PileupGetReducedFeatures', {
-            sessionId,
-            regions: view.staticBlocks.contentBlocks,
-            filterBy: getSnapshot(self.filterBy),
-            adapterConfig: self.adapterConfig,
-        }));
-        self.setChainData(ret);
-        self.setLoading(false);
-    }
-    catch (e) {
-        console.error(e);
-        self.setError(e);
+    const { rpcSessionId: sessionId } = getContainingTrack(self);
+    const { rpcManager } = getSession(self);
+    const view = getContainingView(self);
+    if (!view.initialized || self.error || self.regionTooLarge) {
+        return;
     }
+    self.setLoading(true);
+    const ret = (await rpcManager.call(sessionId, 'PileupGetReducedFeatures', {
+        sessionId,
+        regions: view.staticBlocks.contentBlocks,
+        filterBy: getSnapshot(self.filterBy),
+        adapterConfig: self.adapterConfig,
+    }));
+    self.setChainData(ret);
+    self.setLoading(false);
 }
 //# sourceMappingURL=fetchChains.js.map

package/esm/shared/fetchChains.js.map

@@ -1 +1 @@
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package/esm/shared/renderSvg.d.ts

@@ -0,0 +1,7 @@
+import React from 'react';
+export declare function renderSvg<T extends {
+    id: string;
+    height: number;
+}>(self: T, opts: {
+    rasterizeLayers?: boolean;
+}, cb: (model: T, ctx: CanvasRenderingContext2D, width: number, height: number) => void): Promise<React.JSX.Element | undefined>;

package/esm/shared/renderSvg.js

@@ -0,0 +1,39 @@
+import React from 'react';
+import { getContainingView } from '@jbrowse/core/util';
+// stabilize clipid under test for snapshot
+function getId(id) {
+    const isJest = typeof jest === 'undefined';
+    return `arc-clip-${isJest ? id : 'jest'}`;
+}
+export async function renderSvg(self, opts, cb) {
+    const view = getContainingView(self);
+    const width = view.dynamicBlocks.totalWidthPx;
+    const height = self.height;
+    if (opts.rasterizeLayers) {
+        const canvas = document.createElement('canvas');
+        canvas.width = width * 2;
+        canvas.height = height * 2;
+        const ctx = canvas.getContext('2d');
+        if (!ctx) {
+            return;
+        }
+        ctx.scale(2, 2);
+        cb(self, ctx, width, height);
+        return (React.createElement("image", { width: width, height: height, xlinkHref: canvas.toDataURL('image/png') }));
+    }
+    else {
+        // @ts-ignore
+        const C2S = await import('canvas2svg');
+        const ctx = new C2S.default(width, height);
+        cb(self, ctx, width, height);
+        const clipid = getId(self.id);
+        return (React.createElement(React.Fragment, null,
+            React.createElement("defs", null,
+                React.createElement("clipPath", { id: clipid },
+                    React.createElement("rect", { x: 0, y: 0, width: width, height: height }))),
+            React.createElement("g", { 
+                /* eslint-disable-next-line react/no-danger */
+                dangerouslySetInnerHTML: { __html: ctx.getSvg().innerHTML }, clipPath: `url(#${clipid})` })));
+    }
+}
+//# sourceMappingURL=renderSvg.js.map

package/esm/shared/renderSvg.js.map

@@ -0,0 +1 @@
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package/esm/shared/util.d.ts

@@ -0,0 +1,2 @@
+import { ChainData } from './fetchChains';
+export declare function hasPairedReads(features: ChainData): boolean;

package/esm/shared/util.js

@@ -0,0 +1,9 @@
+export function hasPairedReads(features) {
+    for (const f of features.chains.values()) {
+        if (f[0].flags & 1) {
+            return true;
+        }
+    }
+    return false;
+}
+//# sourceMappingURL=util.js.map

package/esm/shared/util.js.map

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