@jbrowse/plugin-alignments 2.4.2 → 2.6.0

package/dist/LinearReadArcsDisplay/configSchema.d.ts

@@ -2,5 +2,63 @@ import PluginManager from '@jbrowse/core/PluginManager';
 /**
  * #config LinearReadArcsDisplay
  */
-declare function configSchemaF(pluginManager: PluginManager): import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+declare function configSchemaF(pluginManager: PluginManager): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    /**
+     * #slot
+     */
+    maxFeatureScreenDensity: {
+        type: string;
+        description: string;
+        defaultValue: number;
+    };
+    /**
+     * #slot
+     */
+    lineWidth: {
+        type: string;
+        description: string;
+        defaultValue: number;
+    };
+    /**
+     * #slot
+     */
+    jitter: {
+        type: string;
+        description: string;
+        defaultValue: number;
+    };
+    /**
+     * #slot
+     */
+    colorScheme: {
+        type: string;
+        model: import("mobx-state-tree").ISimpleType<string>;
+        description: string;
+        defaultValue: string;
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    renderer: import("mobx-state-tree").IAnyModelType;
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    maxFeatureScreenDensity: {
+        type: string;
+        description: string;
+        defaultValue: number;
+    };
+    fetchSizeLimit: {
+        type: string;
+        defaultValue: number;
+        description: string;
+    };
+    height: {
+        type: string;
+        defaultValue: number;
+        description: string;
+    };
+    mouseover: {
+        type: string;
+        description: string;
+        defaultValue: string;
+        contextVariable: string[];
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>, undefined>>, undefined>>;
 export default configSchemaF;

package/dist/LinearReadArcsDisplay/drawFeats.d.ts

@@ -1,15 +1,2 @@
-import { ChainData } from '../shared/fetchChains';
-export declare function hasPairedReads(features: ChainData): boolean;
-export default function drawFeats(self: {
-    setLastDrawnOffsetPx: (n: number) => void;
-    drawInter?: boolean;
-    drawLongRange?: boolean;
-    setError: (e: unknown) => void;
-    colorBy?: {
-        type: string;
-    };
-    height: number;
-    chainData?: ChainData;
-    lineWidthSetting: number;
-    jitterVal: number;
-}, ctx: CanvasRenderingContext2D): Promise<void>;
+import { LinearReadArcsDisplayModel } from './model';
+export declare function drawFeats(self: LinearReadArcsDisplayModel, ctx: CanvasRenderingContext2D, width: number, height: number): void;

package/dist/LinearReadArcsDisplay/drawFeats.js

@@ -1,67 +1,59 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.hasPairedReads = void 0;
+exports.drawFeats = void 0;
 const util_1 = require("@jbrowse/core/util");
 // locals
 const color_1 = require("../shared/color");
 const MismatchParser_1 = require("../MismatchParser");
-function hasPairedReads(features) {
-    for (const f of features.chains.values()) {
-        if (f[0].flags & 1) {
-            return true;
-        }
-    }
-    return false;
-}
-exports.hasPairedReads = hasPairedReads;
+const util_2 = require("../shared/util");
 function jitter(n) {
     return Math.random() * 2 * n - n;
 }
-async function drawFeats(self, ctx) {
-    const { chainData, height, colorBy, drawInter, drawLongRange, lineWidthSetting, jitterVal, } = self;
+function drawLineAtOffset(ctx, offset, height, color) {
+    // draws a vertical line off to middle of nowhere if the second end not found
+    ctx.strokeStyle = color;
+    ctx.beginPath();
+    ctx.moveTo(offset, 0);
+    ctx.lineTo(offset, height);
+    ctx.stroke();
+}
+function drawFeats(self, ctx, width, height) {
+    const { chainData, colorBy, drawInter, drawLongRange, lineWidthSetting, jitterVal, } = self;
     if (!chainData) {
         return;
     }
     const view = (0, util_1.getContainingView)(self);
     const { assemblyManager } = (0, util_1.getSession)(self);
-    self.setLastDrawnOffsetPx(view.offsetPx);
-    ctx.lineWidth = lineWidthSetting;
     const { chains, stats } = chainData;
-    const hasPaired = hasPairedReads(chainData);
-    const assemblyName = view.assemblyNames[0];
-    const asm = assemblyManager.get(assemblyName);
+    const hasPaired = (0, util_2.hasPairedReads)(chainData);
+    const asm = assemblyManager.get(view.assemblyNames[0]);
     const type = (colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) || 'insertSizeAndOrientation';
     if (!asm) {
         return;
     }
-    function drawLineAtOffset(p, c) {
-        // draws a vertical line off to middle of nowhere if the second end not found
-        ctx.strokeStyle = c;
-        ctx.beginPath();
-        ctx.moveTo(p, 0);
-        ctx.lineTo(p, height);
-        ctx.stroke();
-    }
+    ctx.lineWidth = lineWidthSetting;
     function draw(k1, k2, assembly, longRange) {
+        var _a, _b, _c;
         const s1 = k1.strand;
         const s2 = k2.strand;
         const f1 = s1 === -1;
         const f2 = s2 === -1;
         const p1 = f1 ? k1.start : k1.end;
         const p2 = hasPaired ? (f2 ? k2.start : k2.end) : f2 ? k2.end : k2.start;
-        const ra1 = assembly.getCanonicalRefName(k1.refName);
-        const ra2 = assembly.getCanonicalRefName(k2.refName);
-        const r1 = view.bpToPx({ refName: ra1, coord: p1 });
-        const r2 = view.bpToPx({ refName: ra2, coord: p2 });
-        if (r1 && r2) {
-            const radius = (r2.offsetPx - r1.offsetPx) / 2;
+        const ra1 = assembly.getCanonicalRefName(k1.refName) || k1.refName;
+        const ra2 = assembly.getCanonicalRefName(k2.refName) || k2.refName;
+        const r1 = (_a = view.bpToPx({ refName: ra1, coord: p1 })) === null || _a === void 0 ? void 0 : _a.offsetPx;
+        const r2 = (_b = view.bpToPx({ refName: ra2, coord: p2 })) === null || _b === void 0 ? void 0 : _b.offsetPx;
+        if (r1 !== undefined && r2 !== undefined) {
+            const radius = (r2 - r1) / 2;
             const absrad = Math.abs(radius);
-            const p = r1.offsetPx - view.offsetPx;
-            const p2 = r2.offsetPx - view.offsetPx;
+            const p = r1 - view.offsetPx;
+            const p2 = r2 - view.offsetPx;
+            const drawArcInsteadOfBezier = absrad > 10000;
             // bezier (used for non-long-range arcs) requires moveTo before beginPath
             // arc (used for long-range) requires moveTo after beginPath (or else a
             // unwanted line at y=0 is rendered along with the arc)
-            if (longRange) {
+            if (longRange && drawArcInsteadOfBezier) {
                 ctx.moveTo(p, 0);
                 ctx.beginPath();
             }
@@ -69,19 +61,20 @@ async function drawFeats(self, ctx) {
                 ctx.beginPath();
                 ctx.moveTo(p, 0);
             }
-            if (longRange) {
+            if (longRange && drawArcInsteadOfBezier) {
                 ctx.strokeStyle = 'red';
             }
             else {
                 if (hasPaired) {
                     if (type === 'insertSizeAndOrientation') {
-                        ctx.strokeStyle = (0, color_1.getInsertSizeAndOrientationColor)(k1, k2, stats);
+                        ctx.strokeStyle = (0, color_1.getPairedInsertSizeAndOrientationColor)(k1, k2, stats)[0];
                     }
                     else if (type === 'orientation') {
-                        ctx.strokeStyle = (0, color_1.getOrientationColor)(k1);
+                        ctx.strokeStyle = (0, color_1.getPairedOrientationColor)(k1)[0];
                     }
                     else if (type === 'insertSize') {
-                        ctx.strokeStyle = (0, color_1.getInsertSizeColor)(k1, k2, stats) || 'grey';
+                        ctx.strokeStyle =
+                            ((_c = (0, color_1.getPairedInsertSizeColor)(k1, k2, stats)) === null || _c === void 0 ? void 0 : _c[0]) || 'grey';
                     }
                     else if (type === 'gradient') {
                         ctx.strokeStyle = `hsl(${Math.log10(absrad) * 10},50%,50%)`;
@@ -110,13 +103,17 @@ async function drawFeats(self, ctx) {
                 // avoid drawing gigantic circles that glitch out the rendering,
                 // instead draw vertical lines
                 if (absrad > 100000) {
-                    drawLineAtOffset(p + jitter(jitterVal), 'red');
-                    drawLineAtOffset(p2 + jitter(jitterVal), 'red');
+                    drawLineAtOffset(ctx, p + jitter(jitterVal), height, 'red');
+                    drawLineAtOffset(ctx, p2 + jitter(jitterVal), height, 'red');
                 }
-                else {
+                else if (drawArcInsteadOfBezier) {
                     ctx.arc(p + radius + jitter(jitterVal), 0, absrad, 0, Math.PI);
                     ctx.stroke();
                 }
+                else {
+                    ctx.bezierCurveTo(p + jitter(jitterVal), destY, destX, destY, destX + jitter(jitterVal), 0);
+                    ctx.stroke();
+                }
             }
             else {
                 ctx.bezierCurveTo(p + jitter(jitterVal), destY, destX, destY, destX + jitter(jitterVal), 0);
@@ -124,26 +121,24 @@ async function drawFeats(self, ctx) {
             }
         }
         else if (r1 && drawInter) {
-            drawLineAtOffset(r1.offsetPx - view.offsetPx, 'purple');
+            drawLineAtOffset(ctx, r1 - view.offsetPx, height, 'purple');
         }
     }
-    for (let i = 0; i < chains.length; i++) {
-        let chain = chains[i];
+    for (const chain of chains) {
+        // chain.length === 1, singleton (other pairs/mates not in view)
         if (chain.length === 1 && drawLongRange) {
-            // singleton feature
             const f = chain[0];
-            // special case where we look at RPOS/RNEXT
-            if (hasPaired) {
-                // eslint-disable-next-line @typescript-eslint/no-non-null-assertion
-                const refName = f.next_ref;
-                // eslint-disable-next-line @typescript-eslint/no-non-null-assertion
-                const coord = f.next_pos;
-                draw(f, { refName, start: coord, end: coord, strand: f.strand }, asm, true);
+            if (hasPaired && !(f.flags & 8)) {
+                const mate = {
+                    refName: f.next_ref || '',
+                    start: f.next_pos || 0,
+                    end: f.next_pos || 0,
+                    strand: f.strand,
+                };
+                draw(f, mate, asm, true);
             }
-            // special case where we look at SA
             else {
-                const suppAlns = (0, MismatchParser_1.featurizeSA)(f.SA, f.id, f.strand, f.name);
-                const features = [f, ...suppAlns].sort((a, b) => a.clipPos - b.clipPos);
+                const features = [f, ...(0, MismatchParser_1.featurizeSA)(f.SA, f.id, f.strand, f.name)].sort((a, b) => a.clipPos - b.clipPos);
                 for (let i = 0; i < features.length - 1; i++) {
                     const f = features[i];
                     const v1 = features[i + 1];
@@ -152,19 +147,16 @@ async function drawFeats(self, ctx) {
             }
         }
         else {
-            if (!hasPaired) {
-                chain.sort((a, b) => a.clipPos - b.clipPos);
-                chain = chain.filter(f => !(f.flags & 256));
-            }
-            else {
-                // ignore split/supplementary reads for hasPaired=true for now
-                chain = chain.filter(f => !(f.flags & 2048));
-            }
-            for (let i = 0; i < chain.length - 1; i++) {
-                draw(chain[i], chain[i + 1], asm, false);
+            const res = hasPaired
+                ? chain.filter(f => !(f.flags & 2048) && !(f.flags & 8))
+                : chain
+                    .sort((a, b) => a.clipPos - b.clipPos)
+                    .filter(f => !(f.flags & 256));
+            for (let i = 0; i < res.length - 1; i++) {
+                draw(res[i], res[i + 1], asm, false);
             }
         }
     }
 }
-exports.default = drawFeats;
+exports.drawFeats = drawFeats;
 //# sourceMappingURL=drawFeats.js.map

package/dist/LinearReadArcsDisplay/drawFeats.js.map

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