@jbrowse/plugin-wiggle 2.16.0 → 2.17.0

package/esm/util.js

@@ -1,9 +1,4 @@
 import { scaleLinear, scaleLog, scaleQuantize, } from '@mui/x-charts-vendor/d3-scale';
-import { autorun } from 'mobx';
-import { isAbortException, getSession, getContainingView, } from '@jbrowse/core/util';
-import { getRpcSessionId } from '@jbrowse/core/util/tracks';
-import { addDisposer, isAlive } from 'mobx-state-tree';
-import { getConf } from '@jbrowse/core/configuration';
 export const YSCALEBAR_LABEL_OFFSET = 5;
 /**
  * produces a d3-scale from arguments. applies a "nice domain" adjustment
@@ -44,7 +39,8 @@ export function getScale({ domain = [], range = [], scaleType, pivotValue, inver
     return scale;
 }
 /**
- * gets the origin for drawing the graph. for linear this is 0, for log this is arbitrarily set to log(1)==0
+ * gets the origin for drawing the graph. for linear this is 0, for log this is
+ * arbitrarily set to log(1)==0
  *
  * @param scaleType -
  */
@@ -67,8 +63,8 @@ export function getOrigin(scaleType /* , pivot, stats */) {
     return 0;
 }
 /**
- * produces a "nice" domain that actually rounds down to 0 for the min
- * or 0 to the max depending on if all values are positive or negative
+ * produces a "nice" domain that actually rounds down to 0 for the min or 0 to
+ * the max depending on if all values are positive or negative
  *
  * @param object - containing attributes
  *   - domain [min,max]
@@ -121,96 +117,6 @@ export function getNiceDomain({ scaleType, domain, bounds, }) {
     scale.nice();
     return scale.domain();
 }
-export async function getQuantitativeStats(self, opts) {
-    const { rpcManager } = getSession(self);
-    const numStdDev = getConf(self, 'numStdDev') || 3;
-    const { adapterConfig, autoscaleType } = self;
-    const sessionId = getRpcSessionId(self);
-    const params = {
-        sessionId,
-        adapterConfig,
-        statusCallback: (message) => {
-            if (isAlive(self)) {
-                self.setMessage(message);
-            }
-        },
-        ...opts,
-    };
-    if (autoscaleType === 'global' || autoscaleType === 'globalsd') {
-        const results = (await rpcManager.call(sessionId, 'WiggleGetGlobalQuantitativeStats', params));
-        const { scoreMin, scoreMean, scoreStdDev } = results;
-        // globalsd uses heuristic to avoid unnecessary scoreMin<0
-        // if the scoreMin is never less than 0
-        // helps with most coverage bigwigs just being >0
-        return autoscaleType === 'globalsd'
-            ? {
-                ...results,
-                scoreMin: scoreMin >= 0 ? 0 : scoreMean - numStdDev * scoreStdDev,
-                scoreMax: scoreMean + numStdDev * scoreStdDev,
-            }
-            : results;
-    }
-    if (autoscaleType === 'local' || autoscaleType === 'localsd') {
-        const { dynamicBlocks, bpPerPx } = getContainingView(self);
-        const results = (await rpcManager.call(sessionId, 'WiggleGetMultiRegionQuantitativeStats', {
-            ...params,
-            regions: dynamicBlocks.contentBlocks.map(region => {
-                const { start, end } = region;
-                return {
-                    ...JSON.parse(JSON.stringify(region)),
-                    start: Math.floor(start),
-                    end: Math.ceil(end),
-                };
-            }),
-            bpPerPx,
-        }));
-        const { scoreMin, scoreMean, scoreStdDev } = results;
-        // localsd uses heuristic to avoid unnecessary scoreMin<0 if the
-        // scoreMin is never less than 0 helps with most coverage bigwigs
-        // just being >0
-        return autoscaleType === 'localsd'
-            ? {
-                ...results,
-                scoreMin: scoreMin >= 0 ? 0 : scoreMean - numStdDev * scoreStdDev,
-                scoreMax: scoreMean + numStdDev * scoreStdDev,
-            }
-            : results;
-    }
-    if (autoscaleType === 'zscale') {
-        return rpcManager.call(sessionId, 'WiggleGetGlobalQuantitativeStats', params);
-    }
-    throw new Error(`invalid autoscaleType '${autoscaleType}'`);
-}
-export function quantitativeStatsAutorun(self) {
-    addDisposer(self, autorun(async () => {
-        try {
-            const aborter = new AbortController();
-            const view = getContainingView(self);
-            self.setLoading(aborter);
-            if (!view.initialized ||
-                !self.featureDensityStatsReady ||
-                self.regionTooLarge ||
-                self.error) {
-                return;
-            }
-            const statsRegion = JSON.stringify(view.dynamicBlocks);
-            const wiggleStats = await getQuantitativeStats(self, {
-                signal: aborter.signal,
-                filters: [],
-                ...self.renderProps(),
-            });
-            if (isAlive(self)) {
-                self.updateQuantitativeStats(wiggleStats, statsRegion);
-            }
-        }
-        catch (e) {
-            if (!isAbortException(e) && isAlive(self)) {
-                console.error(e);
-                self.setError(e);
-            }
-        }
-    }, { delay: 1000 }));
-}
 export function toP(s = 0) {
     return +(+s).toPrecision(6);
 }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-wiggle",
-  "version": "2.16.0",
+  "version": "2.17.0",
   "description": "JBrowse 2 wiggle adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -65,5 +65,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "1e6d4fbc27ce684eed19e3c217f34bd2da24ab75"
+  "gitHead": "eed30b5e671f8f7823652d7cecc51aa89226de46"
 }