Much faster SASA calculation. Quite fine tracks (7620805d) · Commits · Visitlab / Chromatin / chromoskein

app/package-lock.json

+296 −0

Original line number	Diff line number	Diff line
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		"integrity": "sha512-a4pASwB1jQyJcKLYrwrladVfDZDUGc78qLJZbHyb1Q4rhte0URhzc6ALQpBcauwgov0sXLwZz3vYH5jKAhSMIg==",
		"requires": {
		"ndarray": "^1.0.14",
		"ndarray-ops": "^1.2.1",
		"typedarray-pool": "^1.0.2"
		}
		},
		"ndarray-select": {
		"version": "1.0.1",
		"resolved": "https://registry.npmjs.org/ndarray-select/-/ndarray-select-1.0.1.tgz",
		"integrity": "sha512-bUQH+V2TQnPA0tiB6pliaUSYUTld6Il3UILaH/7T3S7RKzuW9RdA08hayeRJr04Xu4yNTpccLL3YYz7rNd7ffw=="
		},
		"negotiator": {
		"version": "0.6.3",
		"resolved": "https://registry.npmjs.org/negotiator/-/negotiator-0.6.3.tgz",
		@@ -17169,6 +17436,21 @@
		"stacktrace-gps": "^3.0.4"
		}
		},
		"static-kdtree": {
		"version": "1.0.2",
		"resolved": "https://registry.npmjs.org/static-kdtree/-/static-kdtree-1.0.2.tgz",
		"integrity": "sha512-0EnWbb9V5TKZp+SvS59wzXGDFzA02YTpOfE73R1Exj2MK7fNyJELtAeSMW/p23nc2HFV1HqHxTS19aflt6f83g==",
		"requires": {
		"bit-twiddle": "^1.0.0",
		"inorder-tree-layout": "^1.0.0",
		"ndarray": "^1.0.13",
		"ndarray-ops": "^1.2.1",
		"ndarray-pack": "^1.1.0",
		"ndarray-scratch": "^1.0.0",
		"ndarray-select": "^1.0.0",
		"typedarray-pool": "^1.0.0"
		}
		},
		"statuses": {
		"version": "1.5.0",
		"resolved": "https://registry.npmjs.org/statuses/-/statuses-1.5.0.tgz",
		@@ -17612,6 +17894,15 @@
		"mime-types": "~2.1.24"
		}
		},
		"typedarray-pool": {
		"version": "1.2.0",
		"resolved": "https://registry.npmjs.org/typedarray-pool/-/typedarray-pool-1.2.0.tgz",
		"integrity": "sha512-YTSQbzX43yvtpfRtIDAYygoYtgT+Rpjuxy9iOpczrjpXLgGoyG7aS5USJXV2d3nn8uHTeb9rXDvzS27zUg5KYQ==",
		"requires": {
		"bit-twiddle": "^1.0.0",
		"dup": "^1.0.0"
		}
		},
		"typescript": {
		"version": "4.5.5",
		"resolved": "https://registry.npmjs.org/typescript/-/typescript-4.5.5.tgz",
		@@ -17657,6 +17948,11 @@
		"which-boxed-primitive": "^1.0.2"
		}
		},
		"uniq": {
		"version": "1.0.1",
		"resolved": "https://registry.npmjs.org/uniq/-/uniq-1.0.1.tgz",
		"integrity": "sha512-Gw+zz50YNKPDKXs+9d+aKAjVwpjNwqzvNpLigIruT4HA9lMZNdMqs9x07kKHB/L9WRzqp4+DlTU5s4wG2esdoA=="
		},
		"universalify": {
		"version": "2.0.0",
		"resolved": "https://registry.npmjs.org/universalify/-/universalify-2.0.0.tgz",

app/package.json

+2 −0

Original line number	Diff line number	Diff line
		@@ -16,6 +16,7 @@
		"@gmod/gff": "^1.1.2",
		"@types/chroma-js": "^2.1.3",
		"@types/ua-parser-js": "^0.7.36",
		"buffer": "^6.0.3",
		"chroma-js": "^2.4.2",
		"d3": "^7.2.1",
		"file-saver": "^2.0.5",
		@@ -46,6 +47,7 @@
		"rooks": "^5.7.3",
		"sigma": "^2.2.0",
		"simple-statistics": "^7.7.0",
		"static-kdtree": "^1.0.2",
		"stream": "^0.0.2",
		"ua-parser-js": "^1.0.2",
		"use-deep-compare-effect": "^1.8.1",

app/src/components/RightPanel/ChromatinViewportConfigurationPanel.tsx

+1 −1

Original line number	Diff line number	Diff line
		@@ -646,7 +646,7 @@ export function ChromatinViewportConfigurationPanel(props: {
		{configuration.selectedDatum != null && configuration.data.length > configuration.selectedDatum && (<Slider
		label="Radius"
		min={0.0}
		max={configuration.data[configuration.selectedDatum].radiusRange.max * 2.0}
		max={configuration.data[configuration.selectedDatum].radiusRange.max}
		step={(configuration.data[configuration.selectedDatum].radiusRange.max - configuration.data[configuration.selectedDatum].radiusRange.min) / 100.0}
		value={toNumber(configuration.data[configuration.selectedDatum].radius)}
		showValue={false}

app/src/components/RightPanel/tracks/SelectionsTrack.tsx

+2 −1

Original line number	Diff line number	Diff line
		@@ -30,7 +30,8 @@ export function SelectionsTrack(props: {
		throw "";
		}

		const selectionsList = allSelections.selections.map(s => {
		const d = configuration.data as DistanceDataConfiguration;
		const selectionsList = allSelections.selections.filter(s => s.dataID == d.id).map(s => {
		return {
		key: isoSelectionID.unwrap(s.id),
		text: s.name,

app/src/components/viewports/ChromatinViewport.tsx

+3 −2

Original line number	Diff line number	Diff line
		@@ -553,7 +553,7 @@ export function ChromatinViewport(props: {
		}, [viewport, configuration.cutaways]);

		//#region Labels
		let labelsWorldSpace: Array<[vec3, string \| number, IColor]> = [];
		let labelsWorldSpace: Array<[vec4, string \| number, IColor]> = [];

		// Create Labels
		for (const [configurationDatumIndex, configurationDatum] of configuration.data.entries()) {
		@@ -566,7 +566,7 @@ export function ChromatinViewport(props: {

		if (data3D) {
		labelsWorldSpace = (primaryData.values as BEDAnnotations).map((annotation: BEDAnnotation) => [
		vec3.fromValues(data3D.positions[annotation.from].x, data3D.positions[annotation.from].y, data3D.positions[annotation.from].z),
		vec4.fromValues(data3D.positions[annotation.from].x, data3D.positions[annotation.from].y, data3D.positions[annotation.from].z, configurationDatum.radius),
		// annotation.attributes[0] \|\| 'None'
		annotation.attributes[4] \|\| 'None',
		markerColor
		@@ -605,6 +605,7 @@ export function ChromatinViewport(props: {
		let i = 0;
		for (const [position, marker, color] of labelsWorldSpace) {
		const viewSpacePosition = vec4.transformMat4(vec4.create(), vec4.fromValues(position[0], position[1], position[2], 1.0), mvm);
		viewSpacePosition[2] += 2.0 * position[3];
		const clipSpacePosition = vec4.transformMat4(vec4.create(), viewSpacePosition, pm);
		const w = clipSpacePosition[3];