Commit 23937808 authored by MatusT's avatar MatusT
Browse files

Fix spline (a little). Annotations are now in basepairs.

parent b93d7727

app/demo-workspace.png

−323 KiB (1.35 MiB)
Loading image diff...

app/src/components/viewports/ChromatinViewport.tsx

+49 −10
Original line number Diff line number Diff line
@@ -2,17 +2,16 @@ import { useEffect, useRef, useState, Dispatch } from "react"; 
import * as GraphicsModule from "../../modules/graphics";

import { sasa } from "../../modules/sasa";

import { ChromatinViewportConfiguration, ConfigurationAction, ConfigurationState, getDefaultViewportSelectionOptions, ChromatinViewportToolType } from "../../modules/storage/models/viewports";

import { useDeepCompareEffect, useMouseHovered, usePrevious } from "react-use";

import { useDeepCompareEffect, useMouseHovered } from "react-use";

import { ChromatinIntersection, ContinuousTube, Sphere, CullPlane } from "../../modules/graphics";

import { vec2, vec3, vec4 } from "gl-matrix";

import { BEDAnnotations, BEDAnnotation, BinPositionsData, Data, DataAction, DataState, isoDataID, Positions3D, Sparse1DNumericData, Sparse1DTextData } from "../../modules/storage/models/data";

import { BEDAnnotations, BinPositionsData, Data, DataAction, DataState, isoDataID, Positions3D, Sparse1DNumericData, Sparse1DTextData, Position3D } from "../../modules/storage/models/data";

import { SelectionAction, SelectionActionKind, SelectionState } from "../../modules/storage/models/selections";

import { useConfiguration } from "../hooks";

import { useKey } from "rooks";

import * as chroma from "chroma-js";

import { CoordinatePreviewAction, CoordinatePreviewState } from "../../modules/storage/models/coordinatePreview";

import { LabelingOverlay } from "./LabelingOverlay"

import { LabelingDebugViewport } from "./LabelingDebugViewport";

import { IColor } from "@fluentui/react";



const SphereSelectionName = 'SPHERE_SELECTION';
@@ -145,6 +144,7 @@ export function ChromatinViewport(props: { 


        for (const [configurationDatumIndex, configurationDatum] of configuration.data.entries()) {

            const primaryData = data.data.find((d: Data) => d.id == configurationDatum.id);



            if (primaryData?.type == '3d-positions') {

                const datum = primaryData as BinPositionsData;

                const positions = datum.values.positions;
@@ -152,13 +152,33 @@ export function ChromatinViewport(props: { 
                const chromatinPart = viewport.addPart(datum.name, positions, datum.values.connectivity || null, configurationDatumIndex, configurationDatum.representation, false);

                chromatinPart.structure.radius = configurationDatum.radius;

            } else if (primaryData?.type == 'bed-annotation' && configurationDatum.secondaryID) {

                const data3D = data.data.find((d: Data) => d.id == configurationDatum.secondaryID)?.values as Positions3D | undefined;

                const data3D: BinPositionsData | undefined = data.data.find((d: Data) => d.id == configurationDatum.secondaryID) as BinPositionsData | undefined;



                if (data3D) {

                    const positions = (primaryData.values as BEDAnnotations).map((annotation: BEDAnnotation) => data3D.positions[annotation.from]);

                    const positions = data3D.values.positions;

                    const resolution = data3D.basePairsResolution;

                    const annotations = (primaryData.values as BEDAnnotations);



                    const interpolatedPositions: Position3D[] = [];

                    for(const annotation of annotations) {

                        const startBin = Math.floor(annotation.from / resolution);

                        const endBin = Math.ceil(annotation.from / resolution);



                        const startPosition = positions[startBin];

                        const endPosition = positions[endBin];



                        const tBegin = (annotation.from - startBin * resolution) / resolution;



                        interpolatedPositions.push({

                            x: startPosition.x + tBegin * (endPosition.x - startPosition.x),

                            y: startPosition.y + tBegin * (endPosition.y - startPosition.y),

                            z: startPosition.z + tBegin * (endPosition.z - startPosition.z),

                        });

                    }



                    const chromatinPart = viewport.addPart(primaryData.name, positions, null, configurationDatumIndex, configurationDatum.representation, false);

                    const chromatinPart = viewport.addPart(primaryData.name, interpolatedPositions, null, configurationDatumIndex, configurationDatum.representation, false);

                    chromatinPart.structure.radius = configurationDatum.radius;

                    // chromatinPart.structure.partOfBVH = false;

                }

            }

        }
@@ -561,13 +581,32 @@ export function ChromatinViewport(props: { 


        // Let's only go through markers

        if (primaryData?.type == 'bed-annotation' && configurationDatum.secondaryID) {

            const data3D = data.data.find((d: Data) => d.id == configurationDatum.secondaryID)?.values as Positions3D | undefined;

            const data3D: BinPositionsData | undefined = data.data.find((d: Data) => d.id == configurationDatum.secondaryID) as BinPositionsData | undefined;

            const markerColor = configurationDatum.color;



            if (data3D) {

                labelsWorldSpace = (primaryData.values as BEDAnnotations).map((annotation: BEDAnnotation) => [

                    vec4.fromValues(data3D.positions[annotation.from].x, data3D.positions[annotation.from].y, data3D.positions[annotation.from].z, configurationDatum.radius),

                    // annotation.attributes[0] || 'None'

                const positions = data3D.values.positions;

                const resolution = data3D.basePairsResolution;

                const annotations = (primaryData.values as BEDAnnotations);



                const interpolatedPositions: Position3D[] = [];

                for(const annotation of annotations) {

                    const startBin = Math.floor(annotation.from / resolution);

                    const endBin = Math.ceil(annotation.from / resolution);



                    const startPosition = positions[startBin];

                    const endPosition = positions[endBin];



                    const tBegin = (annotation.from - startBin * resolution) / resolution;



                    interpolatedPositions.push({

                        x: startPosition.x + tBegin * (endPosition.x - startPosition.x),

                        y: startPosition.y + tBegin * (endPosition.y - startPosition.y),

                        z: startPosition.z + tBegin * (endPosition.z - startPosition.z),

                    });

                }

                labelsWorldSpace = annotations.map((annotation, annotationIndex) => [

                    vec4.fromValues(interpolatedPositions[annotationIndex].x, interpolatedPositions[annotationIndex].y, interpolatedPositions[annotationIndex].z, configurationDatum.radius),

                    annotation.attributes[4] || 'None',

                    markerColor

                ]);

app/src/exemplaryWorkspace.chromoskein

+1 −1

File changed.

Preview size limit exceeded, changes collapsed.

app/src/overviewWorkspace.chromoskein

deleted100644 → 0
+0 −1

File deleted.

Preview size limit exceeded, changes collapsed.

libs/graphics/package-lock.json

+3009 −1779

File changed.

Preview size limit exceeded, changes collapsed.