/** * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info. * * @author Alexander Rose * @author David Sehnal */ import * as React from 'react'; import { PluginUIComponent } from '../base'; import { MarkerAction } from '../../mol-util/marker-action'; import { ButtonsType, ModifiersKeys, getButtons, getModifiers, getButton } from '../../mol-util/input/input-observer'; import { SequenceWrapper } from './wrapper'; import { StructureElement, StructureProperties, Unit } from '../../mol-model/structure'; import { Subject } from 'rxjs'; import { debounceTime } from 'rxjs/operators'; import { OrderedSet } from '../../mol-data/int'; import { Representation } from '../../mol-repr/representation'; type SequenceProps = { sequenceWrapper: SequenceWrapper.Any, sequenceNumberPeriod?: number, hideSequenceNumbers?: boolean, } /** Note, if this is changed, the CSS for `msp-sequence-number` needs adjustment too */ const MaxSequenceNumberSize = 5; // TODO: this is somewhat inefficient and should be done using a canvas. export class Sequence

extends PluginUIComponent

{ private parentDiv = React.createRef(); private lastMouseOverSeqIdx = -1; private highlightQueue = new Subject<{ seqIdx: number, buttons: number, button: number, modifiers: ModifiersKeys }>(); private lociHighlightProvider = (loci: Representation.Loci, action: MarkerAction) => { const changed = this.props.sequenceWrapper.markResidue(loci.loci, action); if (changed) this.updateMarker(); }; private lociSelectionProvider = (loci: Representation.Loci, action: MarkerAction) => { const changed = this.props.sequenceWrapper.markResidue(loci.loci, action); if (changed) this.updateMarker(); }; private get sequenceNumberPeriod() { if (this.props.sequenceNumberPeriod !== undefined) { return this.props.sequenceNumberPeriod as number; } if (this.props.sequenceWrapper.length > 10) return 10; const lastSeqNum = this.getSequenceNumber(this.props.sequenceWrapper.length - 1); if (lastSeqNum.length > 1) return 5; return 1; } componentDidMount() { this.plugin.managers.interactivity.lociHighlights.addProvider(this.lociHighlightProvider); this.plugin.managers.interactivity.lociSelects.addProvider(this.lociSelectionProvider); this.subscribe(debounceTime<{ seqIdx: number, buttons: number, button: number, modifiers: ModifiersKeys }>(15)(this.highlightQueue), (e) => { const loci = this.getLoci(e.seqIdx < 0 ? void 0 : e.seqIdx); this.hover(loci, e.buttons, e.button, e.modifiers); }); // this.updateMarker() } componentWillUnmount() { super.componentWillUnmount(); this.plugin.managers.interactivity.lociHighlights.removeProvider(this.lociHighlightProvider); this.plugin.managers.interactivity.lociSelects.removeProvider(this.lociSelectionProvider); } getLoci(seqIdx: number | undefined) { if (seqIdx !== undefined) { const loci = this.props.sequenceWrapper.getLoci(seqIdx); if (!StructureElement.Loci.isEmpty(loci)) return loci; } } getSeqIdx(e: React.MouseEvent) { let seqIdx: number | undefined = undefined; const el = e.target as HTMLElement; if (el && el.getAttribute) { seqIdx = el.hasAttribute('data-seqid') ? +el.getAttribute('data-seqid')! : undefined; } return seqIdx; } hover(loci: StructureElement.Loci | undefined, buttons: ButtonsType, button: ButtonsType.Flag, modifiers: ModifiersKeys) { const ev = { current: Representation.Loci.Empty, buttons, button, modifiers }; if (loci !== undefined && !StructureElement.Loci.isEmpty(loci)) { ev.current = { loci }; } this.plugin.behaviors.interaction.hover.next(ev); } click(loci: StructureElement.Loci | undefined, buttons: ButtonsType, button: ButtonsType.Flag, modifiers: ModifiersKeys) { const ev = { current: Representation.Loci.Empty, buttons, button, modifiers }; if (loci !== undefined && !StructureElement.Loci.isEmpty(loci)) { ev.current = { loci }; } this.plugin.behaviors.interaction.click.next(ev); } contextMenu = (e: React.MouseEvent) => { e.preventDefault(); }; private mouseDownLoci: StructureElement.Loci | undefined = undefined; mouseDown = (e: React.MouseEvent) => { e.stopPropagation(); const seqIdx = this.getSeqIdx(e); const loci = this.getLoci(seqIdx); const buttons = getButtons(e.nativeEvent); const button = getButton(e.nativeEvent); const modifiers = getModifiers(e.nativeEvent); this.click(loci, buttons, button, modifiers); this.mouseDownLoci = loci; }; mouseUp = (e: React.MouseEvent) => { e.stopPropagation(); // ignore mouse-up events without a bound loci if (this.mouseDownLoci === undefined) return; const seqIdx = this.getSeqIdx(e); const loci = this.getLoci(seqIdx); if (loci && !StructureElement.Loci.areEqual(this.mouseDownLoci, loci)) { const buttons = getButtons(e.nativeEvent); const button = getButton(e.nativeEvent); const modifiers = getModifiers(e.nativeEvent); const ref = this.mouseDownLoci.elements[0]; const ext = loci.elements[0]; const min = Math.min(OrderedSet.min(ref.indices), OrderedSet.min(ext.indices)); const max = Math.max(OrderedSet.max(ref.indices), OrderedSet.max(ext.indices)); const range = StructureElement.Loci(loci.structure, [{ unit: ref.unit, indices: OrderedSet.ofRange(min as StructureElement.UnitIndex, max as StructureElement.UnitIndex) }]); this.click(StructureElement.Loci.subtract(range, this.mouseDownLoci), buttons, button, modifiers); } this.mouseDownLoci = undefined; }; private getBackgroundColor(marker: number) { // TODO: make marker color configurable if (typeof marker === 'undefined') console.error('unexpected marker value'); return marker === 0 ? '' : marker % 2 === 0 ? 'rgb(51, 255, 25)' // selected : 'rgb(255, 102, 153)'; // highlighted } private getResidueClass(seqIdx: number, label: string) { return label.length > 1 ? this.props.sequenceWrapper.residueClass(seqIdx) + (seqIdx === 0 ? ' msp-sequence-residue-long-begin' : ' msp-sequence-residue-long') : this.props.sequenceWrapper.residueClass(seqIdx); } private residue(seqIdx: number, label: string, marker: number) { return {`\u200b${label}\u200b`}; } private getSequenceNumberClass(seqIdx: number, seqNum: string, label: string) { const classList = ['msp-sequence-number']; if (seqNum.startsWith('-')) { if (label.length > 1 && seqIdx > 0) classList.push('msp-sequence-number-long-negative'); else classList.push('msp-sequence-number-negative'); } else { if (label.length > 1 && seqIdx > 0) classList.push('msp-sequence-number-long'); } return classList.join(' '); } private location = StructureElement.Location.create(void 0); private getSequenceNumber(seqIdx: number) { let seqNum = ''; const loci = this.props.sequenceWrapper.getLoci(seqIdx); const l = StructureElement.Loci.getFirstLocation(loci, this.location); if (l) { if (Unit.isAtomic(l.unit)) { const seqId = StructureProperties.residue.auth_seq_id(l); const insCode = StructureProperties.residue.pdbx_PDB_ins_code(l); seqNum = `${seqId}${insCode ? insCode : ''}`; } else if (Unit.isCoarse(l.unit)) { seqNum = `${seqIdx + 1}`; } } return seqNum; } private padSeqNum(n: string) { if (n.length < MaxSequenceNumberSize) return n + new Array(MaxSequenceNumberSize - n.length + 1).join('\u00A0'); return n; } private getSequenceNumberSpan(seqIdx: number, label: string) { const seqNum = this.getSequenceNumber(seqIdx); return {this.padSeqNum(seqNum)}; } private updateMarker() { if (!this.parentDiv.current) return; const xs = this.parentDiv.current.children; const { markerArray } = this.props.sequenceWrapper; const hasNumbers = !this.props.hideSequenceNumbers, period = this.sequenceNumberPeriod; // let first: HTMLSpanElement | undefined; let o = 0; for (let i = 0, il = markerArray.length; i < il; i++) { if (hasNumbers && i % period === 0 && i < il) o++; // o + 1 to account for help icon const span = xs[o] as HTMLSpanElement; if (!span) return; o++; // if (!first && markerArray[i] > 0) { // first = span; // } const backgroundColor = this.getBackgroundColor(markerArray[i]); if (span.style.backgroundColor !== backgroundColor) span.style.backgroundColor = backgroundColor; } // if (first) { // first.scrollIntoView({ block: 'nearest' }); // } } mouseMove = (e: React.MouseEvent) => { e.stopPropagation(); const buttons = getButtons(e.nativeEvent); const button = getButton(e.nativeEvent); const modifiers = getModifiers(e.nativeEvent); const el = e.target as HTMLElement; if (!el || !el.getAttribute) { if (this.lastMouseOverSeqIdx === -1) return; this.lastMouseOverSeqIdx = -1; this.highlightQueue.next({ seqIdx: -1, buttons, button, modifiers }); return; } const seqIdx = el.hasAttribute('data-seqid') ? +el.getAttribute('data-seqid')! : -1; if (this.lastMouseOverSeqIdx === seqIdx) { return; } else { this.lastMouseOverSeqIdx = seqIdx; if (this.mouseDownLoci !== undefined) { const loci = this.getLoci(seqIdx); this.hover(loci, ButtonsType.Flag.None, ButtonsType.Flag.None, { ...modifiers, shift: true }); } else { this.highlightQueue.next({ seqIdx, buttons, button, modifiers }); } } }; mouseLeave = (e: React.MouseEvent) => { e.stopPropagation(); this.mouseDownLoci = undefined; if (this.lastMouseOverSeqIdx === -1) return; this.lastMouseOverSeqIdx = -1; const buttons = getButtons(e.nativeEvent); const button = getButton(e.nativeEvent); const modifiers = getModifiers(e.nativeEvent); this.highlightQueue.next({ seqIdx: -1, buttons, button, modifiers }); }; render() { const sw = this.props.sequenceWrapper; const elems: JSX.Element[] = []; const hasNumbers = !this.props.hideSequenceNumbers, period = this.sequenceNumberPeriod; for (let i = 0, il = sw.length; i < il; ++i) { const label = sw.residueLabel(i); // add sequence number before name so the html element do not get separated by a line-break if (hasNumbers && i % period === 0 && i < il) { elems[elems.length] = this.getSequenceNumberSpan(i, label); } elems[elems.length] = this.residue(i, label, sw.markerArray[i]); } // calling .updateMarker here is neccesary to ensure existing // residue spans are updated as react won't update them this.updateMarker(); return

{elems}
; } }