diff --git a/src/mol-model/structure/structure/element.ts b/src/mol-model/structure/structure/element.ts
index 5e4809a5e9fae1ef367f66ab6a6f8e3a52fd9265..8fcb7e512d4b1cfd6cc7dee866ad8e68c2b81a53 100644
--- a/src/mol-model/structure/structure/element.ts
+++ b/src/mol-model/structure/structure/element.ts
@@ -38,6 +38,12 @@ namespace StructureElement {
return a;
}
+ export function copy(out: StructureElement, a: StructureElement): StructureElement {
+ out.unit = a.unit
+ out.element = a.element
+ return out
+ }
+
// TODO: when nominal types are available, make this indexed by UnitIndex
export type Set = SortedArray<ElementIndex>
@@ -483,6 +489,8 @@ namespace StructureElement {
}
}
+ //
+
interface QueryElement {
/**
* Array (sorted by first element in sub-array) of
@@ -675,6 +683,122 @@ namespace StructureElement {
return true
}
}
+
+ //
+
+ export interface Stats {
+ elementCount: number
+ residueCount: number
+ unitCount: number
+
+ firstElementLoc: StructureElement
+ firstResidueLoc: StructureElement
+ firstUnitLoc: StructureElement
+ }
+
+ export namespace Stats {
+ export function create(): Stats {
+ return {
+ elementCount: 0,
+ residueCount: 0,
+ unitCount: 0,
+
+ firstElementLoc: StructureElement.create(),
+ firstResidueLoc: StructureElement.create(),
+ firstUnitLoc: StructureElement.create(),
+ }
+ }
+
+ function handleElement(stats: Stats, element: StructureElement.Loci['elements'][0]) {
+ const { indices, unit } = element
+ const { elements } = unit
+ const size = OrderedSet.size(indices)
+ if (size === 1) {
+ stats.elementCount += 1
+ if (stats.elementCount === 1) {
+ StructureElement.set(stats.firstElementLoc, unit, elements[OrderedSet.start(indices)])
+ }
+ } else if (size === elements.length) {
+ stats.unitCount += 1
+ if (stats.unitCount === 1) {
+ StructureElement.set(stats.firstUnitLoc, unit, elements[OrderedSet.start(indices)])
+ }
+ } else {
+ if (Unit.isAtomic(unit)) {
+ const { index, offsets } = unit.model.atomicHierarchy.residueAtomSegments
+ let i = 0
+ while (i < size) {
+ const eI = elements[OrderedSet.getAt(indices, i)]
+ const rI = index[eI]
+ if (offsets[rI] !== eI) {
+ // partial residue, start missing
+ ++i
+ stats.elementCount += 1
+ while (i < size && index[elements[OrderedSet.getAt(indices, i)]] === rI) {
+ ++i
+ stats.elementCount += 1
+ }
+ } else {
+ ++i
+ while (i < size && index[elements[OrderedSet.getAt(indices, i)]] === rI) {
+ ++i
+ }
+
+ if (offsets[rI + 1] - 1 === elements[OrderedSet.getAt(indices, i - 1)]) {
+ // full residue
+ stats.residueCount += 1
+ if (stats.residueCount === 1) {
+ StructureElement.set(stats.firstResidueLoc, unit, elements[OrderedSet.start(indices)])
+ }
+ } else {
+ // partial residue, end missing
+ stats.elementCount += offsets[rI + 1] - 1 - elements[OrderedSet.getAt(indices, i - 1)]
+ }
+ }
+ }
+ } else {
+ // TODO
+ stats.elementCount += size
+ if (stats.elementCount === 1) {
+ StructureElement.set(stats.firstElementLoc, unit, elements[OrderedSet.start(indices)])
+ }
+ }
+ }
+ }
+
+ export function ofLoci(loci: StructureElement.Loci) {
+ const stats = create()
+ if (loci.elements.length > 0) {
+ for (const e of loci.elements) handleElement(stats, e)
+ }
+ return stats
+ }
+
+ export function add(out: Stats, a: Stats, b: Stats) {
+ if (a.elementCount === 1 && b.elementCount === 0) {
+ StructureElement.copy(out.firstElementLoc, a.firstElementLoc)
+ } else if (a.elementCount === 0 && b.elementCount === 1) {
+ StructureElement.copy(out.firstElementLoc, b.firstElementLoc)
+ }
+
+ if (a.residueCount === 1 && b.residueCount === 0) {
+ StructureElement.copy(out.firstResidueLoc, a.firstResidueLoc)
+ } else if (a.residueCount === 0 && b.residueCount === 1) {
+ StructureElement.copy(out.firstResidueLoc, b.firstResidueLoc)
+ }
+
+ if (a.unitCount === 1 && b.unitCount === 0) {
+ StructureElement.copy(out.firstUnitLoc, a.firstUnitLoc)
+ } else if (a.unitCount === 0 && b.unitCount === 1) {
+ StructureElement.copy(out.firstUnitLoc, b.firstUnitLoc)
+ }
+
+ out.elementCount = a.elementCount + b.elementCount
+ out.residueCount = a.residueCount + b.residueCount
+ out.unitCount = a.unitCount + b.unitCount
+ return out
+ }
+ }
}
export default StructureElement
\ No newline at end of file
diff --git a/src/mol-plugin/behavior/dynamic/representation.ts b/src/mol-plugin/behavior/dynamic/representation.ts
index 09fab185318486ab21feee5601ae390708520b67..d1e11929ac2284a6a5f8ee23db21157293bd5698 100644
--- a/src/mol-plugin/behavior/dynamic/representation.ts
+++ b/src/mol-plugin/behavior/dynamic/representation.ts
@@ -8,7 +8,7 @@
import { MarkerAction } from '../../../mol-util/marker-action';
import { PluginContext } from '../../../mol-plugin/context';
import { PluginStateObject as SO } from '../../state/objects';
-import { labelFirst } from '../../../mol-theme/label';
+import { lociLabel } from '../../../mol-theme/label';
import { PluginBehavior } from '../behavior';
import { Interactivity } from '../../util/interactivity';
import { StateTreeSpine } from '../../../mol-state/tree/spine';
@@ -70,7 +70,7 @@ export const DefaultLociLabelProvider = PluginBehavior.create({
name: 'default-loci-label-provider',
category: 'interaction',
ctor: class implements PluginBehavior<undefined> {
- private f = labelFirst;
+ private f = lociLabel;
register() { this.ctx.lociLabels.addProvider(this.f); }
unregister() { this.ctx.lociLabels.removeProvider(this.f); }
constructor(protected ctx: PluginContext) { }
diff --git a/src/mol-plugin/ui/structure/selection.tsx b/src/mol-plugin/ui/structure/selection.tsx
index 36ac44600da2ef4f57bb16736c9f8a587c35bfea..ae3df5a7ca139041c1fa3aa9caa42b016b72a5c0 100644
--- a/src/mol-plugin/ui/structure/selection.tsx
+++ b/src/mol-plugin/ui/structure/selection.tsx
@@ -6,8 +6,7 @@
import * as React from 'react';
import { PluginUIComponent } from '../base';
-import { formatStructureSelectionStats } from '../../util/structure-element-selection';
-import { StructureSelectionQueries } from '../../util/structure-selection-helper';
+import { StructureSelectionQueries, SelectionModifier } from '../../util/structure-selection-helper';
import { ButtonSelect, Options } from '../controls/common';
import { PluginCommands } from '../../command';
import { ParamDefinition as PD } from '../../../mol-util/param-definition';
@@ -33,7 +32,12 @@ export class StructureSelectionControls extends PluginUIComponent<{}, {}> {
}
get stats() {
- return formatStructureSelectionStats(this.plugin.helpers.structureSelectionManager.stats)
+ const stats = this.plugin.helpers.structureSelectionManager.stats
+ if (stats.structureCount === 0 || stats.elementCount === 0) {
+ return 'Selected nothing'
+ } else {
+ return `Selected ${stats.label}`
+ }
}
setProps = (p: { param: PD.Base<any>, name: string, value: any }) => {
diff --git a/src/mol-plugin/util/loci-label-manager.ts b/src/mol-plugin/util/loci-label-manager.ts
index d6d6f53993749676adafc8e1a715800eb30c6b9b..a0b9f85729ea371251d4aa1e9d1a22b0b25ab27b 100644
--- a/src/mol-plugin/util/loci-label-manager.ts
+++ b/src/mol-plugin/util/loci-label-manager.ts
@@ -1,7 +1,8 @@
/**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author David Sehnal <david.sehnal@gmail.com>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
import { PluginContext } from '../../mol-plugin/context';
@@ -35,6 +36,6 @@ export class LociLabelManager {
}
constructor(public ctx: PluginContext) {
- ctx.behaviors.interaction.highlight.subscribe(ev => ctx.behaviors.labels.highlight.next({ entries: this.getInfo(ev.current) }));
+ ctx.interactivity.lociHighlights.addProvider((loci) => ctx.behaviors.labels.highlight.next({ entries: this.getInfo(loci) }))
}
}
\ No newline at end of file
diff --git a/src/mol-plugin/util/structure-element-selection.ts b/src/mol-plugin/util/structure-element-selection.ts
index 8c60270ea2a54c8ec92819e17d670d0aede03c01..441b7c51c6fcb3b80819c4d8c818f0dda4d7b3a7 100644
--- a/src/mol-plugin/util/structure-element-selection.ts
+++ b/src/mol-plugin/util/structure-element-selection.ts
@@ -11,18 +11,7 @@ import { Structure, StructureElement } from '../../mol-model/structure';
import { StateObject } from '../../mol-state';
import { PluginContext } from '../context';
import { PluginStateObject } from '../state/objects';
-
-export type StructureSelectionStats = { structureCount: number, elementCount: number }
-
-export function formatStructureSelectionStats(stats: StructureSelectionStats) {
- if (stats.structureCount === 0 || stats.elementCount === 0) {
- return 'Selected nothing'
- } else if (stats.structureCount === 1) {
- return `Selected ${stats.elementCount} elements`
- }
- return `Selected ${stats.elementCount} elements in ${stats.structureCount} structures`
-}
-
+import { structureElementStatsLabel } from '../../mol-theme/label';
export { StructureElementSelectionManager };
class StructureElementSelectionManager {
@@ -44,6 +33,7 @@ class StructureElementSelectionManager {
get stats() {
let structureCount = 0
let elementCount = 0
+ const stats = StructureElement.Stats.create()
this.entries.forEach(v => {
const { elements } = v.selection
@@ -52,10 +42,13 @@ class StructureElementSelectionManager {
for (let i = 0, il = elements.length; i < il; ++i) {
elementCount += OrderedSet.size(elements[i].indices)
}
+ StructureElement.Stats.add(stats, stats, StructureElement.Stats.ofLoci(v.selection))
}
})
- return { structureCount, elementCount }
+ const label = structureElementStatsLabel(stats, true)
+
+ return { structureCount, elementCount, label }
}
add(loci: Loci): Loci {
diff --git a/src/mol-theme/label.ts b/src/mol-theme/label.ts
index 791bffec731ed57539863ada9df944bedca80937..3724e4106ee360c0a13956bbdb1b6a1c68d0a0e4 100644
--- a/src/mol-theme/label.ts
+++ b/src/mol-theme/label.ts
@@ -1,5 +1,5 @@
/**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
* @author David Sehnal <david.sehnal@gmail.com>
@@ -18,18 +18,12 @@ function setElementLocation(loc: StructureElement, unit: Unit, index: StructureE
loc.element = unit.elements[index]
}
-export function labelFirst(loci: Loci): string {
+export function lociLabel(loci: Loci): string {
switch (loci.kind) {
case 'structure-loci':
- return loci.structure.models.map(m => m.label).join(', ')
+ return loci.structure.models.map(m => m.entry).join(', ')
case 'element-loci':
- const e = loci.elements[0]
- if (e) {
- const el = e.unit.elements[OrderedSet.getAt(e.indices, 0)];
- return elementLabel(StructureElement.create(e.unit, el))
- } else {
- return 'Unknown'
- }
+ return structureElementStatsLabel(StructureElement.Stats.ofLoci(loci))
case 'link-loci':
const link = loci.links[0]
return link ? linkLabel(link) : 'Unknown'
@@ -37,11 +31,7 @@ export function labelFirst(loci: Loci): string {
return loci.shape.name
case 'group-loci':
const g = loci.groups[0]
- if (g) {
- return loci.shape.getLabel(OrderedSet.getAt(g.ids, 0), loci.instance)
- } else {
- return 'Unknown'
- }
+ return g ? loci.shape.getLabel(OrderedSet.start(g.ids), loci.instance) : 'Unknown'
case 'every-loci':
return 'Everything'
case 'empty-loci':
@@ -51,6 +41,39 @@ export function labelFirst(loci: Loci): string {
}
}
+function countLabel(count: number, label: string) {
+ return count === 1 ? `1 ${label}` : `${count} ${label}s`
+}
+
+/** Gets residue count of the model chain segments the unit is a subset of */
+function getResidueCount(unit: Unit.Atomic) {
+ const { elements, model } = unit
+ const { chainAtomSegments, residueAtomSegments } = model.atomicHierarchy
+ const elementStart = chainAtomSegments.offsets[chainAtomSegments.index[elements[0]]]
+ const elementEnd = chainAtomSegments.offsets[chainAtomSegments.index[elements[elements.length - 1]] + 1]
+ return residueAtomSegments.index[elementEnd] - residueAtomSegments.index[elementStart]
+}
+
+export function structureElementStatsLabel(stats: StructureElement.Stats, countsOnly = false) {
+ const { unitCount, residueCount, elementCount } = stats
+
+ if (!countsOnly && elementCount === 1 && residueCount === 0 && unitCount === 0) {
+ return elementLabel(stats.firstElementLoc, 'element')
+ } else if (!countsOnly && elementCount === 0 && residueCount === 1 && unitCount === 0) {
+ return elementLabel(stats.firstResidueLoc, 'residue')
+ } else if (!countsOnly && elementCount === 0 && residueCount === 0 && unitCount === 1) {
+ const { unit } = stats.firstUnitLoc
+ const granularity = (Unit.isAtomic(unit) && getResidueCount(unit) === 1) ? 'residue' : 'chain'
+ return elementLabel(stats.firstUnitLoc, granularity)
+ } else {
+ const label: string[] = []
+ if (unitCount > 0) label.push(countLabel(unitCount, 'Chain'))
+ if (residueCount > 0) label.push(countLabel(residueCount, 'Residue'))
+ if (elementCount > 0) label.push(countLabel(elementCount, 'Element'))
+ return label.join(', ')
+ }
+}
+
export function linkLabel(link: Link.Location) {
if (!elementLocA) elementLocA = StructureElement.create()
if (!elementLocB) elementLocB = StructureElement.create()
@@ -59,33 +82,57 @@ export function linkLabel(link: Link.Location) {
return `${elementLabel(elementLocA)} - ${elementLabel(elementLocB)}`
}
-export function elementLabel(location: StructureElement) {
+export type LabelGranularity = 'element' | 'residue' | 'chain' | 'structure'
+
+export function elementLabel(location: StructureElement, granularity: LabelGranularity = 'element') {
const model = location.unit.model.entry
const instance = location.unit.conformation.operator.name
- let label = ''
+ const label = [model, instance]
if (Unit.isAtomic(location.unit)) {
- const asym_id = Props.chain.auth_asym_id(location)
- const seq_id = location.unit.model.atomicHierarchy.residues.auth_seq_id.isDefined ? Props.residue.auth_seq_id(location) : Props.residue.label_seq_id(location)
- const comp_id = Props.residue.label_comp_id(location)
- const atom_id = Props.atom.label_atom_id(location)
- const alt_id = Props.atom.label_alt_id(location)
- label = `[${comp_id}]${seq_id}:${asym_id}.${atom_id}${alt_id ? `%${alt_id}` : ''}`
+ label.push(atomicElementLabel(location as StructureElement<Unit.Atomic>, granularity))
} else if (Unit.isCoarse(location.unit)) {
- const asym_id = Props.coarse.asym_id(location)
- const seq_id_begin = Props.coarse.seq_id_begin(location)
- const seq_id_end = Props.coarse.seq_id_end(location)
- if (seq_id_begin === seq_id_end) {
- const entityIndex = Props.coarse.entityKey(location)
- const seq = location.unit.model.sequence.byEntityKey[entityIndex]
- const comp_id = seq.compId.value(seq_id_begin - 1) // 1-indexed
- label = `[${comp_id}]${seq_id_begin}:${asym_id}`
- } else {
- label = `${seq_id_begin}-${seq_id_end}:${asym_id}`
- }
+ label.push(coarseElementLabel(location as StructureElement<Unit.Spheres | Unit.Gaussians>, granularity))
} else {
- label = 'unknown'
+ label.push('Unknown')
}
- return `${model} ${instance} ${label}`
+ return label.join(' | ')
+}
+
+export function atomicElementLabel(location: StructureElement<Unit.Atomic>, granularity: LabelGranularity) {
+ const label_asym_id = Props.chain.label_asym_id(location)
+ const auth_asym_id = Props.chain.auth_asym_id(location)
+ const seq_id = location.unit.model.atomicHierarchy.residues.auth_seq_id.isDefined ? Props.residue.auth_seq_id(location) : Props.residue.label_seq_id(location)
+ const comp_id = Props.residue.label_comp_id(location)
+ const atom_id = Props.atom.label_atom_id(location)
+ const alt_id = Props.atom.label_alt_id(location)
+
+ const label: string[] = []
+
+ switch (granularity) {
+ case 'element':
+ label.push(`${atom_id}${alt_id ? `%${alt_id}` : ''}`)
+ case 'residue':
+ label.push(`${comp_id} ${seq_id}`)
+ case 'chain':
+ label.push(`Chain ${label_asym_id}:${auth_asym_id}`)
+ }
+
+ return label.reverse().join(' | ')
+}
+
+export function coarseElementLabel(location: StructureElement<Unit.Spheres | Unit.Gaussians>, granularity: LabelGranularity) {
+ // TODO handle granularity
+ const asym_id = Props.coarse.asym_id(location)
+ const seq_id_begin = Props.coarse.seq_id_begin(location)
+ const seq_id_end = Props.coarse.seq_id_end(location)
+ if (seq_id_begin === seq_id_end) {
+ const entityIndex = Props.coarse.entityKey(location)
+ const seq = location.unit.model.sequence.byEntityKey[entityIndex]
+ const comp_id = seq.compId.value(seq_id_begin - 1) // 1-indexed
+ return `${comp_id} ${seq_id_begin}:${asym_id}`
+ } else {
+ return `${seq_id_begin}-${seq_id_end}:${asym_id}`
+ }
}
\ No newline at end of file
diff --git a/src/tests/browser/render-shape.ts b/src/tests/browser/render-shape.ts
index d06d257ce4dd1e1dd4a434015d84617df3948d20..ac2153ce5d55f3069be39ccb5cb08700833dc2d0 100644
--- a/src/tests/browser/render-shape.ts
+++ b/src/tests/browser/render-shape.ts
@@ -8,7 +8,7 @@ import './index.html'
import { resizeCanvas } from '../../mol-canvas3d/util';
import { Representation } from '../../mol-repr/representation';
import { Canvas3D } from '../../mol-canvas3d/canvas3d';
-import { labelFirst } from '../../mol-theme/label';
+import { lociLabel } from '../../mol-theme/label';
import { MarkerAction } from '../../mol-util/marker-action';
import { EveryLoci } from '../../mol-model/loci';
import { RuntimeContext, Progress } from '../../mol-task';
@@ -45,7 +45,7 @@ canvas3d.input.move.subscribe(({x, y}) => {
let label = ''
if (pickingId) {
const reprLoci = canvas3d.getLoci(pickingId)
- label = labelFirst(reprLoci.loci)
+ label = lociLabel(reprLoci.loci)
if (!Representation.Loci.areEqual(prevReprLoci, reprLoci)) {
canvas3d.mark(prevReprLoci, MarkerAction.RemoveHighlight)
canvas3d.mark(reprLoci, MarkerAction.Highlight)