molstar
Version:
A comprehensive macromolecular library.
85 lines • 3.78 kB
JavaScript
/**
* Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
import { __extends } from "tslib";
import { Structure, StructureElement, StructureProperties } from '../../mol-model/structure';
import { SequenceWrapper } from './wrapper';
import { OrderedSet, Interval } from '../../mol-data/int';
import { ColorNames } from '../../mol-util/color/names';
import { applyMarkerAction } from '../../mol-util/marker-action';
var ChainSequenceWrapper = /** @class */ (function (_super) {
__extends(ChainSequenceWrapper, _super);
function ChainSequenceWrapper(data) {
var _this = this;
var residueCount = 0;
var elementCount = 0;
var counts = [];
var l = StructureElement.Location.create(data.structure);
var unitIndices = new Map();
var lociElements = [];
for (var i = 0, il = data.units.length; i < il; ++i) {
var unit = data.units[i];
StructureElement.Location.set(l, data.structure, unit, unit.elements[0]);
var entitySeq = unit.model.sequence.byEntityKey[StructureProperties.entity.key(l)];
if (entitySeq)
residueCount += entitySeq.sequence.length;
elementCount += unit.elements.length;
var indices = Interval.ofBounds(0, unit.elements.length);
unitIndices.set(unit.id, indices);
lociElements.push({ unit: unit, indices: indices });
}
if (residueCount > 0)
counts.push(residueCount + " residues");
counts.push(elementCount + " elements");
var length = 1;
var markerArray = new Uint8Array(length);
_this = _super.call(this, data, markerArray, length) || this;
_this.label = "Whole Chain (" + counts.join(', ') + ")";
_this.unitIndices = unitIndices;
_this.loci = StructureElement.Loci(_this.data.structure, lociElements);
return _this;
}
ChainSequenceWrapper.prototype.residueLabel = function (seqIdx) {
return this.label;
};
ChainSequenceWrapper.prototype.residueColor = function (seqIdx) {
return ColorNames.black;
};
ChainSequenceWrapper.prototype.residueClass = function (seqIdx) {
return 'msp-sequence-present';
};
ChainSequenceWrapper.prototype.mark = function (loci, action) {
var changed = false;
var structure = this.data.structure;
if (StructureElement.Loci.is(loci)) {
if (!Structure.areRootsEquivalent(loci.structure, structure))
return false;
loci = StructureElement.Loci.remap(loci, structure);
for (var _i = 0, _a = loci.elements; _i < _a.length; _i++) {
var e = _a[_i];
var indices = this.unitIndices.get(e.unit.id);
if (indices) {
if (OrderedSet.isSubset(indices, e.indices)) {
if (applyMarkerAction(this.markerArray, Interval.ofSingleton(0), action))
changed = true;
}
}
}
}
else if (Structure.isLoci(loci)) {
if (!Structure.areRootsEquivalent(loci.structure, structure))
return false;
if (applyMarkerAction(this.markerArray, Interval.ofSingleton(0), action))
changed = true;
}
return changed;
};
ChainSequenceWrapper.prototype.getLoci = function (seqIdx) {
return this.loci;
};
return ChainSequenceWrapper;
}(SequenceWrapper));
export { ChainSequenceWrapper };
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