molstar 3.3.1 → 3.4.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/README.md +3 -0
- package/build/viewer/molstar.js +1 -1
- package/lib/apps/docking-viewer/viewport.js +1 -1
- package/lib/apps/viewer/app.d.ts +7 -6
- package/lib/apps/viewer/app.js +2 -0
- package/lib/cli/chem-comp-dict/create-saccharides.d.ts +7 -0
- package/lib/cli/chem-comp-dict/create-saccharides.js +67 -0
- package/lib/commonjs/apps/docking-viewer/index.js +12 -12
- package/lib/commonjs/apps/docking-viewer/viewport.js +33 -33
- package/lib/commonjs/apps/viewer/app.d.ts +7 -6
- package/lib/commonjs/apps/viewer/app.js +24 -22
- package/lib/commonjs/apps/viewer/index.js +1 -1
- package/lib/commonjs/cli/chem-comp-dict/create-ions.js +6 -6
- package/lib/commonjs/cli/chem-comp-dict/create-saccharides.d.ts +7 -0
- package/lib/commonjs/cli/chem-comp-dict/create-saccharides.js +69 -0
- package/lib/commonjs/cli/chem-comp-dict/create-table.js +8 -8
- package/lib/commonjs/cli/chem-comp-dict/util.js +17 -17
- package/lib/commonjs/cli/cif2bcif/converter.js +9 -9
- package/lib/commonjs/cli/cif2bcif/index.js +8 -8
- package/lib/commonjs/cli/cifschema/index.js +27 -27
- package/lib/commonjs/cli/cifschema/util/cif-dic.js +1 -1
- package/lib/commonjs/cli/lipid-params/index.js +9 -9
- package/lib/commonjs/cli/state-docs/index.js +2 -2
- package/lib/commonjs/cli/structure-info/helpers.js +11 -11
- package/lib/commonjs/cli/structure-info/model.js +15 -15
- package/lib/commonjs/cli/structure-info/volume.js +9 -9
- package/lib/commonjs/examples/alpha-orbitals/controls.js +3 -3
- package/lib/commonjs/examples/alpha-orbitals/index.js +11 -11
- package/lib/commonjs/examples/basic-wrapper/controls.js +2 -2
- package/lib/commonjs/examples/basic-wrapper/index.js +22 -22
- package/lib/commonjs/examples/basic-wrapper/superposition.js +8 -8
- package/lib/commonjs/examples/domain-annotation-server/mapping.js +3 -3
- package/lib/commonjs/examples/domain-annotation-server/server.js +6 -6
- package/lib/commonjs/examples/domain-annotation-server/test.js +3 -3
- package/lib/commonjs/examples/lighting/index.js +6 -6
- package/lib/commonjs/examples/proteopedia-wrapper/annotation.js +2 -2
- package/lib/commonjs/examples/proteopedia-wrapper/helpers.js +4 -4
- package/lib/commonjs/examples/proteopedia-wrapper/index.js +26 -26
- package/lib/commonjs/examples/proteopedia-wrapper/ui/controls.js +2 -2
- package/lib/commonjs/examples/task.js +15 -15
- package/lib/commonjs/extensions/alpha-orbitals/collocation.js +2 -2
- package/lib/commonjs/extensions/alpha-orbitals/data-model.js +1 -1
- package/lib/commonjs/extensions/alpha-orbitals/density.js +2 -2
- package/lib/commonjs/extensions/alpha-orbitals/gpu/compute.js +2 -2
- package/lib/commonjs/extensions/alpha-orbitals/orbitals.js +2 -2
- package/lib/commonjs/extensions/alpha-orbitals/transforms.js +13 -13
- package/lib/commonjs/extensions/anvil/algorithm.js +13 -13
- package/lib/commonjs/extensions/anvil/behavior.js +14 -14
- package/lib/commonjs/extensions/anvil/prop.js +7 -7
- package/lib/commonjs/extensions/anvil/representation.js +5 -5
- package/lib/commonjs/extensions/cellpack/index.js +1 -1
- package/lib/commonjs/extensions/cellpack/model.js +26 -24
- package/lib/commonjs/extensions/cellpack/preset.js +6 -6
- package/lib/commonjs/extensions/cellpack/property.js +3 -3
- package/lib/commonjs/extensions/cellpack/representation.js +2 -2
- package/lib/commonjs/extensions/cellpack/state.js +13 -13
- package/lib/commonjs/extensions/cellpack/util.js +14 -14
- package/lib/commonjs/extensions/dnatco/confal-pyramids/behavior.js +7 -7
- package/lib/commonjs/extensions/dnatco/confal-pyramids/property.js +5 -5
- package/lib/commonjs/extensions/dnatco/confal-pyramids/representation.js +2 -2
- package/lib/commonjs/extensions/dnatco/confal-pyramids/util.js +1 -1
- package/lib/commonjs/extensions/g3d/data.js +6 -6
- package/lib/commonjs/extensions/g3d/format.js +14 -14
- package/lib/commonjs/extensions/g3d/model.js +4 -4
- package/lib/commonjs/extensions/geo-export/controls.js +3 -3
- package/lib/commonjs/extensions/geo-export/glb-exporter.js +9 -9
- package/lib/commonjs/extensions/geo-export/index.js +1 -1
- package/lib/commonjs/extensions/geo-export/mesh-exporter.js +12 -12
- package/lib/commonjs/extensions/geo-export/obj-exporter.js +7 -7
- package/lib/commonjs/extensions/geo-export/stl-exporter.js +7 -7
- package/lib/commonjs/extensions/geo-export/ui.js +7 -7
- package/lib/commonjs/extensions/geo-export/usdz-exporter.js +9 -9
- package/lib/commonjs/extensions/model-archive/quality-assessment/behavior.js +9 -9
- package/lib/commonjs/extensions/model-archive/quality-assessment/color/plddt.js +4 -4
- package/lib/commonjs/extensions/model-archive/quality-assessment/color/qmean.js +4 -4
- package/lib/commonjs/extensions/model-archive/quality-assessment/prop.js +5 -5
- package/lib/commonjs/extensions/model-export/export.js +4 -4
- package/lib/commonjs/extensions/model-export/index.js +1 -1
- package/lib/commonjs/extensions/model-export/ui.js +5 -5
- package/lib/commonjs/extensions/mp4-export/controls.js +5 -5
- package/lib/commonjs/extensions/mp4-export/encoder.js +4 -4
- package/lib/commonjs/extensions/mp4-export/index.js +1 -1
- package/lib/commonjs/extensions/mp4-export/ui.js +5 -5
- package/lib/commonjs/extensions/pdbe/preferred-assembly.js +2 -2
- package/lib/commonjs/extensions/pdbe/struct-ref-domain.js +2 -2
- package/lib/commonjs/extensions/pdbe/structure-quality-report/behavior.js +1 -1
- package/lib/commonjs/extensions/pdbe/structure-quality-report/prop.js +8 -8
- package/lib/commonjs/extensions/rcsb/assembly-symmetry/behavior.js +17 -17
- package/lib/commonjs/extensions/rcsb/assembly-symmetry/color.js +2 -2
- package/lib/commonjs/extensions/rcsb/assembly-symmetry/prop.js +9 -9
- package/lib/commonjs/extensions/rcsb/assembly-symmetry/representation.js +6 -6
- package/lib/commonjs/extensions/rcsb/assembly-symmetry/ui.js +9 -9
- package/lib/commonjs/extensions/rcsb/validation-report/behavior.js +17 -17
- package/lib/commonjs/extensions/rcsb/validation-report/prop.js +15 -15
- package/lib/commonjs/extensions/rcsb/validation-report/representation.js +3 -3
- package/lib/commonjs/extensions/zenodo/index.d.ts +7 -0
- package/lib/commonjs/extensions/zenodo/index.js +35 -0
- package/lib/commonjs/extensions/zenodo/ui.d.ts +61 -0
- package/lib/commonjs/extensions/zenodo/ui.js +306 -0
- package/lib/commonjs/mol-canvas3d/camera/stereo.js +1 -1
- package/lib/commonjs/mol-canvas3d/camera/util.js +1 -1
- package/lib/commonjs/mol-canvas3d/camera.js +2 -1
- package/lib/commonjs/mol-canvas3d/canvas3d.js +14 -14
- package/lib/commonjs/mol-canvas3d/controls/trackball.js +1 -1
- package/lib/commonjs/mol-canvas3d/helper/bounding-sphere-helper.js +1 -1
- package/lib/commonjs/mol-canvas3d/helper/camera-helper.js +5 -5
- package/lib/commonjs/mol-canvas3d/helper/handle-helper.js +5 -5
- package/lib/commonjs/mol-canvas3d/helper/helper.js +1 -1
- package/lib/commonjs/mol-canvas3d/helper/interaction-events.js +2 -2
- package/lib/commonjs/mol-canvas3d/passes/draw.js +3 -3
- package/lib/commonjs/mol-canvas3d/passes/fxaa.js +3 -3
- package/lib/commonjs/mol-canvas3d/passes/image.js +1 -1
- package/lib/commonjs/mol-canvas3d/passes/marking.js +6 -6
- package/lib/commonjs/mol-canvas3d/passes/multi-sample.js +3 -3
- package/lib/commonjs/mol-canvas3d/passes/postprocessing.js +12 -12
- package/lib/commonjs/mol-canvas3d/passes/smaa.js +9 -9
- package/lib/commonjs/mol-canvas3d/passes/wboit.js +3 -3
- package/lib/commonjs/mol-canvas3d/util.js +2 -2
- package/lib/commonjs/mol-data/db/column.js +2 -2
- package/lib/commonjs/mol-data/db/table.js +1 -1
- package/lib/commonjs/mol-data/db.js +1 -1
- package/lib/commonjs/mol-data/generic.js +3 -3
- package/lib/commonjs/mol-data/index.js +4 -4
- package/lib/commonjs/mol-data/int/interval.js +1 -1
- package/lib/commonjs/mol-data/int/ordered-set.js +1 -1
- package/lib/commonjs/mol-data/int/segmentation.js +1 -1
- package/lib/commonjs/mol-data/int/sorted-array.js +1 -1
- package/lib/commonjs/mol-data/util.js +7 -7
- package/lib/commonjs/mol-geo/geometry/cylinders/cylinders.js +3 -3
- package/lib/commonjs/mol-geo/geometry/direct-volume/direct-volume.js +3 -3
- package/lib/commonjs/mol-geo/geometry/direct-volume/transfer-function.js +1 -1
- package/lib/commonjs/mol-geo/geometry/image/image.js +3 -3
- package/lib/commonjs/mol-geo/geometry/lines/lines.js +3 -3
- package/lib/commonjs/mol-geo/geometry/mesh/mesh.js +3 -3
- package/lib/commonjs/mol-geo/geometry/points/points.js +3 -3
- package/lib/commonjs/mol-geo/geometry/size-data.js +1 -1
- package/lib/commonjs/mol-geo/geometry/spheres/spheres.js +3 -3
- package/lib/commonjs/mol-geo/geometry/text/font-atlas.js +1 -1
- package/lib/commonjs/mol-geo/geometry/text/text-builder.js +3 -2
- package/lib/commonjs/mol-geo/geometry/text/text.js +3 -3
- package/lib/commonjs/mol-geo/geometry/texture-mesh/color-smoothing.js +4 -4
- package/lib/commonjs/mol-geo/geometry/texture-mesh/texture-mesh.js +3 -3
- package/lib/commonjs/mol-geo/primitive/circle.js +1 -1
- package/lib/commonjs/mol-geo/primitive/cylinder.js +1 -1
- package/lib/commonjs/mol-geo/primitive/polyhedron.js +1 -1
- package/lib/commonjs/mol-geo/primitive/prism.js +1 -1
- package/lib/commonjs/mol-geo/primitive/star.js +1 -1
- package/lib/commonjs/mol-geo/primitive/torus.js +1 -1
- package/lib/commonjs/mol-geo/util/marching-cubes/algorithm.js +9 -9
- package/lib/commonjs/mol-gl/compute/grid3d.js +5 -5
- package/lib/commonjs/mol-gl/compute/histogram-pyramid/reduction.js +3 -3
- package/lib/commonjs/mol-gl/compute/histogram-pyramid/sum.js +3 -3
- package/lib/commonjs/mol-gl/compute/marching-cubes/active-voxels.js +3 -3
- package/lib/commonjs/mol-gl/compute/marching-cubes/isosurface.js +3 -3
- package/lib/commonjs/mol-gl/compute/util.js +3 -3
- package/lib/commonjs/mol-gl/renderable/cylinders.js +3 -3
- package/lib/commonjs/mol-gl/renderable/direct-volume.js +3 -3
- package/lib/commonjs/mol-gl/renderable/image.js +3 -3
- package/lib/commonjs/mol-gl/renderable/lines.js +3 -3
- package/lib/commonjs/mol-gl/renderable/mesh.js +3 -3
- package/lib/commonjs/mol-gl/renderable/points.js +3 -3
- package/lib/commonjs/mol-gl/renderable/schema.js +1 -1
- package/lib/commonjs/mol-gl/renderable/spheres.js +3 -3
- package/lib/commonjs/mol-gl/renderable/text.js +3 -3
- package/lib/commonjs/mol-gl/renderable/texture-mesh.js +3 -3
- package/lib/commonjs/mol-gl/renderable/util.js +1 -1
- package/lib/commonjs/mol-gl/shader-code.js +2 -1
- package/lib/commonjs/mol-gl/webgl/buffer.js +4 -5
- package/lib/commonjs/mol-gl/webgl/context.js +3 -3
- package/lib/commonjs/mol-gl/webgl/render-item.js +1 -1
- package/lib/commonjs/mol-gl/webgl/resources.js +2 -2
- package/lib/commonjs/mol-io/common/binary-cif/classifier.js +7 -6
- package/lib/commonjs/mol-io/common/binary-cif/decoder.js +4 -3
- package/lib/commonjs/mol-io/common/binary-cif.js +3 -3
- package/lib/commonjs/mol-io/common/io-buffer.d.ts +206 -0
- package/lib/commonjs/mol-io/common/io-buffer.js +408 -0
- package/lib/commonjs/mol-io/common/netcdf/reader.d.ts +78 -0
- package/lib/commonjs/mol-io/common/netcdf/reader.js +459 -0
- package/lib/commonjs/mol-io/common/typed-array.js +2 -2
- package/lib/commonjs/mol-io/reader/ccp4/parser.js +8 -8
- package/lib/commonjs/mol-io/reader/cif/binary/parser.js +3 -3
- package/lib/commonjs/mol-io/reader/cif/data-model.js +1 -1
- package/lib/commonjs/mol-io/reader/cif/schema/mmcif-extras.js +2 -2
- package/lib/commonjs/mol-io/reader/cif/schema/mmcif.d.ts +1 -1
- package/lib/commonjs/mol-io/reader/cif/schema.js +2 -2
- package/lib/commonjs/mol-io/reader/cif/text/parser.js +7 -7
- package/lib/commonjs/mol-io/reader/cif.js +1 -1
- package/lib/commonjs/mol-io/reader/common/text/tokenizer.js +4 -4
- package/lib/commonjs/mol-io/reader/csv/data-model.js +1 -1
- package/lib/commonjs/mol-io/reader/csv/parser.js +7 -7
- package/lib/commonjs/mol-io/reader/cube/parser.js +2 -2
- package/lib/commonjs/mol-io/reader/dcd/parser.js +2 -2
- package/lib/commonjs/mol-io/reader/dsn6/parser.js +8 -8
- package/lib/commonjs/mol-io/reader/dx/parser.js +4 -4
- package/lib/commonjs/mol-io/reader/gro/parser.js +6 -6
- package/lib/commonjs/mol-io/reader/mol/parser.js +2 -2
- package/lib/commonjs/mol-io/reader/mol2/parser.js +8 -8
- package/lib/commonjs/mol-io/reader/nctraj/parser.d.ts +18 -0
- package/lib/commonjs/mol-io/reader/nctraj/parser.js +101 -0
- package/lib/commonjs/mol-io/reader/obj/parser.js +4 -4
- package/lib/commonjs/mol-io/reader/pdb/parser.js +2 -2
- package/lib/commonjs/mol-io/reader/ply/parser.js +4 -4
- package/lib/commonjs/mol-io/reader/prmtop/parser.d.ts +58 -0
- package/lib/commonjs/mol-io/reader/prmtop/parser.js +172 -0
- package/lib/commonjs/mol-io/reader/psf/parser.js +8 -8
- package/lib/commonjs/mol-io/reader/sdf/parser.js +2 -2
- package/lib/commonjs/mol-io/reader/top/parser.d.ts +37 -0
- package/lib/commonjs/mol-io/reader/top/parser.js +303 -0
- package/lib/commonjs/mol-io/reader/trr/parser.d.ts +22 -0
- package/lib/commonjs/mol-io/reader/trr/parser.js +146 -0
- package/lib/commonjs/mol-io/reader/xtc/parser.js +4 -4
- package/lib/commonjs/mol-io/reader/xyz/parser.js +2 -2
- package/lib/commonjs/mol-io/writer/cif/encoder.js +3 -2
- package/lib/commonjs/mol-io/writer/cif.js +1 -1
- package/lib/commonjs/mol-io/writer/ligand-encoder.js +1 -1
- package/lib/commonjs/mol-io/writer/mol/encoder.js +1 -1
- package/lib/commonjs/mol-io/writer/mol2/encoder.js +1 -1
- package/lib/commonjs/mol-math/geometry/boundary-helper.js +5 -5
- package/lib/commonjs/mol-math/geometry/gaussian-density/cpu.js +4 -4
- package/lib/commonjs/mol-math/geometry/gaussian-density/gpu.js +1 -1
- package/lib/commonjs/mol-math/geometry/gaussian-density.js +4 -4
- package/lib/commonjs/mol-math/geometry/molecular-surface.js +8 -8
- package/lib/commonjs/mol-math/geometry/primitives/sphere3d.js +1 -1
- package/lib/commonjs/mol-math/geometry.js +8 -8
- package/lib/commonjs/mol-math/graph/inter-unit-graph.js +1 -1
- package/lib/commonjs/mol-math/graph.js +1 -1
- package/lib/commonjs/mol-math/linear-algebra.js +2 -2
- package/lib/commonjs/mol-model/sequence/alignment/alignment.js +1 -1
- package/lib/commonjs/mol-model/sequence/sequence.js +2 -1
- package/lib/commonjs/mol-model/sequence.js +1 -1
- package/lib/commonjs/mol-model/shape.js +1 -1
- package/lib/commonjs/mol-model/structure/coordinates.js +1 -1
- package/lib/commonjs/mol-model/structure/export/categories/secondary-structure.js +2 -2
- package/lib/commonjs/mol-model/structure/model/model.js +3 -3
- package/lib/commonjs/mol-model/structure/model/properties/atomic.js +3 -3
- package/lib/commonjs/mol-model/structure/model/properties/coarse.js +2 -2
- package/lib/commonjs/mol-model/structure/model/types/saccharides.d.ts +8 -0
- package/lib/commonjs/mol-model/structure/model/types/saccharides.js +11 -0
- package/lib/commonjs/mol-model/structure/model.js +3 -3
- package/lib/commonjs/mol-model/structure/query/queries/generators.js +2 -2
- package/lib/commonjs/mol-model/structure/query/queries/modifiers.js +2 -2
- package/lib/commonjs/mol-model/structure/query.js +6 -6
- package/lib/commonjs/mol-model/structure/structure/carbohydrates/compute.js +1 -1
- package/lib/commonjs/mol-model/structure/structure/carbohydrates/constants.d.ts +1 -1
- package/lib/commonjs/mol-model/structure/structure/carbohydrates/constants.js +6 -9
- package/lib/commonjs/mol-model/structure/structure/element/element.js +5 -5
- package/lib/commonjs/mol-model/structure/structure/element.js +1 -1
- package/lib/commonjs/mol-model/structure/structure/structure.js +5 -5
- package/lib/commonjs/mol-model/structure/structure/symmetry.js +10 -10
- package/lib/commonjs/mol-model/structure/structure/unit/bonds/data.js +2 -2
- package/lib/commonjs/mol-model/structure/structure/unit/bonds/inter-compute.js +3 -3
- package/lib/commonjs/mol-model/structure/structure/unit/bonds/intra-compute.js +1 -1
- package/lib/commonjs/mol-model/structure/structure/unit/bonds.js +3 -3
- package/lib/commonjs/mol-model/structure/structure/unit.js +4 -4
- package/lib/commonjs/mol-model/structure/structure/util/superposition.js +1 -1
- package/lib/commonjs/mol-model/structure/structure.js +2 -2
- package/lib/commonjs/mol-model/structure/topology.js +1 -1
- package/lib/commonjs/mol-model/structure.js +6 -6
- package/lib/commonjs/mol-model/volume.js +2 -2
- package/lib/commonjs/mol-model-formats/shape/ply.js +7 -7
- package/lib/commonjs/mol-model-formats/structure/basic/atomic.d.ts +1 -1
- package/lib/commonjs/mol-model-formats/structure/basic/atomic.js +2 -15
- package/lib/commonjs/mol-model-formats/structure/basic/coarse.js +3 -3
- package/lib/commonjs/mol-model-formats/structure/basic/entities.js +1 -1
- package/lib/commonjs/mol-model-formats/structure/basic/parser.d.ts +1 -1
- package/lib/commonjs/mol-model-formats/structure/basic/parser.js +10 -10
- package/lib/commonjs/mol-model-formats/structure/basic/schema.d.ts +2 -2
- package/lib/commonjs/mol-model-formats/structure/basic/schema.js +7 -2
- package/lib/commonjs/mol-model-formats/structure/basic/sort.js +2 -2
- package/lib/commonjs/mol-model-formats/structure/basic/util.d.ts +33 -2
- package/lib/commonjs/mol-model-formats/structure/basic/util.js +26 -2
- package/lib/commonjs/mol-model-formats/structure/cif-core.js +6 -6
- package/lib/commonjs/mol-model-formats/structure/common/component.js +5 -1
- package/lib/commonjs/mol-model-formats/structure/cube.js +5 -5
- package/lib/commonjs/mol-model-formats/structure/dcd.js +2 -2
- package/lib/commonjs/mol-model-formats/structure/gro.js +5 -3
- package/lib/commonjs/mol-model-formats/structure/mmcif.d.ts +1 -1
- package/lib/commonjs/mol-model-formats/structure/mmcif.js +4 -2
- package/lib/commonjs/mol-model-formats/structure/mol.js +5 -5
- package/lib/commonjs/mol-model-formats/structure/mol2.js +6 -6
- package/lib/commonjs/mol-model-formats/structure/nctraj.d.ts +9 -0
- package/lib/commonjs/mol-model-formats/structure/nctraj.js +60 -0
- package/lib/commonjs/mol-model-formats/structure/pdb/to-cif.js +2 -2
- package/lib/commonjs/mol-model-formats/structure/pdb.d.ts +1 -1
- package/lib/commonjs/mol-model-formats/structure/pdb.js +7 -5
- package/lib/commonjs/mol-model-formats/structure/prmtop.d.ts +16 -0
- package/lib/commonjs/mol-model-formats/structure/prmtop.js +147 -0
- package/lib/commonjs/mol-model-formats/structure/property/bonds/index-pair.js +1 -1
- package/lib/commonjs/mol-model-formats/structure/property/symmetry.js +11 -1
- package/lib/commonjs/mol-model-formats/structure/psf.js +5 -3
- package/lib/commonjs/mol-model-formats/structure/top.d.ts +16 -0
- package/lib/commonjs/mol-model-formats/structure/top.js +189 -0
- package/lib/commonjs/mol-model-formats/structure/trr.d.ts +9 -0
- package/lib/commonjs/mol-model-formats/structure/trr.js +46 -0
- package/lib/commonjs/mol-model-formats/structure/util.d.ts +2 -2
- package/lib/commonjs/mol-model-formats/structure/util.js +19 -20
- package/lib/commonjs/mol-model-formats/structure/xtc.js +2 -2
- package/lib/commonjs/mol-model-formats/structure/xyz.js +2 -2
- package/lib/commonjs/mol-model-formats/volume/ccp4.js +2 -2
- package/lib/commonjs/mol-model-formats/volume/cube.js +2 -2
- package/lib/commonjs/mol-model-formats/volume/density-server.js +2 -2
- package/lib/commonjs/mol-model-formats/volume/dsn6.js +2 -2
- package/lib/commonjs/mol-model-formats/volume/dx.js +2 -2
- package/lib/commonjs/mol-model-props/common/custom-element-property.js +2 -2
- package/lib/commonjs/mol-model-props/common/custom-model-property.js +5 -5
- package/lib/commonjs/mol-model-props/common/custom-property.js +1 -1
- package/lib/commonjs/mol-model-props/common/custom-structure-property.js +6 -6
- package/lib/commonjs/mol-model-props/computed/accessible-surface-area/shrake-rupley/area.js +2 -2
- package/lib/commonjs/mol-model-props/computed/accessible-surface-area/shrake-rupley.js +5 -5
- package/lib/commonjs/mol-model-props/computed/accessible-surface-area.js +4 -4
- package/lib/commonjs/mol-model-props/computed/chemistry/valence-model.js +3 -3
- package/lib/commonjs/mol-model-props/computed/helix-orientation.js +2 -2
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- package/lib/commonjs/servers/volume/pack.js +1 -1
- package/lib/commonjs/servers/volume/query.js +4 -4
- package/lib/commonjs/servers/volume/server/algebra/box.js +1 -1
- package/lib/commonjs/servers/volume/server/api.js +8 -8
- package/lib/commonjs/servers/volume/server/local-api.js +8 -8
- package/lib/commonjs/servers/volume/server/query/compose.js +8 -8
- package/lib/commonjs/servers/volume/server/query/execute.js +10 -10
- package/lib/commonjs/servers/volume/server/query/identify.js +2 -2
- package/lib/commonjs/servers/volume/server/web-api.js +7 -7
- package/lib/commonjs/servers/volume/server.js +2 -2
- package/lib/examples/alpha-orbitals/controls.js +2 -2
- package/lib/examples/basic-wrapper/controls.js +1 -1
- package/lib/examples/proteopedia-wrapper/ui/controls.js +1 -1
- package/lib/extensions/cellpack/model.js +4 -2
- package/lib/extensions/cellpack/state.js +2 -2
- package/lib/extensions/geo-export/ui.js +2 -2
- package/lib/extensions/model-export/ui.js +2 -2
- package/lib/extensions/mp4-export/ui.js +2 -2
- package/lib/extensions/rcsb/assembly-symmetry/ui.js +3 -3
- package/lib/extensions/zenodo/index.d.ts +7 -0
- package/lib/extensions/zenodo/index.js +32 -0
- package/lib/extensions/zenodo/ui.d.ts +61 -0
- package/lib/extensions/zenodo/ui.js +303 -0
- package/lib/mol-canvas3d/camera.js +2 -1
- package/lib/mol-canvas3d/helper/camera-helper.js +1 -1
- package/lib/mol-canvas3d/helper/handle-helper.js +1 -1
- package/lib/mol-canvas3d/helper/interaction-events.js +1 -1
- package/lib/mol-geo/geometry/text/text-builder.js +2 -1
- package/lib/mol-gl/shader-code.js +2 -1
- package/lib/mol-gl/webgl/buffer.js +2 -3
- package/lib/mol-io/common/binary-cif/classifier.js +3 -2
- package/lib/mol-io/common/binary-cif/decoder.js +4 -3
- package/lib/mol-io/common/io-buffer.d.ts +206 -0
- package/lib/mol-io/common/io-buffer.js +405 -0
- package/lib/mol-io/common/netcdf/reader.d.ts +78 -0
- package/lib/mol-io/common/netcdf/reader.js +456 -0
- package/lib/mol-io/reader/cif/schema/mmcif.d.ts +1 -1
- package/lib/mol-io/reader/nctraj/parser.d.ts +18 -0
- package/lib/mol-io/reader/nctraj/parser.js +97 -0
- package/lib/mol-io/reader/prmtop/parser.d.ts +58 -0
- package/lib/mol-io/reader/prmtop/parser.js +168 -0
- package/lib/mol-io/reader/top/parser.d.ts +37 -0
- package/lib/mol-io/reader/top/parser.js +299 -0
- package/lib/mol-io/reader/trr/parser.d.ts +22 -0
- package/lib/mol-io/reader/trr/parser.js +142 -0
- package/lib/mol-io/writer/cif/encoder.js +2 -1
- package/lib/mol-model/sequence/sequence.js +2 -1
- package/lib/mol-model/structure/model/types/saccharides.d.ts +8 -0
- package/lib/mol-model/structure/model/types/saccharides.js +8 -0
- package/lib/mol-model/structure/structure/carbohydrates/constants.d.ts +1 -1
- package/lib/mol-model/structure/structure/carbohydrates/constants.js +6 -9
- package/lib/mol-model-formats/structure/basic/atomic.d.ts +1 -1
- package/lib/mol-model-formats/structure/basic/atomic.js +1 -14
- package/lib/mol-model-formats/structure/basic/parser.d.ts +1 -1
- package/lib/mol-model-formats/structure/basic/parser.js +1 -1
- package/lib/mol-model-formats/structure/basic/schema.d.ts +2 -2
- package/lib/mol-model-formats/structure/basic/schema.js +7 -2
- package/lib/mol-model-formats/structure/basic/util.d.ts +33 -2
- package/lib/mol-model-formats/structure/basic/util.js +24 -1
- package/lib/mol-model-formats/structure/cif-core.js +4 -4
- package/lib/mol-model-formats/structure/common/component.js +5 -1
- package/lib/mol-model-formats/structure/cube.js +3 -3
- package/lib/mol-model-formats/structure/gro.js +3 -1
- package/lib/mol-model-formats/structure/mmcif.d.ts +1 -1
- package/lib/mol-model-formats/structure/mmcif.js +4 -2
- package/lib/mol-model-formats/structure/mol.js +3 -3
- package/lib/mol-model-formats/structure/mol2.js +4 -4
- package/lib/mol-model-formats/structure/nctraj.d.ts +9 -0
- package/lib/mol-model-formats/structure/nctraj.js +56 -0
- package/lib/mol-model-formats/structure/pdb.d.ts +1 -1
- package/lib/mol-model-formats/structure/pdb.js +5 -3
- package/lib/mol-model-formats/structure/prmtop.d.ts +16 -0
- package/lib/mol-model-formats/structure/prmtop.js +144 -0
- package/lib/mol-model-formats/structure/property/symmetry.js +11 -1
- package/lib/mol-model-formats/structure/psf.js +3 -1
- package/lib/mol-model-formats/structure/top.d.ts +16 -0
- package/lib/mol-model-formats/structure/top.js +186 -0
- package/lib/mol-model-formats/structure/trr.d.ts +9 -0
- package/lib/mol-model-formats/structure/trr.js +42 -0
- package/lib/mol-model-formats/structure/util.d.ts +2 -2
- package/lib/mol-model-formats/structure/util.js +19 -20
- package/lib/mol-model-formats/structure/xyz.js +2 -2
- package/lib/mol-plugin/context.d.ts +2 -1
- package/lib/mol-plugin/context.js +4 -3
- package/lib/mol-plugin/spec.js +1 -1
- package/lib/mol-plugin/version.js +2 -2
- package/lib/mol-plugin-state/actions/file.d.ts +1 -1
- package/lib/mol-plugin-state/actions/file.js +88 -55
- package/lib/mol-plugin-state/actions/structure.d.ts +11 -2
- package/lib/mol-plugin-state/actions/structure.js +174 -4
- package/lib/mol-plugin-state/actions/volume.js +3 -2
- package/lib/mol-plugin-state/formats/{structure.d.ts → coordinates.d.ts} +34 -18
- package/lib/mol-plugin-state/formats/coordinates.js +67 -0
- package/lib/mol-plugin-state/formats/registry.d.ts +3 -3
- package/lib/mol-plugin-state/formats/registry.js +13 -8
- package/lib/mol-plugin-state/formats/topology.d.ts +73 -0
- package/lib/mol-plugin-state/formats/topology.js +84 -0
- package/lib/mol-plugin-state/helpers/structure-component.js +2 -1
- package/lib/mol-plugin-state/manager/snapshots.js +4 -4
- package/lib/mol-plugin-state/objects.d.ts +47 -1
- package/lib/mol-plugin-state/objects.js +17 -1
- package/lib/mol-plugin-state/transforms/data.d.ts +6 -0
- package/lib/mol-plugin-state/transforms/data.js +61 -9
- package/lib/mol-plugin-state/transforms/model.d.ts +14 -2
- package/lib/mol-plugin-state/transforms/model.js +112 -3
- package/lib/mol-plugin-ui/base.js +1 -1
- package/lib/mol-plugin-ui/controls/action-menu.js +7 -7
- package/lib/mol-plugin-ui/controls/color.js +3 -3
- package/lib/mol-plugin-ui/controls/common.js +10 -10
- package/lib/mol-plugin-ui/controls/icons.js +70 -70
- package/lib/mol-plugin-ui/controls/legend.js +3 -3
- package/lib/mol-plugin-ui/controls/line-graph/line-graph-component.js +1 -1
- package/lib/mol-plugin-ui/controls/parameters.js +51 -51
- package/lib/mol-plugin-ui/controls/screenshot.js +2 -2
- package/lib/mol-plugin-ui/controls/slider.js +5 -5
- package/lib/mol-plugin-ui/controls.js +7 -7
- package/lib/mol-plugin-ui/custom/volume.js +4 -4
- package/lib/mol-plugin-ui/left-panel.d.ts +8 -1
- package/lib/mol-plugin-ui/left-panel.js +33 -12
- package/lib/mol-plugin-ui/plugin.js +10 -10
- package/lib/mol-plugin-ui/sequence/sequence.js +1 -1
- package/lib/mol-plugin-ui/sequence.js +5 -5
- package/lib/mol-plugin-ui/state/actions.js +1 -1
- package/lib/mol-plugin-ui/state/animation.js +1 -1
- package/lib/mol-plugin-ui/state/common.js +7 -7
- package/lib/mol-plugin-ui/state/snapshots.js +9 -9
- package/lib/mol-plugin-ui/state/tree.js +14 -14
- package/lib/mol-plugin-ui/state/update-transform.js +1 -1
- package/lib/mol-plugin-ui/structure/components.js +10 -10
- package/lib/mol-plugin-ui/structure/focus.js +1 -1
- package/lib/mol-plugin-ui/structure/generic.js +4 -4
- package/lib/mol-plugin-ui/structure/measurements.js +8 -8
- package/lib/mol-plugin-ui/structure/quick-styles.js +2 -2
- package/lib/mol-plugin-ui/structure/selection.js +7 -7
- package/lib/mol-plugin-ui/structure/source.js +4 -4
- package/lib/mol-plugin-ui/structure/superposition.js +8 -8
- package/lib/mol-plugin-ui/structure/volume.js +4 -4
- package/lib/mol-plugin-ui/task.js +5 -5
- package/lib/mol-plugin-ui/toast.js +4 -4
- package/lib/mol-plugin-ui/viewport/canvas.js +3 -3
- package/lib/mol-plugin-ui/viewport/help.js +8 -8
- package/lib/mol-plugin-ui/viewport/screenshot.js +3 -3
- package/lib/mol-plugin-ui/viewport/simple-settings.js +1 -1
- package/lib/mol-plugin-ui/viewport.js +4 -4
- package/lib/mol-script/language/parser.js +7 -4
- package/lib/mol-task/util/scheduler.d.ts +2 -2
- package/lib/mol-task/util/scheduler.js +7 -7
- package/lib/mol-theme/color/hydrophobicity.js +2 -2
- package/lib/mol-util/data-source.js +2 -1
- package/lib/mol-util/file-info.d.ts +1 -3
- package/lib/mol-util/file-info.js +2 -10
- package/lib/mol-util/index.d.ts +1 -0
- package/lib/mol-util/index.js +5 -0
- package/lib/mol-util/zip/deflate.js +2 -1
- package/lib/mol-util/zip/zip.d.ts +7 -1
- package/lib/mol-util/zip/zip.js +5 -1
- package/lib/servers/model/config.d.ts +2 -2
- package/package.json +16 -16
- package/lib/commonjs/mol-plugin-state/formats/structure.js +0 -64
- package/lib/mol-plugin-state/formats/structure.js +0 -61
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return _jsxs(_Fragment, { children: [_jsxs("div", __assign({ className: 'msp-flex-row' }, { children: [_jsx(ToggleButton, { icon: BookmarksOutlinedSvg, label: 'Preset', title: 'Apply a representation preset for the current structure(s).', toggle: this.togglePreset, isSelected: this.state.action === 'preset', disabled: this.isDisabled }), _jsx(ToggleButton, { icon: AddSvg, label: 'Add', title: 'Add a new representation component for a selection.', toggle: this.toggleAdd, isSelected: this.state.action === 'add', disabled: this.isDisabled }), _jsx(ToggleButton, { icon: TuneSvg, label: '', title: 'Options that are applied to all applicable representations.', style: { flex: '0 0 40px', padding: 0 }, toggle: this.toggleOptions, isSelected: this.state.action === 'options', disabled: this.isDisabled }), _jsx(IconButton, { svg: RestoreSvg, className: 'msp-flex-item', flex: '40px', onClick: this.undo, disabled: !this.state.canUndo || this.isDisabled, title: undoTitle })] })), this.state.action === 'preset' && this.presetControls, this.state.action === 'add' && _jsx("div", __assign({ className: 'msp-control-offset' }, { children: _jsx(AddComponentControls, { onApply: this.hideAction }) })), this.state.action === 'options' && _jsx("div", __assign({ className: 'msp-control-offset' }, { children: _jsx(ComponentOptionsControls, { isDisabled: this.isDisabled }) }))] });
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return _jsxs(_Fragment, { children: [_jsxs("div", __assign({ className: 'msp-flex-row' }, { children: [_jsxs(Button, __assign({ noOverflow: true, className: 'msp-control-button-label', title: "".concat(label, ". Click to focus."), onClick: this.focus, onMouseEnter: this.highlight, onMouseLeave: this.clearHighlight, style: { textAlign: 'left' } }, { children: [label, _jsx("small", __assign({ className: 'msp-25-lower-contrast-text', style: { float: 'right' } }, { children: reprLabel }))] })), _jsx(IconButton, { svg: cell.state.isHidden ? VisibilityOffOutlinedSvg : VisibilityOutlinedSvg, toggleState: false, onClick: this.toggleVisible, title: "".concat(cell.state.isHidden ? 'Show' : 'Hide', " component"), small: true, className: 'msp-form-control', flex: true }), _jsx(IconButton, { svg: DeleteOutlinedSvg, toggleState: false, onClick: this.remove, title: 'Remove', small: true, className: 'msp-form-control', flex: true }), _jsx(IconButton, { svg: MoreHorizSvg, onClick: this.toggleAction, title: 'Actions', toggleState: this.state.action === 'action', className: 'msp-form-control', flex: true })] })), this.state.action === 'label' && _jsx("div", __assign({ className: 'msp-control-offset', style: { marginBottom: '6px' } }, { children: _jsx(ControlRow, { label: 'Label', control: _jsxs("div", __assign({ style: { display: 'flex', textAlignLast: 'center' } }, { children: [_jsx(TextInput, { onChange: this.updateLabel, value: label, style: { flex: '1 1 auto', minWidth: 0 }, className: 'msp-form-control', blurOnEnter: true, blurOnEscape: true }), _jsx(IconButton, { svg: CheckSvg, onClick: this.toggleLabel, className: 'msp-form-control msp-control-button-label', flex: true })] })) }) })), this.state.action === 'action' && _jsxs("div", __assign({ className: 'msp-accent-offset' }, { children: [_jsx("div", __assign({ style: { marginBottom: '6px' } }, { children: _jsx(ActionMenu, { items: this.actions, onSelect: this.selectAction, noOffset: true }) })), _jsx("div", __assign({ style: { marginBottom: '6px' } }, { children: component.representations.map(function (r) { return _jsx(StructureRepresentationEntry, { group: _this.props.group, representation: r }, r.cell.transform.ref); }) }))] }))] });
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return _jsxs("div", __assign({ className: 'msp-representation-entry' }, { children: [repr.parent && _jsx(ExpandGroup, __assign({ header: "".concat(((_a = repr.obj) === null || _a === void 0 ? void 0 : _a.label) || '', " Representation"), noOffset: true }, { children: _jsx(UpdateTransformControl, { state: repr.parent, transform: repr.transform, customHeader: 'none', customUpdate: this.update, noMargin: true }) })), _jsx(IconButton, { svg: DeleteOutlinedSvg, onClick: this.remove, title: 'Remove', small: true, className: 'msp-default-bg', toggleState: false, style: {
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} }), _jsx(IconButton, { svg: this.props.representation.cell.state.isHidden ? VisibilityOffOutlinedSvg : VisibilityOutlinedSvg, toggleState: false, onClick: this.toggleVisible, title: 'Toggle Visibility', small: true, className: 'msp-default-bg', style: {
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return _jsxs(_Fragment, { children: [_jsxs("div", __assign({ className: 'msp-flex-row' }, { children: [_jsx(Button, __assign({ noOverflow: true, onClick: this.focusCamera, title: title, onMouseEnter: this.highlightCurrent, onMouseLeave: this.clearHighlights, disabled: this.isDisabled || !current, style: { textAlignLast: current ? 'left' : void 0 } }, { children: label })
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return _jsxs(_Fragment, { children: [_jsxs("div", __assign({ className: 'msp-flex-row' }, { children: [_jsx(Button, __assign({ noOverflow: true, onClick: this.focusCamera, title: title, onMouseEnter: this.highlightCurrent, onMouseLeave: this.clearHighlights, disabled: this.isDisabled || !current, style: { textAlignLast: current ? 'left' : void 0 } }, { children: label })), current && _jsx(IconButton, { svg: CancelOutlinedSvg, onClick: this.clear, title: 'Clear', className: 'msp-form-control', flex: true, disabled: this.isDisabled }), _jsx(ToggleButton, { icon: CenterFocusStrongSvg, title: 'Select a focus target to center on an show its surroundings. Hold shift to focus on multiple targets.', toggle: this.toggleAction, isSelected: this.state.showAction, disabled: this.isDisabled, style: { flex: '0 0 40px', padding: 0 } })] })), this.state.showAction && _jsx(ActionMenu, { items: this.actionItems, onSelect: this.selectAction })] });
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return _jsx(GenericEntry, { refs: refs, labelMultiple: 'Unit Cells' }
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return _jsx(GenericEntry, { refs: refs, labelMultiple: 'Unit Cells' });
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controls.push(_jsx("div", { children: _jsx(GenericEntry, { refs: refs, labelMultiple: labelMultiple }) }, key));
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return _jsx(_Fragment, { children: _jsxs("div", __assign({ style: { marginTop: '6px' } }, { children: [this.unitcell, this.customControls] })) });
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return _jsxs(_Fragment, { children: [_jsxs("div", __assign({ className: 'msp-flex-row' }, { children: [_jsxs("button", __assign({ className: 'msp-form-control msp-control-button-label', title: "".concat(label, ". Click to focus."), onClick: this.focus, onMouseEnter: this.highlight, onMouseLeave: this.clearHighlight, style: { textAlign: 'left' } }, { children: [label, " ", _jsx("small", { children: description }
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return _jsxs(_Fragment, { children: [_jsxs("div", __assign({ className: 'msp-flex-row' }, { children: [_jsxs("button", __assign({ className: 'msp-form-control msp-control-button-label', title: "".concat(label, ". Click to focus."), onClick: this.focus, onMouseEnter: this.highlight, onMouseLeave: this.clearHighlight, style: { textAlign: 'left' } }, { children: [label, " ", _jsx("small", { children: description })] })), _jsx(IconButton, { svg: pivot.cell.state.isHidden ? VisibilityOffOutlinedSvg : VisibilityOutlinedSvg, toggleState: false, className: 'msp-form-control', onClick: this.toggleVisibility, title: "".concat(pivot.cell.state.isHidden ? 'Show' : 'Hide'), small: true, flex: true }), refs.length === 1 && _jsx(IconButton, { svg: MoreHorizSvg, className: 'msp-form-control', onClick: this.toggleOptions, title: 'Options', toggleState: this.state.showOptions, flex: true })] })), (refs.length === 1 && this.state.showOptions && pivot.cell.parent) && _jsx(_Fragment, { children: _jsx("div", __assign({ className: 'msp-control-offset' }, { children: _jsx(UpdateTransformControl, { state: pivot.cell.parent, transform: pivot.cell.transform, customHeader: 'none', autoHideApply: true }) })) })] });
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@@ -25,7 +25,7 @@ var StructureMeasurementsControls = /** @class */ (function (_super) {
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return _jsxs(_Fragment, { children: [_jsx(MeasurementControls, {}), _jsx(MeasurementList, {})] });
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@@ -48,11 +48,11 @@ var MeasurementList = /** @class */ (function (_super) {
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group.push(_jsx(MeasurementEntry, { cell: cell }, cell.obj.id));
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}
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return group.length ? _jsx(ExpandGroup, __assign({ header: header, initiallyExpanded: true }, { children: group })
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return group.length ? _jsx(ExpandGroup, __assign({ header: header, initiallyExpanded: true }, { children: group })) : null;
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var measurements = this.plugin.managers.structure.measurement.state;
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return _jsxs("div", __assign({ style: { marginTop: '6px' } }, { children: [this.renderGroup(measurements.labels, 'Labels'), this.renderGroup(measurements.distances, 'Distances'), this.renderGroup(measurements.angles, 'Angles'), this.renderGroup(measurements.dihedrals, 'Dihedrals'), this.renderGroup(measurements.orientations, 'Orientations'), this.renderGroup(measurements.planes, 'Planes')] })
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return _jsxs("div", __assign({ style: { marginTop: '6px' } }, { children: [this.renderGroup(measurements.labels, 'Labels'), this.renderGroup(measurements.distances, 'Distances'), this.renderGroup(measurements.angles, 'Angles'), this.renderGroup(measurements.dihedrals, 'Dihedrals'), this.renderGroup(measurements.orientations, 'Orientations'), this.renderGroup(measurements.planes, 'Planes')] }));
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@@ -169,7 +169,7 @@ var MeasurementControls = /** @class */ (function (_super) {
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return _jsxs("div", __assign({ className: 'msp-flex-row', onMouseEnter: function () { return _this.highlight(e.loci); }, onMouseLeave: function () { return _this.plugin.managers.interactivity.lociHighlights.clearHighlights(); } }, { children: [_jsxs(Button, __assign({ noOverflow: true, title: 'Click to focus. Hover to highlight.', onClick: function () { return _this.focusLoci(e.loci); }, style: { width: 'auto', textAlign: 'left' } }, { children: [idx, ". ", _jsx("span", { dangerouslySetInnerHTML: { __html: e.label } }
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return _jsxs("div", __assign({ className: 'msp-flex-row', onMouseEnter: function () { return _this.highlight(e.loci); }, onMouseLeave: function () { return _this.plugin.managers.interactivity.lociHighlights.clearHighlights(); } }, { children: [_jsxs(Button, __assign({ noOverflow: true, title: 'Click to focus. Hover to highlight.', onClick: function () { return _this.focusLoci(e.loci); }, style: { width: 'auto', textAlign: 'left' } }, { children: [idx, ". ", _jsx("span", { dangerouslySetInnerHTML: { __html: e.label } })] })), history.length > 1 && _jsx(IconButton, { svg: ArrowUpwardSvg, small: true, className: 'msp-form-control', onClick: function () { return _this.moveHistory(e, 'up'); }, flex: '20px', title: 'Move up' }), history.length > 1 && _jsx(IconButton, { svg: ArrowDownwardSvg, small: true, className: 'msp-form-control', onClick: function () { return _this.moveHistory(e, 'down'); }, flex: '20px', title: 'Move down' }), _jsx(IconButton, { svg: DeleteOutlinedSvg, small: true, className: 'msp-form-control', onClick: function () { return _this.plugin.managers.structure.selection.modifyHistory(e, 'remove'); }, flex: true, title: 'Remove' })] }), e.id);
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@@ -177,10 +177,10 @@ var MeasurementControls = /** @class */ (function (_super) {
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for (var i = 0, _i = Math.min(history.length, 4); i < _i; i++) {
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entries.push(this.historyEntry(history[i], i + 1));
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}
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return _jsxs(_Fragment, { children: [_jsx(ActionMenu, { items: this.actions, onSelect: this.selectAction }
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return _jsxs(_Fragment, { children: [_jsx(ActionMenu, { items: this.actions, onSelect: this.selectAction }), entries.length > 0 && _jsx("div", __assign({ className: 'msp-control-offset' }, { children: entries })), entries.length === 0 && _jsx("div", __assign({ className: 'msp-control-offset msp-help-text' }, { children: _jsxs("div", __assign({ className: 'msp-help-description' }, { children: [_jsx(Icon, { svg: HelpOutlineSvg, inline: true }), "Add one or more selections (toggle ", _jsx(ToggleSelectionModeButton, { inline: true }), " mode)"] })) }))] });
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return _jsxs(_Fragment, { children: [_jsxs("div", __assign({ className: 'msp-flex-row' }, { children: [_jsx(ToggleButton, { icon: AddSvg, label: 'Add', toggle: this.toggleAdd, isSelected: this.state.action === 'add', disabled: this.state.isBusy, className: 'msp-btn-apply-simple' }
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return _jsxs(_Fragment, { children: [_jsxs("div", __assign({ className: 'msp-flex-row' }, { children: [_jsx(ToggleButton, { icon: AddSvg, label: 'Add', toggle: this.toggleAdd, isSelected: this.state.action === 'add', disabled: this.state.isBusy, className: 'msp-btn-apply-simple' }), _jsx(ToggleButton, { icon: TuneSvg, label: '', title: 'Options', toggle: this.toggleOptions, isSelected: this.state.action === 'options', disabled: this.state.isBusy, style: { flex: '0 0 40px', padding: 0 } })] })), this.state.action === 'add' && this.add(), this.state.action === 'options' && _jsx(MeasurementsOptions, {})] });
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@@ -206,7 +206,7 @@ var MeasurementsOptions = /** @class */ (function (_super) {
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return _jsx("div", __assign({ className: 'msp-control-offset' }, { children: _jsx(ParameterControls, { params: StructureMeasurementParams, values: measurements.options, onChangeValues: this.changed, isDisabled: this.state.isDisabled }
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return _jsx("div", __assign({ className: 'msp-control-offset' }, { children: _jsx(ParameterControls, { params: StructureMeasurementParams, values: measurements.options, onChangeValues: this.changed, isDisabled: this.state.isDisabled }) }));
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}(PurePluginUIComponent));
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@@ -324,7 +324,7 @@ var MeasurementEntry = /** @class */ (function (_super) {
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return _jsxs(_Fragment, { children: [_jsxs("div", __assign({ className: 'msp-flex-row', onMouseEnter: this.highlight, onMouseLeave: this.clearHighlight }, { children: [_jsx("button", __assign({ className: 'msp-form-control msp-control-button-label msp-no-overflow', title: 'Click to focus. Hover to highlight.', onClick: this.focus, style: { width: 'auto', textAlign: 'left' } }, { children: _jsx("span", { dangerouslySetInnerHTML: { __html: this.label } }
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return _jsxs(_Fragment, { children: [_jsxs("div", __assign({ className: 'msp-flex-row', onMouseEnter: this.highlight, onMouseLeave: this.clearHighlight }, { children: [_jsx("button", __assign({ className: 'msp-form-control msp-control-button-label msp-no-overflow', title: 'Click to focus. Hover to highlight.', onClick: this.focus, style: { width: 'auto', textAlign: 'left' } }, { children: _jsx("span", { dangerouslySetInnerHTML: { __html: this.label } }) })), _jsx(IconButton, { svg: cell.state.isHidden ? VisibilityOffOutlinedSvg : VisibilityOutlinedSvg, toggleState: false, small: true, className: 'msp-form-control', onClick: this.toggleVisibility, flex: true, title: cell.state.isHidden ? 'Show' : 'Hide' }), _jsx(IconButton, { svg: DeleteOutlinedSvg, small: true, className: 'msp-form-control', onClick: this.delete, flex: true, title: 'Delete', toggleState: false }), _jsx(IconButton, { svg: MoreHorizSvg, className: 'msp-form-control', onClick: this.toggleUpdate, flex: true, title: 'Actions', toggleState: this.state.showUpdate })] }), obj.id), this.state.showUpdate && cell.parent && _jsx(_Fragment, { children: _jsxs("div", __assign({ className: 'msp-accent-offset' }, { children: [_jsx(ActionMenu, { items: this.actions, onSelect: this.selectAction, noOffset: true }), _jsx(ExpandGroup, __assign({ header: 'Options', noOffset: true }, { children: _jsx(UpdateTransformControl, { state: cell.parent, transform: cell.transform, customHeader: 'none', autoHideApply: true }) }))] })) })] });
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};
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}(PurePluginUIComponent));
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@@ -27,7 +27,7 @@ var StructureQuickStylesControls = /** @class */ (function (_super) {
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};
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};
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StructureQuickStylesControls.prototype.renderControls = function () {
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return _jsx(_Fragment, { children: _jsx(QuickStyles, {}
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+
return _jsx(_Fragment, { children: _jsx(QuickStyles, {}) });
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}(CollapsableControls));
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@@ -120,7 +120,7 @@ var QuickStyles = /** @class */ (function (_super) {
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};
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QuickStyles.prototype.render = function () {
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return _jsxs("div", __assign({ className: 'msp-flex-row' }, { children: [_jsx(Button, __assign({ noOverflow: true, title: 'Applies default representation preset. Set outline and occlusion effects to defaults.', onClick: function () { return _this.default(); }, style: { width: 'auto' } }, { children: "Default" })
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return _jsxs("div", __assign({ className: 'msp-flex-row' }, { children: [_jsx(Button, __assign({ noOverflow: true, title: 'Applies default representation preset. Set outline and occlusion effects to defaults.', onClick: function () { return _this.default(); }, style: { width: 'auto' } }, { children: "Default" })), _jsx(Button, __assign({ noOverflow: true, title: 'Applies no representation preset. Enables outline and occlusion effects. Enables ignore-light representation parameter.', onClick: function () { return _this.stylized(); }, style: { width: 'auto' } }, { children: "Stylized" })), _jsx(Button, __assign({ noOverflow: true, title: 'Applies illustrative representation preset. Enables outline and occlusion effects. Enables ignore-light parameter.', onClick: function () { return _this.illustrative(); }, style: { width: 'auto' } }, { children: "Illustrative" }))] }));
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};
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return QuickStyles;
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}(PurePluginUIComponent));
|
|
@@ -40,7 +40,7 @@ var ToggleSelectionModeButton = /** @class */ (function (_super) {
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40
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var style = this.props.inline
|
|
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|
? { background: 'transparent', width: 'auto', height: 'auto', lineHeight: 'unset' }
|
|
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: { background: 'transparent' };
|
|
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-
return _jsx(IconButton, { svg: SelectionModeSvg, onClick: this._toggleSelMode, title: 'Toggle Selection Mode', style: style, toggleState: this.plugin.selectionMode }
|
|
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|
+
return _jsx(IconButton, { svg: SelectionModeSvg, onClick: this._toggleSelMode, title: 'Toggle Selection Mode', style: style, toggleState: this.plugin.selectionMode });
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|
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|
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|
46
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}(PurePluginUIComponent));
|
|
@@ -219,13 +219,13 @@ var StructureSelectionActionsControls = /** @class */ (function (_super) {
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: 'Some mistakes of the past can be undone.';
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var children = void 0;
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if (this.state.action && !this.state.helper) {
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children = _jsxs(_Fragment, { children: [(this.state.action && this.state.action !== 'theme' && this.state.action !== 'add-component' && this.state.action !== 'help') && _jsxs("div", __assign({ className: 'msp-selection-viewport-controls-actions' }, { children: [_jsx(ActionMenu, { header: ActionHeader.get(this.state.action), title: 'Click to close.', items: this.queries, onSelect: this.selectQuery, noOffset: true }
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+
children = _jsxs(_Fragment, { children: [(this.state.action && this.state.action !== 'theme' && this.state.action !== 'add-component' && this.state.action !== 'help') && _jsxs("div", __assign({ className: 'msp-selection-viewport-controls-actions' }, { children: [_jsx(ActionMenu, { header: ActionHeader.get(this.state.action), title: 'Click to close.', items: this.queries, onSelect: this.selectQuery, noOffset: true }), _jsx(ActionMenu, { items: this.helpers, onSelect: this.selectHelper, noOffset: true })] })), this.state.action === 'theme' && _jsx("div", __assign({ className: 'msp-selection-viewport-controls-actions' }, { children: _jsx(ControlGroup, __assign({ header: 'Theme', title: 'Click to close.', initialExpanded: true, hideExpander: true, hideOffset: true, onHeaderClick: this.toggleTheme, topRightIcon: CloseSvg }, { children: _jsx(ApplyThemeControls, { onApply: this.toggleTheme }) })) })), this.state.action === 'add-component' && _jsx("div", __assign({ className: 'msp-selection-viewport-controls-actions' }, { children: _jsx(ControlGroup, __assign({ header: 'Add Component', title: 'Click to close.', initialExpanded: true, hideExpander: true, hideOffset: true, onHeaderClick: this.toggleAddComponent, topRightIcon: CloseSvg }, { children: _jsx(AddComponentControls, { onApply: this.toggleAddComponent, forSelection: true }) })) })), this.state.action === 'help' && _jsx("div", __assign({ className: 'msp-selection-viewport-controls-actions' }, { children: _jsxs(ControlGroup, __assign({ header: 'Help', title: 'Click to close.', initialExpanded: true, hideExpander: true, hideOffset: true, onHeaderClick: this.toggleHelp, topRightIcon: CloseSvg, maxHeight: '300px' }, { children: [_jsx(HelpGroup, __assign({ header: 'Selection Operations' }, { children: _jsxs(HelpText, { children: ["Use ", _jsx(Icon, { svg: UnionSvg, inline: true }), " ", _jsx(Icon, { svg: SubtractSvg, inline: true }), " ", _jsx(Icon, { svg: IntersectSvg, inline: true }), " ", _jsx(Icon, { svg: SetSvg, inline: true }), " to modify the selection."] }) })), _jsx(HelpGroup, __assign({ header: 'Representation Operations' }, { children: _jsxs(HelpText, { children: ["Use ", _jsx(Icon, { svg: BrushSvg, inline: true }), " ", _jsx(Icon, { svg: CubeOutlineSvg, inline: true }), " ", _jsx(Icon, { svg: RemoveSvg, inline: true }), " ", _jsx(Icon, { svg: RestoreSvg, inline: true }), " to color, create components, remove from components, or undo actions."] }) })), _jsx(ViewportHelpContent, { selectOnly: true })] })) }))] });
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}
|
|
224
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|
else if (ActionHeader.has(this.state.action) && this.state.helper === 'residue-list') {
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var close_1 = function () { return _this.setState({ action: void 0, helper: void 0 }); };
|
|
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-
children = _jsx("div", __assign({ className: 'msp-selection-viewport-controls-actions' }, { children: _jsx(ControlGroup, __assign({ header: 'Atom/Residue Identifier List', title: 'Click to close.', initialExpanded: true, hideExpander: true, hideOffset: true, onHeaderClick: close_1, topRightIcon: CloseSvg }, { children: _jsx(ResidueListSelectionHelper, { modifier: this.state.action, plugin: this.plugin, close: close_1 }
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children = _jsx("div", __assign({ className: 'msp-selection-viewport-controls-actions' }, { children: _jsx(ControlGroup, __assign({ header: 'Atom/Residue Identifier List', title: 'Click to close.', initialExpanded: true, hideExpander: true, hideOffset: true, onHeaderClick: close_1, topRightIcon: CloseSvg }, { children: _jsx(ResidueListSelectionHelper, { modifier: this.state.action, plugin: this.plugin, close: close_1 }) })) }));
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return _jsxs(_Fragment, { children: [_jsxs("div", __assign({ className: 'msp-flex-row', style: { background: 'none' } }, { children: [_jsx(PureSelectControl, { title: "Picking Level for selecting and highlighting", param: StructureSelectionParams.granularity, name: 'granularity', value: granularity, onChange: this.setGranuality, isDisabled: this.isDisabled }), _jsx(ToggleButton, { icon: UnionSvg, title: "".concat(ActionHeader.get('add'), ". Hold shift key to keep menu open."), toggle: this.toggleAdd, isSelected: this.state.action === 'add', disabled: this.isDisabled }), _jsx(ToggleButton, { icon: SubtractSvg, title: "".concat(ActionHeader.get('remove'), ". Hold shift key to keep menu open."), toggle: this.toggleRemove, isSelected: this.state.action === 'remove', disabled: this.isDisabled }), _jsx(ToggleButton, { icon: IntersectSvg, title: "".concat(ActionHeader.get('intersect'), ". Hold shift key to keep menu open."), toggle: this.toggleIntersect, isSelected: this.state.action === 'intersect', disabled: this.isDisabled }), _jsx(ToggleButton, { icon: SetSvg, title: "".concat(ActionHeader.get('set'), ". Hold shift key to keep menu open."), toggle: this.toggleSet, isSelected: this.state.action === 'set', disabled: this.isDisabled }), _jsx(ToggleButton, { icon: BrushSvg, title: 'Apply Theme to Selection', toggle: this.toggleTheme, isSelected: this.state.action === 'theme', disabled: this.isDisabled, style: { marginLeft: '10px' } }), _jsx(ToggleButton, { icon: CubeOutlineSvg, title: 'Create Component of Selection with Representation', toggle: this.toggleAddComponent, isSelected: this.state.action === 'add-component', disabled: this.isDisabled }), _jsx(IconButton, { svg: RemoveSvg, title: 'Remove/subtract Selection from all Components', onClick: this.subtract, disabled: this.isDisabled }), _jsx(IconButton, { svg: RestoreSvg, onClick: this.undo, disabled: !this.state.canUndo || this.isDisabled, title: undoTitle }), _jsx(ToggleButton, { icon: HelpOutlineSvg, title: 'Show/hide help', toggle: this.toggleHelp, style: { marginLeft: '10px' }, isSelected: this.state.action === 'help' }), _jsx(IconButton, { svg: CancelOutlinedSvg, title: 'Turn selection mode off', onClick: this.turnOff })] })), children] });
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return _jsx(_Fragment, { children: _jsxs("div", __assign({ className: 'msp-flex-row' }, { children: [_jsx(Button, __assign({ noOverflow: true, onClick: this.focus, title: 'Click to Focus Selection', disabled: empty, onMouseEnter: this.highlight, onMouseLeave: this.clearHighlight, style: { textAlignLast: !empty ? 'left' : void 0 } }, { children: this.stats })), !empty && _jsx(IconButton, { svg: CancelOutlinedSvg, onClick: this.clear, title: 'Clear', className: 'msp-form-control', flex: true })] })) });
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return _jsxs(_Fragment, { children: [_jsx(ParameterControls, { params: this.params, values: this.state.values, onChangeValues: this.paramsChanged }), _jsx(Button, __assign({ icon: BrushSvg, className: 'msp-btn-commit msp-btn-commit-on', onClick: this.apply, style: { marginTop: '1px' } }, { children: "Apply Theme" }))] });
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return _jsxs(_Fragment, { children: [_jsx(ParameterControls, { params: ResidueListIdTypeParams, values: state, onChangeValues: setState, onEnter: apply }), _jsxs(Button, __assign({ className: 'msp-btn-commit msp-btn-commit-on', disabled: state.identifiers.trim().length === 0, onClick: apply, style: { marginTop: '1px' } }, { children: [capitalize(modifier), " Selection"] }))] });
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return _jsx(ParameterControls, { params: params, values: (_b = m.cell.params) === null || _b === void 0 ? void 0 : _b.values, onChangeValues: this.updateStructureModel, isDisabled: this.state.isBusy });
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return _jsx(UpdateTransformControl, { state: s.cell.parent, transform: s.cell.transform, customHeader: 'none', customUpdate: this.updateStructure, noMargin: true, autoHideApply: true }
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return _jsx(UpdateTransformControl, { state: s.cell.parent, transform: s.cell.transform, customHeader: 'none', customUpdate: this.updateStructure, noMargin: true, autoHideApply: true });
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return _jsx(ExpandGroup, __assign({ header: "Conformation Transform" }, { children: _jsx(UpdateTransformControl, { state: t.parent, transform: t.transform, customHeader: 'none', noMargin: true, autoHideApply: true }
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return _jsx(ExpandGroup, __assign({ header: "Conformation Transform" }, { children: _jsx(UpdateTransformControl, { state: t.parent, transform: t.transform, customHeader: 'none', noMargin: true, autoHideApply: true }) }));
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return _jsxs(_Fragment, { children: [_jsxs("div", __assign({ className: 'msp-flex-row', style: { marginTop: '1px' } }, { children: [_jsx(Button, __assign({ noOverflow: true, flex: true, onClick: this.toggleHierarchy, disabled: disabled, title: label }, { children: label })
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return _jsxs(_Fragment, { children: [_jsxs("div", __assign({ className: 'msp-flex-row', style: { marginTop: '1px' } }, { children: [_jsx(Button, __assign({ noOverflow: true, flex: true, onClick: this.toggleHierarchy, disabled: disabled, title: label }, { children: label })), presets.length > 0 && _jsx(IconButton, { svg: BookmarksOutlinedSvg, className: 'msp-form-control', flex: '40px', onClick: this.togglePreset, title: 'Apply a structure presets to the current hierarchy.', toggleState: this.state.show === 'presets', disabled: disabled })] })), this.state.show === 'hierarchy' && _jsx(ActionMenu, { items: this.hierarchyItems, onSelect: this.selectHierarchy, multiselect: true }), this.state.show === 'presets' && _jsx(ActionMenu, { items: presets, onSelect: this.applyPreset }), this.modelIndex, this.structureType, this.transform, _jsxs("div", __assign({ style: { marginTop: '6px' } }, { children: [_jsx(StructureFocusControls, {}), _jsx(StructureSelectionStatsControls, { hideOnEmpty: true })] }))] });
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return _jsx(_Fragment, { children: _jsx(SuperpositionControls, {}) });
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return _jsx("div", __assign({ className: 'msp-flex-row' }, { children: _jsx(Button, __assign({ noOverflow: true, title: 'Click to focus. Hover to highlight.', onClick: function () { return _this.focusLoci(e.loci); }, style: { width: 'auto', textAlign: 'left' }, onMouseEnter: function () { return _this.highlight(e.loci); }, onMouseLeave: function () { return _this.plugin.managers.interactivity.lociHighlights.clearHighlights(); } }, { children: _jsx("span", { dangerouslySetInnerHTML: { __html: e.label } }
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return _jsx("div", __assign({ className: 'msp-flex-row' }, { children: _jsx(Button, __assign({ noOverflow: true, title: 'Click to focus. Hover to highlight.', onClick: function () { return _this.focusLoci(e.loci); }, style: { width: 'auto', textAlign: 'left' }, onMouseEnter: function () { return _this.highlight(e.loci); }, onMouseLeave: function () { return _this.plugin.managers.interactivity.lociHighlights.clearHighlights(); } }, { children: _jsx("span", { dangerouslySetInnerHTML: { __html: e.label } }) })) }), idx);
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return _jsxs("div", __assign({ className: 'msp-flex-row' }, { children: [_jsxs(Button, __assign({ noOverflow: true, title: 'Click to focus. Hover to highlight.', onClick: function () { return _this.focusLoci(e.loci); }, style: { width: 'auto', textAlign: 'left' }, onMouseEnter: function () { return _this.highlight(e.loci); }, onMouseLeave: function () { return _this.plugin.managers.interactivity.lociHighlights.clearHighlights(); } }, { children: [idx, ". ", _jsx("span", { dangerouslySetInnerHTML: { __html: e.label } }
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return _jsxs("div", __assign({ className: 'msp-flex-row' }, { children: [_jsxs(Button, __assign({ noOverflow: true, title: 'Click to focus. Hover to highlight.', onClick: function () { return _this.focusLoci(e.loci); }, style: { width: 'auto', textAlign: 'left' }, onMouseEnter: function () { return _this.highlight(e.loci); }, onMouseLeave: function () { return _this.plugin.managers.interactivity.lociHighlights.clearHighlights(); } }, { children: [idx, ". ", _jsx("span", { dangerouslySetInnerHTML: { __html: e.label } })] })), history.length > 1 && _jsx(IconButton, { svg: ArrowUpwardSvg, small: true, className: 'msp-form-control', onClick: function () { return _this.moveHistory(e, 'up'); }, flex: '20px', title: 'Move up' }), history.length > 1 && _jsx(IconButton, { svg: ArrowDownwardSvg, small: true, className: 'msp-form-control', onClick: function () { return _this.moveHistory(e, 'down'); }, flex: '20px', title: 'Move down' }), _jsx(IconButton, { svg: DeleteOutlinedSvg, small: true, className: 'msp-form-control', onClick: function () { return _this.plugin.managers.structure.selection.modifyHistory(e, 'remove'); }, flex: true, title: 'Remove' })] }), e.id);
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SuperpositionControls.prototype.atomsLociEntry = function (e, idx) {
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return _jsxs("div", { children: [_jsx("div", __assign({ className: 'msp-control-group-header' }, { children: _jsx("div", __assign({ className: 'msp-no-overflow', title: e.label }, { children: e.label })
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return _jsxs("div", { children: [_jsx("div", __assign({ className: 'msp-control-group-header' }, { children: _jsx("div", __assign({ className: 'msp-no-overflow', title: e.label }, { children: e.label })) })), _jsx("div", __assign({ className: 'msp-control-offset' }, { children: e.atoms.map(function (h, i) { return _this.historyEntry(h, i); }) }))] }, idx);
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};
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Object.defineProperty(SuperpositionControls.prototype, "chainEntries", {
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@@ -346,18 +346,18 @@ var SuperpositionControls = /** @class */ (function (_super) {
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SuperpositionControls.prototype.addByChains = function () {
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return _jsxs(_Fragment, { children: [entries.length > 0 && _jsx("div", __assign({ className: 'msp-control-offset' }, { children: entries.map(function (e, i) { return _this.lociEntry(e, i); }) })
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return _jsxs(_Fragment, { children: [entries.length > 0 && _jsx("div", __assign({ className: 'msp-control-offset' }, { children: entries.map(function (e, i) { return _this.lociEntry(e, i); }) })), entries.length < 2 && _jsx("div", __assign({ className: 'msp-control-offset msp-help-text' }, { children: _jsxs("div", __assign({ className: 'msp-help-description' }, { children: [_jsx(Icon, { svg: HelpOutlineSvg, inline: true }), "Add 2 or more selections (toggle ", _jsx(ToggleSelectionModeButton, { inline: true }), " mode) from separate structures. Selections must be limited to single polymer chains or residues therein."] })) })), entries.length > 1 && _jsx(Button, __assign({ title: 'Superpose structures by selected chains.', className: 'msp-btn-commit msp-btn-commit-on', onClick: this.superposeChains, style: { marginTop: '1px' } }, { children: "Superpose" }))] });
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};
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return _jsxs(_Fragment, { children: [entries.length > 0 && _jsx("div", __assign({ className: 'msp-control-offset' }, { children: entries.map(function (e, i) { return _this.atomsLociEntry(e, i); }) })
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return _jsxs(_Fragment, { children: [entries.length > 0 && _jsx("div", __assign({ className: 'msp-control-offset' }, { children: entries.map(function (e, i) { return _this.atomsLociEntry(e, i); }) })), entries.length < 2 && _jsx("div", __assign({ className: 'msp-control-offset msp-help-text' }, { children: _jsxs("div", __assign({ className: 'msp-help-description' }, { children: [_jsx(Icon, { svg: HelpOutlineSvg, inline: true }), "Add 1 or more selections (toggle ", _jsx(ToggleSelectionModeButton, { inline: true }), " mode) from separate structures. Selections must be limited to single atoms."] })) })), entries.length > 1 && _jsx(Button, __assign({ title: 'Superpose structures by selected atoms.', className: 'msp-btn-commit msp-btn-commit-on', onClick: this.superposeAtoms, style: { marginTop: '1px' } }, { children: "Superpose" }))] });
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};
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SuperpositionControls.prototype.superposeByDbMapping = function () {
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return _jsx(_Fragment, { children: _jsx(Button, __assign({ icon: SuperposeChainsSvg, title: 'Superpose structures using intersection of residues from SIFTS UNIPROT mapping.', className: 'msp-btn msp-btn-block', onClick: this.superposeDb, style: { marginTop: '1px' }, disabled: this.state.isBusy }, { children: "Uniprot" })
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+
return _jsx(_Fragment, { children: _jsx(Button, __assign({ icon: SuperposeChainsSvg, title: 'Superpose structures using intersection of residues from SIFTS UNIPROT mapping.', className: 'msp-btn msp-btn-block', onClick: this.superposeDb, style: { marginTop: '1px' }, disabled: this.state.isBusy }, { children: "Uniprot" })) });
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return _jsxs(_Fragment, { children: [_jsxs("div", __assign({ className: 'msp-flex-row' }, { children: [_jsx(ToggleButton, { icon: SuperposeChainsSvg, label: 'Chains', toggle: this.toggleByChains, isSelected: this.state.action === 'byChains', disabled: this.state.isBusy }
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+
return _jsxs(_Fragment, { children: [_jsxs("div", __assign({ className: 'msp-flex-row' }, { children: [_jsx(ToggleButton, { icon: SuperposeChainsSvg, label: 'Chains', toggle: this.toggleByChains, isSelected: this.state.action === 'byChains', disabled: this.state.isBusy }), _jsx(ToggleButton, { icon: SuperposeAtomsSvg, label: 'Atoms', toggle: this.toggleByAtoms, isSelected: this.state.action === 'byAtoms', disabled: this.state.isBusy }), this.state.canUseDb && this.superposeByDbMapping(), _jsx(ToggleButton, { icon: TuneSvg, label: '', title: 'Options', toggle: this.toggleOptions, isSelected: this.state.action === 'options', disabled: this.state.isBusy, style: { flex: '0 0 40px', padding: 0 } })] })), this.state.action === 'byChains' && this.addByChains(), this.state.action === 'byAtoms' && this.addByAtoms(), this.state.action === 'options' && _jsx("div", __assign({ className: 'msp-control-offset' }, { children: _jsx(ParameterControls, { params: StructureSuperpositionParams, values: this.state.options, onChangeValues: this.setOptions, isDisabled: this.state.isBusy }) }))] });
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};
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return SuperpositionControls;
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}(PurePluginUIComponent));
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@@ -76,7 +76,7 @@ var VolumeStreamingControls = /** @class */ (function (_super) {
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: rootCell && ((_b = rootCell.obj) === null || _b === void 0 ? void 0 : _b.data.entries.length) === 0
|
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? { header: 'Error Enabling', icon: ErrorSvg, title: 'No Entry for Streaming Found' }
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: { header: 'Enable', icon: CheckSvg, title: 'Enable' };
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return _jsx(ApplyActionControl, { state: pivot.cell.parent, action: InitVolumeStreaming, initiallyCollapsed: true, nodeRef: pivot.cell.transform.ref, simpleApply: simpleApply }
|
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+
return _jsx(ApplyActionControl, { state: pivot.cell.parent, action: InitVolumeStreaming, initiallyCollapsed: true, nodeRef: pivot.cell.transform.ref, simpleApply: simpleApply });
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};
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VolumeStreamingControls.prototype.renderParams = function () {
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|
var _a, _b, _c, _d, _e;
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@@ -84,7 +84,7 @@ var VolumeStreamingControls = /** @class */ (function (_super) {
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|
if (!pivot.cell.parent)
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|
return null;
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|
var bindings = ((_b = (_a = pivot.volumeStreaming) === null || _a === void 0 ? void 0 : _a.cell.transform.params) === null || _b === void 0 ? void 0 : _b.entry.params.view.name) === 'selection-box' && ((_e = (_d = (_c = this.plugin.state.behaviors.cells.get(FocusLoci.id)) === null || _c === void 0 ? void 0 : _c.params) === null || _d === void 0 ? void 0 : _d.values) === null || _e === void 0 ? void 0 : _e.bindings);
|
|
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return _jsxs(_Fragment, { children: [_jsx(UpdateTransformControl, { state: pivot.cell.parent, transform: pivot.volumeStreaming.cell.transform, customHeader: 'none', noMargin: true }
|
|
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+
return _jsxs(_Fragment, { children: [_jsx(UpdateTransformControl, { state: pivot.cell.parent, transform: pivot.volumeStreaming.cell.transform, customHeader: 'none', noMargin: true }), bindings && _jsx(ExpandGroup, __assign({ header: 'Controls Help' }, { children: _jsx(BindingsHelp, { bindings: bindings }) }))] });
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};
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VolumeStreamingControls.prototype.renderControls = function () {
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var pivot = this.pivot;
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@@ -267,7 +267,7 @@ var VolumeSourceControls = /** @class */ (function (_super) {
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var disabled = this.state.isBusy || this.isEmpty;
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var label = this.label;
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var selected = this.plugin.managers.volume.hierarchy.selection;
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return _jsxs(_Fragment, { children: [_jsxs("div", __assign({ className: 'msp-flex-row', style: { marginTop: '1px' } }, { children: [_jsx(Button, __assign({ noOverflow: true, flex: true, onClick: this.toggleHierarchy, disabled: disabled, title: label }, { children: label })
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return _jsxs(_Fragment, { children: [_jsxs("div", __assign({ className: 'msp-flex-row', style: { marginTop: '1px' } }, { children: [_jsx(Button, __assign({ noOverflow: true, flex: true, onClick: this.toggleHierarchy, disabled: disabled, title: label }, { children: label })), !this.isEmpty && selected && _jsx(IconButton, { svg: AddSvg, onClick: this.toggleAddRepr, title: 'Apply a structure presets to the current hierarchy.', toggleState: this.state.show === 'add-repr', disabled: disabled })] })), this.state.show === 'hierarchy' && _jsx(ActionMenu, { items: this.hierarchyItems, onSelect: this.selectCurrent }), this.state.show === 'add-repr' && _jsx(ActionMenu, { items: this.addActions, onSelect: this.selectAdd }), selected && selected.representations.length > 0 && _jsx("div", __assign({ style: { marginTop: '6px' } }, { children: selected.representations.map(function (r) { return _jsx(VolumeRepresentationControls, { representation: r }, r.cell.transform.ref); }) }))] });
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};
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return VolumeSourceControls;
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}(CollapsableControls));
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@@ -314,7 +314,7 @@ var VolumeRepresentationControls = /** @class */ (function (_super) {
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VolumeRepresentationControls.prototype.render = function () {
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var _a, _b, _c;
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var repr = this.props.representation.cell;
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return _jsxs(_Fragment, { children: [_jsxs("div", __assign({ className: 'msp-flex-row' }, { children: [_jsxs(Button, __assign({ noOverflow: true, className: 'msp-control-button-label', title: "".concat((_a = repr.obj) === null || _a === void 0 ? void 0 : _a.label, ". Click to focus."), onClick: this.focus, onMouseEnter: this.highlight, onMouseLeave: this.clearHighlight, style: { textAlign: 'left' } }, { children: [(_b = repr.obj) === null || _b === void 0 ? void 0 : _b.label, _jsx("small", __assign({ className: 'msp-25-lower-contrast-text', style: { float: 'right' } }, { children: (_c = repr.obj) === null || _c === void 0 ? void 0 : _c.description })
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return _jsxs(_Fragment, { children: [_jsxs("div", __assign({ className: 'msp-flex-row' }, { children: [_jsxs(Button, __assign({ noOverflow: true, className: 'msp-control-button-label', title: "".concat((_a = repr.obj) === null || _a === void 0 ? void 0 : _a.label, ". Click to focus."), onClick: this.focus, onMouseEnter: this.highlight, onMouseLeave: this.clearHighlight, style: { textAlign: 'left' } }, { children: [(_b = repr.obj) === null || _b === void 0 ? void 0 : _b.label, _jsx("small", __assign({ className: 'msp-25-lower-contrast-text', style: { float: 'right' } }, { children: (_c = repr.obj) === null || _c === void 0 ? void 0 : _c.description }))] })), _jsx(IconButton, { svg: repr.state.isHidden ? VisibilityOffOutlinedSvg : VisibilityOutlinedSvg, toggleState: false, onClick: this.toggleVisible, title: "".concat(repr.state.isHidden ? 'Show' : 'Hide', " component"), small: true, className: 'msp-form-control', flex: true }), _jsx(IconButton, { svg: DeleteOutlinedSvg, onClick: this.remove, title: 'Remove', small: true }), _jsx(IconButton, { svg: MoreHorizSvg, onClick: this.toggleUpdate, title: 'Actions', toggleState: this.state.action === 'update' })] })), this.state.action === 'update' && !!repr.parent && _jsx("div", __assign({ style: { marginBottom: '6px' }, className: 'msp-accent-offset' }, { children: _jsx(UpdateTransformControl, { state: repr.parent, transform: repr.transform, customHeader: 'none', noMargin: true }) }))] });
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};
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return VolumeRepresentationControls;
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}(PurePluginUIComponent));
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@@ -30,7 +30,7 @@ var BackgroundTaskProgress = /** @class */ (function (_super) {
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});
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};
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BackgroundTaskProgress.prototype.render = function () {
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return _jsx("div", __assign({ className: 'msp-background-tasks' }, { children: this.state.tracked.valueSeq().map(function (e) { return _jsx(ProgressEntry, { event: e }, e.id); }) })
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return _jsx("div", __assign({ className: 'msp-background-tasks' }, { children: this.state.tracked.valueSeq().map(function (e) { return _jsx(ProgressEntry, { event: e }, e.id); }) }));
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};
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return BackgroundTaskProgress;
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}(PluginUIComponent));
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@@ -49,11 +49,11 @@ var ProgressEntry = /** @class */ (function (_super) {
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var subtaskCount = countSubtasks(this.props.event.progress.root) - 1;
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var pr = root.progress.isIndeterminate
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? void 0
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: _jsxs(_Fragment, { children: ["[", root.progress.current, "/", root.progress.max, "]"] }
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: _jsxs(_Fragment, { children: ["[", root.progress.current, "/", root.progress.max, "]"] });
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var subtasks = subtaskCount > 0
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? _jsxs(_Fragment, { children: ["[", subtaskCount, " subtask(s)]"] }
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? _jsxs(_Fragment, { children: ["[", subtaskCount, " subtask(s)]"] })
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: void 0;
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-
return _jsx("div", __assign({ className: 'msp-task-state' }, { children: _jsxs("div", { children: [root.progress.canAbort && _jsx(IconButton, { svg: CancelSvg, onClick: this.abort, title: 'Abort' }
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+
return _jsx("div", __assign({ className: 'msp-task-state' }, { children: _jsxs("div", { children: [root.progress.canAbort && _jsx(IconButton, { svg: CancelSvg, onClick: this.abort, title: 'Abort' }), _jsxs("div", { children: [root.progress.message, " ", pr, " ", subtasks] })] }) }));
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};
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return ProgressEntry;
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}(PluginUIComponent));
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@@ -87,7 +87,7 @@ var OverlayTaskProgress = /** @class */ (function (_super) {
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OverlayTaskProgress.prototype.render = function () {
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if (this.state.tracked.size === 0)
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return null;
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return _jsx("div", __assign({ className: 'msp-overlay-tasks' }, { children: this.state.tracked.valueSeq().map(function (e) { return _jsx(ProgressEntry, { event: e }, e.id); }) })
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return _jsx("div", __assign({ className: 'msp-overlay-tasks' }, { children: this.state.tracked.valueSeq().map(function (e) { return _jsx(ProgressEntry, { event: e }, e.id); }) }));
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};
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return OverlayTaskProgress;
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}(PluginUIComponent));
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@@ -24,9 +24,9 @@ var ToastEntry = /** @class */ (function (_super) {
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var _this = this;
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var entry = this.props.entry;
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var message = typeof entry.message === 'string'
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-
? _jsx("div", { dangerouslySetInnerHTML: { __html: entry.message } }
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: _jsx("div", { children: _jsx(entry.message, {}
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-
return _jsxs("div", __assign({ className: 'msp-toast-entry' }, { children: [_jsx("div", __assign({ className: 'msp-toast-title', onClick: function () { return _this.hide(); } }, { children: entry.title })
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+
? _jsx("div", { dangerouslySetInnerHTML: { __html: entry.message } })
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+
: _jsx("div", { children: _jsx(entry.message, {}) });
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+
return _jsxs("div", __assign({ className: 'msp-toast-entry' }, { children: [_jsx("div", __assign({ className: 'msp-toast-title', onClick: function () { return _this.hide(); } }, { children: entry.title })), _jsx("div", __assign({ className: 'msp-toast-message' }, { children: message })), _jsx("div", { className: 'msp-toast-clear' }), _jsx("div", __assign({ className: 'msp-toast-hide' }, { children: _jsx(IconButton, { svg: CancelSvg, onClick: this.hide, title: 'Hide', className: 'msp-no-hover-outline' }) }))] }));
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};
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return ToastEntry;
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}(PluginUIComponent));
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@@ -46,7 +46,7 @@ var Toasts = /** @class */ (function (_super) {
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var entries = [];
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state.entries.forEach(function (t, k) { return entries.push(t); });
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|
entries.sort(function (x, y) { return x.serialNumber - y.serialNumber; });
|
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-
return _jsx("div", __assign({ className: 'msp-toast-container' }, { children: entries.map(function (e) { return _jsx(ToastEntry, { entry: e }, e.serialNumber); }) })
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+
return _jsx("div", __assign({ className: 'msp-toast-container' }, { children: entries.map(function (e) { return _jsx(ToastEntry, { entry: e }, e.serialNumber); }) }));
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};
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return Toasts;
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}(PluginUIComponent));
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@@ -39,15 +39,15 @@ var ViewportCanvas = /** @class */ (function (_super) {
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|
ViewportCanvas.prototype.renderMissing = function () {
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|
if (this.props.noWebGl) {
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|
var C = this.props.noWebGl;
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|
-
return _jsx(C, {}
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+
return _jsx(C, {});
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}
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-
return _jsx("div", __assign({ className: 'msp-no-webgl' }, { children: _jsxs("div", { children: [_jsx("p", { children: _jsx("b", { children: "WebGL does not seem to be available." }
|
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|
+
return _jsx("div", __assign({ className: 'msp-no-webgl' }, { children: _jsxs("div", { children: [_jsx("p", { children: _jsx("b", { children: "WebGL does not seem to be available." }) }), _jsx("p", { children: "This can be caused by an outdated browser, graphics card driver issue, or bad weather. Sometimes, just restarting the browser helps." }), _jsxs("p", { children: ["For a list of supported browsers, refer to ", _jsx("a", __assign({ href: 'http://caniuse.com/#feat=webgl', target: '_blank' }, { children: "http://caniuse.com/#feat=webgl" })), "."] })] }) }));
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|
};
|
|
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|
ViewportCanvas.prototype.render = function () {
|
|
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|
if (this.state.noWebGl)
|
|
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|
return this.renderMissing();
|
|
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|
var Logo = this.props.logo;
|
|
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|
-
return _jsxs("div", __assign({ className: this.props.parentClassName || 'msp-viewport', style: this.props.parentStyle }, { children: [_jsx("div", __assign({ className: this.props.hostClassName || 'msp-viewport-host3d', style: this.props.hostStyle, ref: this.container }, { children: _jsx("canvas", { ref: this.canvas }
|
|
50
|
+
return _jsxs("div", __assign({ className: this.props.parentClassName || 'msp-viewport', style: this.props.parentStyle }, { children: [_jsx("div", __assign({ className: this.props.hostClassName || 'msp-viewport-host3d', style: this.props.hostStyle, ref: this.container }, { children: _jsx("canvas", { ref: this.canvas }) })), (this.state.showLogo && Logo) && _jsx(Logo, {})] }));
|
|
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|
};
|
|
52
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|
return ViewportCanvas;
|
|
53
53
|
}(PluginUIComponent));
|