molstar 3.2.0 → 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/LICENSE +20 -20
- package/README.md +197 -194
- package/build/viewer/embedded.html +43 -43
- package/build/viewer/index.html +106 -106
- package/build/viewer/molstar.css +1 -1
- package/build/viewer/molstar.js +1 -1
- package/lib/apps/docking-viewer/index.html +36 -36
- package/lib/apps/docking-viewer/index.js +0 -1
- package/lib/apps/docking-viewer/viewport.js +6 -6
- package/lib/apps/viewer/app.d.ts +7 -6
- package/lib/apps/viewer/app.js +2 -1
- package/lib/apps/viewer/embedded.html +43 -43
- package/lib/apps/viewer/index.html +106 -106
- package/lib/apps/viewer/index.js +0 -1
- package/lib/cli/chem-comp-dict/create-ions.js +0 -1
- 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/cli/chem-comp-dict/create-table.js +0 -1
- package/lib/cli/chem-comp-dict/util.js +0 -1
- package/lib/cli/cif2bcif/converter.js +0 -1
- package/lib/cli/cif2bcif/index.js +0 -1
- package/lib/cli/cifschema/index.js +0 -1
- package/lib/cli/cifschema/util/cif-dic.js +0 -1
- package/lib/cli/cifschema/util/generate.js +0 -1
- package/lib/cli/cifschema/util/helper.js +0 -1
- package/lib/cli/cifschema/util/schema.js +0 -1
- package/lib/cli/lipid-params/index.js +0 -1
- package/lib/cli/state-docs/index.js +0 -1
- package/lib/cli/state-docs/pd-to-md.js +0 -1
- package/lib/cli/structure-info/helpers.js +0 -1
- package/lib/cli/structure-info/model.js +0 -1
- package/lib/cli/structure-info/volume.js +0 -1
- package/lib/commonjs/apps/docking-viewer/index.js +12 -13
- package/lib/commonjs/apps/docking-viewer/viewport.js +38 -38
- package/lib/commonjs/apps/viewer/app.d.ts +7 -6
- package/lib/commonjs/apps/viewer/app.js +24 -23
- package/lib/commonjs/apps/viewer/index.js +1 -2
- package/lib/commonjs/cli/chem-comp-dict/create-ions.js +6 -7
- 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 -9
- package/lib/commonjs/cli/chem-comp-dict/util.js +17 -18
- package/lib/commonjs/cli/cif2bcif/converter.js +9 -10
- package/lib/commonjs/cli/cif2bcif/index.js +8 -9
- package/lib/commonjs/cli/cifschema/index.js +27 -28
- package/lib/commonjs/cli/cifschema/util/cif-dic.js +1 -2
- package/lib/commonjs/cli/cifschema/util/generate.js +0 -1
- package/lib/commonjs/cli/cifschema/util/helper.js +0 -1
- package/lib/commonjs/cli/cifschema/util/schema.js +0 -1
- package/lib/commonjs/cli/lipid-params/index.js +9 -10
- package/lib/commonjs/cli/state-docs/index.js +2 -3
- package/lib/commonjs/cli/state-docs/pd-to-md.js +0 -1
- package/lib/commonjs/cli/structure-info/helpers.js +11 -12
- package/lib/commonjs/cli/structure-info/model.js +15 -16
- package/lib/commonjs/cli/structure-info/volume.js +9 -10
- package/lib/commonjs/examples/alpha-orbitals/controls.js +3 -4
- package/lib/commonjs/examples/alpha-orbitals/example-data.js +0 -1
- package/lib/commonjs/examples/alpha-orbitals/index.js +11 -12
- package/lib/commonjs/examples/basic-wrapper/coloring.js +0 -1
- package/lib/commonjs/examples/basic-wrapper/controls.js +2 -3
- package/lib/commonjs/examples/basic-wrapper/custom-theme.js +0 -1
- package/lib/commonjs/examples/basic-wrapper/index.js +22 -23
- package/lib/commonjs/examples/basic-wrapper/superposition.js +8 -9
- package/lib/commonjs/examples/domain-annotation-server/mapping.js +3 -4
- package/lib/commonjs/examples/domain-annotation-server/schemas.js +0 -1
- package/lib/commonjs/examples/domain-annotation-server/server.js +6 -7
- package/lib/commonjs/examples/domain-annotation-server/test.js +3 -4
- package/lib/commonjs/examples/lighting/index.js +8 -9
- package/lib/commonjs/examples/proteopedia-wrapper/annotation.js +2 -3
- package/lib/commonjs/examples/proteopedia-wrapper/coloring.js +0 -1
- package/lib/commonjs/examples/proteopedia-wrapper/helpers.js +4 -5
- package/lib/commonjs/examples/proteopedia-wrapper/index.js +26 -27
- package/lib/commonjs/examples/proteopedia-wrapper/ui/controls.js +2 -3
- package/lib/commonjs/examples/task.js +15 -16
- package/lib/commonjs/extensions/alpha-orbitals/collocation.js +2 -3
- package/lib/commonjs/extensions/alpha-orbitals/data-model.js +1 -2
- package/lib/commonjs/extensions/alpha-orbitals/density.js +2 -3
- package/lib/commonjs/extensions/alpha-orbitals/gpu/compute.js +2 -3
- package/lib/commonjs/extensions/alpha-orbitals/gpu/shader.frag.js +0 -1
- package/lib/commonjs/extensions/alpha-orbitals/orbitals.js +2 -3
- package/lib/commonjs/extensions/alpha-orbitals/spherical-functions.js +0 -1
- package/lib/commonjs/extensions/alpha-orbitals/transforms.js +13 -14
- package/lib/commonjs/extensions/anvil/algorithm.js +13 -14
- package/lib/commonjs/extensions/anvil/behavior.js +14 -15
- package/lib/commonjs/extensions/anvil/prop.js +7 -8
- package/lib/commonjs/extensions/anvil/representation.js +5 -6
- package/lib/commonjs/extensions/cellpack/color/generate.js +0 -1
- package/lib/commonjs/extensions/cellpack/color/provided.js +0 -1
- package/lib/commonjs/extensions/cellpack/curve.js +0 -1
- package/lib/commonjs/extensions/cellpack/data.js +0 -1
- package/lib/commonjs/extensions/cellpack/index.js +1 -2
- package/lib/commonjs/extensions/cellpack/model.js +26 -25
- package/lib/commonjs/extensions/cellpack/preset.js +6 -7
- package/lib/commonjs/extensions/cellpack/property.js +3 -4
- package/lib/commonjs/extensions/cellpack/representation.js +2 -3
- package/lib/commonjs/extensions/cellpack/state.js +13 -14
- package/lib/commonjs/extensions/cellpack/util.js +14 -15
- package/lib/commonjs/extensions/dnatco/confal-pyramids/behavior.js +7 -8
- package/lib/commonjs/extensions/dnatco/confal-pyramids/color.js +0 -1
- package/lib/commonjs/extensions/dnatco/confal-pyramids/property.js +5 -6
- package/lib/commonjs/extensions/dnatco/confal-pyramids/representation.js +2 -3
- package/lib/commonjs/extensions/dnatco/confal-pyramids/types.js +0 -1
- package/lib/commonjs/extensions/dnatco/confal-pyramids/util.js +1 -2
- package/lib/commonjs/extensions/dnatco/index.js +0 -1
- package/lib/commonjs/extensions/g3d/data.js +6 -7
- package/lib/commonjs/extensions/g3d/format.js +14 -15
- package/lib/commonjs/extensions/g3d/model.js +4 -5
- package/lib/commonjs/extensions/geo-export/controls.js +3 -4
- package/lib/commonjs/extensions/geo-export/glb-exporter.js +9 -10
- package/lib/commonjs/extensions/geo-export/index.js +1 -2
- package/lib/commonjs/extensions/geo-export/mesh-exporter.js +12 -13
- package/lib/commonjs/extensions/geo-export/obj-exporter.js +7 -8
- package/lib/commonjs/extensions/geo-export/render-object-exporter.js +0 -1
- package/lib/commonjs/extensions/geo-export/stl-exporter.js +7 -8
- package/lib/commonjs/extensions/geo-export/ui.js +7 -8
- package/lib/commonjs/extensions/geo-export/usdz-exporter.js +9 -10
- package/lib/commonjs/extensions/model-archive/quality-assessment/behavior.js +9 -10
- package/lib/commonjs/extensions/model-archive/quality-assessment/color/plddt.js +4 -5
- package/lib/commonjs/extensions/model-archive/quality-assessment/color/qmean.js +4 -5
- package/lib/commonjs/extensions/model-archive/quality-assessment/prop.js +5 -6
- package/lib/commonjs/extensions/model-export/export.js +4 -5
- package/lib/commonjs/extensions/model-export/index.js +1 -2
- package/lib/commonjs/extensions/model-export/ui.js +5 -6
- package/lib/commonjs/extensions/mp4-export/controls.js +5 -6
- package/lib/commonjs/extensions/mp4-export/encoder.js +4 -5
- package/lib/commonjs/extensions/mp4-export/index.js +1 -2
- package/lib/commonjs/extensions/mp4-export/ui.js +5 -6
- package/lib/commonjs/extensions/pdbe/index.js +0 -1
- package/lib/commonjs/extensions/pdbe/preferred-assembly.js +2 -3
- package/lib/commonjs/extensions/pdbe/struct-ref-domain.js +2 -3
- package/lib/commonjs/extensions/pdbe/structure-quality-report/behavior.js +1 -2
- package/lib/commonjs/extensions/pdbe/structure-quality-report/color.js +0 -1
- package/lib/commonjs/extensions/pdbe/structure-quality-report/prop.js +8 -9
- package/lib/commonjs/extensions/rcsb/assembly-symmetry/behavior.js +17 -18
- package/lib/commonjs/extensions/rcsb/assembly-symmetry/color.js +2 -3
- package/lib/commonjs/extensions/rcsb/assembly-symmetry/prop.js +9 -10
- package/lib/commonjs/extensions/rcsb/assembly-symmetry/representation.js +6 -7
- package/lib/commonjs/extensions/rcsb/assembly-symmetry/ui.js +9 -10
- package/lib/commonjs/extensions/rcsb/graphql/symmetry.gql.js +0 -1
- package/lib/commonjs/extensions/rcsb/graphql/types.d.ts +158 -1
- package/lib/commonjs/extensions/rcsb/graphql/types.js +0 -1
- package/lib/commonjs/extensions/rcsb/index.js +0 -1
- package/lib/commonjs/extensions/rcsb/validation-report/behavior.js +17 -18
- package/lib/commonjs/extensions/rcsb/validation-report/color/density-fit.js +0 -1
- package/lib/commonjs/extensions/rcsb/validation-report/color/geometry-quality.js +0 -1
- package/lib/commonjs/extensions/rcsb/validation-report/color/random-coil-index.js +0 -1
- package/lib/commonjs/extensions/rcsb/validation-report/prop.js +15 -16
- package/lib/commonjs/extensions/rcsb/validation-report/representation.js +22 -6
- 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 -2
- package/lib/commonjs/mol-canvas3d/camera/transition.js +0 -1
- package/lib/commonjs/mol-canvas3d/camera/util.js +1 -2
- package/lib/commonjs/mol-canvas3d/camera.js +2 -2
- package/lib/commonjs/mol-canvas3d/canvas3d.d.ts +3 -1
- package/lib/commonjs/mol-canvas3d/canvas3d.js +46 -39
- package/lib/commonjs/mol-canvas3d/controls/object.js +0 -1
- package/lib/commonjs/mol-canvas3d/controls/trackball.js +1 -2
- package/lib/commonjs/mol-canvas3d/helper/bounding-sphere-helper.js +1 -2
- package/lib/commonjs/mol-canvas3d/helper/camera-helper.js +5 -6
- package/lib/commonjs/mol-canvas3d/helper/handle-helper.js +5 -6
- package/lib/commonjs/mol-canvas3d/helper/helper.js +1 -2
- package/lib/commonjs/mol-canvas3d/helper/interaction-events.js +2 -3
- package/lib/commonjs/mol-canvas3d/passes/draw.js +15 -13
- package/lib/commonjs/mol-canvas3d/passes/fxaa.js +3 -4
- package/lib/commonjs/mol-canvas3d/passes/image.d.ts +1 -0
- package/lib/commonjs/mol-canvas3d/passes/image.js +1 -2
- package/lib/commonjs/mol-canvas3d/passes/marking.js +6 -7
- package/lib/commonjs/mol-canvas3d/passes/multi-sample.d.ts +1 -1
- package/lib/commonjs/mol-canvas3d/passes/multi-sample.js +23 -10
- package/lib/commonjs/mol-canvas3d/passes/passes.js +0 -1
- package/lib/commonjs/mol-canvas3d/passes/pick.js +0 -1
- package/lib/commonjs/mol-canvas3d/passes/postprocessing.d.ts +8 -1
- package/lib/commonjs/mol-canvas3d/passes/postprocessing.js +60 -31
- package/lib/commonjs/mol-canvas3d/passes/smaa.js +9 -10
- package/lib/commonjs/mol-canvas3d/passes/wboit.js +3 -4
- package/lib/commonjs/mol-canvas3d/util.js +2 -3
- package/lib/commonjs/mol-data/db/column-helpers.js +0 -1
- package/lib/commonjs/mol-data/db/column.js +2 -3
- package/lib/commonjs/mol-data/db/database.js +0 -1
- package/lib/commonjs/mol-data/db/table.js +1 -2
- package/lib/commonjs/mol-data/db.js +1 -2
- package/lib/commonjs/mol-data/generic/hash-set.js +0 -1
- package/lib/commonjs/mol-data/generic/linked-list.js +0 -1
- package/lib/commonjs/mol-data/generic/unique-array.js +0 -1
- package/lib/commonjs/mol-data/generic.js +3 -4
- package/lib/commonjs/mol-data/index.js +4 -5
- package/lib/commonjs/mol-data/int/impl/interval.js +0 -1
- package/lib/commonjs/mol-data/int/impl/ordered-set.js +0 -1
- package/lib/commonjs/mol-data/int/impl/segmentation.js +0 -1
- package/lib/commonjs/mol-data/int/impl/sorted-array.js +0 -1
- package/lib/commonjs/mol-data/int/interval.js +1 -2
- package/lib/commonjs/mol-data/int/linked-index.js +0 -1
- package/lib/commonjs/mol-data/int/map.js +0 -1
- package/lib/commonjs/mol-data/int/ordered-set.js +1 -2
- package/lib/commonjs/mol-data/int/segmentation.js +1 -2
- package/lib/commonjs/mol-data/int/sorted-array.js +1 -2
- package/lib/commonjs/mol-data/int/sorted-ranges.js +0 -1
- package/lib/commonjs/mol-data/int/tuple.js +0 -1
- package/lib/commonjs/mol-data/int.js +0 -1
- package/lib/commonjs/mol-data/iterator.js +0 -1
- package/lib/commonjs/mol-data/util/array.js +0 -1
- package/lib/commonjs/mol-data/util/buckets.js +0 -1
- package/lib/commonjs/mol-data/util/chunked-array.js +0 -1
- package/lib/commonjs/mol-data/util/combination.js +0 -1
- package/lib/commonjs/mol-data/util/equivalence-classes.js +0 -1
- package/lib/commonjs/mol-data/util/grouping.js +0 -1
- package/lib/commonjs/mol-data/util/hash-functions.js +0 -1
- package/lib/commonjs/mol-data/util/interval-iterator.js +0 -1
- package/lib/commonjs/mol-data/util/sort.js +0 -1
- package/lib/commonjs/mol-data/util.js +7 -8
- package/lib/commonjs/mol-geo/geometry/base.js +0 -1
- package/lib/commonjs/mol-geo/geometry/clipping-data.js +0 -1
- package/lib/commonjs/mol-geo/geometry/color-data.js +0 -1
- package/lib/commonjs/mol-geo/geometry/cylinders/cylinders-builder.js +0 -1
- package/lib/commonjs/mol-geo/geometry/cylinders/cylinders.d.ts +2 -2
- package/lib/commonjs/mol-geo/geometry/cylinders/cylinders.js +3 -4
- package/lib/commonjs/mol-geo/geometry/direct-volume/direct-volume.js +3 -4
- package/lib/commonjs/mol-geo/geometry/direct-volume/transfer-function.js +1 -2
- package/lib/commonjs/mol-geo/geometry/geometry.js +0 -1
- package/lib/commonjs/mol-geo/geometry/image/image.js +3 -4
- package/lib/commonjs/mol-geo/geometry/lines/lines-builder.js +0 -1
- package/lib/commonjs/mol-geo/geometry/lines/lines.d.ts +2 -1
- package/lib/commonjs/mol-geo/geometry/lines/lines.js +4 -5
- package/lib/commonjs/mol-geo/geometry/marker-data.js +0 -1
- package/lib/commonjs/mol-geo/geometry/mesh/builder/axes.js +0 -1
- package/lib/commonjs/mol-geo/geometry/mesh/builder/box.js +0 -1
- package/lib/commonjs/mol-geo/geometry/mesh/builder/cylinder.js +0 -1
- package/lib/commonjs/mol-geo/geometry/mesh/builder/ellipsoid.js +0 -1
- package/lib/commonjs/mol-geo/geometry/mesh/builder/ribbon.js +0 -1
- package/lib/commonjs/mol-geo/geometry/mesh/builder/sheet.js +0 -1
- package/lib/commonjs/mol-geo/geometry/mesh/builder/sphere.js +0 -1
- package/lib/commonjs/mol-geo/geometry/mesh/builder/tube.js +0 -1
- package/lib/commonjs/mol-geo/geometry/mesh/color-smoothing.js +0 -1
- package/lib/commonjs/mol-geo/geometry/mesh/laplacian-smoothing.js +0 -1
- package/lib/commonjs/mol-geo/geometry/mesh/mesh-builder.js +0 -1
- package/lib/commonjs/mol-geo/geometry/mesh/mesh.js +3 -4
- package/lib/commonjs/mol-geo/geometry/overpaint-data.js +0 -1
- package/lib/commonjs/mol-geo/geometry/picking.js +0 -1
- package/lib/commonjs/mol-geo/geometry/points/points-builder.js +0 -1
- package/lib/commonjs/mol-geo/geometry/points/points.d.ts +1 -1
- package/lib/commonjs/mol-geo/geometry/points/points.js +3 -4
- package/lib/commonjs/mol-geo/geometry/size-data.js +1 -2
- package/lib/commonjs/mol-geo/geometry/spheres/spheres-builder.js +0 -1
- package/lib/commonjs/mol-geo/geometry/spheres/spheres.js +3 -4
- package/lib/commonjs/mol-geo/geometry/substance-data.js +0 -1
- package/lib/commonjs/mol-geo/geometry/text/font-atlas.js +1 -2
- package/lib/commonjs/mol-geo/geometry/text/text-builder.js +3 -3
- package/lib/commonjs/mol-geo/geometry/text/text.js +3 -4
- package/lib/commonjs/mol-geo/geometry/texture-mesh/color-smoothing.js +4 -5
- package/lib/commonjs/mol-geo/geometry/texture-mesh/texture-mesh.js +3 -4
- package/lib/commonjs/mol-geo/geometry/transform-data.js +0 -1
- package/lib/commonjs/mol-geo/geometry/transparency-data.js +0 -1
- package/lib/commonjs/mol-geo/primitive/box.js +0 -1
- package/lib/commonjs/mol-geo/primitive/cage.js +0 -1
- package/lib/commonjs/mol-geo/primitive/circle.js +1 -2
- package/lib/commonjs/mol-geo/primitive/cylinder.js +1 -2
- package/lib/commonjs/mol-geo/primitive/dodecahedron.js +0 -1
- package/lib/commonjs/mol-geo/primitive/icosahedron.js +0 -1
- package/lib/commonjs/mol-geo/primitive/octahedron.js +0 -1
- package/lib/commonjs/mol-geo/primitive/plane.js +0 -1
- package/lib/commonjs/mol-geo/primitive/polygon.js +0 -1
- package/lib/commonjs/mol-geo/primitive/polyhedron.js +1 -2
- package/lib/commonjs/mol-geo/primitive/primitive.js +0 -1
- package/lib/commonjs/mol-geo/primitive/prism.js +1 -2
- package/lib/commonjs/mol-geo/primitive/pyramid.js +0 -1
- package/lib/commonjs/mol-geo/primitive/sphere.js +0 -1
- package/lib/commonjs/mol-geo/primitive/spiked-ball.js +0 -1
- package/lib/commonjs/mol-geo/primitive/star.js +1 -2
- package/lib/commonjs/mol-geo/primitive/tetrahedron.js +0 -1
- package/lib/commonjs/mol-geo/primitive/torus.js +1 -2
- package/lib/commonjs/mol-geo/primitive/wedge.js +0 -1
- package/lib/commonjs/mol-geo/util/location-iterator.js +0 -1
- package/lib/commonjs/mol-geo/util/marching-cubes/algorithm.js +9 -10
- package/lib/commonjs/mol-geo/util/marching-cubes/builder.js +0 -1
- package/lib/commonjs/mol-geo/util/marching-cubes/tables.js +0 -1
- package/lib/commonjs/mol-geo/util.js +0 -1
- package/lib/commonjs/mol-gl/commit-queue.js +0 -1
- package/lib/commonjs/mol-gl/compute/grid3d.js +5 -6
- package/lib/commonjs/mol-gl/compute/histogram-pyramid/reduction.js +3 -4
- package/lib/commonjs/mol-gl/compute/histogram-pyramid/sum.js +3 -4
- package/lib/commonjs/mol-gl/compute/marching-cubes/active-voxels.js +3 -4
- package/lib/commonjs/mol-gl/compute/marching-cubes/isosurface.js +3 -4
- package/lib/commonjs/mol-gl/compute/marching-cubes/tables.js +0 -1
- package/lib/commonjs/mol-gl/compute/util.js +3 -4
- package/lib/commonjs/mol-gl/object3d.js +0 -1
- package/lib/commonjs/mol-gl/render-object.js +0 -1
- package/lib/commonjs/mol-gl/renderable/cylinders.js +3 -4
- package/lib/commonjs/mol-gl/renderable/direct-volume.js +3 -4
- package/lib/commonjs/mol-gl/renderable/image.js +3 -4
- package/lib/commonjs/mol-gl/renderable/lines.js +3 -4
- package/lib/commonjs/mol-gl/renderable/mesh.js +3 -4
- package/lib/commonjs/mol-gl/renderable/points.js +3 -4
- package/lib/commonjs/mol-gl/renderable/schema.js +1 -2
- package/lib/commonjs/mol-gl/renderable/spheres.js +3 -4
- package/lib/commonjs/mol-gl/renderable/text.js +3 -4
- package/lib/commonjs/mol-gl/renderable/texture-mesh.js +3 -4
- package/lib/commonjs/mol-gl/renderable/util.js +1 -2
- package/lib/commonjs/mol-gl/renderable.js +0 -1
- package/lib/commonjs/mol-gl/renderer.js +3 -5
- package/lib/commonjs/mol-gl/scene.d.ts +2 -1
- package/lib/commonjs/mol-gl/scene.js +14 -3
- package/lib/commonjs/mol-gl/shader/chunks/apply-fog.glsl.js +0 -1
- package/lib/commonjs/mol-gl/shader/chunks/apply-interior-color.glsl.js +0 -1
- package/lib/commonjs/mol-gl/shader/chunks/apply-light-color.glsl.js +0 -1
- package/lib/commonjs/mol-gl/shader/chunks/apply-marker-color.glsl.js +0 -1
- package/lib/commonjs/mol-gl/shader/chunks/assign-clipping-varying.glsl.js +0 -1
- package/lib/commonjs/mol-gl/shader/chunks/assign-color-varying.glsl.js +0 -1
- package/lib/commonjs/mol-gl/shader/chunks/assign-group.glsl.js +0 -1
- package/lib/commonjs/mol-gl/shader/chunks/assign-marker-varying.glsl.js +0 -1
- package/lib/commonjs/mol-gl/shader/chunks/assign-material-color.glsl.js +0 -1
- package/lib/commonjs/mol-gl/shader/chunks/assign-position.glsl.js +0 -1
- package/lib/commonjs/mol-gl/shader/chunks/assign-size.glsl.js +0 -1
- package/lib/commonjs/mol-gl/shader/chunks/check-picking-alpha.glsl.js +0 -1
- package/lib/commonjs/mol-gl/shader/chunks/clip-instance.glsl.js +0 -1
- package/lib/commonjs/mol-gl/shader/chunks/clip-pixel.glsl.js +0 -1
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- package/lib/mol-script/script/mol-script/script-macro.js +0 -1
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- package/lib/mol-task/execution/runtime-context.js +0 -1
- package/lib/mol-task/execution/synchronous.js +0 -1
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- package/lib/mol-task/util/user-timing.js +0 -1
- package/lib/mol-theme/clipping.js +0 -1
- package/lib/mol-theme/color/atom-id.js +0 -1
- package/lib/mol-theme/color/carbohydrate-symbol.js +0 -1
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- package/lib/mol-theme/color/hydrophobicity.js +2 -3
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- package/lib/mol-theme/color/model-index.js +0 -1
- package/lib/mol-theme/color/molecule-type.js +0 -1
- package/lib/mol-theme/color/occupancy.js +0 -1
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entries.push((0, jsx_runtime_1.jsxs)("li", { children: [(0, jsx_runtime_1.jsx)("div", { className: 'msp-log-entry-badge msp-log-entry-' + e.type }), (0, jsx_runtime_1.jsx)("div", tslib_1.__assign({ className: 'msp-log-timestamp' }, { children: (0, mol_util_1.formatTime)(e.timestamp) })), (0, jsx_runtime_1.jsx)("div", tslib_1.__assign({ className: 'msp-log-entry' }, { children: e.message }))] }, o++));
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|
@@ -13,7 +13,7 @@ var int_1 = require("../../mol-data/int");
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var names_1 = require("../../mol-util/color/names");
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var marker_action_1 = require("../../mol-util/marker-action");
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var HeteroSequenceWrapper = /** @class */ (function (_super) {
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tslib_1.__extends(HeteroSequenceWrapper, _super);
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function HeteroSequenceWrapper(data) {
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var sequence = [];
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@@ -103,4 +103,3 @@ var HeteroSequenceWrapper = /** @class */ (function (_super) {
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return HeteroSequenceWrapper;
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}(wrapper_1.SequenceWrapper));
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exports.HeteroSequenceWrapper = HeteroSequenceWrapper;
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//# sourceMappingURL=hetero.js.map
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var names_1 = require("../../mol-util/color/names");
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var marker_action_1 = require("../../mol-util/marker-action");
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var PolymerSequenceWrapper = /** @class */ (function (_super) {
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tslib_1.__extends(PolymerSequenceWrapper, _super);
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function PolymerSequenceWrapper(data) {
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var _this = this;
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var l = structure_1.StructureElement.Location.create(data.structure, data.units[0], data.units[0].elements[0]);
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return true;
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}
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//# sourceMappingURL=polymer.js.map
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* @author David Sehnal <david.sehnal@gmail.com>
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*/
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import * as React from 'react';
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import {
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import { StructureElement } from '../../mol-model/structure';
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import { ButtonsType, ModifiersKeys } from '../../mol-util/input/input-observer';
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import { PluginUIComponent } from '../base';
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import { SequenceWrapper } from './wrapper';
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import { StructureElement } from '../../mol-model/structure';
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declare type SequenceProps = {
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sequenceWrapper: SequenceWrapper.Any;
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sequenceNumberPeriod?: number;
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* @author Alexander Rose <alexander.rose@weirdbyte.de>
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* @author David Sehnal <david.sehnal@gmail.com>
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*/
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var React =
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var base_1 = require("../base");
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var input_observer_1 = require("../../mol-util/input/input-observer");
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var structure_1 = require("../../mol-model/structure");
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var React = tslib_1.__importStar(require("react"));
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var rxjs_1 = require("rxjs");
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var operators_1 = require("rxjs/operators");
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var int_1 = require("../../mol-data/int");
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var structure_1 = require("../../mol-model/structure");
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var representation_1 = require("../../mol-repr/representation");
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var input_observer_1 = require("../../mol-util/input/input-observer");
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var base_1 = require("../base");
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/** Note, if this is changed, the CSS for `msp-sequence-number` needs adjustment too */
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var MaxSequenceNumberSize = 5;
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// TODO: this is somewhat inefficient and should be done using a canvas.
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var Sequence = /** @class */ (function (_super) {
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tslib_1.__extends(Sequence, _super);
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function Sequence() {
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var _this = _super !== null && _super.apply(this, arguments) || this;
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_this.parentDiv = React.createRef();
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@@ -96,7 +96,7 @@ var Sequence = /** @class */ (function (_super) {
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_this.lastMouseOverSeqIdx = seqIdx;
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if (_this.mouseDownLoci !== undefined) {
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var loci = _this.getLoci(seqIdx);
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_this.hover(loci, 0 /* None */, 0 /* None */,
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_this.hover(loci, 0 /* None */, 0 /* None */, tslib_1.__assign(tslib_1.__assign({}, modifiers), { shift: true }));
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}
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else {
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_this.highlightQueue.next({ seqIdx: seqIdx, buttons: buttons, button: button, modifiers: modifiers });
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var _this = this;
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this.plugin.managers.interactivity.lociHighlights.addProvider(this.lociHighlightProvider);
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this.plugin.managers.interactivity.lociSelects.addProvider(this.lociSelectionProvider);
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this.subscribe((0, operators_1.
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this.subscribe(this.highlightQueue.pipe((0, operators_1.throttleTime)(3 * 16.666, void 0, { leading: true, trailing: true })), function (e) {
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var loci = _this.getLoci(e.seqIdx < 0 ? void 0 : e.seqIdx);
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_this.hover(loci, e.buttons, e.button, e.modifiers);
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});
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// this.updateMarker()
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};
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Sequence.prototype.componentWillUnmount = function () {
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_super.prototype.componentWillUnmount.call(this);
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@@ -191,7 +190,7 @@ var Sequence = /** @class */ (function (_super) {
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: this.props.sequenceWrapper.residueClass(seqIdx);
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};
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Sequence.prototype.residue = function (seqIdx, label, marker) {
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return (0, jsx_runtime_1.jsx)("span",
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return (0, jsx_runtime_1.jsx)("span", tslib_1.__assign({ "data-seqid": seqIdx, style: { backgroundColor: this.getBackgroundColor(marker) }, className: this.getResidueClass(seqIdx, label) }, { children: "\u200B".concat(label, "\u200B") }), seqIdx);
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};
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Sequence.prototype.getSequenceNumberClass = function (seqIdx, seqNum, label) {
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var classList = ['msp-sequence-number'];
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};
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Sequence.prototype.getSequenceNumberSpan = function (seqIdx, label) {
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var seqNum = this.getSequenceNumber(seqIdx);
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return (0, jsx_runtime_1.jsx)("span",
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return (0, jsx_runtime_1.jsx)("span", tslib_1.__assign({ className: this.getSequenceNumberClass(seqIdx, seqNum, label) }, { children: this.padSeqNum(seqNum) }), "marker-".concat(seqIdx));
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};
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Sequence.prototype.updateMarker = function () {
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if (!this.parentDiv.current)
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// calling .updateMarker here is neccesary to ensure existing
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// residue spans are updated as react won't update them
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this.updateMarker();
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return (0, jsx_runtime_1.jsx)("div",
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return (0, jsx_runtime_1.jsx)("div", tslib_1.__assign({ className: 'msp-sequence-wrapper', onContextMenu: this.contextMenu, onMouseDown: this.mouseDown, onMouseUp: this.mouseUp, onMouseMove: this.mouseMove, onMouseLeave: this.mouseLeave, ref: this.parentDiv }, { children: elems }));
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};
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return Sequence;
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}(base_1.PluginUIComponent));
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exports.Sequence = Sequence;
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//# sourceMappingURL=sequence.js.map
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@@ -9,7 +9,7 @@ var jsx_runtime_1 = require("react/jsx-runtime");
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*/
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var React =
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var React = tslib_1.__importStar(require("react"));
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var base_1 = require("./base");
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var objects_1 = require("../mol-plugin-state/objects");
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var sequence_1 = require("./sequence/sequence");
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}
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var SequenceViewModeParam = param_definition_1.ParamDefinition.Select('single', [['single', 'Chain'], ['polymers', 'Polymers'], ['all', 'Everything']]);
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var SequenceView = /** @class */ (function (_super) {
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tslib_1.__extends(SequenceView, _super);
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function SequenceView() {
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var _this = _super !== null && _super.apply(this, arguments) || this;
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_this.state = { structureOptions: { options: [], all: [] }, structure: structure_1.Structure.Empty, structureRef: '', modelEntityId: '', chainGroupId: -1, operatorKey: '', mode: 'single' };
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_this.setParamProps = function (p) {
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var state =
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var state = tslib_1.__assign({}, _this.state);
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switch (p.name) {
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case 'mode':
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state.mode = p.value;
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});
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SequenceView.prototype.render = function () {
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if (this.getStructure(this.state.structureRef) === structure_1.Structure.Empty) {
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return (0, jsx_runtime_1.jsx)("div",
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return (0, jsx_runtime_1.jsx)("div", tslib_1.__assign({ className: 'msp-sequence' }, { children: (0, jsx_runtime_1.jsxs)("div", tslib_1.__assign({ className: 'msp-sequence-select' }, { children: [(0, jsx_runtime_1.jsx)(icons_1.Icon, { svg: icons_1.HelpOutlineSvg, style: { cursor: 'help', position: 'absolute', right: 0, top: 0 }, title: 'Shows a sequence of one or more chains. Use the controls to alter selection.' }), (0, jsx_runtime_1.jsx)("span", { children: "Sequence" }), (0, jsx_runtime_1.jsx)("span", tslib_1.__assign({ style: { fontWeight: 'normal' } }, { children: "No structure available" }))] })) }));
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}
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var params = this.params;
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var values = this.values;
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var sequenceWrappers = this.getSequenceWrappers(params);
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return (0, jsx_runtime_1.jsxs)("div",
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return (0, jsx_runtime_1.jsxs)("div", tslib_1.__assign({ className: 'msp-sequence' }, { children: [(0, jsx_runtime_1.jsxs)("div", tslib_1.__assign({ className: 'msp-sequence-select' }, { children: [(0, jsx_runtime_1.jsx)(icons_1.Icon, { svg: icons_1.HelpOutlineSvg, style: { cursor: 'help', position: 'absolute', right: 0, top: 0 }, title: 'This shows a single sequence. Use the controls to show a different sequence.' }), (0, jsx_runtime_1.jsx)("span", { children: "Sequence of" }), (0, jsx_runtime_1.jsx)(parameters_1.PureSelectControl, { title: "[Structure] ".concat(param_definition_1.ParamDefinition.optionLabel(params.structure, values.structure)), param: params.structure, name: 'structure', value: values.structure, onChange: this.setParamProps }), (0, jsx_runtime_1.jsx)(parameters_1.PureSelectControl, { title: "[Mode]", param: SequenceViewModeParam, name: 'mode', value: values.mode, onChange: this.setParamProps }), values.mode === 'single' && (0, jsx_runtime_1.jsx)(parameters_1.PureSelectControl, { title: "[Entity] ".concat(param_definition_1.ParamDefinition.optionLabel(params.entity, values.entity)), param: params.entity, name: 'entity', value: values.entity, onChange: this.setParamProps }), values.mode === 'single' && (0, jsx_runtime_1.jsx)(parameters_1.PureSelectControl, { title: "[Chain] ".concat(param_definition_1.ParamDefinition.optionLabel(params.chain, values.chain)), param: params.chain, name: 'chain', value: values.chain, onChange: this.setParamProps }), params.operator.options.length > 1 && (0, jsx_runtime_1.jsx)(jsx_runtime_1.Fragment, { children: (0, jsx_runtime_1.jsx)(parameters_1.PureSelectControl, { title: "[Instance] ".concat(param_definition_1.ParamDefinition.optionLabel(params.operator, values.operator)), param: params.operator, name: 'operator', value: values.operator, onChange: this.setParamProps }) })] })), (0, jsx_runtime_1.jsx)(NonEmptySequenceWrapper, { children: sequenceWrappers.map(function (s, i) {
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var elem = typeof s.wrapper === 'string'
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? (0, jsx_runtime_1.jsx)("div",
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? (0, jsx_runtime_1.jsx)("div", tslib_1.__assign({ className: 'msp-sequence-wrapper' }, { children: s.wrapper }), i)
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: (0, jsx_runtime_1.jsx)(sequence_1.Sequence, { sequenceWrapper: s.wrapper }, i);
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if (values.mode === 'single')
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return elem;
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return (0, jsx_runtime_1.jsxs)(React.Fragment, { children: [(0, jsx_runtime_1.jsx)("div",
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}) }
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return (0, jsx_runtime_1.jsxs)(React.Fragment, { children: [(0, jsx_runtime_1.jsx)("div", tslib_1.__assign({ className: 'msp-sequence-chain-label' }, { children: s.label })), elem] }, i);
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}) })] }));
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};
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return SequenceView;
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}(base_1.PluginUIComponent));
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exports.SequenceView = SequenceView;
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function NonEmptySequenceWrapper(_a) {
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var children = _a.children;
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return (0, jsx_runtime_1.jsx)("div",
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return (0, jsx_runtime_1.jsx)("div", tslib_1.__assign({ className: 'msp-sequence-wrapper-non-empty' }, { children: children }));
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}
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//# sourceMappingURL=sequence.js.map
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var transformers_1 = require("../mol-plugin/behavior/dynamic/volume-streaming/transformers");
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var spec_1 = require("../mol-plugin/spec");
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var volume_1 = require("./custom/volume");
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var DefaultPluginUISpec = function () { return (
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var DefaultPluginUISpec = function () { return (tslib_1.__assign(tslib_1.__assign({}, (0, spec_1.DefaultPluginSpec)()), { customParamEditors: [
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[transformers_1.CreateVolumeStreamingBehavior, volume_1.VolumeStreamingCustomControls]
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] })); };
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exports.DefaultPluginUISpec = DefaultPluginUISpec;
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//# sourceMappingURL=spec.js.map
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var icons_1 = require("../controls/icons");
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var apply_action_1 = require("./apply-action");
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var StateObjectActions = /** @class */ (function (_super) {
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tslib_1.__extends(StateObjectActions, _super);
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function StateObjectActions() {
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return _super !== null && _super.apply(this, arguments) || this;
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}
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return null;
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var def = cell.transform.transformer.definition;
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var display = cell.obj ? cell.obj.label : (def.display && def.display.name) || def.name;
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return (0, jsx_runtime_1.jsxs)("div",
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return (0, jsx_runtime_1.jsxs)("div", tslib_1.__assign({ className: 'msp-state-actions' }, { children: [!this.props.hideHeader && (0, jsx_runtime_1.jsxs)("div", tslib_1.__assign({ className: 'msp-section-header' }, { children: [(0, jsx_runtime_1.jsx)(icons_1.Icon, { svg: icons_1.CodeSvg }), " ", "Actions (".concat(display, ")")] })), actions.map(function (act, i) { return (0, jsx_runtime_1.jsx)(apply_action_1.ApplyActionControl, { state: state, action: act, nodeRef: ref, initiallyCollapsed: i === 0 ? !_this.props.alwaysExpandFirst && _this.props.initiallyCollapsed : _this.props.initiallyCollapsed }, "".concat(act.id)); })] }));
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};
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return StateObjectActions;
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}(base_1.PluginUIComponent));
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exports.StateObjectActions = StateObjectActions;
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//# sourceMappingURL=actions.js.map
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var common_1 = require("../controls/common");
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var icons_1 = require("../controls/icons");
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var AnimationControls = /** @class */ (function (_super) {
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tslib_1.__extends(AnimationControls, _super);
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function AnimationControls() {
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var _this = _super !== null && _super.apply(this, arguments) || this;
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_this.updateParams = function (p) {
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return null;
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var isDisabled = anim.state.animationState === 'playing';
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var canApply = (_b = (_a = anim.current.anim).canApply) === null || _b === void 0 ? void 0 : _b.call(_a, this.plugin);
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return (0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)(parameters_1.ParameterControls, { params: anim.getParams(), values: anim.state.params, onChange: this.updateParams, isDisabled: isDisabled }
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return (0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)(parameters_1.ParameterControls, { params: anim.getParams(), values: anim.state.params, onChange: this.updateParams, isDisabled: isDisabled }), (0, jsx_runtime_1.jsx)(parameters_1.ParameterControls, { params: anim.current.params, values: anim.current.paramValues, onChange: this.updateCurrentParams, isDisabled: isDisabled }), (0, jsx_runtime_1.jsx)("div", tslib_1.__assign({ className: 'msp-flex-row' }, { children: (0, jsx_runtime_1.jsx)(common_1.Button, tslib_1.__assign({ icon: anim.state.animationState !== 'playing' ? void 0 : icons_1.PlayArrowSvg, onClick: this.startOrStop, disabled: canApply !== void 0 && canApply.canApply === false }, { children: anim.state.animationState === 'playing' ? 'Stop' : canApply === void 0 || canApply.canApply ? 'Start' : canApply.reason || 'Start' })) }))] });
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};
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52
52
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return AnimationControls;
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53
53
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}(base_1.PluginUIComponent));
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54
54
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exports.AnimationControls = AnimationControls;
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55
|
-
//# sourceMappingURL=animation.js.map
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@@ -12,7 +12,7 @@ var memoize_1 = require("../../mol-util/memoize");
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12
12
|
var common_1 = require("./common");
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13
13
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var param_definition_1 = require("../../mol-util/param-definition");
|
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14
14
|
var ApplyActionControl = /** @class */ (function (_super) {
|
|
15
|
-
|
|
15
|
+
tslib_1.__extends(ApplyActionControl, _super);
|
|
16
16
|
function ApplyActionControl() {
|
|
17
17
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var _this = _super !== null && _super.apply(this, arguments) || this;
|
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18
18
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_this._getInfo = (0, memoize_1.memoizeLatest)(function (t, v) { return common_1.StateTransformParameters.infoFromAction(_this.plugin, _this.props.state, _this.props.action, _this.props.nodeRef); });
|
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@@ -56,4 +56,3 @@ var ApplyActionControl = /** @class */ (function (_super) {
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56
56
|
return ApplyActionControl;
|
|
57
57
|
}(common_1.TransformControlBase));
|
|
58
58
|
exports.ApplyActionControl = ApplyActionControl;
|
|
59
|
-
//# sourceMappingURL=apply-action.js.map
|