molstar 3.3.0 → 3.5.0
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 +202 -194
- package/build/viewer/embedded.html +43 -43
- package/build/viewer/index.html +106 -106
- package/build/viewer/molstar.js +1 -1
- package/lib/apps/docking-viewer/index.html +36 -36
- 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/apps/viewer/embedded.html +43 -43
- package/lib/apps/viewer/index.html +106 -106
- 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/cif2bcif/converter.js +1 -1
- package/lib/cli/cif2bcif/index.js +4 -4
- 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 +12 -12
- 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/color.d.ts +397 -2
- package/lib/commonjs/extensions/dnatco/confal-pyramids/color.js +223 -131
- package/lib/commonjs/extensions/dnatco/confal-pyramids/property.js +6 -8
- package/lib/commonjs/extensions/dnatco/confal-pyramids/representation.js +2 -2
- package/lib/commonjs/extensions/dnatco/confal-pyramids/util.js +19 -20
- 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 +22 -5
- 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.d.ts +2 -2
- 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.d.ts +0 -1
- package/lib/commonjs/mol-geo/geometry/lines/lines.js +3 -3
- package/lib/commonjs/mol-geo/geometry/mesh/color-smoothing.d.ts +1 -1
- package/lib/commonjs/mol-geo/geometry/mesh/color-smoothing.js +5 -3
- package/lib/commonjs/mol-geo/geometry/mesh/mesh.js +3 -3
- package/lib/commonjs/mol-geo/geometry/points/points.d.ts +1 -1
- 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.d.ts +1 -1
- package/lib/commonjs/mol-geo/geometry/texture-mesh/color-smoothing.js +10 -8
- 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.d.ts +1 -1
- package/lib/commonjs/mol-gl/webgl/context.js +5 -5
- 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/common.d.ts +2 -1
- package/lib/commonjs/mol-math/geometry/common.js +1 -1
- package/lib/commonjs/mol-math/geometry/gaussian-density/cpu.d.ts +1 -1
- package/lib/commonjs/mol-math/geometry/gaussian-density/cpu.js +6 -6
- package/lib/commonjs/mol-math/geometry/gaussian-density/gpu.d.ts +1 -1
- package/lib/commonjs/mol-math/geometry/gaussian-density/gpu.js +8 -8
- package/lib/commonjs/mol-math/geometry/gaussian-density.d.ts +2 -2
- package/lib/commonjs/mol-math/geometry/gaussian-density.js +5 -5
- package/lib/commonjs/mol-math/geometry/molecular-surface.d.ts +2 -1
- package/lib/commonjs/mol-math/geometry/molecular-surface.js +10 -10
- package/lib/commonjs/mol-math/geometry/primitives/box3d.js +2 -1
- package/lib/commonjs/mol-math/geometry/primitives/sphere3d.js +13 -7
- 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 +9 -6
- 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.d.ts +1 -0
- package/lib/commonjs/mol-model/structure/structure/unit/bonds/inter-compute.js +6 -4
- 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 +5 -22
- 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
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- package/lib/mol-plugin-ui/skin/base/components/toast.scss +83 -83
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- package/lib/mol-plugin-ui/skin/colors/blue.scss +23 -23
- package/lib/mol-plugin-ui/skin/colors/dark.scss +23 -23
- package/lib/mol-plugin-ui/skin/colors/light.scss +29 -29
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- package/lib/mol-plugin-ui/skin/light.scss +1 -1
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- 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
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- 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
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- package/lib/mol-repr/structure/visual/bond-inter-unit-cylinder.js +20 -10
- package/lib/mol-repr/structure/visual/bond-inter-unit-line.d.ts +1 -1
- package/lib/mol-repr/structure/visual/bond-inter-unit-line.js +10 -5
- package/lib/mol-repr/structure/visual/bond-intra-unit-cylinder.js +16 -6
- package/lib/mol-repr/structure/visual/bond-intra-unit-line.js +8 -3
- package/lib/mol-repr/structure/visual/carbohydrate-link-cylinder.js +10 -1
- package/lib/mol-repr/structure/visual/carbohydrate-terminal-link-cylinder.js +10 -1
- package/lib/mol-repr/structure/visual/element-point.d.ts +1 -1
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- package/lib/mol-repr/structure/visual/gaussian-density-volume.js +2 -3
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- package/lib/mol-repr/structure/visual/molecular-surface-mesh.js +4 -4
- package/lib/mol-repr/structure/visual/molecular-surface-wireframe.d.ts +1 -1
- package/lib/mol-repr/structure/visual/molecular-surface-wireframe.js +5 -5
- package/lib/mol-repr/structure/visual/util/common.d.ts +1 -3
- package/lib/mol-repr/structure/visual/util/common.js +1 -24
- package/lib/mol-repr/structure/visual/util/element.js +36 -2
- package/lib/mol-repr/structure/visual/util/link.d.ts +13 -3
- package/lib/mol-repr/structure/visual/util/link.js +55 -6
- package/lib/mol-script/language/builder.d.ts +1 -0
- 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 +160 -160
- 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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var HistopyramidReductionSchema = tslib_1.__assign(tslib_1.__assign({}, util_1.QuadSchema), { tInputLevel: (0, schema_1.TextureSpec)('texture', 'rgba', 'float', 'nearest'), tPreviousLevel: (0, schema_1.TextureSpec)('texture', 'rgba', 'float', 'nearest'), uSize: (0, schema_1.UniformSpec)('f'), uTexSize: (0, schema_1.UniformSpec)('f'), uFirst: (0, schema_1.UniformSpec)('b') });
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var values = tslib_1.__assign(tslib_1.__assign({}, util_1.QuadValues), { tInputLevel: mol_util_1.ValueCell.create(inputLevel), tPreviousLevel: mol_util_1.ValueCell.create(previousLevel), uSize: mol_util_1.ValueCell.create(0), uTexSize: mol_util_1.ValueCell.create(0), uFirst: mol_util_1.ValueCell.create(true) });
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var HistopyramidSumSchema = tslib_1.__assign(tslib_1.__assign({}, util_1.QuadSchema), { tTexture: (0, schema_1.TextureSpec)('texture', 'rgba', 'float', 'nearest') });
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var ActiveVoxelsSchema = tslib_1.__assign(tslib_1.__assign({}, util_1.QuadSchema), { tTriCount: (0, schema_1.TextureSpec)('image-uint8', 'alpha', 'ubyte', 'nearest'), tVolumeData: (0, schema_1.TextureSpec)('texture', 'rgba', 'ubyte', 'nearest'), uIsoValue: (0, schema_1.UniformSpec)('f'), uGridDim: (0, schema_1.UniformSpec)('v3'), uGridTexDim: (0, schema_1.UniformSpec)('v3'), uScale: (0, schema_1.UniformSpec)('v2') });
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@@ -35,8 +35,8 @@ function getActiveVoxelsRenderable(ctx, volumeData, gridDim, gridTexDim, isoValu
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function createActiveVoxelsRenderable(ctx, volumeData, gridDim, gridTexDim, isoValue, scale) {
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|
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var schema =
|
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var values = tslib_1.__assign(tslib_1.__assign({}, util_1.QuadValues), { tTriCount: mol_util_1.ValueCell.create((0, tables_1.getTriCount)()), uQuadScale: mol_util_1.ValueCell.create(scale), tVolumeData: mol_util_1.ValueCell.create(volumeData), uIsoValue: mol_util_1.ValueCell.create(isoValue), uGridDim: mol_util_1.ValueCell.create(gridDim), uGridTexDim: mol_util_1.ValueCell.create(gridTexDim), uScale: mol_util_1.ValueCell.create(scale) });
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var schema = tslib_1.__assign({}, ActiveVoxelsSchema);
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var shaderCode = (0, shader_code_1.ShaderCode)('active-voxels', quad_vert_1.quad_vert, active_voxels_frag_1.activeVoxels_frag);
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var renderItem = (0, render_item_1.createComputeRenderItem)(ctx, 'triangles', shaderCode, schema, values);
|
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return (0, renderable_1.createComputeRenderable)(renderItem, values);
|
|
@@ -19,7 +19,7 @@ var quad_vert_1 = require("../../../mol-gl/shader/quad.vert");
|
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var isosurface_frag_1 = require("../../../mol-gl/shader/marching-cubes/isosurface.frag");
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var active_voxels_1 = require("./active-voxels");
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|
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|
|
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var IsosurfaceSchema =
|
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+
var IsosurfaceSchema = tslib_1.__assign(tslib_1.__assign({}, util_1.QuadSchema), { tTriIndices: (0, schema_1.TextureSpec)('image-uint8', 'alpha', 'ubyte', 'nearest'), tActiveVoxelsPyramid: (0, schema_1.TextureSpec)('texture', 'rgba', 'float', 'nearest'), tActiveVoxelsBase: (0, schema_1.TextureSpec)('texture', 'rgba', 'float', 'nearest'), tVolumeData: (0, schema_1.TextureSpec)('texture', 'rgba', 'ubyte', 'nearest'), uIsoValue: (0, schema_1.UniformSpec)('f'), uSize: (0, schema_1.UniformSpec)('f'), uLevels: (0, schema_1.UniformSpec)('f'), uCount: (0, schema_1.UniformSpec)('f'), uInvert: (0, schema_1.UniformSpec)('b'), uGridDim: (0, schema_1.UniformSpec)('v3'), uGridTexDim: (0, schema_1.UniformSpec)('v3'), uGridTransform: (0, schema_1.UniformSpec)('m4'), uScale: (0, schema_1.UniformSpec)('v2'), dPackedGroup: (0, schema_1.DefineSpec)('boolean'), dAxisOrder: (0, schema_1.DefineSpec)('string', ['012', '021', '102', '120', '201', '210']) });
|
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var IsosurfaceName = 'isosurface';
|
|
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|
function getIsosurfaceRenderable(ctx, activeVoxelsPyramid, activeVoxelsBase, volumeData, gridDim, gridTexDim, transform, isoValue, levels, scale, count, invert, packedGroup, axisOrder) {
|
|
25
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|
if (ctx.namedComputeRenderables[IsosurfaceName]) {
|
|
@@ -47,8 +47,8 @@ function getIsosurfaceRenderable(ctx, activeVoxelsPyramid, activeVoxelsBase, vol
|
|
|
47
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|
}
|
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function createIsosurfaceRenderable(ctx, activeVoxelsPyramid, activeVoxelsBase, volumeData, gridDim, gridTexDim, transform, isoValue, levels, scale, count, invert, packedGroup, axisOrder) {
|
|
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// console.log('uSize', Math.pow(2, levels))
|
|
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var values =
|
|
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-
var schema =
|
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+
var values = tslib_1.__assign(tslib_1.__assign({}, util_1.QuadValues), { tTriIndices: mol_util_1.ValueCell.create((0, tables_1.getTriIndices)()), tActiveVoxelsPyramid: mol_util_1.ValueCell.create(activeVoxelsPyramid), tActiveVoxelsBase: mol_util_1.ValueCell.create(activeVoxelsBase), tVolumeData: mol_util_1.ValueCell.create(volumeData), uIsoValue: mol_util_1.ValueCell.create(isoValue), uSize: mol_util_1.ValueCell.create(Math.pow(2, levels)), uLevels: mol_util_1.ValueCell.create(levels), uCount: mol_util_1.ValueCell.create(count), uInvert: mol_util_1.ValueCell.create(invert), uGridDim: mol_util_1.ValueCell.create(gridDim), uGridTexDim: mol_util_1.ValueCell.create(gridTexDim), uGridTransform: mol_util_1.ValueCell.create(transform), uScale: mol_util_1.ValueCell.create(scale), dPackedGroup: mol_util_1.ValueCell.create(packedGroup), dAxisOrder: mol_util_1.ValueCell.create(axisOrder.join('')) });
|
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|
+
var schema = tslib_1.__assign({}, IsosurfaceSchema);
|
|
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|
var shaderCode = (0, shader_code_1.ShaderCode)('isosurface', quad_vert_1.quad_vert, isosurface_frag_1.isosurface_frag, { drawBuffers: 'required' });
|
|
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|
var renderItem = (0, render_item_1.createComputeRenderItem)(ctx, 'triangles', shaderCode, schema, values);
|
|
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|
return (0, renderable_1.createComputeRenderable)(renderItem, values);
|
|
@@ -33,11 +33,11 @@ exports.QuadValues = {
|
|
|
33
33
|
uQuadScale: mol_util_1.ValueCell.create(linear_algebra_1.Vec2.create(1, 1)),
|
|
34
34
|
};
|
|
35
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|
//
|
|
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|
-
var CopySchema =
|
|
36
|
+
var CopySchema = tslib_1.__assign(tslib_1.__assign({}, exports.QuadSchema), { tColor: (0, schema_1.TextureSpec)('texture', 'rgba', 'ubyte', 'nearest'), uTexSize: (0, schema_1.UniformSpec)('v2') });
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var CopyShaderCode = (0, shader_code_1.ShaderCode)('copy', quad_vert_1.quad_vert, copy_frag_1.copy_frag);
|
|
38
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|
function createCopyRenderable(ctx, texture) {
|
|
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|
-
var values =
|
|
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|
-
var schema =
|
|
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|
+
var values = tslib_1.__assign(tslib_1.__assign({}, exports.QuadValues), { tColor: mol_util_1.ValueCell.create(texture), uTexSize: mol_util_1.ValueCell.create(linear_algebra_1.Vec2.create(texture.getWidth(), texture.getHeight())) });
|
|
40
|
+
var schema = tslib_1.__assign({}, CopySchema);
|
|
41
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|
var renderItem = (0, render_item_1.createComputeRenderItem)(ctx, 'triangles', CopyShaderCode, schema, values);
|
|
42
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|
return (0, renderable_1.createComputeRenderable)(renderItem, values);
|
|
43
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|
}
|
|
@@ -12,14 +12,14 @@ var render_item_1 = require("../webgl/render-item");
|
|
|
12
12
|
var schema_1 = require("./schema");
|
|
13
13
|
var shader_code_1 = require("../shader-code");
|
|
14
14
|
var mol_util_1 = require("../../mol-util");
|
|
15
|
-
exports.CylindersSchema =
|
|
15
|
+
exports.CylindersSchema = tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({}, schema_1.BaseSchema), schema_1.SizeSchema), { aGroup: (0, schema_1.AttributeSpec)('float32', 1, 0), aStart: (0, schema_1.AttributeSpec)('float32', 3, 0), aEnd: (0, schema_1.AttributeSpec)('float32', 3, 0), aMapping: (0, schema_1.AttributeSpec)('float32', 3, 0), aScale: (0, schema_1.AttributeSpec)('float32', 1, 0), aCap: (0, schema_1.AttributeSpec)('float32', 1, 0), elements: (0, schema_1.ElementsSpec)('uint32'), padding: (0, schema_1.ValueSpec)('number'), uDoubleSided: (0, schema_1.UniformSpec)('b'), dIgnoreLight: (0, schema_1.DefineSpec)('boolean'), dXrayShaded: (0, schema_1.DefineSpec)('boolean'), uBumpFrequency: (0, schema_1.UniformSpec)('f'), uBumpAmplitude: (0, schema_1.UniformSpec)('f') });
|
|
16
16
|
function CylindersRenderable(ctx, id, values, state, materialId, variants) {
|
|
17
|
-
var schema =
|
|
17
|
+
var schema = tslib_1.__assign(tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({}, schema_1.GlobalUniformSchema), schema_1.GlobalTextureSchema), schema_1.InternalSchema), exports.CylindersSchema);
|
|
18
18
|
var internalValues = {
|
|
19
19
|
uObjectId: mol_util_1.ValueCell.create(id),
|
|
20
20
|
};
|
|
21
21
|
var shaderCode = shader_code_1.CylindersShaderCode;
|
|
22
|
-
var renderItem = (0, render_item_1.createGraphicsRenderItem)(ctx, 'triangles', shaderCode, schema,
|
|
22
|
+
var renderItem = (0, render_item_1.createGraphicsRenderItem)(ctx, 'triangles', shaderCode, schema, tslib_1.__assign(tslib_1.__assign({}, values), internalValues), materialId, variants);
|
|
23
23
|
return (0, renderable_1.createRenderable)(renderItem, values, state);
|
|
24
24
|
}
|
|
25
25
|
exports.CylindersRenderable = CylindersRenderable;
|
|
@@ -12,9 +12,9 @@ var render_item_1 = require("../webgl/render-item");
|
|
|
12
12
|
var schema_1 = require("./schema");
|
|
13
13
|
var shader_code_1 = require("../shader-code");
|
|
14
14
|
var mol_util_1 = require("../../mol-util");
|
|
15
|
-
exports.DirectVolumeSchema =
|
|
15
|
+
exports.DirectVolumeSchema = tslib_1.__assign(tslib_1.__assign({}, schema_1.BaseSchema), { aPosition: (0, schema_1.AttributeSpec)('float32', 3, 0), elements: (0, schema_1.ElementsSpec)('uint32'), uBboxMin: (0, schema_1.UniformSpec)('v3'), uBboxMax: (0, schema_1.UniformSpec)('v3'), uBboxSize: (0, schema_1.UniformSpec)('v3'), uMaxSteps: (0, schema_1.UniformSpec)('i'), uStepScale: (0, schema_1.UniformSpec)('f'), uJumpLength: (0, schema_1.UniformSpec)('f'), uTransform: (0, schema_1.UniformSpec)('m4'), uGridDim: (0, schema_1.UniformSpec)('v3'), tTransferTex: (0, schema_1.TextureSpec)('image-uint8', 'alpha', 'ubyte', 'linear'), uTransferScale: (0, schema_1.UniformSpec)('f'), dGridTexType: (0, schema_1.DefineSpec)('string', ['2d', '3d']), uGridTexDim: (0, schema_1.UniformSpec)('v3'), tGridTex: (0, schema_1.TextureSpec)('texture', 'rgba', 'ubyte', 'linear'), uGridStats: (0, schema_1.UniformSpec)('v4'), uCellDim: (0, schema_1.UniformSpec)('v3'), uCartnToUnit: (0, schema_1.UniformSpec)('m4'), uUnitToCartn: (0, schema_1.UniformSpec)('m4'), dPackedGroup: (0, schema_1.DefineSpec)('boolean'), dAxisOrder: (0, schema_1.DefineSpec)('string', ['012', '021', '102', '120', '201', '210']), dIgnoreLight: (0, schema_1.DefineSpec)('boolean'), dXrayShaded: (0, schema_1.DefineSpec)('boolean') });
|
|
16
16
|
function DirectVolumeRenderable(ctx, id, values, state, materialId, variants) {
|
|
17
|
-
var schema =
|
|
17
|
+
var schema = tslib_1.__assign(tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({}, schema_1.GlobalUniformSchema), schema_1.GlobalTextureSchema), schema_1.InternalSchema), exports.DirectVolumeSchema);
|
|
18
18
|
if (!ctx.isWebGL2) {
|
|
19
19
|
// workaround for webgl1 limitation that loop counters need to be `const`
|
|
20
20
|
schema.uMaxSteps = (0, schema_1.DefineSpec)('number');
|
|
@@ -23,7 +23,7 @@ function DirectVolumeRenderable(ctx, id, values, state, materialId, variants) {
|
|
|
23
23
|
uObjectId: mol_util_1.ValueCell.create(id),
|
|
24
24
|
};
|
|
25
25
|
var shaderCode = shader_code_1.DirectVolumeShaderCode;
|
|
26
|
-
var renderItem = (0, render_item_1.createGraphicsRenderItem)(ctx, 'triangles', shaderCode, schema,
|
|
26
|
+
var renderItem = (0, render_item_1.createGraphicsRenderItem)(ctx, 'triangles', shaderCode, schema, tslib_1.__assign(tslib_1.__assign({}, values), internalValues), materialId, variants);
|
|
27
27
|
return (0, renderable_1.createRenderable)(renderItem, values, state);
|
|
28
28
|
}
|
|
29
29
|
exports.DirectVolumeRenderable = DirectVolumeRenderable;
|
|
@@ -13,14 +13,14 @@ var schema_1 = require("./schema");
|
|
|
13
13
|
var shader_code_1 = require("../shader-code");
|
|
14
14
|
var mol_util_1 = require("../../mol-util");
|
|
15
15
|
var image_1 = require("../../mol-geo/geometry/image/image");
|
|
16
|
-
exports.ImageSchema =
|
|
16
|
+
exports.ImageSchema = tslib_1.__assign(tslib_1.__assign({}, schema_1.BaseSchema), { aGroup: (0, schema_1.AttributeSpec)('float32', 1, 0), aPosition: (0, schema_1.AttributeSpec)('float32', 3, 0), aUv: (0, schema_1.AttributeSpec)('float32', 2, 0), elements: (0, schema_1.ElementsSpec)('uint32'), uImageTexDim: (0, schema_1.UniformSpec)('v2'), tImageTex: (0, schema_1.TextureSpec)('image-uint8', 'rgba', 'ubyte', 'nearest'), tGroupTex: (0, schema_1.TextureSpec)('image-uint8', 'rgba', 'ubyte', 'nearest'), dInterpolation: (0, schema_1.DefineSpec)('string', image_1.InterpolationTypeNames) });
|
|
17
17
|
function ImageRenderable(ctx, id, values, state, materialId, variants) {
|
|
18
|
-
var schema =
|
|
18
|
+
var schema = tslib_1.__assign(tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({}, schema_1.GlobalUniformSchema), schema_1.GlobalTextureSchema), schema_1.InternalSchema), exports.ImageSchema);
|
|
19
19
|
var internalValues = {
|
|
20
20
|
uObjectId: mol_util_1.ValueCell.create(id),
|
|
21
21
|
};
|
|
22
22
|
var shaderCode = shader_code_1.ImageShaderCode;
|
|
23
|
-
var renderItem = (0, render_item_1.createGraphicsRenderItem)(ctx, 'triangles', shaderCode, schema,
|
|
23
|
+
var renderItem = (0, render_item_1.createGraphicsRenderItem)(ctx, 'triangles', shaderCode, schema, tslib_1.__assign(tslib_1.__assign({}, values), internalValues), materialId, variants);
|
|
24
24
|
return (0, renderable_1.createRenderable)(renderItem, values, state);
|
|
25
25
|
}
|
|
26
26
|
exports.ImageRenderable = ImageRenderable;
|
|
@@ -12,14 +12,14 @@ var render_item_1 = require("../webgl/render-item");
|
|
|
12
12
|
var schema_1 = require("./schema");
|
|
13
13
|
var mol_util_1 = require("../../mol-util");
|
|
14
14
|
var shader_code_1 = require("../shader-code");
|
|
15
|
-
exports.LinesSchema =
|
|
15
|
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exports.LinesSchema = tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({}, schema_1.BaseSchema), schema_1.SizeSchema), { aGroup: (0, schema_1.AttributeSpec)('float32', 1, 0), aMapping: (0, schema_1.AttributeSpec)('float32', 2, 0), aStart: (0, schema_1.AttributeSpec)('float32', 3, 0), aEnd: (0, schema_1.AttributeSpec)('float32', 3, 0), elements: (0, schema_1.ElementsSpec)('uint32'), dLineSizeAttenuation: (0, schema_1.DefineSpec)('boolean'), uDoubleSided: (0, schema_1.UniformSpec)('b'), dFlipSided: (0, schema_1.DefineSpec)('boolean') });
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exports.SpheresSchema = tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({}, schema_1.BaseSchema), schema_1.SizeSchema), { aGroup: (0, schema_1.AttributeSpec)('float32', 1, 0), aPosition: (0, schema_1.AttributeSpec)('float32', 3, 0), aMapping: (0, schema_1.AttributeSpec)('float32', 2, 0), elements: (0, schema_1.ElementsSpec)('uint32'), padding: (0, schema_1.ValueSpec)('number'), uDoubleSided: (0, schema_1.UniformSpec)('b'), dIgnoreLight: (0, schema_1.DefineSpec)('boolean'), dXrayShaded: (0, schema_1.DefineSpec)('boolean'), uBumpFrequency: (0, schema_1.UniformSpec)('f'), uBumpAmplitude: (0, schema_1.UniformSpec)('f') });
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var schema = tslib_1.__assign(tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({}, schema_1.GlobalUniformSchema), schema_1.GlobalTextureSchema), schema_1.InternalSchema), exports.SpheresSchema);
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var renderItem = (0, render_item_1.createGraphicsRenderItem)(ctx, 'triangles', shaderCode, schema, tslib_1.__assign(tslib_1.__assign({}, values), internalValues), materialId, variants);
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exports.TextSchema =
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exports.TextSchema = tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({}, schema_1.BaseSchema), schema_1.SizeSchema), { aGroup: (0, schema_1.AttributeSpec)('float32', 1, 0), aPosition: (0, schema_1.AttributeSpec)('float32', 3, 0), aMapping: (0, schema_1.AttributeSpec)('float32', 2, 0), aDepth: (0, schema_1.AttributeSpec)('float32', 1, 0), elements: (0, schema_1.ElementsSpec)('uint32'), aTexCoord: (0, schema_1.AttributeSpec)('float32', 2, 0), tFont: (0, schema_1.TextureSpec)('image-uint8', 'alpha', 'ubyte', 'linear'), padding: (0, schema_1.ValueSpec)('number'), uBorderWidth: (0, schema_1.UniformSpec)('f'), uBorderColor: (0, schema_1.UniformSpec)('v3'), uOffsetX: (0, schema_1.UniformSpec)('f'), uOffsetY: (0, schema_1.UniformSpec)('f'), uOffsetZ: (0, schema_1.UniformSpec)('f'), uBackgroundColor: (0, schema_1.UniformSpec)('v3'), uBackgroundOpacity: (0, schema_1.UniformSpec)('f') });
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var schema = tslib_1.__assign(tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({}, schema_1.GlobalUniformSchema), schema_1.GlobalTextureSchema), schema_1.InternalSchema), exports.TextSchema);
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var renderItem = (0, render_item_1.createGraphicsRenderItem)(ctx, 'triangles', shaderCode, schema, tslib_1.__assign(tslib_1.__assign({}, values), internalValues), materialId, variants);
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@@ -12,14 +12,14 @@ var render_item_1 = require("../webgl/render-item");
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exports.TextureMeshSchema =
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exports.TextureMeshSchema = tslib_1.__assign(tslib_1.__assign({}, schema_1.BaseSchema), { uGeoTexDim: (0, schema_1.UniformSpec)('v2', 'buffered'), tPosition: (0, schema_1.TextureSpec)('texture', 'rgb', 'float', 'nearest'), tGroup: (0, schema_1.TextureSpec)('texture', 'alpha', 'float', 'nearest'), tNormal: (0, schema_1.TextureSpec)('texture', 'rgb', 'float', 'nearest'), dFlatShaded: (0, schema_1.DefineSpec)('boolean'), uDoubleSided: (0, schema_1.UniformSpec)('b'), dFlipSided: (0, schema_1.DefineSpec)('boolean'), dIgnoreLight: (0, schema_1.DefineSpec)('boolean'), dXrayShaded: (0, schema_1.DefineSpec)('boolean'), uBumpFrequency: (0, schema_1.UniformSpec)('f'), uBumpAmplitude: (0, schema_1.UniformSpec)('f'), meta: (0, schema_1.ValueSpec)('unknown') });
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var schema = tslib_1.__assign(tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({}, schema_1.GlobalUniformSchema), schema_1.GlobalTextureSchema), schema_1.InternalSchema), exports.TextureMeshSchema);
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|
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var renderItem = (0, render_item_1.createGraphicsRenderItem)(ctx, 'triangles', shaderCode, schema, tslib_1.__assign(tslib_1.__assign({}, values), internalValues), materialId, variants);
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|
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|
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exports.TextureMeshRenderable = TextureMeshRenderable;
|
|
@@ -56,7 +56,7 @@ var tmpCanvasCtx;
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|
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|
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|
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@@ -167,6 +167,7 @@ var direct_volume_frag_1 = require("./shader/direct-volume.frag");
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|
exports.DirectVolumeShaderCode = ShaderCode('direct-volume', direct_volume_vert_1.directVolume_vert, direct_volume_frag_1.directVolume_frag, { fragDepth: 'optional', drawBuffers: 'optional' }, {}, ignoreDefine);
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|
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|
|
@@ -191,7 +192,7 @@ function getDefinesCode(defines, ignore) {
|
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|
|
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(0, type_helpers_1.assertUnreachable)(v);
|
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|
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|
|
@@ -8,6 +8,7 @@ Object.defineProperty(exports, "__esModule", { value: true });
|
|
|
8
8
|
exports.createElementsBuffer = exports.createAttributeBuffers = exports.createAttributeBuffer = exports.getAttribType = exports.getBufferType = exports.getDataType = exports.getUsageHint = void 0;
|
|
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|
var tslib_1 = require("tslib");
|
|
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|
var id_factory_1 = require("../../mol-util/id-factory");
|
|
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|
+
var type_helpers_1 = require("../../mol-util/type-helpers");
|
|
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|
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|
|
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|
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|
|
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|
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|
|
@@ -51,9 +52,7 @@ function dataTypeFromArray(gl, array) {
|
|
|
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|
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|
|
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|
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|
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|
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|
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|
-
|
|
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|
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throw new Error('Should nevver happen');
|
|
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|
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}
|
|
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|
+
(0, type_helpers_1.assertUnreachable)(array);
|
|
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|
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|
|
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|
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|
|
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|
switch (bufferType) {
|
|
@@ -141,7 +140,7 @@ function createAttributeBuffer(gl, state, extensions, array, itemSize, divisor,
|
|
|
141
140
|
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|
|
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|
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|
|
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|
var _bufferType = buffer._bufferType, _dataType = buffer._dataType, _bpe = buffer._bpe;
|
|
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|
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return
|
|
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|
+
return tslib_1.__assign(tslib_1.__assign({}, buffer), { bind: function (location) {
|
|
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|
gl.bindBuffer(_bufferType, buffer.getBuffer());
|
|
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|
if (itemSize === 16) {
|
|
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|
for (var i = 0; i < 4; ++i) {
|
|
@@ -172,7 +171,7 @@ exports.createAttributeBuffers = createAttributeBuffers;
|
|
|
172
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|
function createElementsBuffer(gl, array, usageHint) {
|
|
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|
if (usageHint === void 0) { usageHint = 'static'; }
|
|
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|
var buffer = createBuffer(gl, array, usageHint, 'elements');
|
|
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|
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return
|
|
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|
+
return tslib_1.__assign(tslib_1.__assign({}, buffer), { bind: function () {
|
|
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|
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|
|
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|
} });
|
|
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|
}
|
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
"use strict";
|
|
2
2
|
/**
|
|
3
|
-
* Copyright (c) 2018-
|
|
3
|
+
* Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
|
|
4
4
|
*
|
|
5
5
|
* @author Alexander Rose <alexander.rose@weirdbyte.de>
|
|
6
6
|
*/
|
|
@@ -221,8 +221,8 @@ function createContext(gl, props) {
|
|
|
221
221
|
}); };
|
|
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|
}
|
|
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|
else {
|
|
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|
-
readPixelsAsync = function (x, y, width, height, buffer) { return
|
|
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|
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return
|
|
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|
+
readPixelsAsync = function (x, y, width, height, buffer) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
|
|
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|
+
return tslib_1.__generator(this, function (_a) {
|
|
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|
readPixels(gl, x, y, width, height, buffer);
|
|
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|
return [2 /*return*/];
|
|
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|
});
|
|
@@ -233,7 +233,7 @@ function createContext(gl, props) {
|
|
|
233
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|
gl: gl,
|
|
234
234
|
isWebGL2: (0, compat_1.isWebGL2)(gl),
|
|
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235
|
get pixelRatio() {
|
|
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|
-
var dpr = (typeof window !== 'undefined') ? window.devicePixelRatio : 1;
|
|
236
|
+
var dpr = (typeof window !== 'undefined') ? (window.devicePixelRatio || 1) : 1;
|
|
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|
return dpr * (props.pixelScale || 1);
|
|
238
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|
},
|
|
239
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|
extensions: extensions,
|
|
@@ -270,7 +270,7 @@ function createContext(gl, props) {
|
|
|
270
270
|
createRenderTarget: function (width, height, depth, type, filter) {
|
|
271
271
|
var renderTarget = (0, render_target_1.createRenderTarget)(gl, resources, width, height, depth, type, filter);
|
|
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|
renderTargets.add(renderTarget);
|
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-
return
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+
return tslib_1.__assign(tslib_1.__assign({}, renderTarget), { destroy: function () {
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renderTarget.destroy();
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renderTargets.delete(renderTarget);
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} });
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@@ -40,7 +40,7 @@ exports.GraphicsRenderVariantsWboit = exports.GraphicsRenderVariants.filter(func
|
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40
40
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var ComputeRenderVariant = { compute: '' };
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41
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exports.ComputeRenderVariants = Object.keys(ComputeRenderVariant);
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42
42
|
function createProgramVariant(ctx, variant, defineValues, shaderCode, schema) {
|
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43
|
-
defineValues =
|
|
43
|
+
defineValues = tslib_1.__assign(tslib_1.__assign({}, defineValues), { dRenderVariant: mol_util_1.ValueCell.create(variant) });
|
|
44
44
|
if (schema.dRenderVariant === undefined) {
|
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45
45
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Object.defineProperty(schema, 'dRenderVariant', { value: (0, schema_1.DefineSpec)('string') });
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46
46
|
}
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|
@@ -21,7 +21,7 @@ function defineValueHash(v) {
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21
21
|
typeof v === 'number' ? (v * 10000) : (0, util_1.hashString)(v);
|
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22
22
|
}
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|
23
23
|
function wrapCached(resourceItem) {
|
|
24
|
-
var wrapped =
|
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24
|
+
var wrapped = tslib_1.__assign(tslib_1.__assign({}, resourceItem.value), { destroy: function () {
|
|
25
25
|
resourceItem.free();
|
|
26
26
|
} });
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|
27
27
|
return wrapped;
|
|
@@ -40,7 +40,7 @@ function createResources(gl, state, stats, extensions) {
|
|
|
40
40
|
function wrap(name, resource) {
|
|
41
41
|
sets[name].add(resource);
|
|
42
42
|
stats.resourceCounts[name] += 1;
|
|
43
|
-
return
|
|
43
|
+
return tslib_1.__assign(tslib_1.__assign({}, resource), { destroy: function () {
|
|
44
44
|
resource.destroy();
|
|
45
45
|
sets[name].delete(resource);
|
|
46
46
|
stats.resourceCounts[name] -= 1;
|
|
@@ -9,6 +9,7 @@ exports.classifyFloatArray = exports.classifyIntArray = void 0;
|
|
|
9
9
|
var tslib_1 = require("tslib");
|
|
10
10
|
var array_encoder_1 = require("./array-encoder");
|
|
11
11
|
var number_1 = require("../../../mol-util/number");
|
|
12
|
+
var type_helpers_1 = require("../../../mol-util/type-helpers");
|
|
12
13
|
function classifyIntArray(xs) {
|
|
13
14
|
return IntClassifier.classify(xs);
|
|
14
15
|
}
|
|
@@ -59,7 +60,7 @@ var IntClassifier;
|
|
|
59
60
|
for (var i = 0, n = data.length; i < n; i++) {
|
|
60
61
|
incSize(info, size, data[i]);
|
|
61
62
|
}
|
|
62
|
-
return
|
|
63
|
+
return tslib_1.__assign(tslib_1.__assign({}, byteSize(size)), { kind: 'pack' });
|
|
63
64
|
}
|
|
64
65
|
function deltaSize(data, info) {
|
|
65
66
|
var size = SizeInfo();
|
|
@@ -68,7 +69,7 @@ var IntClassifier;
|
|
|
68
69
|
incSizeSigned(size, data[i] - prev);
|
|
69
70
|
prev = data[i];
|
|
70
71
|
}
|
|
71
|
-
return
|
|
72
|
+
return tslib_1.__assign(tslib_1.__assign({}, byteSize(size)), { kind: 'delta' });
|
|
72
73
|
}
|
|
73
74
|
function rleSize(data, info) {
|
|
74
75
|
var size = SizeInfo();
|
|
@@ -85,7 +86,7 @@ var IntClassifier;
|
|
|
85
86
|
}
|
|
86
87
|
incSize(info, size, data[data.length - 1]);
|
|
87
88
|
incSize(info, size, run);
|
|
88
|
-
return
|
|
89
|
+
return tslib_1.__assign(tslib_1.__assign({}, byteSize(size)), { kind: 'rle' });
|
|
89
90
|
}
|
|
90
91
|
function deltaRleSize(data, info) {
|
|
91
92
|
var size = SizeInfo();
|
|
@@ -105,7 +106,7 @@ var IntClassifier;
|
|
|
105
106
|
}
|
|
106
107
|
incSizeSigned(size, prevValue);
|
|
107
108
|
incSizeSigned(size, run);
|
|
108
|
-
return
|
|
109
|
+
return tslib_1.__assign(tslib_1.__assign({}, byteSize(size)), { kind: 'delta-rle' });
|
|
109
110
|
}
|
|
110
111
|
function getSize(data) {
|
|
111
112
|
var info = getInfo(data);
|
|
@@ -124,8 +125,8 @@ var IntClassifier;
|
|
|
124
125
|
case 'rle': return array_encoder_1.ArrayEncoding.by(array_encoder_1.ArrayEncoding.runLength).and(array_encoder_1.ArrayEncoding.integerPacking);
|
|
125
126
|
case 'delta': return array_encoder_1.ArrayEncoding.by(array_encoder_1.ArrayEncoding.delta).and(array_encoder_1.ArrayEncoding.integerPacking);
|
|
126
127
|
case 'delta-rle': return array_encoder_1.ArrayEncoding.by(array_encoder_1.ArrayEncoding.delta).and(array_encoder_1.ArrayEncoding.runLength).and(array_encoder_1.ArrayEncoding.integerPacking);
|
|
128
|
+
default: (0, type_helpers_1.assertUnreachable)(size);
|
|
127
129
|
}
|
|
128
|
-
throw new Error('should not happen :)');
|
|
129
130
|
}
|
|
130
131
|
IntClassifier.classify = classify;
|
|
131
132
|
})(IntClassifier || (IntClassifier = {}));
|
|
@@ -159,8 +160,8 @@ var FloatClassifier;
|
|
|
159
160
|
case 'rle': return fp.and(array_encoder_1.ArrayEncoding.runLength).and(array_encoder_1.ArrayEncoding.integerPacking);
|
|
160
161
|
case 'delta': return fp.and(array_encoder_1.ArrayEncoding.delta).and(array_encoder_1.ArrayEncoding.integerPacking);
|
|
161
162
|
case 'delta-rle': return fp.and(array_encoder_1.ArrayEncoding.delta).and(array_encoder_1.ArrayEncoding.runLength).and(array_encoder_1.ArrayEncoding.integerPacking);
|
|
163
|
+
default: (0, type_helpers_1.assertUnreachable)(size);
|
|
162
164
|
}
|
|
163
|
-
throw new Error('should not happen :)');
|
|
164
165
|
}
|
|
165
166
|
FloatClassifier.classify = classify;
|
|
166
167
|
function getMultiplier(mantissaDigits) {
|