genome-spy-python 0.1.0__py3-none-any.whl

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Files changed (64) hide show
  1. genome_spy/__init__.py +199 -0
  2. genome_spy/_chart_authoring.py +231 -0
  3. genome_spy/_conditions.py +72 -0
  4. genome_spy/_embed.py +87 -0
  5. genome_spy/_expressions.py +271 -0
  6. genome_spy/_parameters.py +267 -0
  7. genome_spy/_render.py +207 -0
  8. genome_spy/_utils.py +75 -0
  9. genome_spy/_widget.py +262 -0
  10. genome_spy/api.py +198 -0
  11. genome_spy/arrow.py +155 -0
  12. genome_spy/channels.py +193 -0
  13. genome_spy/chart.py +1240 -0
  14. genome_spy/data.py +56 -0
  15. genome_spy/data_transformers.py +267 -0
  16. genome_spy/datasets/__init__.py +189 -0
  17. genome_spy/datasets/_airway.py +219 -0
  18. genome_spy/datasets/_annotations.py +37 -0
  19. genome_spy/datasets/_gistic.py +43 -0
  20. genome_spy/datasets/_grammar.py +66 -0
  21. genome_spy/datasets/_hapmap.py +180 -0
  22. genome_spy/datasets/_mutation.py +289 -0
  23. genome_spy/datasets/_oncoprint.py +523 -0
  24. genome_spy/datasets/data/airway_metadata.csv +9 -0
  25. genome_spy/datasets/data/airway_scaledcounts.csv +38695 -0
  26. genome_spy/datasets/data/brca.maf.gz +0 -0
  27. genome_spy/datasets/data/hapmap_gwas.csv +14413 -0
  28. genome_spy/datasets/data/mutation_impact_reference.json +27 -0
  29. genome_spy/datasets/data/oncoprint_dataset3.json +266 -0
  30. genome_spy/datasets/data/p53_sequence_comparison.json.gz +0 -0
  31. genome_spy/datasets/data/pik3ca_mutations.json +1 -0
  32. genome_spy/datasets/data/pik3ca_tcga_brca_lollipop.json +38 -0
  33. genome_spy/datasets/data/refseq_gene_bodies.csv.gz +0 -0
  34. genome_spy/datasets/data/tal1_alphagenome_reference.json.gz +0 -0
  35. genome_spy/datasets/data/tcga.tsv +146 -0
  36. genome_spy/datasets/data/tcga_laml.maf.gz +0 -0
  37. genome_spy/datasets/data/tcga_laml_annot.tsv +201 -0
  38. genome_spy/datasets/data/tcga_laml_combined_oncoplot.json.gz +0 -0
  39. genome_spy/datasets/data/tcga_ov_gistic_lesions.tsv.gz +0 -0
  40. genome_spy/datasets/data/tcga_ov_gistic_scores.tsv.gz +0 -0
  41. genome_spy/helpers.py +185 -0
  42. genome_spy/jupyter.py +5 -0
  43. genome_spy/py.typed +0 -0
  44. genome_spy/schema/__init__.py +784 -0
  45. genome_spy/schema/_kwds.py +1394 -0
  46. genome_spy/schema/_typing.py +186 -0
  47. genome_spy/schema/capabilities.json +593 -0
  48. genome_spy/schema/channels.py +8943 -0
  49. genome_spy/schema/composition.py +1064 -0
  50. genome_spy/schema/core.py +51821 -0
  51. genome_spy/schema/ergonomics.py +2056 -0
  52. genome_spy/schema/expressions.py +476 -0
  53. genome_spy/schema/genome-spy-schema.json +33657 -0
  54. genome_spy/schema/lazy.py +326 -0
  55. genome_spy/schema/mixins.py +11684 -0
  56. genome_spy/schemapi.py +264 -0
  57. genome_spy/static/widget.js +345 -0
  58. genome_spy_python-0.1.0.dist-info/METADATA +185 -0
  59. genome_spy_python-0.1.0.dist-info/RECORD +64 -0
  60. genome_spy_python-0.1.0.dist-info/WHEEL +4 -0
  61. genome_spy_python-0.1.0.dist-info/licenses/LICENSE +21 -0
  62. genome_spy_python-0.1.0.dist-info/licenses/LICENSES/ALTAIR-BSD-3-Clause.txt +27 -0
  63. genome_spy_python-0.1.0.dist-info/licenses/LICENSES/GALLERY-DATA-MIT.txt +22 -0
  64. genome_spy_python-0.1.0.dist-info/licenses/THIRD_PARTY_NOTICES.md +42 -0
genome_spy/schema/_typing.py ADDED
@@ -0,0 +1,186 @@
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+ """Generated from the GenomeSpy JSON Schema. Do not edit by hand."""
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+
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+ from __future__ import annotations
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+ from collections.abc import Sequence
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+ from typing import TypeAlias, Literal
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+
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+ AggregateOp_T: TypeAlias = Literal[
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+ "count", "valid", "sum", "min", "max", "mean", "q1", "median", "q3", "variance"
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+ ]
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+ Align_T: TypeAlias = Literal["left", "center", "right"]
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+ ArrowDirection_T: TypeAlias = Literal["forward", "reverse"]
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+ AxisOrient_T: TypeAlias = Literal["top", "bottom", "left", "right"]
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+ AxisPlacement_T: TypeAlias = Literal["outside", "inside"]
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+ Baseline_T: TypeAlias = Literal["top", "middle", "bottom", "alphabetic", "baseline"]
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+ BuiltInThemeName_T: TypeAlias = Literal[
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+ "genomespy", "vegalite", "quartz", "dark", "fivethirtyeight", "urbaninstitute"
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+ ]
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+ FieldName_T: TypeAlias = str
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+ Field_T: TypeAlias = str
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+ FontStyle_T: TypeAlias = Literal["normal", "italic"]
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+ FontWeight_T: TypeAlias = (
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+ float
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+ | Literal["thin"]
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+ | Literal["light"]
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+ | Literal["regular"]
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+ | Literal["normal"]
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+ | Literal["medium"]
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+ | Literal["bold"]
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+ | Literal["black"]
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+ )
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+ InteractionEventType_T: TypeAlias = Literal[
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+ "click",
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+ "dblclick",
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+ "mouseenter",
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+ "mouseleave",
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+ "mouseover",
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+ "mousemove",
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+ "mousedown",
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+ "wheel",
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+ ]
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+ DomEventType_T: TypeAlias = InteractionEventType_T | Literal["pointerover"]
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+ LegendDirection_T: TypeAlias = Literal["vertical", "horizontal"]
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+ LegendOrient_T: TypeAlias = Literal[
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+ "left",
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+ "right",
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+ "top",
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+ "bottom",
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+ "top-left",
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+ "top-right",
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+ "bottom-left",
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+ "bottom-right",
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+ ]
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+ LegendRegionAnchor_T: TypeAlias = Literal["start", "middle", "end"]
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+ LegendTitleOrient_T: TypeAlias = Literal["top", "bottom", "left", "right"]
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+ MarkType_T: TypeAlias = Literal[
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+ "rect", "point", "rule", "tick", "text", "link", "arrow"
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+ ]
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+ NumericDomain_T: TypeAlias = Sequence[float]
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+ OffsetChannel_T: TypeAlias = Literal["xOffset", "yOffset"]
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+ ParseValue_T: TypeAlias = str | None
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+ PrimaryPositionalChannel_T: TypeAlias = Literal["x", "y"]
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+ ResolutionBehavior_T: TypeAlias = Literal["independent", "shared", "excluded", "forced"]
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+ LegendResolutionBehavior_T: TypeAlias = ResolutionBehavior_T | Literal["collected"]
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+ RulerClear_T: TypeAlias = Literal["mouseleave", "mouseup", False]
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+ RulerDisplay_T: TypeAlias = Literal["line", "center", "band", "none"]
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+ RulerEventType_T: TypeAlias = Literal["mousemove", "mousedown"]
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+ RulerExtent_T: TypeAlias = Literal["auto", "view", "container"]
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+ RulerSnap_T: TypeAlias = Literal["auto", "integer", False]
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+ RulerSource_T: TypeAlias = Literal["pointer", "viewport"]
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+ ScalarDomain_T: TypeAlias = NumericDomain_T | Sequence[str] | Sequence[bool]
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+ Scalar_T: TypeAlias = str | float | bool
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+ ScaleInterpolate_T: TypeAlias = Literal[
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+ "rgb", "lab", "hcl", "hsl", "hsl-long", "hcl-long", "cubehelix", "cubehelix-long"
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+ ]
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+ ScaleType_T: TypeAlias = Literal[
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+ "null",
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+ "linear",
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+ "log",
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+ "pow",
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+ "sqrt",
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+ "symlog",
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+ "identity",
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+ "sequential",
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+ "quantize",
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+ "threshold",
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+ "ordinal",
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+ "point",
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+ "band",
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+ "index",
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+ "locus",
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+ ]
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+ SecondaryPositionalChannel_T: TypeAlias = Literal["x2", "y2"]
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+ PositionalChannel_T: TypeAlias = (
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+ PrimaryPositionalChannel_T | SecondaryPositionalChannel_T
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+ )
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+ ChannelWithScale_T: TypeAlias = (
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+ PositionalChannel_T
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+ | OffsetChannel_T
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+ | Literal["color"]
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+ | Literal["fill"]
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+ | Literal["stroke"]
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+ | Literal["opacity"]
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+ | Literal["fillOpacity"]
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+ | Literal["strokeOpacity"]
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+ | Literal["strokeWidth"]
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+ | Literal["size"]
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+ | Literal["shape"]
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+ | Literal["direction"]
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+ | Literal["angle"]
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+ | Literal["dx"]
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+ | Literal["dy"]
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+ )
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+ SelectionExtent_T: TypeAlias = Literal["auto", "view", "container"]
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+ SelectionType_T: TypeAlias = Literal["point", "interval"]
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+ SortOrder_T: TypeAlias = Literal["ascending", "descending"]
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+ TitleAnchor_T: TypeAlias = Literal[None, "start", "middle", "end"]
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+ TitleFrame_T: TypeAlias = Literal["bounds", "group"]
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+ TitleOrient_T: TypeAlias = Literal["none", "left", "right", "top", "bottom"]
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+ TypeForShape_T: TypeAlias = Literal["ordinal", "nominal"]
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+ Type_T: TypeAlias = Literal["quantitative", "ordinal", "nominal", "index", "locus"]
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+ WindowOnlyOp_T: TypeAlias = Literal[
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+ "row_number",
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+ "rank",
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+ "dense_rank",
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+ "percent_rank",
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+ "cume_dist",
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+ "ntile",
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+ "lag",
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+ "lead",
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+ "first_value",
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+ "last_value",
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+ "nth_value",
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+ "prev_value",
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+ "next_value",
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+ ]
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+ WindowOp_T: TypeAlias = WindowOnlyOp_T | AggregateOp_T
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+
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+ __all__ = [
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+ "AggregateOp_T",
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+ "Align_T",
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+ "ArrowDirection_T",
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+ "AxisOrient_T",
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+ "AxisPlacement_T",
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+ "Baseline_T",
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+ "BuiltInThemeName_T",
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+ "FieldName_T",
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+ "Field_T",
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+ "FontStyle_T",
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+ "FontWeight_T",
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+ "InteractionEventType_T",
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+ "DomEventType_T",
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+ "LegendDirection_T",
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+ "LegendOrient_T",
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+ "LegendRegionAnchor_T",
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+ "LegendTitleOrient_T",
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+ "MarkType_T",
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+ "NumericDomain_T",
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+ "OffsetChannel_T",
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+ "ParseValue_T",
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+ "PrimaryPositionalChannel_T",
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+ "ResolutionBehavior_T",
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+ "LegendResolutionBehavior_T",
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+ "RulerClear_T",
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+ "RulerDisplay_T",
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+ "RulerEventType_T",
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+ "RulerExtent_T",
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+ "RulerSnap_T",
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+ "RulerSource_T",
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+ "ScalarDomain_T",
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+ "Scalar_T",
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+ "ScaleInterpolate_T",
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+ "ScaleType_T",
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+ "SecondaryPositionalChannel_T",
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+ "PositionalChannel_T",
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+ "ChannelWithScale_T",
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+ "SelectionExtent_T",
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+ "SelectionType_T",
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+ "SortOrder_T",
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+ "TitleAnchor_T",
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+ "TitleFrame_T",
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+ "TitleOrient_T",
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+ "TypeForShape_T",
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+ "Type_T",
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+ "WindowOnlyOp_T",
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+ "WindowOp_T",
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+ ]