@czi-sds/data-viz 2.4.2 → 2.5.0

package/dist/shared/index3.cjs.d.ts

@@ -1,166 +1,69 @@
 /// <reference types="react" />
-import { HTMLAttributes } from "react";
-import { DiscreteColorGeneratorOptions, TooltipTableContentProps } from "@czi-sds/components";
-
-//#region src/core/StackedBarChart/StackedBarChart.types.d.ts
-interface StackedBarChartDataItem {
-  /**
-   * The segment's label in the legend, and the key the animations track it by.
-   * Must be unique within the chart.
-   */
-  name: string;
-  /**
-   * The quantity the segment stands for.
-   */
-  value: number;
-  /**
-   * Any CSS color. Without it the segment takes a generated palette color,
-   * which can shift as categories come and go.
-   */
-  color?: string;
-  /**
-   * A unit for this item's counted value, for data that mixes units across
-   * categories.
-   */
-  unit?: string;
-  /**
-   * Takes the segment and its legend item out of every interaction: no hover,
-   * no tooltip, no selection.
-   * @default false
-   */
-  disabled?: boolean;
-  /**
-   * Content for a TooltipTable shown above the segment on hover. Use it for the
-   * breakdown behind the number; a segment without it has no tooltip.
-   */
-  tooltip?: TooltipTableContentProps;
-}
-interface StackedBarChartProps extends HTMLAttributes<HTMLDivElement> {
-  /**
-   * A heading above the bar. It is also what makes room for the badge; with no
-   * title, no badge is drawn.
-   */
-  title?: string;
-  /**
-   * Overrides the badge text, which otherwise counts the data and the selection
-   * ("7", or "3 of 7").
-   */
-  badge?: string;
-  /**
-   * Removes the badge, leaving the title on its own.
-   * @default false
-   */
-  hideBadge?: boolean;
-  /**
-   * The segments, in the order they are drawn.
-   */
-  data: StackedBarChartDataItem[];
-  /**
-   * Any CSS width; a number is read as pixels. It sets the width of the whole
-   * chart, legend included.
-   * @default 100%
-   */
-  width?: number | string;
-  /**
-   * Height of the bar in pixels. Values below 1 are clamped to 1, so the bar
-   * cannot disappear.
-   * @default 16
-   */
-  barHeight?: number;
-  /**
-   * Draws the legend below the bar. It is the only place segment names appear,
-   * and the only part of the chart a keyboard can reach.
-   * @default true
-   */
-  showLegend?: boolean;
-  /**
-   * Shows each item's value beside its name in the legend.
-   * @default true
-   */
-  showLegendValues?: boolean;
-  /**
-   * "percentage" shows the segment's share of the bar, rounded. "count" shows
-   * the raw value followed by the item's unit, or the chart's unit if the item
-   * has none.
-   * @default "percentage"
-   */
-  legendValueFormat?: "percentage" | "count";
-  /**
-   * Indices into data that are currently selected. The chart is controlled: it
-   * draws this and never changes it.
-   */
-  selectedIndices?: number[];
-  /**
-   * Called with the next selection when a segment or legend item is clicked.
-   * Without it, clicking selects nothing.
-   */
-  onSelectionChange?: (selectedIndices: number[], selectedData: StackedBarChartDataItem[]) => void;
-  /**
-   * Called when the pointer enters a segment. The chart already syncs its own
-   * hover highlight between bar and legend, so this is for driving something
-   * outside it.
-   */
-  onSegmentMouseEnter?: (item: StackedBarChartDataItem, index: number) => void;
-  /**
-   * Called when the pointer leaves a segment.
-   */
-  onSegmentMouseLeave?: (item: StackedBarChartDataItem, index: number) => void;
-  /**
-   * Called when the pointer enters a legend item.
-   */
-  onLegendItemMouseEnter?: (item: StackedBarChartDataItem, index: number) => void;
-  /**
-   * Called when the pointer leaves a legend item.
-   */
-  onLegendItemMouseLeave?: (item: StackedBarChartDataItem, index: number) => void;
-  /**
-   * Fires on a segment click, alongside any selection change rather than
-   * instead of it.
-   */
-  onSegmentClick?: (item: StackedBarChartDataItem, index: number) => void;
-  /**
-   * The same, for a click on a legend item.
-   */
-  onLegendItemClick?: (item: StackedBarChartDataItem, index: number) => void;
-  /**
-   * What a selection does to the unselected segments: fade them to 20% opacity,
-   * or drop them from the bar and let the rest take the space.
-   * @default "dim"
-   */
-  selectionBehavior?: "dim" | "hide";
-  /**
-   * Whether the bar shows a breakdown of the data (segments always fill it) or
-   * progress towards maxAmount.
-   * @default "proportional"
-   */
-  mode?: "proportional" | "cumulative";
-  /**
-   * Cumulative mode only. The value the full bar represents. Any difference
-   * between it and the sum of the data is drawn as the Remaining segment.
-   */
-  maxAmount?: number;
-  /**
-   * Name of the grey gap segment in cumulative mode.
-   * @default "Remaining"
-   */
-  remainingLabel?: string;
-  /**
-   * A unit for the Remaining segment's value alone.
-   */
-  remainingUnit?: string;
-  /**
-   * The unit appended to counted values, for items that do not carry one of
-   * their own.
-   */
-  unit?: string;
-  /**
-   * Tunes the generated palette (start hue, rotations, lightness range, gamma).
-   * Items with their own color are untouched by it.
-   */
-  colorGeneratorOptions?: DiscreteColorGeneratorOptions;
-}
+import { t as ColorScale } from "./colorScales.cjs.js";
+import { u as ProteinStructureViewerProps } from "./index2.cjs.js";
+//#region src/core/ProteinStructureViewer/utils/structureFormat.d.ts
+/**
+ * Structure text formats Mol* can parse from the viewer's `structure` prop.
+ *
+ * `"mmcif"` covers both mmCIF and PDBx; they are the same text format, and
+ * that is the name Mol*'s trajectory parser uses. Binary CIF (`.bcif`) is not
+ * accepted: the prop is a string.
+ */
+type StructureFormat = "pdb" | "mmcif";
+/**
+ * Infers whether `text` is PDB or mmCIF (PDBx).
+ *
+ * mmCIF documents start with a `data_` block and name their coordinates
+ * `_atom_site.`. PDB never does either, so either marker is enough. A leading
+ * comment (`# ...`) before `data_` is still mmCIF.
+ */
+declare function detectStructureFormat(text: string): StructureFormat;
 //#endregion
-//#region src/core/StackedBarChart/index.d.ts
-declare const StackedBarChart: (props: StackedBarChartProps) => JSX.Element;
+//#region src/core/ProteinStructureViewer/utils/plddt.d.ts
+/**
+ * AlphaFold's pLDDT confidence bands. Thresholds are on the 0-1 scale that
+ * `plddt` values use, ascending from lowest to highest confidence.
+ */
+declare const PLDDT_COLOR_SCALE: ColorScale;
+/**
+ * Rewrites a PDB file's B-factor column with pLDDT scores so Mol* can read them
+ * off the parsed model. B-factors occupy columns 60-66 of ATOM/HETATM lines;
+ * scores arrive on a 0-1 scale and are stored on the conventional 0-100 one.
+ * Residues past the end of `plddtValues` fall back to a mid-confidence 50.
+ *
+ * A residue is identified by chain, sequence number and insertion code. The
+ * code has to be part of that: `10` and `10A` are two residues, Mol* counts
+ * them as two, and treating them as one here would hand every residue after
+ * them its neighbour's score.
+ */
+declare function injectPlddtIntoPdb(pdbData: string, plddtValues: number[]): string;
+/**
+ * Rewrites an mmCIF (PDBx) file's `_atom_site.B_iso_or_equiv` column with
+ * pLDDT scores so Mol* can read them off the parsed model, the same way
+ * `injectPlddtIntoPdb` rewrites the PDB B-factor column. Scores arrive on a
+ * 0-1 scale and are stored on the conventional 0-100 one. Residues past the
+ * end of `plddtValues` fall back to a mid-confidence 50.
+ *
+ * If the file has no B-factor column, one is appended to the atom-site loop
+ * rather than leaving the scores behind.
+ */
+declare function injectPlddtIntoMmcif(mmcifData: string, plddtValues: number[]): string;
+/**
+ * Rewrites a structure file's B-factors with pLDDT scores. Dispatches to
+ * `injectPlddtIntoPdb` or `injectPlddtIntoMmcif` from `format`, or from
+ * detecting the format of `data` when `format` is omitted.
+ */
+declare function injectPlddt(data: string, plddtValues: number[], format?: StructureFormat): string;
 //#endregion
-export { StackedBarChartDataItem as n, StackedBarChartProps as r, StackedBarChart as t };
+//#region src/core/ProteinStructureViewer/utils/highlights.d.ts
+/**
+ * Colors for highlights that name none, in the order the highlights are given.
+ * Saturated enough to stand out over a chain, pLDDT or overlay coloring, and
+ * wrapping around once they run out.
+ */
+declare const HIGHLIGHT_COLOR_PALETTE: readonly ["#E64545", "#F0C229", "#12A9A0", "#BD57D4", "#FF8A32", "#559DF3"];
+//#endregion
+//#region src/core/ProteinStructureViewer/index.d.ts
+declare const _default: import("react").MemoExoticComponent<import("react").ForwardRefExoticComponent<ProteinStructureViewerProps & import("react").RefAttributes<HTMLDivElement>>>;
+//#endregion
+export { injectPlddtIntoMmcif as a, detectStructureFormat as c, injectPlddt as i, HIGHLIGHT_COLOR_PALETTE as n, injectPlddtIntoPdb as o, PLDDT_COLOR_SCALE as r, StructureFormat as s, _default as t };

package/dist/shared/index3.esm.d.ts

@@ -1,166 +1,71 @@
 /// <reference types="react" />
-import { HTMLAttributes } from "react";
-import { DiscreteColorGeneratorOptions, TooltipTableContentProps } from "@czi-sds/components";
+import { t as ColorScale } from "./colorScales.esm.js";
+import { u as ProteinStructureViewerProps } from "./index2.esm.js";
+import { Color } from "molstar/lib/mol-util/color";
 
-//#region src/core/StackedBarChart/StackedBarChart.types.d.ts
-interface StackedBarChartDataItem {
-  /**
-   * The segment's label in the legend, and the key the animations track it by.
-   * Must be unique within the chart.
-   */
-  name: string;
-  /**
-   * The quantity the segment stands for.
-   */
-  value: number;
-  /**
-   * Any CSS color. Without it the segment takes a generated palette color,
-   * which can shift as categories come and go.
-   */
-  color?: string;
-  /**
-   * A unit for this item's counted value, for data that mixes units across
-   * categories.
-   */
-  unit?: string;
-  /**
-   * Takes the segment and its legend item out of every interaction: no hover,
-   * no tooltip, no selection.
-   * @default false
-   */
-  disabled?: boolean;
-  /**
-   * Content for a TooltipTable shown above the segment on hover. Use it for the
-   * breakdown behind the number; a segment without it has no tooltip.
-   */
-  tooltip?: TooltipTableContentProps;
-}
-interface StackedBarChartProps extends HTMLAttributes<HTMLDivElement> {
-  /**
-   * A heading above the bar. It is also what makes room for the badge; with no
-   * title, no badge is drawn.
-   */
-  title?: string;
-  /**
-   * Overrides the badge text, which otherwise counts the data and the selection
-   * ("7", or "3 of 7").
-   */
-  badge?: string;
-  /**
-   * Removes the badge, leaving the title on its own.
-   * @default false
-   */
-  hideBadge?: boolean;
-  /**
-   * The segments, in the order they are drawn.
-   */
-  data: StackedBarChartDataItem[];
-  /**
-   * Any CSS width; a number is read as pixels. It sets the width of the whole
-   * chart, legend included.
-   * @default 100%
-   */
-  width?: number | string;
-  /**
-   * Height of the bar in pixels. Values below 1 are clamped to 1, so the bar
-   * cannot disappear.
-   * @default 16
-   */
-  barHeight?: number;
-  /**
-   * Draws the legend below the bar. It is the only place segment names appear,
-   * and the only part of the chart a keyboard can reach.
-   * @default true
-   */
-  showLegend?: boolean;
-  /**
-   * Shows each item's value beside its name in the legend.
-   * @default true
-   */
-  showLegendValues?: boolean;
-  /**
-   * "percentage" shows the segment's share of the bar, rounded. "count" shows
-   * the raw value followed by the item's unit, or the chart's unit if the item
-   * has none.
-   * @default "percentage"
-   */
-  legendValueFormat?: "percentage" | "count";
-  /**
-   * Indices into data that are currently selected. The chart is controlled: it
-   * draws this and never changes it.
-   */
-  selectedIndices?: number[];
-  /**
-   * Called with the next selection when a segment or legend item is clicked.
-   * Without it, clicking selects nothing.
-   */
-  onSelectionChange?: (selectedIndices: number[], selectedData: StackedBarChartDataItem[]) => void;
-  /**
-   * Called when the pointer enters a segment. The chart already syncs its own
-   * hover highlight between bar and legend, so this is for driving something
-   * outside it.
-   */
-  onSegmentMouseEnter?: (item: StackedBarChartDataItem, index: number) => void;
-  /**
-   * Called when the pointer leaves a segment.
-   */
-  onSegmentMouseLeave?: (item: StackedBarChartDataItem, index: number) => void;
-  /**
-   * Called when the pointer enters a legend item.
-   */
-  onLegendItemMouseEnter?: (item: StackedBarChartDataItem, index: number) => void;
-  /**
-   * Called when the pointer leaves a legend item.
-   */
-  onLegendItemMouseLeave?: (item: StackedBarChartDataItem, index: number) => void;
-  /**
-   * Fires on a segment click, alongside any selection change rather than
-   * instead of it.
-   */
-  onSegmentClick?: (item: StackedBarChartDataItem, index: number) => void;
-  /**
-   * The same, for a click on a legend item.
-   */
-  onLegendItemClick?: (item: StackedBarChartDataItem, index: number) => void;
-  /**
-   * What a selection does to the unselected segments: fade them to 20% opacity,
-   * or drop them from the bar and let the rest take the space.
-   * @default "dim"
-   */
-  selectionBehavior?: "dim" | "hide";
-  /**
-   * Whether the bar shows a breakdown of the data (segments always fill it) or
-   * progress towards maxAmount.
-   * @default "proportional"
-   */
-  mode?: "proportional" | "cumulative";
-  /**
-   * Cumulative mode only. The value the full bar represents. Any difference
-   * between it and the sum of the data is drawn as the Remaining segment.
-   */
-  maxAmount?: number;
-  /**
-   * Name of the grey gap segment in cumulative mode.
-   * @default "Remaining"
-   */
-  remainingLabel?: string;
-  /**
-   * A unit for the Remaining segment's value alone.
-   */
-  remainingUnit?: string;
-  /**
-   * The unit appended to counted values, for items that do not carry one of
-   * their own.
-   */
-  unit?: string;
-  /**
-   * Tunes the generated palette (start hue, rotations, lightness range, gamma).
-   * Items with their own color are untouched by it.
-   */
-  colorGeneratorOptions?: DiscreteColorGeneratorOptions;
-}
+//#region src/core/ProteinStructureViewer/utils/structureFormat.d.ts
+/**
+ * Structure text formats Mol* can parse from the viewer's `structure` prop.
+ *
+ * `"mmcif"` covers both mmCIF and PDBx; they are the same text format, and
+ * that is the name Mol*'s trajectory parser uses. Binary CIF (`.bcif`) is not
+ * accepted: the prop is a string.
+ */
+type StructureFormat = "pdb" | "mmcif";
+/**
+ * Infers whether `text` is PDB or mmCIF (PDBx).
+ *
+ * mmCIF documents start with a `data_` block and name their coordinates
+ * `_atom_site.`. PDB never does either, so either marker is enough. A leading
+ * comment (`# ...`) before `data_` is still mmCIF.
+ */
+declare function detectStructureFormat(text: string): StructureFormat;
 //#endregion
-//#region src/core/StackedBarChart/index.d.ts
-declare const StackedBarChart: (props: StackedBarChartProps) => JSX.Element;
+//#region src/core/ProteinStructureViewer/utils/plddt.d.ts
+/**
+ * AlphaFold's pLDDT confidence bands. Thresholds are on the 0-1 scale that
+ * `plddt` values use, ascending from lowest to highest confidence.
+ */
+declare const PLDDT_COLOR_SCALE: ColorScale;
+/**
+ * Rewrites a PDB file's B-factor column with pLDDT scores so Mol* can read them
+ * off the parsed model. B-factors occupy columns 60-66 of ATOM/HETATM lines;
+ * scores arrive on a 0-1 scale and are stored on the conventional 0-100 one.
+ * Residues past the end of `plddtValues` fall back to a mid-confidence 50.
+ *
+ * A residue is identified by chain, sequence number and insertion code. The
+ * code has to be part of that: `10` and `10A` are two residues, Mol* counts
+ * them as two, and treating them as one here would hand every residue after
+ * them its neighbour's score.
+ */
+declare function injectPlddtIntoPdb(pdbData: string, plddtValues: number[]): string;
+/**
+ * Rewrites an mmCIF (PDBx) file's `_atom_site.B_iso_or_equiv` column with
+ * pLDDT scores so Mol* can read them off the parsed model, the same way
+ * `injectPlddtIntoPdb` rewrites the PDB B-factor column. Scores arrive on a
+ * 0-1 scale and are stored on the conventional 0-100 one. Residues past the
+ * end of `plddtValues` fall back to a mid-confidence 50.
+ *
+ * If the file has no B-factor column, one is appended to the atom-site loop
+ * rather than leaving the scores behind.
+ */
+declare function injectPlddtIntoMmcif(mmcifData: string, plddtValues: number[]): string;
+/**
+ * Rewrites a structure file's B-factors with pLDDT scores. Dispatches to
+ * `injectPlddtIntoPdb` or `injectPlddtIntoMmcif` from `format`, or from
+ * detecting the format of `data` when `format` is omitted.
+ */
+declare function injectPlddt(data: string, plddtValues: number[], format?: StructureFormat): string;
 //#endregion
-export { StackedBarChartDataItem as n, StackedBarChartProps as r, StackedBarChart as t };
+//#region src/core/ProteinStructureViewer/utils/highlights.d.ts
+/**
+ * Colors for highlights that name none, in the order the highlights are given.
+ * Saturated enough to stand out over a chain, pLDDT or overlay coloring, and
+ * wrapping around once they run out.
+ */
+declare const HIGHLIGHT_COLOR_PALETTE: readonly ["#E64545", "#F0C229", "#12A9A0", "#BD57D4", "#FF8A32", "#559DF3"];
+//#endregion
+//#region src/core/ProteinStructureViewer/index.d.ts
+declare const _default: import("react").MemoExoticComponent<import("react").ForwardRefExoticComponent<ProteinStructureViewerProps & import("react").RefAttributes<HTMLDivElement>>>;
+//#endregion
+export { injectPlddtIntoMmcif as a, detectStructureFormat as c, injectPlddt as i, HIGHLIGHT_COLOR_PALETTE as n, injectPlddtIntoPdb as o, PLDDT_COLOR_SCALE as r, StructureFormat as s, _default as t };

package/dist/shared/index4.cjs.d.ts

@@ -0,0 +1,166 @@
+/// <reference types="react" />
+import { HTMLAttributes } from "react";
+import { DiscreteColorGeneratorOptions, TooltipTableContentProps } from "@czi-sds/components";
+
+//#region src/core/StackedBarChart/StackedBarChart.types.d.ts
+interface StackedBarChartDataItem {
+  /**
+   * The segment's label in the legend, and the key the animations track it by.
+   * Must be unique within the chart.
+   */
+  name: string;
+  /**
+   * The quantity the segment stands for.
+   */
+  value: number;
+  /**
+   * Any CSS color. Without it the segment takes a generated palette color,
+   * which can shift as categories come and go.
+   */
+  color?: string;
+  /**
+   * A unit for this item's counted value, for data that mixes units across
+   * categories.
+   */
+  unit?: string;
+  /**
+   * Takes the segment and its legend item out of every interaction: no hover,
+   * no tooltip, no selection.
+   * @default false
+   */
+  disabled?: boolean;
+  /**
+   * Content for a TooltipTable shown above the segment on hover. Use it for the
+   * breakdown behind the number; a segment without it has no tooltip.
+   */
+  tooltip?: TooltipTableContentProps;
+}
+interface StackedBarChartProps extends HTMLAttributes<HTMLDivElement> {
+  /**
+   * A heading above the bar. It is also what makes room for the badge; with no
+   * title, no badge is drawn.
+   */
+  title?: string;
+  /**
+   * Overrides the badge text, which otherwise counts the data and the selection
+   * ("7", or "3 of 7").
+   */
+  badge?: string;
+  /**
+   * Removes the badge, leaving the title on its own.
+   * @default false
+   */
+  hideBadge?: boolean;
+  /**
+   * The segments, in the order they are drawn.
+   */
+  data: StackedBarChartDataItem[];
+  /**
+   * Any CSS width; a number is read as pixels. It sets the width of the whole
+   * chart, legend included.
+   * @default 100%
+   */
+  width?: number | string;
+  /**
+   * Height of the bar in pixels. Values below 1 are clamped to 1, so the bar
+   * cannot disappear.
+   * @default 16
+   */
+  barHeight?: number;
+  /**
+   * Draws the legend below the bar. It is the only place segment names appear,
+   * and the only part of the chart a keyboard can reach.
+   * @default true
+   */
+  showLegend?: boolean;
+  /**
+   * Shows each item's value beside its name in the legend.
+   * @default true
+   */
+  showLegendValues?: boolean;
+  /**
+   * "percentage" shows the segment's share of the bar, rounded. "count" shows
+   * the raw value followed by the item's unit, or the chart's unit if the item
+   * has none.
+   * @default "percentage"
+   */
+  legendValueFormat?: "percentage" | "count";
+  /**
+   * Indices into data that are currently selected. The chart is controlled: it
+   * draws this and never changes it.
+   */
+  selectedIndices?: number[];
+  /**
+   * Called with the next selection when a segment or legend item is clicked.
+   * Without it, clicking selects nothing.
+   */
+  onSelectionChange?: (selectedIndices: number[], selectedData: StackedBarChartDataItem[]) => void;
+  /**
+   * Called when the pointer enters a segment. The chart already syncs its own
+   * hover highlight between bar and legend, so this is for driving something
+   * outside it.
+   */
+  onSegmentMouseEnter?: (item: StackedBarChartDataItem, index: number) => void;
+  /**
+   * Called when the pointer leaves a segment.
+   */
+  onSegmentMouseLeave?: (item: StackedBarChartDataItem, index: number) => void;
+  /**
+   * Called when the pointer enters a legend item.
+   */
+  onLegendItemMouseEnter?: (item: StackedBarChartDataItem, index: number) => void;
+  /**
+   * Called when the pointer leaves a legend item.
+   */
+  onLegendItemMouseLeave?: (item: StackedBarChartDataItem, index: number) => void;
+  /**
+   * Fires on a segment click, alongside any selection change rather than
+   * instead of it.
+   */
+  onSegmentClick?: (item: StackedBarChartDataItem, index: number) => void;
+  /**
+   * The same, for a click on a legend item.
+   */
+  onLegendItemClick?: (item: StackedBarChartDataItem, index: number) => void;
+  /**
+   * What a selection does to the unselected segments: fade them to 20% opacity,
+   * or drop them from the bar and let the rest take the space.
+   * @default "dim"
+   */
+  selectionBehavior?: "dim" | "hide";
+  /**
+   * Whether the bar shows a breakdown of the data (segments always fill it) or
+   * progress towards maxAmount.
+   * @default "proportional"
+   */
+  mode?: "proportional" | "cumulative";
+  /**
+   * Cumulative mode only. The value the full bar represents. Any difference
+   * between it and the sum of the data is drawn as the Remaining segment.
+   */
+  maxAmount?: number;
+  /**
+   * Name of the grey gap segment in cumulative mode.
+   * @default "Remaining"
+   */
+  remainingLabel?: string;
+  /**
+   * A unit for the Remaining segment's value alone.
+   */
+  remainingUnit?: string;
+  /**
+   * The unit appended to counted values, for items that do not carry one of
+   * their own.
+   */
+  unit?: string;
+  /**
+   * Tunes the generated palette (start hue, rotations, lightness range, gamma).
+   * Items with their own color are untouched by it.
+   */
+  colorGeneratorOptions?: DiscreteColorGeneratorOptions;
+}
+//#endregion
+//#region src/core/StackedBarChart/index.d.ts
+declare const StackedBarChart: (props: StackedBarChartProps) => JSX.Element;
+//#endregion
+export { StackedBarChartDataItem as n, StackedBarChartProps as r, StackedBarChart as t };