react-msaview 9.0.0 → 9.1.0

package/dist/viewerSnapshot.d.ts

@@ -0,0 +1,169 @@
+import type { MSAViewerProps } from './components/MSAViewer.tsx';
+import type { ColorScheme, Highlight } from './types.ts';
+export declare function colorSchemeSnapshot(scheme: ColorScheme | undefined): {
+    colorSchemeName: string;
+    customColorScheme?: undefined;
+} | {
+    colorSchemeName?: undefined;
+    customColorScheme: Record<string, string>;
+} | {
+    colorSchemeName?: undefined;
+    customColorScheme?: undefined;
+};
+/**
+ * The `highlightColumns` prop as `highlights`: one `{start, end}` per run of
+ * adjacent 1-based alignment columns
+ */
+export declare function columnHighlights(columns?: number[]): {
+    start: number;
+    end: number;
+}[];
+export declare function viewerHighlights({ highlights, highlightColumns, }: Pick<MSAViewerProps, 'highlights' | 'highlightColumns'>): Highlight[];
+/** each filehandle prop, or the URL prop standing in for it */
+export declare function fileLocations({ msaFilehandle, treeFilehandle, gffFilehandle, msaUrl, treeUrl, gffUrl, }: MSAViewerProps): {
+    msaFilehandle: import("@jbrowse/core/util").BlobLocation | import("@jbrowse/core/util").FileHandleLocation | import("@jbrowse/core/util").LocalPathLocation | {
+        uri: string;
+        locationType: 'UriLocation';
+    } | undefined;
+    treeFilehandle: import("@jbrowse/core/util").BlobLocation | import("@jbrowse/core/util").FileHandleLocation | import("@jbrowse/core/util").LocalPathLocation | {
+        uri: string;
+        locationType: 'UriLocation';
+    } | undefined;
+    gffFilehandle: import("@jbrowse/core/util").BlobLocation | import("@jbrowse/core/util").FileHandleLocation | import("@jbrowse/core/util").LocalPathLocation | {
+        uri: string;
+        locationType: 'UriLocation';
+    } | undefined;
+};
+export declare function resolveTheme(theme: MSAViewerProps['theme']): import("@mui/material").Theme;
+/**
+ * The model snapshot `MSAViewer` creates from its props. The CLI's `--props`
+ * reads the same JSON the R and Python widgets send, so a figure exported
+ * headlessly draws what the widget drew.
+ */
+export declare function viewerSnapshot(props: MSAViewerProps): {
+    colorSchemeName: string;
+    customColorScheme?: undefined;
+    type: 'MsaView';
+    data?: {
+        msa: string;
+        tree: string;
+        gff: string | undefined;
+        treeMetadata?: string | undefined;
+    } | undefined;
+    msaFilehandle?: import("@jbrowse/core/util").BlobLocation | import("@jbrowse/core/util").FileHandleLocation | import("@jbrowse/core/util").LocalPathLocation | {
+        uri: string;
+        locationType: 'UriLocation';
+    } | undefined;
+    treeFilehandle?: import("@jbrowse/core/util").BlobLocation | import("@jbrowse/core/util").FileHandleLocation | import("@jbrowse/core/util").LocalPathLocation | {
+        uri: string;
+        locationType: 'UriLocation';
+    } | undefined;
+    gffFilehandle?: import("@jbrowse/core/util").BlobLocation | import("@jbrowse/core/util").FileHandleLocation | import("@jbrowse/core/util").LocalPathLocation | {
+        uri: string;
+        locationType: 'UriLocation';
+    } | undefined;
+    height?: number | undefined;
+    colWidth?: number | undefined;
+    rowHeight?: number | undefined;
+    allowedGappyness?: number | undefined;
+    highlights?: Highlight[] | undefined;
+    features?: import("./types.ts").Feature[] | undefined;
+    selection?: import("./types.ts").MsaSelection | undefined;
+    clades?: import("./types.ts").Clade[] | undefined;
+    relativeTo?: string | undefined;
+    columnTracks?: import("./types.ts").ColumnTrackSpec[] | undefined;
+    residueMappings?: import("./types.ts").ResidueMapping[] | undefined;
+    encodings?: import("./types.ts").Encoding[] | undefined;
+    rowPanels?: import("./types.ts").RowPanelSpec[] | undefined;
+    drawTree?: boolean | undefined;
+    treeAreaWidth?: number | undefined;
+    showBranchLen?: boolean | undefined;
+    treeOrder?: import("./types.ts").TreeOrder | undefined;
+    treeRoot?: import("./types.ts").TreeRoot | undefined;
+    region?: import("./types.ts").Region | undefined;
+    bgColor?: boolean | undefined;
+} | {
+    colorSchemeName?: undefined;
+    customColorScheme: Record<string, string>;
+    type: 'MsaView';
+    data?: {
+        msa: string;
+        tree: string;
+        gff: string | undefined;
+        treeMetadata?: string | undefined;
+    } | undefined;
+    msaFilehandle?: import("@jbrowse/core/util").BlobLocation | import("@jbrowse/core/util").FileHandleLocation | import("@jbrowse/core/util").LocalPathLocation | {
+        uri: string;
+        locationType: 'UriLocation';
+    } | undefined;
+    treeFilehandle?: import("@jbrowse/core/util").BlobLocation | import("@jbrowse/core/util").FileHandleLocation | import("@jbrowse/core/util").LocalPathLocation | {
+        uri: string;
+        locationType: 'UriLocation';
+    } | undefined;
+    gffFilehandle?: import("@jbrowse/core/util").BlobLocation | import("@jbrowse/core/util").FileHandleLocation | import("@jbrowse/core/util").LocalPathLocation | {
+        uri: string;
+        locationType: 'UriLocation';
+    } | undefined;
+    height?: number | undefined;
+    colWidth?: number | undefined;
+    rowHeight?: number | undefined;
+    allowedGappyness?: number | undefined;
+    highlights?: Highlight[] | undefined;
+    features?: import("./types.ts").Feature[] | undefined;
+    selection?: import("./types.ts").MsaSelection | undefined;
+    clades?: import("./types.ts").Clade[] | undefined;
+    relativeTo?: string | undefined;
+    columnTracks?: import("./types.ts").ColumnTrackSpec[] | undefined;
+    residueMappings?: import("./types.ts").ResidueMapping[] | undefined;
+    encodings?: import("./types.ts").Encoding[] | undefined;
+    rowPanels?: import("./types.ts").RowPanelSpec[] | undefined;
+    drawTree?: boolean | undefined;
+    treeAreaWidth?: number | undefined;
+    showBranchLen?: boolean | undefined;
+    treeOrder?: import("./types.ts").TreeOrder | undefined;
+    treeRoot?: import("./types.ts").TreeRoot | undefined;
+    region?: import("./types.ts").Region | undefined;
+    bgColor?: boolean | undefined;
+} | {
+    colorSchemeName?: undefined;
+    customColorScheme?: undefined;
+    type: 'MsaView';
+    data?: {
+        msa: string;
+        tree: string;
+        gff: string | undefined;
+        treeMetadata?: string | undefined;
+    } | undefined;
+    msaFilehandle?: import("@jbrowse/core/util").BlobLocation | import("@jbrowse/core/util").FileHandleLocation | import("@jbrowse/core/util").LocalPathLocation | {
+        uri: string;
+        locationType: 'UriLocation';
+    } | undefined;
+    treeFilehandle?: import("@jbrowse/core/util").BlobLocation | import("@jbrowse/core/util").FileHandleLocation | import("@jbrowse/core/util").LocalPathLocation | {
+        uri: string;
+        locationType: 'UriLocation';
+    } | undefined;
+    gffFilehandle?: import("@jbrowse/core/util").BlobLocation | import("@jbrowse/core/util").FileHandleLocation | import("@jbrowse/core/util").LocalPathLocation | {
+        uri: string;
+        locationType: 'UriLocation';
+    } | undefined;
+    height?: number | undefined;
+    colWidth?: number | undefined;
+    rowHeight?: number | undefined;
+    allowedGappyness?: number | undefined;
+    highlights?: Highlight[] | undefined;
+    features?: import("./types.ts").Feature[] | undefined;
+    selection?: import("./types.ts").MsaSelection | undefined;
+    clades?: import("./types.ts").Clade[] | undefined;
+    relativeTo?: string | undefined;
+    columnTracks?: import("./types.ts").ColumnTrackSpec[] | undefined;
+    residueMappings?: import("./types.ts").ResidueMapping[] | undefined;
+    encodings?: import("./types.ts").Encoding[] | undefined;
+    rowPanels?: import("./types.ts").RowPanelSpec[] | undefined;
+    drawTree?: boolean | undefined;
+    treeAreaWidth?: number | undefined;
+    showBranchLen?: boolean | undefined;
+    treeOrder?: import("./types.ts").TreeOrder | undefined;
+    treeRoot?: import("./types.ts").TreeRoot | undefined;
+    region?: import("./types.ts").Region | undefined;
+    bgColor?: boolean | undefined;
+};

package/dist/viewerSnapshot.js

@@ -0,0 +1,100 @@
+import { createJBrowseTheme } from '@jbrowse/core/ui/theme';
+export function colorSchemeSnapshot(scheme) {
+    return typeof scheme === 'string'
+        ? { colorSchemeName: scheme }
+        : scheme
+            ? { customColorScheme: scheme.map }
+            : {};
+}
+/**
+ * The `highlightColumns` prop as `highlights`: one `{start, end}` per run of
+ * adjacent 1-based alignment columns
+ */
+export function columnHighlights(columns = []) {
+    const sorted = [...new Set(columns)].sort((a, b) => a - b);
+    const runs = [];
+    for (const column of sorted) {
+        const last = runs.at(-1);
+        if (last?.end === column - 1) {
+            last.end = column;
+        }
+        else {
+            runs.push({ start: column, end: column });
+        }
+    }
+    return runs;
+}
+export function viewerHighlights({ highlights = [], highlightColumns, }) {
+    return [...highlights, ...columnHighlights(highlightColumns)];
+}
+function urlLocation(uri) {
+    return uri ? { uri, locationType: 'UriLocation' } : undefined;
+}
+/** each filehandle prop, or the URL prop standing in for it */
+export function fileLocations({ msaFilehandle, treeFilehandle, gffFilehandle, msaUrl, treeUrl, gffUrl, }) {
+    return {
+        msaFilehandle: msaFilehandle ?? urlLocation(msaUrl),
+        treeFilehandle: treeFilehandle ?? urlLocation(treeUrl),
+        gffFilehandle: gffFilehandle ?? urlLocation(gffUrl),
+    };
+}
+export function resolveTheme(theme) {
+    return createJBrowseTheme(theme === 'dark'
+        ? { palette: { mode: 'dark' } }
+        : typeof theme === 'object'
+            ? theme
+            : undefined);
+}
+/**
+ * The model snapshot `MSAViewer` creates from its props. The CLI's `--props`
+ * reads the same JSON the R and Python widgets send, so a figure exported
+ * headlessly draws what the widget drew.
+ */
+export function viewerSnapshot(props) {
+    const { msa, tree, gff, rowData, colorScheme, height, colWidth, rowHeight, allowedGappyness, highlightColumns, highlights, features, selection, clades, relativeTo, columnTracks, residueMappings, encodings, rowPanels, drawTree, treeAreaWidth, showBranchLen, treeOrder, treeRoot, region, residueEncoding, } = props;
+    const { msaFilehandle, treeFilehandle, gffFilehandle } = fileLocations(props);
+    return {
+        type: 'MsaView',
+        ...(msa || tree || gff || rowData
+            ? {
+                data: {
+                    msa: msa ?? '',
+                    tree: tree ?? '',
+                    gff,
+                    // the row table is stored as this JSON string, which is what a
+                    // shared URL and the size limit already cover
+                    ...(rowData ? { treeMetadata: JSON.stringify(rowData) } : {}),
+                },
+            }
+            : {}),
+        ...(msaFilehandle ? { msaFilehandle } : {}),
+        ...(treeFilehandle ? { treeFilehandle } : {}),
+        ...(gffFilehandle ? { gffFilehandle } : {}),
+        ...colorSchemeSnapshot(colorScheme),
+        ...(height ? { height } : {}),
+        ...(colWidth ? { colWidth } : {}),
+        ...(rowHeight ? { rowHeight } : {}),
+        ...(allowedGappyness !== undefined ? { allowedGappyness } : {}),
+        ...(highlights || highlightColumns
+            ? { highlights: viewerHighlights({ highlights, highlightColumns }) }
+            : {}),
+        ...(features ? { features } : {}),
+        ...(selection ? { selection } : {}),
+        ...(clades ? { clades } : {}),
+        ...(relativeTo ? { relativeTo } : {}),
+        ...(columnTracks ? { columnTracks } : {}),
+        ...(residueMappings ? { residueMappings } : {}),
+        ...(encodings ? { encodings } : {}),
+        ...(rowPanels ? { rowPanels } : {}),
+        ...(drawTree !== undefined ? { drawTree } : {}),
+        ...(treeAreaWidth ? { treeAreaWidth } : {}),
+        ...(showBranchLen !== undefined ? { showBranchLen } : {}),
+        ...(treeOrder ? { treeOrder } : {}),
+        ...(treeRoot ? { treeRoot } : {}),
+        ...(region ? { region } : {}),
+        ...(residueEncoding !== undefined
+            ? { bgColor: residueEncoding === 'fill' }
+            : {}),
+    };
+}
+//# sourceMappingURL=viewerSnapshot.js.map

package/dist/viewerSnapshot.js.map

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package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "react-msaview",
   "author": "Colin",
-  "version": "9.0.0",
+  "version": "9.1.0",
   "license": "MIT",
   "type": "module",
   "repository": {
@@ -50,10 +50,10 @@
   },
   "dependencies": {
     "@gmod/newick": "^1.0.3",
-    "@jbrowse/svgcanvas": "9.0.0",
+    "@jbrowse/svgcanvas": "9.1.0",
     "colord": "^2.10.0",
     "flatbush": "^4.6.2",
-    "msa-parsers": "9.0.0"
+    "msa-parsers": "9.1.0"
   },
   "scripts": {
     "clean": "rimraf dist bundle",

package/src/colorSchemes.ts

@@ -1,11 +1,8 @@
 import { blue, green, orange, red } from '@mui/material/colors'
-import { colord, extend } from 'colord'
-import namesPlugin from 'colord/plugins/names'
+import { colord } from 'colord'
 
 import { transform } from './util.ts'
 
-extend([namesPlugin])
-
 // standard A/C/G/T(/U) coloring, shared by the `jbrowse_dna` and `nucleotide`
 // scheme names
 const dna = {

package/src/columnCounts.ts

@@ -44,7 +44,7 @@ function slotOf(code: number) {
   return code < 128 ? slotOfCode[code]! : OTHER
 }
 
-export function isGapSlot(slot: number) {
+function isGapSlot(slot: number) {
   return slot === DASH || slot === DOT
 }
 

package/src/components/Loading.tsx

@@ -21,15 +21,17 @@ const Reset = observer(function ({
   return (
     <div>
       <ErrorMessage error={error} />
-      <Button
-        variant="contained"
-        color="primary"
-        onClick={() => {
-          model.reset()
-        }}
-      >
-        Return to import form
-      </Button>
+      {model.importForm ? (
+        <Button
+          variant="contained"
+          color="primary"
+          onClick={() => {
+            model.reset()
+          }}
+        >
+          Return to import form
+        </Button>
+      ) : null}
     </div>
   )
 })
@@ -43,6 +45,7 @@ const Loading = observer(function ({ model }: { model: MsaViewModel }) {
     resetCount,
     msaFilehandle,
     treeFilehandle,
+    importForm,
   } = model
   const hasData = !!(data.msa || data.tree)
   // a failed load keeps its filehandle, so the error outranks the spinner
@@ -68,9 +71,13 @@ const Loading = observer(function ({ model }: { model: MsaViewModel }) {
         ) : (
           <>
             {loading ? <StatusMessage model={model} variant="page" /> : null}
-            <div style={{ display: loading ? 'none' : undefined }}>
-              <ImportForm model={model} />
-            </div>
+            {importForm ? (
+              <div style={{ display: loading ? 'none' : undefined }}>
+                <ImportForm model={model} />
+              </div>
+            ) : error ? (
+              <ErrorMessage error={error} />
+            ) : null}
           </>
         )}
       </ErrorBoundary>