react-msaview 5.10.0 → 6.0.0

package/dist/model.d.ts

@@ -1,14 +1,14 @@
 import type { HierarchyNode } from './hierarchy.ts';
-import type { InterProScanResults } from './launchInterProScan.ts';
-import type { BasicTrack, DomainBand, NodeWithIds, NodeWithIdsAndLength } from './types.ts';
+import type { Annotation, BasicTrack, DomainBand, NodeWithIds, NodeWithIdsAndLength } from './types.ts';
 import type { FileLocation as FileLocationType } from '@jbrowse/core/util/types';
 import type { Instance } from '@jbrowse/mobx-state-tree';
 import type { Theme } from '@mui/material';
+import type { InterProScanResults } from 'msa-parsers';
 /**
  * #stateModel MsaView
  *
  * The main MSAView state model. Holds the loaded alignment, tree, and optional
- * InterProScan domain annotations, plus all display state (color scheme, zoom,
+ * overlay annotations, plus all display state (color scheme, zoom,
  * scroll, collapsed clades). It composes in members from `DialogQueueSessionMixin`,
  * `Tree`, and `MSAModel` (see Inherited members below). Data is loaded reactively
  * from the `msaFilehandle` / `treeFilehandle` / `gffFilehandle` properties, or set
@@ -405,7 +405,7 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
     }>, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
     /**
      * #property
-     * filehandle object for InterProScan GFF file
+     * filehandle object for a GFF file of overlay annotations
      */
     gffFilehandle: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISnapshotProcessor<import("@jbrowse/mobx-state-tree").ITypeUnion<import("@jbrowse/mobx-state-tree").ModelCreationType<{
         locationType: "LocalPathLocation";
@@ -674,8 +674,12 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
     error: unknown;
     /**
      * #volatile
+     * overlay annotations drawn on the alignment, whatever their source.
+     * Every source -- InterProScan, GFF, a user upload -- converts to this
+     * flat list before it reaches the model, so nothing downstream of here
+     * knows which one it came from
      */
-    interProAnnotations: undefined | Record<string, InterProScanResults>;
+    annotations: Annotation[];
 } & {
     /**
      * #action
@@ -740,7 +744,7 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
     setHighlightedColumns(columns?: number[]): void;
     /**
      * #action
-     * toggle the InterProScan protein-domain overlay on the alignment
+     * toggle the annotation overlay on the alignment
      */
     setShowDomains(arg: boolean): void;
     /**
@@ -767,11 +771,6 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
      * set col width (px)
      */
     setColWidth(n: number): void;
-    /**
-     * #action
-     * set scroll Y-offset (px)
-     */
-    setScrollY(n: number): void;
     /**
      * #action
      *
@@ -938,10 +937,6 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
      * #getter
      */
     readonly blanks: number[];
-    /**
-     * #getter
-     */
-    readonly blanksSet: Set<number>;
     /**
      * #getter
      * Returns a map of row name to array of insertions with display position and letters
@@ -989,11 +984,6 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
      * #getter
      */
     readonly colStats: import("./columnCounts.ts").ColumnCounts;
-    /**
-     * #getter
-     * per-column residue totals (gaps included)
-     */
-    readonly colStatsSums: Uint32Array<ArrayBufferLike>;
     /**
      * #getter
      * Detects sequence type based on letters present in the alignment.
@@ -1173,9 +1163,21 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
     doScrollY(deltaY: number): void;
     /**
      * #action
-     * Set domain annotations and reveal the overlay in a single step (or clear
-     * both when passed undefined). Shared by every domain source: InterProScan,
-     * GFF, user-provided uploads, and NCBI CDD.
+     * set scroll Y-offset (px), clamped to keep the alignment in view
+     */
+    setScrollY(n: number): void;
+    /**
+     * #action
+     * Set the overlay annotations and reveal the overlay in a single step (an
+     * empty list clears both). Every source funnels through here after its
+     * own adapter has flattened it: InterProScan, GFF, user uploads, NCBI CDD.
+     */
+    setAnnotations(annotations: Annotation[]): void;
+    /**
+     * #action
+     * set the overlay from raw InterProScan results keyed by row name. Kept
+     * for downstream plugins that hold the EBI wire format; new code should
+     * adapt to Annotation[] and call setAnnotations.
      */
     setDomains(data?: Record<string, InterProScanResults>): void;
     applyGFFText(gffText: string): void;
@@ -1303,46 +1305,13 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
      * total height of track area (px)
      */
     readonly totalTrackAreaHeight: number;
-    readonly tidyInterProAnnotationTypes: Map<string, {
-        id: string;
-        name: string;
-        accession: string;
-        description: string;
-        featureType: string | undefined;
-        start: number;
-        end: number;
-        strand: number | undefined;
-    }>;
-    readonly tidyInterProAnnotations: {
-        id: string;
-        name: string;
-        accession: string;
-        description: string;
-        featureType: string | undefined;
-        start: number;
-        end: number;
-        strand: number | undefined;
-    }[];
-    readonly tidyFilteredInterProAnnotations: {
-        id: string;
-        name: string;
-        accession: string;
-        description: string;
-        featureType: string | undefined;
-        start: number;
-        end: number;
-        strand: number | undefined;
-    }[];
-    readonly tidyFilteredGatheredInterProAnnotations: Record<string, {
-        id: string;
-        name: string;
-        accession: string;
-        description: string;
-        featureType: string | undefined;
-        start: number;
-        end: number;
-        strand: number | undefined;
-    }[]>;
+    /**
+     * one representative annotation per accession, which is what the legend,
+     * the filter dialog and the palettes key off
+     */
+    readonly annotationTypes: Map<string, Annotation>;
+    readonly filteredAnnotations: Annotation[];
+    readonly annotationsByRow: Record<string, Annotation[]>;
 } & {
     /**
      * #getter
@@ -1353,37 +1322,26 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
      * #getter
      */
     readonly verticalScrollbarWidth: 0 | 20;
+    /**
+     * #getter
+     * width of the alignment canvas itself: the msa area less the vertical
+     * scrollbar sitting in it. Not usable from showHorizontalScrollbar, which
+     * feeds msaAreaHeight -> showVerticalScrollbar and would close a cycle
+     */
+    readonly msaCanvasWidth: number;
     /**
      * #getter
      * ordinal segment types (exons etc.), ordered by sequence position so
      * exon-1..exon-14 read left-to-right; colored by alternating shade and
      * labeled by number rather than each getting a distinct hue + legend row
      */
-    readonly segmentDomainTypes: {
-        id: string;
-        name: string;
-        accession: string;
-        description: string;
-        featureType: string | undefined;
-        start: number;
-        end: number;
-        strand: number | undefined;
-    }[];
+    readonly segmentDomainTypes: Annotation[];
     /**
      * #getter
      * categorical feature types (InterPro domains and the like) that each get
      * their own color and a legend entry
      */
-    readonly categoricalDomainTypes: {
-        id: string;
-        name: string;
-        accession: string;
-        description: string;
-        featureType: string | undefined;
-        start: number;
-        end: number;
-        strand: number | undefined;
-    }[];
+    readonly categoricalDomainTypes: Annotation[];
     readonly fillPalette: {
         [x: string]: string;
     };
@@ -1403,24 +1361,16 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
      * (exons) are excluded — they read as a numbered gene model, not a color
      * key — so this is the categorical types ordered by sequence position
      */
-    readonly visibleDomainTypes: {
-        id: string;
-        name: string;
-        accession: string;
-        description: string;
-        featureType: string | undefined;
-        start: number;
-        end: number;
-        strand: number | undefined;
-    }[];
+    readonly visibleDomainTypes: Annotation[];
     /**
      * #getter
-     * every filtered-on domain annotation resolved to the visible column span
-     * it is drawn across, keyed by row name and in draw order (largest first,
-     * as tidyInterProAnnotations orders them). Resolving these once here rather
-     * than inside each canvas block removes a per-feature, per-block sequence
-     * position conversion from every redraw, and gives the letter renderer the
-     * band colors it needs to keep residues readable on top of the boxes.
+     * every filtered-on annotation resolved to the visible column span it is
+     * drawn across, keyed by row name. Each row is ordered longest-first so a
+     * short domain nested inside a long one draws on top of it rather than
+     * under it. Resolving these once here rather than inside each canvas
+     * block removes a per-feature, per-block sequence position conversion
+     * from every redraw, and gives the letter renderer the band colors it
+     * needs to keep residues readable on top of the boxes.
      */
     readonly domainBands: Map<string, DomainBand[]>;
     /**
@@ -1434,7 +1384,7 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
      * domain annotations under the mouse, hit-tested against the exact visible
      * column span each box is drawn at (so it matches the overlay across gaps)
      */
-    readonly mouseOverDomains: import("./types.ts").TidyDomainAnnotation[];
+    readonly mouseOverDomains: Annotation[];
     /**
      * #getter
      * row index of the reference row (`relativeTo`), undefined when unset