react-msaview 6.4.2 → 7.0.0

package/dist/rowCoordinateCalculations.js

@@ -1,4 +1,3 @@
-import { isBlank } from './util.js';
 /**
  * MSA Coordinate Systems:
  *
@@ -82,44 +81,21 @@ export function visibleColsBefore(blanks, globalCol) {
     return globalCol - countBlanksBefore(blanks, globalCol);
 }
 /**
- * Convert a visible column to a row-specific sequence position.
- * Returns undefined if the position is a gap in the sequence.
+ * The ungapped position a row holds at a global column, or undefined when that
+ * column is a gap in the row or past its end.
  *
- * @param seq - The row's sequence string (including gaps)
- * @param blanks - Sorted array of global column indices that are hidden
- * @param visibleCol - The visible column index
- * @returns The sequence position, or undefined if it's a gap
+ * A binary search of the row's seqPos index (ascending), not a scan of the row:
+ * this answers on every mouse move, and scanning a 30k-column row per event is
+ * the whole frame.
+ *
+ * @param index - The row's seqPos -> global column index (buildSeqPosIndex)
+ * @param globalCol - The global column index in the full MSA
  */
-export function visibleColToSeqPos({ seq, blanks, visibleCol, }) {
-    // First convert the visible column to global column
-    const globalCol = visibleColToGlobalCol(blanks, visibleCol);
-    const seqLen = seq.length;
-    // Check if the position in the sequence is a gap
-    if (globalCol < seqLen && isBlank(seq[globalCol])) {
+export function seqPosOfGlobalCol(index, globalCol) {
+    if (!index) {
         return undefined;
     }
-    // Count non-gap characters up to the global position
-    let seqPos = 0;
-    for (let i = 0; i < globalCol && i < seqLen; i++) {
-        if (!isBlank(seq[i])) {
-            seqPos++;
-        }
-    }
-    return globalCol < seqLen ? seqPos : undefined;
-}
-/**
- * Convert a visible column to a row-specific sequence position, with row lookup.
- *
- * @param rowName - The name of the row
- * @param visibleCol - The visible column index
- * @param rowMap - Map from row name to sequence string
- * @param blanks - Sorted array of global column indices that are hidden
- * @returns The sequence position, or undefined if row not found or position is a gap
- */
-export function visibleColToSeqPosForRow({ rowName, visibleCol, rowMap, blanks, }) {
-    const seq = rowMap.get(rowName);
-    return seq !== undefined
-        ? visibleColToSeqPos({ seq, visibleCol, blanks })
-        : undefined;
+    const seqPos = partitionPoint(index.length, i => index[i] >= globalCol);
+    return index[seqPos] === globalCol ? seqPos : undefined;
 }
 //# sourceMappingURL=rowCoordinateCalculations.js.map

package/dist/rowCoordinateCalculations.js.map

@@ -1 +1 @@
-{"version":3,"file":"rowCoordinateCalculations.js","sourceRoot":"","sources":["../src/rowCoordinateCalculations.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAA;AAEnC;;;;;;;;;;;;;;;;GAgBG;AAEH;;;;GAIG;AACH,SAAS,cAAc,CAAC,GAAW,EAAE,IAA4B;IAC/D,IAAI,IAAI,GAAG,CAAC,CAAA;IACZ,IAAI,KAAK,GAAG,GAAG,CAAA;IACf,OAAO,IAAI,GAAG,KAAK,EAAE,CAAC;QACpB,MAAM,GAAG,GAAG,CAAC,IAAI,GAAG,KAAK,CAAC,KAAK,CAAC,CAAA;QAChC,IAAI,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC;YACd,KAAK,GAAG,GAAG,CAAA;QACb,CAAC;aAAM,CAAC;YACN,IAAI,GAAG,GAAG,GAAG,CAAC,CAAA;QAChB,CAAC;IACH,CAAC;IACD,OAAO,IAAI,CAAA;AACb,CAAC;AAED;;;;;;;GAOG;AACH,MAAM,UAAU,qBAAqB,CAAC,MAAgB,EAAE,UAAkB;IACxE,2EAA2E;IAC3E,4EAA4E;IAC5E,6EAA6E;IAC7E,OAAO,CACL,UAAU,GAAG,cAAc,CAAC,MAAM,CAAC,MAAM,EAAE,CAAC,CAAC,EAAE,CAAC,MAAM,CAAC,CAAC,CAAE,GAAG,CAAC,GAAG,UAAU,CAAC,CAC7E,CAAA;AACH,CAAC;AAED;;;;;;;GAOG;AACH,MAAM,UAAU,qBAAqB,CACnC,MAAgB,EAChB,SAAiB;IAEjB,MAAM,YAAY,GAAG,iBAAiB,CAAC,MAAM,EAAE,SAAS,CAAC,CAAA;IACzD,OAAO,MAAM,CAAC,YAAY,CAAC,KAAK,SAAS;QACvC,CAAC,CAAC,SAAS,CAAC,mBAAmB;QAC/B,CAAC,CAAC,SAAS,GAAG,YAAY,CAAA;AAC9B,CAAC;AAED,SAAS,iBAAiB,CAAC,MAAgB,EAAE,SAAiB;IAC5D,OAAO,cAAc,CAAC,MAAM,CAAC,MAAM,EAAE,CAAC,CAAC,EAAE,CAAC,MAAM,CAAC,CAAC,CAAE,IAAI,SAAS,CAAC,CAAA;AACpE,CAAC;AAED;;;;;;;;;;;GAWG;AACH,MAAM,UAAU,iBAAiB,CAAC,MAAgB,EAAE,SAAiB;IACnE,OAAO,SAAS,GAAG,iBAAiB,CAAC,MAAM,EAAE,SAAS,CAAC,CAAA;AACzD,CAAC;AAED;;;;;;;;GAQG;AACH,MAAM,UAAU,kBAAkB,CAAC,EACjC,GAAG,EACH,MAAM,EACN,UAAU,GAKX;IACC,oDAAoD;IACpD,MAAM,SAAS,GAAG,qBAAqB,CAAC,MAAM,EAAE,UAAU,CAAC,CAAA;IAC3D,MAAM,MAAM,GAAG,GAAG,CAAC,MAAM,CAAA;IAEzB,iDAAiD;IACjD,IAAI,SAAS,GAAG,MAAM,IAAI,OAAO,CAAC,GAAG,CAAC,SAAS,CAAC,CAAC,EAAE,CAAC;QAClD,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,qDAAqD;IACrD,IAAI,MAAM,GAAG,CAAC,CAAA;IACd,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,SAAS,IAAI,CAAC,GAAG,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;QACjD,IAAI,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC;YACrB,MAAM,EAAE,CAAA;QACV,CAAC;IACH,CAAC;IAED,OAAO,SAAS,GAAG,MAAM,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,SAAS,CAAA;AAChD,CAAC;AAED;;;;;;;;GAQG;AACH,MAAM,UAAU,wBAAwB,CAAC,EACvC,OAAO,EACP,UAAU,EACV,MAAM,EACN,MAAM,GAMP;IACC,MAAM,GAAG,GAAG,MAAM,CAAC,GAAG,CAAC,OAAO,CAAC,CAAA;IAC/B,OAAO,GAAG,KAAK,SAAS;QACtB,CAAC,CAAC,kBAAkB,CAAC,EAAE,GAAG,EAAE,UAAU,EAAE,MAAM,EAAE,CAAC;QACjD,CAAC,CAAC,SAAS,CAAA;AACf,CAAC"}
+{"version":3,"file":"rowCoordinateCalculations.js","sourceRoot":"","sources":["../src/rowCoordinateCalculations.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;GAgBG;AAEH;;;;GAIG;AACH,SAAS,cAAc,CAAC,GAAW,EAAE,IAA4B;IAC/D,IAAI,IAAI,GAAG,CAAC,CAAA;IACZ,IAAI,KAAK,GAAG,GAAG,CAAA;IACf,OAAO,IAAI,GAAG,KAAK,EAAE,CAAC;QACpB,MAAM,GAAG,GAAG,CAAC,IAAI,GAAG,KAAK,CAAC,KAAK,CAAC,CAAA;QAChC,IAAI,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC;YACd,KAAK,GAAG,GAAG,CAAA;QACb,CAAC;aAAM,CAAC;YACN,IAAI,GAAG,GAAG,GAAG,CAAC,CAAA;QAChB,CAAC;IACH,CAAC;IACD,OAAO,IAAI,CAAA;AACb,CAAC;AAED;;;;;;;GAOG;AACH,MAAM,UAAU,qBAAqB,CAAC,MAAgB,EAAE,UAAkB;IACxE,2EAA2E;IAC3E,4EAA4E;IAC5E,6EAA6E;IAC7E,OAAO,CACL,UAAU,GAAG,cAAc,CAAC,MAAM,CAAC,MAAM,EAAE,CAAC,CAAC,EAAE,CAAC,MAAM,CAAC,CAAC,CAAE,GAAG,CAAC,GAAG,UAAU,CAAC,CAC7E,CAAA;AACH,CAAC;AAED;;;;;;;GAOG;AACH,MAAM,UAAU,qBAAqB,CACnC,MAAgB,EAChB,SAAiB;IAEjB,MAAM,YAAY,GAAG,iBAAiB,CAAC,MAAM,EAAE,SAAS,CAAC,CAAA;IACzD,OAAO,MAAM,CAAC,YAAY,CAAC,KAAK,SAAS;QACvC,CAAC,CAAC,SAAS,CAAC,mBAAmB;QAC/B,CAAC,CAAC,SAAS,GAAG,YAAY,CAAA;AAC9B,CAAC;AAED,SAAS,iBAAiB,CAAC,MAAgB,EAAE,SAAiB;IAC5D,OAAO,cAAc,CAAC,MAAM,CAAC,MAAM,EAAE,CAAC,CAAC,EAAE,CAAC,MAAM,CAAC,CAAC,CAAE,IAAI,SAAS,CAAC,CAAA;AACpE,CAAC;AAED;;;;;;;;;;;GAWG;AACH,MAAM,UAAU,iBAAiB,CAAC,MAAgB,EAAE,SAAiB;IACnE,OAAO,SAAS,GAAG,iBAAiB,CAAC,MAAM,EAAE,SAAS,CAAC,CAAA;AACzD,CAAC;AAED;;;;;;;;;;GAUG;AACH,MAAM,UAAU,iBAAiB,CAC/B,KAA6B,EAC7B,SAAiB;IAEjB,IAAI,CAAC,KAAK,EAAE,CAAC;QACX,OAAO,SAAS,CAAA;IAClB,CAAC;IACD,MAAM,MAAM,GAAG,cAAc,CAAC,KAAK,CAAC,MAAM,EAAE,CAAC,CAAC,EAAE,CAAC,KAAK,CAAC,CAAC,CAAE,IAAI,SAAS,CAAC,CAAA;IACxE,OAAO,KAAK,CAAC,MAAM,CAAC,KAAK,SAAS,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,SAAS,CAAA;AACzD,CAAC"}

package/dist/seqPosToGlobalCol.js

@@ -19,6 +19,8 @@ export function buildSeqPosIndex(row) {
             index[n++] = col;
         }
     }
-    return index.subarray(0, n);
+    // slice, not subarray: a subarray keeps the whole row-length buffer alive,
+    // and a gappy alignment's indexes are held for as long as the parse is
+    return index.slice(0, n);
 }
 //# sourceMappingURL=seqPosToGlobalCol.js.map

package/dist/seqPosToGlobalCol.js.map

@@ -1 +1 @@
-{"version":3,"file":"seqPosToGlobalCol.js","sourceRoot":"","sources":["../src/seqPosToGlobalCol.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;GAWG;AACH,MAAM,UAAU,gBAAgB,CAAC,GAAW;IAC1C,MAAM,KAAK,GAAG,IAAI,UAAU,CAAC,GAAG,CAAC,MAAM,CAAC,CAAA;IACxC,IAAI,CAAC,GAAG,CAAC,CAAA;IACT,KAAK,IAAI,GAAG,GAAG,CAAC,EAAE,GAAG,GAAG,GAAG,CAAC,MAAM,EAAE,GAAG,EAAE,EAAE,CAAC;QAC1C,oEAAoE;QACpE,IAAI,CAAC,CAAC,CAAC,GAAG,CAAC,UAAU,CAAC,GAAG,CAAC,GAAG,EAAE,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC,EAAE,CAAC;YAC7C,KAAK,CAAC,CAAC,EAAE,CAAC,GAAG,GAAG,CAAA;QAClB,CAAC;IACH,CAAC;IACD,OAAO,KAAK,CAAC,QAAQ,CAAC,CAAC,EAAE,CAAC,CAAC,CAAA;AAC7B,CAAC"}
+{"version":3,"file":"seqPosToGlobalCol.js","sourceRoot":"","sources":["../src/seqPosToGlobalCol.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;GAWG;AACH,MAAM,UAAU,gBAAgB,CAAC,GAAW;IAC1C,MAAM,KAAK,GAAG,IAAI,UAAU,CAAC,GAAG,CAAC,MAAM,CAAC,CAAA;IACxC,IAAI,CAAC,GAAG,CAAC,CAAA;IACT,KAAK,IAAI,GAAG,GAAG,CAAC,EAAE,GAAG,GAAG,GAAG,CAAC,MAAM,EAAE,GAAG,EAAE,EAAE,CAAC;QAC1C,oEAAoE;QACpE,IAAI,CAAC,CAAC,CAAC,GAAG,CAAC,UAAU,CAAC,GAAG,CAAC,GAAG,EAAE,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC,EAAE,CAAC;YAC7C,KAAK,CAAC,CAAC,EAAE,CAAC,GAAG,GAAG,CAAA;QAClB,CAAC;IACH,CAAC;IACD,2EAA2E;IAC3E,uEAAuE;IACvE,OAAO,KAAK,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,CAAC,CAAA;AAC1B,CAAC"}

package/dist/svgTestUtil.d.ts

@@ -15,7 +15,7 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     colorSchemeName: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
     showColumnStats: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     msaFormat: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<import("msa-parsers").MSAFormat>>;
-}, "allowedGappyness" | "colWidth" | "collapsed" | "columnTracks" | "currentAlignment" | "data" | "drawMsaLetters" | "featureFilters" | "gffFilehandle" | "height" | "hideGaps" | "highlightColumns" | "highlights" | "id" | "msaFilehandle" | "relativeTo" | "rowHeight" | "scrollX" | "scrollY" | "scrollZoom" | "showDomainLegend" | "showDomains" | "showOnly" | "subFeatureRows" | "treeFilehandle" | "treeMetadataFilehandle" | "turnedOffTracks" | "type"> & {
+}, "allowedGappyness" | "colWidth" | "collapsed" | "columnTracks" | "currentAlignment" | "data" | "drawMsaLetters" | "gffFilehandle" | "height" | "hideGaps" | "highlightColumns" | "highlights" | "id" | "msaFilehandle" | "relativeTo" | "residueMappings" | "rowHeight" | "scrollX" | "scrollY" | "scrollZoom" | "showDomainLegend" | "showDomains" | "showOnly" | "subFeatureRows" | "treeFilehandle" | "treeMetadataFilehandle" | "turnedOffFeatures" | "turnedOffTracks" | "type"> & {
     id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
     showDomains: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     showDomainLegend: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
@@ -411,6 +411,7 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     showOnly: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
     turnedOffTracks: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>, [undefined]>;
     columnTracks: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<import("./types.ts").ColumnTrackSpec, import("./types.ts").ColumnTrackSpec, import("./types.ts").ColumnTrackSpec>>, [undefined]>;
+    residueMappings: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<import("./types.ts").ResidueMapping, import("./types.ts").ResidueMapping, import("./types.ts").ResidueMapping>>, [undefined]>;
     data: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IModelType<{
         tree: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
         msa: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
@@ -424,7 +425,7 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     }, import("@jbrowse/mobx-state-tree")._NotCustomized, {
         [k: string]: string | undefined;
     }>, [undefined]>;
-    featureFilters: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>, [undefined]>;
+    turnedOffFeatures: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>, [undefined]>;
     relativeTo: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
     highlightColumns: import("@jbrowse/mobx-state-tree").IType<number[] | undefined, number[] | undefined, number[] | undefined>;
     highlights: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<import("./types.ts").Highlight, import("./types.ts").Highlight, import("./types.ts").Highlight>>, [undefined]>;
@@ -454,7 +455,6 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     headerHeight: number;
     status: {
         msg: string;
-        url?: string;
         onCancel?: () => void;
     } | undefined;
     highResScaleFactor: number;
@@ -472,11 +472,17 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
         descendantNames: string[];
     } | undefined;
     highlightedColumns: number[] | undefined;
+    transientHighlights: Record<string, import("./types.ts").Highlight[]>;
     minimapHeight: number;
     conservationTrackHeight: number;
+    columnTrackHeights: Record<string, number>;
     sequenceLogoTrackHeight: number;
+    arcTrackHeight: number;
     marginLeft: number;
     error: unknown;
+    warnings: string[];
+    resetCount: number;
+    hostCarriesData: boolean;
     annotations: import("msa-parsers").Annotation[];
 } & {
     drawRelativeTo(id: string | undefined): void;
@@ -488,9 +494,14 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     setHighResScaleFactor(arg: number): void;
     setHeight(height: number): void;
     setError(error?: unknown): void;
+    addWarning(warning: string): void;
+    clearWarnings(): void;
+    setHostCarriesData(arg: boolean): void;
     setMousePos(col?: number, row?: number): void;
     setHighlightedColumns(columns?: number[]): void;
     setHighlights(highlights: import("./types.ts").Highlight[]): void;
+    applyHighlight(owner: string, highlights: import("./types.ts").Highlight[]): void;
+    clearHighlight(owner: string): void;
     setShowDomains(arg: boolean): void;
     setShowDomainLegend(arg: boolean): void;
     setSubFeatureRows(arg: boolean): void;
@@ -513,14 +524,15 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     setMSA(result: string): void;
     setTree(result: string): void;
     setTreeMetadata(result: string): void;
+    setGFF(result: string): void;
 } & {
     readonly hideGapsEffective: boolean;
     readonly realAllowedGappyness: number;
     readonly actuallyShowDomains: boolean;
+    readonly hostRestoresData: boolean;
     readonly viewInitialized: boolean;
     readonly width: number;
 } & {
-    extraViewMenuItems(): never[];
     readonly colorScheme: Record<string, string>;
     readonly header: Record<string, unknown> | {
         info: string;
@@ -537,6 +549,7 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     readonly alignmentNames: string[];
     readonly noTree: boolean;
     readonly noDomains: boolean;
+    readonly unshareableData: import("./types.ts").UnshareableData[];
     menuItems(): never[];
     readonly treeMetadata: Record<string, Record<string, string> | undefined>;
     readonly MSA: import("msa-parsers").MSAParserType | null;
@@ -560,7 +573,7 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     }[]>;
     readonly rows: [string, string][];
     readonly numRows: number;
-    readonly seqPosGlobalColIndex: Map<string, Int32Array<ArrayBuffer>>;
+    seqPosIndex(rowName: string): Int32Array | undefined;
     readonly rowMap: Map<string, string>;
     readonly columns: Map<string, string>;
     readonly columns2d: string[];
@@ -578,29 +591,74 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     readonly hierarchy: import("./hierarchy.ts").HierarchyNode<import("./types.ts").NodeWithIdsAndLength>;
     readonly totalHeight: number;
     readonly leaves: import("./hierarchy.ts").HierarchyNode<import("./types.ts").NodeWithIdsAndLength>[];
+    readonly rootToTipLength: number;
     readonly maxBranchLength: number;
+    readonly pxPerBranchLength: number;
     readonly maxDepthToLeaf: number;
     readonly allBranchesLength0: boolean;
     readonly showBranchLenEffective: boolean;
 } & {
     readonly totalWidth: number;
+} & {
+    readonly showMsaLetters: boolean;
+    readonly showTreeText: boolean;
+} & {
+    readonly labelWidthMap: Map<string, number>;
+    readonly labelWidthScale: number;
+    readonly labelsWidth: number;
+    readonly secondaryStructureConsensus: string | undefined;
+    readonly seqConsensus: string | undefined;
+    readonly secondaryStructureArcs: import("./types.ts").Arc[] | undefined;
+    readonly adapterTrackModels: import("./types.ts").BasicTrack[];
+    readonly columnTrackContent: Map<string, {
+        values?: number[];
+        data?: string;
+        arcs?: import("./types.ts").Arc[];
+    }>;
+    readonly columnTrackModels: import("./types.ts").BasicTrack[];
+    readonly basePairTrackModels: import("./types.ts").BasicTrack[];
+    readonly computedTrackModels: import("./types.ts").BasicTrack[];
+    readonly tracks: import("./types.ts").BasicTrack[];
+    readonly turnedOnTracks: import("./types.ts").BasicTrack[];
+    readonly showHorizontalScrollbar: boolean;
+    visibleColToRowLetter(rowName: string, visibleCol: number): string | undefined;
+    visibleColToSeqPos(rowName: string, visibleCol: number): number | undefined;
+    visibleColToSeqPosOneBased(rowName: string, visibleCol: number): number | undefined;
+    globalColToVisibleCol(globalCol: number): number | undefined;
+    visibleColToGlobalCol(visibleCol: number): number;
+    seqPosToGlobalCol(rowName: string, seqPos: number): number | undefined;
+    seqPosToVisibleCol(rowName: string, seqPos: number): number | undefined;
+    readonly residueMappingProblems: import("./types.ts").ResidueMappingProblem[];
+    readonly usableResidueMappings: import("./types.ts").ResidueMapping[];
+    readonly mappedStructures: {
+        row: string;
+        structure: import("./types.ts").MappedStructure;
+    }[];
+    structureResidue(rowName: string, seqPos: number, structureId?: string): import("./types.ts").StructureResidue | undefined;
+    rowResidue(structureId: string, position: number, asymId?: string): import("./types.ts").RowResidue | undefined;
+} & {
+    readonly msaAreaHeight: number;
+    readonly totalTrackAreaHeight: number;
+    readonly annotationTypes: Map<string, import("msa-parsers").Annotation>;
+    readonly filteredAnnotations: import("msa-parsers").Annotation[];
+    readonly annotationsByRow: Record<string, import("msa-parsers").Annotation[]>;
+} & {
+    readonly showVerticalScrollbar: boolean;
 } & {
     readonly dataInitialized: boolean;
     readonly blocksX: number[];
     readonly blocksY: number[];
-    readonly visibleMsaHeight: number;
 } & {
     readonly blocks2d: (readonly [number, number])[];
     readonly isLoading: boolean;
     readonly maxScrollX: number;
     readonly maxScrollY: number;
-    readonly showMsaLetters: boolean;
-    readonly showTreeText: boolean;
 } & {
     setDrawMsaLetters(arg: boolean): void;
     setScrollZoom(arg: boolean): void;
     setHoveredTreeNode(nodeId?: string): void;
     calculateNeighborJoiningTreeFromMSA(): void;
+    replaceTree(newick: string): void;
     resetZoom(): void;
     zoomOutHorizontal(): void;
     zoomInHorizontal(): void;
@@ -617,41 +675,12 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     doScrollX(deltaX: number): void;
     setScrollX(n: number): void;
     setColumnTracks(tracks: import("./types.ts").ColumnTrackSpec[]): void;
+    setResidueMappings(mappings: import("./types.ts").ResidueMapping[]): void;
     toggleTrack(id: string): void;
     setStatus(status?: {
         msg: string;
-        url?: string;
         onCancel?: () => void;
     }): void;
-} & {
-    readonly labelWidthMap: Map<string, number>;
-    readonly labelWidthScale: number;
-    readonly labelsWidth: number;
-    readonly secondaryStructureConsensus: string | undefined;
-    readonly seqConsensus: string | undefined;
-    readonly adapterTrackModels: import("./types.ts").BasicTrack[];
-    readonly columnTrackContent: Map<string, {
-        values?: number[];
-        data?: string;
-    }>;
-    readonly columnTrackModels: import("./types.ts").BasicTrack[];
-    readonly tracks: import("./types.ts").BasicTrack[];
-    readonly turnedOnTracks: import("./types.ts").BasicTrack[];
-    readonly showHorizontalScrollbar: boolean;
-    visibleColToRowLetter(rowName: string, visibleCol: number): string | undefined;
-    visibleColToSeqPos(rowName: string, visibleCol: number): number | undefined;
-    visibleColToSeqPosOneBased(rowName: string, visibleCol: number): number | undefined;
-    globalColToVisibleCol(globalCol: number): number | undefined;
-    seqPosToGlobalCol(rowName: string, seqPos: number): number;
-    seqPosToVisibleCol(rowName: string, seqPos: number): number | undefined;
-} & {
-    readonly msaAreaHeight: number;
-    readonly totalTrackAreaHeight: number;
-    readonly annotationTypes: Map<string, import("msa-parsers").Annotation>;
-    readonly filteredAnnotations: import("msa-parsers").Annotation[];
-    readonly annotationsByRow: Record<string, import("msa-parsers").Annotation[]>;
-} & {
-    readonly showVerticalScrollbar: boolean;
 } & {
     readonly verticalScrollbarWidth: 0 | 20;
     readonly msaCanvasWidth: number;
@@ -698,11 +727,12 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
 } & {
     setHeaderHeight(arg: number): void;
     setConservationTrackHeight(arg: number): void;
+    setColumnTrackHeight(id: string, height: number): void;
     setSequenceLogoTrackHeight(arg: number): void;
+    setArcTrackHeight(arg: number): void;
     reset(): void;
     exportSVG(opts: import("./renderToSvg.tsx").ExportSvgOptions): Promise<void>;
-    initFilter(arg: string): void;
-    setFilter(arg: string, flag: boolean): void;
+    setFilter(accession: string, shown: boolean): void;
     fit(): void;
     fitVertically(): void;
     fitHorizontally(): void;
@@ -721,7 +751,7 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     colorSchemeName: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
     showColumnStats: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     msaFormat: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<import("msa-parsers").MSAFormat>>;
-}, "allowedGappyness" | "colWidth" | "collapsed" | "columnTracks" | "currentAlignment" | "data" | "drawMsaLetters" | "featureFilters" | "gffFilehandle" | "height" | "hideGaps" | "highlightColumns" | "highlights" | "id" | "msaFilehandle" | "relativeTo" | "rowHeight" | "scrollX" | "scrollY" | "scrollZoom" | "showDomainLegend" | "showDomains" | "showOnly" | "subFeatureRows" | "treeFilehandle" | "treeMetadataFilehandle" | "turnedOffTracks" | "type"> & {
+}, "allowedGappyness" | "colWidth" | "collapsed" | "columnTracks" | "currentAlignment" | "data" | "drawMsaLetters" | "gffFilehandle" | "height" | "hideGaps" | "highlightColumns" | "highlights" | "id" | "msaFilehandle" | "relativeTo" | "residueMappings" | "rowHeight" | "scrollX" | "scrollY" | "scrollZoom" | "showDomainLegend" | "showDomains" | "showOnly" | "subFeatureRows" | "treeFilehandle" | "treeMetadataFilehandle" | "turnedOffFeatures" | "turnedOffTracks" | "type"> & {
     id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
     showDomains: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     showDomainLegend: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
@@ -1117,6 +1147,7 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     showOnly: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
     turnedOffTracks: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>, [undefined]>;
     columnTracks: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<import("./types.ts").ColumnTrackSpec, import("./types.ts").ColumnTrackSpec, import("./types.ts").ColumnTrackSpec>>, [undefined]>;
+    residueMappings: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<import("./types.ts").ResidueMapping, import("./types.ts").ResidueMapping, import("./types.ts").ResidueMapping>>, [undefined]>;
     data: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IModelType<{
         tree: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
         msa: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
@@ -1130,7 +1161,7 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     }, import("@jbrowse/mobx-state-tree")._NotCustomized, {
         [k: string]: string | undefined;
     }>, [undefined]>;
-    featureFilters: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>, [undefined]>;
+    turnedOffFeatures: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>, [undefined]>;
     relativeTo: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
     highlightColumns: import("@jbrowse/mobx-state-tree").IType<number[] | undefined, number[] | undefined, number[] | undefined>;
     highlights: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<import("./types.ts").Highlight, import("./types.ts").Highlight, import("./types.ts").Highlight>>, [undefined]>;
@@ -1160,7 +1191,6 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     headerHeight: number;
     status: {
         msg: string;
-        url?: string;
         onCancel?: () => void;
     } | undefined;
     highResScaleFactor: number;
@@ -1178,11 +1208,17 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
         descendantNames: string[];
     } | undefined;
     highlightedColumns: number[] | undefined;
+    transientHighlights: Record<string, import("./types.ts").Highlight[]>;
     minimapHeight: number;
     conservationTrackHeight: number;
+    columnTrackHeights: Record<string, number>;
     sequenceLogoTrackHeight: number;
+    arcTrackHeight: number;
     marginLeft: number;
     error: unknown;
+    warnings: string[];
+    resetCount: number;
+    hostCarriesData: boolean;
     annotations: import("msa-parsers").Annotation[];
 } & {
     drawRelativeTo(id: string | undefined): void;
@@ -1194,9 +1230,14 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     setHighResScaleFactor(arg: number): void;
     setHeight(height: number): void;
     setError(error?: unknown): void;
+    addWarning(warning: string): void;
+    clearWarnings(): void;
+    setHostCarriesData(arg: boolean): void;
     setMousePos(col?: number, row?: number): void;
     setHighlightedColumns(columns?: number[]): void;
     setHighlights(highlights: import("./types.ts").Highlight[]): void;
+    applyHighlight(owner: string, highlights: import("./types.ts").Highlight[]): void;
+    clearHighlight(owner: string): void;
     setShowDomains(arg: boolean): void;
     setShowDomainLegend(arg: boolean): void;
     setSubFeatureRows(arg: boolean): void;
@@ -1219,14 +1260,15 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     setMSA(result: string): void;
     setTree(result: string): void;
     setTreeMetadata(result: string): void;
+    setGFF(result: string): void;
 } & {
     readonly hideGapsEffective: boolean;
     readonly realAllowedGappyness: number;
     readonly actuallyShowDomains: boolean;
+    readonly hostRestoresData: boolean;
     readonly viewInitialized: boolean;
     readonly width: number;
 } & {
-    extraViewMenuItems(): never[];
     readonly colorScheme: Record<string, string>;
     readonly header: Record<string, unknown> | {
         info: string;
@@ -1243,6 +1285,7 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     readonly alignmentNames: string[];
     readonly noTree: boolean;
     readonly noDomains: boolean;
+    readonly unshareableData: import("./types.ts").UnshareableData[];
     menuItems(): never[];
     readonly treeMetadata: Record<string, Record<string, string> | undefined>;
     readonly MSA: import("msa-parsers").MSAParserType | null;
@@ -1266,7 +1309,7 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     }[]>;
     readonly rows: [string, string][];
     readonly numRows: number;
-    readonly seqPosGlobalColIndex: Map<string, Int32Array<ArrayBuffer>>;
+    seqPosIndex(rowName: string): Int32Array | undefined;
     readonly rowMap: Map<string, string>;
     readonly columns: Map<string, string>;
     readonly columns2d: string[];
@@ -1284,29 +1327,74 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     readonly hierarchy: import("./hierarchy.ts").HierarchyNode<import("./types.ts").NodeWithIdsAndLength>;
     readonly totalHeight: number;
     readonly leaves: import("./hierarchy.ts").HierarchyNode<import("./types.ts").NodeWithIdsAndLength>[];
+    readonly rootToTipLength: number;
     readonly maxBranchLength: number;
+    readonly pxPerBranchLength: number;
     readonly maxDepthToLeaf: number;
     readonly allBranchesLength0: boolean;
     readonly showBranchLenEffective: boolean;
 } & {
     readonly totalWidth: number;
+} & {
+    readonly showMsaLetters: boolean;
+    readonly showTreeText: boolean;
+} & {
+    readonly labelWidthMap: Map<string, number>;
+    readonly labelWidthScale: number;
+    readonly labelsWidth: number;
+    readonly secondaryStructureConsensus: string | undefined;
+    readonly seqConsensus: string | undefined;
+    readonly secondaryStructureArcs: import("./types.ts").Arc[] | undefined;
+    readonly adapterTrackModels: import("./types.ts").BasicTrack[];
+    readonly columnTrackContent: Map<string, {
+        values?: number[];
+        data?: string;
+        arcs?: import("./types.ts").Arc[];
+    }>;
+    readonly columnTrackModels: import("./types.ts").BasicTrack[];
+    readonly basePairTrackModels: import("./types.ts").BasicTrack[];
+    readonly computedTrackModels: import("./types.ts").BasicTrack[];
+    readonly tracks: import("./types.ts").BasicTrack[];
+    readonly turnedOnTracks: import("./types.ts").BasicTrack[];
+    readonly showHorizontalScrollbar: boolean;
+    visibleColToRowLetter(rowName: string, visibleCol: number): string | undefined;
+    visibleColToSeqPos(rowName: string, visibleCol: number): number | undefined;
+    visibleColToSeqPosOneBased(rowName: string, visibleCol: number): number | undefined;
+    globalColToVisibleCol(globalCol: number): number | undefined;
+    visibleColToGlobalCol(visibleCol: number): number;
+    seqPosToGlobalCol(rowName: string, seqPos: number): number | undefined;
+    seqPosToVisibleCol(rowName: string, seqPos: number): number | undefined;
+    readonly residueMappingProblems: import("./types.ts").ResidueMappingProblem[];
+    readonly usableResidueMappings: import("./types.ts").ResidueMapping[];
+    readonly mappedStructures: {
+        row: string;
+        structure: import("./types.ts").MappedStructure;
+    }[];
+    structureResidue(rowName: string, seqPos: number, structureId?: string): import("./types.ts").StructureResidue | undefined;
+    rowResidue(structureId: string, position: number, asymId?: string): import("./types.ts").RowResidue | undefined;
+} & {
+    readonly msaAreaHeight: number;
+    readonly totalTrackAreaHeight: number;
+    readonly annotationTypes: Map<string, import("msa-parsers").Annotation>;
+    readonly filteredAnnotations: import("msa-parsers").Annotation[];
+    readonly annotationsByRow: Record<string, import("msa-parsers").Annotation[]>;
+} & {
+    readonly showVerticalScrollbar: boolean;
 } & {
     readonly dataInitialized: boolean;
     readonly blocksX: number[];
     readonly blocksY: number[];
-    readonly visibleMsaHeight: number;
 } & {
     readonly blocks2d: (readonly [number, number])[];
     readonly isLoading: boolean;
     readonly maxScrollX: number;
     readonly maxScrollY: number;
-    readonly showMsaLetters: boolean;
-    readonly showTreeText: boolean;
 } & {
     setDrawMsaLetters(arg: boolean): void;
     setScrollZoom(arg: boolean): void;
     setHoveredTreeNode(nodeId?: string): void;
     calculateNeighborJoiningTreeFromMSA(): void;
+    replaceTree(newick: string): void;
     resetZoom(): void;
     zoomOutHorizontal(): void;
     zoomInHorizontal(): void;
@@ -1323,41 +1411,12 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     doScrollX(deltaX: number): void;
     setScrollX(n: number): void;
     setColumnTracks(tracks: import("./types.ts").ColumnTrackSpec[]): void;
+    setResidueMappings(mappings: import("./types.ts").ResidueMapping[]): void;
     toggleTrack(id: string): void;
     setStatus(status?: {
         msg: string;
-        url?: string;
         onCancel?: () => void;
     }): void;
-} & {
-    readonly labelWidthMap: Map<string, number>;
-    readonly labelWidthScale: number;
-    readonly labelsWidth: number;
-    readonly secondaryStructureConsensus: string | undefined;
-    readonly seqConsensus: string | undefined;
-    readonly adapterTrackModels: import("./types.ts").BasicTrack[];
-    readonly columnTrackContent: Map<string, {
-        values?: number[];
-        data?: string;
-    }>;
-    readonly columnTrackModels: import("./types.ts").BasicTrack[];
-    readonly tracks: import("./types.ts").BasicTrack[];
-    readonly turnedOnTracks: import("./types.ts").BasicTrack[];
-    readonly showHorizontalScrollbar: boolean;
-    visibleColToRowLetter(rowName: string, visibleCol: number): string | undefined;
-    visibleColToSeqPos(rowName: string, visibleCol: number): number | undefined;
-    visibleColToSeqPosOneBased(rowName: string, visibleCol: number): number | undefined;
-    globalColToVisibleCol(globalCol: number): number | undefined;
-    seqPosToGlobalCol(rowName: string, seqPos: number): number;
-    seqPosToVisibleCol(rowName: string, seqPos: number): number | undefined;
-} & {
-    readonly msaAreaHeight: number;
-    readonly totalTrackAreaHeight: number;
-    readonly annotationTypes: Map<string, import("msa-parsers").Annotation>;
-    readonly filteredAnnotations: import("msa-parsers").Annotation[];
-    readonly annotationsByRow: Record<string, import("msa-parsers").Annotation[]>;
-} & {
-    readonly showVerticalScrollbar: boolean;
 } & {
     readonly verticalScrollbarWidth: 0 | 20;
     readonly msaCanvasWidth: number;
@@ -1404,11 +1463,12 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
 } & {
     setHeaderHeight(arg: number): void;
     setConservationTrackHeight(arg: number): void;
+    setColumnTrackHeight(id: string, height: number): void;
     setSequenceLogoTrackHeight(arg: number): void;
+    setArcTrackHeight(arg: number): void;
     reset(): void;
     exportSVG(opts: import("./renderToSvg.tsx").ExportSvgOptions): Promise<void>;
-    initFilter(arg: string): void;
-    setFilter(arg: string, flag: boolean): void;
+    setFilter(accession: string, shown: boolean): void;
     fit(): void;
     fitVertically(): void;
     fitHorizontally(): void;
@@ -1525,7 +1585,8 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     collapsed: string[];
     showOnly: string | undefined;
     turnedOffTracks: import("mobx").IKeyValueMap<boolean>;
-    featureFilters: import("mobx").IKeyValueMap<boolean>;
+    residueMappings: import("./types.ts").ResidueMapping[];
+    turnedOffFeatures: import("mobx").IKeyValueMap<boolean>;
     relativeTo: string | undefined;
     highlightColumns: number[] | undefined;
     highlights: import("./types.ts").Highlight[];
@@ -1647,7 +1708,8 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     collapsed: string[];
     showOnly: string | undefined;
     turnedOffTracks: import("mobx").IKeyValueMap<boolean>;
-    featureFilters: import("mobx").IKeyValueMap<boolean>;
+    residueMappings: import("./types.ts").ResidueMapping[];
+    turnedOffFeatures: import("mobx").IKeyValueMap<boolean>;
     relativeTo: string | undefined;
     highlightColumns: number[] | undefined;
     highlights: import("./types.ts").Highlight[];