react-msaview 5.0.6 → 5.0.13

package/dist/components/tree/renderTreeCanvas.js

@@ -1,3 +1,4 @@
+import { descendants, links } from "../../hierarchy.js";
 export const padding = 600;
 const extendBounds = 5;
 const radius = 2.5;
@@ -6,7 +7,7 @@ export function renderTree({ offsetY, ctx, model, theme, blockSizeYOverride, })
     const { hierarchy, showBranchLenEffective: showBranchLen, blockSize } = model;
     const by = blockSizeYOverride || blockSize;
     ctx.strokeStyle = theme.palette.text.primary;
-    for (const link of hierarchy.links()) {
+    for (const link of links(hierarchy)) {
         const { source, target } = link;
         if (target.height === 0 && !showBranchLen) {
             continue;
@@ -35,7 +36,7 @@ export function renderTree({ offsetY, ctx, model, theme, blockSizeYOverride, })
 export function renderNodeBubbles({ ctx, clickMap, offsetY, model, blockSizeYOverride, }) {
     const { hierarchy, showBranchLenEffective: showBranchLen, collapsed, blockSize, marginLeft: ml, } = model;
     const by = blockSizeYOverride || blockSize;
-    for (const node of hierarchy.descendants()) {
+    for (const node of descendants(hierarchy)) {
         const x = showBranchLen ? node.len : node.y;
         if (x === undefined) {
             continue;
@@ -65,7 +66,7 @@ export function renderNodeBubbles({ ctx, clickMap, offsetY, model, blockSizeYOve
     }
 }
 export function renderTreeLabels({ theme, model, offsetY, ctx, clickMap, blockSizeYOverride, }) {
-    const { fontSize, showBranchLenEffective: showBranchLen, treeMetadata, hierarchy, collapsed, collapsedLeaves, blockSize, labelsAlignRight, drawTree, treeAreaWidth, treeWidth, treeAreaWidthMinusMargin, marginLeft, leaves, noTree, } = model;
+    const { fontSize, showBranchLenEffective: showBranchLen, treeMetadata, blockSize, labelsAlignRight, drawTree, treeAreaWidth, treeAreaWidthMinusMargin, marginLeft, leaves, noTree, } = model;
     const by = blockSizeYOverride || blockSize;
     const emHeight = ctx.measureText('M').width;
     if (labelsAlignRight) {
@@ -87,15 +88,6 @@ export function renderTreeLabels({ theme, model, offsetY, ctx, clickMap, blockSi
             let xp = 0;
             if (!noTree) {
                 xp = (showBranchLen ? len : x) || 0;
-                if (!showBranchLen &&
-                    !collapsed.includes(id) &&
-                    !collapsedLeaves.includes(id)) {
-                    // this subtraction is a hack to compensate for the leafnode rendering
-                    // glitch (issue #71). the context is that an extra leaf node is added
-                    // so that 'collapsing/hiding leaf nodes is possible' but this causes
-                    // weird workarounds
-                    xp -= treeWidth / hierarchy.height;
-                }
             }
             const { width } = ctx.measureText(displayName);
             ctx.fillStyle = theme.palette.text.primary;

package/dist/components/tree/renderTreeCanvas.js.map

@@ -1 +1 @@
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package/dist/constants.d.ts

@@ -7,7 +7,6 @@ export declare const defaultCurrentAlignment = 0;
 export declare const defaultShowDomains = false;
 export declare const defaultHideGaps = true;
 export declare const defaultAllowedGappyness = 100;
-export declare const defaultContrastLettering = true;
 export declare const defaultSubFeatureRows = false;
 export declare const defaultDrawMsaLetters = true;
 export declare const defaultBgColor = true;
@@ -16,7 +15,6 @@ export declare const defaultDrawLabels = true;
 export declare const defaultLabelsAlignRight = false;
 export declare const defaultTreeAreaWidth = 400;
 export declare const defaultTreeWidth = 300;
-export declare const defaultTreeWidthMatchesArea = true;
 export declare const defaultShowBranchLen = true;
 export declare const defaultDrawTree = true;
 export declare const defaultDrawNodeBubbles = true;

package/dist/constants.js

@@ -8,7 +8,6 @@ export const defaultCurrentAlignment = 0;
 export const defaultShowDomains = false;
 export const defaultHideGaps = true;
 export const defaultAllowedGappyness = 100;
-export const defaultContrastLettering = true;
 export const defaultSubFeatureRows = false;
 export const defaultDrawMsaLetters = true;
 // MSA model defaults
@@ -19,7 +18,6 @@ export const defaultDrawLabels = true;
 export const defaultLabelsAlignRight = false;
 export const defaultTreeAreaWidth = 400;
 export const defaultTreeWidth = 300;
-export const defaultTreeWidthMatchesArea = true;
 export const defaultShowBranchLen = true;
 export const defaultDrawTree = true;
 export const defaultDrawNodeBubbles = true;

package/dist/constants.js.map

@@ -1 +1 @@
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+{"version":3,"file":"constants.js","sourceRoot":"","sources":["../src/constants.ts"],"names":[],"mappings":"AAAA,sBAAsB;AACtB,MAAM,CAAC,MAAM,gBAAgB,GAAG,EAAE,CAAA;AAClC,MAAM,CAAC,MAAM,eAAe,GAAG,EAAE,CAAA;AACjC,MAAM,CAAC,MAAM,aAAa,GAAG,GAAG,CAAA;AAChC,MAAM,CAAC,MAAM,cAAc,GAAG,CAAC,CAAA;AAC/B,MAAM,CAAC,MAAM,cAAc,GAAG,CAAC,CAAA;AAC/B,MAAM,CAAC,MAAM,uBAAuB,GAAG,CAAC,CAAA;AACxC,MAAM,CAAC,MAAM,kBAAkB,GAAG,KAAK,CAAA;AACvC,MAAM,CAAC,MAAM,eAAe,GAAG,IAAI,CAAA;AACnC,MAAM,CAAC,MAAM,uBAAuB,GAAG,GAAG,CAAA;AAC1C,MAAM,CAAC,MAAM,qBAAqB,GAAG,KAAK,CAAA;AAC1C,MAAM,CAAC,MAAM,qBAAqB,GAAG,IAAI,CAAA;AAEzC,qBAAqB;AACrB,MAAM,CAAC,MAAM,cAAc,GAAG,IAAI,CAAA;AAClC,MAAM,CAAC,MAAM,sBAAsB,GAAG,UAAU,CAAA;AAEhD,sBAAsB;AACtB,MAAM,CAAC,MAAM,iBAAiB,GAAG,IAAI,CAAA;AACrC,MAAM,CAAC,MAAM,uBAAuB,GAAG,KAAK,CAAA;AAC5C,MAAM,CAAC,MAAM,oBAAoB,GAAG,GAAG,CAAA;AACvC,MAAM,CAAC,MAAM,gBAAgB,GAAG,GAAG,CAAA;AACnC,MAAM,CAAC,MAAM,oBAAoB,GAAG,IAAI,CAAA;AACxC,MAAM,CAAC,MAAM,eAAe,GAAG,IAAI,CAAA;AACnC,MAAM,CAAC,MAAM,sBAAsB,GAAG,IAAI,CAAA"}

package/dist/fetchUtils.d.ts

@@ -1,5 +1,4 @@
 export declare function myfetch(url: string, args?: RequestInit): Promise<Response>;
 export declare function textfetch(url: string, args?: RequestInit): Promise<string>;
 export declare function jsonfetch<T>(url: string, args?: RequestInit): Promise<T>;
-export declare function arraybufferfetch(url: string): Promise<ArrayBuffer>;
 export declare function timeout(time: number): Promise<unknown>;

package/dist/fetchUtils.js

@@ -13,10 +13,6 @@ export async function jsonfetch(url, args) {
     const response = await myfetch(url, args);
     return response.json();
 }
-export async function arraybufferfetch(url) {
-    const res = await myfetch(url);
-    return res.arrayBuffer();
-}
 export function timeout(time) {
     return new Promise(res => setTimeout(res, time));
 }

package/dist/fetchUtils.js.map

@@ -1 +1 @@
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package/dist/flatToTree.d.ts

@@ -8,10 +8,5 @@ interface TreeNode {
     parent?: string;
     children: TreeNode[];
 }
-/**
- * Parses a flat list of items into a tree structure
- * @param items - Array of flat items with id and optional parent
- * @returns Array of root tree nodes
- */
 export declare function flatToTree(items: FlatItem[]): TreeNode;
 export {};

package/dist/flatToTree.js

@@ -1,41 +1,24 @@
-/**
- * Parses a flat list of items into a tree structure
- * @param items - Array of flat items with id and optional parent
- * @returns Array of root tree nodes
- */
 export function flatToTree(items) {
-    // Create a map to store all nodes by their id for quick lookup
-    const nodeMap = new Map();
-    // First pass: Create all tree nodes
-    items.forEach(item => {
-        nodeMap.set(item.id, {
-            ...item,
+    const nodeMap = new Map(items.map(item => [
+        item.id,
+        {
             id: `${item.id}`,
             name: `${item.id}`,
             parent: item.parent !== undefined ? `${item.parent}` : undefined,
             children: [],
-        });
-    });
-    // Second pass: Build parent-child relationships
-    const roots = [];
-    items.forEach(item => {
+        },
+    ]));
+    let root;
+    for (const item of items) {
         const node = nodeMap.get(item.id);
-        if (item.parent !== undefined) {
-            // This item has a parent, add it to parent's children
-            const parentNode = nodeMap.get(item.parent);
-            if (parentNode) {
-                parentNode.children.push(node);
-            }
-            else {
-                // Parent doesn't exist, treat as root
-                roots.push(node);
-            }
+        const parent = item.parent !== undefined ? nodeMap.get(item.parent) : undefined;
+        if (parent) {
+            parent.children.push(node);
         }
         else {
-            // This item has no parent, it's a root node
-            roots.push(node);
+            root ??= node;
         }
-    });
-    return roots[0];
+    }
+    return root;
 }
 //# sourceMappingURL=flatToTree.js.map

package/dist/flatToTree.js.map

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package/dist/hierarchy.d.ts

@@ -0,0 +1,28 @@
+import type { NodeWithIds } from './types.ts';
+export interface HierarchyNode<T = NodeWithIds> {
+    data: T;
+    children: HierarchyNode<T>[] | null;
+    parent: HierarchyNode<T> | null;
+    depth: number;
+    height: number;
+    value?: number;
+    x?: number;
+    y?: number;
+    len?: number;
+    _children?: HierarchyNode<T>[] | null;
+}
+export interface HierarchyLink<T = NodeWithIds> {
+    source: HierarchyNode<T>;
+    target: HierarchyNode<T>;
+}
+export declare function hierarchy<T>(data: T, childrenAccessor: (d: T) => T[] | undefined): HierarchyNode<T>;
+export declare function sum<T>(node: HierarchyNode<T>, valueFn: (d: T) => number): HierarchyNode<T>;
+export declare function sort<T>(node: HierarchyNode<T>, compareFn: (a: HierarchyNode<T>, b: HierarchyNode<T>) => number): HierarchyNode<T>;
+export declare function find<T>(node: HierarchyNode<T>, predicate: (n: HierarchyNode<T>) => boolean): HierarchyNode<T> | undefined;
+export declare function leaves<T>(node: HierarchyNode<T>): HierarchyNode<T>[];
+export declare function descendants<T>(node: HierarchyNode<T>): HierarchyNode<T>[];
+export declare function links<T>(node: HierarchyNode<T>): HierarchyLink<T>[];
+export declare function clusterLayout<T>(root: HierarchyNode<T>, sizeX: number, sizeY: number): void;
+export declare function collapse<T>(node: HierarchyNode<T>): void;
+export declare function maxLength(d: HierarchyNode): number;
+export declare function setBrLength(d: HierarchyNode, y0: number, k: number): void;

package/dist/hierarchy.js

@@ -0,0 +1,164 @@
+function computeHeight(node) {
+    let h = 0;
+    if (node.children) {
+        for (const child of node.children) {
+            const ch = computeHeight(child) + 1;
+            if (ch > h) {
+                h = ch;
+            }
+        }
+    }
+    node.height = h;
+    return h;
+}
+function wrap(data, childrenAccessor, parent, depth) {
+    const kids = childrenAccessor(data);
+    const node = {
+        data,
+        children: null,
+        parent,
+        depth,
+        height: 0,
+    };
+    if (kids?.length) {
+        node.children = kids.map(d => wrap(d, childrenAccessor, node, depth + 1));
+    }
+    return node;
+}
+export function hierarchy(data, childrenAccessor) {
+    const root = wrap(data, childrenAccessor, null, 0);
+    computeHeight(root);
+    return root;
+}
+export function sum(node, valueFn) {
+    function visit(n) {
+        let s = valueFn(n.data);
+        if (n.children) {
+            for (const child of n.children) {
+                s += visit(child);
+            }
+        }
+        n.value = s;
+        return s;
+    }
+    visit(node);
+    return node;
+}
+export function sort(node, compareFn) {
+    function visit(n) {
+        if (n.children) {
+            n.children.sort(compareFn);
+            for (const child of n.children) {
+                visit(child);
+            }
+        }
+    }
+    visit(node);
+    return node;
+}
+export function find(node, predicate) {
+    if (predicate(node)) {
+        return node;
+    }
+    if (node.children) {
+        for (const child of node.children) {
+            const result = find(child, predicate);
+            if (result) {
+                return result;
+            }
+        }
+    }
+    return undefined;
+}
+export function leaves(node) {
+    const result = [];
+    function visit(n) {
+        if (n.children) {
+            for (const child of n.children) {
+                visit(child);
+            }
+        }
+        else {
+            result.push(n);
+        }
+    }
+    visit(node);
+    return result;
+}
+export function descendants(node) {
+    const result = [];
+    function visit(n) {
+        result.push(n);
+        if (n.children) {
+            for (const child of n.children) {
+                visit(child);
+            }
+        }
+    }
+    visit(node);
+    return result;
+}
+export function links(node) {
+    const result = [];
+    function visit(n) {
+        if (n.children) {
+            for (const child of n.children) {
+                result.push({ source: n, target: child });
+                visit(child);
+            }
+        }
+    }
+    visit(node);
+    return result;
+}
+export function clusterLayout(root, sizeX, sizeY) {
+    const leafNodes = leaves(root);
+    const n = leafNodes.length;
+    const step = sizeX / n;
+    for (let i = 0; i < n; i++) {
+        leafNodes[i].x = (i + 0.5) * step;
+    }
+    function assignX(node) {
+        if (!node.children) {
+            return;
+        }
+        for (const child of node.children) {
+            assignX(child);
+        }
+        let sum = 0;
+        for (const child of node.children) {
+            sum += child.x;
+        }
+        node.x = sum / node.children.length;
+    }
+    assignX(root);
+    const rootHeight = root.height;
+    function assignY(node, depth) {
+        node.y = rootHeight === 0 ? sizeY : (depth / rootHeight) * sizeY;
+        if (node.children) {
+            for (const child of node.children) {
+                assignY(child, depth + 1);
+            }
+        }
+    }
+    assignY(root, 0);
+}
+export function collapse(node) {
+    if (node.children) {
+        node._children = node.children;
+        node.children = null;
+    }
+}
+export function maxLength(d) {
+    return ((d.data.length || 0) +
+        (d.children ? d.children.reduce((m, c) => Math.max(m, maxLength(c)), 0) : 0));
+}
+export function setBrLength(d, y0, k) {
+    d.len = (y0 += Math.max(d.data.length || 0, 0)) * k;
+    if (d.children) {
+        for (const child of d.children) {
+            setBrLength(child, y0, k);
+        }
+    }
+}
+//# sourceMappingURL=hierarchy.js.map

package/dist/hierarchy.js.map

@@ -0,0 +1 @@
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package/dist/index.d.ts

@@ -1,5 +1,7 @@
 export { default as MSAView } from './components/Loading.tsx';
+export { default as MSAViewer } from './components/MSAViewer.tsx';
 export { type MsaViewModel, default as MSAModelF } from './model.ts';
 export type { MSAParserType } from 'msa-parsers';
+export type { HierarchyNode } from './hierarchy.ts';
 export type { InterProScanResults } from './launchInterProScan.ts';
 export type { Accession, BasicTrack, BasicTrackModel, Node, NodeWithIds, NodeWithIdsAndLength, TextTrackModel, } from './types.ts';

package/dist/index.js

@@ -1,3 +1,4 @@
 export { default as MSAView } from "./components/Loading.js";
+export { default as MSAViewer } from "./components/MSAViewer.js";
 export { default as MSAModelF } from "./model.js";
 //# sourceMappingURL=index.js.map

package/dist/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,IAAI,OAAO,EAAE,MAAM,yBAA0B,CAAA;AAC7D,OAAO,EAAqB,OAAO,IAAI,SAAS,EAAE,MAAM,YAAY,CAAA"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,IAAI,OAAO,EAAE,MAAM,yBAA0B,CAAA;AAC7D,OAAO,EAAE,OAAO,IAAI,SAAS,EAAE,MAAM,2BAA4B,CAAA;AACjE,OAAO,EAAqB,OAAO,IAAI,SAAS,EAAE,MAAM,YAAY,CAAA"}

package/dist/launchInterProScan.d.ts

@@ -20,7 +20,6 @@ export interface InterProScanResults {
 export interface InterProScanResponse {
     results: InterProScanResults[];
 }
-export declare function loadInterProScanResults(jobId: string): Promise<InterProScanResponse>;
 export declare function launchInterProScan({ algorithm, seq, programs, onJobId, onProgress, model, }: {
     algorithm: string;
     seq: string;
@@ -32,7 +31,3 @@ export declare function launchInterProScan({ algorithm, seq, programs, onJobId,
     onJobId?: (arg: string) => void;
     model: MsaViewModel;
 }): Promise<void>;
-export declare function loadInterProScanResultsWithStatus({ jobId, model, }: {
-    jobId: string;
-    model: MsaViewModel;
-}): Promise<void>;

package/dist/launchInterProScan.js

@@ -17,7 +17,7 @@ async function runInterProScan({ seq, onProgress, onJobId, programs, model, }) {
     });
     await loadInterProScanResultsWithStatus({ jobId, model });
 }
-export function loadInterProScanResults(jobId) {
+function loadInterProScanResults(jobId) {
     return jsonfetch(`${base}/iprscan5/result/${jobId}/json`);
 }
 async function wait({ onProgress, jobId, }) {
@@ -54,13 +54,15 @@ export async function launchInterProScan({ algorithm, seq, programs, onJobId, on
                 model,
             });
         }
-        throw new Error('unknown algorithm');
+        else {
+            throw new Error('unknown algorithm');
+        }
     }
     finally {
         onProgress();
     }
 }
-export async function loadInterProScanResultsWithStatus({ jobId, model, }) {
+async function loadInterProScanResultsWithStatus({ jobId, model, }) {
     try {
         model.setStatus({
             msg: `Downloading results of ${jobId} (for larger sequences this can be slow, click status to download and upload in the manual tab)`,

package/dist/launchInterProScan.js.map

@@ -1 +1 @@
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+{"version":3,"file":"launchInterProScan.js","sourceRoot":"","sources":["../src/launchInterProScan.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAA;AAE/C,OAAO,EAAE,SAAS,EAAE,SAAS,EAAE,OAAO,EAAE,MAAM,iBAAiB,CAAA;AAI/D,MAAM,IAAI,GAAG,2CAA2C,CAAA;AAmBxD,KAAK,UAAU,eAAe,CAAC,EAC7B,GAAG,EACH,UAAU,EACV,OAAO,EACP,QAAQ,EACR,KAAK,GAON;IACC,MAAM,KAAK,GAAG,MAAM,SAAS,CAAC,GAAG,IAAI,eAAe,EAAE;QACpD,MAAM,EAAE,MAAM;QACd,IAAI,EAAE,IAAI,eAAe,CAAC;YACxB,KAAK,EAAE,uBAAuB;YAC9B,QAAQ,EAAE,GAAG;YACb,QAAQ,EAAE,QAAQ,CAAC,IAAI,CAAC,GAAG,CAAC;SAC7B,CAAC;KACH,CAAC,CAAA;IACF,OAAO,EAAE,CAAC,KAAK,CAAC,CAAA;IAChB,MAAM,IAAI,CAAC;QACT,KAAK;QACL,UAAU;KACX,CAAC,CAAA;IACF,MAAM,iCAAiC,CAAC,EAAE,KAAK,EAAE,KAAK,EAAE,CAAC,CAAA;AAC3D,CAAC;AAED,SAAS,uBAAuB,CAAC,KAAa;IAC5C,OAAO,SAAS,CACd,GAAG,IAAI,oBAAoB,KAAK,OAAO,CACxC,CAAA;AACH,CAAC;AAED,KAAK,UAAU,IAAI,CAAC,EAClB,UAAU,EACV,KAAK,GAIN;IACC,MAAM,GAAG,GAAG,GAAG,IAAI,oBAAoB,KAAK,EAAE,CAAA;IAC9C,IAAI,CAAC;QACH,uEAAuE;QACvE,OAAO,IAAI,EAAE,CAAC;YACZ,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,EAAE,EAAE,CAAC,EAAE,EAAE,CAAC;gBAC5B,MAAM,OAAO,CAAC,IAAI,CAAC,CAAA;gBACnB,UAAU,CAAC,EAAE,GAAG,EAAE,mBAAmB,EAAE,GAAG,CAAC,EAAE,EAAE,GAAG,EAAE,CAAC,CAAA;YACvD,CAAC;YACD,MAAM,MAAM,GAAG,MAAM,SAAS,CAAC,GAAG,CAAC,CAAA;YACnC,IAAI,MAAM,CAAC,QAAQ,CAAC,UAAU,CAAC,EAAE,CAAC;gBAChC,MAAK;YACP,CAAC;YACD,IAAI,MAAM,CAAC,QAAQ,CAAC,SAAS,CAAC,EAAE,CAAC;gBAC/B,MAAM,IAAI,KAAK,CAAC,wBAAwB,KAAK,EAAE,CAAC,CAAA;YAClD,CAAC;QACH,CAAC;IACH,CAAC;YAAS,CAAC;QACT,UAAU,EAAE,CAAA;IACd,CAAC;AACH,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,kBAAkB,CAAC,EACvC,SAAS,EACT,GAAG,EACH,QAAQ,EACR,OAAO,EACP,UAAU,EACV,KAAK,GAQN;IACC,IAAI,CAAC;QACH,UAAU,CAAC,EAAE,GAAG,EAAE,aAAa,SAAS,MAAM,EAAE,CAAC,CAAA;QACjD,IAAI,SAAS,KAAK,cAAc,EAAE,CAAC;YACjC,MAAM,eAAe,CAAC;gBACpB,GAAG;gBACH,OAAO;gBACP,UAAU;gBACV,QAAQ;gBACR,KAAK;aACN,CAAC,CAAA;QACJ,CAAC;aAAM,CAAC;YACN,MAAM,IAAI,KAAK,CAAC,mBAAmB,CAAC,CAAA;QACtC,CAAC;IACH,CAAC;YAAS,CAAC;QACT,UAAU,EAAE,CAAA;IACd,CAAC;AACH,CAAC;AAED,KAAK,UAAU,iCAAiC,CAAC,EAC/C,KAAK,EACL,KAAK,GAIN;IACC,IAAI,CAAC;QACH,KAAK,CAAC,SAAS,CAAC;YACd,GAAG,EAAE,0BAA0B,KAAK,iGAAiG;YACrI,GAAG,EAAE,6DAA6D,KAAK,OAAO;SAC/E,CAAC,CAAA;QACF,MAAM,GAAG,GAAG,MAAM,uBAAuB,CAAC,KAAK,CAAC,CAAA;QAChD,KAAK,CAAC,sBAAsB,CAC1B,MAAM,CAAC,WAAW,CAAC,GAAG,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,CAC7D,CAAA;QACD,KAAK,CAAC,cAAc,CAAC,IAAI,CAAC,CAAA;QAC1B,UAAU,CAAC,KAAK,CAAC,CAAC,MAAM,CAAC,uBAAuB,KAAK,UAAU,EAAE,SAAS,CAAC,CAAA;IAC7E,CAAC;IAAC,OAAO,CAAC,EAAE,CAAC;QACX,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;QAChB,UAAU,CAAC,KAAK,CAAC,CAAC,WAAW,CAAC,GAAG,CAAC,EAAE,EAAE,CAAC,CAAC,CAAA;IAC1C,CAAC;YAAS,CAAC;QACT,KAAK,CAAC,SAAS,EAAE,CAAA;IACnB,CAAC;AACH,CAAC"}

package/dist/model/DataModel.d.ts

@@ -18,6 +18,10 @@ export declare function DataModelF(): import("@jbrowse/mobx-state-tree").IModelT
      * #property
      */
     treeMetadata: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+    /**
+     * #property
+     */
+    gff: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
 }, {
     /**
      * #action
@@ -31,8 +35,13 @@ export declare function DataModelF(): import("@jbrowse/mobx-state-tree").IModelT
      * #action
      */
     setTreeMetadata(treeMetadata?: string): void;
+    /**
+     * #action
+     */
+    setGFF(gff?: string): void;
 }, import("@jbrowse/mobx-state-tree")._NotCustomized, {
     tree: string | undefined;
     msa: string | undefined;
     treeMetadata: string | undefined;
+    gff: string | undefined;
 }>;

package/dist/model/DataModel.js

@@ -21,6 +21,10 @@ export function DataModelF() {
          * #property
          */
         treeMetadata: types.maybe(types.string),
+        /**
+         * #property
+         */
+        gff: types.maybe(types.string),
     })
         .actions(self => ({
         /**
@@ -41,14 +45,21 @@ export function DataModelF() {
         setTreeMetadata(treeMetadata) {
             self.treeMetadata = treeMetadata;
         },
+        /**
+         * #action
+         */
+        setGFF(gff) {
+            self.gff = gff;
+        },
     }))
         .postProcessSnapshot(snap => {
-        const { tree, msa, treeMetadata } = snap;
+        const { tree, msa, treeMetadata, gff } = snap;
         const max = 50_000;
         return {
             tree: tree && tree.length > max ? undefined : tree,
             msa: msa && msa.length > max ? undefined : msa,
             treeMetadata: treeMetadata && treeMetadata.length > max ? undefined : treeMetadata,
+            gff: gff && gff.length > max ? undefined : gff,
         };
     });
 }

package/dist/model/DataModel.js.map

@@ -1 +1 @@
-{"version":3,"file":"DataModel.js","sourceRoot":"","sources":["../../src/model/DataModel.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAE,MAAM,0BAA0B,CAAA;AAEhD;;;;;;GAMG;AACH,MAAM,UAAU,UAAU;IACxB,OAAO,KAAK;SACT,KAAK,CAAC;QACL;;WAEG;QACH,IAAI,EAAE,KAAK,CAAC,KAAK,CAAC,KAAK,CAAC,MAAM,CAAC;QAC/B;;WAEG;QACH,GAAG,EAAE,KAAK,CAAC,KAAK,CAAC,KAAK,CAAC,MAAM,CAAC;QAC9B;;WAEG;QACH,YAAY,EAAE,KAAK,CAAC,KAAK,CAAC,KAAK,CAAC,MAAM,CAAC;KACxC,CAAC;SACD,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAChB;;WAEG;QACH,OAAO,CAAC,IAAa;YACnB,IAAI,CAAC,IAAI,GAAG,IAAI,CAAA;QAClB,CAAC;QACD;;WAEG;QACH,MAAM,CAAC,GAAY;YACjB,IAAI,CAAC,GAAG,GAAG,GAAG,CAAA;QAChB,CAAC;QACD;;WAEG;QACH,eAAe,CAAC,YAAqB;YACnC,IAAI,CAAC,YAAY,GAAG,YAAY,CAAA;QAClC,CAAC;KACF,CAAC,CAAC;SACF,mBAAmB,CAAC,IAAI,CAAC,EAAE;QAC1B,MAAM,EAAE,IAAI,EAAE,GAAG,EAAE,YAAY,EAAE,GAAG,IAAI,CAAA;QACxC,MAAM,GAAG,GAAG,MAAM,CAAA;QAClB,OAAO;YACL,IAAI,EAAE,IAAI,IAAI,IAAI,CAAC,MAAM,GAAG,GAAG,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI;YAClD,GAAG,EAAE,GAAG,IAAI,GAAG,CAAC,MAAM,GAAG,GAAG,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,GAAG;YAC9C,YAAY,EACV,YAAY,IAAI,YAAY,CAAC,MAAM,GAAG,GAAG,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,YAAY;SACvE,CAAA;IACH,CAAC,CAAC,CAAA;AACN,CAAC"}
+{"version":3,"file":"DataModel.js","sourceRoot":"","sources":["../../src/model/DataModel.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAE,MAAM,0BAA0B,CAAA;AAEhD;;;;;;GAMG;AACH,MAAM,UAAU,UAAU;IACxB,OAAO,KAAK;SACT,KAAK,CAAC;QACL;;WAEG;QACH,IAAI,EAAE,KAAK,CAAC,KAAK,CAAC,KAAK,CAAC,MAAM,CAAC;QAC/B;;WAEG;QACH,GAAG,EAAE,KAAK,CAAC,KAAK,CAAC,KAAK,CAAC,MAAM,CAAC;QAC9B;;WAEG;QACH,YAAY,EAAE,KAAK,CAAC,KAAK,CAAC,KAAK,CAAC,MAAM,CAAC;QACvC;;WAEG;QACH,GAAG,EAAE,KAAK,CAAC,KAAK,CAAC,KAAK,CAAC,MAAM,CAAC;KAC/B,CAAC;SACD,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAChB;;WAEG;QACH,OAAO,CAAC,IAAa;YACnB,IAAI,CAAC,IAAI,GAAG,IAAI,CAAA;QAClB,CAAC;QACD;;WAEG;QACH,MAAM,CAAC,GAAY;YACjB,IAAI,CAAC,GAAG,GAAG,GAAG,CAAA;QAChB,CAAC;QACD;;WAEG;QACH,eAAe,CAAC,YAAqB;YACnC,IAAI,CAAC,YAAY,GAAG,YAAY,CAAA;QAClC,CAAC;QACD;;WAEG;QACH,MAAM,CAAC,GAAY;YACjB,IAAI,CAAC,GAAG,GAAG,GAAG,CAAA;QAChB,CAAC;KACF,CAAC,CAAC;SACF,mBAAmB,CAAC,IAAI,CAAC,EAAE;QAC1B,MAAM,EAAE,IAAI,EAAE,GAAG,EAAE,YAAY,EAAE,GAAG,EAAE,GAAG,IAAI,CAAA;QAC7C,MAAM,GAAG,GAAG,MAAM,CAAA;QAClB,OAAO;YACL,IAAI,EAAE,IAAI,IAAI,IAAI,CAAC,MAAM,GAAG,GAAG,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI;YAClD,GAAG,EAAE,GAAG,IAAI,GAAG,CAAC,MAAM,GAAG,GAAG,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,GAAG;YAC9C,YAAY,EACV,YAAY,IAAI,YAAY,CAAC,MAAM,GAAG,GAAG,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,YAAY;YACtE,GAAG,EAAE,GAAG,IAAI,GAAG,CAAC,MAAM,GAAG,GAAG,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,GAAG;SAC/C,CAAA;IACH,CAAC,CAAC,CAAA;AACN,CAAC"}

package/dist/model/msaModel.d.ts

@@ -1,3 +1,6 @@
+/**
+ * #stateModel MSAModel
+ */
 export declare function MSAModelF(): import("@jbrowse/mobx-state-tree").IModelType<{
     bgColor: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     colorSchemeName: import("@jbrowse/mobx-state-tree").IType<string | undefined, string, string>;

package/dist/model/msaModel.js

@@ -3,7 +3,6 @@ import { defaultBgColor, defaultColorSchemeName } from "../constants.js";
 /**
  * #stateModel MSAModel
  */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
 export function MSAModelF() {
     return types
         .model({

package/dist/model/msaModel.js.map

@@ -1 +1 @@
-{"version":3,"file":"msaModel.js","sourceRoot":"","sources":["../../src/model/msaModel.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAE,MAAM,0BAA0B,CAAA;AAEhD,OAAO,EAAE,cAAc,EAAE,sBAAsB,EAAE,MAAM,iBAAiB,CAAA;AAExE;;GAEG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,UAAU,SAAS;IACvB,OAAO,KAAK;SACT,KAAK,CAAC;QACL;;;WAGG;QACH,OAAO,EAAE,cAAc;QAEvB;;;WAGG;QACH,eAAe,EAAE,sBAAsB;KACxC,CAAC;SACD,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAChB;;;WAGG;QACH,kBAAkB,CAAC,IAAY;YAC7B,IAAI,CAAC,eAAe,GAAG,IAAI,CAAA;QAC7B,CAAC;QAED;;WAEG;QACH,UAAU,CAAC,GAAY;YACrB,IAAI,CAAC,OAAO,GAAG,GAAG,CAAA;QACpB,CAAC;KACF,CAAC,CAAC,CAAA;AACP,CAAC"}
+{"version":3,"file":"msaModel.js","sourceRoot":"","sources":["../../src/model/msaModel.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAE,MAAM,0BAA0B,CAAA;AAEhD,OAAO,EAAE,cAAc,EAAE,sBAAsB,EAAE,MAAM,iBAAiB,CAAA;AAExE;;GAEG;AACH,MAAM,UAAU,SAAS;IACvB,OAAO,KAAK;SACT,KAAK,CAAC;QACL;;;WAGG;QACH,OAAO,EAAE,cAAc;QAEvB;;;WAGG;QACH,eAAe,EAAE,sBAAsB;KACxC,CAAC;SACD,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAChB;;;WAGG;QACH,kBAAkB,CAAC,IAAY;YAC7B,IAAI,CAAC,eAAe,GAAG,IAAI,CAAA;QAC7B,CAAC;QAED;;WAEG;QACH,UAAU,CAAC,GAAY;YACrB,IAAI,CAAC,OAAO,GAAG,GAAG,CAAA;QACpB,CAAC;KACF,CAAC,CAAC,CAAA;AACP,CAAC"}

package/dist/model/treeModel.d.ts

@@ -1,18 +1,15 @@
+/**
+ * #stateModel Tree
+ */
 export declare function TreeModelF(): import("@jbrowse/mobx-state-tree").IModelType<{
     drawLabels: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     labelsAlignRight: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     treeAreaWidth: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
     treeWidth: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
-    treeWidthMatchesArea: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     showBranchLen: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     drawTree: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     drawNodeBubbles: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
 }, {
-    /**
-     * #action
-     * synchronize the treewidth and treeareawidth
-     */
-    setTreeWidthMatchesArea(arg: boolean): void;
     /**
      * #action
      * set tree area width (px)