react-msaview 5.3.0 → 5.4.1

package/dist/hierarchy.js

@@ -179,10 +179,47 @@ export function clusterLayout(root, sizeX, sizeY) {
 }
 export function collapse(node) {
     if (node.children) {
+        // memoize the real subtree depth onto the node before detaching its
+        // children, so cladogram positioning keeps the node (now the apex of a
+        // collapsed-clade triangle) at its true branch point rather than snapping
+        // it to the tip-alignment line. This also keeps the rest of the tree's
+        // horizontal layout stable when a clade is collapsed.
+        calcDepthToLeaf(node);
         node._children = node.children;
         node.children = null;
     }
 }
+// Min/max cumulative raw branch length from a collapsed node down to the tips of
+// its detached subtree (excludes the node's own branch). Used to size the
+// collapsed-clade triangle in phylogram mode.
+export function collapsedSubtreeLengthExtent(node) {
+    const roots = node._children ?? node.children;
+    let min = Infinity;
+    let max = 0;
+    if (roots) {
+        const stack = roots.map(child => ({
+            node: child,
+            acc: Math.max(child.data.length ?? 0, 0),
+        }));
+        while (stack.length > 0) {
+            const { node: n, acc } = stack.pop();
+            const kids = n.children ?? n._children;
+            if (kids?.length) {
+                for (const child of kids) {
+                    stack.push({
+                        node: child,
+                        acc: acc + Math.max(child.data.length ?? 0, 0),
+                    });
+                }
+            }
+            else {
+                min = Math.min(min, acc);
+                max = Math.max(max, acc);
+            }
+        }
+    }
+    return { min: min === Infinity ? 0 : min, max };
+}
 // Cladogram positioning based on ape's plot.phylo: uses topological depth (max
 // steps to a tip) instead of branch length so all leaves align at the rightmost
 // x. Memoizes onto node.depthToLeaf since the layout walks the tree repeatedly.

package/dist/hierarchy.js.map

@@ -1 +1 @@
-{"version":3,"file":"hierarchy.js","sourceRoot":"","sources":["../src/hierarchy.ts"],"names":[],"mappings":"AAqBA,iFAAiF;AACjF,kFAAkF;AAClF,4EAA4E;AAE5E,gFAAgF;AAChF,kFAAkF;AAClF,oCAAoC;AACpC,MAAM,UAAU,WAAW,CAAI,IAAsB;IACnD,MAAM,MAAM,GAAuB,EAAE,CAAA;IACrC,MAAM,KAAK,GAAG,CAAC,IAAI,CAAC,CAAA;IACpB,OAAO,KAAK,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;QACxB,MAAM,CAAC,GAAG,KAAK,CAAC,GAAG,EAAG,CAAA;QACtB,MAAM,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;QACd,IAAI,CAAC,CAAC,QAAQ,EAAE,CAAC;YACf,KAAK,IAAI,CAAC,GAAG,CAAC,CAAC,QAAQ,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC;gBAChD,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAE,CAAC,CAAA;YAC5B,CAAC;QACH,CAAC;IACH,CAAC;IACD,OAAO,MAAM,CAAA;AACf,CAAC;AAED,SAAS,aAAa,CAAI,IAAsB;IAC9C,MAAM,KAAK,GAAG,WAAW,CAAC,IAAI,CAAC,CAAA;IAC/B,KAAK,IAAI,CAAC,GAAG,KAAK,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC;QAC3C,MAAM,CAAC,GAAG,KAAK,CAAC,CAAC,CAAE,CAAA;QACnB,IAAI,CAAC,GAAG,CAAC,CAAA;QACT,IAAI,CAAC,CAAC,QAAQ,EAAE,CAAC;YACf,KAAK,MAAM,KAAK,IAAI,CAAC,CAAC,QAAQ,EAAE,CAAC;gBAC/B,IAAI,KAAK,CAAC,MAAM,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC;oBACzB,CAAC,GAAG,KAAK,CAAC,MAAM,GAAG,CAAC,CAAA;gBACtB,CAAC;YACH,CAAC;QACH,CAAC;QACD,CAAC,CAAC,MAAM,GAAG,CAAC,CAAA;IACd,CAAC;AACH,CAAC;AAED,MAAM,UAAU,SAAS,CACvB,IAAO,EACP,gBAA2C;IAE3C,MAAM,IAAI,GAAqB;QAC7B,IAAI;QACJ,QAAQ,EAAE,IAAI;QACd,MAAM,EAAE,IAAI;QACZ,KAAK,EAAE,CAAC;QACR,MAAM,EAAE,CAAC;KACV,CAAA;IACD,MAAM,KAAK,GAAG,CAAC,IAAI,CAAC,CAAA;IACpB,OAAO,KAAK,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;QACxB,MAAM,IAAI,GAAG,KAAK,CAAC,GAAG,EAAG,CAAA;QACzB,MAAM,IAAI,GAAG,gBAAgB,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;QACxC,IAAI,IAAI,EAAE,MAAM,EAAE,CAAC;YACjB,IAAI,CAAC,QAAQ,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC;gBAC7B,IAAI,EAAE,CAAC;gBACP,QAAQ,EAAE,IAAI;gBACd,MAAM,EAAE,IAAI;gBACZ,KAAK,EAAE,IAAI,CAAC,KAAK,GAAG,CAAC;gBACrB,MAAM,EAAE,CAAC;aACV,CAAC,CAAC,CAAA;YACH,KAAK,MAAM,KAAK,IAAI,IAAI,CAAC,QAAQ,EAAE,CAAC;gBAClC,KAAK,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;YACnB,CAAC;QACH,CAAC;IACH,CAAC;IACD,aAAa,CAAC,IAAI,CAAC,CAAA;IACnB,OAAO,IAAI,CAAA;AACb,CAAC;AAED,MAAM,UAAU,GAAG,CACjB,IAAsB,EACtB,OAAyB;IAEzB,MAAM,KAAK,GAAG,WAAW,CAAC,IAAI,CAAC,CAAA;IAC/B,KAAK,IAAI,CAAC,GAAG,KAAK,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC;QAC3C,MAAM,CAAC,GAAG,KAAK,CAAC,CAAC,CAAE,CAAA;QACnB,IAAI,CAAC,GAAG,OAAO,CAAC,CAAC,CAAC,IAAI,CAAC,CAAA;QACvB,IAAI,CAAC,CAAC,QAAQ,EAAE,CAAC;YACf,KAAK,MAAM,KAAK,IAAI,CAAC,CAAC,QAAQ,EAAE,CAAC;gBAC/B,CAAC,IAAI,KAAK,CAAC,KAAM,CAAA;YACnB,CAAC;QACH,CAAC;QACD,CAAC,CAAC,KAAK,GAAG,CAAC,CAAA;IACb,CAAC;IACD,OAAO,IAAI,CAAA;AACb,CAAC;AAED,MAAM,UAAU,IAAI,CAClB,IAAsB,EACtB,SAA+D;IAE/D,MAAM,KAAK,GAAG,CAAC,IAAI,CAAC,CAAA;IACpB,OAAO,KAAK,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;QACxB,MAAM,CAAC,GAAG,KAAK,CAAC,GAAG,EAAG,CAAA;QACtB,IAAI,CAAC,CAAC,QAAQ,EAAE,CAAC;YACf,CAAC,CAAC,QAAQ,CAAC,IAAI,CAAC,SAAS,CAAC,CAAA;YAC1B,KAAK,MAAM,KAAK,IAAI,CAAC,CAAC,QAAQ,EAAE,CAAC;gBAC/B,KAAK,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;YACnB,CAAC;QACH,CAAC;IACH,CAAC;IACD,OAAO,IAAI,CAAA;AACb,CAAC;AAED,MAAM,UAAU,IAAI,CAClB,IAAsB,EACtB,SAA2C;IAE3C,MAAM,KAAK,GAAG,CAAC,IAAI,CAAC,CAAA;IACpB,IAAI,KAAmC,CAAA;IACvC,OAAO,KAAK,CAAC,MAAM,GAAG,CAAC,IAAI,KAAK,KAAK,SAAS,EAAE,CAAC;QAC/C,MAAM,CAAC,GAAG,KAAK,CAAC,GAAG,EAAG,CAAA;QACtB,IAAI,SAAS,CAAC,CAAC,CAAC,EAAE,CAAC;YACjB,KAAK,GAAG,CAAC,CAAA;QACX,CAAC;aAAM,IAAI,CAAC,CAAC,QAAQ,EAAE,CAAC;YACtB,KAAK,IAAI,CAAC,GAAG,CAAC,CAAC,QAAQ,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC;gBAChD,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAE,CAAC,CAAA;YAC5B,CAAC;QACH,CAAC;IACH,CAAC;IACD,OAAO,KAAK,CAAA;AACd,CAAC;AAED,MAAM,UAAU,MAAM,CAAI,IAAsB;IAC9C,MAAM,MAAM,GAAuB,EAAE,CAAA;IACrC,MAAM,KAAK,GAAG,CAAC,IAAI,CAAC,CAAA;IACpB,OAAO,KAAK,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;QACxB,MAAM,CAAC,GAAG,KAAK,CAAC,GAAG,EAAG,CAAA;QACtB,IAAI,CAAC,CAAC,QAAQ,EAAE,CAAC;YACf,KAAK,IAAI,CAAC,GAAG,CAAC,CAAC,QAAQ,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC;gBAChD,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAE,CAAC,CAAA;YAC5B,CAAC;QACH,CAAC;aAAM,CAAC;YACN,MAAM,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;QAChB,CAAC;IACH,CAAC;IACD,OAAO,MAAM,CAAA;AACf,CAAC;AAED,MAAM,UAAU,KAAK,CAAI,IAAsB;IAC7C,MAAM,MAAM,GAAuB,EAAE,CAAA;IACrC,WAAW,CAAC,IAAI,EAAE,CAAC,MAAM,EAAE,MAAM,EAAE,EAAE;QACnC,MAAM,CAAC,IAAI,CAAC,EAAE,MAAM,EAAE,MAAM,EAAE,CAAC,CAAA;IACjC,CAAC,CAAC,CAAA;IACF,OAAO,MAAM,CAAA;AACf,CAAC;AAED,MAAM,UAAU,WAAW,CACzB,IAAsB,EACtB,EAAgE;IAEhE,MAAM,KAAK,GAAG,CAAC,IAAI,CAAC,CAAA;IACpB,OAAO,KAAK,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;QACxB,MAAM,CAAC,GAAG,KAAK,CAAC,GAAG,EAAG,CAAA;QACtB,IAAI,CAAC,CAAC,QAAQ,EAAE,CAAC;YACf,KAAK,IAAI,CAAC,GAAG,CAAC,CAAC,QAAQ,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC;gBAChD,MAAM,KAAK,GAAG,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAE,CAAA;gBAC5B,EAAE,CAAC,CAAC,EAAE,KAAK,CAAC,CAAA;gBACZ,KAAK,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;YACnB,CAAC;QACH,CAAC;IACH,CAAC;AACH,CAAC;AAED,MAAM,UAAU,iBAAiB,CAC/B,IAAsB,EACtB,EAAiC;IAEjC,KAAK,MAAM,CAAC,IAAI,WAAW,CAAC,IAAI,CAAC,EAAE,CAAC;QAClC,EAAE,CAAC,CAAC,CAAC,CAAA;IACP,CAAC;AACH,CAAC;AAED,MAAM,UAAU,aAAa,CAC3B,IAAsB,EACtB,KAAa,EACb,KAAa;IAEb,MAAM,SAAS,GAAG,MAAM,CAAC,IAAI,CAAC,CAAA;IAC9B,MAAM,CAAC,GAAG,SAAS,CAAC,MAAM,CAAA;IAC1B,MAAM,IAAI,GAAG,KAAK,GAAG,CAAC,CAAA;IAEtB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC;QAC3B,SAAS,CAAC,CAAC,CAAE,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAC,GAAG,IAAI,CAAA;IACpC,CAAC;IAED,uEAAuE;IACvE,uCAAuC;IACvC,MAAM,KAAK,GAAG,WAAW,CAAC,IAAI,CAAC,CAAA;IAC/B,KAAK,IAAI,CAAC,GAAG,KAAK,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC;QAC3C,MAAM,IAAI,GAAG,KAAK,CAAC,CAAC,CAAE,CAAA;QACtB,IAAI,IAAI,CAAC,QAAQ,EAAE,CAAC;YAClB,IAAI,GAAG,GAAG,CAAC,CAAA;YACX,KAAK,MAAM,KAAK,IAAI,IAAI,CAAC,QAAQ,EAAE,CAAC;gBAClC,GAAG,IAAI,KAAK,CAAC,CAAE,CAAA;YACjB,CAAC;YACD,IAAI,CAAC,CAAC,GAAG,GAAG,GAAG,IAAI,CAAC,QAAQ,CAAC,MAAM,CAAA;QACrC,CAAC;IACH,CAAC;IAED,MAAM,UAAU,GAAG,IAAI,CAAC,MAAM,CAAA;IAC9B,MAAM,KAAK,GAAG,CAAC,EAAE,IAAI,EAAE,IAAI,EAAE,KAAK,EAAE,CAAC,EAAE,CAAC,CAAA;IACxC,OAAO,KAAK,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;QACxB,MAAM,EAAE,IAAI,EAAE,KAAK,EAAE,GAAG,KAAK,CAAC,GAAG,EAAG,CAAA;QACpC,IAAI,CAAC,CAAC,GAAG,UAAU,KAAK,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,KAAK,GAAG,UAAU,CAAC,GAAG,KAAK,CAAA;QAChE,IAAI,IAAI,CAAC,QAAQ,EAAE,CAAC;YAClB,KAAK,MAAM,KAAK,IAAI,IAAI,CAAC,QAAQ,EAAE,CAAC;gBAClC,KAAK,CAAC,IAAI,CAAC,EAAE,IAAI,EAAE,KAAK,EAAE,KAAK,EAAE,KAAK,GAAG,CAAC,EAAE,CAAC,CAAA;YAC/C,CAAC;QACH,CAAC;IACH,CAAC;AACH,CAAC;AAED,MAAM,UAAU,QAAQ,CAAI,IAAsB;IAChD,IAAI,IAAI,CAAC,QAAQ,EAAE,CAAC;QAClB,IAAI,CAAC,SAAS,GAAG,IAAI,CAAC,QAAQ,CAAA;QAC9B,IAAI,CAAC,QAAQ,GAAG,IAAI,CAAA;IACtB,CAAC;AACH,CAAC;AAED,+EAA+E;AAC/E,gFAAgF;AAChF,gFAAgF;AAChF,wEAAwE;AACxE,MAAM,UAAU,eAAe,CAAC,IAAmB;IACjD,MAAM,KAAK,GAAG,WAAW,CAAC,IAAI,CAAC,CAAA;IAC/B,KAAK,IAAI,CAAC,GAAG,KAAK,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC;QAC3C,MAAM,CAAC,GAAG,KAAK,CAAC,CAAC,CAAE,CAAA;QACnB,IAAI,CAAC,CAAC,WAAW,KAAK,SAAS,EAAE,CAAC;YAChC,IAAI,QAAQ,GAAG,CAAC,CAAA;YAChB,IAAI,CAAC,CAAC,QAAQ,EAAE,CAAC;gBACf,KAAK,MAAM,KAAK,IAAI,CAAC,CAAC,QAAQ,EAAE,CAAC;oBAC/B,QAAQ,GAAG,IAAI,CAAC,GAAG,CAAC,QAAQ,EAAE,CAAC,GAAG,KAAK,CAAC,WAAY,CAAC,CAAA;gBACvD,CAAC;YACH,CAAC;YACD,CAAC,CAAC,WAAW,GAAG,QAAQ,CAAA;QAC1B,CAAC;IACH,CAAC;IACD,OAAO,IAAI,CAAC,WAAY,CAAA;AAC1B,CAAC;AAED,MAAM,UAAU,gBAAgB,CAAC,IAAmB;IAClD,IAAI,MAAM,GAAG,CAAC,CAAA;IACd,KAAK,MAAM,CAAC,IAAI,WAAW,CAAC,IAAI,CAAC,EAAE,CAAC;QAClC,MAAM,GAAG,IAAI,CAAC,GAAG,CAAC,MAAM,EAAE,CAAC,CAAC,GAAG,IAAI,CAAC,CAAC,CAAA;IACvC,CAAC;IACD,OAAO,MAAM,CAAA;AACf,CAAC;AAED,iEAAiE;AACjE,MAAM,UAAU,SAAS,CAAC,CAAgB;IACxC,MAAM,KAAK,GAAG,WAAW,CAAC,CAAC,CAAC,CAAA;IAC5B,MAAM,OAAO,GAAG,IAAI,GAAG,EAAyB,CAAA;IAChD,KAAK,IAAI,CAAC,GAAG,KAAK,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC;QAC3C,MAAM,CAAC,GAAG,KAAK,CAAC,CAAC,CAAE,CAAA;QACnB,IAAI,QAAQ,GAAG,CAAC,CAAA;QAChB,IAAI,CAAC,CAAC,QAAQ,EAAE,CAAC;YACf,KAAK,MAAM,KAAK,IAAI,CAAC,CAAC,QAAQ,EAAE,CAAC;gBAC/B,QAAQ,GAAG,IAAI,CAAC,GAAG,CAAC,QAAQ,EAAE,OAAO,CAAC,GAAG,CAAC,KAAK,CAAE,CAAC,CAAA;YACpD,CAAC;QACH,CAAC;QACD,OAAO,CAAC,GAAG,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,MAAM,IAAI,CAAC,CAAC,GAAG,QAAQ,CAAC,CAAA;IACjD,CAAC;IACD,OAAO,OAAO,CAAC,GAAG,CAAC,CAAC,CAAE,CAAA;AACxB,CAAC;AAED,MAAM,UAAU,WAAW,CAAC,CAAgB,EAAE,EAAU,EAAE,CAAS;IACjE,MAAM,KAAK,GAAG,CAAC,EAAE,IAAI,EAAE,CAAC,EAAE,EAAE,EAAE,CAAC,CAAA;IAC/B,OAAO,KAAK,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;QACxB,MAAM,EAAE,IAAI,EAAE,EAAE,EAAE,GAAG,EAAE,GAAG,KAAK,CAAC,GAAG,EAAG,CAAA;QACtC,MAAM,IAAI,GAAG,GAAG,GAAG,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,IAAI,CAAC,MAAM,IAAI,CAAC,EAAE,CAAC,CAAC,CAAA;QACrD,IAAI,CAAC,GAAG,GAAG,IAAI,GAAG,CAAC,CAAA;QACnB,IAAI,IAAI,CAAC,QAAQ,EAAE,CAAC;YAClB,KAAK,MAAM,KAAK,IAAI,IAAI,CAAC,QAAQ,EAAE,CAAC;gBAClC,KAAK,CAAC,IAAI,CAAC,EAAE,IAAI,EAAE,KAAK,EAAE,EAAE,EAAE,IAAI,EAAE,CAAC,CAAA;YACvC,CAAC;QACH,CAAC;IACH,CAAC;AACH,CAAC"}
+{"version":3,"file":"hierarchy.js","sourceRoot":"","sources":["../src/hierarchy.ts"],"names":[],"mappings":"AAyBA,iFAAiF;AACjF,kFAAkF;AAClF,4EAA4E;AAE5E,gFAAgF;AAChF,kFAAkF;AAClF,oCAAoC;AACpC,MAAM,UAAU,WAAW,CAAI,IAAsB;IACnD,MAAM,MAAM,GAAuB,EAAE,CAAA;IACrC,MAAM,KAAK,GAAG,CAAC,IAAI,CAAC,CAAA;IACpB,OAAO,KAAK,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;QACxB,MAAM,CAAC,GAAG,KAAK,CAAC,GAAG,EAAG,CAAA;QACtB,MAAM,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;QACd,IAAI,CAAC,CAAC,QAAQ,EAAE,CAAC;YACf,KAAK,IAAI,CAAC,GAAG,CAAC,CAAC,QAAQ,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC;gBAChD,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAE,CAAC,CAAA;YAC5B,CAAC;QACH,CAAC;IACH,CAAC;IACD,OAAO,MAAM,CAAA;AACf,CAAC;AAED,SAAS,aAAa,CAAI,IAAsB;IAC9C,MAAM,KAAK,GAAG,WAAW,CAAC,IAAI,CAAC,CAAA;IAC/B,KAAK,IAAI,CAAC,GAAG,KAAK,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC;QAC3C,MAAM,CAAC,GAAG,KAAK,CAAC,CAAC,CAAE,CAAA;QACnB,IAAI,CAAC,GAAG,CAAC,CAAA;QACT,IAAI,CAAC,CAAC,QAAQ,EAAE,CAAC;YACf,KAAK,MAAM,KAAK,IAAI,CAAC,CAAC,QAAQ,EAAE,CAAC;gBAC/B,IAAI,KAAK,CAAC,MAAM,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC;oBACzB,CAAC,GAAG,KAAK,CAAC,MAAM,GAAG,CAAC,CAAA;gBACtB,CAAC;YACH,CAAC;QACH,CAAC;QACD,CAAC,CAAC,MAAM,GAAG,CAAC,CAAA;IACd,CAAC;AACH,CAAC;AAED,MAAM,UAAU,SAAS,CACvB,IAAO,EACP,gBAA2C;IAE3C,MAAM,IAAI,GAAqB;QAC7B,IAAI;QACJ,QAAQ,EAAE,IAAI;QACd,MAAM,EAAE,IAAI;QACZ,KAAK,EAAE,CAAC;QACR,MAAM,EAAE,CAAC;KACV,CAAA;IACD,MAAM,KAAK,GAAG,CAAC,IAAI,CAAC,CAAA;IACpB,OAAO,KAAK,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;QACxB,MAAM,IAAI,GAAG,KAAK,CAAC,GAAG,EAAG,CAAA;QACzB,MAAM,IAAI,GAAG,gBAAgB,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;QACxC,IAAI,IAAI,EAAE,MAAM,EAAE,CAAC;YACjB,IAAI,CAAC,QAAQ,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC;gBAC7B,IAAI,EAAE,CAAC;gBACP,QAAQ,EAAE,IAAI;gBACd,MAAM,EAAE,IAAI;gBACZ,KAAK,EAAE,IAAI,CAAC,KAAK,GAAG,CAAC;gBACrB,MAAM,EAAE,CAAC;aACV,CAAC,CAAC,CAAA;YACH,KAAK,MAAM,KAAK,IAAI,IAAI,CAAC,QAAQ,EAAE,CAAC;gBAClC,KAAK,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;YACnB,CAAC;QACH,CAAC;IACH,CAAC;IACD,aAAa,CAAC,IAAI,CAAC,CAAA;IACnB,OAAO,IAAI,CAAA;AACb,CAAC;AAED,MAAM,UAAU,GAAG,CACjB,IAAsB,EACtB,OAAyB;IAEzB,MAAM,KAAK,GAAG,WAAW,CAAC,IAAI,CAAC,CAAA;IAC/B,KAAK,IAAI,CAAC,GAAG,KAAK,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC;QAC3C,MAAM,CAAC,GAAG,KAAK,CAAC,CAAC,CAAE,CAAA;QACnB,IAAI,CAAC,GAAG,OAAO,CAAC,CAAC,CAAC,IAAI,CAAC,CAAA;QACvB,IAAI,CAAC,CAAC,QAAQ,EAAE,CAAC;YACf,KAAK,MAAM,KAAK,IAAI,CAAC,CAAC,QAAQ,EAAE,CAAC;gBAC/B,CAAC,IAAI,KAAK,CAAC,KAAM,CAAA;YACnB,CAAC;QACH,CAAC;QACD,CAAC,CAAC,KAAK,GAAG,CAAC,CAAA;IACb,CAAC;IACD,OAAO,IAAI,CAAA;AACb,CAAC;AAED,MAAM,UAAU,IAAI,CAClB,IAAsB,EACtB,SAA+D;IAE/D,MAAM,KAAK,GAAG,CAAC,IAAI,CAAC,CAAA;IACpB,OAAO,KAAK,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;QACxB,MAAM,CAAC,GAAG,KAAK,CAAC,GAAG,EAAG,CAAA;QACtB,IAAI,CAAC,CAAC,QAAQ,EAAE,CAAC;YACf,CAAC,CAAC,QAAQ,CAAC,IAAI,CAAC,SAAS,CAAC,CAAA;YAC1B,KAAK,MAAM,KAAK,IAAI,CAAC,CAAC,QAAQ,EAAE,CAAC;gBAC/B,KAAK,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;YACnB,CAAC;QACH,CAAC;IACH,CAAC;IACD,OAAO,IAAI,CAAA;AACb,CAAC;AAED,MAAM,UAAU,IAAI,CAClB,IAAsB,EACtB,SAA2C;IAE3C,MAAM,KAAK,GAAG,CAAC,IAAI,CAAC,CAAA;IACpB,IAAI,KAAmC,CAAA;IACvC,OAAO,KAAK,CAAC,MAAM,GAAG,CAAC,IAAI,KAAK,KAAK,SAAS,EAAE,CAAC;QAC/C,MAAM,CAAC,GAAG,KAAK,CAAC,GAAG,EAAG,CAAA;QACtB,IAAI,SAAS,CAAC,CAAC,CAAC,EAAE,CAAC;YACjB,KAAK,GAAG,CAAC,CAAA;QACX,CAAC;aAAM,IAAI,CAAC,CAAC,QAAQ,EAAE,CAAC;YACtB,KAAK,IAAI,CAAC,GAAG,CAAC,CAAC,QAAQ,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC;gBAChD,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAE,CAAC,CAAA;YAC5B,CAAC;QACH,CAAC;IACH,CAAC;IACD,OAAO,KAAK,CAAA;AACd,CAAC;AAED,MAAM,UAAU,MAAM,CAAI,IAAsB;IAC9C,MAAM,MAAM,GAAuB,EAAE,CAAA;IACrC,MAAM,KAAK,GAAG,CAAC,IAAI,CAAC,CAAA;IACpB,OAAO,KAAK,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;QACxB,MAAM,CAAC,GAAG,KAAK,CAAC,GAAG,EAAG,CAAA;QACtB,IAAI,CAAC,CAAC,QAAQ,EAAE,CAAC;YACf,KAAK,IAAI,CAAC,GAAG,CAAC,CAAC,QAAQ,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC;gBAChD,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAE,CAAC,CAAA;YAC5B,CAAC;QACH,CAAC;aAAM,CAAC;YACN,MAAM,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;QAChB,CAAC;IACH,CAAC;IACD,OAAO,MAAM,CAAA;AACf,CAAC;AAED,MAAM,UAAU,KAAK,CAAI,IAAsB;IAC7C,MAAM,MAAM,GAAuB,EAAE,CAAA;IACrC,WAAW,CAAC,IAAI,EAAE,CAAC,MAAM,EAAE,MAAM,EAAE,EAAE;QACnC,MAAM,CAAC,IAAI,CAAC,EAAE,MAAM,EAAE,MAAM,EAAE,CAAC,CAAA;IACjC,CAAC,CAAC,CAAA;IACF,OAAO,MAAM,CAAA;AACf,CAAC;AAED,MAAM,UAAU,WAAW,CACzB,IAAsB,EACtB,EAAgE;IAEhE,MAAM,KAAK,GAAG,CAAC,IAAI,CAAC,CAAA;IACpB,OAAO,KAAK,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;QACxB,MAAM,CAAC,GAAG,KAAK,CAAC,GAAG,EAAG,CAAA;QACtB,IAAI,CAAC,CAAC,QAAQ,EAAE,CAAC;YACf,KAAK,IAAI,CAAC,GAAG,CAAC,CAAC,QAAQ,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC;gBAChD,MAAM,KAAK,GAAG,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAE,CAAA;gBAC5B,EAAE,CAAC,CAAC,EAAE,KAAK,CAAC,CAAA;gBACZ,KAAK,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;YACnB,CAAC;QACH,CAAC;IACH,CAAC;AACH,CAAC;AAED,MAAM,UAAU,iBAAiB,CAC/B,IAAsB,EACtB,EAAiC;IAEjC,KAAK,MAAM,CAAC,IAAI,WAAW,CAAC,IAAI,CAAC,EAAE,CAAC;QAClC,EAAE,CAAC,CAAC,CAAC,CAAA;IACP,CAAC;AACH,CAAC;AAED,MAAM,UAAU,aAAa,CAC3B,IAAsB,EACtB,KAAa,EACb,KAAa;IAEb,MAAM,SAAS,GAAG,MAAM,CAAC,IAAI,CAAC,CAAA;IAC9B,MAAM,CAAC,GAAG,SAAS,CAAC,MAAM,CAAA;IAC1B,MAAM,IAAI,GAAG,KAAK,GAAG,CAAC,CAAA;IAEtB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC;QAC3B,SAAS,CAAC,CAAC,CAAE,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAC,GAAG,IAAI,CAAA;IACpC,CAAC;IAED,uEAAuE;IACvE,uCAAuC;IACvC,MAAM,KAAK,GAAG,WAAW,CAAC,IAAI,CAAC,CAAA;IAC/B,KAAK,IAAI,CAAC,GAAG,KAAK,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC;QAC3C,MAAM,IAAI,GAAG,KAAK,CAAC,CAAC,CAAE,CAAA;QACtB,IAAI,IAAI,CAAC,QAAQ,EAAE,CAAC;YAClB,IAAI,GAAG,GAAG,CAAC,CAAA;YACX,KAAK,MAAM,KAAK,IAAI,IAAI,CAAC,QAAQ,EAAE,CAAC;gBAClC,GAAG,IAAI,KAAK,CAAC,CAAE,CAAA;YACjB,CAAC;YACD,IAAI,CAAC,CAAC,GAAG,GAAG,GAAG,IAAI,CAAC,QAAQ,CAAC,MAAM,CAAA;QACrC,CAAC;IACH,CAAC;IAED,MAAM,UAAU,GAAG,IAAI,CAAC,MAAM,CAAA;IAC9B,MAAM,KAAK,GAAG,CAAC,EAAE,IAAI,EAAE,IAAI,EAAE,KAAK,EAAE,CAAC,EAAE,CAAC,CAAA;IACxC,OAAO,KAAK,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;QACxB,MAAM,EAAE,IAAI,EAAE,KAAK,EAAE,GAAG,KAAK,CAAC,GAAG,EAAG,CAAA;QACpC,IAAI,CAAC,CAAC,GAAG,UAAU,KAAK,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,KAAK,GAAG,UAAU,CAAC,GAAG,KAAK,CAAA;QAChE,IAAI,IAAI,CAAC,QAAQ,EAAE,CAAC;YAClB,KAAK,MAAM,KAAK,IAAI,IAAI,CAAC,QAAQ,EAAE,CAAC;gBAClC,KAAK,CAAC,IAAI,CAAC,EAAE,IAAI,EAAE,KAAK,EAAE,KAAK,EAAE,KAAK,GAAG,CAAC,EAAE,CAAC,CAAA;YAC/C,CAAC;QACH,CAAC;IACH,CAAC;AACH,CAAC;AAED,MAAM,UAAU,QAAQ,CAAI,IAAsB;IAChD,IAAI,IAAI,CAAC,QAAQ,EAAE,CAAC;QAClB,oEAAoE;QACpE,uEAAuE;QACvE,0EAA0E;QAC1E,uEAAuE;QACvE,sDAAsD;QACtD,eAAe,CAAC,IAAI,CAAC,CAAA;QACrB,IAAI,CAAC,SAAS,GAAG,IAAI,CAAC,QAAQ,CAAA;QAC9B,IAAI,CAAC,QAAQ,GAAG,IAAI,CAAA;IACtB,CAAC;AACH,CAAC;AAED,iFAAiF;AACjF,0EAA0E;AAC1E,8CAA8C;AAC9C,MAAM,UAAU,4BAA4B,CAC1C,IAAsB;IAEtB,MAAM,KAAK,GAAG,IAAI,CAAC,SAAS,IAAI,IAAI,CAAC,QAAQ,CAAA;IAC7C,IAAI,GAAG,GAAG,QAAQ,CAAA;IAClB,IAAI,GAAG,GAAG,CAAC,CAAA;IACX,IAAI,KAAK,EAAE,CAAC;QACV,MAAM,KAAK,GAAG,KAAK,CAAC,GAAG,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;YAChC,IAAI,EAAE,KAAK;YACX,GAAG,EAAE,IAAI,CAAC,GAAG,CAAC,KAAK,CAAC,IAAI,CAAC,MAAM,IAAI,CAAC,EAAE,CAAC,CAAC;SACzC,CAAC,CAAC,CAAA;QACH,OAAO,KAAK,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;YACxB,MAAM,EAAE,IAAI,EAAE,CAAC,EAAE,GAAG,EAAE,GAAG,KAAK,CAAC,GAAG,EAAG,CAAA;YACrC,MAAM,IAAI,GAAG,CAAC,CAAC,QAAQ,IAAI,CAAC,CAAC,SAAS,CAAA;YACtC,IAAI,IAAI,EAAE,MAAM,EAAE,CAAC;gBACjB,KAAK,MAAM,KAAK,IAAI,IAAI,EAAE,CAAC;oBACzB,KAAK,CAAC,IAAI,CAAC;wBACT,IAAI,EAAE,KAAK;wBACX,GAAG,EAAE,GAAG,GAAG,IAAI,CAAC,GAAG,CAAC,KAAK,CAAC,IAAI,CAAC,MAAM,IAAI,CAAC,EAAE,CAAC,CAAC;qBAC/C,CAAC,CAAA;gBACJ,CAAC;YACH,CAAC;iBAAM,CAAC;gBACN,GAAG,GAAG,IAAI,CAAC,GAAG,CAAC,GAAG,EAAE,GAAG,CAAC,CAAA;gBACxB,GAAG,GAAG,IAAI,CAAC,GAAG,CAAC,GAAG,EAAE,GAAG,CAAC,CAAA;YAC1B,CAAC;QACH,CAAC;IACH,CAAC;IACD,OAAO,EAAE,GAAG,EAAE,GAAG,KAAK,QAAQ,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,EAAE,GAAG,EAAE,CAAA;AACjD,CAAC;AAED,+EAA+E;AAC/E,gFAAgF;AAChF,gFAAgF;AAChF,wEAAwE;AACxE,MAAM,UAAU,eAAe,CAAI,IAAsB;IACvD,MAAM,KAAK,GAAG,WAAW,CAAC,IAAI,CAAC,CAAA;IAC/B,KAAK,IAAI,CAAC,GAAG,KAAK,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC;QAC3C,MAAM,CAAC,GAAG,KAAK,CAAC,CAAC,CAAE,CAAA;QACnB,IAAI,CAAC,CAAC,WAAW,KAAK,SAAS,EAAE,CAAC;YAChC,IAAI,QAAQ,GAAG,CAAC,CAAA;YAChB,IAAI,CAAC,CAAC,QAAQ,EAAE,CAAC;gBACf,KAAK,MAAM,KAAK,IAAI,CAAC,CAAC,QAAQ,EAAE,CAAC;oBAC/B,QAAQ,GAAG,IAAI,CAAC,GAAG,CAAC,QAAQ,EAAE,CAAC,GAAG,KAAK,CAAC,WAAY,CAAC,CAAA;gBACvD,CAAC;YACH,CAAC;YACD,CAAC,CAAC,WAAW,GAAG,QAAQ,CAAA;QAC1B,CAAC;IACH,CAAC;IACD,OAAO,IAAI,CAAC,WAAY,CAAA;AAC1B,CAAC;AAED,MAAM,UAAU,gBAAgB,CAAC,IAAmB;IAClD,IAAI,MAAM,GAAG,CAAC,CAAA;IACd,KAAK,MAAM,CAAC,IAAI,WAAW,CAAC,IAAI,CAAC,EAAE,CAAC;QAClC,MAAM,GAAG,IAAI,CAAC,GAAG,CAAC,MAAM,EAAE,CAAC,CAAC,GAAG,IAAI,CAAC,CAAC,CAAA;IACvC,CAAC;IACD,OAAO,MAAM,CAAA;AACf,CAAC;AAED,iEAAiE;AACjE,MAAM,UAAU,SAAS,CAAC,CAAgB;IACxC,MAAM,KAAK,GAAG,WAAW,CAAC,CAAC,CAAC,CAAA;IAC5B,MAAM,OAAO,GAAG,IAAI,GAAG,EAAyB,CAAA;IAChD,KAAK,IAAI,CAAC,GAAG,KAAK,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC;QAC3C,MAAM,CAAC,GAAG,KAAK,CAAC,CAAC,CAAE,CAAA;QACnB,IAAI,QAAQ,GAAG,CAAC,CAAA;QAChB,IAAI,CAAC,CAAC,QAAQ,EAAE,CAAC;YACf,KAAK,MAAM,KAAK,IAAI,CAAC,CAAC,QAAQ,EAAE,CAAC;gBAC/B,QAAQ,GAAG,IAAI,CAAC,GAAG,CAAC,QAAQ,EAAE,OAAO,CAAC,GAAG,CAAC,KAAK,CAAE,CAAC,CAAA;YACpD,CAAC;QACH,CAAC;QACD,OAAO,CAAC,GAAG,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,MAAM,IAAI,CAAC,CAAC,GAAG,QAAQ,CAAC,CAAA;IACjD,CAAC;IACD,OAAO,OAAO,CAAC,GAAG,CAAC,CAAC,CAAE,CAAA;AACxB,CAAC;AAED,MAAM,UAAU,WAAW,CAAC,CAAgB,EAAE,EAAU,EAAE,CAAS;IACjE,MAAM,KAAK,GAAG,CAAC,EAAE,IAAI,EAAE,CAAC,EAAE,EAAE,EAAE,CAAC,CAAA;IAC/B,OAAO,KAAK,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;QACxB,MAAM,EAAE,IAAI,EAAE,EAAE,EAAE,GAAG,EAAE,GAAG,KAAK,CAAC,GAAG,EAAG,CAAA;QACtC,MAAM,IAAI,GAAG,GAAG,GAAG,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,IAAI,CAAC,MAAM,IAAI,CAAC,EAAE,CAAC,CAAC,CAAA;QACrD,IAAI,CAAC,GAAG,GAAG,IAAI,GAAG,CAAC,CAAA;QACnB,IAAI,IAAI,CAAC,QAAQ,EAAE,CAAC;YAClB,KAAK,MAAM,KAAK,IAAI,IAAI,CAAC,QAAQ,EAAE,CAAC;gBAClC,KAAK,CAAC,IAAI,CAAC,EAAE,IAAI,EAAE,KAAK,EAAE,EAAE,EAAE,IAAI,EAAE,CAAC,CAAA;YACvC,CAAC;QACH,CAAC;IACH,CAAC;AACH,CAAC"}

package/dist/model/msaModel.d.ts

@@ -1,9 +1,11 @@
+import type { MSAFormat } from 'msa-parsers';
 /**
  * #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>;
+    msaFormat: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<MSAFormat>>;
 }, {
     /**
      * #action
@@ -14,4 +16,9 @@ export declare function MSAModelF(): import("@jbrowse/mobx-state-tree").IModelTy
      * #action
      */
     setBgColor(arg: boolean): void;
+    /**
+     * #action
+     * force a specific MSA parser, or pass undefined to auto-detect
+     */
+    setMSAFormat(arg?: MSAFormat): void;
 }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>;

package/dist/model/msaModel.js

@@ -1,5 +1,6 @@
 import { types } from '@jbrowse/mobx-state-tree';
 import { defaultBgColor, defaultColorSchemeName } from "../constants.js";
+const msaFormats = ['stockholm', 'a3m', 'fasta', 'emf', 'clustal'];
 /**
  * #stateModel MSAModel
  */
@@ -16,6 +17,12 @@ export function MSAModelF() {
          * default color scheme name
          */
         colorSchemeName: defaultColorSchemeName,
+        /**
+         * #property
+         * force the MSA data to be parsed as a specific format instead of relying
+         * on auto-detection (which is ambiguous between e.g. fasta and a3m)
+         */
+        msaFormat: types.maybe(types.enumeration('MSAFormat', msaFormats)),
     })
         .actions(self => ({
         /**
@@ -31,6 +38,13 @@ export function MSAModelF() {
         setBgColor(arg) {
             self.bgColor = arg;
         },
+        /**
+         * #action
+         * force a specific MSA parser, or pass undefined to auto-detect
+         */
+        setMSAFormat(arg) {
+            self.msaFormat = arg;
+        },
     }));
 }
 //# sourceMappingURL=msaModel.js.map

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,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;AAIxE,MAAM,UAAU,GAAgB,CAAC,WAAW,EAAE,KAAK,EAAE,OAAO,EAAE,KAAK,EAAE,SAAS,CAAC,CAAA;AAE/E;;GAEG;AACH,MAAM,UAAU,SAAS;IACvB,OAAO,KAAK;SACT,KAAK,CAAC;QACL;;;WAGG;QACH,OAAO,EAAE,cAAc;QAEvB;;;WAGG;QACH,eAAe,EAAE,sBAAsB;QAEvC;;;;WAIG;QACH,SAAS,EAAE,KAAK,CAAC,KAAK,CACpB,KAAK,CAAC,WAAW,CAAY,WAAW,EAAE,UAAU,CAAC,CACtD;KACF,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;QAED;;;WAGG;QACH,YAAY,CAAC,GAAe;YAC1B,IAAI,CAAC,SAAS,GAAG,GAAG,CAAA;QACtB,CAAC;KACF,CAAC,CAAC,CAAA;AACP,CAAC"}

package/dist/model.d.ts

@@ -24,10 +24,11 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
     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>;
-}, "bgColor" | "colorSchemeName"> & {
+}, "bgColor" | "colorSchemeName" | "msaFormat"> & {
     bgColor: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     colorSchemeName: import("@jbrowse/mobx-state-tree").IType<string | undefined, string, string>;
-}, "type" | "id" | "data" | "showDomains" | "hideGaps" | "allowedGappyness" | "subFeatureRows" | "drawMsaLetters" | "scrollZoom" | "rowHeight" | "scrollY" | "scrollX" | "colWidth" | "currentAlignment" | "height" | "treeFilehandle" | "msaFilehandle" | "treeMetadataFilehandle" | "gffFilehandle" | "collapsed" | "showOnly" | "turnedOffTracks" | "featureFilters" | "relativeTo"> & {
+    msaFormat: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<import("msa-parsers").MSAFormat>>;
+}, "type" | "id" | "data" | "showDomains" | "hideGaps" | "allowedGappyness" | "subFeatureRows" | "drawMsaLetters" | "scrollZoom" | "rowHeight" | "scrollY" | "scrollX" | "colWidth" | "currentAlignment" | "height" | "treeFilehandle" | "msaFilehandle" | "treeMetadataFilehandle" | "gffFilehandle" | "collapsed" | "showOnly" | "turnedOffTracks" | "featureFilters" | "relativeTo" | "highlightColumns"> & {
     id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
     showDomains: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     hideGaps: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
@@ -143,6 +144,7 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
     }>, [undefined]>;
     featureFilters: import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>;
     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>;
 }, {
     queueOfDialogs: [import("@jbrowse/core/util").DialogComponentType, any][];
 } & {
@@ -162,6 +164,7 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
 } & {
     setColorSchemeName(name: string): void;
     setBgColor(arg: boolean): void;
+    setMSAFormat(arg?: import("msa-parsers").MSAFormat): void;
 } & {
     /**
      * #volatile
@@ -949,10 +952,11 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
     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>;
-}, "bgColor" | "colorSchemeName"> & {
+}, "bgColor" | "colorSchemeName" | "msaFormat"> & {
     bgColor: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     colorSchemeName: import("@jbrowse/mobx-state-tree").IType<string | undefined, string, string>;
-}, "type" | "id" | "data" | "showDomains" | "hideGaps" | "allowedGappyness" | "subFeatureRows" | "drawMsaLetters" | "scrollZoom" | "rowHeight" | "scrollY" | "scrollX" | "colWidth" | "currentAlignment" | "height" | "treeFilehandle" | "msaFilehandle" | "treeMetadataFilehandle" | "gffFilehandle" | "collapsed" | "showOnly" | "turnedOffTracks" | "featureFilters" | "relativeTo"> & {
+    msaFormat: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<import("msa-parsers").MSAFormat>>;
+}, "type" | "id" | "data" | "showDomains" | "hideGaps" | "allowedGappyness" | "subFeatureRows" | "drawMsaLetters" | "scrollZoom" | "rowHeight" | "scrollY" | "scrollX" | "colWidth" | "currentAlignment" | "height" | "treeFilehandle" | "msaFilehandle" | "treeMetadataFilehandle" | "gffFilehandle" | "collapsed" | "showOnly" | "turnedOffTracks" | "featureFilters" | "relativeTo" | "highlightColumns"> & {
     id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
     showDomains: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     hideGaps: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
@@ -1068,6 +1072,7 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
     }>, [undefined]>;
     featureFilters: import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>;
     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>;
 }>, symbol>>;
 export default stateModelFactory;
 export type MsaViewStateModel = ReturnType<typeof stateModelFactory>;

package/dist/model.js

@@ -1,4 +1,4 @@
-import { clamp, fetchAndMaybeUnzipText, groupBy, notEmpty, sum, } from '@jbrowse/core/util';
+import { clamp, groupBy, notEmpty, sum } from '@jbrowse/core/util';
 import { openLocation } from '@jbrowse/core/util/io';
 import { ElementId, FileLocation } from '@jbrowse/core/util/types/mst';
 import { addDisposer, cast, types } from '@jbrowse/mobx-state-tree';
@@ -12,8 +12,9 @@ import ConservationTrack from "./components/ConservationTrack.js";
 import TextTrack from "./components/TextTrack.js";
 import { defaultAllowedGappyness, defaultBgColor, defaultColWidth, defaultColorSchemeName, defaultCurrentAlignment, defaultDrawLabels, defaultDrawMsaLetters, defaultDrawNodeBubbles, defaultDrawTree, defaultHeight, defaultHideGaps, defaultLabelsAlignRight, defaultRowHeight, defaultScrollX, defaultScrollY, defaultScrollZoom, defaultShowBranchLen, defaultShowDomains, defaultSubFeatureRows, defaultTreeAreaWidth, defaultTreeWidth, maxCellSize, minColWidth, minRowHeight, } from "./constants.js";
 import { createPaletteMap } from "./createPaletteMap.js";
+import { fetchTextWithProgress, isAbortError } from "./fetchUtils.js";
 import { flatToTree } from "./flatToTree.js";
-import { calcDepthToLeaf, clusterLayout, collapse, find, findMaxBranchLen, hierarchy, leaves, links, maxLength, setBrLength, sort, sum as hierarchySum, } from "./hierarchy.js";
+import { calcDepthToLeaf, clusterLayout, collapse, collapsedSubtreeLengthExtent, find, findMaxBranchLen, forEachDescendant, hierarchy, leaves, links, maxLength, setBrLength, sort, sum as hierarchySum, } from "./hierarchy.js";
 import { measureTextCanvas } from "./measureTextCanvas.js";
 import { DataModelF } from "./model/DataModel.js";
 import { DialogQueueSessionMixin } from "./model/DialogQueue.js";
@@ -165,6 +166,15 @@ function stateModelFactory() {
          * #property
          */
         relativeTo: types.maybe(types.string),
+        /**
+         * #property
+         * declarative seed for the highlighted-columns overlay (visible column
+         * indices). Unlike the volatile `highlightedColumns` (driven by
+         * transient genome-hover sync), this persists in the snapshot/URL so a
+         * shared link can open with specific columns highlighted. Applied once
+         * in afterCreate.
+         */
+        highlightColumns: types.frozen(),
     }))
         .volatile(() => ({
         /**
@@ -534,7 +544,9 @@ function stateModelFactory() {
             const text = self.data.msa;
             // uses parseMSA so the named MSAParserType return type is portable
             // to downstream consumers (avoids TS2883 with default exports)
-            return text ? parseMSA(text, self.currentAlignment) : null;
+            return text
+                ? parseMSA(text, self.currentAlignment, self.msaFormat)
+                : null;
         },
         /**
          * #getter
@@ -791,6 +803,9 @@ function stateModelFactory() {
             const { colStats, colStatsSums } = this;
             return colStats.map((stats, i) => {
                 const total = colStatsSums[i];
+                if (!total) {
+                    return { letter: '', color: undefined };
+                }
                 let maxCount = 0;
                 let letter = '';
                 for (const [key, val] of Object.entries(stats)) {
@@ -859,7 +874,18 @@ function stateModelFactory() {
             clusterLayout(r, this.totalHeight, self.treeWidth);
             r.data.length = 0;
             const max = maxLength(r);
-            setBrLength(r, 0, max ? self.treeWidth / max : 0);
+            const k = max ? self.treeWidth / max : 0;
+            setBrLength(r, 0, k);
+            // for each collapsed clade, record the pixel x-positions of its
+            // nearest/farthest tips so the renderer can draw a triangle that spans
+            // the branch-length extent of the hidden subtree
+            forEachDescendant(r, node => {
+                if (node._children) {
+                    const { min, max: mx } = collapsedSubtreeLengthExtent(node);
+                    node.collapsedTipXNear = (node.len ?? 0) + min * k;
+                    node.collapsedTipXFar = (node.len ?? 0) + mx * k;
+                }
+            });
             return r;
         },
         /**
@@ -1066,9 +1092,8 @@ function stateModelFactory() {
          */
         zoomIn() {
             transaction(() => {
-                self.colWidth = Math.min(maxCellSize, Math.ceil(self.colWidth * 1.5));
-                self.rowHeight = Math.min(maxCellSize, Math.ceil(self.rowHeight * 1.5));
-                self.scrollX = clamp(self.scrollX, self.maxScrollX, 0);
+                this.zoomInHorizontal();
+                this.zoomInVertical();
             });
         },
         /**
@@ -1076,9 +1101,8 @@ function stateModelFactory() {
          */
         zoomOut() {
             transaction(() => {
-                self.colWidth = Math.max(minColWidth, Math.floor(self.colWidth * 0.75));
-                self.rowHeight = Math.max(minRowHeight, Math.floor(self.rowHeight * 0.75));
-                self.scrollX = clamp(self.scrollX, self.maxScrollX, 0);
+                this.zoomOutHorizontal();
+                this.zoomOutVertical();
             });
         },
         /**
@@ -1099,8 +1123,12 @@ function stateModelFactory() {
                 self.rowHeight = clamp(self.rowHeight * scaleFactor, minRowHeight, maxCellSize);
                 self.scrollX = clamp(offsetX - colInView * self.colWidth, self.maxScrollX, 0);
                 const anchoredScrollY = offsetY - rowInView * self.rowHeight;
-                const overflow = Math.max(0, self.totalHeight - self.height);
-                const topBias = self.height > 0 ? clamp(1 - overflow / self.height, 0, 1) : 0;
+                // maxScrollY is -(totalHeight - visibleMsaHeight) when the alignment
+                // overflows, so -maxScrollY is exactly that overflow past the
+                // scrollable MSA viewport (0 when it fits)
+                const overflow = Math.max(0, -self.maxScrollY);
+                const visibleHeight = self.totalHeight - overflow;
+                const topBias = visibleHeight > 0 ? clamp(1 - overflow / visibleHeight, 0, 1) : 1;
                 self.scrollY = clamp(anchoredScrollY * (1 - topBias), self.maxScrollY, 0);
             });
         },
@@ -1448,14 +1476,8 @@ function stateModelFactory() {
          * #action
          */
         fit() {
-            if (self.numRows > 0) {
-                self.rowHeight = clamp(self.msaAreaHeight / self.numRows, minRowHeight, maxCellSize);
-            }
-            if (self.numColumns > 0) {
-                self.colWidth = clamp(self.msaAreaWidth / self.numColumns, minColWidth, maxCellSize);
-            }
-            self.scrollX = 0;
-            self.scrollY = 0;
+            this.fitVertically();
+            this.fitHorizontally();
         },
         /**
          * #action
@@ -1476,6 +1498,12 @@ function stateModelFactory() {
             self.scrollX = 0;
         },
         afterCreate() {
+            // seed the highlighted-columns overlay from the declarative property so
+            // a shared snapshot/URL opens with those columns highlighted (the
+            // volatile highlightedColumns can later be driven by genome-hover sync)
+            if (self.highlightColumns?.length) {
+                self.setHighlightedColumns(self.highlightColumns);
+            }
             addDisposer(self, autorun(() => {
                 for (const key of self.tidyInterProAnnotationTypes.keys()) {
                     this.initFilter(key);
@@ -1491,7 +1519,11 @@ function stateModelFactory() {
                     const generation = ++treeGeneration;
                     try {
                         self.setLoadingTree(true);
-                        const text = await fetchAndMaybeUnzipText(openLocation(treeFilehandle));
+                        const text = await fetchTextWithProgress(openLocation(treeFilehandle), status => {
+                            if (generation === treeGeneration) {
+                                self.setStatus(status);
+                            }
+                        });
                         if (generation === treeGeneration) {
                             transaction(() => {
                                 self.setTree(text);
@@ -1504,8 +1536,15 @@ function stateModelFactory() {
                     }
                     catch (e) {
                         if (generation === treeGeneration) {
-                            console.error(e);
-                            self.setError(e);
+                            if (isAbortError(e)) {
+                                // cancelled by the user: drop the filehandle so the view
+                                // returns to the import form instead of a stuck spinner
+                                self.setTreeFilehandle(undefined);
+                            }
+                            else {
+                                console.error(e);
+                                self.setError(e);
+                            }
                         }
                     }
                     finally {
@@ -1520,11 +1559,16 @@ function stateModelFactory() {
                 const { treeMetadataFilehandle } = self;
                 if (treeMetadataFilehandle) {
                     try {
-                        self.setTreeMetadata(await fetchAndMaybeUnzipText(openLocation(treeMetadataFilehandle)));
+                        self.setTreeMetadata(await fetchTextWithProgress(openLocation(treeMetadataFilehandle), status => {
+                            self.setStatus(status);
+                        }));
                     }
                     catch (e) {
-                        console.error(e);
-                        self.setError(e);
+                        // ignore user cancel (isAbortError); treeMetadata is optional
+                        if (!isAbortError(e)) {
+                            console.error(e);
+                            self.setError(e);
+                        }
                     }
                 }
             }));
@@ -1546,15 +1590,23 @@ function stateModelFactory() {
                 const { gffFilehandle } = self;
                 if (gffFilehandle) {
                     try {
-                        const gffText = await fetchAndMaybeUnzipText(openLocation(gffFilehandle));
+                        const gffText = await fetchTextWithProgress(openLocation(gffFilehandle), status => {
+                            self.setStatus(status);
+                        });
                         self.applyGFFText(gffText);
                         if (gffFilehandle.locationType === 'BlobLocation') {
                             self.setGFFFilehandle(undefined);
                         }
                     }
                     catch (e) {
-                        console.error(e);
-                        self.setError(e);
+                        // on user cancel (isAbortError) drop the filehandle
+                        if (isAbortError(e)) {
+                            self.setGFFFilehandle(undefined);
+                        }
+                        else {
+                            console.error(e);
+                            self.setError(e);
+                        }
                     }
                 }
             }));
@@ -1567,7 +1619,11 @@ function stateModelFactory() {
                     try {
                         self.setLoadingMSA(true);
                         self.setError(undefined);
-                        const txt = await fetchAndMaybeUnzipText(openLocation(msaFilehandle));
+                        const txt = await fetchTextWithProgress(openLocation(msaFilehandle), status => {
+                            if (generation === msaGeneration) {
+                                self.setStatus(status);
+                            }
+                        });
                         if (generation === msaGeneration) {
                             transaction(() => {
                                 self.setMSA(txt);
@@ -1580,8 +1636,15 @@ function stateModelFactory() {
                     }
                     catch (e) {
                         if (generation === msaGeneration) {
-                            console.error(e);
-                            self.setError(e);
+                            if (isAbortError(e)) {
+                                // cancelled by the user: drop the filehandle so the view
+                                // returns to the import form instead of a stuck spinner
+                                self.setMSAFilehandle(undefined);
+                            }
+                            else {
+                                console.error(e);
+                                self.setError(e);
+                            }
                         }
                     }
                     finally {