react-msaview 5.10.0 → 6.1.0

package/dist/hierarchy.js

@@ -56,12 +56,11 @@ export function collapse(node) {
         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
+// Cumulative raw branch length from a collapsed node down to the farthest tip of
+// its detached subtree (excludes the node's own branch). Sizes the base of the
 // collapsed-clade triangle in phylogram mode.
-export function collapsedSubtreeLengthExtent(node) {
+export function collapsedSubtreeMaxLength(node) {
     const roots = node._children ?? node.children;
-    let min = Infinity;
     let max = 0;
     if (roots) {
         const stack = roots.map(child => ({
@@ -80,12 +79,11 @@ export function collapsedSubtreeLengthExtent(node) {
                 }
             }
             else {
-                min = Math.min(min, acc);
                 max = Math.max(max, acc);
             }
         }
     }
-    return { min: min === Infinity ? 0 : min, max };
+    return 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

package/dist/hierarchy.js.map

@@ -1 +1 @@
-{"version":3,"file":"hierarchy.js","sourceRoot":"","sources":["../src/hierarchy.ts"],"names":[],"mappings":"AAAA,OAAO,EACL,WAAW,EACX,IAAI,EACJ,iBAAiB,EACjB,WAAW,EACX,SAAS,IAAI,aAAa,EAC1B,MAAM,EACN,KAAK,EACL,IAAI,EACJ,GAAG,GACJ,MAAM,cAAc,CAAA;AA0BrB,gFAAgF;AAChF,iFAAiF;AACjF,+EAA+E;AAC/E,uEAAuE;AACvE,OAAO,EACL,WAAW,EACX,IAAI,EACJ,iBAAiB,EACjB,WAAW,EACX,MAAM,EACN,KAAK,EACL,IAAI,EACJ,GAAG,GACJ,CAAA;AAGD,gFAAgF;AAChF,iFAAiF;AACjF,6EAA6E;AAC7E,wEAAwE;AACxE,yBAAyB;AACzB,MAAM,UAAU,SAAS,CACvB,IAAO,EACP,gBAA2C;IAE3C,OAAO,aAAa,CAAC,IAAI,EAAE,gBAAgB,CAAC,CAAA;AAC9C,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,+EAA+E;IAC/E,+EAA+E;IAC/E,+EAA+E;IAC/E,gEAAgE;IAChE,IAAI,IAAI,CAAC,WAAW,KAAK,SAAS,EAAE,CAAC;QACnC,MAAM,KAAK,GAAG,WAAW,CAAC,IAAI,CAAC,CAAA;QAC/B,KAAK,IAAI,CAAC,GAAG,KAAK,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC;YAC3C,MAAM,CAAC,GAAG,KAAK,CAAC,CAAC,CAAE,CAAA;YACnB,IAAI,CAAC,CAAC,WAAW,KAAK,SAAS,EAAE,CAAC;gBAChC,IAAI,QAAQ,GAAG,CAAC,CAAA;gBAChB,IAAI,CAAC,CAAC,QAAQ,EAAE,CAAC;oBACf,KAAK,MAAM,KAAK,IAAI,CAAC,CAAC,QAAQ,EAAE,CAAC;wBAC/B,QAAQ,GAAG,IAAI,CAAC,GAAG,CAAC,QAAQ,EAAE,CAAC,GAAG,KAAK,CAAC,WAAY,CAAC,CAAA;oBACvD,CAAC;gBACH,CAAC;gBACD,CAAC,CAAC,WAAW,GAAG,QAAQ,CAAA;YAC1B,CAAC;QACH,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":"AAAA,OAAO,EACL,WAAW,EACX,IAAI,EACJ,iBAAiB,EACjB,WAAW,EACX,SAAS,IAAI,aAAa,EAC1B,MAAM,EACN,KAAK,EACL,IAAI,EACJ,GAAG,GACJ,MAAM,cAAc,CAAA;AAyBrB,gFAAgF;AAChF,iFAAiF;AACjF,+EAA+E;AAC/E,uEAAuE;AACvE,OAAO,EACL,WAAW,EACX,IAAI,EACJ,iBAAiB,EACjB,WAAW,EACX,MAAM,EACN,KAAK,EACL,IAAI,EACJ,GAAG,GACJ,CAAA;AAGD,gFAAgF;AAChF,iFAAiF;AACjF,6EAA6E;AAC7E,wEAAwE;AACxE,yBAAyB;AACzB,MAAM,UAAU,SAAS,CACvB,IAAO,EACP,gBAA2C;IAE3C,OAAO,aAAa,CAAC,IAAI,EAAE,gBAAgB,CAAC,CAAA;AAC9C,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,+EAA+E;AAC/E,8CAA8C;AAC9C,MAAM,UAAU,yBAAyB,CACvC,IAAsB;IAEtB,MAAM,KAAK,GAAG,IAAI,CAAC,SAAS,IAAI,IAAI,CAAC,QAAQ,CAAA;IAC7C,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;YAC1B,CAAC;QACH,CAAC;IACH,CAAC;IACD,OAAO,GAAG,CAAA;AACZ,CAAC;AAED,+EAA+E;AAC/E,gFAAgF;AAChF,gFAAgF;AAChF,wEAAwE;AACxE,MAAM,UAAU,eAAe,CAAI,IAAsB;IACvD,+EAA+E;IAC/E,+EAA+E;IAC/E,+EAA+E;IAC/E,gEAAgE;IAChE,IAAI,IAAI,CAAC,WAAW,KAAK,SAAS,EAAE,CAAC;QACnC,MAAM,KAAK,GAAG,WAAW,CAAC,IAAI,CAAC,CAAA;QAC/B,KAAK,IAAI,CAAC,GAAG,KAAK,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC;YAC3C,MAAM,CAAC,GAAG,KAAK,CAAC,CAAC,CAAE,CAAA;YACnB,IAAI,CAAC,CAAC,WAAW,KAAK,SAAS,EAAE,CAAC;gBAChC,IAAI,QAAQ,GAAG,CAAC,CAAA;gBAChB,IAAI,CAAC,CAAC,QAAQ,EAAE,CAAC;oBACf,KAAK,MAAM,KAAK,IAAI,CAAC,CAAC,QAAQ,EAAE,CAAC;wBAC/B,QAAQ,GAAG,IAAI,CAAC,GAAG,CAAC,QAAQ,EAAE,CAAC,GAAG,KAAK,CAAC,WAAY,CAAC,CAAA;oBACvD,CAAC;gBACH,CAAC;gBACD,CAAC,CAAC,WAAW,GAAG,QAAQ,CAAA;YAC1B,CAAC;QACH,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/index.d.ts

@@ -4,6 +4,6 @@ export { default as MSAViewer } from './components/MSAViewer.tsx';
 export { type MsaViewModel, default as MSAModelF } from './model.ts';
 export type { MSAFormat, MSAParserType } from 'msa-parsers';
 export type { HierarchyNode } from './hierarchy.ts';
-export type { InterProScanResults } from './launchInterProScan.ts';
+export type { InterProScanResults } from 'msa-parsers';
 export type { ColumnCounts } from './columnCounts.ts';
-export type { Accession, BasicTrack, BasicTrackModel, DomainBand, Node, NodeWithIds, NodeWithIdsAndLength, TextTrackModel, TidyDomainAnnotation, } from './types.ts';
+export type { Accession, Annotation, BasicTrack, BasicTrackModel, DomainBand, Node, NodeWithIds, NodeWithIdsAndLength, TextTrackModel, TidyDomainAnnotation, } from './types.ts';

package/dist/launchInterProScan.d.ts

@@ -1,27 +1,4 @@
 import type { MsaViewModel } from './model.ts';
-export interface InterProScanResults {
-    matches: {
-        signature: {
-            entry?: {
-                name: string;
-                description: string;
-                accession: string;
-                featureType?: string;
-            };
-        };
-        locations: {
-            start: number;
-            end: number;
-            strand?: number;
-        }[];
-    }[];
-    xref: {
-        id: string;
-    }[];
-}
-export interface InterProScanResponse {
-    results: InterProScanResults[];
-}
 export declare function launchInterProScan({ algorithm, seq, programs, onJobId, onProgress, model, signal, }: {
     algorithm: string;
     seq: string;

package/dist/launchInterProScan.js

@@ -1,4 +1,5 @@
 import { getSession } from '@jbrowse/core/util';
+import { interProScanResponseToAnnotations } from 'msa-parsers';
 import { isAbortError, jsonfetch, textfetch, timeout } from './fetchUtils.js';
 const base = 'https://www.ebi.ac.uk/Tools/services/rest';
 async function runInterProScan({ seq, onProgress, onJobId, programs, model, signal, }) {
@@ -90,11 +91,7 @@ async function loadInterProScanResultsWithStatus({ jobId, model, onProgress, sig
             url: `https://www.ebi.ac.uk/Tools/services/rest/iprscan5/result/${jobId}/json`,
         });
         const ret = await loadInterProScanResults(jobId, signal);
-        // key each result by its xref id; skip any result lacking an xref entry
-        // rather than crashing the whole load on one malformed result
-        model.setDomains(Object.fromEntries(ret.results
-            .map(r => [r.xref[0]?.id, r])
-            .filter((e) => e[0] !== undefined)));
+        model.setAnnotations(interProScanResponseToAnnotations(ret));
         getSession(model).notify(`Loaded interproscan ${jobId} results`, 'success');
     }
     catch (e) {

package/dist/launchInterProScan.js.map

@@ -1 +1 @@
-{"version":3,"file":"launchInterProScan.js","sourceRoot":"","sources":["../src/launchInterProScan.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAA;AAE/C,OAAO,EAAE,YAAY,EAAE,SAAS,EAAE,SAAS,EAAE,OAAO,EAAE,MAAM,iBAAiB,CAAA;AAI7E,MAAM,IAAI,GAAG,2CAA2C,CAAA;AAqBxD,KAAK,UAAU,eAAe,CAAC,EAC7B,GAAG,EACH,UAAU,EACV,OAAO,EACP,QAAQ,EACR,KAAK,EACL,MAAM,GAQP;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;QACF,MAAM;KACP,CAAC,CAAA;IACF,OAAO,EAAE,CAAC,KAAK,CAAC,CAAA;IAChB,MAAM,IAAI,CAAC;QACT,KAAK;QACL,UAAU;QACV,MAAM;KACP,CAAC,CAAA;IACF,MAAM,iCAAiC,CAAC,EAAE,KAAK,EAAE,KAAK,EAAE,UAAU,EAAE,MAAM,EAAE,CAAC,CAAA;AAC/E,CAAC;AAED,SAAS,uBAAuB,CAAC,KAAa,EAAE,MAAoB;IAClE,OAAO,SAAS,CACd,GAAG,IAAI,oBAAoB,KAAK,OAAO,EACvC,EAAE,MAAM,EAAE,CACX,CAAA;AACH,CAAC;AAED,KAAK,UAAU,IAAI,CAAC,EAClB,UAAU,EACV,KAAK,EACL,MAAM,GAKP;IACC,MAAM,GAAG,GAAG,GAAG,IAAI,oBAAoB,KAAK,EAAE,CAAA;IAC9C,4EAA4E;IAC5E,4EAA4E;IAC5E,MAAM,SAAS,GAAG,GAAG,CAAA;IACrB,IAAI,CAAC;QACH,IAAI,QAAQ,GAAG,KAAK,CAAA;QACpB,KAAK,IAAI,KAAK,GAAG,CAAC,EAAE,KAAK,GAAG,SAAS,IAAI,CAAC,QAAQ,EAAE,KAAK,EAAE,EAAE,CAAC;YAC5D,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,EAAE,EAAE,CAAC,EAAE,EAAE,CAAC;gBAC5B,MAAM,OAAO,CAAC,IAAI,EAAE,MAAM,CAAC,CAAA;gBAC3B,UAAU,CAAC,EAAE,GAAG,EAAE,mBAAmB,EAAE,GAAG,CAAC,EAAE,EAAE,GAAG,EAAE,CAAC,CAAA;YACvD,CAAC;YACD,yEAAyE;YACzE,wEAAwE;YACxE,MAAM,MAAM,GAAG,CAAC,MAAM,SAAS,CAAC,GAAG,EAAE,EAAE,MAAM,EAAE,CAAC,CAAC,CAAC,IAAI,EAAE,CAAA;YACxD,IAAI,MAAM,KAAK,UAAU,EAAE,CAAC;gBAC1B,QAAQ,GAAG,IAAI,CAAA;YACjB,CAAC;iBAAM,IACL,MAAM,KAAK,SAAS;gBACpB,MAAM,KAAK,OAAO;gBAClB,MAAM,KAAK,WAAW,EACtB,CAAC;gBACD,MAAM,IAAI,KAAK,CACb,oBAAoB,KAAK,uBAAuB,MAAM,EAAE,CACzD,CAAA;YACH,CAAC;QACH,CAAC;QACD,IAAI,CAAC,QAAQ,EAAE,CAAC;YACd,MAAM,IAAI,KAAK,CACb,oBAAoB,KAAK,yBAAyB,SAAS,gBAAgB,CAC5E,CAAA;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,EACL,MAAM,GASP;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;gBACL,MAAM;aACP,CAAC,CAAA;QACJ,CAAC;aAAM,CAAC;YACN,MAAM,IAAI,KAAK,CAAC,mBAAmB,CAAC,CAAA;QACtC,CAAC;IACH,CAAC;IAAC,OAAO,CAAC,EAAE,CAAC;QACX,IAAI,YAAY,CAAC,CAAC,CAAC,EAAE,CAAC;YACpB,UAAU,CAAC,KAAK,CAAC,CAAC,MAAM,CAAC,8BAA8B,EAAE,MAAM,CAAC,CAAA;QAClE,CAAC;aAAM,CAAC;YACN,MAAM,CAAC,CAAA;QACT,CAAC;IACH,CAAC;YAAS,CAAC;QACT,UAAU,EAAE,CAAA;IACd,CAAC;AACH,CAAC;AAED,KAAK,UAAU,iCAAiC,CAAC,EAC/C,KAAK,EACL,KAAK,EACL,UAAU,EACV,MAAM,GAMP;IACC,IAAI,CAAC;QACH,UAAU,CAAC;YACT,GAAG,EAAE,0BAA0B,KAAK,iGAAiG;YACrI,GAAG,EAAE,6DAA6D,KAAK,OAAO;SAC/E,CAAC,CAAA;QACF,MAAM,GAAG,GAAG,MAAM,uBAAuB,CAAC,KAAK,EAAE,MAAM,CAAC,CAAA;QACxD,wEAAwE;QACxE,8DAA8D;QAC9D,KAAK,CAAC,UAAU,CACd,MAAM,CAAC,WAAW,CAChB,GAAG,CAAC,OAAO;aACR,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,EAAE,EAAE,CAAC,CAAU,CAAC;aACrC,MAAM,CACL,CAAC,CAAC,EAAsC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,KAAK,SAAS,CAC9D,CACJ,CACF,CAAA;QACD,UAAU,CAAC,KAAK,CAAC,CAAC,MAAM,CAAC,uBAAuB,KAAK,UAAU,EAAE,SAAS,CAAC,CAAA;IAC7E,CAAC;IAAC,OAAO,CAAC,EAAE,CAAC;QACX,IAAI,YAAY,CAAC,CAAC,CAAC,EAAE,CAAC;YACpB,UAAU,CAAC,KAAK,CAAC,CAAC,MAAM,CAAC,8BAA8B,EAAE,MAAM,CAAC,CAAA;QAClE,CAAC;aAAM,CAAC;YACN,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;YAChB,UAAU,CAAC,KAAK,CAAC,CAAC,WAAW,CAAC,GAAG,CAAC,EAAE,EAAE,CAAC,CAAC,CAAA;QAC1C,CAAC;IACH,CAAC;YAAS,CAAC;QACT,UAAU,EAAE,CAAA;IACd,CAAC;AACH,CAAC"}
+{"version":3,"file":"launchInterProScan.js","sourceRoot":"","sources":["../src/launchInterProScan.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAA;AAC/C,OAAO,EAAE,iCAAiC,EAAE,MAAM,aAAa,CAAA;AAE/D,OAAO,EAAE,YAAY,EAAE,SAAS,EAAE,SAAS,EAAE,OAAO,EAAE,MAAM,iBAAiB,CAAA;AAK7E,MAAM,IAAI,GAAG,2CAA2C,CAAA;AAExD,KAAK,UAAU,eAAe,CAAC,EAC7B,GAAG,EACH,UAAU,EACV,OAAO,EACP,QAAQ,EACR,KAAK,EACL,MAAM,GAQP;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;QACF,MAAM;KACP,CAAC,CAAA;IACF,OAAO,EAAE,CAAC,KAAK,CAAC,CAAA;IAChB,MAAM,IAAI,CAAC;QACT,KAAK;QACL,UAAU;QACV,MAAM;KACP,CAAC,CAAA;IACF,MAAM,iCAAiC,CAAC,EAAE,KAAK,EAAE,KAAK,EAAE,UAAU,EAAE,MAAM,EAAE,CAAC,CAAA;AAC/E,CAAC;AAED,SAAS,uBAAuB,CAAC,KAAa,EAAE,MAAoB;IAClE,OAAO,SAAS,CACd,GAAG,IAAI,oBAAoB,KAAK,OAAO,EACvC,EAAE,MAAM,EAAE,CACX,CAAA;AACH,CAAC;AAED,KAAK,UAAU,IAAI,CAAC,EAClB,UAAU,EACV,KAAK,EACL,MAAM,GAKP;IACC,MAAM,GAAG,GAAG,GAAG,IAAI,oBAAoB,KAAK,EAAE,CAAA;IAC9C,4EAA4E;IAC5E,4EAA4E;IAC5E,MAAM,SAAS,GAAG,GAAG,CAAA;IACrB,IAAI,CAAC;QACH,IAAI,QAAQ,GAAG,KAAK,CAAA;QACpB,KAAK,IAAI,KAAK,GAAG,CAAC,EAAE,KAAK,GAAG,SAAS,IAAI,CAAC,QAAQ,EAAE,KAAK,EAAE,EAAE,CAAC;YAC5D,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,EAAE,EAAE,CAAC,EAAE,EAAE,CAAC;gBAC5B,MAAM,OAAO,CAAC,IAAI,EAAE,MAAM,CAAC,CAAA;gBAC3B,UAAU,CAAC,EAAE,GAAG,EAAE,mBAAmB,EAAE,GAAG,CAAC,EAAE,EAAE,GAAG,EAAE,CAAC,CAAA;YACvD,CAAC;YACD,yEAAyE;YACzE,wEAAwE;YACxE,MAAM,MAAM,GAAG,CAAC,MAAM,SAAS,CAAC,GAAG,EAAE,EAAE,MAAM,EAAE,CAAC,CAAC,CAAC,IAAI,EAAE,CAAA;YACxD,IAAI,MAAM,KAAK,UAAU,EAAE,CAAC;gBAC1B,QAAQ,GAAG,IAAI,CAAA;YACjB,CAAC;iBAAM,IACL,MAAM,KAAK,SAAS;gBACpB,MAAM,KAAK,OAAO;gBAClB,MAAM,KAAK,WAAW,EACtB,CAAC;gBACD,MAAM,IAAI,KAAK,CACb,oBAAoB,KAAK,uBAAuB,MAAM,EAAE,CACzD,CAAA;YACH,CAAC;QACH,CAAC;QACD,IAAI,CAAC,QAAQ,EAAE,CAAC;YACd,MAAM,IAAI,KAAK,CACb,oBAAoB,KAAK,yBAAyB,SAAS,gBAAgB,CAC5E,CAAA;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,EACL,MAAM,GASP;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;gBACL,MAAM;aACP,CAAC,CAAA;QACJ,CAAC;aAAM,CAAC;YACN,MAAM,IAAI,KAAK,CAAC,mBAAmB,CAAC,CAAA;QACtC,CAAC;IACH,CAAC;IAAC,OAAO,CAAC,EAAE,CAAC;QACX,IAAI,YAAY,CAAC,CAAC,CAAC,EAAE,CAAC;YACpB,UAAU,CAAC,KAAK,CAAC,CAAC,MAAM,CAAC,8BAA8B,EAAE,MAAM,CAAC,CAAA;QAClE,CAAC;aAAM,CAAC;YACN,MAAM,CAAC,CAAA;QACT,CAAC;IACH,CAAC;YAAS,CAAC;QACT,UAAU,EAAE,CAAA;IACd,CAAC;AACH,CAAC;AAED,KAAK,UAAU,iCAAiC,CAAC,EAC/C,KAAK,EACL,KAAK,EACL,UAAU,EACV,MAAM,GAMP;IACC,IAAI,CAAC;QACH,UAAU,CAAC;YACT,GAAG,EAAE,0BAA0B,KAAK,iGAAiG;YACrI,GAAG,EAAE,6DAA6D,KAAK,OAAO;SAC/E,CAAC,CAAA;QACF,MAAM,GAAG,GAAG,MAAM,uBAAuB,CAAC,KAAK,EAAE,MAAM,CAAC,CAAA;QACxD,KAAK,CAAC,cAAc,CAAC,iCAAiC,CAAC,GAAG,CAAC,CAAC,CAAA;QAC5D,UAAU,CAAC,KAAK,CAAC,CAAC,MAAM,CAAC,uBAAuB,KAAK,UAAU,EAAE,SAAS,CAAC,CAAA;IAC7E,CAAC;IAAC,OAAO,CAAC,EAAE,CAAC;QACX,IAAI,YAAY,CAAC,CAAC,CAAC,EAAE,CAAC;YACpB,UAAU,CAAC,KAAK,CAAC,CAAC,MAAM,CAAC,8BAA8B,EAAE,MAAM,CAAC,CAAA;QAClE,CAAC;aAAM,CAAC;YACN,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;YAChB,UAAU,CAAC,KAAK,CAAC,CAAC,WAAW,CAAC,GAAG,CAAC,EAAE,EAAE,CAAC,CAAC,CAAA;QAC1C,CAAC;IACH,CAAC;YAAS,CAAC;QACT,UAAU,EAAE,CAAA;IACd,CAAC;AACH,CAAC"}

package/dist/measureTextCanvas.js

@@ -1,12 +1,27 @@
 import { setFontSize } from './setFontSize.js';
-let canvasHandle;
-export function measureTextCanvas(text, fontSize) {
-    if (!canvasHandle) {
-        canvasHandle = document.createElement('canvas');
+// Cached across calls: labelWidthMap measures every leaf label on every layout,
+// and both createElement and getContext are far more expensive than measureText.
+// `null` records that this environment has no 2d context, so the lookup is not
+// retried on every label.
+let ctxHandle;
+function getCtx() {
+    if (ctxHandle === undefined) {
+        ctxHandle =
+            typeof document === 'undefined'
+                ? null
+                : document.createElement('canvas').getContext('2d');
     }
-    const ctx = canvasHandle.getContext('2d');
+    return ctxHandle;
+}
+// Rough average glyph width as a fraction of the font size for the sans-serif
+// stack the tree labels use. Only reached where there is no canvas to measure
+// with (jsdom, SSR); estimating the label gutter beats throwing out of the
+// layout getters that read this on every render.
+const fallbackGlyphWidthRatio = 0.6;
+export function measureTextCanvas(text, fontSize) {
+    const ctx = getCtx();
     if (!ctx) {
-        throw new Error('no canvas context');
+        return text.length * fontSize * fallbackGlyphWidthRatio;
     }
     setFontSize(ctx, fontSize);
     return ctx.measureText(text).width;

package/dist/measureTextCanvas.js.map

@@ -1 +1 @@
-{"version":3,"file":"measureTextCanvas.js","sourceRoot":"","sources":["../src/measureTextCanvas.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,WAAW,EAAE,MAAM,kBAAkB,CAAA;AAE9C,IAAI,YAA2C,CAAA;AAE/C,MAAM,UAAU,iBAAiB,CAAC,IAAY,EAAE,QAAgB;IAC9D,IAAI,CAAC,YAAY,EAAE,CAAC;QAClB,YAAY,GAAG,QAAQ,CAAC,aAAa,CAAC,QAAQ,CAAC,CAAA;IACjD,CAAC;IAED,MAAM,GAAG,GAAG,YAAY,CAAC,UAAU,CAAC,IAAI,CAAC,CAAA;IACzC,IAAI,CAAC,GAAG,EAAE,CAAC;QACT,MAAM,IAAI,KAAK,CAAC,mBAAmB,CAAC,CAAA;IACtC,CAAC;IACD,WAAW,CAAC,GAAG,EAAE,QAAQ,CAAC,CAAA;IAC1B,OAAO,GAAG,CAAC,WAAW,CAAC,IAAI,CAAC,CAAC,KAAK,CAAA;AACpC,CAAC"}
+{"version":3,"file":"measureTextCanvas.js","sourceRoot":"","sources":["../src/measureTextCanvas.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,WAAW,EAAE,MAAM,kBAAkB,CAAA;AAE9C,gFAAgF;AAChF,iFAAiF;AACjF,+EAA+E;AAC/E,0BAA0B;AAC1B,IAAI,SAAsD,CAAA;AAE1D,SAAS,MAAM;IACb,IAAI,SAAS,KAAK,SAAS,EAAE,CAAC;QAC5B,SAAS;YACP,OAAO,QAAQ,KAAK,WAAW;gBAC7B,CAAC,CAAC,IAAI;gBACN,CAAC,CAAC,QAAQ,CAAC,aAAa,CAAC,QAAQ,CAAC,CAAC,UAAU,CAAC,IAAI,CAAC,CAAA;IACzD,CAAC;IACD,OAAO,SAAS,CAAA;AAClB,CAAC;AAED,8EAA8E;AAC9E,8EAA8E;AAC9E,2EAA2E;AAC3E,iDAAiD;AACjD,MAAM,uBAAuB,GAAG,GAAG,CAAA;AAEnC,MAAM,UAAU,iBAAiB,CAAC,IAAY,EAAE,QAAgB;IAC9D,MAAM,GAAG,GAAG,MAAM,EAAE,CAAA;IACpB,IAAI,CAAC,GAAG,EAAE,CAAC;QACT,OAAO,IAAI,CAAC,MAAM,GAAG,QAAQ,GAAG,uBAAuB,CAAA;IACzD,CAAC;IACD,WAAW,CAAC,GAAG,EAAE,QAAQ,CAAC,CAAA;IAC1B,OAAO,GAAG,CAAC,WAAW,CAAC,IAAI,CAAC,CAAC,KAAK,CAAA;AACpC,CAAC"}

package/dist/model/DataModel.d.ts

@@ -40,8 +40,5 @@ export declare function DataModelF(): import("@jbrowse/mobx-state-tree").IModelT
      */
     setGFF(gff?: string): void;
 }, import("@jbrowse/mobx-state-tree")._NotCustomized, {
-    tree: string | undefined;
-    msa: string | undefined;
-    treeMetadata: string | undefined;
-    gff: string | undefined;
+    [k: string]: string | undefined;
 }>;

package/dist/model/DataModel.js

@@ -52,15 +52,13 @@ export function DataModelF() {
             self.gff = gff;
         },
     }))
-        .postProcessSnapshot(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,
-        };
-    });
+        .postProcessSnapshot(snap => 
+    // a large document is dropped from the snapshot rather than inlined
+    // into a session or a shared URL, and every field here holds one, so
+    // the rule is the same for all of them
+    Object.fromEntries(Object.entries(snap).map(([key, text]) => [
+        key,
+        text && text.length > 50_000 ? undefined : text,
+    ])));
 }
 //# sourceMappingURL=DataModel.js.map

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;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"}
+{"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;IAC1B,oEAAoE;IACpE,qEAAqE;IACrE,uCAAuC;IACvC,MAAM,CAAC,WAAW,CAChB,MAAM,CAAC,OAAO,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,EAAE,IAAI,CAAC,EAAE,EAAE,CAAC;QACxC,GAAG;QACH,IAAI,IAAI,IAAI,CAAC,MAAM,GAAG,MAAM,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI;KAChD,CAAC,CACH,CACF,CAAA;AACL,CAAC"}

package/dist/model.d.ts

@@ -1,14 +1,14 @@
 import type { HierarchyNode } from './hierarchy.ts';
-import type { InterProScanResults } from './launchInterProScan.ts';
-import type { BasicTrack, DomainBand, NodeWithIds, NodeWithIdsAndLength } from './types.ts';
+import type { Annotation, BasicTrack, DomainBand, NodeWithIds, NodeWithIdsAndLength } from './types.ts';
 import type { FileLocation as FileLocationType } from '@jbrowse/core/util/types';
 import type { Instance } from '@jbrowse/mobx-state-tree';
 import type { Theme } from '@mui/material';
+import type { InterProScanResults } from 'msa-parsers';
 /**
  * #stateModel MsaView
  *
  * The main MSAView state model. Holds the loaded alignment, tree, and optional
- * InterProScan domain annotations, plus all display state (color scheme, zoom,
+ * overlay annotations, plus all display state (color scheme, zoom,
  * scroll, collapsed clades). It composes in members from `DialogQueueSessionMixin`,
  * `Tree`, and `MSAModel` (see Inherited members below). Data is loaded reactively
  * from the `msaFilehandle` / `treeFilehandle` / `gffFilehandle` properties, or set
@@ -405,7 +405,7 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
     }>, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
     /**
      * #property
-     * filehandle object for InterProScan GFF file
+     * filehandle object for a GFF file of overlay annotations
      */
     gffFilehandle: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISnapshotProcessor<import("@jbrowse/mobx-state-tree").ITypeUnion<import("@jbrowse/mobx-state-tree").ModelCreationType<{
         locationType: "LocalPathLocation";
@@ -518,7 +518,10 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
     showOnly: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
     /**
      * #property
-     * turned off tracks
+     * the user's explicit show/hide choice per track id, keyed by id with
+     * the value meaning "off". A track the user has never touched is absent
+     * and falls back to its own default (see `defaultOffTracks`), so a
+     * hidden-by-default track adds nothing to the shared URL.
      */
     turnedOffTracks: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>, [undefined]>;
     /**
@@ -537,10 +540,7 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
         setTreeMetadata(treeMetadata?: string): void;
         setGFF(gff?: string): void;
     }, import("@jbrowse/mobx-state-tree")._NotCustomized, {
-        tree: string | undefined;
-        msa: string | undefined;
-        treeMetadata: string | undefined;
-        gff: string | undefined;
+        [k: string]: string | undefined;
     }>, [undefined]>;
     /**
      * #property
@@ -664,6 +664,13 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
      * #volatile
      */
     conservationTrackHeight: number;
+    /**
+     * #volatile
+     * taller than the conservation track by default: the logo spends its
+     * height on stacked glyphs, and a 40px stack of four residues leaves each
+     * one too short to identify
+     */
+    sequenceLogoTrackHeight: number;
     /**
      * #volatile
      */
@@ -674,8 +681,12 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
     error: unknown;
     /**
      * #volatile
+     * overlay annotations drawn on the alignment, whatever their source.
+     * Every source -- InterProScan, GFF, a user upload -- converts to this
+     * flat list before it reaches the model, so nothing downstream of here
+     * knows which one it came from
      */
-    interProAnnotations: undefined | Record<string, InterProScanResults>;
+    annotations: Annotation[];
 } & {
     /**
      * #action
@@ -740,7 +751,7 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
     setHighlightedColumns(columns?: number[]): void;
     /**
      * #action
-     * toggle the InterProScan protein-domain overlay on the alignment
+     * toggle the annotation overlay on the alignment
      */
     setShowDomains(arg: boolean): void;
     /**
@@ -767,11 +778,6 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
      * set col width (px)
      */
     setColWidth(n: number): void;
-    /**
-     * #action
-     * set scroll Y-offset (px)
-     */
-    setScrollY(n: number): void;
     /**
      * #action
      *
@@ -938,10 +944,6 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
      * #getter
      */
     readonly blanks: number[];
-    /**
-     * #getter
-     */
-    readonly blanksSet: Set<number>;
     /**
      * #getter
      * Returns a map of row name to array of insertions with display position and letters
@@ -989,11 +991,6 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
      * #getter
      */
     readonly colStats: import("./columnCounts.ts").ColumnCounts;
-    /**
-     * #getter
-     * per-column residue totals (gaps included)
-     */
-    readonly colStatsSums: Uint32Array<ArrayBufferLike>;
     /**
      * #getter
      * Detects sequence type based on letters present in the alignment.
@@ -1023,6 +1020,13 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
      * Returns values 0-1 where 1 = fully conserved, 0 = no conservation.
      */
     readonly conservation: number[];
+    /**
+     * #getter
+     * The information content of a fully conserved column, in bits, which
+     * depends on the alphabet. Both the entropy ceiling `conservation`
+     * normalizes against and the y-axis ceiling of the sequence logo track.
+     */
+    readonly alphabetMaxBits: number;
     /**
      * #getter
      * Per-column conservation of physicochemical property class (amino acids
@@ -1080,6 +1084,12 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
      * #getter
      */
     readonly blocksY: number[];
+    /**
+     * #getter
+     * height of the alignment viewport, px. The same subtraction as
+     * msaAreaHeight, which is defined later in the views chain
+     */
+    readonly visibleMsaHeight: number;
 } & {
     /**
      * #getter
@@ -1096,8 +1106,7 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
     /**
      * #getter
      * most-negative allowed scrollY, keeping the last row in view rather than
-     * letting the whole alignment scroll off the top. visible MSA height is
-     * computed inline here because msaAreaHeight is defined later in the chain.
+     * letting the whole alignment scroll off the top.
      */
     readonly maxScrollY: number;
     /**
@@ -1173,9 +1182,21 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
     doScrollY(deltaY: number): void;
     /**
      * #action
-     * Set domain annotations and reveal the overlay in a single step (or clear
-     * both when passed undefined). Shared by every domain source: InterProScan,
-     * GFF, user-provided uploads, and NCBI CDD.
+     * set scroll Y-offset (px), clamped to keep the alignment in view
+     */
+    setScrollY(n: number): void;
+    /**
+     * #action
+     * Set the overlay annotations and reveal the overlay in a single step (an
+     * empty list clears both). Every source funnels through here after its
+     * own adapter has flattened it: InterProScan, GFF, user uploads, NCBI CDD.
+     */
+    setAnnotations(annotations: Annotation[]): void;
+    /**
+     * #action
+     * set the overlay from raw InterProScan results keyed by row name. Kept
+     * for downstream plugins that hold the EBI wire format; new code should
+     * adapt to Annotation[] and call setAnnotations.
      */
     setDomains(data?: Record<string, InterProScanResults>): void;
     applyGFFText(gffText: string): void;
@@ -1204,6 +1225,12 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
      * #getter
      */
     readonly labelWidthMap: Map<string, number>;
+    /**
+     * #getter
+     * factor turning a labelWidthMap entry into its width at the current
+     * font size
+     */
+    readonly labelWidthScale: number;
     readonly labelsWidth: number;
     /**
      * #getter
@@ -1303,46 +1330,13 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
      * total height of track area (px)
      */
     readonly totalTrackAreaHeight: number;
-    readonly tidyInterProAnnotationTypes: Map<string, {
-        id: string;
-        name: string;
-        accession: string;
-        description: string;
-        featureType: string | undefined;
-        start: number;
-        end: number;
-        strand: number | undefined;
-    }>;
-    readonly tidyInterProAnnotations: {
-        id: string;
-        name: string;
-        accession: string;
-        description: string;
-        featureType: string | undefined;
-        start: number;
-        end: number;
-        strand: number | undefined;
-    }[];
-    readonly tidyFilteredInterProAnnotations: {
-        id: string;
-        name: string;
-        accession: string;
-        description: string;
-        featureType: string | undefined;
-        start: number;
-        end: number;
-        strand: number | undefined;
-    }[];
-    readonly tidyFilteredGatheredInterProAnnotations: Record<string, {
-        id: string;
-        name: string;
-        accession: string;
-        description: string;
-        featureType: string | undefined;
-        start: number;
-        end: number;
-        strand: number | undefined;
-    }[]>;
+    /**
+     * one representative annotation per accession, which is what the legend,
+     * the filter dialog and the palettes key off
+     */
+    readonly annotationTypes: Map<string, Annotation>;
+    readonly filteredAnnotations: Annotation[];
+    readonly annotationsByRow: Record<string, Annotation[]>;
 } & {
     /**
      * #getter
@@ -1353,37 +1347,26 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
      * #getter
      */
     readonly verticalScrollbarWidth: 0 | 20;
+    /**
+     * #getter
+     * width of the alignment canvas itself: the msa area less the vertical
+     * scrollbar sitting in it. Not usable from showHorizontalScrollbar, which
+     * feeds msaAreaHeight -> showVerticalScrollbar and would close a cycle
+     */
+    readonly msaCanvasWidth: number;
     /**
      * #getter
      * ordinal segment types (exons etc.), ordered by sequence position so
      * exon-1..exon-14 read left-to-right; colored by alternating shade and
      * labeled by number rather than each getting a distinct hue + legend row
      */
-    readonly segmentDomainTypes: {
-        id: string;
-        name: string;
-        accession: string;
-        description: string;
-        featureType: string | undefined;
-        start: number;
-        end: number;
-        strand: number | undefined;
-    }[];
+    readonly segmentDomainTypes: Annotation[];
     /**
      * #getter
      * categorical feature types (InterPro domains and the like) that each get
      * their own color and a legend entry
      */
-    readonly categoricalDomainTypes: {
-        id: string;
-        name: string;
-        accession: string;
-        description: string;
-        featureType: string | undefined;
-        start: number;
-        end: number;
-        strand: number | undefined;
-    }[];
+    readonly categoricalDomainTypes: Annotation[];
     readonly fillPalette: {
         [x: string]: string;
     };
@@ -1403,24 +1386,16 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
      * (exons) are excluded — they read as a numbered gene model, not a color
      * key — so this is the categorical types ordered by sequence position
      */
-    readonly visibleDomainTypes: {
-        id: string;
-        name: string;
-        accession: string;
-        description: string;
-        featureType: string | undefined;
-        start: number;
-        end: number;
-        strand: number | undefined;
-    }[];
+    readonly visibleDomainTypes: Annotation[];
     /**
      * #getter
-     * every filtered-on domain annotation resolved to the visible column span
-     * it is drawn across, keyed by row name and in draw order (largest first,
-     * as tidyInterProAnnotations orders them). Resolving these once here rather
-     * than inside each canvas block removes a per-feature, per-block sequence
-     * position conversion from every redraw, and gives the letter renderer the
-     * band colors it needs to keep residues readable on top of the boxes.
+     * every filtered-on annotation resolved to the visible column span it is
+     * drawn across, keyed by row name. Each row is ordered longest-first so a
+     * short domain nested inside a long one draws on top of it rather than
+     * under it. Resolving these once here rather than inside each canvas
+     * block removes a per-feature, per-block sequence position conversion
+     * from every redraw, and gives the letter renderer the band colors it
+     * needs to keep residues readable on top of the boxes.
      */
     readonly domainBands: Map<string, DomainBand[]>;
     /**
@@ -1434,7 +1409,7 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
      * domain annotations under the mouse, hit-tested against the exact visible
      * column span each box is drawn at (so it matches the overlay across gaps)
      */
-    readonly mouseOverDomains: import("./types.ts").TidyDomainAnnotation[];
+    readonly mouseOverDomains: Annotation[];
     /**
      * #getter
      * row index of the reference row (`relativeTo`), undefined when unset
@@ -1496,6 +1471,10 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
      * #action
      */
     setConservationTrackHeight(arg: number): void;
+    /**
+     * #action
+     */
+    setSequenceLogoTrackHeight(arg: number): void;
     /**
      * #action
      */