react-msaview 5.7.3 → 5.8.0

package/dist/components/SequenceTextArea.js

@@ -1,6 +1,7 @@
 import React, { useState } from 'react';
 import { makeStyles } from '@jbrowse/core/util/tss-react';
 import { Button, TextField } from '@mui/material';
+import { getUngappedSequence } from 'msa-parsers';
 import copy from '../vendor/copyToClipboard.js';
 import Checkbox2 from './Checkbox2.js';
 const useStyles = makeStyles()({
@@ -19,9 +20,8 @@ export default function SequenceTextArea({ str }) {
     const [copied, setCopied] = useState(false);
     const [showGaps, setShowGaps] = useState(false);
     const [showEmpty, setShowEmpty] = useState(false);
-    const removeGaps = (s) => s.replaceAll('-', '').replaceAll('.', '');
     const disp = str
-        .map(([s1, s2]) => [s1, showGaps ? s2 : removeGaps(s2)])
+        .map(([s1, s2]) => [s1, showGaps ? s2 : getUngappedSequence(s2)])
         .filter(([, s2]) => showEmpty || !!s2)
         .map(([s1, s2]) => `>${s1}\n${s2}`)
         .join('\n');

package/dist/components/SequenceTextArea.js.map

@@ -1 +1 @@
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+{"version":3,"file":"SequenceTextArea.js","sourceRoot":"","sources":["../../src/components/SequenceTextArea.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAEvC,OAAO,EAAE,UAAU,EAAE,MAAM,8BAA8B,CAAA;AACzD,OAAO,EAAE,MAAM,EAAE,SAAS,EAAE,MAAM,eAAe,CAAA;AACjD,OAAO,EAAE,mBAAmB,EAAE,MAAM,aAAa,CAAA;AAEjD,OAAO,IAAI,MAAM,8BAA8B,CAAA;AAC/C,OAAO,SAAS,MAAM,gBAAiB,CAAA;AAEvC,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC;IAC7B,YAAY,EAAE;QACZ,UAAU,EAAE,aAAa;QACzB,QAAQ,EAAE,YAAY;KACvB;IACD,aAAa,EAAE;QACb,UAAU,EAAE,WAAW;QACvB,MAAM,EAAE,CAAC;QACT,QAAQ,EAAE,MAAM;KACjB;CACF,CAAC,CAAA;AAEF,MAAM,CAAC,OAAO,UAAU,gBAAgB,CAAC,EAAE,GAAG,EAA+B;IAC3E,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,CAAC,MAAM,EAAE,SAAS,CAAC,GAAG,QAAQ,CAAC,KAAK,CAAC,CAAA;IAC3C,MAAM,CAAC,QAAQ,EAAE,WAAW,CAAC,GAAG,QAAQ,CAAC,KAAK,CAAC,CAAA;IAC/C,MAAM,CAAC,SAAS,EAAE,YAAY,CAAC,GAAG,QAAQ,CAAC,KAAK,CAAC,CAAA;IAEjD,MAAM,IAAI,GAAG,GAAG;SACb,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,EAAE,EAAE,QAAQ,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,mBAAmB,CAAC,EAAE,CAAC,CAAU,CAAC;SACzE,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,EAAE,EAAE,CAAC,SAAS,IAAI,CAAC,CAAC,EAAE,CAAC;SACrC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,EAAE,CAAC,EAAE,EAAE,CAAC,IAAI,EAAE,KAAK,EAAE,EAAE,CAAC;SAClC,IAAI,CAAC,IAAI,CAAC,CAAA;IACb,OAAO,CACL;QACE,oBAAC,MAAM,IACL,KAAK,EAAC,SAAS,EACf,OAAO,EAAC,WAAW,EACnB,OAAO,EAAE,GAAG,EAAE;gBACZ,IAAI,CAAC,IAAI,CAAC,CAAA;gBACV,SAAS,CAAC,IAAI,CAAC,CAAA;gBACf,UAAU,CAAC,GAAG,EAAE;oBACd,SAAS,CAAC,KAAK,CAAC,CAAA;gBAClB,CAAC,EAAE,GAAG,CAAC,CAAA;YACT,CAAC,IAEA,MAAM,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,mBAAmB,CAClC;QACT,oBAAC,SAAS,IACR,KAAK,EAAC,WAAW,EACjB,OAAO,EAAE,QAAQ,EACjB,QAAQ,EAAE,GAAG,EAAE;gBACb,WAAW,CAAC,CAAC,QAAQ,CAAC,CAAA;YACxB,CAAC,GACD;QACF,oBAAC,SAAS,IACR,KAAK,EAAC,YAAY,EAClB,OAAO,EAAE,SAAS,EAClB,QAAQ,EAAE,GAAG,EAAE;gBACb,YAAY,CAAC,CAAC,SAAS,CAAC,CAAA;YAC1B,CAAC,GACD;QACF,oBAAC,SAAS,IACR,OAAO,EAAC,UAAU,EAClB,SAAS,QACT,SAAS,EAAE,OAAO,CAAC,aAAa,EAChC,OAAO,EAAE,CAAC,EACV,OAAO,EAAE,EAAE,EACX,SAAS,QACT,KAAK,EAAE,IAAI,EACX,SAAS,EAAE;gBACT,KAAK,EAAE;oBACL,QAAQ,EAAE,IAAI;oBACd,SAAS,EAAE,OAAO,CAAC,YAAY;iBAChC;aACF,GACD,CACD,CACJ,CAAA;AACH,CAAC"}

package/dist/components/dialogs/UserProvidedDomainsDialog.js

@@ -45,7 +45,12 @@ const UserProvidedDomainsDialog = observer(function ({ handleClose, model, }) {
                             const ret = file
                                 ? JSON.parse(await file.text())
                                 : await jsonfetch(interProURL);
-                            model.setDomains(Object.fromEntries(ret.results.map(r => [r.xref[0].id, r])));
+                            // key each result by its xref id; a result without one has no
+                            // row to attach to, and keying it `undefined` would draw a
+                            // phantom row's worth of domains
+                            model.setDomains(Object.fromEntries(ret.results
+                                .map(r => [r.xref[0]?.id, r])
+                                .filter(e => e[0] !== undefined)));
                             getSession(model).notify('Loaded interproscan results', 'success');
                         }
                         catch (e) {

package/dist/components/dialogs/UserProvidedDomainsDialog.js.map

@@ -1 +1 @@
-{"version":3,"file":"UserProvidedDomainsDialog.js","sourceRoot":"","sources":["../../../src/components/dialogs/UserProvidedDomainsDialog.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAEvC,OAAO,EAAE,MAAM,EAAE,MAAM,kBAAkB,CAAA;AACzC,OAAO,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAA;AAC/C,OAAO,EACL,MAAM,EACN,aAAa,EACb,aAAa,EACb,WAAW,EACX,gBAAgB,EAChB,KAAK,EACL,UAAU,EACV,SAAS,EACT,UAAU,GACX,MAAM,eAAe,CAAA;AACtB,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,EAAE,SAAS,EAAE,MAAM,qBAAqB,CAAA;AAK/C,MAAM,yBAAyB,GAAG,QAAQ,CAAC,UAAU,EACnD,WAAW,EACX,KAAK,GAIN;IACC,MAAM,CAAC,IAAI,EAAE,OAAO,CAAC,GAAG,QAAQ,EAAQ,CAAA;IACxC,MAAM,CAAC,MAAM,EAAE,SAAS,CAAC,GAAG,QAAQ,CAAC,MAAM,CAAC,CAAA;IAC5C,MAAM,CAAC,WAAW,EAAE,cAAc,CAAC,GAAG,QAAQ,CAAC,EAAE,CAAC,CAAA;IAElD,OAAO,CACL,oBAAC,MAAM,IACL,QAAQ,EAAC,IAAI,EACb,KAAK,EAAC,gCAAgC,EACtC,OAAO,EAAE,GAAG,EAAE;YACZ,WAAW,EAAE,CAAA;QACf,CAAC,EACD,IAAI;QAEJ,oBAAC,aAAa;YACZ;gBACE,oBAAC,UAAU,mGAGE;gBAEb,6BAAK,KAAK,EAAE,EAAE,OAAO,EAAE,MAAM,EAAE,MAAM,EAAE,EAAE,EAAE;oBACzC,oBAAC,WAAW,IAAC,SAAS,EAAC,UAAU;wBAC/B,oBAAC,UAAU,IACT,KAAK,EAAE,MAAM,EACb,QAAQ,EAAE,KAAK,CAAC,EAAE;gCAChB,SAAS,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,CAAA;4BAC/B,CAAC;4BAED,oBAAC,gBAAgB,IAAC,KAAK,EAAC,KAAK,EAAC,OAAO,EAAE,oBAAC,KAAK,OAAG,EAAE,KAAK,EAAC,KAAK,GAAG;4BAChE,oBAAC,gBAAgB,IACf,KAAK,EAAC,MAAM,EACZ,OAAO,EAAE,oBAAC,KAAK,OAAG,EAClB,KAAK,EAAC,MAAM,GACZ,CACS,CACD;oBACb,MAAM,KAAK,KAAK,CAAC,CAAC,CAAC,CAClB;wBACE,oBAAC,UAAU,mDAEE;wBACb,oBAAC,SAAS,IACR,KAAK,EAAC,KAAK,EACX,KAAK,EAAE,WAAW,EAClB,QAAQ,EAAE,KAAK,CAAC,EAAE;gCAChB,cAAc,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,CAAA;4BACpC,CAAC,GACD,CACE,CACP,CAAC,CAAC,CAAC,IAAI;oBACP,MAAM,KAAK,MAAM,CAAC,CAAC,CAAC,CACnB,6BAAK,KAAK,EAAE,EAAE,UAAU,EAAE,EAAE,EAAE;wBAC5B,oBAAC,UAAU,mEAEE;wBACb,oBAAC,MAAM,IAAC,OAAO,EAAC,UAAU,EAAC,SAAS,EAAC,OAAO;;4BAE1C,+BACE,IAAI,EAAC,MAAM,EACX,MAAM,QACN,QAAQ,EAAE,CAAC,EAAE,MAAM,EAAE,EAAE,EAAE;oCACvB,MAAM,IAAI,GAAG,MAAM,CAAC,KAAK,EAAE,CAAC,CAAC,CAAC,CAAA;oCAC9B,IAAI,IAAI,EAAE,CAAC;wCACT,OAAO,CAAC,IAAI,CAAC,CAAA;oCACf,CAAC;gCACH,CAAC,GACD,CACK,CACL,CACP,CAAC,CAAC,CAAC,IAAI,CACJ,CACF,CACQ;QAChB,oBAAC,aAAa;YACZ,oBAAC,MAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,SAAS,EACf,OAAO,EAAE,GAAG,EAAE;oBACZ,mEAAmE;oBACnE,CAAC;oBAAA,CAAC,KAAK,IAAI,EAAE;wBACX,IAAI,CAAC;4BACH,MAAM,GAAG,GAAyB,IAAI;gCACpC,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,MAAM,IAAI,CAAC,IAAI,EAAE,CAAC;gCAC/B,CAAC,CAAC,MAAM,SAAS,CAAC,WAAW,CAAC,CAAA;4BAEhC,KAAK,CAAC,UAAU,CACd,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;4BACD,UAAU,CAAC,KAAK,CAAC,CAAC,MAAM,CACtB,6BAA6B,EAC7B,SAAS,CACV,CAAA;wBACH,CAAC;wBAAC,OAAO,CAAC,EAAE,CAAC;4BACX,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;4BAChB,UAAU,CAAC,KAAK,CAAC,CAAC,WAAW,CAAC,GAAG,CAAC,EAAE,EAAE,CAAC,CAAC,CAAA;wBAC1C,CAAC;gCAAS,CAAC;4BACT,KAAK,CAAC,SAAS,EAAE,CAAA;wBACnB,CAAC;oBACH,CAAC,CAAC,EAAE,CAAA;oBACJ,WAAW,EAAE,CAAA;gBACf,CAAC,mBAGM,CACK,CACT,CACV,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,yBAAyB,CAAA"}
+{"version":3,"file":"UserProvidedDomainsDialog.js","sourceRoot":"","sources":["../../../src/components/dialogs/UserProvidedDomainsDialog.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAEvC,OAAO,EAAE,MAAM,EAAE,MAAM,kBAAkB,CAAA;AACzC,OAAO,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAA;AAC/C,OAAO,EACL,MAAM,EACN,aAAa,EACb,aAAa,EACb,WAAW,EACX,gBAAgB,EAChB,KAAK,EACL,UAAU,EACV,SAAS,EACT,UAAU,GACX,MAAM,eAAe,CAAA;AACtB,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,EAAE,SAAS,EAAE,MAAM,qBAAqB,CAAA;AAK/C,MAAM,yBAAyB,GAAG,QAAQ,CAAC,UAAU,EACnD,WAAW,EACX,KAAK,GAIN;IACC,MAAM,CAAC,IAAI,EAAE,OAAO,CAAC,GAAG,QAAQ,EAAQ,CAAA;IACxC,MAAM,CAAC,MAAM,EAAE,SAAS,CAAC,GAAG,QAAQ,CAAC,MAAM,CAAC,CAAA;IAC5C,MAAM,CAAC,WAAW,EAAE,cAAc,CAAC,GAAG,QAAQ,CAAC,EAAE,CAAC,CAAA;IAElD,OAAO,CACL,oBAAC,MAAM,IACL,QAAQ,EAAC,IAAI,EACb,KAAK,EAAC,gCAAgC,EACtC,OAAO,EAAE,GAAG,EAAE;YACZ,WAAW,EAAE,CAAA;QACf,CAAC,EACD,IAAI;QAEJ,oBAAC,aAAa;YACZ;gBACE,oBAAC,UAAU,mGAGE;gBAEb,6BAAK,KAAK,EAAE,EAAE,OAAO,EAAE,MAAM,EAAE,MAAM,EAAE,EAAE,EAAE;oBACzC,oBAAC,WAAW,IAAC,SAAS,EAAC,UAAU;wBAC/B,oBAAC,UAAU,IACT,KAAK,EAAE,MAAM,EACb,QAAQ,EAAE,KAAK,CAAC,EAAE;gCAChB,SAAS,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,CAAA;4BAC/B,CAAC;4BAED,oBAAC,gBAAgB,IAAC,KAAK,EAAC,KAAK,EAAC,OAAO,EAAE,oBAAC,KAAK,OAAG,EAAE,KAAK,EAAC,KAAK,GAAG;4BAChE,oBAAC,gBAAgB,IACf,KAAK,EAAC,MAAM,EACZ,OAAO,EAAE,oBAAC,KAAK,OAAG,EAClB,KAAK,EAAC,MAAM,GACZ,CACS,CACD;oBACb,MAAM,KAAK,KAAK,CAAC,CAAC,CAAC,CAClB;wBACE,oBAAC,UAAU,mDAEE;wBACb,oBAAC,SAAS,IACR,KAAK,EAAC,KAAK,EACX,KAAK,EAAE,WAAW,EAClB,QAAQ,EAAE,KAAK,CAAC,EAAE;gCAChB,cAAc,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,CAAA;4BACpC,CAAC,GACD,CACE,CACP,CAAC,CAAC,CAAC,IAAI;oBACP,MAAM,KAAK,MAAM,CAAC,CAAC,CAAC,CACnB,6BAAK,KAAK,EAAE,EAAE,UAAU,EAAE,EAAE,EAAE;wBAC5B,oBAAC,UAAU,mEAEE;wBACb,oBAAC,MAAM,IAAC,OAAO,EAAC,UAAU,EAAC,SAAS,EAAC,OAAO;;4BAE1C,+BACE,IAAI,EAAC,MAAM,EACX,MAAM,QACN,QAAQ,EAAE,CAAC,EAAE,MAAM,EAAE,EAAE,EAAE;oCACvB,MAAM,IAAI,GAAG,MAAM,CAAC,KAAK,EAAE,CAAC,CAAC,CAAC,CAAA;oCAC9B,IAAI,IAAI,EAAE,CAAC;wCACT,OAAO,CAAC,IAAI,CAAC,CAAA;oCACf,CAAC;gCACH,CAAC,GACD,CACK,CACL,CACP,CAAC,CAAC,CAAC,IAAI,CACJ,CACF,CACQ;QAChB,oBAAC,aAAa;YACZ,oBAAC,MAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,SAAS,EACf,OAAO,EAAE,GAAG,EAAE;oBACZ,mEAAmE;oBACnE,CAAC;oBAAA,CAAC,KAAK,IAAI,EAAE;wBACX,IAAI,CAAC;4BACH,MAAM,GAAG,GAAyB,IAAI;gCACpC,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,MAAM,IAAI,CAAC,IAAI,EAAE,CAAC;gCAC/B,CAAC,CAAC,MAAM,SAAS,CAAC,WAAW,CAAC,CAAA;4BAEhC,8DAA8D;4BAC9D,2DAA2D;4BAC3D,iCAAiC;4BACjC,KAAK,CAAC,UAAU,CACd,MAAM,CAAC,WAAW,CAChB,GAAG,CAAC,OAAO;iCACR,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,EAAE,EAAE,CAAC,CAAU,CAAC;iCACrC,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,KAAK,SAAS,CAAC,CACnC,CACF,CAAA;4BACD,UAAU,CAAC,KAAK,CAAC,CAAC,MAAM,CACtB,6BAA6B,EAC7B,SAAS,CACV,CAAA;wBACH,CAAC;wBAAC,OAAO,CAAC,EAAE,CAAC;4BACX,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;4BAChB,UAAU,CAAC,KAAK,CAAC,CAAC,WAAW,CAAC,GAAG,CAAC,EAAE,EAAE,CAAC,CAAC,CAAA;wBAC1C,CAAC;gCAAS,CAAC;4BACT,KAAK,CAAC,SAAS,EAAE,CAAA;wBACnB,CAAC;oBACH,CAAC,CAAC,EAAE,CAAA;oBACJ,WAAW,EAAE,CAAA;gBACf,CAAC,mBAGM,CACK,CACT,CACV,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,yBAAyB,CAAA"}

package/dist/components/header/getDomainsMenu.js

@@ -40,7 +40,7 @@ export function getDomainMenu({ model }) {
             label: `Show domains${noDomains ? ' (no domains loaded)' : ''}`,
             disabled: noDomains,
             icon: Visibility,
-            checked: actuallyShowDomains ? showDomains : false,
+            checked: actuallyShowDomains,
             type: 'checkbox',
             onClick: () => {
                 model.setShowDomains(!showDomains);

package/dist/components/header/getDomainsMenu.js.map

@@ -1 +1 @@
-{"version":3,"file":"getDomainsMenu.js","sourceRoot":"","sources":["../../../src/components/header/getDomainsMenu.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,IAAI,EAAE,MAAM,OAAO,CAAA;AAE5B,OAAO,SAAS,MAAM,+BAA+B,CAAA;AACrD,OAAO,UAAU,MAAM,gCAAgC,CAAA;AACvD,OAAO,MAAM,MAAM,4BAA4B,CAAA;AAC/C,OAAO,IAAI,MAAM,0BAA0B,CAAA;AAC3C,OAAO,UAAU,MAAM,gCAAgC,CAAA;AAIvD,MAAM,mBAAmB,GAAG,IAAI,CAAC,GAAG,EAAE,CAAC,MAAM,CAAC,6BAA8B,CAAC,CAAC,CAAA;AAC9E,MAAM,yBAAyB,GAAG,IAAI,CACpC,GAAG,EAAE,CAAC,MAAM,CAAC,yCAA0C,CAAC,CACzD,CAAA;AACD,MAAM,kBAAkB,GAAG,IAAI,CAC7B,GAAG,EAAE,CAAC,MAAM,CAAC,kCAAmC,CAAC,CAClD,CAAA;AAED,MAAM,UAAU,aAAa,CAAC,EAAE,KAAK,EAA2B;IAC9D,MAAM,EAAE,WAAW,EAAE,mBAAmB,EAAE,cAAc,EAAE,SAAS,EAAE,GAAG,KAAK,CAAA;IAC7E,OAAO;QACL;YACE,KAAK,EAAE,iBAAiB;YACxB,IAAI,EAAE,UAAU;YAChB,OAAO,EAAE,GAAG,EAAE;gBACZ,KAAK,CAAC,WAAW,CAAC,WAAW,CAAC,EAAE,CAAC;oBAC/B,yBAAyB;oBACzB;wBACE,WAAW;wBACX,KAAK;qBACN;iBACF,CAAC,CAAA;YACJ,CAAC;SACF;QACD;YACE,KAAK,EAAE,mCAAmC;YAC1C,IAAI,EAAE,MAAM;YACZ,OAAO,EAAE,GAAG,EAAE;gBACZ,KAAK,CAAC,WAAW,CAAC,WAAW,CAAC,EAAE,CAAC;oBAC/B,kBAAkB;oBAClB;wBACE,WAAW;wBACX,KAAK;qBACN;iBACF,CAAC,CAAA;YACJ,CAAC;SACF;QACD;YACE,KAAK,EAAE,eAAe,SAAS,CAAC,CAAC,CAAC,sBAAsB,CAAC,CAAC,CAAC,EAAE,EAAE;YAC/D,QAAQ,EAAE,SAAS;YACnB,IAAI,EAAE,UAAU;YAChB,OAAO,EAAE,mBAAmB,CAAC,CAAC,CAAC,WAAW,CAAC,CAAC,CAAC,KAAK;YAClD,IAAI,EAAE,UAAmB;YACzB,OAAO,EAAE,GAAG,EAAE;gBACZ,KAAK,CAAC,cAAc,CAAC,CAAC,WAAW,CAAC,CAAA;YACpC,CAAC;SACF;QACD;YACE,KAAK,EAAE,qBAAqB,SAAS,CAAC,CAAC,CAAC,sBAAsB,CAAC,CAAC,CAAC,EAAE,EAAE;YACrE,QAAQ,EAAE,SAAS;YACnB,OAAO,EAAE,mBAAmB,CAAC,CAAC,CAAC,cAAc,CAAC,CAAC,CAAC,KAAK;YACrD,IAAI,EAAE,IAAI;YACV,IAAI,EAAE,UAAmB;YACzB,OAAO,EAAE,GAAG,EAAE;gBACZ,KAAK,CAAC,iBAAiB,CAAC,CAAC,cAAc,CAAC,CAAA;YAC1C,CAAC;SACF;QACD;YACE,KAAK,EAAE,iBAAiB,SAAS,CAAC,CAAC,CAAC,sBAAsB,CAAC,CAAC,CAAC,EAAE,EAAE;YACjE,IAAI,EAAE,SAAS;YACf,QAAQ,EAAE,SAAS;YACnB,OAAO,EAAE,GAAG,EAAE;gBACZ,KAAK,CAAC,WAAW,CAAC,OAAO,CAAC,EAAE,CAAC;oBAC3B,mBAAmB;oBACnB;wBACE,OAAO;wBACP,KAAK;qBACN;iBACF,CAAC,CAAA;YACJ,CAAC;SACF;KACF,CAAA;AACH,CAAC"}
+{"version":3,"file":"getDomainsMenu.js","sourceRoot":"","sources":["../../../src/components/header/getDomainsMenu.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,IAAI,EAAE,MAAM,OAAO,CAAA;AAE5B,OAAO,SAAS,MAAM,+BAA+B,CAAA;AACrD,OAAO,UAAU,MAAM,gCAAgC,CAAA;AACvD,OAAO,MAAM,MAAM,4BAA4B,CAAA;AAC/C,OAAO,IAAI,MAAM,0BAA0B,CAAA;AAC3C,OAAO,UAAU,MAAM,gCAAgC,CAAA;AAIvD,MAAM,mBAAmB,GAAG,IAAI,CAAC,GAAG,EAAE,CAAC,MAAM,CAAC,6BAA8B,CAAC,CAAC,CAAA;AAC9E,MAAM,yBAAyB,GAAG,IAAI,CACpC,GAAG,EAAE,CAAC,MAAM,CAAC,yCAA0C,CAAC,CACzD,CAAA;AACD,MAAM,kBAAkB,GAAG,IAAI,CAC7B,GAAG,EAAE,CAAC,MAAM,CAAC,kCAAmC,CAAC,CAClD,CAAA;AAED,MAAM,UAAU,aAAa,CAAC,EAAE,KAAK,EAA2B;IAC9D,MAAM,EAAE,WAAW,EAAE,mBAAmB,EAAE,cAAc,EAAE,SAAS,EAAE,GAAG,KAAK,CAAA;IAC7E,OAAO;QACL;YACE,KAAK,EAAE,iBAAiB;YACxB,IAAI,EAAE,UAAU;YAChB,OAAO,EAAE,GAAG,EAAE;gBACZ,KAAK,CAAC,WAAW,CAAC,WAAW,CAAC,EAAE,CAAC;oBAC/B,yBAAyB;oBACzB;wBACE,WAAW;wBACX,KAAK;qBACN;iBACF,CAAC,CAAA;YACJ,CAAC;SACF;QACD;YACE,KAAK,EAAE,mCAAmC;YAC1C,IAAI,EAAE,MAAM;YACZ,OAAO,EAAE,GAAG,EAAE;gBACZ,KAAK,CAAC,WAAW,CAAC,WAAW,CAAC,EAAE,CAAC;oBAC/B,kBAAkB;oBAClB;wBACE,WAAW;wBACX,KAAK;qBACN;iBACF,CAAC,CAAA;YACJ,CAAC;SACF;QACD;YACE,KAAK,EAAE,eAAe,SAAS,CAAC,CAAC,CAAC,sBAAsB,CAAC,CAAC,CAAC,EAAE,EAAE;YAC/D,QAAQ,EAAE,SAAS;YACnB,IAAI,EAAE,UAAU;YAChB,OAAO,EAAE,mBAAmB;YAC5B,IAAI,EAAE,UAAmB;YACzB,OAAO,EAAE,GAAG,EAAE;gBACZ,KAAK,CAAC,cAAc,CAAC,CAAC,WAAW,CAAC,CAAA;YACpC,CAAC;SACF;QACD;YACE,KAAK,EAAE,qBAAqB,SAAS,CAAC,CAAC,CAAC,sBAAsB,CAAC,CAAC,CAAC,EAAE,EAAE;YACrE,QAAQ,EAAE,SAAS;YACnB,OAAO,EAAE,mBAAmB,CAAC,CAAC,CAAC,cAAc,CAAC,CAAC,CAAC,KAAK;YACrD,IAAI,EAAE,IAAI;YACV,IAAI,EAAE,UAAmB;YACzB,OAAO,EAAE,GAAG,EAAE;gBACZ,KAAK,CAAC,iBAAiB,CAAC,CAAC,cAAc,CAAC,CAAA;YAC1C,CAAC;SACF;QACD;YACE,KAAK,EAAE,iBAAiB,SAAS,CAAC,CAAC,CAAC,sBAAsB,CAAC,CAAC,CAAC,EAAE,EAAE;YACjE,IAAI,EAAE,SAAS;YACf,QAAQ,EAAE,SAAS;YACnB,OAAO,EAAE,GAAG,EAAE;gBACZ,KAAK,CAAC,WAAW,CAAC,OAAO,CAAC,EAAE,CAAC;oBAC3B,mBAAmB;oBACnB;wBACE,OAAO;wBACP,KAAK;qBACN;iBACF,CAAC,CAAA;YACJ,CAAC;SACF;KACF,CAAA;AACH,CAAC"}

package/dist/components/import/ImportForm.js

@@ -32,17 +32,13 @@ const ImportForm = observer(function ({ model }) {
                     React.createElement(FileSelector, { location: gffFile, setLocation: setGffFile }))),
             React.createElement("div", null,
                 React.createElement(Button, { onClick: () => {
-                        // eslint-disable-next-line @typescript-eslint/no-floating-promises
-                        ;
-                        (async () => {
-                            try {
-                                await load(model, msaFile, treeFile, gffFile);
-                            }
-                            catch (e) {
-                                console.error(e);
-                                model.setError(e);
-                            }
-                        })();
+                        try {
+                            load(model, msaFile, treeFile, gffFile);
+                        }
+                        catch (e) {
+                            console.error(e);
+                            model.setError(e);
+                        }
                     }, variant: "contained", color: "primary", disabled: !msaFile && !treeFile }, "Open")),
             React.createElement("div", null,
                 React.createElement(Typography, null, "Examples"),

package/dist/components/import/ImportForm.js.map

@@ -1 +1 @@
-{"version":3,"file":"ImportForm.js","sourceRoot":"","sources":["../../../src/components/import/ImportForm.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAEvC,OAAO,EAAE,YAAY,EAAE,YAAY,EAAE,MAAM,kBAAkB,CAAA;AAC7D,OAAO,EAAE,MAAM,EAAE,SAAS,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAC7D,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,kBAAkB,MAAM,yBAA0B,CAAA;AACzD,OAAO,EAAE,IAAI,EAAE,MAAM,WAAW,CAAA;AAKhC,MAAM,UAAU,GAAG,QAAQ,CAAC,UAAU,EAAE,KAAK,EAA2B;IACtE,MAAM,CAAC,OAAO,EAAE,UAAU,CAAC,GAAG,QAAQ,EAAgB,CAAA;IACtD,MAAM,CAAC,QAAQ,EAAE,WAAW,CAAC,GAAG,QAAQ,EAAgB,CAAA;IACxD,MAAM,CAAC,OAAO,EAAE,UAAU,CAAC,GAAG,QAAQ,EAAgB,CAAA;IACtD,MAAM,EAAE,KAAK,EAAE,GAAG,KAAK,CAAA;IAEvB,OAAO,CACL,oBAAC,SAAS;QACR,6BAAK,KAAK,EAAE,EAAE,KAAK,EAAE,KAAK,EAAE;YACzB,KAAK,CAAC,CAAC,CAAC,oBAAC,YAAY,IAAC,KAAK,EAAE,KAAK,GAAI,CAAC,CAAC,CAAC,IAAI;YAC9C,oBAAC,UAAU,6FAGE;YACb,oBAAC,UAAU,IAAC,KAAK,EAAC,OAAO,mNAKZ,CACT;QAEN,6BACE,KAAK,EAAE;gBACL,OAAO,EAAE,MAAM;gBACf,cAAc,EAAE,QAAQ;gBACxB,UAAU,EAAE,QAAQ;gBACpB,GAAG,EAAE,EAAE;aACR;YAED;gBACE;oBACE,oBAAC,UAAU,0BAA6B;oBACxC,oBAAC,YAAY,IAAC,QAAQ,EAAE,OAAO,EAAE,WAAW,EAAE,UAAU,GAAI,CACxD;gBACN;oBACE,oBAAC,UAAU,2BAA8B;oBACzC,oBAAC,YAAY,IAAC,QAAQ,EAAE,QAAQ,EAAE,WAAW,EAAE,WAAW,GAAI,CAC1D;gBACN;oBACE,oBAAC,UAAU,kDAAqD;oBAChE,oBAAC,YAAY,IAAC,QAAQ,EAAE,OAAO,EAAE,WAAW,EAAE,UAAU,GAAI,CACxD,CACF;YACN;gBACE,oBAAC,MAAM,IACL,OAAO,EAAE,GAAG,EAAE;wBACZ,mEAAmE;wBACnE,CAAC;wBAAA,CAAC,KAAK,IAAI,EAAE;4BACX,IAAI,CAAC;gCACH,MAAM,IAAI,CAAC,KAAK,EAAE,OAAO,EAAE,QAAQ,EAAE,OAAO,CAAC,CAAA;4BAC/C,CAAC;4BAAC,OAAO,CAAC,EAAE,CAAC;gCACX,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;gCAChB,KAAK,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAA;4BACnB,CAAC;wBACH,CAAC,CAAC,EAAE,CAAA;oBACN,CAAC,EACD,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,SAAS,EACf,QAAQ,EAAE,CAAC,OAAO,IAAI,CAAC,QAAQ,WAGxB,CACL;YAEN;gBACE,oBAAC,UAAU,mBAAsB;gBACjC,oBAAC,kBAAkB,IAAC,KAAK,EAAE,KAAK,GAAI,CAChC,CACF,CACI,CACb,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,UAAU,CAAA"}
+{"version":3,"file":"ImportForm.js","sourceRoot":"","sources":["../../../src/components/import/ImportForm.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAEvC,OAAO,EAAE,YAAY,EAAE,YAAY,EAAE,MAAM,kBAAkB,CAAA;AAC7D,OAAO,EAAE,MAAM,EAAE,SAAS,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAC7D,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,kBAAkB,MAAM,yBAA0B,CAAA;AACzD,OAAO,EAAE,IAAI,EAAE,MAAM,WAAW,CAAA;AAKhC,MAAM,UAAU,GAAG,QAAQ,CAAC,UAAU,EAAE,KAAK,EAA2B;IACtE,MAAM,CAAC,OAAO,EAAE,UAAU,CAAC,GAAG,QAAQ,EAAgB,CAAA;IACtD,MAAM,CAAC,QAAQ,EAAE,WAAW,CAAC,GAAG,QAAQ,EAAgB,CAAA;IACxD,MAAM,CAAC,OAAO,EAAE,UAAU,CAAC,GAAG,QAAQ,EAAgB,CAAA;IACtD,MAAM,EAAE,KAAK,EAAE,GAAG,KAAK,CAAA;IAEvB,OAAO,CACL,oBAAC,SAAS;QACR,6BAAK,KAAK,EAAE,EAAE,KAAK,EAAE,KAAK,EAAE;YACzB,KAAK,CAAC,CAAC,CAAC,oBAAC,YAAY,IAAC,KAAK,EAAE,KAAK,GAAI,CAAC,CAAC,CAAC,IAAI;YAC9C,oBAAC,UAAU,6FAGE;YACb,oBAAC,UAAU,IAAC,KAAK,EAAC,OAAO,mNAKZ,CACT;QAEN,6BACE,KAAK,EAAE;gBACL,OAAO,EAAE,MAAM;gBACf,cAAc,EAAE,QAAQ;gBACxB,UAAU,EAAE,QAAQ;gBACpB,GAAG,EAAE,EAAE;aACR;YAED;gBACE;oBACE,oBAAC,UAAU,0BAA6B;oBACxC,oBAAC,YAAY,IAAC,QAAQ,EAAE,OAAO,EAAE,WAAW,EAAE,UAAU,GAAI,CACxD;gBACN;oBACE,oBAAC,UAAU,2BAA8B;oBACzC,oBAAC,YAAY,IAAC,QAAQ,EAAE,QAAQ,EAAE,WAAW,EAAE,WAAW,GAAI,CAC1D;gBACN;oBACE,oBAAC,UAAU,kDAAqD;oBAChE,oBAAC,YAAY,IAAC,QAAQ,EAAE,OAAO,EAAE,WAAW,EAAE,UAAU,GAAI,CACxD,CACF;YACN;gBACE,oBAAC,MAAM,IACL,OAAO,EAAE,GAAG,EAAE;wBACZ,IAAI,CAAC;4BACH,IAAI,CAAC,KAAK,EAAE,OAAO,EAAE,QAAQ,EAAE,OAAO,CAAC,CAAA;wBACzC,CAAC;wBAAC,OAAO,CAAC,EAAE,CAAC;4BACX,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;4BAChB,KAAK,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAA;wBACnB,CAAC;oBACH,CAAC,EACD,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,SAAS,EACf,QAAQ,EAAE,CAAC,OAAO,IAAI,CAAC,QAAQ,WAGxB,CACL;YAEN;gBACE,oBAAC,UAAU,mBAAsB;gBACjC,oBAAC,kBAAkB,IAAC,KAAK,EAAE,KAAK,GAAI,CAChC,CACF,CACI,CACb,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,UAAU,CAAA"}

package/dist/components/import/ImportFormExamples.js

@@ -15,17 +15,13 @@ function ListItem({ onClick, model, children, }) {
 const BASE = 'https://jbrowse.org/genomes/multiple_sequence_alignments';
 const ImportFormExamples = observer(function ({ model, }) {
     function loadUris({ msa, tree, gff, }) {
-        // eslint-disable-next-line @typescript-eslint/no-floating-promises
-        ;
-        (async () => {
-            try {
-                await load(model, msa ? { uri: msa, locationType: 'UriLocation' } : undefined, tree ? { uri: tree, locationType: 'UriLocation' } : undefined, gff ? { uri: gff, locationType: 'UriLocation' } : undefined);
-            }
-            catch (e) {
-                console.error(e);
-                model.setError(e);
-            }
-        })();
+        try {
+            load(model, msa ? { uri: msa, locationType: 'UriLocation' } : undefined, tree ? { uri: tree, locationType: 'UriLocation' } : undefined, gff ? { uri: gff, locationType: 'UriLocation' } : undefined);
+        }
+        catch (e) {
+            console.error(e);
+            model.setError(e);
+        }
     }
     return (React.createElement("ul", null,
         React.createElement(ListItem, { model: model, onClick: () => {

package/dist/components/import/ImportFormExamples.js.map

@@ -1 +1 @@
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package/dist/components/import/util.d.ts

@@ -1,3 +1,3 @@
 import type { MsaViewModel } from '../../model.ts';
 import type { FileLocation } from '@jbrowse/core/util';
-export declare function load(model: MsaViewModel, msaFile?: FileLocation, treeFile?: FileLocation, gffFile?: FileLocation): Promise<void>;
+export declare function load(model: MsaViewModel, msaFile?: FileLocation, treeFile?: FileLocation, gffFile?: FileLocation): void;

package/dist/components/import/util.js

@@ -1,4 +1,4 @@
-export async function load(model, msaFile, treeFile, gffFile) {
+export function load(model, msaFile, treeFile, gffFile) {
     model.setError(undefined);
     if (msaFile) {
         model.setMSAFilehandle(msaFile);

package/dist/components/import/util.js.map

@@ -1 +1 @@
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package/dist/components/msa/renderBoxFeatureCanvasBlock.js

@@ -1,8 +1,8 @@
 import { subFeatureRowHeight } from '../../constants.js';
 import { getVisibleLeaves } from '../getVisibleLeaves.js';
 export function renderBoxFeatureCanvasBlock({ model, offsetX, offsetY, ctx, highResScaleFactorOverride, blockSizeXOverride, blockSizeYOverride, }) {
-    const { blockSize, rowHeight, highResScaleFactor, showDomains } = model;
-    if (showDomains) {
+    const { blockSize, rowHeight, highResScaleFactor, actuallyShowDomains } = model;
+    if (actuallyShowDomains) {
         const k = highResScaleFactorOverride ?? highResScaleFactor;
         const bx = blockSizeXOverride ?? blockSize;
         const by = blockSizeYOverride ?? blockSize;

package/dist/components/msa/renderBoxFeatureCanvasBlock.js.map

@@ -1 +1 @@
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package/dist/components/tree/renderTreeCanvas.d.ts

@@ -4,42 +4,42 @@ import type { RenderCtx } from '../renderCtx.ts';
 import type { ClickMapIndex } from './clickMap.ts';
 import type { Theme } from '@mui/material';
 export declare const padding = 600;
-export declare function getNodeX(node: HierarchyNode, showBranchLen: boolean, maxBranchLen: number, maxDepthToLeaf: number): number | undefined;
-export declare function renderTree({ offsetY, ctx, model, theme, maxBranchLen, maxDepthToLeaf, blockSizeYOverride, }: {
+export declare function getNodeX(node: HierarchyNode, showBranchLen: boolean, tipX: number, maxDepthToLeaf: number): number | undefined;
+export declare function renderTree({ offsetY, ctx, model, theme, tipX, maxDepthToLeaf, blockSizeYOverride, }: {
     offsetY: number;
     ctx: RenderCtx;
     model: MsaViewModel;
     theme: Theme;
-    maxBranchLen: number;
+    tipX: number;
     maxDepthToLeaf: number;
     blockSizeYOverride?: number;
 }): void;
-export declare function renderCollapsedTriangles({ ctx, clickMap, offsetY, model, theme, maxBranchLen, maxDepthToLeaf, blockSizeYOverride, }: {
+export declare function renderCollapsedTriangles({ ctx, clickMap, offsetY, model, theme, tipX, maxDepthToLeaf, blockSizeYOverride, }: {
     ctx: RenderCtx;
     clickMap?: ClickMapIndex;
     offsetY: number;
     model: MsaViewModel;
     theme: Theme;
-    maxBranchLen: number;
+    tipX: number;
     maxDepthToLeaf: number;
     blockSizeYOverride?: number;
 }): void;
-export declare function renderNodeBubbles({ ctx, clickMap, offsetY, model, maxBranchLen, maxDepthToLeaf, blockSizeYOverride, }: {
+export declare function renderNodeBubbles({ ctx, clickMap, offsetY, model, tipX, maxDepthToLeaf, blockSizeYOverride, }: {
     ctx: RenderCtx;
     clickMap?: ClickMapIndex;
     offsetY: number;
     model: MsaViewModel;
-    maxBranchLen: number;
+    tipX: number;
     maxDepthToLeaf: number;
     blockSizeYOverride?: number;
 }): void;
-export declare function renderTreeLabels({ theme, model, offsetY, ctx, clickMap, maxBranchLen, maxDepthToLeaf, blockSizeYOverride, }: {
+export declare function renderTreeLabels({ theme, model, offsetY, ctx, clickMap, tipX, maxDepthToLeaf, blockSizeYOverride, }: {
     model: MsaViewModel;
     offsetY: number;
     ctx: RenderCtx;
     clickMap?: ClickMapIndex;
     theme: Theme;
-    maxBranchLen: number;
+    tipX: number;
     maxDepthToLeaf: number;
     blockSizeYOverride?: number;
 }): void;

package/dist/components/tree/renderTreeCanvas.js

@@ -10,11 +10,12 @@ const d = radius * 2;
 function inYBlock(y, offsetY, by) {
     return y > offsetY - extendBounds && y < offsetY + by + extendBounds;
 }
-// Calculate node x-coordinate for both phylogram (with branch lengths) and cladogram (topology only) modes
-// For cladograms: x = (maxDepthToLeaf - nodeDepthToLeaf) / maxDepthToLeaf * maxWidth
-// This positions: leaves at maxWidth (rightmost), root at 0 (leftmost), internal nodes proportionally in between
+// Calculate node x-coordinate for both phylogram (with branch lengths) and
+// cladogram (topology only) modes. tipX is the pixel x the tips sit at.
+// For cladograms: x = (maxDepthToLeaf - nodeDepthToLeaf) / maxDepthToLeaf * tipX
+// This positions: leaves at tipX (rightmost), root at 0 (leftmost), internal nodes proportionally in between
 // Matches ape's: xx <- max(xx) - xx (where xx is depth from each node to tips)
-export function getNodeX(node, showBranchLen, maxBranchLen, maxDepthToLeaf) {
+export function getNodeX(node, showBranchLen, tipX, maxDepthToLeaf) {
     if (showBranchLen) {
         return node.len;
     }
@@ -22,17 +23,17 @@ export function getNodeX(node, showBranchLen, maxBranchLen, maxDepthToLeaf) {
         return 0;
     }
     const depthToLeaf = calcDepthToLeaf(node);
-    return ((maxDepthToLeaf - depthToLeaf) / maxDepthToLeaf) * maxBranchLen;
+    return ((maxDepthToLeaf - depthToLeaf) / maxDepthToLeaf) * tipX;
 }
-export function renderTree({ offsetY, ctx, model, theme, maxBranchLen, maxDepthToLeaf, blockSizeYOverride, }) {
+export function renderTree({ offsetY, ctx, model, theme, tipX, maxDepthToLeaf, blockSizeYOverride, }) {
     const { hierarchy, showBranchLenEffective: showBranchLen, blockSize } = model;
     const by = blockSizeYOverride ?? blockSize;
     ctx.strokeStyle = theme.palette.text.primary;
     forEachLink(hierarchy, (source, target) => {
         const sy = source.x;
         const ty = target.x;
-        const tx = getNodeX(target, showBranchLen, maxBranchLen, maxDepthToLeaf);
-        const sx = getNodeX(source, showBranchLen, maxBranchLen, maxDepthToLeaf);
+        const tx = getNodeX(target, showBranchLen, tipX, maxDepthToLeaf);
+        const sx = getNodeX(source, showBranchLen, tipX, maxDepthToLeaf);
         if (tx === undefined || sx === undefined) {
             return;
         }
@@ -50,21 +51,25 @@ export function renderTree({ offsetY, ctx, model, theme, maxBranchLen, maxDepthT
         }
     });
 }
-export function renderCollapsedTriangles({ ctx, clickMap, offsetY, model, theme, maxBranchLen, maxDepthToLeaf, blockSizeYOverride, }) {
+export function renderCollapsedTriangles({ ctx, clickMap, offsetY, model, theme, tipX, maxDepthToLeaf, blockSizeYOverride, }) {
     const { hierarchy, showBranchLenEffective: showBranchLen, collapsed, blockSize, rowHeight, fontSize, marginLeft: ml, } = model;
+    // nothing collapsed is the common case, and the traversal below visits every
+    // node in the tree on every block of every redraw
+    if (collapsed.length === 0) {
+        return;
+    }
+    const collapsedSet = new Set(collapsed);
     const by = blockSizeYOverride ?? blockSize;
     const halfHeight = Math.max(2, rowHeight * 0.42);
     forEachDescendant(hierarchy, node => {
         const { id, name } = node.data;
-        if (collapsed.includes(id)) {
-            const apexX = getNodeX(node, showBranchLen, maxBranchLen, maxDepthToLeaf);
+        if (collapsedSet.has(id)) {
+            const apexX = getNodeX(node, showBranchLen, tipX, maxDepthToLeaf);
             const y = node.x;
             const inBlock = inYBlock(y, offsetY, by);
             // in cladogram mode the hidden tips align at the right edge, otherwise use
             // the branch-length extent recorded in the model's hierarchy getter
-            const baseX = showBranchLen
-                ? (node.collapsedTipXFar ?? maxBranchLen)
-                : maxBranchLen;
+            const baseX = showBranchLen ? (node.collapsedTipXFar ?? tipX) : tipX;
             if (apexX !== undefined && inBlock && baseX > apexX) {
                 ctx.beginPath();
                 ctx.moveTo(apexX, y);
@@ -99,11 +104,12 @@ export function renderCollapsedTriangles({ ctx, clickMap, offsetY, model, theme,
         }
     });
 }
-export function renderNodeBubbles({ ctx, clickMap, offsetY, model, maxBranchLen, maxDepthToLeaf, blockSizeYOverride, }) {
+export function renderNodeBubbles({ ctx, clickMap, offsetY, model, tipX, maxDepthToLeaf, blockSizeYOverride, }) {
     const { hierarchy, showBranchLenEffective: showBranchLen, collapsed, blockSize, marginLeft: ml, } = model;
     const by = blockSizeYOverride ?? blockSize;
+    const collapsedSet = new Set(collapsed);
     forEachDescendant(hierarchy, node => {
-        const x = getNodeX(node, showBranchLen, maxBranchLen, maxDepthToLeaf);
+        const x = getNodeX(node, showBranchLen, tipX, maxDepthToLeaf);
         if (x === undefined) {
             return;
         }
@@ -111,7 +117,7 @@ export function renderNodeBubbles({ ctx, clickMap, offsetY, model, maxBranchLen,
         const y = node.x;
         const { id, name } = data;
         if (node.height >= 1 && inYBlock(y, offsetY, by)) {
-            const isCollapsed = collapsed.includes(id);
+            const isCollapsed = collapsedSet.has(id);
             ctx.strokeStyle = 'black';
             ctx.fillStyle = isCollapsed ? 'black' : 'white';
             ctx.beginPath();
@@ -134,7 +140,7 @@ export function renderNodeBubbles({ ctx, clickMap, offsetY, model, maxBranchLen,
         }
     });
 }
-export function renderTreeLabels({ theme, model, offsetY, ctx, clickMap, maxBranchLen, maxDepthToLeaf, blockSizeYOverride, }) {
+export function renderTreeLabels({ theme, model, offsetY, ctx, clickMap, tipX, maxDepthToLeaf, blockSizeYOverride, }) {
     const { fontSize, showBranchLenEffective: showBranchLen, treeMetadata, blockSize, labelsAlignRight, drawTree, treeAreaWidth, treeAreaWidthMinusMargin, marginLeft, noTree, labelWidthMap, collapsed, } = model;
     // labels only exist for leaves, which are laid out top to bottom, so take the
     // same slice the MSA renderer uses instead of walking every tip per block
@@ -165,7 +171,7 @@ export function renderTreeLabels({ theme, model, offsetY, ctx, clickMap, maxBran
             const yp = y + fontSize / 4;
             let xp = 0;
             if (!noTree) {
-                xp = getNodeX(node, showBranchLen, maxBranchLen, maxDepthToLeaf) ?? 0;
+                xp = getNodeX(node, showBranchLen, tipX, maxDepthToLeaf) ?? 0;
             }
             const width = labelWidthMap.get(name) ?? ctx.measureText(displayName).width;
             ctx.fillStyle = theme.palette.text.primary;
@@ -220,14 +226,20 @@ export function renderTreeCanvas({ model, clickMap, ctx, offsetY, theme, highRes
     setFontSize(ctx, fontSize);
     // memoized on the model and shared across the tree/bubble/label passes (and
     // across all tree blocks) rather than re-traversing the hierarchy in each
-    const { maxBranchLength: maxBranchLen, maxDepthToLeaf } = model;
+    const { maxBranchLength, maxDepthToLeaf, showBranchLenEffective, treeWidth } = model;
+    // pixel x of the tips. A phylogram scales branch lengths so the longest
+    // root-to-tip path lands at maxBranchLength; a cladogram ignores lengths and
+    // spreads topological depth across the whole tree area instead. Reusing
+    // maxBranchLength for the cladogram would pin every node to x=0 for a tree
+    // with no branch lengths -- which is exactly what forces cladogram mode.
+    const tipX = showBranchLenEffective ? maxBranchLength : treeWidth;
     if (!noTree && drawTree) {
         renderTree({
             ctx,
             offsetY,
             model,
             theme,
-            maxBranchLen,
+            tipX,
             maxDepthToLeaf,
             blockSizeYOverride,
         });
@@ -237,7 +249,7 @@ export function renderTreeCanvas({ model, clickMap, ctx, offsetY, theme, highRes
             offsetY,
             model,
             theme,
-            maxBranchLen,
+            tipX,
             maxDepthToLeaf,
             blockSizeYOverride,
         });
@@ -247,7 +259,7 @@ export function renderTreeCanvas({ model, clickMap, ctx, offsetY, theme, highRes
                 offsetY,
                 clickMap,
                 model,
-                maxBranchLen,
+                tipX,
                 maxDepthToLeaf,
                 blockSizeYOverride,
             });
@@ -260,7 +272,7 @@ export function renderTreeCanvas({ model, clickMap, ctx, offsetY, theme, highRes
             model,
             clickMap,
             theme,
-            maxBranchLen,
+            tipX,
             maxDepthToLeaf,
             blockSizeYOverride,
         });

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

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

@@ -1,11 +1,13 @@
 interface FlatItem {
     id: number;
     parent?: number;
+    label?: string;
+    dist?: string;
 }
 interface TreeNode {
     id: string;
     name: string;
-    parent?: string;
+    length?: number;
     children: TreeNode[];
 }
 export declare function flatToTree(items: FlatItem[]): TreeNode;

package/dist/flatToTree.js

@@ -1,13 +1,20 @@
 export function flatToTree(items) {
-    const nodeMap = new Map(items.map(item => [
-        item.id,
-        {
-            id: `${item.id}`,
-            name: `${item.id}`,
-            parent: item.parent !== undefined ? `${item.parent}` : undefined,
-            children: [],
-        },
-    ]));
+    const nodeMap = new Map(items.map(item => {
+        const length = item.dist === undefined ? undefined : Number(item.dist);
+        return [
+            item.id,
+            {
+                id: `${item.id}`,
+                // the label is what NCBI's own tree viewer shows; falling back to the
+                // node id would render a tree of bare numbers
+                name: item.label || `${item.id}`,
+                ...(length !== undefined && Number.isFinite(length)
+                    ? { length }
+                    : {}),
+                children: [],
+            },
+        ];
+    }));
     let root;
     for (const item of items) {
         const node = nodeMap.get(item.id);

package/dist/flatToTree.js.map

@@ -1 +1 @@
-{"version":3,"file":"flatToTree.js","sourceRoot":"","sources":["../src/flatToTree.ts"],"names":[],"mappings":"AAYA,MAAM,UAAU,UAAU,CAAC,KAAiB;IAC1C,MAAM,OAAO,GAAG,IAAI,GAAG,CACrB,KAAK,CAAC,GAAG,CAAC,IAAI,CAAC,EAAE,CAAC;QAChB,IAAI,CAAC,EAAE;QACP;YACE,EAAE,EAAE,GAAG,IAAI,CAAC,EAAE,EAAE;YAChB,IAAI,EAAE,GAAG,IAAI,CAAC,EAAE,EAAE;YAClB,MAAM,EAAE,IAAI,CAAC,MAAM,KAAK,SAAS,CAAC,CAAC,CAAC,GAAG,IAAI,CAAC,MAAM,EAAE,CAAC,CAAC,CAAC,SAAS;YAChE,QAAQ,EAAE,EAAgB;SAC3B;KACF,CAAC,CACH,CAAA;IAED,IAAI,IAA0B,CAAA;IAC9B,KAAK,MAAM,IAAI,IAAI,KAAK,EAAE,CAAC;QACzB,MAAM,IAAI,GAAG,OAAO,CAAC,GAAG,CAAC,IAAI,CAAC,EAAE,CAAE,CAAA;QAClC,MAAM,MAAM,GACV,IAAI,CAAC,MAAM,KAAK,SAAS,CAAC,CAAC,CAAC,OAAO,CAAC,GAAG,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,SAAS,CAAA;QAClE,IAAI,MAAM,EAAE,CAAC;YACX,MAAM,CAAC,QAAQ,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;QAC5B,CAAC;aAAM,CAAC;YACN,IAAI,KAAK,IAAI,CAAA;QACf,CAAC;IACH,CAAC;IAED,IAAI,IAAI,KAAK,SAAS,EAAE,CAAC;QACvB,2EAA2E;QAC3E,2EAA2E;QAC3E,qEAAqE;QACrE,MAAM,IAAI,KAAK,CACb,sGAAsG,CACvG,CAAA;IACH,CAAC;IAED,OAAO,IAAI,CAAA;AACb,CAAC"}
+{"version":3,"file":"flatToTree.js","sourceRoot":"","sources":["../src/flatToTree.ts"],"names":[],"mappings":"AAgBA,MAAM,UAAU,UAAU,CAAC,KAAiB;IAC1C,MAAM,OAAO,GAAG,IAAI,GAAG,CACrB,KAAK,CAAC,GAAG,CAAC,IAAI,CAAC,EAAE;QACf,MAAM,MAAM,GAAG,IAAI,CAAC,IAAI,KAAK,SAAS,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;QACtE,OAAO;YACL,IAAI,CAAC,EAAE;YACP;gBACE,EAAE,EAAE,GAAG,IAAI,CAAC,EAAE,EAAE;gBAChB,sEAAsE;gBACtE,8CAA8C;gBAC9C,IAAI,EAAE,IAAI,CAAC,KAAK,IAAI,GAAG,IAAI,CAAC,EAAE,EAAE;gBAChC,GAAG,CAAC,MAAM,KAAK,SAAS,IAAI,MAAM,CAAC,QAAQ,CAAC,MAAM,CAAC;oBACjD,CAAC,CAAC,EAAE,MAAM,EAAE;oBACZ,CAAC,CAAC,EAAE,CAAC;gBACP,QAAQ,EAAE,EAAgB;aAC3B;SACF,CAAA;IACH,CAAC,CAAC,CACH,CAAA;IAED,IAAI,IAA0B,CAAA;IAC9B,KAAK,MAAM,IAAI,IAAI,KAAK,EAAE,CAAC;QACzB,MAAM,IAAI,GAAG,OAAO,CAAC,GAAG,CAAC,IAAI,CAAC,EAAE,CAAE,CAAA;QAClC,MAAM,MAAM,GACV,IAAI,CAAC,MAAM,KAAK,SAAS,CAAC,CAAC,CAAC,OAAO,CAAC,GAAG,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,SAAS,CAAA;QAClE,IAAI,MAAM,EAAE,CAAC;YACX,MAAM,CAAC,QAAQ,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;QAC5B,CAAC;aAAM,CAAC;YACN,IAAI,KAAK,IAAI,CAAA;QACf,CAAC;IACH,CAAC;IAED,IAAI,IAAI,KAAK,SAAS,EAAE,CAAC;QACvB,2EAA2E;QAC3E,2EAA2E;QAC3E,qEAAqE;QACrE,MAAM,IAAI,KAAK,CACb,sGAAsG,CACvG,CAAA;IACH,CAAC;IAED,OAAO,IAAI,CAAA;AACb,CAAC"}

package/dist/hierarchy.d.ts

@@ -1,11 +1,16 @@
+import { descendants, find, forEachDescendant, forEachLink, leaves, links, sort, sum } from '@gmod/newick';
 import type { NodeWithIds } from './types.ts';
-export interface HierarchyNode<T = NodeWithIds> {
-    data: T;
+import type { HierarchyNode as CoreHierarchyNode } from '@gmod/newick';
+/**
+ * A hierarchy node plus the fields this viewer hangs off it during layout.
+ *
+ * The traversals in `@gmod/newick` are generic over the node type rather than
+ * over its data, so they take and return this extended node rather than the base
+ * one, and no call site has to cast.
+ */
+export interface HierarchyNode<T = NodeWithIds> extends CoreHierarchyNode<T> {
     children: HierarchyNode<T>[] | null;
     parent: HierarchyNode<T> | null;
-    depth: number;
-    height: number;
-    value?: number;
     x?: number;
     y?: number;
     len?: number;
@@ -14,19 +19,9 @@ export interface HierarchyNode<T = NodeWithIds> {
     collapsedTipXNear?: number;
     collapsedTipXFar?: number;
 }
-export interface HierarchyLink<T = NodeWithIds> {
-    source: HierarchyNode<T>;
-    target: HierarchyNode<T>;
-}
-export declare function descendants<T>(node: HierarchyNode<T>): HierarchyNode<T>[];
+export { descendants, find, forEachDescendant, forEachLink, leaves, links, sort, sum, };
+export type { HierarchyLink } from '@gmod/newick';
 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 links<T>(node: HierarchyNode<T>): HierarchyLink<T>[];
-export declare function forEachLink<T>(node: HierarchyNode<T>, cb: (source: HierarchyNode<T>, target: HierarchyNode<T>) => void): void;
-export declare function forEachDescendant<T>(node: HierarchyNode<T>, cb: (n: HierarchyNode<T>) => void): void;
 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 collapsedSubtreeLengthExtent<T extends {