react-msaview 4.6.0 → 4.8.0

package/dist/components/header/HeaderInfoArea.js

@@ -14,10 +14,9 @@ const HeaderInfoArea = observer(function ({ model }) {
     return mouseOverRowName && mouseCol !== undefined ? (React.createElement(Typography, { className: classes.margin },
         mouseOverRowName,
         ":",
-        model.mouseOverCoordToGapRemovedRowCoordOneBased(mouseOverRowName, mouseCol),
-        ' ',
-        "(",
-        model.mouseOverCoordToRowLetter(mouseOverRowName, mouseCol),
+        model.visibleColToSeqPosOneBased(mouseOverRowName, mouseCol),
+        " (",
+        model.visibleColToRowLetter(mouseOverRowName, mouseCol),
         ")")) : null;
 });
 export default HeaderInfoArea;

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

@@ -1 +1 @@
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+{"version":3,"file":"HeaderInfoArea.js","sourceRoot":"","sources":["../../../src/components/header/HeaderInfoArea.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAC1C,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAI1C,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC;IAC7B,MAAM,EAAE;QACN,MAAM,EAAE,MAAM;QACd,UAAU,EAAE,EAAE;KACf;CACF,CAAC,CAAA;AAEF,MAAM,cAAc,GAAG,QAAQ,CAAC,UAAU,EAAE,KAAK,EAA2B;IAC1E,MAAM,EAAE,gBAAgB,EAAE,QAAQ,EAAE,GAAG,KAAK,CAAA;IAC5C,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,OAAO,gBAAgB,IAAI,QAAQ,KAAK,SAAS,CAAC,CAAC,CAAC,CAClD,oBAAC,UAAU,IAAC,SAAS,EAAE,OAAO,CAAC,MAAM;QAClC,gBAAgB;;QAChB,KAAK,CAAC,0BAA0B,CAAC,gBAAgB,EAAE,QAAQ,CAAC;;QAC5D,KAAK,CAAC,qBAAqB,CAAC,gBAAgB,EAAE,QAAQ,CAAC;YAC7C,CACd,CAAC,CAAC,CAAC,IAAI,CAAA;AACV,CAAC,CAAC,CAAA;AAEF,eAAe,cAAc,CAAA"}

package/dist/components/import/ImportForm.js

@@ -7,6 +7,7 @@ import { load } from './util';
 const ImportForm = observer(function ({ model }) {
     const [msaFile, setMsaFile] = useState();
     const [treeFile, setTreeFile] = useState();
+    const [gffFile, setGffFile] = useState();
     const { error } = model;
     return (React.createElement(Container, null,
         React.createElement("div", { style: { width: '50%' } },
@@ -25,14 +26,17 @@ const ImportForm = observer(function ({ model }) {
                     React.createElement(FileSelector, { location: msaFile, setLocation: setMsaFile })),
                 React.createElement("div", null,
                     React.createElement(Typography, null, "Tree file or URL"),
-                    React.createElement(FileSelector, { location: treeFile, setLocation: setTreeFile }))),
+                    React.createElement(FileSelector, { location: treeFile, setLocation: setTreeFile })),
+                React.createElement("div", null,
+                    React.createElement(Typography, null, "InterProScan GFF file or URL (optional)"),
+                    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);
+                                await load(model, msaFile, treeFile, gffFile);
                             }
                             catch (e) {
                                 console.error(e);

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

@@ -1 +1 @@
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+{"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,sBAAsB,CAAA;AACrD,OAAO,EAAE,IAAI,EAAE,MAAM,QAAQ,CAAA;AAK7B,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"}

package/dist/components/import/util.d.ts

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

package/dist/components/import/util.js

@@ -1,4 +1,4 @@
-export async function load(model, msaFile, treeFile) {
+export async function load(model, msaFile, treeFile, gffFile) {
     model.setError(undefined);
     if (msaFile) {
         model.setMSAFilehandle(msaFile);
@@ -6,5 +6,8 @@ export async function load(model, msaFile, treeFile) {
     if (treeFile) {
         model.setTreeFilehandle(treeFile);
     }
+    if (gffFile) {
+        model.setGFFFilehandle(gffFile);
+    }
 }
 //# sourceMappingURL=util.js.map

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

@@ -1 +1 @@
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+{"version":3,"file":"util.js","sourceRoot":"","sources":["../../../src/components/import/util.ts"],"names":[],"mappings":"AAGA,MAAM,CAAC,KAAK,UAAU,IAAI,CACxB,KAAmB,EACnB,OAAsB,EACtB,QAAuB,EACvB,OAAsB;IAEtB,KAAK,CAAC,QAAQ,CAAC,SAAS,CAAC,CAAA;IACzB,IAAI,OAAO,EAAE,CAAC;QACZ,KAAK,CAAC,gBAAgB,CAAC,OAAO,CAAC,CAAA;IACjC,CAAC;IACD,IAAI,QAAQ,EAAE,CAAC;QACb,KAAK,CAAC,iBAAiB,CAAC,QAAQ,CAAC,CAAA;IACnC,CAAC;IACD,IAAI,OAAO,EAAE,CAAC;QACZ,KAAK,CAAC,gBAAgB,CAAC,OAAO,CAAC,CAAA;IACjC,CAAC;AACH,CAAC"}

package/dist/components/msa/renderBoxFeatureCanvasBlock.js

@@ -26,8 +26,13 @@ function drawTiles({ model, ctx, visibleLeaves, }) {
         if (entry) {
             for (let j = 0, l2 = entry.length; j < l2; j++) {
                 const { start, end, accession } = entry[j];
-                const m1 = model.seqCoordToRowSpecificGlobalCoord(name, start - 1);
-                const m2 = model.seqCoordToRowSpecificGlobalCoord(name, end);
+                // Convert sequence positions to visible column positions
+                // seqPos is 1-based from InterPro, so subtract 1 for 0-based
+                const m1 = model.seqPosToVisibleCol(name, start - 1);
+                const m2 = model.seqPosToVisibleCol(name, end);
+                if (m1 === undefined || m2 === undefined) {
+                    continue; // Skip if either position is hidden
+                }
                 const x = m1 * colWidth;
                 ctx.fillStyle = fillPalette[accession];
                 ctx.strokeStyle = strokePalette[accession];

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

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

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+{"version":3,"file":"renderMSABlock.js","sourceRoot":"","sources":["../../../src/components/msa/renderMSABlock.ts"],"names":[],"mappings":"AAKA,MAAM,UAAU,cAAc,CAAC,EAC7B,KAAK,EACL,OAAO,EACP,OAAO,EACP,cAAc,EACd,GAAG,EACH,KAAK,EACL,0BAA0B,EAC1B,kBAAkB,EAClB,kBAAkB,GAWnB;IACC,MAAM,EACJ,QAAQ,EACR,SAAS,EACT,SAAS,EACT,QAAQ,EACR,kBAAkB,EAClB,mBAAmB,EACnB,MAAM,EACN,OAAO,GACR,GAAG,KAAK,CAAA;IACT,MAAM,CAAC,GAAG,0BAA0B,IAAI,kBAAkB,CAAA;IAC1D,MAAM,EAAE,GAAG,kBAAkB,IAAI,SAAS,CAAA;IAC1C,MAAM,EAAE,GAAG,kBAAkB,IAAI,SAAS,CAAA;IAC1C,GAAG,CAAC,cAAc,EAAE,CAAA;IACpB,GAAG,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,CAAC,CAAA;IACf,GAAG,CAAC,SAAS,CAAC,CAAC,OAAO,EAAE,SAAS,GAAG,CAAC,GAAG,OAAO,CAAC,CAAA;IAChD,GAAG,CAAC,SAAS,GAAG,QAAQ,CAAA;IACxB,GAAG,CAAC,IAAI,GAAG,GAAG,CAAC,IAAI,CAAC,OAAO,CAAC,OAAO,EAAE,GAAG,OAAO,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,GAAG,QAAQ,IAAI,CAAC,CAAA;IAE9E,MAAM,MAAM,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,IAAI,CAAC,KAAK,CAAC,CAAC,OAAO,GAAG,SAAS,CAAC,GAAG,SAAS,CAAC,CAAC,CAAA;IACzE,MAAM,IAAI,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,IAAI,CAAC,IAAI,CAAC,CAAC,OAAO,GAAG,EAAE,GAAG,SAAS,CAAC,GAAG,SAAS,CAAC,CAAC,CAAA;IAC3E,MAAM,MAAM,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,IAAI,CAAC,KAAK,CAAC,OAAO,GAAG,QAAQ,CAAC,CAAC,CAAA;IAC1D,MAAM,IAAI,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,IAAI,CAAC,IAAI,CAAC,CAAC,OAAO,GAAG,EAAE,CAAC,GAAG,QAAQ,CAAC,CAAC,CAAA;IAC9D,MAAM,aAAa,GAAG,MAAM,CAAC,KAAK,CAAC,MAAM,EAAE,IAAI,CAAC,CAAA;IAEhD,IAAI,CAAC,mBAAmB,EAAE,CAAC;QACzB,SAAS,CAAC;YACR,KAAK;YACL,GAAG;YACH,KAAK;YACL,OAAO;YACP,MAAM;YACN,IAAI;YACJ,aAAa;SACd,CAAC,CAAA;IACJ,CAAC;IACD,QAAQ,CAAC;QACP,KAAK;QACL,GAAG;QACH,OAAO;QACP,cAAc;QACd,MAAM;QACN,IAAI;QACJ,aAAa;KACd,CAAC,CAAA;IACF,uBAAuB,CAAC;QACtB,KAAK;QACL,GAAG;QACH,MAAM;QACN,IAAI;QACJ,aAAa;KACd,CAAC,CAAA;IACF,GAAG,CAAC,cAAc,EAAE,CAAA;AACtB,CAAC;AAED,SAAS,SAAS,CAAC,EACjB,KAAK,EACL,OAAO,EACP,GAAG,EACH,aAAa,EACb,KAAK,EACL,MAAM,EACN,IAAI,GASL;IACC,MAAM,EACJ,OAAO,EACP,eAAe,EACf,WAAW,EACX,OAAO,EACP,QAAQ,EACR,SAAS,EACT,UAAU,GACX,GAAG,KAAK,CAAA;IAET,8CAA8C;IAC9C,MAAM,YAAY,GAAG,UAAU;QAC7B,CAAC,CAAC,OAAO,CAAC,UAAU,CAAC,EAAE,KAAK,CAAC,MAAM,EAAE,IAAI,CAAC;QAC1C,CAAC,CAAC,IAAI,CAAA;IAER,MAAM,UAAU,GAAG,eAAe,KAAK,0BAA0B,CAAA;IACjE,MAAM,iBAAiB,GAAG,eAAe,KAAK,0BAA0B,CAAA;IACxE,MAAM,cAAc,GAAG,OAAO,GAAG,CAAC,OAAO,GAAG,QAAQ,CAAC,CAAA;IAErD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,GAAG,aAAa,CAAC,MAAM,EAAE,CAAC,GAAG,EAAE,EAAE,CAAC,EAAE,EAAE,CAAC;QACvD,MAAM,IAAI,GAAG,aAAa,CAAC,CAAC,CAAE,CAAA;QAC9B,MAAM,EACJ,IAAI,EAAE,EAAE,IAAI,EAAE,GACf,GAAG,IAAI,CAAA;QACR,MAAM,CAAC,GAAG,IAAI,CAAC,CAAE,CAAA;QACjB,MAAM,GAAG,GAAG,OAAO,CAAC,IAAI,CAAC,EAAE,KAAK,CAAC,MAAM,EAAE,IAAI,CAAC,CAAA;QAC9C,IAAI,GAAG,EAAE,CAAC;YACR,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,GAAG,GAAG,CAAC,MAAM,EAAE,CAAC,GAAG,EAAE,EAAE,CAAC,EAAE,EAAE,CAAC;gBAC7C,MAAM,MAAM,GAAG,GAAG,CAAC,CAAC,CAAE,CAAA;gBAEtB,4DAA4D;gBAC5D,MAAM,mBAAmB,GACvB,YAAY,IAAI,IAAI,KAAK,UAAU,IAAI,MAAM,KAAK,YAAY,CAAC,CAAC,CAAC,CAAA;gBAEnE,MAAM,KAAK,GAAG,UAAU;oBACtB,CAAC,CAAC,KAAK,CAAC,WAAW,CAAC,MAAM,GAAG,CAAC,CAAE,CAAC,MAAM,CAAC;oBACxC,CAAC,CAAC,iBAAiB;wBACjB,CAAC,CAAC,CAAC,GAAG,EAAE;4BACJ,MAAM,SAAS,GAAG,KAAK,CAAC,YAAY,CAAC,MAAM,GAAG,CAAC,CAAE,CAAA;4BACjD,OAAO,MAAM,KAAK,SAAS,CAAC,MAAM,CAAC,CAAC,CAAC,SAAS,CAAC,KAAK,CAAC,CAAC,CAAC,SAAS,CAAA;wBAClE,CAAC,CAAC,EAAE;wBACN,CAAC,CAAC,WAAW,CAAC,MAAM,CAAC,WAAW,EAAE,CAAC,CAAA;gBACvC,IAAI,OAAO,IAAI,UAAU,IAAI,iBAAiB,EAAE,CAAC;oBAC/C,sEAAsE;oBACtE,MAAM,UAAU,GAAG,mBAAmB;wBACpC,CAAC,CAAC,KAAK,CAAC,OAAO,CAAC,MAAM,CAAC,KAAK;wBAC5B,CAAC,CAAC,KAAK,IAAI,KAAK,CAAC,OAAO,CAAC,UAAU,CAAC,OAAO,CAAA;oBAC7C,GAAG,CAAC,SAAS,GAAG,UAAU,CAAA;oBAC1B,GAAG,CAAC,QAAQ,CACV,CAAC,GAAG,QAAQ,GAAG,cAAc,EAC7B,CAAC,GAAG,SAAS,EACb,QAAQ,EACR,SAAS,CACV,CAAA;gBACH,CAAC;YACH,CAAC;QACH,CAAC;IACH,CAAC;AACH,CAAC;AAED,SAAS,QAAQ,CAAC,EAChB,KAAK,EACL,OAAO,EACP,cAAc,EACd,GAAG,EACH,aAAa,EACb,MAAM,EACN,IAAI,GASL;IACC,MAAM,EACJ,OAAO,EACP,mBAAmB,EACnB,cAAc,EACd,WAAW,EACX,OAAO,EACP,QAAQ,EACR,iBAAiB,EACjB,SAAS,EACT,UAAU,GACX,GAAG,KAAK,CAAA;IAET,8CAA8C;IAC9C,MAAM,YAAY,GAAG,UAAU;QAC7B,CAAC,CAAC,OAAO,CAAC,UAAU,CAAC,EAAE,KAAK,CAAC,MAAM,EAAE,IAAI,CAAC;QAC1C,CAAC,CAAC,IAAI,CAAA;IAER,IAAI,cAAc,EAAE,CAAC;QACnB,MAAM,cAAc,GAAG,OAAO,GAAG,CAAC,OAAO,GAAG,QAAQ,CAAC,CAAA;QACrD,MAAM,YAAY,GAAG,QAAQ,GAAG,CAAC,CAAA;QACjC,MAAM,gBAAgB,GAAG,SAAS,GAAG,CAAC,CAAA;QAEtC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,GAAG,aAAa,CAAC,MAAM,EAAE,CAAC,GAAG,EAAE,EAAE,CAAC,EAAE,EAAE,CAAC;YACvD,MAAM,IAAI,GAAG,aAAa,CAAC,CAAC,CAAE,CAAA;YAC9B,MAAM,EACJ,IAAI,EAAE,EAAE,IAAI,EAAE,GACf,GAAG,IAAI,CAAA;YACR,MAAM,CAAC,GAAG,IAAI,CAAC,CAAE,GAAG,gBAAgB,CAAA;YACpC,MAAM,GAAG,GAAG,OAAO,CAAC,IAAI,CAAC,EAAE,KAAK,CAAC,MAAM,EAAE,IAAI,CAAC,CAAA;YAC9C,IAAI,GAAG,EAAE,CAAC;gBACR,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,GAAG,GAAG,CAAC,MAAM,EAAE,CAAC,GAAG,EAAE,EAAE,CAAC,EAAE,EAAE,CAAC;oBAC7C,MAAM,MAAM,GAAG,GAAG,CAAC,CAAC,CAAE,CAAA;oBAEtB,+CAA+C;oBAC/C,MAAM,mBAAmB,GACvB,YAAY,IAAI,IAAI,KAAK,UAAU,IAAI,MAAM,KAAK,YAAY,CAAC,CAAC,CAAC,CAAA;oBAEnE,mEAAmE;oBACnE,MAAM,aAAa,GAAG,mBAAmB,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,MAAM,CAAA;oBAExD,MAAM,KAAK,GAAG,WAAW,CAAC,MAAM,CAAC,WAAW,EAAE,CAAC,CAAA;oBAC/C,MAAM,QAAQ,GAAG,iBAAiB;wBAChC,CAAC,CAAC,cA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package/dist/components/tree/renderTreeCanvas.js

@@ -13,10 +13,11 @@ export function renderTree({ offsetY, ctx, model, theme, blockSizeYOverride, })
         }
         const sy = source.x;
         const ty = target.x;
-        // @ts-expect-error
         const tx = showBranchLen ? target.len : target.y;
-        // @ts-expect-error
         const sx = showBranchLen ? source.len : source.y;
+        if (tx === undefined || sx === undefined) {
+            continue;
+        }
         const y1 = Math.min(sy, ty);
         const y2 = Math.max(sy, ty);
         // 1d line intersection to check if line crosses block at all, this is an
@@ -35,9 +36,11 @@ export function renderNodeBubbles({ ctx, clickMap, offsetY, model, blockSizeYOve
     const { hierarchy, showBranchLenEffective: showBranchLen, collapsed, blockSize, marginLeft: ml, } = model;
     const by = blockSizeYOverride || blockSize;
     for (const node of hierarchy.descendants()) {
-        const val = showBranchLen ? 'len' : 'y';
-        // @ts-expect-error
-        const { [val]: x, data } = node;
+        const x = showBranchLen ? node.len : node.y;
+        if (x === undefined) {
+            continue;
+        }
+        const { data } = node;
         const y = node.x;
         const { id, name } = data;
         if (node.height > 1 &&
@@ -73,9 +76,8 @@ export function renderTreeLabels({ theme, model, offsetY, ctx, clickMap, blockSi
         ctx.textAlign = 'start';
     }
     for (const node of leaves) {
-        const { data: { name, id }, 
-        // @ts-expect-error
-        len, } = node;
+        const { data: { name, id }, } = node;
+        const len = node.len;
         const y = node.x;
         const x = node.y;
         const displayName = treeMetadata[name]?.genome || name;

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

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

@@ -1,8 +1,4 @@
-import A3mMSA from './parsers/A3mMSA';
-import ClustalMSA from './parsers/ClustalMSA';
-import EmfMSA from './parsers/EmfMSA';
-import FastaMSA from './parsers/FastaMSA';
-import StockholmMSA from './parsers/StockholmMSA';
+import { A3mMSA, ClustalMSA, EmfMSA, FastaMSA, StockholmMSA } from '@react-msaview/parsers';
 import type { InterProScanResults } from './launchInterProScan';
 import type { Accession, BasicTrack, NodeWithIds, NodeWithIdsAndLength } from './types';
 import type { FileLocation as FileLocationType } from '@jbrowse/core/util/types';
@@ -195,6 +191,57 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
             authInfo: import("mobx-state-tree").IType<any, any, any>;
         }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
     }>> & import("mobx-state-tree/dist/internal").NonEmptyObject)>, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+    gffFilehandle: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISnapshotProcessor<import("mobx-state-tree").ITypeUnion<import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
+        locationType: import("mobx-state-tree").ISimpleType<"UriLocation">;
+        uri: import("mobx-state-tree").ISimpleType<string>;
+        baseUri: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+        internetAccountId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+        internetAccountPreAuthorization: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IModelType<{
+            internetAccountType: import("mobx-state-tree").ISimpleType<string>;
+            authInfo: import("mobx-state-tree").IType<any, any, any>;
+        }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+    }>> | import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
+        locationType: import("mobx-state-tree").ISimpleType<"BlobLocation">;
+        name: import("mobx-state-tree").ISimpleType<string>;
+        blobId: import("mobx-state-tree").ISimpleType<string>;
+    }>> | import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
+        locationType: import("mobx-state-tree").ISimpleType<"LocalPathLocation">;
+        localPath: import("mobx-state-tree").ISimpleType<string>;
+    }>>, {
+        locationType: "UriLocation";
+        uri: string;
+        internetAccountId: string | undefined;
+        internetAccountPreAuthorization: import("mobx-state-tree").ModelSnapshotType<{
+            internetAccountType: import("mobx-state-tree").ISimpleType<string>;
+            authInfo: import("mobx-state-tree").IType<any, any, any>;
+        }> | undefined;
+    } | import("mobx-state-tree").ModelSnapshotType<{
+        locationType: import("mobx-state-tree").ISimpleType<"BlobLocation">;
+        name: import("mobx-state-tree").ISimpleType<string>;
+        blobId: import("mobx-state-tree").ISimpleType<string>;
+    }> | import("mobx-state-tree").ModelSnapshotType<{
+        locationType: import("mobx-state-tree").ISimpleType<"LocalPathLocation">;
+        localPath: import("mobx-state-tree").ISimpleType<string>;
+    }>, import("mobx-state-tree").ModelInstanceType<{
+        locationType: import("mobx-state-tree").ISimpleType<"BlobLocation">;
+        name: import("mobx-state-tree").ISimpleType<string>;
+        blobId: import("mobx-state-tree").ISimpleType<string>;
+    }, {}> | import("mobx-state-tree").ModelInstanceType<{
+        locationType: import("mobx-state-tree").ISimpleType<"LocalPathLocation">;
+        localPath: import("mobx-state-tree").ISimpleType<string>;
+    }, {}> | ({
+        locationType: "UriLocation";
+        uri: string;
+    } & Partial<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
+        locationType: import("mobx-state-tree").ISimpleType<"UriLocation">;
+        uri: import("mobx-state-tree").ISimpleType<string>;
+        baseUri: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+        internetAccountId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+        internetAccountPreAuthorization: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IModelType<{
+            internetAccountType: import("mobx-state-tree").ISimpleType<string>;
+            authInfo: import("mobx-state-tree").IType<any, any, any>;
+        }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+    }>> & import("mobx-state-tree/dist/internal").NonEmptyObject)>, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
     currentAlignment: import("mobx-state-tree").IType<number | undefined, number, number>;
     collapsed: import("mobx-state-tree").IArrayType<import("mobx-state-tree").ISimpleType<string>>;
     collapsedLeaves: import("mobx-state-tree").IArrayType<import("mobx-state-tree").ISimpleType<string>>;
@@ -461,6 +508,10 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
      * #action
      */
     setTreeFilehandle(treeFilehandle?: FileLocationType): void;
+    /**
+     * #action
+     */
+    setGFFFilehandle(gffFilehandle?: FileLocationType): void;
     /**
      * #action
      */
@@ -805,27 +856,62 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
     readonly rowNamesSet: Map<string, number>;
     /**
      * #method
-     * return a row-specific letter, or undefined if gap
+     * Return a row-specific letter at a visible column, or undefined if gap.
+     *
+     * @param rowName - The name of the row
+     * @param visibleCol - The visible column index (what the user sees on screen)
+     * @returns The letter at that position, or undefined if it's a gap
      */
-    mouseOverCoordToRowLetter(rowName: string, pos: number): string | undefined;
+    visibleColToRowLetter(rowName: string, visibleCol: number): string | undefined;
     /**
      * #method
-     * return a row-specific sequence coordinate, skipping gaps, given a
-     * global coordinate
+     * Convert a visible column to a row-specific sequence position (0-based).
+     * Returns undefined if the position is a gap in the sequence.
+     *
+     * @param rowName - The name of the row
+     * @param visibleCol - The visible column index
+     * @returns The sequence position (0-based), or undefined if it's a gap
      */
-    mouseOverCoordToGapRemovedRowCoord(rowName: string, position: number): number | undefined;
+    visibleColToSeqPos(rowName: string, visibleCol: number): number | undefined;
     /**
      * #method
-     * return a row-specific sequence coordinate, skipping gaps, given a
-     * global coordinate
+     * Convert a visible column to a row-specific sequence position (1-based).
+     * Returns undefined if the position is a gap in the sequence.
+     *
+     * @param rowName - The name of the row
+     * @param visibleCol - The visible column index
+     * @returns The sequence position (1-based), or undefined if it's a gap
      */
-    mouseOverCoordToGapRemovedRowCoordOneBased(rowName: string, position: number): number | undefined;
+    visibleColToSeqPosOneBased(rowName: string, visibleCol: number): number | undefined;
     /**
      * #method
-     * return a global coordinate given a row-specific sequence coordinate
-     * which does not not include gaps
+     * Convert a global column index to a visible column index.
+     * Returns undefined if the column is hidden (in blanks).
+     * This is the inverse of visibleColToGlobalCol.
+     *
+     * @param globalCol - The global column index in the full MSA
+     * @returns The visible column index, or undefined if the column is hidden
      */
-    seqCoordToRowSpecificGlobalCoord(rowName: string, position: number): number;
+    globalColToVisibleCol(globalCol: number): number | undefined;
+    /**
+     * #method
+     * Convert a sequence position (ungapped) to a global column index.
+     *
+     * @param rowName - The name of the row
+     * @param seqPos - The sequence position (0-based, ungapped)
+     * @returns The global column index in the full MSA
+     */
+    seqPosToGlobalCol(rowName: string, seqPos: number): number;
+    /**
+     * #method
+     * Convert a sequence position (ungapped) directly to a visible column index.
+     * This combines seqPosToGlobalCol and globalColToVisibleCol.
+     *
+     * @param rowName - The name of the row
+     * @param seqPos - The sequence position (0-based, ungapped)
+     * @returns The visible column index, or undefined if the column is hidden
+     */
+    seqPosToVisibleCol(rowName: string, seqPos: number): number | undefined;
 } & {
     /**
      * #getter
@@ -1128,6 +1214,57 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
             authInfo: import("mobx-state-tree").IType<any, any, any>;
         }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
     }>> & import("mobx-state-tree/dist/internal").NonEmptyObject)>, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+    gffFilehandle: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISnapshotProcessor<import("mobx-state-tree").ITypeUnion<import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
+        locationType: import("mobx-state-tree").ISimpleType<"UriLocation">;
+        uri: import("mobx-state-tree").ISimpleType<string>;
+        baseUri: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+        internetAccountId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+        internetAccountPreAuthorization: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IModelType<{
+            internetAccountType: import("mobx-state-tree").ISimpleType<string>;
+            authInfo: import("mobx-state-tree").IType<any, any, any>;
+        }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+    }>> | import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
+        locationType: import("mobx-state-tree").ISimpleType<"BlobLocation">;
+        name: import("mobx-state-tree").ISimpleType<string>;
+        blobId: import("mobx-state-tree").ISimpleType<string>;
+    }>> | import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
+        locationType: import("mobx-state-tree").ISimpleType<"LocalPathLocation">;
+        localPath: import("mobx-state-tree").ISimpleType<string>;
+    }>>, {
+        locationType: "UriLocation";
+        uri: string;
+        internetAccountId: string | undefined;
+        internetAccountPreAuthorization: import("mobx-state-tree").ModelSnapshotType<{
+            internetAccountType: import("mobx-state-tree").ISimpleType<string>;
+            authInfo: import("mobx-state-tree").IType<any, any, any>;
+        }> | undefined;
+    } | import("mobx-state-tree").ModelSnapshotType<{
+        locationType: import("mobx-state-tree").ISimpleType<"BlobLocation">;
+        name: import("mobx-state-tree").ISimpleType<string>;
+        blobId: import("mobx-state-tree").ISimpleType<string>;
+    }> | import("mobx-state-tree").ModelSnapshotType<{
+        locationType: import("mobx-state-tree").ISimpleType<"LocalPathLocation">;
+        localPath: import("mobx-state-tree").ISimpleType<string>;
+    }>, import("mobx-state-tree").ModelInstanceType<{
+        locationType: import("mobx-state-tree").ISimpleType<"BlobLocation">;
+        name: import("mobx-state-tree").ISimpleType<string>;
+        blobId: import("mobx-state-tree").ISimpleType<string>;
+    }, {}> | import("mobx-state-tree").ModelInstanceType<{
+        locationType: import("mobx-state-tree").ISimpleType<"LocalPathLocation">;
+        localPath: import("mobx-state-tree").ISimpleType<string>;
+    }, {}> | ({
+        locationType: "UriLocation";
+        uri: string;
+    } & Partial<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
+        locationType: import("mobx-state-tree").ISimpleType<"UriLocation">;
+        uri: import("mobx-state-tree").ISimpleType<string>;
+        baseUri: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+        internetAccountId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+        internetAccountPreAuthorization: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IModelType<{
+            internetAccountType: import("mobx-state-tree").ISimpleType<string>;
+            authInfo: import("mobx-state-tree").IType<any, any, any>;
+        }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+    }>> & import("mobx-state-tree/dist/internal").NonEmptyObject)>, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
     currentAlignment: import("mobx-state-tree").IType<number | undefined, number, number>;
     collapsed: import("mobx-state-tree").IArrayType<import("mobx-state-tree").ISimpleType<string>>;
     collapsedLeaves: import("mobx-state-tree").IArrayType<import("mobx-state-tree").ISimpleType<string>>;