react-msaview 3.2.0 → 3.2.2

package/dist/model.js

@@ -23,6 +23,7 @@ import palettes from './ggplotPalettes';
 import TextTrack from './components/TextTrack';
 // parsers
 import ClustalMSA from './parsers/ClustalMSA';
+import EmfMSA from './parsers/EmfMSA';
 import StockholmMSA from './parsers/StockholmMSA';
 import FastaMSA from './parsers/FastaMSA';
 import parseNewick from './parseNewick';
@@ -32,6 +33,8 @@ import { DataModelF } from './model/DataModel';
 import { DialogQueueSessionMixin } from './model/DialogQueue';
 import { TreeF } from './model/treeModel';
 import { MSAModelF } from './model/msaModel';
+import { mouseOverCoordToGlobalCoord, globalCoordToRowSpecificCoord, } from './rowCoordinateCalculations';
+import EmfTree from './parsers/EmfTree';
 /**
  * #stateModel MsaView
  * extends
@@ -89,7 +92,7 @@ function stateModelFactory() {
          * #property
          * height of each row, px
          */
-        rowHeight: 20,
+        rowHeight: 18,
         /**
          * #property
          * scroll position, Y-offset, px
@@ -104,7 +107,7 @@ function stateModelFactory() {
          * #property
          * width of columns, px
          */
-        colWidth: 16,
+        colWidth: 14,
         /**
          * #property
          * filehandle object for the tree
@@ -153,7 +156,11 @@ function stateModelFactory() {
          * data from the loaded tree/msa/treeMetadata, generally loaded by
          * autorun
          */
-        data: types.optional(DataModelF(), { tree: '', msa: '' }),
+        data: types.optional(DataModelF(), {
+            tree: '',
+            msa: '',
+            treeMetadata: '',
+        }),
         /**
          * #property
          */
@@ -417,6 +424,12 @@ function stateModelFactory() {
         },
     }))
         .views(self => ({
+        /**
+         * #getter
+         */
+        get realAllowedGappyness() {
+            return self.hideGaps ? self.allowedGappyness : 100;
+        },
         /**
          * #getter
          */
@@ -488,7 +501,7 @@ function stateModelFactory() {
         /**
          * #getter
          */
-        get menuItems() {
+        menuItems() {
             return [];
         },
         /**
@@ -506,10 +519,15 @@ function stateModelFactory() {
                 if (Stockholm.sniff(text)) {
                     return new StockholmMSA(text, self.currentAlignment);
                 }
-                if (text.startsWith('>')) {
+                else if (text.startsWith('>')) {
                     return new FastaMSA(text);
                 }
-                return new ClustalMSA(text);
+                else if (text.startsWith('SEQ')) {
+                    return new EmfMSA(text);
+                }
+                else {
+                    return new ClustalMSA(text);
+                }
             }
             return null;
         },
@@ -523,14 +541,27 @@ function stateModelFactory() {
          * #getter
          */
         get tree() {
-            const ret = self.data.tree
-                ? generateNodeIds(parseNewick(self.data.tree))
-                : this.MSA?.getTree() || {
+            const text = self.data.tree;
+            let ret;
+            if (text) {
+                let t;
+                if (text.startsWith('SEQ')) {
+                    const r = new EmfTree(text);
+                    t = r.data.tree;
+                }
+                else {
+                    t = text;
+                }
+                ret = generateNodeIds(parseNewick(t));
+            }
+            else {
+                ret = this.MSA?.getTree() || {
                     noTree: true,
-                    branchset: [],
+                    children: [],
                     id: 'empty',
                     name: 'empty',
                 };
+            }
             return reparseTree(ret);
         },
         /**
@@ -550,8 +581,10 @@ function stateModelFactory() {
          * #getter
          */
         get root() {
-            let hier = hierarchy(this.tree, d => d.branchset)
-                .sum(d => (d.branchset ? 0 : 1))
+            let hier = hierarchy(this.tree, d => d.children)
+                // todo: investigate whether needed, typescript says children always true
+                // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
+                .sum(d => (d.children ? 0 : 1))
                 .sort((a, b) => ascending(a.data.length || 1, b.data.length || 1));
             if (self.showOnly) {
                 const res = hier.find(n => n.data.id === self.showOnly);
@@ -563,7 +596,9 @@ function stateModelFactory() {
             [...self.collapsed, ...self.collapsedLeaves]
                 .map(collapsedId => hier.find(node => node.data.id === collapsedId))
                 .filter(notEmpty)
-                .map(node => collapse(node));
+                .map(node => {
+                collapse(node);
+            });
             return hier;
         },
         /**
@@ -583,24 +618,34 @@ function stateModelFactory() {
          * #getter
          */
         get blanks() {
-            const { allowedGappyness } = self;
+            const { hideGaps, realAllowedGappyness } = self;
             const blanks = [];
-            const strs = this.leaves
-                .map(leaf => this.MSA?.getRow(leaf.data.name))
-                .filter((item) => !!item);
-            for (let i = 0; i < strs[0]?.length; i++) {
-                let counter = 0;
-                for (const str of strs) {
-                    if (str[i] === '-') {
-                        counter++;
+            if (hideGaps) {
+                const strs = this.leaves
+                    .map(leaf => this.MSA?.getRow(leaf.data.name))
+                    .filter((item) => !!item);
+                if (strs.length) {
+                    for (let i = 0; i < strs[0].length; i++) {
+                        let counter = 0;
+                        for (const str of strs) {
+                            if (str[i] === '-') {
+                                counter++;
+                            }
+                        }
+                        if (counter / strs.length >= realAllowedGappyness / 100) {
+                            blanks.push(i);
+                        }
                     }
                 }
-                if (counter / strs.length >= allowedGappyness / 100) {
-                    blanks.push(i);
-                }
             }
             return blanks;
         },
+        /**
+         * #getter
+         */
+        get blanksSet() {
+            return new Set(this.blanks);
+        },
         /**
          * #getter
          */
@@ -610,6 +655,12 @@ function stateModelFactory() {
                 .map(leaf => [leaf.data.name, MSA?.getRow(leaf.data.name)])
                 .filter((f) => !!f[1]);
         },
+        /**
+         * #getter
+         */
+        get rowMap() {
+            return new Map(this.rows);
+        },
         /**
          * #getter
          */
@@ -626,7 +677,7 @@ function stateModelFactory() {
          * #getter
          */
         get fontSize() {
-            return Math.min(Math.max(6, self.rowHeight - 8), 18);
+            return Math.min(Math.max(6, self.rowHeight - 3), 18);
         },
         /**
          * #getter
@@ -637,10 +688,11 @@ function stateModelFactory() {
             for (const column of columns) {
                 for (let j = 0; j < column.length; j++) {
                     const l = r[j] || {};
-                    if (!l[column[j]]) {
-                        l[column[j]] = 0;
+                    const cj = column[j];
+                    if (!l[cj]) {
+                        l[cj] = 0;
                     }
-                    l[column[j]]++;
+                    l[cj]++;
                     r[j] = l;
                 }
             }
@@ -922,28 +974,36 @@ function stateModelFactory() {
         get showHorizontalScrollbar() {
             return self.msaAreaWidth < self.totalWidth;
         },
+        /**
+         * #getter
+         */
+        get rowNamesSet() {
+            return new Map(self.rowNames.map((r, idx) => [r, idx]));
+        },
         /**
          * #method
-         * return a row-specific sequence coordinate, skipping gaps, given a global
-         * coordinate
+         * return a row-specific letter, or undefined if gap
          */
-        globalCoordToRowSpecificSeqCoord(rowName, position) {
-            const { rowNames, rows } = self;
-            const index = rowNames.indexOf(rowName);
-            if (index !== -1 && rows[index]) {
-                const row = rows[index][1];
-                let k = 0;
-                for (let i = 0; i < position; i++) {
-                    if (row[i] !== '-') {
-                        k++;
-                    }
-                    else if (k >= position) {
-                        break;
-                    }
-                }
-                return k;
+        mouseOverCoordToRowLetter(rowName, position) {
+            const { rowMap, blanks } = self;
+            return rowMap.get(rowName)?.[mouseOverCoordToGlobalCoord(blanks, position)];
+        },
+        /**
+         * #method
+         * return a row-specific sequence coordinate, skipping gaps, given a
+         * global coordinate
+         */
+        mouseOverCoordToGapRemovedRowCoord(rowName, position) {
+            const { rowMap, blanks } = self;
+            const seq = rowMap.get(rowName);
+            if (seq !== undefined) {
+                const pos2 = mouseOverCoordToGlobalCoord(blanks, position);
+                const pos1 = globalCoordToRowSpecificCoord(seq, pos2);
+                return seq[pos1] === '-' || !seq[pos1] ? undefined : pos1;
+            }
+            else {
+                return undefined;
             }
-            return 0;
         },
         /**
          * #method
@@ -990,19 +1050,17 @@ function stateModelFactory() {
         /**
          * #getter
          */
-        get tidyTypes() {
+        get tidyInterProAnnotationTypes() {
             const types = new Map();
-            if (this.tidyAnnotations) {
-                for (const { name, accession, description } of this.tidyAnnotations) {
-                    types.set(accession, { name, accession, description });
-                }
+            for (const annot of this.tidyInterProAnnotations) {
+                types.set(annot.accession, annot);
             }
             return types;
         },
         /**
          * #getter
          */
-        get tidyAnnotations() {
+        get tidyInterProAnnotations() {
             const ret = [];
             const { interProAnnotations } = self;
             if (interProAnnotations) {
@@ -1030,14 +1088,14 @@ function stateModelFactory() {
         /**
          * #getter
          */
-        get tidyFilteredAnnotations() {
-            return this.tidyAnnotations.filter(r => self.featureFilters.get(r.accession));
+        get tidyFilteredInterProAnnotations() {
+            return this.tidyInterProAnnotations.filter(r => self.featureFilters.get(r.accession));
         },
         /**
          * #getter
          */
-        get tidyFilteredGatheredAnnotations() {
-            return groupBy(this.tidyFilteredAnnotations, r => r.id);
+        get tidyFilteredGatheredInterProAnnotations() {
+            return groupBy(this.tidyFilteredInterProAnnotations, r => r.id);
         },
     }))
         .views(self => ({
@@ -1059,7 +1117,7 @@ function stateModelFactory() {
          * #getter
          */
         get fillPalette() {
-            const arr = [...self.tidyTypes.keys()];
+            const arr = [...self.tidyInterProAnnotationTypes.keys()];
             let i = 0;
             const map = {};
             for (const key of arr) {
@@ -1131,7 +1189,7 @@ function stateModelFactory() {
         },
         afterCreate() {
             addDisposer(self, autorun(() => {
-                for (const key of self.tidyTypes.keys()) {
+                for (const key of self.tidyInterProAnnotationTypes.keys()) {
                     this.initFilter(key);
                 }
             }));
@@ -1195,12 +1253,15 @@ function stateModelFactory() {
                     }
                 }
             }));
+            // force colStats not to go stale
+            // xref solution https://github.com/mobxjs/mobx/issues/266#issuecomment-222007278
+            // xref problem https://github.com/GMOD/react-msaview/issues/75
             addDisposer(self, autorun(() => {
-                // force colStats not to go stale,
-                // xref solution https://github.com/mobxjs/mobx/issues/266#issuecomment-222007278
-                // xref problem https://github.com/GMOD/react-msaview/issues/75
+                // eslint-disable-next-line  @typescript-eslint/no-unused-expressions
                 self.colStats;
+                // eslint-disable-next-line  @typescript-eslint/no-unused-expressions
                 self.colStatsSums;
+                // eslint-disable-next-line  @typescript-eslint/no-unused-expressions
                 self.columns;
             }));
             // autorun synchronizes treeWidth with treeAreaWidth

package/dist/model.js.map

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package/dist/parseGFF.js

@@ -6,14 +6,14 @@ export function parseGFF(str) {
         .map(f => {
         const [seq_id, source, type, start, end, score, strand, phase, col9] = f.split('\t');
         return {
-            seq_id,
-            source,
-            type,
+            seq_id: seq_id,
+            source: source,
+            type: type,
             start: +start,
             end: +end,
             score: +score,
-            strand,
-            phase,
+            strand: strand,
+            phase: phase,
             ...Object.fromEntries(col9
                 .split(';')
                 .map(f => f.trim())
@@ -21,7 +21,9 @@ export function parseGFF(str) {
                 .map(f => f.split('='))
                 .map(([key, val]) => [
                 key.trim(),
-                decodeURIComponent(val).trim().split(',').join(' '),
+                val
+                    ? decodeURIComponent(val).trim().split(',').join(' ')
+                    : undefined,
             ])),
         };
     });

package/dist/parseGFF.js.map

@@ -1 +1 @@
-{"version":3,"file":"parseGFF.js","sourceRoot":"","sources":["../src/parseGFF.ts"],"names":[],"mappings":"AAAA,MAAM,UAAU,QAAQ,CAAC,GAAY;IACnC,OAAO,GAAG;QACR,EAAE,KAAK,CAAC,IAAI,CAAC;SACZ,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC;SAClB,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,UAAU,CAAC,GAAG,CAAC,CAAC;SACtC,GAAG,CAAC,CAAC,CAAC,EAAE;QACP,MAAM,CAAC,MAAM,EAAE,MAAM,EAAE,IAAI,EAAE,KAAK,EAAE,GAAG,EAAE,KAAK,EAAE,MAAM,EAAE,KAAK,EAAE,IAAI,CAAC,GAClE,CAAC,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QAEf,OAAO;YACL,MAAM;YACN,MAAM;YACN,IAAI;YACJ,KAAK,EAAE,CAAC,KAAK;YACb,GAAG,EAAE,CAAC,GAAG;YACT,KAAK,EAAE,CAAC,KAAK;YACb,MAAM;YACN,KAAK;YACL,GAAG,MAAM,CAAC,WAAW,CACnB,IAAI;iBACD,KAAK,CAAC,GAAG,CAAC;iBACV,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC;iBAClB,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC;iBAChB,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC;iBACtB,GAAG,CAAC,CAAC,CAAC,GAAG,EAAE,GAAG,CAAC,EAAE,EAAE,CAAC;gBACnB,GAAG,CAAC,IAAI,EAAE;gBACV,kBAAkB,CAAC,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC;aACpD,CAAC,CACL;SACF,CAAA;IACH,CAAC,CAAC,CAAA;AACN,CAAC"}
+{"version":3,"file":"parseGFF.js","sourceRoot":"","sources":["../src/parseGFF.ts"],"names":[],"mappings":"AAAA,MAAM,UAAU,QAAQ,CAAC,GAAY;IACnC,OAAO,GAAG;QACR,EAAE,KAAK,CAAC,IAAI,CAAC;SACZ,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC;SAClB,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,UAAU,CAAC,GAAG,CAAC,CAAC;SACtC,GAAG,CAAC,CAAC,CAAC,EAAE;QACP,MAAM,CAAC,MAAM,EAAE,MAAM,EAAE,IAAI,EAAE,KAAK,EAAE,GAAG,EAAE,KAAK,EAAE,MAAM,EAAE,KAAK,EAAE,IAAI,CAAC,GAClE,CAAC,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QAEf,OAAO;YACL,MAAM,EAAE,MAAO;YACf,MAAM,EAAE,MAAO;YACf,IAAI,EAAE,IAAK;YACX,KAAK,EAAE,CAAC,KAAM;YACd,GAAG,EAAE,CAAC,GAAI;YACV,KAAK,EAAE,CAAC,KAAM;YACd,MAAM,EAAE,MAAO;YACf,KAAK,EAAE,KAAM;YACb,GAAG,MAAM,CAAC,WAAW,CACnB,IAAK;iBACF,KAAK,CAAC,GAAG,CAAC;iBACV,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC;iBAClB,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC;iBAChB,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC;iBACtB,GAAG,CAAC,CAAC,CAAC,GAAG,EAAE,GAAG,CAAC,EAAE,EAAE,CAAC;gBACnB,GAAI,CAAC,IAAI,EAAE;gBACX,GAAG;oBACD,CAAC,CAAC,kBAAkB,CAAC,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC;oBACrD,CAAC,CAAC,SAAS;aACd,CAAC,CACL;SACF,CAAA;IACH,CAAC,CAAC,CAAA;AACN,CAAC"}

package/dist/parseNewick.d.ts

@@ -34,13 +34,13 @@
  * Converted to JSON:
  * {
  *   name: "F",
- *   branchset: [
+ *   children: [
  *     {name: "A", length: 0.1},
  *     {name: "B", length: 0.2},
  *     {
  *       name: "E",
  *       length: 0.5,
- *       branchset: [
+ *       children: [
  *         {name: "C", length: 0.3},
  *         {name: "D", length: 0.4}
  *       ]
@@ -50,9 +50,9 @@
  *
  * Converted to JSON, but with no names or lengths:
  * {
- *   branchset: [
+ *   children: [
  *     {}, {}, {
- *       branchset: [{}, {}]
+ *       children: [{}, {}]
  *     }
  *   ]
  * }

package/dist/parseNewick.js

@@ -34,13 +34,13 @@
  * Converted to JSON:
  * {
  *   name: "F",
- *   branchset: [
+ *   children: [
  *     {name: "A", length: 0.1},
  *     {name: "B", length: 0.2},
  *     {
  *       name: "E",
  *       length: 0.5,
- *       branchset: [
+ *       children: [
  *         {name: "C", length: 0.3},
  *         {name: "D", length: 0.4}
  *       ]
@@ -50,29 +50,28 @@
  *
  * Converted to JSON, but with no names or lengths:
  * {
- *   branchset: [
+ *   children: [
  *     {}, {}, {
- *       branchset: [{}, {}]
+ *       children: [{}, {}]
  *     }
  *   ]
  * }
  */
 export default function parse(s) {
     const ancestors = [];
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any
     let tree = {};
     const tokens = s.split(/\s*(;|\(|\)|,|:)\s*/);
     for (let i = 0; i < tokens.length; i++) {
         const token = tokens[i];
         const subtree = {};
         switch (token) {
-            case '(': // new branchset
-                tree.branchset = [subtree];
+            case '(': // new children
+                tree.children = [subtree];
                 ancestors.push(tree);
                 tree = subtree;
                 break;
             case ',': // another branch
-                ancestors.at(-1)?.branchset.push(subtree);
+                ancestors.at(-1)?.children.push(subtree);
                 tree = subtree;
                 break;
             case ')': // optional name next

package/dist/parseNewick.js.map

@@ -1 +1 @@
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+{"version":3,"file":"parseNewick.js","sourceRoot":"","sources":["../src/parseNewick.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GA0DG;AACH,MAAM,CAAC,OAAO,UAAU,KAAK,CAAC,CAAS;IACrC,MAAM,SAAS,GAAG,EAAE,CAAA;IAEpB,IAAI,IAAI,GAAG,EAAyB,CAAA;IACpC,MAAM,MAAM,GAAG,CAAC,CAAC,KAAK,CAAC,qBAAqB,CAAC,CAAA;IAC7C,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,MAAM,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;QACvC,MAAM,KAAK,GAAG,MAAM,CAAC,CAAC,CAAE,CAAA;QACxB,MAAM,OAAO,GAAG,EAAE,CAAA;QAClB,QAAQ,KAAK,EAAE,CAAC;YACd,KAAK,GAAG,EAAE,eAAe;gBACvB,IAAI,CAAC,QAAQ,GAAG,CAAC,OAAO,CAAC,CAAA;gBACzB,SAAS,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;gBACpB,IAAI,GAAG,OAAO,CAAA;gBACd,MAAK;YACP,KAAK,GAAG,EAAE,iBAAiB;gBACzB,SAAS,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,EAAE,QAAQ,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;gBACxC,IAAI,GAAG,OAAO,CAAA;gBACd,MAAK;YACP,KAAK,GAAG,EAAE,qBAAqB;gBAC7B,IAAI,GAAG,SAAS,CAAC,GAAG,EAAG,CAAA;gBACvB,MAAK;YACP,KAAK,GAAG,EAAE,uBAAuB;gBAC/B,MAAK;YACP,OAAO,CAAC,CAAC,CAAC;gBACR,MAAM,CAAC,GAAG,MAAM,CAAC,CAAC,GAAG,CAAC,CAAE,CAAA;gBACxB,IAAI,CAAC,KAAK,GAAG,IAAI,CAAC,KAAK,GAAG,IAAI,CAAC,KAAK,GAAG,EAAE,CAAC;oBACxC,IAAI,CAAC,IAAI,GAAG,KAAK,CAAA;gBACnB,CAAC;qBAAM,IAAI,CAAC,KAAK,GAAG,EAAE,CAAC;oBACrB,IAAI,CAAC,MAAM,GAAG,MAAM,CAAC,UAAU,CAAC,KAAK,CAAC,CAAA;gBACxC,CAAC;YACH,CAAC;QACH,CAAC;IACH,CAAC;IACD,OAAO,IAAI,CAAA;AACb,CAAC"}

package/dist/parsers/ClustalMSA.d.ts

@@ -5,22 +5,22 @@ export default class ClustalMSA {
     getMSA(): {
         consensus: string;
         alns: {
-            id: any;
-            seq: any;
+            id: string;
+            seq: string;
         }[];
         header: {
             info: string;
             version: string;
         };
     };
-    getRow(name: string): any;
-    getWidth(): any;
+    getRow(name: string): string;
+    getWidth(): number;
     getRowData(): undefined;
     getHeader(): {
         info: string;
         version: string;
     };
-    getNames(): any[];
+    getNames(): string[];
     getStructures(): {};
     get alignmentNames(): never[];
     getTree(): NodeWithIds;

package/dist/parsers/ClustalMSA.js

@@ -33,10 +33,10 @@ export default class ClustalMSA {
             id: 'root',
             name: 'root',
             noTree: true,
-            branchset: this.getNames().map(name => ({
+            children: this.getNames().map(name => ({
                 id: name,
                 name,
-                branchset: [],
+                children: [],
             })),
         };
     }