jbrowse-plugin-msaview 2.2.3 → 2.2.5

package/dist/MsaViewPanel/pairwiseAlignment.js.map

@@ -0,0 +1 @@
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package/dist/MsaViewPanel/pairwiseAlignment.test.d.ts

@@ -0,0 +1 @@
+export {};

package/dist/MsaViewPanel/pairwiseAlignment.test.js

@@ -0,0 +1,112 @@
+import { describe, expect, test } from 'vitest';
+import { buildAlignmentMaps, needlemanWunsch, runPairwiseAlignment, } from './pairwiseAlignment';
+describe('needlemanWunsch', () => {
+    test('identical sequences align perfectly', () => {
+        const result = needlemanWunsch('MKAA', 'MKAA');
+        expect(result.alignedSeq1).toBe('MKAA');
+        expect(result.alignedSeq2).toBe('MKAA');
+        expect(result.score).toBeGreaterThan(0);
+    });
+    test('aligned sequences have same length', () => {
+        const result = needlemanWunsch('MKAAYLSMFG', 'MKAYLSMFG');
+        expect(result.alignedSeq1.length).toBe(result.alignedSeq2.length);
+    });
+    test('aligned sequences preserve original characters', () => {
+        const seq1 = 'MKAAYLSMFG';
+        const seq2 = 'MKAYLSMFG';
+        const result = needlemanWunsch(seq1, seq2);
+        expect(result.alignedSeq1.replaceAll('-', '')).toBe(seq1);
+        expect(result.alignedSeq2.replaceAll('-', '')).toBe(seq2);
+    });
+    test('handles empty sequences', () => {
+        const result = needlemanWunsch('', '');
+        expect(result.alignedSeq1).toBe('');
+        expect(result.alignedSeq2).toBe('');
+    });
+    test('handles one empty sequence', () => {
+        const result = needlemanWunsch('MKA', '');
+        expect(result.alignedSeq1.replaceAll('-', '')).toBe('MKA');
+        expect(result.alignedSeq2.replaceAll('-', '')).toBe('');
+        expect(result.alignedSeq1.length).toBe(result.alignedSeq2.length);
+    });
+});
+describe('runPairwiseAlignment', () => {
+    test('returns PairwiseAlignment format', () => {
+        const result = runPairwiseAlignment('MKAA', 'MKAA');
+        expect(result.consensus).toBeDefined();
+        expect(result.alns).toHaveLength(2);
+        expect(result.alns[0].id).toBe('msa');
+        expect(result.alns[1].id).toBe('structure');
+    });
+    test('consensus marks matches with pipe', () => {
+        const result = runPairwiseAlignment('MKAA', 'MKAA');
+        expect(result.consensus).toBe('||||');
+    });
+    test('consensus marks gaps with space', () => {
+        const result = runPairwiseAlignment('MKAA', 'MKA');
+        expect(result.consensus).toContain(' ');
+    });
+    test('consensus marks mismatches with space', () => {
+        const result = runPairwiseAlignment('MKAA', 'MKBA');
+        // A vs B should be a space in consensus
+        expect(result.consensus).toContain(' ');
+    });
+});
+describe('buildAlignmentMaps', () => {
+    test('builds bidirectional maps for identical sequences', () => {
+        const alignment = runPairwiseAlignment('MKAA', 'MKAA');
+        const { seq1ToSeq2, seq2ToSeq1 } = buildAlignmentMaps(alignment);
+        expect(seq1ToSeq2.get(0)).toBe(0);
+        expect(seq1ToSeq2.get(1)).toBe(1);
+        expect(seq1ToSeq2.get(2)).toBe(2);
+        expect(seq1ToSeq2.get(3)).toBe(3);
+        expect(seq2ToSeq1.get(0)).toBe(0);
+        expect(seq2ToSeq1.get(1)).toBe(1);
+        expect(seq2ToSeq1.get(2)).toBe(2);
+        expect(seq2ToSeq1.get(3)).toBe(3);
+    });
+    test('maps are inverses of each other for matched positions', () => {
+        const alignment = runPairwiseAlignment('MKAAYLSMFG', 'MKAYLSMFG');
+        const { seq1ToSeq2, seq2ToSeq1 } = buildAlignmentMaps(alignment);
+        // For every mapped position, the inverse should return the original
+        for (const [pos1, pos2] of seq1ToSeq2) {
+            expect(seq2ToSeq1.get(pos2)).toBe(pos1);
+        }
+    });
+    test('handles gaps correctly - positions without counterpart are not in map', () => {
+        // Aligning 'MKAAA' with 'MKA' should result in gaps
+        const alignment = runPairwiseAlignment('MKAAA', 'MKA');
+        const { seq1ToSeq2 } = buildAlignmentMaps(alignment);
+        // seq1 has 5 positions, seq2 has 3
+        // Only matched positions should be in the map
+        expect(seq1ToSeq2.size).toBeLessThanOrEqual(3);
+    });
+    test('handles real protein sequence alignment', () => {
+        const msaSeq = 'MKAAYLSMFGKEDHKPFGDDEVELFRAVPGLKLKIAG';
+        const structureSeq = 'MKAAYLSMFGKEDHKPFGDDEVELFRAVPGLKLKIAG';
+        const alignment = runPairwiseAlignment(msaSeq, structureSeq);
+        const { seq1ToSeq2, seq2ToSeq1 } = buildAlignmentMaps(alignment);
+        // Identical sequences should have 1:1 mapping
+        expect(seq1ToSeq2.size).toBe(msaSeq.length);
+        expect(seq2ToSeq1.size).toBe(structureSeq.length);
+        // Check a few positions
+        expect(seq1ToSeq2.get(0)).toBe(0);
+        expect(seq1ToSeq2.get(10)).toBe(10);
+        expect(seq2ToSeq1.get(20)).toBe(20);
+    });
+    test('handles sequences with insertions/deletions', () => {
+        // MSA sequence has an extra 'X' in the middle
+        const msaSeq = 'MKAXYLSMFG';
+        const structureSeq = 'MKAYLSMFG';
+        const alignment = runPairwiseAlignment(msaSeq, structureSeq);
+        const { seq1ToSeq2 } = buildAlignmentMaps(alignment);
+        // Positions before the insertion should map correctly
+        expect(seq1ToSeq2.get(0)).toBe(0); // M
+        expect(seq1ToSeq2.get(1)).toBe(1); // K
+        expect(seq1ToSeq2.get(2)).toBe(2); // A
+        // The mapping should handle the offset after insertion
+        // (exact behavior depends on alignment algorithm)
+        expect(seq1ToSeq2.size).toBeLessThanOrEqual(structureSeq.length);
+    });
+});
+//# sourceMappingURL=pairwiseAlignment.test.js.map

package/dist/MsaViewPanel/pairwiseAlignment.test.js.map

@@ -0,0 +1 @@
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package/dist/MsaViewPanel/structureConnection.d.ts

@@ -0,0 +1,27 @@
+/**
+ * Represents a connection between the MSA view and a protein structure
+ */
+export interface StructureConnection {
+    /** ID of the ProteinView containing the structure */
+    proteinViewId: string;
+    /** Index of the structure within the ProteinView's structures array */
+    structureIdx: number;
+    /** Name of the MSA row that corresponds to this structure */
+    msaRowName: string;
+    /** Map from MSA ungapped position to structure sequence position */
+    msaToStructure: Record<number, number>;
+    /** Map from structure sequence position to MSA ungapped position */
+    structureToMsa: Record<number, number>;
+}
+/**
+ * Helper to convert gapped MSA column to ungapped position for a specific row
+ */
+export declare function gappedToUngappedPosition(sequence: string, gappedPosition: number): number | undefined;
+/**
+ * Helper to convert ungapped position to gapped MSA column for a specific row
+ */
+export declare function ungappedToGappedPosition(sequence: string, ungappedPosition: number): number | undefined;
+/**
+ * Convert Map to plain object for MST frozen storage
+ */
+export declare function mapToRecord(map: Map<number, number>): Record<number, number>;

package/dist/MsaViewPanel/structureConnection.js

@@ -0,0 +1,46 @@
+/**
+ * Helper to convert gapped MSA column to ungapped position for a specific row
+ */
+export function gappedToUngappedPosition(sequence, gappedPosition) {
+    if (gappedPosition < 0 || gappedPosition >= sequence.length) {
+        return undefined;
+    }
+    let ungapped = 0;
+    for (let i = 0; i < gappedPosition; i++) {
+        if (sequence[i] !== '-') {
+            ungapped++;
+        }
+    }
+    // If the position itself is a gap, return undefined
+    if (sequence[gappedPosition] === '-') {
+        return undefined;
+    }
+    return ungapped;
+}
+/**
+ * Helper to convert ungapped position to gapped MSA column for a specific row
+ */
+export function ungappedToGappedPosition(sequence, ungappedPosition) {
+    let ungapped = 0;
+    for (let i = 0; i < sequence.length; i++) {
+        const element = sequence[i];
+        if (element !== '-') {
+            if (ungapped === ungappedPosition) {
+                return i;
+            }
+            ungapped++;
+        }
+    }
+    return undefined;
+}
+/**
+ * Convert Map to plain object for MST frozen storage
+ */
+export function mapToRecord(map) {
+    const record = {};
+    for (const [key, value] of map) {
+        record[key] = value;
+    }
+    return record;
+}
+//# sourceMappingURL=structureConnection.js.map

package/dist/MsaViewPanel/structureConnection.js.map

@@ -0,0 +1 @@
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package/dist/MsaViewPanel/structureConnection.test.d.ts

@@ -0,0 +1 @@
+export {};

package/dist/MsaViewPanel/structureConnection.test.js

@@ -0,0 +1,122 @@
+import { describe, expect, test } from 'vitest';
+import { gappedToUngappedPosition, mapToRecord, ungappedToGappedPosition, } from './structureConnection';
+describe('gappedToUngappedPosition', () => {
+    test('returns correct ungapped position for non-gap character', () => {
+        const seq = 'M-KA-A';
+        //           0 12 34  (gapped positions)
+        //           0  1  2  (ungapped positions for M, K, A, A)
+        expect(gappedToUngappedPosition(seq, 0)).toBe(0); // M -> 0
+        expect(gappedToUngappedPosition(seq, 2)).toBe(1); // K -> 1
+        expect(gappedToUngappedPosition(seq, 3)).toBe(2); // A -> 2
+        expect(gappedToUngappedPosition(seq, 5)).toBe(3); // A -> 3
+    });
+    test('returns undefined for gap position', () => {
+        const seq = 'M-KA-A';
+        expect(gappedToUngappedPosition(seq, 1)).toBeUndefined(); // gap
+        expect(gappedToUngappedPosition(seq, 4)).toBeUndefined(); // gap
+    });
+    test('returns undefined for out-of-bounds position', () => {
+        const seq = 'MKA';
+        expect(gappedToUngappedPosition(seq, -1)).toBeUndefined();
+        expect(gappedToUngappedPosition(seq, 3)).toBeUndefined();
+        expect(gappedToUngappedPosition(seq, 100)).toBeUndefined();
+    });
+    test('handles sequence with no gaps', () => {
+        const seq = 'MKAA';
+        expect(gappedToUngappedPosition(seq, 0)).toBe(0);
+        expect(gappedToUngappedPosition(seq, 1)).toBe(1);
+        expect(gappedToUngappedPosition(seq, 2)).toBe(2);
+        expect(gappedToUngappedPosition(seq, 3)).toBe(3);
+    });
+    test('handles sequence with leading gaps', () => {
+        const seq = '--MKA';
+        expect(gappedToUngappedPosition(seq, 0)).toBeUndefined();
+        expect(gappedToUngappedPosition(seq, 1)).toBeUndefined();
+        expect(gappedToUngappedPosition(seq, 2)).toBe(0); // M
+        expect(gappedToUngappedPosition(seq, 3)).toBe(1); // K
+    });
+    test('handles sequence with trailing gaps', () => {
+        const seq = 'MKA--';
+        expect(gappedToUngappedPosition(seq, 2)).toBe(2); // A
+        expect(gappedToUngappedPosition(seq, 3)).toBeUndefined();
+        expect(gappedToUngappedPosition(seq, 4)).toBeUndefined();
+    });
+    test('handles empty sequence', () => {
+        expect(gappedToUngappedPosition('', 0)).toBeUndefined();
+    });
+    test('handles all-gap sequence', () => {
+        const seq = '---';
+        expect(gappedToUngappedPosition(seq, 0)).toBeUndefined();
+        expect(gappedToUngappedPosition(seq, 1)).toBeUndefined();
+        expect(gappedToUngappedPosition(seq, 2)).toBeUndefined();
+    });
+});
+describe('ungappedToGappedPosition', () => {
+    test('returns correct gapped position', () => {
+        const seq = 'M-KA-A';
+        //           0 12 34  (gapped)
+        //           0  1  23 (ungapped)
+        expect(ungappedToGappedPosition(seq, 0)).toBe(0); // M
+        expect(ungappedToGappedPosition(seq, 1)).toBe(2); // K
+        expect(ungappedToGappedPosition(seq, 2)).toBe(3); // A
+        expect(ungappedToGappedPosition(seq, 3)).toBe(5); // A
+    });
+    test('returns undefined for out-of-bounds ungapped position', () => {
+        const seq = 'M-KA';
+        expect(ungappedToGappedPosition(seq, 4)).toBeUndefined();
+        expect(ungappedToGappedPosition(seq, 100)).toBeUndefined();
+    });
+    test('handles sequence with no gaps', () => {
+        const seq = 'MKAA';
+        expect(ungappedToGappedPosition(seq, 0)).toBe(0);
+        expect(ungappedToGappedPosition(seq, 1)).toBe(1);
+        expect(ungappedToGappedPosition(seq, 2)).toBe(2);
+        expect(ungappedToGappedPosition(seq, 3)).toBe(3);
+    });
+    test('handles sequence with leading gaps', () => {
+        const seq = '--MKA';
+        expect(ungappedToGappedPosition(seq, 0)).toBe(2); // M
+        expect(ungappedToGappedPosition(seq, 1)).toBe(3); // K
+        expect(ungappedToGappedPosition(seq, 2)).toBe(4); // A
+    });
+    test('handles empty sequence', () => {
+        expect(ungappedToGappedPosition('', 0)).toBeUndefined();
+    });
+    test('handles all-gap sequence', () => {
+        const seq = '---';
+        expect(ungappedToGappedPosition(seq, 0)).toBeUndefined();
+    });
+});
+describe('gappedToUngappedPosition and ungappedToGappedPosition are inverses', () => {
+    test('round-trip conversion works', () => {
+        const seq = 'M-KA--YL-S';
+        // For each non-gap position, converting to ungapped and back should return original
+        for (let i = 0; i < seq.length; i++) {
+            if (seq[i] !== '-') {
+                const ungapped = gappedToUngappedPosition(seq, i);
+                expect(ungapped).toBeDefined();
+                const backToGapped = ungappedToGappedPosition(seq, ungapped);
+                expect(backToGapped).toBe(i);
+            }
+        }
+    });
+});
+describe('mapToRecord', () => {
+    test('converts Map to Record', () => {
+        const map = new Map([
+            [0, 5],
+            [1, 10],
+            [2, 15],
+        ]);
+        const record = mapToRecord(map);
+        expect(record[0]).toBe(5);
+        expect(record[1]).toBe(10);
+        expect(record[2]).toBe(15);
+    });
+    test('handles empty Map', () => {
+        const map = new Map();
+        const record = mapToRecord(map);
+        expect(Object.keys(record)).toHaveLength(0);
+    });
+});
+//# sourceMappingURL=structureConnection.test.js.map

package/dist/MsaViewPanel/structureConnection.test.js.map

@@ -0,0 +1 @@
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package/dist/MsaViewPanel/types.d.ts

@@ -0,0 +1,13 @@
+export interface MsaViewInitState {
+    msaData?: string;
+    msaUrl?: string;
+    treeData?: string;
+    treeUrl?: string;
+    querySeqName?: string;
+}
+export interface MafRegion {
+    refName: string;
+    start: number;
+    end: number;
+    assemblyName: string;
+}

package/dist/MsaViewPanel/types.js

@@ -0,0 +1,2 @@
+export {};
+//# sourceMappingURL=types.js.map

package/dist/MsaViewPanel/types.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"types.js","sourceRoot":"","sources":["../../src/MsaViewPanel/types.ts"],"names":[],"mappings":""}

package/dist/MsaViewPanel/util.d.ts

@@ -6,3 +6,10 @@ export declare function checkHovered(hovered: unknown): hovered is {
         refName: string;
     };
 };
+/**
+ * Extracts UniProt ID from an AlphaFold URL
+ * Examples:
+ * - https://alphafold.ebi.ac.uk/files/AF-P12345-F1-model_v6.cif -> P12345
+ * - https://alphafold.ebi.ac.uk/files/msa/AF-P12345-F1-msa_v6.a3m -> P12345
+ */
+export declare function getUniprotIdFromAlphaFoldUrl(url: string): string | undefined;

package/dist/MsaViewPanel/util.js

@@ -4,4 +4,14 @@ export function checkHovered(hovered) {
         'hoverFeature' in hovered &&
         'hoverPosition' in hovered);
 }
+/**
+ * Extracts UniProt ID from an AlphaFold URL
+ * Examples:
+ * - https://alphafold.ebi.ac.uk/files/AF-P12345-F1-model_v6.cif -> P12345
+ * - https://alphafold.ebi.ac.uk/files/msa/AF-P12345-F1-msa_v6.a3m -> P12345
+ */
+export function getUniprotIdFromAlphaFoldUrl(url) {
+    const match = /AF-([A-Z0-9]+)-F\d+/.exec(url);
+    return match?.[1];
+}
 //# sourceMappingURL=util.js.map

package/dist/MsaViewPanel/util.js.map

@@ -1 +1 @@
-{"version":3,"file":"util.js","sourceRoot":"","sources":["../../src/MsaViewPanel/util.ts"],"names":[],"mappings":"AAEA,MAAM,UAAU,YAAY,CAAC,OAAgB;IAI3C,OAAO,CACL,OAAO,OAAO,KAAK,QAAQ;QAC3B,OAAO,KAAK,IAAI;QAChB,cAAc,IAAI,OAAO;QACzB,eAAe,IAAI,OAAO,CAC3B,CAAA;AACH,CAAC"}
+{"version":3,"file":"util.js","sourceRoot":"","sources":["../../src/MsaViewPanel/util.ts"],"names":[],"mappings":"AAEA,MAAM,UAAU,YAAY,CAAC,OAAgB;IAI3C,OAAO,CACL,OAAO,OAAO,KAAK,QAAQ;QAC3B,OAAO,KAAK,IAAI;QAChB,cAAc,IAAI,OAAO;QACzB,eAAe,IAAI,OAAO,CAC3B,CAAA;AACH,CAAC;AAED;;;;;GAKG;AACH,MAAM,UAAU,4BAA4B,CAAC,GAAW;IACtD,MAAM,KAAK,GAAG,qBAAqB,CAAC,IAAI,CAAC,GAAG,CAAC,CAAA;IAC7C,OAAO,KAAK,EAAE,CAAC,CAAC,CAAC,CAAA;AACnB,CAAC"}

package/dist/index.d.ts

@@ -6,8 +6,8 @@ export default class MsaViewPlugin extends Plugin {
     install(pluginManager: PluginManager): void;
     configure(pluginManager: PluginManager): void;
     rootConfigurationSchema(pluginManager: PluginManager): {
-        msa: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-            datasets: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IArrayType<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        msa: import("@jbrowse/core/esm/configuration/configurationSchema").ConfigurationSchemaType<{
+            datasets: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/core/esm/configuration/configurationSchema").ConfigurationSchemaType<{
                 datasetId: {
                     type: string;
                     defaultValue: string;
@@ -20,8 +20,8 @@ export default class MsaViewPlugin extends Plugin {
                     type: string;
                     defaultValue: string;
                 };
-                adapter: import("mobx-state-tree").IAnyModelType;
-            }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>>>;
-        }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+                adapter: import("@jbrowse/mobx-state-tree").IAnyModelType;
+            }, import("@jbrowse/core/esm/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>>>;
+        }, import("@jbrowse/core/esm/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
     };
 }

package/dist/index.js

@@ -1,12 +1,13 @@
 import Plugin from '@jbrowse/core/Plugin';
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
 import { isAbstractMenuManager } from '@jbrowse/core/util';
+import { types } from '@jbrowse/mobx-state-tree';
 import GridOn from '@mui/icons-material/GridOn';
-import { types } from 'mobx-state-tree';
 import { version } from '../package.json';
 import AddHighlightModelF from './AddHighlightModel';
 import BgzipFastaMsaAdapterF from './BgzipFastaMsaAdapter';
 import LaunchMsaViewF from './LaunchMsaView';
+import LaunchMsaViewExtensionPointF from './LaunchMsaViewExtensionPoint';
 import MsaViewF from './MsaViewPanel';
 export default class MsaViewPlugin extends Plugin {
     constructor() {
@@ -17,6 +18,7 @@ export default class MsaViewPlugin extends Plugin {
     install(pluginManager) {
         MsaViewF(pluginManager);
         LaunchMsaViewF(pluginManager);
+        LaunchMsaViewExtensionPointF(pluginManager);
         AddHighlightModelF(pluginManager);
         BgzipFastaMsaAdapterF(pluginManager);
     }

package/dist/index.js.map

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