jbrowse-plugin-protein3d 0.0.2 → 0.0.4

package/dist/ProteinView/components/SplitString.js

@@ -1,9 +1,9 @@
 import React from 'react';
-export default function SplitString({ str, col, set, onMouseOver, onClick, showHighlight, }) {
+export default function SplitString({ str, gapSet, hoveredPosition, showHighlight, onMouseOver, onClick, }) {
     return str.split('').map((d, i) => (React.createElement("span", { key: `${d}-${i}`, onMouseOver: () => onMouseOver?.(i), onClick: () => onClick?.(i), style: {
-            background: col !== undefined && i === col
-                ? '#f69'
-                : set?.has(i) && showHighlight
+            background: hoveredPosition !== undefined && i === hoveredPosition
+                ? '#f698'
+                : gapSet?.has(i) && showHighlight
                     ? '#33ff19'
                     : undefined,
         } }, d === ' ' ? React.createElement(React.Fragment, null, "\u00A0") : d)));

package/dist/ProteinView/components/SplitString.js.map

@@ -1 +1 @@
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+{"version":3,"file":"SplitString.js","sourceRoot":"","sources":["../../../src/ProteinView/components/SplitString.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,MAAM,CAAC,OAAO,UAAU,WAAW,CAAC,EAClC,GAAG,EACH,MAAM,EACN,eAAe,EACf,aAAa,EACb,WAAW,EACX,OAAO,GAQR;IACC,OAAO,GAAG,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CACjC,8BACE,GAAG,EAAE,GAAG,CAAC,IAAI,CAAC,EAAE,EAChB,WAAW,EAAE,GAAG,EAAE,CAAC,WAAW,EAAE,CAAC,CAAC,CAAC,EACnC,OAAO,EAAE,GAAG,EAAE,CAAC,OAAO,EAAE,CAAC,CAAC,CAAC,EAC3B,KAAK,EAAE;YACL,UAAU,EACR,eAAe,KAAK,SAAS,IAAI,CAAC,KAAK,eAAe;gBACpD,CAAC,CAAC,OAAO;gBACT,CAAC,CAAC,MAAM,EAAE,GAAG,CAAC,CAAC,CAAC,IAAI,aAAa;oBAC/B,CAAC,CAAC,SAAS;oBACX,CAAC,CAAC,SAAS;SAClB,IAEA,CAAC,KAAK,GAAG,CAAC,CAAC,CAAC,mDAAW,CAAC,CAAC,CAAC,CAAC,CACvB,CACR,CAAC,CAAA;AACJ,CAAC"}

package/dist/ProteinView/genomeToProtein.d.ts

@@ -1,4 +1,4 @@
-import { JBrowsePluginProteinViewModel } from './model';
+import { JBrowsePluginProteinStructureModel } from './model';
 export declare function genomeToProtein({ model, }: {
-    model: JBrowsePluginProteinViewModel;
+    model: JBrowsePluginProteinStructureModel;
 }): number | undefined;

package/dist/ProteinView/genomeToProtein.js

@@ -3,11 +3,10 @@ import { checkHovered } from './util';
 export function genomeToProtein({ model, }) {
     const { hovered } = getSession(model);
     const { genomeToTranscriptSeqMapping, connectedView } = model;
-    if (!connectedView?.initialized ||
+    return !connectedView?.initialized ||
         !genomeToTranscriptSeqMapping ||
-        !checkHovered(hovered)) {
-        return undefined;
-    }
-    return genomeToTranscriptSeqMapping.g2p[hovered.hoverPosition.coord];
+        !checkHovered(hovered)
+        ? undefined
+        : genomeToTranscriptSeqMapping.g2p[hovered.hoverPosition.coord];
 }
 //# sourceMappingURL=genomeToProtein.js.map

package/dist/ProteinView/genomeToProtein.js.map

@@ -1 +1 @@
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+{"version":3,"file":"genomeToProtein.js","sourceRoot":"","sources":["../../src/ProteinView/genomeToProtein.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAA;AAC/C,OAAO,EAAE,YAAY,EAAE,MAAM,QAAQ,CAAA;AAGrC,MAAM,UAAU,eAAe,CAAC,EAC9B,KAAK,GAGN;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,UAAU,CAAC,KAAK,CAAC,CAAA;IACrC,MAAM,EAAE,4BAA4B,EAAE,aAAa,EAAE,GAAG,KAAK,CAAA;IAC7D,OAAO,CAAC,aAAa,EAAE,WAAW;QAChC,CAAC,4BAA4B;QAC7B,CAAC,YAAY,CAAC,OAAO,CAAC;QACtB,CAAC,CAAC,SAAS;QACX,CAAC,CAAC,4BAA4B,CAAC,GAAG,CAAC,OAAO,CAAC,aAAa,CAAC,KAAK,CAAC,CAAA;AACnE,CAAC"}

package/dist/ProteinView/highlightResidue.js

@@ -6,8 +6,8 @@ export default function highlightResidue({ structure, selectedResidue, plugin, }
         selectedResidue: selectedResidue + 1,
     });
     const loci = StructureSelection.toLociWithSourceUnits(sel);
-    plugin?.managers.interactivity.lociHighlights.clearHighlights();
-    plugin?.managers.interactivity.lociHighlights.highlight({
+    plugin.managers.interactivity.lociHighlights.clearHighlights();
+    plugin.managers.interactivity.lociHighlights.highlight({
         loci,
     });
 }

package/dist/ProteinView/highlightResidue.js.map

@@ -1 +1 @@
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+{"version":3,"file":"highlightResidue.js","sourceRoot":"","sources":["../../src/ProteinView/highlightResidue.ts"],"names":[],"mappings":"AACA,OAAO,EAAa,kBAAkB,EAAE,MAAM,iCAAiC,CAAA;AAC/E,OAAO,EAAE,4BAA4B,EAAE,MAAM,QAAQ,CAAA;AAErD,MAAM,CAAC,OAAO,UAAU,gBAAgB,CAAC,EACvC,SAAS,EACT,eAAe,EACf,MAAM,GAKP;IACC,MAAM,GAAG,GAAG,4BAA4B,CAAC;QACvC,SAAS;QACT,eAAe,EAAE,eAAe,GAAG,CAAC;KACrC,CAAC,CAAA;IACF,MAAM,IAAI,GAAG,kBAAkB,CAAC,qBAAqB,CAAC,GAAG,CAAC,CAAA;IAC1D,MAAM,CAAC,QAAQ,CAAC,aAAa,CAAC,cAAc,CAAC,eAAe,EAAE,CAAA;IAC9D,MAAM,CAAC,QAAQ,CAAC,aAAa,CAAC,cAAc,CAAC,SAAS,CAAC;QACrD,IAAI;KACL,CAAC,CAAA;AACJ,CAAC"}

package/dist/ProteinView/launchRemotePairwiseAlignment.d.ts

@@ -4,11 +4,8 @@ export declare function launchPairwiseAlignment({ algorithm, seq1, seq2, onProgr
     seq2: string;
     onProgress: (arg: string) => void;
 }): Promise<{
-    alignment: {
+    pairwiseAlignment: {
         consensus: string;
-        alns: {
-            id: any;
-            seq: any;
-        }[];
+        alns: [import("clustal-js").Row, import("clustal-js").Row];
     };
 }>;

package/dist/ProteinView/launchRemotePairwiseAlignment.js

@@ -17,7 +17,7 @@ async function runEmbossMatcher({ seq1, seq2, onProgress, }) {
     });
     const ret = await textfetch(`${base}/emboss_matcher/result/${jobId}/aln`);
     return {
-        alignment: parsePairwise(ret
+        pairwiseAlignment: parsePairwise(ret
             .split('\n')
             .filter(line => !line.startsWith('#'))
             .join('\n')),
@@ -39,22 +39,26 @@ async function runEmbossNeedle({ seq1, seq2, onProgress, }) {
     });
     const ret = await textfetch(`${base}/emboss_needle/result/${jobId}/aln`);
     return {
-        alignment: parsePairwise(ret
+        pairwiseAlignment: parsePairwise(ret
             .split('\n')
             .filter(line => !line.startsWith('#'))
             .join('\n')),
     };
 }
 async function wait({ onProgress, jobId, algorithm, }) {
+    // eslint-disable-next-line  @typescript-eslint/no-unnecessary-condition
     while (true) {
         for (let i = 0; i < 10; i++) {
             await timeout(1000);
-            onProgress(`Re-checking alignment to PDB seq1,seq2 in... ${10 - i}`);
+            onProgress(`Re-checking pairwiseAlignment to PDB seq1,seq2 in... ${10 - i}`);
         }
         const result = await textfetch(`${base}/${algorithm}/status/${jobId}`);
         if (result === 'FINISHED') {
             break;
         }
+        else if (result.includes('FAILED')) {
+            throw new Error('Remote returned FAILED');
+        }
     }
 }
 export async function launchPairwiseAlignment({ algorithm, seq1, seq2, onProgress, }) {

package/dist/ProteinView/launchRemotePairwiseAlignment.js.map

@@ -1 +1 @@
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