protvista-uniprot 3.0.0 → 3.0.7

package/dist/es/styles/protvista-styles.js

@@ -1,89 +0,0 @@
-import { css } from 'lit';
-export default css `
-  .track-content {
-    width: 80vw;
-  }
-
-  .track-content__coloured-sequence {
-    display: flex;
-    align-items: center;
-  }
-
-  .nav-container,
-  .category__track {
-    display: flex;
-    margin-bottom: 0.1rem;
-  }
-
-  .category {
-    display: none;
-    margin-bottom: 0.1rem;
-  }
-
-  .category-label,
-  .track-label,
-  .nav-track-label,
-  .credits {
-    min-width: 20vw;
-    max-width: 20vw;
-    padding: 0.5em;
-    line-height: normal;
-  }
-
-  .category-label {
-    background-color: #b2f5ff;
-    cursor: pointer;
-  }
-
-  .category-label::before {
-    content: ' ';
-    display: inline-block;
-    width: 0;
-    height: 0;
-    border-top: 5px solid transparent;
-    border-bottom: 5px solid transparent;
-    border-left: 5px solid #333;
-    margin-right: 5px;
-    -webkit-transition: all 0.1s;
-    /* Safari */
-    -o-transition: all 0.1s;
-    transition: all 0.1s;
-  }
-
-  .category-label.open::before {
-    content: ' ';
-    display: inline-block;
-    width: 0;
-    height: 0;
-    border-left: 5px solid transparent;
-    border-right: 5px solid transparent;
-    border-top: 5px solid #333;
-    margin-right: 5px;
-  }
-
-  .track-label {
-    background-color: #d9faff;
-  }
-
-  nightingale-track {
-    border-top: 1px solid #d9faff;
-  }
-
-  nightingale-navigation {
-    .handle {
-      fill: darkgrey;
-      stroke: black;
-      stroke-width: 0.5px;
-      height: 19px;
-    }
-  }
-
-  nightingale-filter {
-    font-size: 0.8rem;
-  }
-
-  .feature {
-    cursor: pointer;
-  }
-`;
-//# sourceMappingURL=protvista-styles.js.map

package/dist/es/styles/protvista-styles.js.map

@@ -1 +0,0 @@
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package/dist/es/tooltips/featureTooltip.js

@@ -1,160 +0,0 @@
-import ecoMap from '../adapters/config/evidence';
-const formatSource = (source) => {
-    var _a;
-    if (((_a = source.name) === null || _a === void 0 ? void 0 : _a.toLowerCase()) === 'PubMed'.toLowerCase()) {
-        return `${source.id}&nbsp;(<a href='${source.url}' style="color:#FFF" target='_blank'>${source.name}</a>&nbsp;<a href='${source.alternativeUrl}' style="color:#FFF" target='_blank'>EuropePMC</a>)`;
-    }
-    const sourceLink = `&nbsp;<a href='${source.url}' style="color:#FFF" target='_blank'>${source.id}</a>`;
-    if (source.name) {
-        // Temporary until we get the expected value as 'PeptideAtlas' instead of 'HppPeptideAtlas'
-        if (source.name.startsWith('Hpp')) {
-            return `${sourceLink}&nbsp;(${source.name.slice(3)})`;
-        }
-        return `${sourceLink}&nbsp;(${source.name})`;
-    }
-    return sourceLink;
-};
-export const getEvidenceFromCodes = (evidenceList) => {
-    if (!evidenceList)
-        return ``;
-    return `
-        <ul>${evidenceList
-        .map((ev) => {
-        const ecoMatch = ecoMap.find((eco) => eco.name === ev.code);
-        if (!ecoMatch)
-            return ``;
-        return `<li title='${ecoMatch.description}' style="padding: .25rem 0">${ecoMatch.shortDescription}:&nbsp;${ev.source ? formatSource(ev.source) : ''}</li>`;
-    })
-        .join('')}</ul>
-      `;
-};
-export const formatXrefs = (xrefs) => {
-    return `<ul>${xrefs
-        .map((xref) => `<li style="padding: .25rem 0">${xref.name} ${xref.url
-        ? `<a href="${xref.url}" style="color:#FFF" target="_blank">${xref.id}</a>`
-        : `${xref.name} ${xref.id}`}</li>`)
-        .join('')}</ul>`;
-};
-const getPTMEvidence = (ptms) => {
-    if (!ptms)
-        return ``;
-    const ids = ptms.flatMap(({ dbReferences }) => dbReferences.map((ref) => ref.id));
-    const uniqueIds = [...new Set(ids.flat())];
-    // Urls in the payload are not relevant. For 'Glue project' dataset, Dataset ID and publication reference is hardcoded. Need to be checked in 2024 if it still exists in the payload
-    const proteomexchange = 'https://proteomecentral.proteomexchange.org/dataset/';
-    return `
-    <ul>${uniqueIds
-        .map((id) => {
-        const datasetID = id === 'Glue project' ? 'PXD012174' : id;
-        return `<li title='${datasetID}' style="padding: .25rem 0">${datasetID}&nbsp;(<a href="${proteomexchange}${datasetID}" style="color:#FFF" target="_blank">ProteomeXchange</a>${id === 'Glue project'
-            ? `)</li><li title="publication" style="padding: .25rem 0">Publication:&nbsp;31819260&nbsp;(<a href="https://pubmed.ncbi.nlm.nih.gov/31819260" style="color:#FFF" target="_blank">PubMed</a>)</li>`
-            : `&nbsp;<a href="http://www.peptideatlas.org/builds/rice/phospho/" style="color:#FFF" target="_blank">PeptideAtlas</a>)</li>`}`;
-    })
-        .join('')}</ul>
-  `;
-};
-const formatPTMPeptidoform = (peptide, ptms) => {
-    if (!ptms)
-        return ``;
-    const modificationValues = ptms.map((ptm) => ({
-        name: ptm.name,
-        position: ptm.position,
-    }));
-    let peptidoform = '';
-    let lastModPosition = 0;
-    modificationValues.forEach((p) => {
-        peptidoform = `${peptidoform}${peptide.slice(lastModPosition, p.position)}[${p.name}]`;
-        lastModPosition = p.position;
-    });
-    // Add last remaining part of the peptide if any
-    peptidoform = `${peptidoform}${peptide.slice(lastModPosition)}`;
-    return `<p>${peptidoform}</p>`;
-};
-// At the moment, there is only phospho data. In future we may have more, the below AA sites have to be updated to accomodate more.
-const AAPhosphoSites = {
-    A: 'alanine',
-    S: 'serine',
-    T: 'threonine',
-    Y: 'tyrosine',
-};
-const findModifiedResidueName = (feature, ptm) => {
-    const { peptide, begin: peptideStart } = feature;
-    const proteinLocation = Number(peptideStart) + ptm.position - 1;
-    const modifiedResidue = peptide.charAt(ptm.position - 1); // CharAt index starts from 0
-    return `${proteinLocation} phospho${AAPhosphoSites[modifiedResidue]}`;
-};
-const formatTooltip = (feature) => {
-    const evidenceHTML = feature.type === 'PROTEOMICS_PTM'
-        ? getPTMEvidence(feature.ptms)
-        : getEvidenceFromCodes(feature.evidences);
-    const ptms = feature.type === 'PROTEOMICS_PTM' &&
-        feature.ptms.map((ptm) => findModifiedResidueName(feature, ptm));
-    const dataset = feature.type === 'PROTEOMICS_PTM' &&
-        feature.ptms.flatMap(({ dbReferences }) => dbReferences.map((ref) => ref.id));
-    let { description } = feature;
-    if (feature.type === 'BINDING' || feature.type === 'Binding site') {
-        let bindingDescription = '';
-        if (feature.ligandPart) {
-            bindingDescription += `${feature.ligandPart.name} of `;
-        }
-        if (feature.ligand) {
-            bindingDescription += feature.ligand.name;
-        }
-        if (feature.description) {
-            bindingDescription += `; ${feature.description}`;
-        }
-        description = bindingDescription;
-    }
-    try {
-        return `
-        ${description ? `<h5>Description</h5><p>${description}</p>` : ``}
-        ${feature.matchScore
-            ? `<h5>Match score</h5><p>${feature.matchScore}%</p>`
-            : ``}
-        ${feature.ftId ? `<h5>Feature ID</h5><p>${feature.ftId}</p>` : ``}
-        ${feature.alternativeSequence
-            ? `<h5>Alternative sequence</h5><p>${feature.alternativeSequence}</p>`
-            : ``}
-        ${ptms
-            ? `<h5 data-article-id="ptm_processing_section">PTMs</h5><ul>${ptms
-                .map((item) => `<li>${item}</li>`)
-                .join('')}</ul>
-              `
-            : ''}
-        ${feature.peptide && feature.type === 'PROTEOMICS_PTM'
-            ? `<h5 data-article-id="mod_res_large_scale#what-is-the-goldsilverbronze-criterion">Peptidoform</h5><p>${formatPTMPeptidoform(feature.peptide, feature.ptms)}</p>`
-            : ``}
-        ${feature.peptide && feature.type !== 'PROTEOMICS_PTM'
-            ? `<h5>Peptide</h5><p>${feature.peptide}</p>`
-            : ``} 
-        ${feature.xrefs
-            ? `<h5>Cross-references</h5>${formatXrefs(feature.xrefs)}`
-            : ``}
-        ${evidenceHTML ? `<h5>Evidence</h5>${evidenceHTML}` : ``}
-        ${feature.ptms && dataset && !dataset.includes('Glue project')
-            ? `<hr /><h5 data-article-id="mod_res_large_scale#what-is-the-goldsilverbronze-criterion">PTM statistical attributes</h5><ul>${feature.ptms
-                .map((ptm) => ptm.dbReferences
-                .map((ref) => `<li><b>${ref.id}</b></li>
-                        <li style="text-indent: 1em"><b>${findModifiedResidueName(feature, ptm)}</b></li>
-                        <li style="text-indent: 2em">PubMed ID: <a href="https://europepmc.org/article/MED/${ref.properties['Pubmed ID']}" style="color:#FFF" target="_blank">
-                        ${ref.properties['Pubmed ID']}</a>
-                        </li>
-                        <li style="text-indent: 2em"><span data-article-id="mod_res_large_scale#confidence-score">Confidence score</span>: ${ref.properties['Confidence score']}</li>
-                        <li style="text-indent: 2em">Universal Spectrum Id: 
-                        <a href="http://proteomecentral.proteomexchange.org/usi/?usi=${ref.properties['Universal Spectrum Id']}" style="color:#FFF" target="_blank">View on ProteomeXchange</a>
-                        </li>
-                        <li style="text-indent: 2em">PSM Count (0.05 gFLR): ${ref.properties['PSM Count (0.05 gFLR)']}</li>
-                        <li style="text-indent: 2em">Final site probability: ${ref.properties['Final site probability']}</li>
-                        `)
-                .join(''))
-                .join('')}</ul>`
-            : ''}
-          `;
-    }
-    catch (error) {
-        console.error(error);
-        return '';
-    }
-};
-export default formatTooltip;
-//# sourceMappingURL=featureTooltip.js.map

package/dist/es/tooltips/featureTooltip.js.map

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package/dist/es/tooltips/structureTooltip.js

@@ -1,15 +0,0 @@
-const getStructuresHTML = (structureList) => {
-    return `<ul>
-              ${structureList
-        .map((structure) => `<li style="margin: 0.25rem 0"><a style="color:#FFF" href='${structure.source.url}' target='_blank'>
-              ${structure.source.id}
-          </a> (${structure.start}-${structure.end})</li>`)
-        .join('')}
-          </ul>`;
-};
-const formatTooltip = (feature) => {
-    const structuresHTML = getStructuresHTML(feature.structures);
-    return `${structuresHTML ? `<h5>Structures</h5>${structuresHTML}` : ``}`;
-};
-export default formatTooltip;
-//# sourceMappingURL=structureTooltip.js.map

package/dist/es/tooltips/structureTooltip.js.map

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package/dist/es/tooltips/variationTooltip.js

@@ -1,82 +0,0 @@
-import groupBy from 'lodash-es/groupBy';
-import { formatXrefs, getEvidenceFromCodes } from './featureTooltip';
-const getDiseaseAssociations = (associations) => associations === null || associations === void 0 ? void 0 : associations.map((association) => `
-              <h4>Disease association</h4><p>${association.name}</p>
-              ${association.description
-    ? `<>${association.description}</p>`
-    : ''}
-              ${association.dbReferences
-    ? `<h5>Cross-references</h5>${formatXrefs(association.dbReferences)}`
-    : ''}
-              ${getEvidenceFromCodes(association.evidences)}
-          `).join('');
-const getDescriptions = (descriptions) => `<hr/><h5>Description</h5>${descriptions
-    .map((description) => `<p>${description.value}</p>`)
-    .join('')}
-  `;
-const getPopulationFrequencies = (popFrequencies) => `<hr/><h5>Population frequencies</h5>${popFrequencies
-    .map((freq) => `<p>${freq.frequency} - ${freq.populationName} (${freq.source})</p>`)
-    .join('')}`;
-const getEnsemblCovidLinks = (variant) => {
-    const shouldGenerateLink = variant.locations.some((location) => location.source === 'EnsemblViruses');
-    if (shouldGenerateLink) {
-        const xref = variant.xrefs.find((xref) => xref.name === 'ENA');
-        return xref.id
-            ? `<h5>Ensembl COVID-19</h5>
-          <p>
-          <a href="https://covid-19.ensembl.org/Sars_cov_2/Variation/Explore?v=${xref.id}" target="_blank" rel="noopener noreferrer">${xref.id}</a>
-        </p>`
-            : '';
-    }
-    return '';
-};
-const getPredictions = (predictions) => {
-    const groupedPredictions = groupBy(predictions, 'predAlgorithmNameType');
-    const counts = Object.keys(groupedPredictions).map((key) => {
-        const valueGroups = groupBy(groupedPredictions[key], 'predictionValType');
-        return {
-            algorithm: key,
-            values: Object.keys(valueGroups).map((valKey) => ({
-                name: valKey,
-                count: valueGroups[valKey].length,
-            })),
-        };
-    });
-    return counts
-        .map((countItem) => `<h6>${countItem.algorithm}</h6><ul class="no-bullet">${countItem.values
-        .map((countValue) => `<li>${countValue.name}</li>`)
-        .join('')}</ul>`)
-        .join('');
-};
-const formatTooltip = (variant) => {
-    var _a;
-    return `
-                <h5>Variant</h5><p>${variant.wildType} > ${variant.alternativeSequence || ''}</p>
-                ${variant.populationFrequencies
-        ? getPopulationFrequencies(variant.populationFrequencies)
-        : ''}
-                ${variant.consequenceType
-        ? `<h5>Consequence</h5><p>${variant.consequenceType}</p>`
-        : ``}
-                ${variant.somaticStatus
-        ? `<h5>Somatic</h5><p>${variant.somaticStatus === 0 ? 'No' : 'Yes'}</p>`
-        : ``}
-                ${((_a = variant.genomicLocation) === null || _a === void 0 ? void 0 : _a.length)
-        ? `<h5>Location</h5><p>${variant.genomicLocation.join(', ')}</p>`
-        : ``}
-                ${variant.ftId
-        ? `<h5>Feature ID</h5><p>${variant.ftId}</p>`
-        : ``}
-                ${variant.descriptions
-        ? getDescriptions(variant.descriptions)
-        : ''}
-                ${variant.association
-        ? getDiseaseAssociations(variant.association)
-        : ''}
-                ${variant.predictions ? getPredictions(variant.predictions) : ''}
-                ${getEnsemblCovidLinks(variant)}
-                
-        `;
-};
-export default formatTooltip;
-//# sourceMappingURL=variationTooltip.js.map

package/dist/es/tooltips/variationTooltip.js.map

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package/dist/es/utils.js

@@ -1,28 +0,0 @@
-export const renameProperties = (features) => features.map((ft) => ({
-    ...ft,
-    start: ft.begin || undefined,
-}));
-export const loadComponent = (name, elementConstructor) => {
-    if (!customElements.get(name)) {
-        customElements.define(name, elementConstructor);
-    }
-};
-// Returns an object of the form url => payload json
-// getUrl optional function modifies url string
-export const fetchAll = async (urls, getUrl = null) => Object.fromEntries(await Promise.all(urls.map(async (url) => {
-    try {
-        const response = await fetch(getUrl ? getUrl(url) : url);
-        if (!response.ok) {
-            // TODO handle this better based on error code
-            // Fail silently for now
-            console.warn(`HTTP error status: ${response.status} at ${url}`);
-            return [url, null];
-        }
-        return [url, await response.json()];
-    }
-    catch (error) {
-        console.warn(`Failed to fetch or parse JSON from ${url}:`, error);
-        return [url, null]; // or handle error data as needed
-    }
-})));
-//# sourceMappingURL=utils.js.map

package/dist/es/utils.js.map

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