Skip to content

Commit

Permalink
More PTM related changes and package updates
Browse files Browse the repository at this point in the history
  • Loading branch information
@Swaathik
Swaathik committed Feb 2, 2023
1 parent 09d6b60 commit bef1b56
Show file tree
Hide file tree
Showing 4 changed files with 64 additions and 56 deletions.
16 changes: 8 additions & 8 deletions package.json
View file
Original file line number Diff line number Diff line change
Expand Up @@ -30,21 +30,21 @@
"file-saver": "^2.0.2",
"lit-element": "^2.2.0",
"protvista-datatable": "3.8.4",
"protvista-feature-adapter": "3.8.8",
"protvista-feature-adapter": "3.8.9",
"protvista-filter": "3.8.4",
"protvista-interpro-adapter": "3.8.4",
"protvista-interpro-track": "3.8.8",
"protvista-interpro-track": "3.8.9",
"protvista-manager": "3.8.4",
"protvista-navigation": "3.8.4",
"protvista-proteomics-adapter": "3.8.8",
"protvista-proteomics-adapter": "3.8.9",
"protvista-sequence": "3.8.4",
"protvista-structure": "3.8.4",
"protvista-structure-adapter": "3.8.8",
"protvista-structure-adapter": "3.8.9",
"protvista-tooltip": "3.8.4",
"protvista-track": "3.8.8",
"protvista-variation": "3.8.8",
"protvista-variation-adapter": "3.8.8",
"protvista-variation-graph": "3.8.8",
"protvista-track": "3.8.9",
"protvista-variation": "3.8.9",
"protvista-variation-adapter": "3.8.9",
"protvista-variation-graph": "3.8.9",
"protvista-zoomable": "3.8.4",
"timing-functions": "^2.0.1",
"url-join": "^4.0.1"
Expand Down
2 changes: 2 additions & 0 deletions public/index.html
View file
Original file line number Diff line number Diff line change
Expand Up @@ -29,6 +29,8 @@
<!-- Not all features -->
<!-- <protvista-uniprot accession="P41892"></protvista-uniprot> -->
<protvista-uniprot accession="P05067"></protvista-uniprot>
<!-- <protvista-uniprot accession="Q653S1"></protvista-uniprot> -->
<!-- <protvista-uniprot accession="B9FXV5"></protvista-uniprot> -->
<!-- <protvista-uniprot-structure
accession="P05067"
></protvista-uniprot-structure> -->
Expand Down
22 changes: 14 additions & 8 deletions src/protvista-ptm-exchange.ts
View file
Original file line number Diff line number Diff line change
Expand Up @@ -82,16 +82,16 @@ const convertPtmExchangePtms = (
];
const confidenceScores = new Set(
ptms.flatMap(({ dbReferences }) =>
dbReferences.map(({ properties }) => properties['Confidence score'])
dbReferences?.map(({ properties }) => properties['Confidence score'])
)
);
let confidenceScore: string;

if (!confidenceScores.size) {
console.error('PTMeXchange PTM has no confidence score');
console.log('PTM has no confidence score');
} else if (confidenceScores.size > 1) {
console.error(
`PTMeXchange PTM has a mixture of confidence scores: ${Array.from(
`PTM has a mixture of confidence scores: ${Array.from(
confidenceScores
)}`
);
Expand All @@ -101,15 +101,21 @@ const convertPtmExchangePtms = (

const tooltip = `
<h5>Description</h5><p>${phosphorylate(aa)}</p>
${confidenceScore ? `<h5>Confidence Score</h5><p>${confidenceScore}</p>` : ''}
${confidenceScore ? `<h5 data-article-id="mod_res_large_scale#confidence-score">Confidence Score</h5><p>${confidenceScore}</p>` : ''}
${
evidences
? `<h5>Evidence</h5><ul>${evidences
.map(
(id) =>
`<li title='${id}' style="padding: .25rem 0">${id}&nbsp;
${id.startsWith('PXD') ? `(<a href="https://www.ebi.ac.uk/pride/archive/projects/${id}" style="color:#FFF" target="_blank">PRIDE</a>)` : ''}
</li>`
(id) => {
const datasetID = id === 'Glue project' ? 'PXD012174' : id;
return `<li title='${datasetID}' style="padding: .25rem 0">${datasetID}&nbsp;
(<a href="https://www.ebi.ac.uk/pride/archive/projects/${id}" style="color:#FFF" target="_blank">PRIDE</a>)
</li>
${id === 'Glue project' ?
`<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>`
: ''}
`
}
)
.join('')}</ul>`
: ''
Expand Down
80 changes: 40 additions & 40 deletions yarn.lock
View file
Original file line number Diff line number Diff line change
Expand Up @@ -6915,12 +6915,12 @@ [email protected]:
type-fest "^1.2.1"
uuid "^8.3.1"

[email protected].8, protvista-feature-adapter@^3.8.8:
version "3.8.8"
resolved "https://registry.yarnpkg.com/protvista-feature-adapter/-/protvista-feature-adapter-3.8.8.tgz#c7805e0a8df39f05c13783b7f8493d005ad1337f"
integrity sha512-pE7649ti4vVczpTq8axWR7qQhYTxkFPu2Z2xZVpMrzSIM6Ij0nBDmlqmvXDdf6u9+r6xgd/azLPSew5EXG5MrQ==
[email protected].9, protvista-feature-adapter@^3.8.9:
version "3.8.9"
resolved "https://registry.yarnpkg.com/protvista-feature-adapter/-/protvista-feature-adapter-3.8.9.tgz#b7da32f1fc77c290ff7103350fcdd1aa740f5a22"
integrity sha512-2C3KhsZ+XEKJ4y83z69zxOJ2KVWrXEHf6EmVbK4KHpyYKWXpuV5BJJtoUGxuzoMNHRn8ex97QbUpeA3XJVkdiQ==
dependencies:
protvista-track "^3.8.8"
protvista-track "^3.8.9"
uuid "^8.3.1"

[email protected]:
Expand All @@ -6936,13 +6936,13 @@ [email protected]:
resolved "https://registry.yarnpkg.com/protvista-interpro-adapter/-/protvista-interpro-adapter-3.8.4.tgz#99743941df0630c03c45ff81fd9ee944a06e93e7"
integrity sha512-gPYgKnYQP4ob2aWHKYjkyQBHVIwBRb27Rstm+cFqdulHpzyszZSzkRIwa81TAogKhVMTVMDR9onqleGBfBriMw==

[email protected].8:
version "3.8.8"
resolved "https://registry.yarnpkg.com/protvista-interpro-track/-/protvista-interpro-track-3.8.8.tgz#65f3b8322be34ca6ca37933c2b7b22898cdf2e06"
integrity sha512-INbP209B18/aE32d5JMn5oNB6fTmV7aVQkUOtZFqbrer421GJ1gnAM+THXcrTLm7V3k8hbdscd6d9Cr90BeN1A==
[email protected].9:
version "3.8.9"
resolved "https://registry.yarnpkg.com/protvista-interpro-track/-/protvista-interpro-track-3.8.9.tgz#95cb988129d3118abba81b3fe6cde407905fcce2"
integrity sha512-QQI/du2oOFtd3jh5S5lwyW/2W7+XYScmZ1clIuK2d+qJKk2aRPdKAsOXc+Ibr2MnKBgG99RJI7sk5yZDwNnf2w==
dependencies:
lodash-es "^4.17.11"
protvista-track "^3.8.8"
protvista-track "^3.8.9"

[email protected]:
version "3.8.4"
Expand All @@ -6959,12 +6959,12 @@ [email protected]:
lodash-es "^4.17.11"
protvista-utils "^3.8.4"

[email protected].8:
version "3.8.8"
resolved "https://registry.yarnpkg.com/protvista-proteomics-adapter/-/protvista-proteomics-adapter-3.8.8.tgz#cdcdf654b409d7afbe7271b32b54d90a1a520d62"
integrity sha512-JHdnC5orGLQAWxIRycoNPRbfNKBqVaFa94XGhDkcXJ5a24onDIxPxzVafC1/MGF0X97qCQ8bsR0VbA2BtD/qYw==
[email protected].9:
version "3.8.9"
resolved "https://registry.yarnpkg.com/protvista-proteomics-adapter/-/protvista-proteomics-adapter-3.8.9.tgz#fab2dcaac314fba2ff61ed2a9ec90ccc10027fec"
integrity sha512-uiq1mr4b7peVz+PHYdFUYe2OyI4SmmySOeEupShpP5uVfOIadgnfe4fCkBfaxXvisO+FfCgmYTdZHQXY1XUN4Q==
dependencies:
protvista-feature-adapter "^3.8.8"
protvista-feature-adapter "^3.8.9"
uuid "^8.3.1"

[email protected]:
Expand All @@ -6975,12 +6975,12 @@ [email protected]:
lodash-es "^4.17.11"
protvista-zoomable "^3.8.4"

[email protected].8:
version "3.8.8"
resolved "https://registry.yarnpkg.com/protvista-structure-adapter/-/protvista-structure-adapter-3.8.8.tgz#d056b23b58c8d110b660fcfe386b2eff3a802476"
integrity sha512-ORmAKt7oTvwCjOQX+ZNp/cO5ptuzC6msqtKCrjmViF1ClfeHJ6OOHRBO3Ef5kH9PNCGt1mklaB+0Kb5UfDpLKg==
[email protected].9:
version "3.8.9"
resolved "https://registry.yarnpkg.com/protvista-structure-adapter/-/protvista-structure-adapter-3.8.9.tgz#b8abbfa9cc729fa93ed16bc4080f7433e8a6c957"
integrity sha512-T6nrqtsptOb8t7nWDaggI0m3MqdXKEhpGHGqC1+2AErAg7WNkBrSU5AMvF6EWYZv6Dt536wDwHw1U2367sd39Q==
dependencies:
protvista-feature-adapter "^3.8.8"
protvista-feature-adapter "^3.8.9"
uuid "^8.3.1"

[email protected]:
Expand All @@ -7001,10 +7001,10 @@ [email protected]:
lit-element "^2.4.0"
lodash-es "^4.17.11"

[email protected].8, protvista-track@^3.8.8:
version "3.8.8"
resolved "https://registry.yarnpkg.com/protvista-track/-/protvista-track-3.8.8.tgz#0d8d41386bb9b14b631d21bfb1328e793d09982c"
integrity sha512-1UaQQhKTQ8fBAs+B51ZCxmfqV8jvKvy5Tu0ESqNupdHHaJC1fya+s6c2QzghERA9YtafVqm0uazeNGYc36wuVw==
[email protected].9, protvista-track@^3.8.9:
version "3.8.9"
resolved "https://registry.yarnpkg.com/protvista-track/-/protvista-track-3.8.9.tgz#1d5441e1114b463e6eabf9e03da41bf6890a79c7"
integrity sha512-Cx8a/BKIaw0IySOU8M5ahfRaTJwVefV4VQGacI1ZfCP9aKR40Ax5eqWsIwoPpjNZzH0wziVKHeF0ZqfcphR0HA==
dependencies:
lodash-es "^4.17.11"
protvista-zoomable "^3.8.4"
Expand All @@ -7014,32 +7014,32 @@ protvista-utils@^3.8.4:
resolved "https://registry.yarnpkg.com/protvista-utils/-/protvista-utils-3.8.4.tgz#04dba3099854389f8f371c44e9cece6ec330329d"
integrity sha512-FRrGMjpwGl5hCIfzl7jHHhRjsbZiQd/1rx2cgKNO016ERTU9KJE4zzSuBGy+mrCLoKjrqSlJCGwrqbawOshhWw==

[email protected].8:
version "3.8.8"
resolved "https://registry.yarnpkg.com/protvista-variation-adapter/-/protvista-variation-adapter-3.8.8.tgz#341629320fd7c827324b2bc738c6fc94c182eb10"
integrity sha512-J0Ml6++Z5yJmTXhmwunEyHpsHkNZm5nkLqn0jBM6qv8eqMsa9aDkqVaq0Nz+AV4Ng728gcYPWVaB5Weq8eX35Q==
[email protected].9:
version "3.8.9"
resolved "https://registry.yarnpkg.com/protvista-variation-adapter/-/protvista-variation-adapter-3.8.9.tgz#cc0031cf6e7847c4c7046662cc35ca7332566539"
integrity sha512-XIWEUntxWzOrk9YdFepX112ftfjROnlh/4Ts77ZHZq3BAD1m4iAqcUDb2nQK9fkltp/F2QRx6rtFkmf3ArfeJw==
dependencies:
d3-scale "^3.2.3"
data-loader "^3.8.4"
lodash-es "^4.17.11"
protvista-feature-adapter "^3.8.8"
protvista-variation "^3.8.8"
protvista-feature-adapter "^3.8.9"
protvista-variation "^3.8.9"
uuid "^8.3.1"

[email protected].8:
version "3.8.8"
resolved "https://registry.yarnpkg.com/protvista-variation-graph/-/protvista-variation-graph-3.8.8.tgz#9f41237a09a73f697fa029b0ec68f7a19e9f568b"
integrity sha512-FGVAWdwVSqPScRqSMxH4+cmkeZSksfpV9AKbmnamCXB+vaFQC9NQ0G/2hJsRV026wIJk0S6hu2PYg6E9P74isQ==
[email protected].9:
version "3.8.9"
resolved "https://registry.yarnpkg.com/protvista-variation-graph/-/protvista-variation-graph-3.8.9.tgz#5ead64673087e7a98ab849025855329f09e9b026"
integrity sha512-jIWXNq9qXwtpNewToAsX34H4LFm/b7StDnf82h9WUy7O6HyRb0hsNdssoGNaRLjVG8fOcfOCZVQuh8xBeRVF2w==
dependencies:
protvista-track "^3.8.8"
protvista-track "^3.8.9"

[email protected].8, protvista-variation@^3.8.8:
version "3.8.8"
resolved "https://registry.yarnpkg.com/protvista-variation/-/protvista-variation-3.8.8.tgz#0caaf40213c40f9adfcd2216d5a0516bec5f9612"
integrity sha512-N0ZQvNFfjvbVEj9izTogP39OvTo6qf4tScOwuEA5M85CKBCqXwSDdNboXCyXEijqwCas+dSYd+Nd7peh/TFrjw==
[email protected].9, protvista-variation@^3.8.9:
version "3.8.9"
resolved "https://registry.yarnpkg.com/protvista-variation/-/protvista-variation-3.8.9.tgz#3d39f645ea2d697915477bbe9fa549247034b0db"
integrity sha512-87bZi0NK3kIJNyP6sb8BTf/wUqAGOy6/koW5o/dqdEeLsfz1NAe0pha4Ne/KMlMZqGn1UfbBQZTQqHRO6mepoA==
dependencies:
lodash-es "^4.17.11"
protvista-track "^3.8.8"
protvista-track "^3.8.9"

[email protected], protvista-zoomable@^3.8.4:
version "3.8.4"
Expand Down

0 comments on commit bef1b56

Please sign in to comment.