@datagrok/bio 2.15.3 → 2.15.5
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/CHANGELOG.md +28 -0
- package/detectors.js +3 -1
- package/dist/284.js +1 -1
- package/dist/284.js.map +1 -1
- package/dist/455.js +2 -0
- package/dist/455.js.map +1 -0
- package/dist/980.js +1 -1
- package/dist/980.js.map +1 -1
- package/dist/package-test.js +3 -3
- package/dist/package-test.js.map +1 -1
- package/dist/package.js +2 -2
- package/dist/package.js.map +1 -1
- package/files/tests/to-atomic-level-msa-fasta-output.csv +683 -683
- package/files/tests/to-atomic-level-msa-separator-output.csv +104 -104
- package/package.json +9 -9
- package/src/analysis/sequence-activity-cliffs.ts +3 -1
- package/src/calculations/monomerLevelMols.ts +2 -1
- package/src/demo/bio03-atomic-level.ts +1 -1
- package/src/package.ts +151 -38
- package/src/tests/WebLogo-positions-test.ts +1 -1
- package/src/tests/bio-tests.ts +1 -1
- package/src/tests/detectors-tests.ts +10 -10
- package/src/tests/monomer-libraries-tests.ts +1 -1
- package/src/tests/seq-handler-splitted-tests.ts +6 -2
- package/src/tests/splitters-test.ts +6 -6
- package/src/tests/to-atomic-level-tests.ts +21 -14
- package/src/tests/to-atomic-level-ui-tests.ts +75 -35
- package/src/tests/utils.ts +2 -2
- package/src/utils/cell-renderer-custom.ts +62 -0
- package/src/utils/cell-renderer.ts +58 -126
- package/src/utils/cyclized.ts +28 -14
- package/src/utils/dimerized.ts +0 -2
- package/src/utils/helm-to-molfile/converter/converter.ts +75 -54
- package/src/utils/helm-to-molfile/converter/monomer-wrapper.ts +2 -2
- package/src/utils/helm-to-molfile/converter/polymer.ts +23 -16
- package/src/utils/helm-to-molfile/converter/types.ts +0 -10
- package/src/utils/helm-to-molfile/utils.ts +10 -7
- package/src/utils/monomer-lib/lib-manager.ts +2 -2
- package/src/utils/monomer-lib/monomer-colors.ts +68 -0
- package/src/utils/monomer-lib/monomer-lib-base.ts +165 -0
- package/src/utils/monomer-lib/monomer-lib.ts +19 -68
- package/src/utils/monomer-lib/web-editor-monomer-dummy.ts +121 -0
- package/src/utils/monomer-lib/web-editor-monomer-of-library.ts +102 -0
- package/src/utils/save-as-fasta.ts +1 -1
- package/src/utils/seq-helper/seq-helper.ts +20 -49
- package/src/utils/sequence-to-mol.ts +24 -28
- package/src/viewers/web-logo-viewer.ts +2 -1
- package/src/widgets/composition-analysis-widget.ts +4 -3
- package/src/widgets/representations.ts +8 -10
- package/dist/248.js +0 -2
- package/dist/248.js.map +0 -1
- package/src/utils/cell-renderer-consts.ts +0 -31
package/CHANGELOG.md
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@@ -1,5 +1,33 @@
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# Bio changelog
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## 2.15.5 (2024-09-25)
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### New features
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* Add custom notation, fix tests
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* Add overriding monomer library for toAtomicLevel
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### Bug fixes
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* Fix skipping tests depending on new Helm
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## 2.15.4 (2024-09-24)
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### New features
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* Add monomer hover handling for substruct
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* Add highlight param for toAtomicLevel
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* Add HelmHelper parse and removeGaps methods
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* Add naturalMonomerColors for monomers of MonomerLib
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* Add MonomerLib.getWebEditorMonomer (for color)
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* Add function Identity for Add new Column
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### Bug fixes
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* Fix toAtomicLevel for sequences with gaps
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* Fix ISeqSplitted remove .canonicals and .originals
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* Fix toAtomicLevel tests for linear with gaps
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## 2.15.3 (2024-09-22)
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Add monomer background coloring
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package/detectors.js
CHANGED
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@@ -183,6 +183,7 @@ class BioPackageDetectors extends DG.Package {
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// col.setTag(SeqHandler.TAGS.alphabetSize, alphabetSize.toString());
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col.setTag(SeqHandler.TAGS.alphabetIsMultichar, alphabetIsMultichar ? 'true' : 'false');
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col.setTag(DG.TAGS.CELL_RENDERER, 'helm');
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return DG.SEMTYPE.MACROMOLECULE;
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}
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@@ -262,6 +263,7 @@ class BioPackageDetectors extends DG.Package {
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const alphabetIsMultichar = Object.keys(stats.freq).some((m) => m.length > 1);
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col.setTag(SeqHandler.TAGS.alphabetIsMultichar, alphabetIsMultichar ? 'true' : 'false');
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}
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col.setTag(DG.TAGS.CELL_RENDERER, 'sequence');
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return DG.SEMTYPE.MACROMOLECULE;
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} else {
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const stats = this.getStats(categoriesSample, seqMinLength, splitter);
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}
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refineSeqSplitter(col, stats, separator).then(() => { });
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col.setTag(DG.TAGS.CELL_RENDERER, 'sequence');
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return DG.SEMTYPE.MACROMOLECULE;
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}
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} catch (err) {
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