@sjcrh/proteinpaint-client 2.207.1 → 2.208.0

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.
Files changed (919) hide show
  1. package/dist/2dmaf-PN5YS362.js +1367 -0
  2. package/dist/AggMatrixInput-NJHU4FU2.js +406 -0
  3. package/dist/AggMatrixInput-NJHU4FU2.js.map +7 -0
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  6. package/dist/BoxPlot-ZIVA55SK.js +1211 -0
  7. package/dist/CorrelationVolcano-33I4FC44.js +617 -0
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  9. package/dist/Cuminc-WKY35UGV.js +1219 -0
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  15. package/dist/Disco-OZY5GW2Z.js +3389 -0
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  173. package/dist/dictionary-WSDD6TFI.js +113 -0
  174. package/dist/dnaMethylation-3IM4OACZ.js +33 -0
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  835. /package/dist/{matrix.unit.spec-DROPHFTM.js.map → matrix.unit.spec-7A6ZFRXI.js.map} +0 -0
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  852. /package/dist/{polar2-GVFQNSLK.js.map → polar2-LA4MSRRN.js.map} +0 -0
  853. /package/dist/{profileForms-Z22CJXI4.js.map → profileForms-BJRNB2ZF.js.map} +0 -0
  854. /package/dist/{profilePlot-IVQZBSID.js.map → profilePlot-DDO53C4T.js.map} +0 -0
  855. /package/dist/{proteinView-AUK634AU.js.map → proteinView-NFUR42XQ.js.map} +0 -0
  856. /package/dist/{proteomeCohortCompare-7G2F35H5.js.map → proteomeCohortCompare-OZVF3X66.js.map} +0 -0
  857. /package/dist/{pseudobulk-QTCUSH5I.js.map → pseudobulk-UVT5G2VL.js.map} +0 -0
  858. /package/dist/{qualitative-7ST7SSBT.js.map → qualitative-X3VXNC7X.js.map} +0 -0
  859. /package/dist/{radar2-CEE6SNBS.js.map → radar2-RTVUJ3AN.js.map} +0 -0
  860. /package/dist/{radarFacility2-OSKDYIK7.js.map → radarFacility2-ZGLZ5AKM.js.map} +0 -0
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  862. /package/dist/{render-MAD3WMVD.js.map → render-LR5BOYW6.js.map} +0 -0
  863. /package/dist/{report-6JXJVSEB.js.map → report-37W5OXUM.js.map} +0 -0
  864. /package/dist/{sampleView-SG3QYZKQ.js.map → sampleView-BDC2WPH7.js.map} +0 -0
  865. /package/dist/{samplelst-R765UFP6.js.map → samplelst-V2EIVZC5.js.map} +0 -0
  866. /package/dist/{samplematrix-EBJYE5SM.js.map → samplematrix-XOSKILUL.js.map} +0 -0
  867. /package/dist/{sc-7ZXPFDHD.js.map → sc-ZVZPWQY7.js.map} +0 -0
  868. /package/dist/{scatter-3GUL4KF3.js.map → scatter-2ZE5MCYH.js.map} +0 -0
  869. /package/dist/{selectGenomeWithTklst-K4YXGJYG.js.map → selectGenomeWithTklst-EF7WYEAJ.js.map} +0 -0
  870. /package/dist/{singleCellCellType-TU5VTPLP.js.map → singleCellCellType-TKCGC3G3.js.map} +0 -0
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  872. /package/dist/{singleCellGeneExpression-3IL52QDK.js.map → singleCellGeneExpression-I2INGXGI.js.map} +0 -0
  873. /package/dist/{singleCellGeneExpression.unit.spec-WXC4C37T.js.map → singleCellGeneExpression.unit.spec-KL77FSHZ.js.map} +0 -0
  874. /package/dist/{singleCellPlot-XG3HZS7I.js.map → singleCellNumericValue-2X5NCEHL.js.map} +0 -0
  875. /package/dist/{snp-RMZRB426.js.map → singleCellPlot-Q6INE54V.js.map} +0 -0
  876. /package/dist/{singlecell-BRF2HAV2.js.map → singlecell-5N2P5ZAT.js.map} +0 -0
  877. /package/dist/{singlecell-KVCJF2HI.js.map → singlecell-NPSWMNI3.js.map} +0 -0
  878. /package/dist/{ssGSEA-7RKWYZKX.js.map → snp-2WPJYPDE.js.map} +0 -0
  879. /package/dist/{snp.unit.spec-JF6KR2NT.js.map → snp.unit.spec-PPWIIOX6.js.map} +0 -0
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  881. /package/dist/{spliceevent.a53ss.diagram-OSZZ2CF2.js.map → spliceevent.a53ss.diagram-APCF4LV5.js.map} +0 -0
  882. /package/dist/{spliceevent.exonskip.diagram-AMA2D2OL.js.map → spliceevent.exonskip.diagram-TT5JGBSC.js.map} +0 -0
  883. /package/dist/{spliceevent.noeventdiagram-RKTUXH5D.js.map → spliceevent.noeventdiagram-CPXQSX3Z.js.map} +0 -0
  884. /package/dist/{summarizeMutationDiagnosis-GCL4SRON.js.map → ssGSEA-FSX6P7HA.js.map} +0 -0
  885. /package/dist/{ssGSEA.unit.spec-XLCZHH7S.js.map → ssGSEA.unit.spec-TXYT665R.js.map} +0 -0
  886. /package/dist/{stattable-NDYUCLVZ.js.map → stattable-BD64SFYV.js.map} +0 -0
  887. /package/dist/{studyCatalog-TAXRF5NS.js.map → studyCatalog-6BOWO4PO.js.map} +0 -0
  888. /package/dist/{summarizeCnvGeneexp-3QLHU6N7.js.map → summarizeCnvGeneexp-AMLYJIPU.js.map} +0 -0
  889. /package/dist/{summarizeGeneexpSurvival-ARI4MPFX.js.map → summarizeGeneexpSurvival-IDM7T333.js.map} +0 -0
  890. /package/dist/{summarizeMutationCnv-W7V7CKPI.js.map → summarizeMutationCnv-R6SYSJQC.js.map} +0 -0
  891. /package/dist/{summary-OUYDWLBF.js.map → summarizeMutationDiagnosis-XZJ4JLW2.js.map} +0 -0
  892. /package/dist/{summarizeMutationSurvival-6TTMSRRX.js.map → summarizeMutationSurvival-ABJ5RL4L.js.map} +0 -0
  893. /package/dist/{termCollection-7P3WU6X6.js.map → summary-NVYCTE6P.js.map} +0 -0
  894. /package/dist/{summary.integration.spec-4GTCG6HY.js.map → summary.integration.spec-SSLTLVNW.js.map} +0 -0
  895. /package/dist/{summaryInput-UK3TLC7M.js.map → summaryInput-SJOZETRP.js.map} +0 -0
  896. /package/dist/{sunburst-2UFHMNH3.js.map → sunburst-RU5ZPJKW.js.map} +0 -0
  897. /package/dist/{survival-SPWYSDVB.js.map → survival-BHJQMXKI.js.map} +0 -0
  898. /package/dist/{survival-TL6UZ6FQ.js.map → survival-DVG6Y2FV.js.map} +0 -0
  899. /package/dist/{svgraph-Z543MLIN.js.map → svgraph-ETFA4GRX.js.map} +0 -0
  900. /package/dist/{svmr-SZCAOAIF.js.map → svmr-AI3RU4JK.js.map} +0 -0
  901. /package/dist/{table-IAQ6J4DO.js.map → table-YCTSMLQL.js.map} +0 -0
  902. /package/dist/{termCollection-3NGHR7QN.js.map → termCollection-GMKEZR6D.js.map} +0 -0
  903. /package/dist/{termCollectionFractionSelection-YKIE6BME.js.map → termCollection-VEVKKJZD.js.map} +0 -0
  904. /package/dist/{termCollection.unit.spec-EPYC7LOA.js.map → termCollection.unit.spec-EU6YCEPX.js.map} +0 -0
  905. /package/dist/{tk-X454XH5N.js.map → termCollectionFractionSelection-UBS74X36.js.map} +0 -0
  906. /package/dist/{termCollectionFractionSelection.unit.spec-AG2CZPGZ.js.map → termCollectionFractionSelection.unit.spec-Y5OJFGDD.js.map} +0 -0
  907. /package/dist/{tk-TOXMU4GT.js.map → tk-HMF4HCNV.js.map} +0 -0
  908. /package/dist/{tvs.dt-U77PCG6X.js.map → tk-W6Z4FJMW.js.map} +0 -0
  909. /package/dist/{tp.ui-FDQ76KPL.js.map → tp.ui-NECRDJCS.js.map} +0 -0
  910. /package/dist/{vocabulary-64GO4YDB.js.map → tvs.dt-2JEH3F35.js.map} +0 -0
  911. /package/dist/{tvs.dtcnv.categorical-XYZU4XLO.js.map → tvs.dtcnv.categorical-YBXKEBR2.js.map} +0 -0
  912. /package/dist/{tvs.dtcnv.continuous-4GJILFGP.js.map → tvs.dtcnv.continuous-AD3SJ6BY.js.map} +0 -0
  913. /package/dist/{tvs.dtfusion-7YROAHVI.js.map → tvs.dtfusion-ODI3CLQS.js.map} +0 -0
  914. /package/dist/{tvs.dtitd-MIYU4ZHH.js.map → tvs.dtitd-V3LYLPJY.js.map} +0 -0
  915. /package/dist/{tvs.dtsnvindel-XLDY7KWB.js.map → tvs.dtsnvindel-R3V5LTNL.js.map} +0 -0
  916. /package/dist/{tvs.dtsv-YMLJ37YR.js.map → tvs.dtsv-ZQLKEDLJ.js.map} +0 -0
  917. /package/dist/{tvs.samplelst-KIVEXJKD.js.map → tvs.samplelst-G25A7HM6.js.map} +0 -0
  918. /package/dist/{tvs.termCollection-4CQV3EB3.js.map → tvs.termCollection-WLVCWDEJ.js.map} +0 -0
  919. /package/dist/{wsi.direct-5MQVRJZX.js.map → wsi.direct-SNPPQPVO.js.map} +0 -0
@@ -0,0 +1,339 @@
1
+ import {
2
+ matchesGvQueryEntry
3
+ } from "./chunk-GMRIEUBW.js";
4
+ import {
5
+ mclass
6
+ } from "./chunk-4EZLVENZ.js";
7
+
8
+ // ../shared/utils/dist/src/termCollection.js
9
+ function validateTermCollectionTerm(term) {
10
+ if (!Array.isArray(term?.termlst) || !term.termlst.length)
11
+ throw new Error("termCollection requires nonempty term.termlst[]");
12
+ const memberIds = /* @__PURE__ */ new Set();
13
+ const types = /* @__PURE__ */ new Set();
14
+ for (const t of term.termlst) {
15
+ if (typeof t.id != "string" || !t.id) throw new Error("member term id not non-empty string");
16
+ if (typeof t.type != "string" || !t.type) throw new Error("member term type not non-empty string");
17
+ if (memberIds.has(t.id)) throw new Error(`duplicate member term id '${t.id}'`);
18
+ memberIds.add(t.id);
19
+ types.add(t.type == "integer" || t.type == "float" ? "numDict" : t.type);
20
+ }
21
+ if (types.size > 1) throw new Error("termCollection.termlst[] not allowed to mix multiple term types");
22
+ return memberIds;
23
+ }
24
+ function validateFractionMembers(numerators, denominators, memberIds) {
25
+ if (!Array.isArray(denominators) || !denominators.length) throw new Error("fraction requires nonempty denominators[]");
26
+ if (!Array.isArray(numerators) || !numerators.length) throw new Error("fraction requires nonempty numerators[]");
27
+ if (new Set(denominators).size !== denominators.length) throw new Error("fraction denominators[] contains duplicates");
28
+ if (new Set(numerators).size !== numerators.length) throw new Error("fraction numerators[] contains duplicates");
29
+ for (const id of denominators) {
30
+ if (typeof id != "string" || !id) throw new Error("fraction denominator id not non-empty string");
31
+ if (!memberIds.has(id)) throw new Error(`fraction denominator '${id}' is not a collection member`);
32
+ }
33
+ for (const id of numerators) {
34
+ if (typeof id != "string" || !id) throw new Error("fraction numerator id not non-empty string");
35
+ if (!denominators.includes(id)) throw new Error(`fraction numerator '${id}' is not included in denominators[]`);
36
+ }
37
+ }
38
+ var FRACTION_TW_TYPE = "TermCollectionTWFraction";
39
+ function isFractionTw(tw) {
40
+ return tw?.type === FRACTION_TW_TYPE && tw?.term?.type === "termCollection";
41
+ }
42
+ function getFractionTvsTerm(tw) {
43
+ if (!isFractionTw(tw)) throw new Error("not a fraction termCollection tw");
44
+ const term = structuredClone(tw.term);
45
+ const memberIds = term.termlst?.length ? validateTermCollectionTerm(term) : new Set(term.termIds || []);
46
+ const denominators = tw.q?.denominators?.length ? [...tw.q.denominators] : [...memberIds];
47
+ const numerators = tw.q?.numerators?.length ? [...tw.q.numerators] : [...denominators];
48
+ validateFractionMembers(numerators, denominators, memberIds);
49
+ term.numerators = numerators;
50
+ term.denominators = denominators;
51
+ return term;
52
+ }
53
+ function validateTermCollectionFraction(q, term) {
54
+ const memberIds = validateTermCollectionTerm(term);
55
+ validateFractionMembers(q?.numerators, q?.denominators, memberIds);
56
+ if (q.mode === "discrete" && q.type !== "regular-bin" && q.type !== "custom-bin")
57
+ throw new Error("discrete fraction termCollection requires regular-bin or custom-bin q.type");
58
+ }
59
+
60
+ // ../shared/utils/dist/src/filter.js
61
+ function getFilteredSamples(sampleAnno, filter) {
62
+ setDatasetAnnotations(filter);
63
+ const samples = /* @__PURE__ */ new Set();
64
+ for (const anno of sampleAnno) {
65
+ if (samples.has(anno.sample)) continue;
66
+ const data = anno.s || anno.data;
67
+ if (data && sample_match_termvaluesetting(data, filter)) {
68
+ samples.add(anno.sample);
69
+ }
70
+ }
71
+ return samples;
72
+ }
73
+ function sample_match_termvaluesetting(row, filter, _term = null, sample = null) {
74
+ const lst = filter.type == "tvslst" ? filter.lst : [filter];
75
+ let numberofmatchedterms = 0;
76
+ for (const item of lst) {
77
+ if ("type" in item && item.type == "tvslst") {
78
+ if (sample_match_termvaluesetting(row, item, _term, sample)) {
79
+ numberofmatchedterms++;
80
+ }
81
+ } else {
82
+ const itemCopy = JSON.parse(JSON.stringify(item));
83
+ const t = itemCopy.tvs;
84
+ if (_term && t.term) {
85
+ if (!(_term.name == t.term.name && _term.type == t.term.type)) {
86
+ numberofmatchedterms++;
87
+ continue;
88
+ }
89
+ }
90
+ let samplevalue;
91
+ if (_term && !t.term) {
92
+ if (t.term$type && t.term$type !== _term.type) {
93
+ numberofmatchedterms++;
94
+ continue;
95
+ }
96
+ t.term = _term;
97
+ samplevalue = typeof row === "object" && t.term.id in row ? row[t.term.id] : row;
98
+ } else if (sample && t.term.$id) {
99
+ samplevalue = sample[t.term.$id].value;
100
+ } else {
101
+ samplevalue = t.term.id in row ? row[t.term.id] : row;
102
+ }
103
+ setDatasetAnnotations(itemCopy);
104
+ let thistermmatch;
105
+ if (t.term.type == "categorical") {
106
+ if (samplevalue === void 0) continue;
107
+ thistermmatch = t.valueset.has(samplevalue);
108
+ } else if (t.term.type == "integer" || t.term.type == "float") {
109
+ if (samplevalue === void 0) continue;
110
+ for (const range of t.ranges) {
111
+ if ("value" in range) {
112
+ thistermmatch = samplevalue === range.value;
113
+ if (thistermmatch) break;
114
+ } else if (samplevalue == range.name) {
115
+ thistermmatch = true;
116
+ break;
117
+ } else {
118
+ if (t.term.values) {
119
+ const v = t.term.values[samplevalue.toString()];
120
+ if (v && v.uncomputable) {
121
+ continue;
122
+ }
123
+ }
124
+ let left, right;
125
+ if (range.startunbounded) {
126
+ left = true;
127
+ } else if ("start" in range) {
128
+ if (range.startinclusive) {
129
+ left = samplevalue >= range.start;
130
+ } else {
131
+ left = samplevalue > range.start;
132
+ }
133
+ }
134
+ if (range.stopunbounded) {
135
+ right = true;
136
+ } else if ("stop" in range) {
137
+ if (range.stopinclusive) {
138
+ right = samplevalue <= range.stop;
139
+ } else {
140
+ right = samplevalue < range.stop;
141
+ }
142
+ }
143
+ thistermmatch = left && right;
144
+ }
145
+ if (thistermmatch) break;
146
+ }
147
+ } else if (t.term.type == "condition") {
148
+ const key = getPrecomputedKey(t);
149
+ const anno = samplevalue && samplevalue[key];
150
+ if (anno) {
151
+ thistermmatch = Array.isArray(anno) ? t.values.find((d) => anno.includes(d.key)) : t.values.find((d) => d.key == anno);
152
+ }
153
+ } else if (t.term.type == "geneVariant") {
154
+ const svalues = samplevalue.values || [samplevalue];
155
+ for (const sv of svalues) {
156
+ thistermmatch = t.values.find(
157
+ (v) => v.dt == sv.dt && (!v.origin || sv.origin == v.origin) && (!v.mclasslst || v.mclasslst.includes(sv.class))
158
+ ) && true;
159
+ if (thistermmatch) break;
160
+ }
161
+ } else {
162
+ throw "unknown term type [sample_match_termvaluesetting() shared/utils/src/filter.ts]";
163
+ }
164
+ if (t.isnot) {
165
+ thistermmatch = !thistermmatch;
166
+ }
167
+ if (thistermmatch) numberofmatchedterms++;
168
+ }
169
+ if (filter.join == "or") {
170
+ if (numberofmatchedterms && filter.in) return true;
171
+ if (!numberofmatchedterms && !filter.in) return true;
172
+ }
173
+ }
174
+ if (!("in" in filter)) filter.in = true;
175
+ return filter.in == (numberofmatchedterms == lst.length);
176
+ }
177
+ function setDatasetAnnotations(item, ds = null) {
178
+ if (item.type == "tvslst") {
179
+ for (const subitem of item.lst) {
180
+ setDatasetAnnotations(subitem, ds);
181
+ }
182
+ } else {
183
+ if (ds && typeof ds.setAnnoByTermId == "function") {
184
+ ds.setAnnoByTermId(item.tvs.term.id);
185
+ }
186
+ if (item.tvs.term.type == "categorical") {
187
+ const tvsAny = item.tvs;
188
+ tvsAny.valueset = new Set(tvsAny.values.map((i) => i.key));
189
+ }
190
+ }
191
+ }
192
+ function getPrecomputedKey(q) {
193
+ const precomputedKey = q.bar_by_children && q.value_by_max_grade ? "childrenAtMaxGrade" : q.bar_by_children && q.value_by_most_recent ? "childrenAtMostRecent" : q.bar_by_children && q.value_by_computable_grade ? "children" : q.bar_by_grade && q.value_by_max_grade ? "maxGrade" : q.bar_by_grade && q.value_by_most_recent ? "mostRecentGrades" : q.bar_by_grade && q.value_by_computable_grade ? "computableGrades" : "";
194
+ if (!precomputedKey) throw `unknown condition term bar_by_* and/or value_by_*`;
195
+ return precomputedKey;
196
+ }
197
+ function getWrappedTvslst(lst = [], join = "", $id = null) {
198
+ const filter = {
199
+ type: "tvslst",
200
+ in: true,
201
+ join,
202
+ lst
203
+ };
204
+ if ($id !== null) filter.$id = $id;
205
+ return filter;
206
+ }
207
+ function getTvsDenominators(term) {
208
+ if (Array.isArray(term?.denominators) && term.denominators.length) return term.denominators;
209
+ return (term?.termlst || []).map((t) => t.id);
210
+ }
211
+ function validateTermCollectionTvs(term) {
212
+ const memberIds = validateTermCollectionTerm(term);
213
+ if (!term.numerators) return;
214
+ validateFractionMembers(term.numerators, getTvsDenominators(term), memberIds);
215
+ }
216
+
217
+ // ../shared/utils/dist/src/geneVariantFilter.js
218
+ var statusClasses = /* @__PURE__ */ new Set(["WT", "Blank"]);
219
+ function unsupported(what) {
220
+ return `tw.q.variantFilter does not support ${what}, which qualifies a sample rather than an individual variant. Use a groupset (q.type='custom-groupset') for a sample-level filter.`;
221
+ }
222
+ function validateVariantFilter(filter, term) {
223
+ if (!filter) return;
224
+ if (filter.type != "tvslst") throw `tw.q.variantFilter.type must be 'tvslst'`;
225
+ if (!Array.isArray(filter.lst) || !filter.lst.length) throw "tw.q.variantFilter.lst[] is empty";
226
+ if (filter.lst.length > 1 && filter.join != "and" && filter.join != "or")
227
+ throw `tw.q.variantFilter.join must be 'and' or 'or' when lst[] has more than one item`;
228
+ const dts = term?.childTerms?.length ? new Set(term.childTerms.map((t) => t.dt)) : null;
229
+ for (const item of filter.lst) {
230
+ if (item.type == "tvslst") {
231
+ validateVariantFilter(item, term);
232
+ continue;
233
+ }
234
+ if (item.type != "tvs") throw `unexpected tw.q.variantFilter item.type='${item.type}'`;
235
+ const tvs = item.tvs;
236
+ if (!tvs) throw "missing tvs of a tw.q.variantFilter item";
237
+ if (!Number.isInteger(tvs.term?.dt)) throw "tw.q.variantFilter tvs.term must be a dt term, with an integer .dt";
238
+ if (dts && !dts.has(tvs.term.dt))
239
+ throw `tw.q.variantFilter tvs.term.dt=${tvs.term.dt} is not a dt of term '${term.name}'`;
240
+ if (!Array.isArray(tvs.values) || !tvs.values.length) throw "tw.q.variantFilter tvs.values[] is empty";
241
+ for (const v of tvs.values) {
242
+ if (!v.key) throw "a tw.q.variantFilter tvs.values[] entry is missing .key";
243
+ if (statusClasses.has(v.key))
244
+ throw `tw.q.variantFilter cannot select the '${v.key}' class, which is a testing status and not a variant`;
245
+ if (v.partnerBreakpointRange) throw unsupported("partnerBreakpointRange");
246
+ }
247
+ if (tvs.genotype && tvs.genotype != "variant") throw unsupported(`genotype='${tvs.genotype}'`);
248
+ if (tvs.mcount && tvs.mcount != "any") throw unsupported(`mcount='${tvs.mcount}'`);
249
+ if (tvs.mafFilter) throw unsupported("mafFilter");
250
+ if (tvs.continuousCnv) throw unsupported("continuousCnv");
251
+ if (tvs.selfBreakpointRange) throw unsupported("selfBreakpointRange");
252
+ }
253
+ }
254
+ function getFilterScope(filter, scope = /* @__PURE__ */ new Set()) {
255
+ for (const item of filter.lst) {
256
+ if (item.type == "tvslst") getFilterScope(item, scope);
257
+ else scope.add(`${item.tvs.term.dt}:${item.tvs.term.origin || "*"}`);
258
+ }
259
+ return scope;
260
+ }
261
+ function isInScope(v, scope) {
262
+ return scope.has(`${v.dt}:*`) || scope.has(`${v.dt}:${v.origin || ""}`);
263
+ }
264
+ function matchTvs(v, tvs) {
265
+ let match = false;
266
+ if (v.dt == tvs.term.dt && (!tvs.term.origin || v.origin == tvs.term.origin)) {
267
+ match = tvs.values.some((e) => e.key == v.class && (!e.mname || e.mname == v.mname && matchesGvQueryEntry(e, v)));
268
+ }
269
+ return tvs.isnot ? !match : match;
270
+ }
271
+ function matchFilter(v, filter) {
272
+ const lst = filter.type == "tvslst" ? filter.lst : [filter];
273
+ let numMatched = 0;
274
+ for (const item of lst) {
275
+ const matched = item.type == "tvslst" ? matchFilter(v, item) : matchTvs(v, item.tvs);
276
+ if (matched) numMatched++;
277
+ if (filter.join == "or" && numMatched) break;
278
+ }
279
+ const pass = filter.join == "or" ? numMatched > 0 : numMatched == lst.length;
280
+ return filter.in === false ? !pass : pass;
281
+ }
282
+ function filterVariantValues(values, filter) {
283
+ if (!filter || !values) return values;
284
+ const scope = getFilterScope(filter);
285
+ const kept = [];
286
+ const annotated = /* @__PURE__ */ new Set();
287
+ const dropped = /* @__PURE__ */ new Map();
288
+ for (const v of values) {
289
+ if (!isInScope(v, scope)) continue;
290
+ const key = `${v.dt}:${v.origin || ""}`;
291
+ if (statusClasses.has(v.class) || matchFilter(v, filter)) {
292
+ kept.push(v);
293
+ annotated.add(key);
294
+ } else if (!dropped.has(key)) {
295
+ dropped.set(key, v);
296
+ }
297
+ }
298
+ for (const [key, v] of dropped) {
299
+ if (annotated.has(key)) continue;
300
+ const wt = { dt: v.dt, class: "WT", label: mclass.WT.label };
301
+ if (v.gene) wt.gene = v.gene;
302
+ if (v.origin) wt.origin = v.origin;
303
+ kept.push(wt);
304
+ }
305
+ return kept;
306
+ }
307
+ function variantFilterLabel(filter, mclassOverride, maxItems = 3) {
308
+ if (!filter) return "";
309
+ const entries = [];
310
+ collect(filter, false);
311
+ function collect(f, negated) {
312
+ const flipped = f.in === false ? !negated : negated;
313
+ for (const item of f.lst) {
314
+ if (item.type == "tvslst") collect(item, flipped);
315
+ else if (flipped === !!item.tvs.isnot) entries.push(...item.tvs.values);
316
+ }
317
+ }
318
+ if (!entries.length) return "";
319
+ const classes = mclass;
320
+ const names = [
321
+ ...new Set(entries.map((e) => e.mname || mclassOverride?.[e.key]?.label || classes[e.key]?.label || e.key))
322
+ ];
323
+ return names.length > maxItems ? `${names.slice(0, maxItems).join("/")}\u2026` : names.join("/");
324
+ }
325
+
326
+ export {
327
+ isFractionTw,
328
+ getFractionTvsTerm,
329
+ validateTermCollectionFraction,
330
+ getFilteredSamples,
331
+ sample_match_termvaluesetting,
332
+ getWrappedTvslst,
333
+ getTvsDenominators,
334
+ validateTermCollectionTvs,
335
+ validateVariantFilter,
336
+ filterVariantValues,
337
+ variantFilterLabel
338
+ };
339
+ //# sourceMappingURL=chunk-HKKTNIMX.js.map
@@ -0,0 +1,26 @@
1
+ import {
2
+ plotColor
3
+ } from "./chunk-4EZLVENZ.js";
4
+
5
+ // plots/boxplot/defaults.ts
6
+ function getDefaultBoxplotSettings(app, overrides = {}) {
7
+ const defaults = {
8
+ plotLength: 550,
9
+ color: plotColor,
10
+ displayMode: "default",
11
+ labelPad: 10,
12
+ isLogScale: false,
13
+ isVertical: false,
14
+ orderByMedian: false,
15
+ rowHeight: 50,
16
+ rowSpace: 15,
17
+ removeOutliers: false,
18
+ showAssocTests: true
19
+ };
20
+ return Object.assign(defaults, overrides);
21
+ }
22
+
23
+ export {
24
+ getDefaultBoxplotSettings
25
+ };
26
+ //# sourceMappingURL=chunk-HKSRIEWJ.js.map
@@ -0,0 +1,70 @@
1
+ import {
2
+ junctionCustomTermSource
3
+ } from "./chunk-OBBR4UYN.js";
4
+ import {
5
+ mayRenderFractionSelection
6
+ } from "./chunk-QJ3HYZH3.js";
7
+
8
+ // termdb/handlers/junction.ts
9
+ var SearchHandler = class {
10
+ async init(opts) {
11
+ if (!opts?.holder) throw new Error("opts.holder is required");
12
+ if (typeof opts.callback != "function") throw new Error("opts.callback is required");
13
+ const entries = getJunctionCustomTerms(opts.app.vocabApi.state?.customTerms);
14
+ render(opts, entries);
15
+ }
16
+ };
17
+ function getJunctionCustomTerms(customTerms) {
18
+ if (!Array.isArray(customTerms)) return [];
19
+ return customTerms.filter((term) => term?.source === junctionCustomTermSource && term.tw?.term);
20
+ }
21
+ function render(opts, entries) {
22
+ const holder = opts.holder;
23
+ holder.selectAll("*").remove();
24
+ const div = holder.append("div").style("padding", "10px 0px");
25
+ if (!entries.length) {
26
+ div.append("div").text("Junctions selected from genome browser will be shown here.");
27
+ return;
28
+ }
29
+ const listDiv = div.append("div");
30
+ const fractionDiv = div.append("div");
31
+ for (const entry of entries) {
32
+ if (entry.eventlabel) renderJunctionEvent(listDiv, fractionDiv, entry, opts);
33
+ else renderJunction(listDiv, entry, opts);
34
+ }
35
+ listDiv.append("div").style("font-size", ".7em").style("margin-top", "10px").style("opacity", 0.7).text("Select additional junctions from genome browser.");
36
+ }
37
+ function renderJunction(holder, entry, opts) {
38
+ const choice = holder.append("div");
39
+ choice.append("div").attr("class", "ts_pill sja_filter_tag_btn sja_tree_click_term").style("display", "inline-block").style("border-radius", "6px").style("margin", "1px 0").text(entry.tw.term.name).on("click", () => opts.callback(entry.tw.term));
40
+ addDeleteButton(choice, entry, opts);
41
+ }
42
+ function renderJunctionEvent(holder, fractionDiv, entry, opts) {
43
+ const eventHolder = holder.append("div");
44
+ const pillRow = eventHolder.append("div");
45
+ pillRow.append("div").attr("class", "ts_pill sja_filter_tag_btn sja_tree_click_term").style("display", "inline-block").style("border-radius", "6px").style("margin", "1px 0").text(entry.eventlabel).on("click", () => selectJunctionEvent(holder, fractionDiv, entry, opts));
46
+ addDeleteButton(pillRow, entry, opts);
47
+ eventHolder.append("div").style("margin-left", "10px").style("font-size", ".7em").selectAll("div").data(entry.tw.term.termlst, (term) => term.id).enter().append("div").text((term) => term.name);
48
+ }
49
+ function selectJunctionEvent(listDiv, fractionDiv, entry, opts) {
50
+ const isStaged = mayRenderFractionSelection({
51
+ term: entry.tw.term,
52
+ selectionMode: opts.termCollectionSelectionMode,
53
+ listDiv,
54
+ fractionDiv,
55
+ callback: (tw) => opts.callback(tw)
56
+ });
57
+ if (!isStaged) opts.callback(entry.tw.term);
58
+ }
59
+ function addDeleteButton(holder, entry, opts) {
60
+ holder.append("button").attr("data-testid", "sjpp-junction-delete").style("margin-left", "4px").attr("aria-label", `Delete ${entry.name}`).text("\xD7").on("click", async () => {
61
+ await opts.app.vocabApi.deleteCustomTermById(entry.id);
62
+ render(opts, getJunctionCustomTerms(opts.app.vocabApi.state?.customTerms));
63
+ });
64
+ }
65
+
66
+ export {
67
+ SearchHandler,
68
+ getJunctionCustomTerms
69
+ };
70
+ //# sourceMappingURL=chunk-IELQ3HMN.js.map
@@ -0,0 +1,103 @@
1
+ import {
2
+ SearchHandler,
3
+ fillTermWrapper,
4
+ table2col,
5
+ termsettingInit
6
+ } from "./chunk-QJ3HYZH3.js";
7
+
8
+ // plots/summarizeMutationDiagnosis.ts
9
+ async function makeChartBtnMenu(holder, chartsInstance) {
10
+ let dictTw;
11
+ {
12
+ const t = chartsInstance.app.vocabApi.termdbConfig.defaultTw4correlationPlot?.disease;
13
+ if (!t) throw "defaultTw4correlationPlot missing";
14
+ dictTw = structuredClone(t);
15
+ await fillTermWrapper(dictTw, chartsInstance.app.vocabApi);
16
+ }
17
+ const table = table2col({
18
+ holder: holder.append("div"),
19
+ margin: "0px 10px 10px 10px",
20
+ cellPadding: "10px"
21
+ });
22
+ {
23
+ const [td1, td2] = table.addRow();
24
+ td1.text("Mutation Variable");
25
+ const searchDiv = td2.append("div");
26
+ const geneSearchInst = new SearchHandler();
27
+ geneSearchInst.init({
28
+ holder: searchDiv,
29
+ app: chartsInstance.app,
30
+ // required to supply "opts.app.vocabApi" for the search ui
31
+ genomeObj: chartsInstance.app.opts.genome,
32
+ msg: "Hit ENTER to launch plot.",
33
+ /* the geneTw below is used as it comes, so a grouping the user built for this gene
34
+ elsewhere can be offered here, see keepsQ in client/termdb/TermTypeSearch.ts */
35
+ keepsQ: true,
36
+ callback: async (geneTw) => {
37
+ await fillTermWrapper(geneTw, chartsInstance.app.vocabApi);
38
+ launchPlot({
39
+ tw1: dictTw,
40
+ tw2: geneTw,
41
+ chartsInstance,
42
+ holder
43
+ });
44
+ }
45
+ });
46
+ searchDiv.style("padding", "0px 0px 5px 0px");
47
+ }
48
+ {
49
+ const [td1, td2] = table.addRow();
50
+ td1.text("Compare Mutations Against");
51
+ const pillDiv = td2.append("div"), waitDiv = td2.append("div").style("font-size", ".7em").text("LOADING ...");
52
+ const pill = await termsettingInit({
53
+ menuOptions: "{edit,replace}",
54
+ /** presumably this usecase let it restrict to dictionary term ui, and hide genomic queries
55
+ target="filter" works for gdc since in gdc ds it is overriding filter to dict
56
+ but is not a general fix for non-gdc ds, which Replace menu will launch genomic+dict options
57
+ maybe this is okay for non-gdc ds as the default dictTw is meaningful
58
+ */
59
+ usecase: { target: "filter" },
60
+ vocabApi: chartsInstance.app.vocabApi,
61
+ holder: pillDiv,
62
+ callback: async (tw) => {
63
+ waitDiv.text("LOADING ...");
64
+ try {
65
+ await pill.main(tw);
66
+ dictTw = tw;
67
+ waitDiv.text("Click to edit/replace the variable before searching gene.");
68
+ } catch (e) {
69
+ waitDiv.text("Error: " + (e.message || e));
70
+ }
71
+ }
72
+ });
73
+ try {
74
+ await fillTermWrapper(dictTw, chartsInstance.app.vocabApi);
75
+ await pill.main(dictTw);
76
+ waitDiv.text("Click to edit/replace the variable before searching gene.");
77
+ } catch (e) {
78
+ waitDiv.text("Error: " + (e.message || e));
79
+ }
80
+ }
81
+ }
82
+ function launchPlot({ tw1, tw2, chartsInstance, holder }) {
83
+ const chart = {
84
+ config: {
85
+ chartType: tw1?.term?.type == "survival" ? "survival" : "summary",
86
+ // TODO define sandbox header with gene+term name
87
+ term: tw1,
88
+ term2: tw2
89
+ }
90
+ };
91
+ chartsInstance.plotCreate(chart);
92
+ holder.selectAll("*").remove();
93
+ holder.append("div").style("margin", "20px").text("LOADING CHART ...");
94
+ setTimeout(() => {
95
+ holder.style("display", "none");
96
+ }, 1e3);
97
+ }
98
+
99
+ export {
100
+ makeChartBtnMenu,
101
+ launchPlot
102
+ };
103
+ //# sourceMappingURL=chunk-IISNWG4X.js.map
@@ -0,0 +1,34 @@
1
+ import {
2
+ appInit
3
+ } from "./chunk-QJ3HYZH3.js";
4
+ import {
5
+ TermTypes
6
+ } from "./chunk-4EZLVENZ.js";
7
+
8
+ // termdb/handlers/ssGSEA.ts
9
+ var SearchHandler = class {
10
+ async init(opts) {
11
+ this.callback = opts.callback;
12
+ this.app = opts.app;
13
+ const genesetDbName = Object.keys(opts.genomeObj.termdbs || {})[0];
14
+ if (!genesetDbName) throw "genesetDbName missing";
15
+ await appInit({
16
+ holder: opts.holder,
17
+ state: {
18
+ dslabel: genesetDbName,
19
+ genome: opts.genomeObj.name,
20
+ nav: { header_mode: "search_only" }
21
+ },
22
+ tree: {
23
+ click_term: (term) => {
24
+ this.callback({ id: term.id, type: TermTypes.SSGSEA, name: term.name });
25
+ }
26
+ }
27
+ });
28
+ }
29
+ };
30
+
31
+ export {
32
+ SearchHandler
33
+ };
34
+ //# sourceMappingURL=chunk-J7KB2MH3.js.map