@jbrowse/plugin-legacy-jbrowse 2.1.0 → 2.1.3
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/dist/JBrowse1Connection/configSchema.js +2 -2
- package/dist/JBrowse1Connection/configSchema.js.map +1 -1
- package/dist/JBrowse1Connection/jb1ConfigLoad.js +132 -285
- package/dist/JBrowse1Connection/jb1ConfigLoad.js.map +1 -1
- package/dist/JBrowse1Connection/jb1ConfigParse.js +58 -127
- package/dist/JBrowse1Connection/jb1ConfigParse.js.map +1 -1
- package/dist/JBrowse1Connection/jb1ToJb2.js +155 -159
- package/dist/JBrowse1Connection/jb1ToJb2.js.map +1 -1
- package/dist/JBrowse1Connection/model.js +20 -20
- package/dist/JBrowse1Connection/model.js.map +1 -1
- package/dist/JBrowse1Connection/util.js +18 -41
- package/dist/JBrowse1Connection/util.js.map +1 -1
- package/dist/JBrowse1TextSeachAdapter/HttpMap.js +58 -168
- package/dist/JBrowse1TextSeachAdapter/HttpMap.js.map +1 -1
- package/dist/JBrowse1TextSeachAdapter/JBrowse1TextSearchAdapter.js +48 -145
- package/dist/JBrowse1TextSeachAdapter/JBrowse1TextSearchAdapter.js.map +1 -1
- package/dist/JBrowse1TextSeachAdapter/configSchema.js +1 -1
- package/dist/JBrowse1TextSeachAdapter/configSchema.js.map +1 -1
- package/dist/NCListAdapter/NCListAdapter.js +38 -147
- package/dist/NCListAdapter/NCListAdapter.js.map +1 -1
- package/dist/NCListAdapter/NCListFeature.js +35 -39
- package/dist/NCListAdapter/NCListFeature.js.map +1 -1
- package/dist/NCListAdapter/configSchema.js +1 -1
- package/dist/NCListAdapter/configSchema.js.map +1 -1
- package/dist/index.js +39 -65
- package/dist/index.js.map +1 -1
- package/package.json +2 -3
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{"version":3,"file":"JBrowse1TextSearchAdapter.js","sourceRoot":"","sources":["../../src/JBrowse1TextSeachAdapter/JBrowse1TextSearchAdapter.ts"],"names":[],"mappings":"
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{"version":3,"file":"JBrowse1TextSearchAdapter.js","sourceRoot":"","sources":["../../src/JBrowse1TextSeachAdapter/JBrowse1TextSearchAdapter.ts"],"names":[],"mappings":";;;;;AAAA,yEAIgD;AAChD,uFAA6D;AAE7D,+DAA4D;AAE5D,wDAA+B;AAgB/B,gCAAgC;AAChC,wCAAwC;AACxC,MAAqB,yBACnB,SAAQ,yBAAW;IAOnB,YACE,MAAuC,EACvC,aAAiC,EACjC,aAA6B;QAE7B,KAAK,CAAC,MAAM,EAAE,aAAa,EAAE,aAAa,CAAC,CAAA;QAC3C,MAAM,kBAAkB,GAAG,IAAA,8BAAc,EAAC,MAAM,EAAE,oBAAoB,CAAC,CAAA;QACvE,IAAI,CAAC,kBAAkB,EAAE;YACvB,MAAM,IAAI,KAAK,CAAC,iCAAiC,CAAC,CAAA;SACnD;QACD,IAAI,CAAC,OAAO,GAAG,IAAI,iBAAO,CAAC;YACzB,GAAG,EAAE,kBAAkB,CAAC,OAAO;gBAC7B,CAAC,CAAC,IAAI,GAAG,CAAC,kBAAkB,CAAC,GAAG,EAAE,kBAAkB,CAAC,OAAO,CAAC,CAAC,IAAI;gBAClE,CAAC,CAAC,kBAAkB,CAAC,GAAG;SAC3B,CAAC,CAAA;IACJ,CAAC;IAED;;;;OAIG;IACH,KAAK,CAAC,aAAa,CAAC,KAAa;QAC/B,OAAO,IAAI,CAAC,OAAO,CAAC,SAAS,CAAC,KAAK,CAAC,CAAA;IACtC,CAAC;IAED,KAAK,CAAC,WAAW,CAAC,IAAc;QAC9B,MAAM,EAAE,UAAU,EAAE,WAAW,EAAE,GAAG,IAAI,CAAA;QACxC,MAAM,MAAM,GAAG,IAAI,CAAC,WAAW,IAAI,CAAC,MAAM,IAAI,CAAC,OAAO,CAAC,aAAa,EAAE,CAAC,CAAA;QACvE,MAAM,OAAO,GAAG,MAAM,IAAI,CAAC,aAAa,CAAC,WAAW,CAAC,WAAW,EAAE,CAAC,CAAA;QACnE,IAAI,OAAO,CAAC,WAAW,CAAC,EAAE;YACxB,OAAO,IAAI,CAAC,aAAa,CAAC,OAAO,CAAC,WAAW,CAAC,EAAE,MAAM,EAAE,UAAU,CAAC,CAAA;SACpE;QACD,OAAO,EAAE,CAAA;IACX,CAAC;IACD,aAAa,CAAC,OAAsB,EAAE,MAAgB,EAAE,UAAmB;QACzE,OAAO;YACL,GAAG,CAAC,UAAU,KAAK,OAAO;gBACxB,CAAC,CAAC,EAAE;gBACJ,CAAC,CAAC,OAAO,CAAC,MAAM,CAAC,GAAG,CAAC,MAAM,CAAC,EAAE;oBAC1B,OAAO,IAAI,qBAAU,CAAC;wBACpB,KAAK,EAAE,OAAO,MAAM,KAAK,QAAQ,CAAC,CAAC,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC,CAAC,MAAM;wBACxD,gBAAgB,EAAE,MAAM;wBACxB,aAAa,EAAE,EAAE,MAAM,EAAE,MAAM,EAAE;qBAClC,CAAC,CAAA;gBACJ,CAAC,CAAC,CAAC;YACP,GAAG,OAAO,CAAC,KAAK,CAAC,GAAG,CAAC,MAAM,CAAC,EAAE;gBAC5B,MAAM,IAAI,GAAG,MAAM,CAAC,CAAC,CAAW,CAAA;gBAChC,MAAM,UAAU,GAAG,MAAM,CAAC,CAAC,CAAW,CAAA;gBACtC,MAAM,OAAO,GAAG,MAAM,CAAC,CAAC,CAAW,CAAA;gBACnC,MAAM,KAAK,GAAG,MAAM,CAAC,CAAC,CAAW,CAAA;gBACjC,MAAM,GAAG,GAAG,MAAM,CAAC,CAAC,CAAW,CAAA;gBAC/B,MAAM,SAAS,GAAG,GAAG,OAAO,IAAI,IAAI,IAAI,KAAK,IAAI,GAAG,EAAE,CAAA;gBACtD,OAAO,IAAI,qBAAU,CAAC;oBACpB,SAAS,EAAE,SAAS;oBACpB,KAAK,EAAE,IAAI;oBACX,gBAAgB,EAAE,MAAM;oBACxB,aAAa,EAAE,MAAM;oBACrB,OAAO,EAAE,MAAM,CAAC,UAAU,CAAC;iBAC5B,CAAC,CAAA;YACJ,CAAC,CAAC;SACH,CAAC,MAAM,CAAC,MAAM,CAAC,EAAE,CAAC,MAAM,CAAC,QAAQ,EAAE,KAAK,kBAAkB,CAAC,CAAA;IAC9D,CAAC;IAED,aAAa,KAAI,CAAC;CACnB;AAzED,4CAyEC"}
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Object.defineProperty(exports, "__esModule", { value: true });
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const configuration_1 = require("@jbrowse/core/configuration");
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exports.default = (0, configuration_1.ConfigurationSchema)('JBrowse1TextSearchAdapter', {
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// metadata about tracks and assemblies covered by text search adapter
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namesIndexLocation: {
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{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/JBrowse1TextSeachAdapter/configSchema.ts"],"names":[],"mappings":";;AAAA
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{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/JBrowse1TextSeachAdapter/configSchema.ts"],"names":[],"mappings":";;AAAA,+DAAiE;AAEjE,kBAAe,IAAA,mCAAmB,EAChC,2BAA2B,EAC3B;IACE,sEAAsE;IACtE,kBAAkB,EAAE;QAClB,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE,EAAE,GAAG,EAAE,eAAe,EAAE,YAAY,EAAE,aAAa,EAAE;QACnE,WAAW,EAAE,yDAAyD;KACvE;IACD,MAAM,EAAE;QACN,IAAI,EAAE,aAAa;QACnB,YAAY,EAAE,EAAE;QAChB,WAAW,EAAE,+CAA+C;KAC7D;IACD,aAAa,EAAE;QACb,IAAI,EAAE,aAAa;QACnB,YAAY,EAAE,EAAE;QAChB,WAAW,EAAE,mDAAmD;KACjE;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,kBAAkB,EAAE,qBAAqB,EAAE,CACrE,CAAA"}
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return new NCListFeature_1.default(ncFeature, undefined, "".concat(this.id, "-").concat(ncFeature.id()));
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return [2 /*return*/, !!(root && root.stats && root.stats.featureCount)];
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return (0, rxjs_1.ObservableCreate)(async (observer) => {
|
|
37
|
+
const { signal } = opts;
|
|
38
|
+
for await (const feature of this.nclist.getFeatures(region, opts)) {
|
|
39
|
+
(0, util_1.checkAbortSignal)(signal);
|
|
40
|
+
observer.next(this.wrapFeature(feature));
|
|
41
|
+
}
|
|
42
|
+
observer.complete();
|
|
159
43
|
});
|
|
160
|
-
}
|
|
44
|
+
}
|
|
45
|
+
// eslint-disable-next-line @typescript-eslint/no-explicit-any
|
|
46
|
+
wrapFeature(ncFeature) {
|
|
47
|
+
return new NCListFeature_1.default(ncFeature, undefined, `${this.id}-${ncFeature.id()}`);
|
|
48
|
+
}
|
|
49
|
+
async hasDataForRefName(refName) {
|
|
50
|
+
const root = await this.nclist.getDataRoot(refName);
|
|
51
|
+
return !!(root && root.stats && root.stats.featureCount);
|
|
52
|
+
}
|
|
161
53
|
/*
|
|
162
54
|
* NCList is unable to get list of ref names so returns empty
|
|
163
55
|
* @return Promise<string[]> of empty list
|
|
164
56
|
*/
|
|
165
|
-
|
|
57
|
+
getRefNames() {
|
|
166
58
|
return Promise.resolve(this.configRefNames || []);
|
|
167
|
-
}
|
|
59
|
+
}
|
|
168
60
|
/**
|
|
169
61
|
* called to provide a hint that data tied to a certain region
|
|
170
62
|
* will not be needed for the forseeable future and can be purged
|
|
171
63
|
* from caches, etc
|
|
172
64
|
*/
|
|
173
|
-
|
|
174
|
-
|
|
175
|
-
}(BaseAdapter_1.BaseFeatureDataAdapter));
|
|
65
|
+
freeResources() { }
|
|
66
|
+
}
|
|
176
67
|
exports.default = NCListAdapter;
|
|
177
68
|
//# sourceMappingURL=NCListAdapter.js.map
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"NCListAdapter.js","sourceRoot":"","sources":["../../src/NCListAdapter/NCListAdapter.ts"],"names":[],"mappings":"
|
|
1
|
+
{"version":3,"file":"NCListAdapter.js","sourceRoot":"","sources":["../../src/NCListAdapter/NCListAdapter.ts"],"names":[],"mappings":";;;;;AAAA,0DAAsC;AAEtC,yEAGgD;AAEhD,kDAA0D;AAC1D,6CAAqD;AACrD,2DAA+C;AAE/C,+DAA4D;AAC5D,oEAA2C;AAK3C,MAAqB,aAAc,SAAQ,oCAAsB;IAM/D,YACE,MAAuC,EACvC,aAAiC,EACjC,aAA6B;QAE7B,KAAK,CAAC,MAAM,EAAE,aAAa,EAAE,aAAa,CAAC,CAAA;QAC3C,MAAM,QAAQ,GAAG,IAAA,8BAAc,EAAC,MAAM,EAAE,UAAU,CAAC,CAAA;QACnD,MAAM,eAAe,GAAG,IAAA,8BAAc,EAAC,MAAM,EAAE,iBAAiB,CAAC,CAAA;QACjE,IAAI,CAAC,cAAc,GAAG,QAAQ,CAAA;QAE9B,IAAI,CAAC,MAAM,GAAG,IAAI,gBAAW,CAAC;YAC5B,OAAO,EAAE,EAAE;YACX,WAAW,EAAE,eAAe,CAAC,GAAG;YAChC,QAAQ,EAAE,CAAC,GAAW,EAAE,EAAE,CACxB,IAAI,+BAAU,CACZ,MAAM,CACJ,eAAe,CAAC,OAAO;gBACrB,CAAC,CAAC,IAAI,GAAG,CAAC,GAAG,EAAE,eAAe,CAAC,OAAO,CAAC,CAAC,QAAQ,EAAE;gBAClD,CAAC,CAAC,GAAG,CACR,CACF,CAAC,QAAQ,EAAE;SACf,CAAC,CAAA;IACJ,CAAC;IAED;;;;;;;OAOG;IACH,WAAW,CAAC,MAAc,EAAE,OAAoB,EAAE;QAChD,OAAO,IAAA,uBAAgB,EAAU,KAAK,EAAC,QAAQ,EAAC,EAAE;YAChD,MAAM,EAAE,MAAM,EAAE,GAAG,IAAI,CAAA;YACvB,IAAI,KAAK,EAAE,MAAM,OAAO,IAAI,IAAI,CAAC,MAAM,CAAC,WAAW,CAAC,MAAM,EAAE,IAAI,CAAC,EAAE;gBACjE,IAAA,uBAAgB,EAAC,MAAM,CAAC,CAAA;gBACxB,QAAQ,CAAC,IAAI,CAAC,IAAI,CAAC,WAAW,CAAC,OAAO,CAAC,CAAC,CAAA;aACzC;YACD,QAAQ,CAAC,QAAQ,EAAE,CAAA;QACrB,CAAC,CAAC,CAAA;IACJ,CAAC;IAED,8DAA8D;IAC9D,WAAW,CAAC,SAAc;QACxB,OAAO,IAAI,uBAAa,CACtB,SAAS,EACT,SAAS,EACT,GAAG,IAAI,CAAC,EAAE,IAAI,SAAS,CAAC,EAAE,EAAE,EAAE,CAC/B,CAAA;IACH,CAAC;IAED,KAAK,CAAC,iBAAiB,CAAC,OAAe;QACrC,MAAM,IAAI,GAAG,MAAM,IAAI,CAAC,MAAM,CAAC,WAAW,CAAC,OAAO,CAAC,CAAA;QACnD,OAAO,CAAC,CAAC,CAAC,IAAI,IAAI,IAAI,CAAC,KAAK,IAAI,IAAI,CAAC,KAAK,CAAC,YAAY,CAAC,CAAA;IAC1D,CAAC;IAED;;;OAGG;IACH,WAAW;QACT,OAAO,OAAO,CAAC,OAAO,CAAC,IAAI,CAAC,cAAc,IAAI,EAAE,CAAC,CAAA;IACnD,CAAC;IAED;;;;OAIG;IACH,aAAa,KAAI,CAAC;CACnB;AA7ED,gCA6EC"}
|
|
@@ -1,76 +1,73 @@
|
|
|
1
1
|
"use strict";
|
|
2
2
|
Object.defineProperty(exports, "__esModule", { value: true });
|
|
3
|
-
|
|
4
|
-
|
|
3
|
+
const jb2ToJb1 = { refName: 'seq_id' };
|
|
4
|
+
const jb1ToJb2 = { seq_id: 'refName' };
|
|
5
5
|
/**
|
|
6
6
|
* wrapper to adapt nclist features to act like jbrowse 2 features
|
|
7
7
|
*/
|
|
8
|
-
|
|
8
|
+
class NCListFeature {
|
|
9
9
|
// eslint-disable-next-line @typescript-eslint/no-explicit-any
|
|
10
|
-
|
|
10
|
+
constructor(ncFeature, parent, id) {
|
|
11
11
|
this.ncFeature = ncFeature;
|
|
12
12
|
this.uniqueId = id || ncFeature.id();
|
|
13
13
|
this.parentHandle = parent;
|
|
14
14
|
}
|
|
15
|
-
|
|
15
|
+
set() {
|
|
16
16
|
throw new Error('not implemented');
|
|
17
|
-
}
|
|
18
|
-
|
|
17
|
+
}
|
|
18
|
+
jb2TagToJb1Tag(tag) {
|
|
19
19
|
// @ts-ignore
|
|
20
|
-
|
|
20
|
+
const mapped = jb2ToJb1[tag] || tag;
|
|
21
21
|
return mapped.toLowerCase();
|
|
22
|
-
}
|
|
23
|
-
|
|
24
|
-
|
|
22
|
+
}
|
|
23
|
+
jb1TagToJb2Tag(tag) {
|
|
24
|
+
const t = tag.toLowerCase();
|
|
25
25
|
// @ts-ignore
|
|
26
|
-
|
|
26
|
+
const mapped = jb1ToJb2[t] || t;
|
|
27
27
|
return mapped;
|
|
28
|
-
}
|
|
28
|
+
}
|
|
29
29
|
// eslint-disable-next-line @typescript-eslint/no-explicit-any
|
|
30
|
-
|
|
31
|
-
|
|
32
|
-
var attr = this.ncFeature.get(this.jb2TagToJb1Tag(attrName));
|
|
30
|
+
get(attrName) {
|
|
31
|
+
const attr = this.ncFeature.get(this.jb2TagToJb1Tag(attrName));
|
|
33
32
|
if (attr && attrName === 'subfeatures') {
|
|
34
33
|
// eslint-disable-next-line @typescript-eslint/no-explicit-any
|
|
35
|
-
return attr.map(
|
|
34
|
+
return attr.map((subfeature) => new NCListFeature(subfeature, this));
|
|
36
35
|
}
|
|
37
36
|
return attr;
|
|
38
|
-
}
|
|
37
|
+
}
|
|
39
38
|
/**
|
|
40
39
|
* Get an array listing which data keys are present in this feature.
|
|
41
40
|
*/
|
|
42
|
-
|
|
43
|
-
|
|
44
|
-
|
|
45
|
-
};
|
|
41
|
+
tags() {
|
|
42
|
+
return this.ncFeature.tags().map((t) => this.jb1TagToJb2Tag(t));
|
|
43
|
+
}
|
|
46
44
|
/**
|
|
47
45
|
* Get the unique ID of this feature.
|
|
48
46
|
*/
|
|
49
|
-
|
|
47
|
+
id() {
|
|
50
48
|
return this.uniqueId;
|
|
51
|
-
}
|
|
49
|
+
}
|
|
52
50
|
/**
|
|
53
51
|
* Get this feature's parent feature, or undefined if none.
|
|
54
52
|
*/
|
|
55
|
-
|
|
53
|
+
parent() {
|
|
56
54
|
return this.parentHandle;
|
|
57
|
-
}
|
|
55
|
+
}
|
|
58
56
|
/**
|
|
59
57
|
* Get an array of child features, or undefined if none.
|
|
60
58
|
*/
|
|
61
|
-
|
|
59
|
+
children() {
|
|
62
60
|
return this.get('subfeatures');
|
|
63
|
-
}
|
|
64
|
-
|
|
65
|
-
|
|
66
|
-
|
|
67
|
-
|
|
68
|
-
|
|
69
|
-
var value = _this.ncFeature.get(tag);
|
|
61
|
+
}
|
|
62
|
+
toJSON() {
|
|
63
|
+
const data = { uniqueId: this.id() };
|
|
64
|
+
this.ncFeature.tags().forEach((tag) => {
|
|
65
|
+
const mappedTag = this.jb1TagToJb2Tag(tag);
|
|
66
|
+
const value = this.ncFeature.get(tag);
|
|
70
67
|
if (mappedTag === 'subfeatures') {
|
|
71
|
-
data.subfeatures = (value || []).map(
|
|
68
|
+
data.subfeatures = (value || []).map((f) => {
|
|
72
69
|
// note: was new NCListFeature(f, `${this.id()}-${i}`, this).toJSON()
|
|
73
|
-
return new NCListFeature(f,
|
|
70
|
+
return new NCListFeature(f, this).toJSON();
|
|
74
71
|
});
|
|
75
72
|
}
|
|
76
73
|
else {
|
|
@@ -78,8 +75,7 @@ var NCListFeature = /** @class */ (function () {
|
|
|
78
75
|
}
|
|
79
76
|
});
|
|
80
77
|
return data;
|
|
81
|
-
}
|
|
82
|
-
|
|
83
|
-
}());
|
|
78
|
+
}
|
|
79
|
+
}
|
|
84
80
|
exports.default = NCListFeature;
|
|
85
81
|
//# sourceMappingURL=NCListFeature.js.map
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"NCListFeature.js","sourceRoot":"","sources":["../../src/NCListAdapter/NCListFeature.ts"],"names":[],"mappings":";;AAKA,
|
|
1
|
+
{"version":3,"file":"NCListFeature.js","sourceRoot":"","sources":["../../src/NCListAdapter/NCListFeature.ts"],"names":[],"mappings":";;AAKA,MAAM,QAAQ,GAAG,EAAE,OAAO,EAAE,QAAQ,EAAE,CAAA;AAEtC,MAAM,QAAQ,GAAG,EAAE,MAAM,EAAE,SAAS,EAAE,CAAA;AAEtC;;GAEG;AACH,MAAqB,aAAa;IAKhC,8DAA8D;IAC9D,YAAoB,SAAc,EAAE,MAAgB,EAAE,EAAW;QAA7C,cAAS,GAAT,SAAS,CAAK;QAChC,IAAI,CAAC,QAAQ,GAAG,EAAE,IAAI,SAAS,CAAC,EAAE,EAAE,CAAA;QACpC,IAAI,CAAC,YAAY,GAAG,MAAM,CAAA;IAC5B,CAAC;IAED,GAAG;QACD,MAAM,IAAI,KAAK,CAAC,iBAAiB,CAAC,CAAA;IACpC,CAAC;IAED,cAAc,CAAC,GAAW;QACxB,aAAa;QACb,MAAM,MAAM,GAAG,QAAQ,CAAC,GAAG,CAAC,IAAI,GAAG,CAAA;QACnC,OAAO,MAAM,CAAC,WAAW,EAAE,CAAA;IAC7B,CAAC;IAED,cAAc,CAAC,GAAW;QACxB,MAAM,CAAC,GAAG,GAAG,CAAC,WAAW,EAAE,CAAA;QAC3B,aAAa;QACb,MAAM,MAAM,GAAG,QAAQ,CAAC,CAAC,CAAC,IAAI,CAAC,CAAA;QAC/B,OAAO,MAAM,CAAA;IACf,CAAC;IAED,8DAA8D;IAC9D,GAAG,CAAC,QAAgB;QAClB,MAAM,IAAI,GAAG,IAAI,CAAC,SAAS,CAAC,GAAG,CAAC,IAAI,CAAC,cAAc,CAAC,QAAQ,CAAC,CAAC,CAAA;QAC9D,IAAI,IAAI,IAAI,QAAQ,KAAK,aAAa,EAAE;YACtC,8DAA8D;YAC9D,OAAO,IAAI,CAAC,GAAG,CAAC,CAAC,UAAe,EAAE,EAAE,CAAC,IAAI,aAAa,CAAC,UAAU,EAAE,IAAI,CAAC,CAAC,CAAA;SAC1E;QACD,OAAO,IAAI,CAAA;IACb,CAAC;IAED;;OAEG;IACH,IAAI;QACF,OAAO,IAAI,CAAC,SAAS,CAAC,IAAI,EAAE,CAAC,GAAG,CAAC,CAAC,CAAS,EAAE,EAAE,CAAC,IAAI,CAAC,cAAc,CAAC,CAAC,CAAC,CAAC,CAAA;IACzE,CAAC;IAED;;OAEG;IACH,EAAE;QACA,OAAO,IAAI,CAAC,QAAQ,CAAA;IACtB,CAAC;IAED;;OAEG;IACH,MAAM;QACJ,OAAO,IAAI,CAAC,YAAY,CAAA;IAC1B,CAAC;IAED;;OAEG;IACH,QAAQ;QACN,OAAO,IAAI,CAAC,GAAG,CAAC,aAAa,CAAC,CAAA;IAChC,CAAC;IAED,MAAM;QACJ,MAAM,IAAI,GAA4B,EAAE,QAAQ,EAAE,IAAI,CAAC,EAAE,EAAE,EAAE,CAAA;QAC7D,IAAI,CAAC,SAAS,CAAC,IAAI,EAAE,CAAC,OAAO,CAAC,CAAC,GAAW,EAAE,EAAE;YAC5C,MAAM,SAAS,GAAG,IAAI,CAAC,cAAc,CAAC,GAAG,CAAC,CAAA;YAC1C,MAAM,KAAK,GAAG,IAAI,CAAC,SAAS,CAAC,GAAG,CAAC,GAAG,CAAC,CAAA;YACrC,IAAI,SAAS,KAAK,aAAa,EAAE;gBAC/B,IAAI,CAAC,WAAW,GAAG,CAAC,KAAK,IAAI,EAAE,CAAC,CAAC,GAAG,CAAC,CAAC,CAAU,EAAE,EAAE;oBAClD,qEAAqE;oBACrE,OAAO,IAAI,aAAa,CAAC,CAAC,EAAE,IAAI,CAAC,CAAC,MAAM,EAAE,CAAA;gBAC5C,CAAC,CAAC,CAAA;aACH;iBAAM;gBACL,IAAI,CAAC,SAAS,CAAC,GAAG,KAAK,CAAA;aACxB;QACH,CAAC,CAAC,CAAA;QACF,OAAO,IAAI,CAAA;IACb,CAAC;CACF;AAlFD,gCAkFC"}
|
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
"use strict";
|
|
2
2
|
Object.defineProperty(exports, "__esModule", { value: true });
|
|
3
|
-
|
|
3
|
+
const configuration_1 = require("@jbrowse/core/configuration");
|
|
4
4
|
exports.default = (0, configuration_1.ConfigurationSchema)('NCListAdapter', {
|
|
5
5
|
rootUrlTemplate: {
|
|
6
6
|
type: 'fileLocation',
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/NCListAdapter/configSchema.ts"],"names":[],"mappings":";;AAAA
|
|
1
|
+
{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/NCListAdapter/configSchema.ts"],"names":[],"mappings":";;AAAA,+DAAiE;AAEjE,kBAAe,IAAA,mCAAmB,EAChC,eAAe,EACf;IACE,eAAe,EAAE;QACf,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE;YACZ,GAAG,EAAE,qCAAqC;YAC1C,YAAY,EAAE,aAAa;SAC5B;KACF;IACD,QAAQ,EAAE;QACR,IAAI,EAAE,aAAa;QACnB,YAAY,EAAE,EAAE;QAChB,WAAW,EAAE,uDAAuD;KACrE;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA"}
|
package/dist/index.js
CHANGED
|
@@ -1,19 +1,4 @@
|
|
|
1
1
|
"use strict";
|
|
2
|
-
var __extends = (this && this.__extends) || (function () {
|
|
3
|
-
var extendStatics = function (d, b) {
|
|
4
|
-
extendStatics = Object.setPrototypeOf ||
|
|
5
|
-
({ __proto__: [] } instanceof Array && function (d, b) { d.__proto__ = b; }) ||
|
|
6
|
-
function (d, b) { for (var p in b) if (Object.prototype.hasOwnProperty.call(b, p)) d[p] = b[p]; };
|
|
7
|
-
return extendStatics(d, b);
|
|
8
|
-
};
|
|
9
|
-
return function (d, b) {
|
|
10
|
-
if (typeof b !== "function" && b !== null)
|
|
11
|
-
throw new TypeError("Class extends value " + String(b) + " is not a constructor or null");
|
|
12
|
-
extendStatics(d, b);
|
|
13
|
-
function __() { this.constructor = d; }
|
|
14
|
-
d.prototype = b === null ? Object.create(b) : (__.prototype = b.prototype, new __());
|
|
15
|
-
};
|
|
16
|
-
})();
|
|
17
2
|
var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
|
|
18
3
|
if (k2 === undefined) k2 = k;
|
|
19
4
|
var desc = Object.getOwnPropertyDescriptor(m, k);
|
|
@@ -41,36 +26,30 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
|
|
|
41
26
|
return (mod && mod.__esModule) ? mod : { "default": mod };
|
|
42
27
|
};
|
|
43
28
|
Object.defineProperty(exports, "__esModule", { value: true });
|
|
44
|
-
|
|
45
|
-
|
|
46
|
-
|
|
47
|
-
|
|
48
|
-
|
|
49
|
-
|
|
50
|
-
|
|
51
|
-
|
|
52
|
-
|
|
53
|
-
|
|
54
|
-
|
|
55
|
-
|
|
56
|
-
_this.name = 'LegacyJBrowsePlugin';
|
|
57
|
-
return _this;
|
|
29
|
+
const AdapterType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/AdapterType"));
|
|
30
|
+
const TextSearchAdapterType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/TextSearchAdapterType"));
|
|
31
|
+
const ConnectionType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/ConnectionType"));
|
|
32
|
+
const Plugin_1 = __importDefault(require("@jbrowse/core/Plugin"));
|
|
33
|
+
const NCListAdapter_1 = require("./NCListAdapter");
|
|
34
|
+
const JBrowse1TextSeachAdapter_1 = require("./JBrowse1TextSeachAdapter");
|
|
35
|
+
const tracks_1 = require("@jbrowse/core/util/tracks");
|
|
36
|
+
const JBrowse1Connection_1 = require("./JBrowse1Connection");
|
|
37
|
+
class LegacyJBrowsePlugin extends Plugin_1.default {
|
|
38
|
+
constructor() {
|
|
39
|
+
super(...arguments);
|
|
40
|
+
this.name = 'LegacyJBrowsePlugin';
|
|
58
41
|
}
|
|
59
|
-
|
|
60
|
-
pluginManager.addAdapterType(
|
|
61
|
-
|
|
62
|
-
|
|
63
|
-
|
|
64
|
-
|
|
65
|
-
|
|
66
|
-
|
|
67
|
-
|
|
68
|
-
|
|
69
|
-
|
|
70
|
-
return function (file, index, adapterHint) {
|
|
71
|
-
var regexGuess = /trackData.jsonz?$/i;
|
|
72
|
-
var adapterName = 'NCListAdapter';
|
|
73
|
-
var fileName = (0, tracks_1.getFileName)(file);
|
|
42
|
+
install(pluginManager) {
|
|
43
|
+
pluginManager.addAdapterType(() => new AdapterType_1.default({
|
|
44
|
+
name: 'NCListAdapter',
|
|
45
|
+
configSchema: NCListAdapter_1.configSchema,
|
|
46
|
+
getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./NCListAdapter/NCListAdapter'))).then(r => r.default),
|
|
47
|
+
}));
|
|
48
|
+
pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
|
|
49
|
+
return (file, index, adapterHint) => {
|
|
50
|
+
const regexGuess = /trackData.jsonz?$/i;
|
|
51
|
+
const adapterName = 'NCListAdapter';
|
|
52
|
+
const fileName = (0, tracks_1.getFileName)(file);
|
|
74
53
|
if (regexGuess.test(fileName) || adapterHint === adapterName) {
|
|
75
54
|
return {
|
|
76
55
|
type: adapterName,
|
|
@@ -80,26 +59,21 @@ var LegacyJBrowsePlugin = /** @class */ (function (_super) {
|
|
|
80
59
|
return adapterGuesser(file, index, adapterHint);
|
|
81
60
|
};
|
|
82
61
|
});
|
|
83
|
-
pluginManager.addTextSearchAdapterType(
|
|
84
|
-
|
|
85
|
-
|
|
86
|
-
|
|
87
|
-
|
|
88
|
-
|
|
89
|
-
|
|
90
|
-
|
|
91
|
-
|
|
92
|
-
|
|
93
|
-
|
|
94
|
-
|
|
95
|
-
|
|
96
|
-
|
|
97
|
-
|
|
98
|
-
|
|
99
|
-
});
|
|
100
|
-
});
|
|
101
|
-
};
|
|
102
|
-
return LegacyJBrowsePlugin;
|
|
103
|
-
}(Plugin_1.default));
|
|
62
|
+
pluginManager.addTextSearchAdapterType(() => new TextSearchAdapterType_1.default({
|
|
63
|
+
name: 'JBrowse1TextSearchAdapter',
|
|
64
|
+
configSchema: JBrowse1TextSeachAdapter_1.configSchema,
|
|
65
|
+
AdapterClass: JBrowse1TextSeachAdapter_1.AdapterClass,
|
|
66
|
+
description: 'A JBrowse 1 text search adapter',
|
|
67
|
+
}));
|
|
68
|
+
pluginManager.addConnectionType(() => new ConnectionType_1.default({
|
|
69
|
+
name: 'JBrowse1Connection',
|
|
70
|
+
configSchema: JBrowse1Connection_1.configSchema,
|
|
71
|
+
stateModel: (0, JBrowse1Connection_1.modelFactory)(pluginManager),
|
|
72
|
+
displayName: 'JBrowse 1 Data',
|
|
73
|
+
description: 'A JBrowse 1 data directory',
|
|
74
|
+
url: '//jbrowse.org/',
|
|
75
|
+
}));
|
|
76
|
+
}
|
|
77
|
+
}
|
|
104
78
|
exports.default = LegacyJBrowsePlugin;
|
|
105
79
|
//# sourceMappingURL=index.js.map
|
package/dist/index.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"
|
|
1
|
+
{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,kGAAyE;AACzE,sHAA6F;AAC7F,wGAA+E;AAC/E,kEAAyC;AAGzC,mDAA2E;AAC3E,yEAGmC;AACnC,sDAAuE;AAEvE,6DAG6B;AAE7B,MAAqB,mBAAoB,SAAQ,gBAAM;IAAvD;;QACE,SAAI,GAAG,qBAAqB,CAAA;IAwD9B,CAAC;IAtDC,OAAO,CAAC,aAA4B;QAClC,aAAa,CAAC,cAAc,CAC1B,GAAG,EAAE,CACH,IAAI,qBAAW,CAAC;YACd,IAAI,EAAE,eAAe;YACrB,YAAY,EAAE,4BAAyB;YACvC,eAAe,EAAE,GAAG,EAAE,CACpB,kDAAO,+BAA+B,IAAE,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC;SAC/D,CAAC,CACL,CAAA;QACD,aAAa,CAAC,mBAAmB,CAC/B,8BAA8B,EAC9B,CAAC,cAA8B,EAAE,EAAE;YACjC,OAAO,CACL,IAAkB,EAClB,KAAoB,EACpB,WAAoB,EACpB,EAAE;gBACF,MAAM,UAAU,GAAG,oBAAoB,CAAA;gBACvC,MAAM,WAAW,GAAG,eAAe,CAAA;gBACnC,MAAM,QAAQ,GAAG,IAAA,oBAAW,EAAC,IAAI,CAAC,CAAA;gBAClC,IAAI,UAAU,CAAC,IAAI,CAAC,QAAQ,CAAC,IAAI,WAAW,KAAK,WAAW,EAAE;oBAC5D,OAAO;wBACL,IAAI,EAAE,WAAW;wBACjB,eAAe,EAAE,IAAI;qBACtB,CAAA;iBACF;gBACD,OAAO,cAAc,CAAC,IAAI,EAAE,KAAK,EAAE,WAAW,CAAC,CAAA;YACjD,CAAC,CAAA;QACH,CAAC,CACF,CAAA;QAED,aAAa,CAAC,wBAAwB,CACpC,GAAG,EAAE,CACH,IAAI,+BAAqB,CAAC;YACxB,IAAI,EAAE,2BAA2B;YACjC,YAAY,EAAE,uCAA2B;YACzC,YAAY,EAAE,uCAA8B;YAC5C,WAAW,EAAE,iCAAiC;SAC/C,CAAC,CACL,CAAA;QAED,aAAa,CAAC,iBAAiB,CAC7B,GAAG,EAAE,CACH,IAAI,wBAAc,CAAC;YACjB,IAAI,EAAE,oBAAoB;YAC1B,YAAY,EAAE,iCAAoB;YAClC,UAAU,EAAE,IAAA,iCAAoB,EAAC,aAAa,CAAC;YAC/C,WAAW,EAAE,gBAAgB;YAC7B,WAAW,EAAE,4BAA4B;YACzC,GAAG,EAAE,gBAAgB;SACtB,CAAC,CACL,CAAA;IACH,CAAC;CACF;AAzDD,sCAyDC"}
|
package/package.json
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "@jbrowse/plugin-legacy-jbrowse",
|
|
3
|
-
"version": "2.1.
|
|
3
|
+
"version": "2.1.3",
|
|
4
4
|
"description": "JBrowse 2 plugin for connecting to and reading JBrowse 1 data",
|
|
5
5
|
"keywords": [
|
|
6
6
|
"jbrowse",
|
|
@@ -37,7 +37,6 @@
|
|
|
37
37
|
"clean": "rimraf dist esm *.tsbuildinfo"
|
|
38
38
|
},
|
|
39
39
|
"dependencies": {
|
|
40
|
-
"@babel/runtime": "^7.17.9",
|
|
41
40
|
"@gmod/nclist": "^0.2.1",
|
|
42
41
|
"buffer-crc32": "^0.2.13",
|
|
43
42
|
"generic-filehandle": "^3.0.0",
|
|
@@ -57,5 +56,5 @@
|
|
|
57
56
|
"distModule": "esm/index.js",
|
|
58
57
|
"srcModule": "src/index.ts",
|
|
59
58
|
"module": "esm/index.js",
|
|
60
|
-
"gitHead": "
|
|
59
|
+
"gitHead": "ebd548ceb52adb36cf6ab437082b5b5feac1338e"
|
|
61
60
|
}
|