@apollo-annotation/shared 0.1.19 → 0.1.21

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Files changed (138) hide show
  1. package/dist/Changes/AddAssemblyAndFeaturesFromFileChange.d.ts +33 -0
  2. package/dist/Changes/AddAssemblyAndFeaturesFromFileChange.js +86 -0
  3. package/dist/Changes/AddAssemblyAndFeaturesFromFileChange.js.map +1 -0
  4. package/dist/Changes/AddAssemblyFromExternalChange.d.ts +34 -0
  5. package/dist/Changes/AddAssemblyFromExternalChange.js +100 -0
  6. package/dist/Changes/AddAssemblyFromExternalChange.js.map +1 -0
  7. package/dist/Changes/AddAssemblyFromFileChange.d.ts +43 -0
  8. package/dist/Changes/AddAssemblyFromFileChange.js +146 -0
  9. package/dist/Changes/AddAssemblyFromFileChange.js.map +1 -0
  10. package/dist/Changes/AddFeatureChange.d.ts +35 -0
  11. package/dist/Changes/AddFeatureChange.js +169 -0
  12. package/dist/Changes/AddFeatureChange.js.map +1 -0
  13. package/dist/Changes/AddFeaturesFromFileChange.d.ts +32 -0
  14. package/dist/Changes/AddFeaturesFromFileChange.js +76 -0
  15. package/dist/Changes/AddFeaturesFromFileChange.js.map +1 -0
  16. package/dist/Changes/AddRefSeqAliasesChange.d.ts +20 -0
  17. package/dist/Changes/AddRefSeqAliasesChange.js +61 -0
  18. package/dist/Changes/AddRefSeqAliasesChange.js.map +1 -0
  19. package/dist/Changes/DeleteAssemblyChange.d.ts +18 -0
  20. package/dist/Changes/DeleteAssemblyChange.js +72 -0
  21. package/dist/Changes/DeleteAssemblyChange.js.map +1 -0
  22. package/dist/Changes/DeleteFeatureChange.d.ts +42 -0
  23. package/dist/Changes/DeleteFeatureChange.js +143 -0
  24. package/dist/Changes/DeleteFeatureChange.js.map +1 -0
  25. package/dist/Changes/DeleteUserChange.d.ts +25 -0
  26. package/dist/Changes/DeleteUserChange.js +53 -0
  27. package/dist/Changes/DeleteUserChange.js.map +1 -0
  28. package/dist/Changes/FeatureAttributeChange.d.ts +31 -0
  29. package/dist/Changes/FeatureAttributeChange.js +112 -0
  30. package/dist/Changes/FeatureAttributeChange.js.map +1 -0
  31. package/dist/Changes/FromFileBaseChange.d.ts +9 -0
  32. package/dist/Changes/FromFileBaseChange.js +187 -0
  33. package/dist/Changes/FromFileBaseChange.js.map +1 -0
  34. package/dist/Changes/ImportJBrowseConfigChange.d.ts +43 -0
  35. package/dist/Changes/ImportJBrowseConfigChange.js +67 -0
  36. package/dist/Changes/ImportJBrowseConfigChange.js.map +1 -0
  37. package/dist/Changes/LocationEndChange.d.ts +32 -0
  38. package/dist/Changes/LocationEndChange.js +129 -0
  39. package/dist/Changes/LocationEndChange.js.map +1 -0
  40. package/dist/Changes/LocationStartChange.d.ts +32 -0
  41. package/dist/Changes/LocationStartChange.js +129 -0
  42. package/dist/Changes/LocationStartChange.js.map +1 -0
  43. package/dist/Changes/StrandChange.d.ts +31 -0
  44. package/dist/Changes/StrandChange.js +114 -0
  45. package/dist/Changes/StrandChange.js.map +1 -0
  46. package/dist/Changes/TypeChange.d.ts +31 -0
  47. package/dist/Changes/TypeChange.js +114 -0
  48. package/dist/Changes/TypeChange.js.map +1 -0
  49. package/dist/Changes/UserChange.d.ts +25 -0
  50. package/dist/Changes/UserChange.js +51 -0
  51. package/dist/Changes/UserChange.js.map +1 -0
  52. package/dist/Changes/index.d.ts +50 -0
  53. package/dist/Changes/index.js +55 -0
  54. package/dist/Changes/index.js.map +1 -0
  55. package/dist/Checks/CDSCheck.d.ts +8 -0
  56. package/dist/Checks/CDSCheck.js +197 -0
  57. package/dist/Checks/CDSCheck.js.map +1 -0
  58. package/dist/Checks/index.d.ts +1 -0
  59. package/dist/Checks/index.js +5 -0
  60. package/dist/Checks/index.js.map +1 -0
  61. package/dist/Common/index.d.ts +1 -0
  62. package/dist/Common/index.js +5 -0
  63. package/dist/Common/index.js.map +1 -0
  64. package/dist/Common/jwtPayload.d.ts +12 -0
  65. package/dist/Common/jwtPayload.js +16 -0
  66. package/dist/Common/jwtPayload.js.map +1 -0
  67. package/dist/GFF3/gff3ToAnnotationFeature.d.ts +3 -0
  68. package/dist/GFF3/gff3ToAnnotationFeature.js +211 -0
  69. package/dist/GFF3/gff3ToAnnotationFeature.js.map +1 -0
  70. package/dist/GFF3/gff3ToAnnotationFeature.test.d.ts +1 -0
  71. package/dist/GFF3/gff3ToAnnotationFeature.test.js +174 -0
  72. package/dist/GFF3/gff3ToAnnotationFeature.test.js.map +1 -0
  73. package/dist/GFF3/gffReservedKeys.d.ts +5 -0
  74. package/dist/GFF3/gffReservedKeys.js +34 -0
  75. package/dist/GFF3/gffReservedKeys.js.map +1 -0
  76. package/dist/GFF3/index.d.ts +2 -0
  77. package/dist/GFF3/index.js +6 -0
  78. package/dist/GFF3/index.js.map +1 -0
  79. package/dist/Messages.d.ts +28 -0
  80. package/dist/Messages.js +3 -0
  81. package/dist/Messages.js.map +1 -0
  82. package/dist/Operations/GetAssembliesOperation.d.ts +13 -0
  83. package/dist/Operations/GetAssembliesOperation.js +20 -0
  84. package/dist/Operations/GetAssembliesOperation.js.map +1 -0
  85. package/dist/Operations/GetFeaturesOperation.d.ts +26 -0
  86. package/dist/Operations/GetFeaturesOperation.js +42 -0
  87. package/dist/Operations/GetFeaturesOperation.js.map +1 -0
  88. package/dist/Operations/index.d.ts +8 -0
  89. package/dist/Operations/index.js +10 -0
  90. package/dist/Operations/index.js.map +1 -0
  91. package/dist/Validations/CoreValidation.d.ts +17 -0
  92. package/dist/Validations/CoreValidation.js +36 -0
  93. package/dist/Validations/CoreValidation.js.map +1 -0
  94. package/dist/Validations/ParentChildValidation.d.ts +17 -0
  95. package/dist/Validations/ParentChildValidation.js +61 -0
  96. package/dist/Validations/ParentChildValidation.js.map +1 -0
  97. package/dist/Validations/Validation.d.ts +27 -0
  98. package/dist/Validations/Validation.js +27 -0
  99. package/dist/Validations/Validation.js.map +1 -0
  100. package/dist/Validations/ValidationSet.d.ts +24 -0
  101. package/dist/Validations/ValidationSet.js +86 -0
  102. package/dist/Validations/ValidationSet.js.map +1 -0
  103. package/dist/Validations/index.d.ts +4 -0
  104. package/dist/Validations/index.js +8 -0
  105. package/dist/Validations/index.js.map +1 -0
  106. package/dist/Validations/soSequenceTypes.d.ts +2 -0
  107. package/dist/Validations/soSequenceTypes.js +1868 -0
  108. package/dist/Validations/soSequenceTypes.js.map +1 -0
  109. package/dist/index.d.ts +8 -0
  110. package/dist/index.js +12 -0
  111. package/dist/index.js.map +1 -0
  112. package/dist/tsconfig.tsbuildinfo +1 -0
  113. package/dist/util.d.ts +4 -0
  114. package/dist/util.js +102 -0
  115. package/dist/util.js.map +1 -0
  116. package/package.json +8 -5
  117. package/src/Changes/AddAssemblyAndFeaturesFromFileChange.ts +10 -6
  118. package/src/Changes/AddAssemblyFromExternalChange.ts +4 -1
  119. package/src/Changes/AddAssemblyFromFileChange.ts +138 -41
  120. package/src/Changes/ImportJBrowseConfigChange.ts +2 -1
  121. package/src/Checks/CDSCheck.ts +202 -252
  122. package/src/GFF3/gff3ToAnnotationFeature.test.ts +165 -5
  123. package/src/GFF3/gff3ToAnnotationFeature.ts +16 -16
  124. package/src/util.ts +1 -0
  125. package/test_data/braker.gff +13 -0
  126. package/test_data/example01.gff3 +26 -0
  127. package/test_data/example01.json +236 -0
  128. package/test_data/example02.json +225 -0
  129. package/test_data/example04.json +225 -0
  130. package/test_data/example05.gff3 +30 -0
  131. package/test_data/example06.gff3 +30 -0
  132. package/test_data/example07.gff3 +30 -0
  133. package/test_data/gene_mrna.gff3 +4 -0
  134. package/test_data/gene_representations.gff3 +1781 -0
  135. package/test_data/one_cds.gff3 +9 -0
  136. package/test_data/one_cds.json +67 -0
  137. package/test_data/two_cds.gff3 +9 -0
  138. package/test_data/two_cds.json +67 -0
package/test_data/one_cds.gff3 ADDED
@@ -0,0 +1,9 @@
1
+ ##gff-version 3
2
+ ##sequence-region chr1 1000 9000
3
+ #example01
4
+ chr1 . gene 1000 9000 . + . ID=gene10001;Name=EDEN;testid=t003
5
+ chr1 . mRNA 1050 9000 . + . ID=mRNA10001;Parent=gene10001;Name=EDEN.1;testid=t004,t001,t004
6
+ chr1 . exon 1050 1500 . + . ID=exon10001;Parent=mRNA10001;testid=t007
7
+ chr1 . exon 5000 5500 . + . ID=exon10004;Parent=mRNA10001;testid=t010
8
+ chr1 . CDS 1201 1500 . + 0 ID=cds10001;Parent=mRNA10001;Name=edenprotein.1;testid=t012,t013,t014
9
+ chr1 . CDS 5000 5000 . + 0 ID=cds10001;Parent=mRNA10001;Name=edenprotein.1;testid=t015,t014
package/test_data/one_cds.json ADDED
@@ -0,0 +1,67 @@
1
+ {
2
+ "_id": "66d70e4ccc30b55b65e5f619",
3
+ "refSeq": "chr1",
4
+ "type": "gene",
5
+ "min": 999,
6
+ "max": 9000,
7
+ "strand": 1,
8
+ "children": {
9
+ "66d70e4ccc30b55b65e5f618": {
10
+ "_id": "66d70e4ccc30b55b65e5f618",
11
+ "refSeq": "chr1",
12
+ "type": "mRNA",
13
+ "min": 1049,
14
+ "max": 9000,
15
+ "strand": 1,
16
+ "children": {
17
+ "66d70e4ccc30b55b65e5f615": {
18
+ "_id": "66d70e4ccc30b55b65e5f615",
19
+ "refSeq": "chr1",
20
+ "type": "exon",
21
+ "min": 1049,
22
+ "max": 1500,
23
+ "strand": 1,
24
+ "attributes": {
25
+ "gff_id": ["exon10001"],
26
+ "testid": ["t007"]
27
+ }
28
+ },
29
+ "66d70e4ccc30b55b65e5f616": {
30
+ "_id": "66d70e4ccc30b55b65e5f616",
31
+ "refSeq": "chr1",
32
+ "type": "exon",
33
+ "min": 4999,
34
+ "max": 5500,
35
+ "strand": 1,
36
+ "attributes": {
37
+ "gff_id": ["exon10004"],
38
+ "testid": ["t010"]
39
+ }
40
+ },
41
+ "66d70e4ccc30b55b65e5f617": {
42
+ "_id": "66d70e4ccc30b55b65e5f617",
43
+ "refSeq": "chr1",
44
+ "type": "CDS",
45
+ "min": 1200,
46
+ "max": 5000,
47
+ "strand": 1,
48
+ "attributes": {
49
+ "gff_id": ["cds10001"],
50
+ "gff_name": ["edenprotein.1"],
51
+ "testid": ["t012", "t013", "t014", "t015"]
52
+ }
53
+ }
54
+ },
55
+ "attributes": {
56
+ "gff_id": ["mRNA10001"],
57
+ "gff_name": ["EDEN.1"],
58
+ "testid": ["t004", "t001", "t004"]
59
+ }
60
+ }
61
+ },
62
+ "attributes": {
63
+ "gff_id": ["gene10001"],
64
+ "gff_name": ["EDEN"],
65
+ "testid": ["t003"]
66
+ }
67
+ }
package/test_data/two_cds.gff3 ADDED
@@ -0,0 +1,9 @@
1
+ ##gff-version 3
2
+ ##sequence-region chr1 1000 9000
3
+ #example01
4
+ chr1 . gene 1000 9000 . + . ID=gene10001;Name=EDEN;testid=t003
5
+ chr1 . mRNA 1050 9000 . + . ID=mRNA10001;Parent=gene10001;Name=EDEN.1;testid=t004,t001,t004
6
+ chr1 . exon 1050 1500 . + . ID=exon10001;Parent=mRNA10001;testid=t007
7
+ chr1 . exon 5000 5500 . + . ID=exon10004;Parent=mRNA10001;testid=t010
8
+ chr1 . CDS 1201 1500 . + 0 ID=cds10001;Parent=mRNA10001;Name=edenprotein.1;testid=t012,t013,t014
9
+ chr1 . CDS 5000 5000 . + 0 ID=cds10001;Parent=mRNA10001;Name=edenprotein.1;testid=t014
package/test_data/two_cds.json ADDED
@@ -0,0 +1,67 @@
1
+ {
2
+ "_id": "66d70f3b9c7a7460925687a3",
3
+ "refSeq": "chr1",
4
+ "type": "gene",
5
+ "min": 999,
6
+ "max": 9000,
7
+ "strand": 1,
8
+ "children": {
9
+ "66d70f3b9c7a7460925687a2": {
10
+ "_id": "66d70f3b9c7a7460925687a2",
11
+ "refSeq": "chr1",
12
+ "type": "mRNA",
13
+ "min": 1049,
14
+ "max": 9000,
15
+ "strand": 1,
16
+ "children": {
17
+ "66d70f3b9c7a74609256879f": {
18
+ "_id": "66d70f3b9c7a74609256879f",
19
+ "refSeq": "chr1",
20
+ "type": "exon",
21
+ "min": 1049,
22
+ "max": 1500,
23
+ "strand": 1,
24
+ "attributes": {
25
+ "gff_id": ["exon10001"],
26
+ "testid": ["t007"]
27
+ }
28
+ },
29
+ "66d70f3b9c7a7460925687a0": {
30
+ "_id": "66d70f3b9c7a7460925687a0",
31
+ "refSeq": "chr1",
32
+ "type": "exon",
33
+ "min": 4999,
34
+ "max": 5500,
35
+ "strand": 1,
36
+ "attributes": {
37
+ "gff_id": ["exon10004"],
38
+ "testid": ["t010"]
39
+ }
40
+ },
41
+ "66d70f3b9c7a7460925687a1": {
42
+ "_id": "66d70f3b9c7a7460925687a1",
43
+ "refSeq": "chr1",
44
+ "type": "CDS",
45
+ "min": 1200,
46
+ "max": 5000,
47
+ "strand": 1,
48
+ "attributes": {
49
+ "gff_id": ["cds10001"],
50
+ "gff_name": ["edenprotein.1"],
51
+ "testid": ["t012", "t013", "t014"]
52
+ }
53
+ }
54
+ },
55
+ "attributes": {
56
+ "gff_id": ["mRNA10001"],
57
+ "gff_name": ["EDEN.1"],
58
+ "testid": ["t004", "t001", "t004"]
59
+ }
60
+ }
61
+ },
62
+ "attributes": {
63
+ "gff_id": ["gene10001"],
64
+ "gff_name": ["EDEN"],
65
+ "testid": ["t003"]
66
+ }
67
+ }