grnsight 4.0.0 → 6.0.0

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Files changed (458) hide show
  1. package/.travis.yml +3 -1
  2. package/GRNsight - Beta.html +194 -0
  3. package/Gemfile.lock +259 -0
  4. package/README.md +2 -2
  5. package/_gh_pages/about.html +360 -45
  6. package/_gh_pages/assets/css/footer.css +3 -0
  7. package/_gh_pages/assets/css/main.css +28 -14
  8. package/_gh_pages/assets/images/21-genes_31-edges_Schade-data_estimation_output_binary-no-targetless-genes_sif.png +0 -0
  9. package/_gh_pages/assets/images/21-genes_31-edges_Schade-data_estimation_output_binary_sif.png +0 -0
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  14. package/_gh_pages/assets/images/21-genes_31-edges_Schade-data_input_binary-no-targetless-genes_sif.png +0 -0
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  16. package/_gh_pages/assets/images/21-genes_31-edges_Schade-data_input_concatenated-no-targetless-genes_sif.png +0 -0
  17. package/_gh_pages/assets/images/21-genes_31-edges_Schade-data_input_concatenated_sif.png +0 -0
  18. package/_gh_pages/assets/images/Choe-Shin_CMSI402-poster-session_20180430.jpg +0 -0
  19. package/_gh_pages/assets/images/Choe_SCCUR_2017.jpg +0 -0
  20. package/_gh_pages/assets/images/Dahlquist-Choe-Shin_CMSI402-poster-session_20180430.jpg +0 -0
  21. package/_gh_pages/assets/images/Dionisio-Dahlquist_GRNsight-shades_20170506.jpg +0 -0
  22. package/_gh_pages/assets/images/Klein_Samdarshi_TriBeta_2018_20180317.jpg +0 -0
  23. package/_gh_pages/assets/images/Shin_SCCUR_2017.jpg +0 -0
  24. package/{documents/manuscripts/peerj-computerscience-2016/figures/submitted-versions/Figure1_zoom145_900pix-wide.png → _gh_pages/assets/images/demo-3_network-sheet.png} +0 -0
  25. package/{documents/manuscripts/peerj-computerscience-2016/figures/submitted-versions/Figure2_zoom145_900pix-wide.png → _gh_pages/assets/images/demo-4_network-optimized-weights-sheet.png} +0 -0
  26. package/_gh_pages/assets/images/gene-pages-0.png +0 -0
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  30. package/_gh_pages/assets/images/grnsight2020.png +0 -0
  31. package/_gh_pages/assets/images/v3demo2-grid+nodecoloring.png +0 -0
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  34. package/_gh_pages/assets/js/ga-report.js +11 -11
  35. package/_gh_pages/assets/js/iframeResizer.min.js +9 -0
  36. package/_gh_pages/assets/js/main.js +43 -43
  37. package/_gh_pages/beta.html +29 -24
  38. package/_gh_pages/contact.html +31 -31
  39. package/_gh_pages/coverage/coverage.json +1 -0
  40. package/_gh_pages/coverage/coverage.raw.json +1 -0
  41. package/_gh_pages/coverage/lcov-report/base.css +223 -0
  42. package/_gh_pages/coverage/lcov-report/block-navigation.js +63 -0
  43. package/_gh_pages/coverage/lcov-report/controllers/additional-sheet-parser.js.html +330 -0
  44. package/_gh_pages/coverage/lcov-report/controllers/constants.js.html +243 -0
  45. package/_gh_pages/coverage/lcov-report/controllers/export-controller.js.html +285 -0
  46. package/_gh_pages/coverage/lcov-report/controllers/exporters/graphml.js.html +405 -0
  47. package/_gh_pages/coverage/lcov-report/controllers/exporters/index.html +110 -0
  48. package/_gh_pages/coverage/lcov-report/controllers/exporters/sif.js.html +150 -0
  49. package/_gh_pages/coverage/lcov-report/controllers/helpers.js.html +114 -0
  50. package/_gh_pages/coverage/lcov-report/controllers/import-controller.js.html +233 -0
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  53. package/_gh_pages/coverage/lcov-report/controllers/importers/sif.js.html +488 -0
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  55. package/_gh_pages/coverage/lcov-report/controllers/semantic-checker.js.html +810 -0
  56. package/_gh_pages/coverage/lcov-report/controllers/spreadsheet-controller.js.html +1779 -0
  57. package/_gh_pages/coverage/lcov-report/index.html +136 -0
  58. package/_gh_pages/coverage/lcov-report/prettify.css +1 -0
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  60. package/_gh_pages/coverage/lcov-report/server/controllers/additional-sheet-parser.js.html +330 -0
  61. package/_gh_pages/coverage/lcov-report/server/controllers/constants.js.html +243 -0
  62. package/_gh_pages/coverage/lcov-report/server/controllers/export-controller.js.html +285 -0
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  73. package/_gh_pages/coverage/lcov-report/server/controllers/semantic-checker.js.html +810 -0
  74. package/_gh_pages/coverage/lcov-report/server/controllers/spreadsheet-controller.js.html +1779 -0
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  77. package/_gh_pages/coverage/lcov-report/web-client/public/js/grnstate.js.html +225 -0
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  79. package/_gh_pages/coverage/lcov.info +49 -0
  80. package/_gh_pages/documentation.html +998 -320
  81. package/_gh_pages/documents/abstracts/SIGGRAPH 2017 Abstract/siggraph-abstract-review.aux +47 -0
  82. package/_gh_pages/documents/abstracts/SIGGRAPH 2017 Abstract/siggraph-abstract-review.bbl +73 -0
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  85. package/_gh_pages/documents/abstracts/SIGGRAPH 2017 Abstract/siggraph-abstract-review.out +7 -0
  86. package/_gh_pages/documents/abstracts/SIGGRAPH 2017 Abstract/siggraph-abstract-review.synctex.gz +0 -0
  87. package/_gh_pages/documents/manuscripts/peerj-computerscience-2016/revisions/GRNsight_PeerJ-CS_manuscript_2016_text-only_revised-Dondi.docx +0 -0
  88. package/_gh_pages/encryption/server.cert +21 -0
  89. package/_gh_pages/encryption/server.key +28 -0
  90. package/_gh_pages/favicon.ico +0 -0
  91. package/_gh_pages/index.html +45 -22
  92. package/_gh_pages/links.html +47 -28
  93. package/_gh_pages/news.html +103 -21
  94. package/_gh_pages/onlyfooter.html +78 -0
  95. package/_gh_pages/onlyheader.html +64 -0
  96. package/_gh_pages/onlysidebar.html +73 -0
  97. package/_gh_pages/package-lock.json +14048 -0
  98. package/_gh_pages/people.html +129 -40
  99. package/_gh_pages/privacy.html +23 -17
  100. package/_gh_pages/publications.html +75 -33
  101. package/_gh_pages/robots.txt +1 -0
  102. package/_gh_pages/sitemap.xml +87 -74
  103. package/_gh_pages/test-files/import-samples/attributes.graphml +40 -0
  104. package/_gh_pages/test-files/import-samples/port.graphml +32 -0
  105. package/_gh_pages/test-files/import-samples/simple.graphml +31 -0
  106. package/_gh_pages/web-client/public/js/grnsight.min.js +2347 -0
  107. package/_gh_pages/web-client/public/stylesheets/grnsight.css +443 -0
  108. package/coverage/coverage.json +1 -1
  109. package/coverage/lcov.info +1847 -1142
  110. package/database/README.md +1 -0
  111. package/database/network-database/README.md +44 -0
  112. package/database/network-database/schema.sql +24 -0
  113. package/database/network-database/scripts/filter_genes.py +76 -0
  114. package/database/network-database/scripts/generate_network.py +199 -0
  115. package/database/network-database/scripts/generate_sgd_network_from_yeastract_network.py +120 -0
  116. package/database/network-database/scripts/loader.py +78 -0
  117. package/package.json +20 -11
  118. package/server/app.js +7 -2
  119. package/server/config/config.js +12 -3
  120. package/server/controllers/additional-sheet-parser.js +292 -55
  121. package/server/controllers/constants.js +4 -37
  122. package/server/controllers/custom-workbook-controller.js +66 -0
  123. package/server/controllers/demo-workbooks.js +5973 -0
  124. package/server/controllers/export-constants.js +78 -0
  125. package/server/controllers/export-controller.js +4 -3
  126. package/server/controllers/exporters/graphml.js +15 -15
  127. package/server/controllers/exporters/sif.js +7 -7
  128. package/server/controllers/exporters/xlsx.js +110 -34
  129. package/server/controllers/expression-database-controller.js +19 -0
  130. package/server/controllers/expression-sheet-parser.js +170 -0
  131. package/server/controllers/graphml-constants.js +0 -17
  132. package/server/controllers/helpers.js +25 -1
  133. package/server/controllers/import-controller.js +2 -2
  134. package/server/controllers/importers/graphml.js +17 -20
  135. package/server/controllers/importers/sif.js +22 -18
  136. package/server/controllers/network-database-controller.js +18 -0
  137. package/server/controllers/network-sheet-parser.js +307 -0
  138. package/server/controllers/semantic-checker.js +30 -162
  139. package/server/controllers/sif-constants.js +36 -0
  140. package/server/controllers/spreadsheet-controller.js +277 -425
  141. package/server/controllers/workbook-constants.js +521 -0
  142. package/server/dals/expression-dal.js +122 -0
  143. package/server/dals/network-dal.js +96 -0
  144. package/test/additional-sheet-parser-tests.js +147 -38
  145. package/test/api-tests.js +3 -6
  146. package/test/errors-adjacency-matrix-modifications.js +30 -29
  147. package/test/errors-graph-tests.js +4 -4
  148. package/test/errors-sheet-modifications.js +10 -2
  149. package/test/export-tests.js +187 -60
  150. package/test/expression-data-import-tests.js +113 -0
  151. package/test/grnstate-tests.js +8 -2
  152. package/test/import-graphml-tests.js +59 -40
  153. package/test/import-sif-tests.js +50 -37
  154. package/test/test.js +554 -91
  155. package/test/warnings-adjacency-matrix-modifications.js +8 -7
  156. package/test-files/additional-sheet-test-files/optimization-diagnostics-default.xlsx +0 -0
  157. package/test-files/additional-sheet-test-files/optimization-diagnostics-extraneous-data.xlsx +0 -0
  158. package/test-files/additional-sheet-test-files/optimization-diagnostics-incorrect-MSE-gene-header.xlsx +0 -0
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  163. package/test-files/additional-sheet-test-files/optimization-diagnostics-missing-MSE-data.xlsx +0 -0
  164. package/test-files/additional-sheet-test-files/optimization-diagnostics-missing-column-headers.xlsx +0 -0
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  166. package/test-files/additional-sheet-test-files/optimization-diagnostics-unknown-parameter.xlsx +0 -0
  167. package/test-files/additional-sheet-test-files/optimization-parameters-default.xlsx +0 -0
  168. package/test-files/additional-sheet-test-files/optimization-parameters-incorrect-headers.xlsx +0 -0
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  170. package/test-files/additional-sheet-test-files/optimization-parameters-missing-headers.xlsx +0 -0
  171. package/test-files/additional-sheet-test-files/optimization-parameters-unknown-parameter.xlsx +0 -0
  172. package/test-files/additional-sheet-test-files/two-column-sheets-extraneous-data.xlsx +0 -0
  173. package/test-files/additional-sheet-test-files/two-column-sheets-incorrect-cell-A1.xlsx +0 -0
  174. package/test-files/additional-sheet-test-files/two-column-sheets-incorrect-column-header.xlsx +0 -0
  175. package/test-files/additional-sheet-test-files/two-column-sheets-invalid-gene-length.xlsx +0 -0
  176. package/test-files/additional-sheet-test-files/two-column-sheets-invalid-gene-type.xlsx +0 -0
  177. package/test-files/additional-sheet-test-files/two-column-sheets-invalid-value.xlsx +0 -0
  178. package/test-files/additional-sheet-test-files/two-column-sheets-missing-column-header.xlsx +0 -0
  179. package/test-files/additional-sheet-test-files/two-column-sheets-special-character.xlsx +0 -0
  180. package/test-files/adjacency-matrix-modifications/asymmetric-gene-order-input.xlsx +0 -0
  181. package/test-files/adjacency-matrix-modifications/asymmetric-gene-order-output.xlsx +0 -0
  182. package/test-files/adjacency-matrix-modifications/extra-column-adjacent-input.xlsx +0 -0
  183. package/test-files/adjacency-matrix-modifications/extra-column-adjacent-output.xlsx +0 -0
  184. package/test-files/adjacency-matrix-modifications/extra-column-end-of-sheet-input.xlsx +0 -0
  185. package/test-files/adjacency-matrix-modifications/extra-column-end-of-sheet-output.xlsx +0 -0
  186. package/test-files/adjacency-matrix-modifications/extra-data-random-cell-both-output.xlsx +0 -0
  187. package/test-files/adjacency-matrix-modifications/extra-data-random-cell-network-only-input.xlsx +0 -0
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  189. package/test-files/adjacency-matrix-modifications/extra-data-random-cell-network-optimized-only-output.xlsx +0 -0
  190. package/test-files/adjacency-matrix-modifications/extra-row-end-of-sheet-input.xlsx +0 -0
  191. package/test-files/adjacency-matrix-modifications/extra-row-end-of-sheet-output.xlsx +0 -0
  192. package/test-files/adjacency-matrix-modifications/incorrect-network-cell-A1.xlsx +0 -0
  193. package/test-files/adjacency-matrix-modifications/missing-column-end-input.xlsx +0 -0
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  196. package/test-files/adjacency-matrix-modifications/missing-data-output.xlsx +0 -0
  197. package/test-files/adjacency-matrix-modifications/missing-row-end-input.xlsx +0 -0
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  199. package/test-files/adjacency-matrix-modifications/missing-row-middle-input.xlsx +0 -0
  200. package/test-files/adjacency-matrix-modifications/missing-row-middle-output.xlsx +0 -0
  201. package/test-files/adjacency-matrix-modifications/missing-value-bottom-corner-input.xlsx +0 -0
  202. package/test-files/adjacency-matrix-modifications/missing-value-bottom-corner-output.xlsx +0 -0
  203. package/test-files/adjacency-matrix-modifications/value-replaced-w-spaces-both-output.xlsx +0 -0
  204. package/test-files/adjacency-matrix-modifications/value-replaced-w-spaces-net-only-input.xlsx +0 -0
  205. package/test-files/adjacency-matrix-modifications/value-replaced-w-spaces-net-op-only-output.xlsx +0 -0
  206. package/test-files/adjacency-matrix-modifications/value-replaced/342/200/223w-spaces-net-only-output.xlsx +0 -0
  207. package/test-files/demo-files/15-genes_28-edges_db5_Dahlquist-data_estimation_output.xlsx +0 -0
  208. package/test-files/demo-files/15-genes_28-edges_db5_Dahlquist-data_input.xlsx +0 -0
  209. package/test-files/expression-data-test-sheets/expression_sheet_correct_numbering.xlsx +0 -0
  210. package/test-files/expression-data-test-sheets/expression_sheet_different_number_of_columns.xlsx +0 -0
  211. package/test-files/expression-data-test-sheets/expression_sheet_empty_column.xlsx +0 -0
  212. package/test-files/expression-data-test-sheets/expression_sheet_empty_row.xlsx +0 -0
  213. package/test-files/expression-data-test-sheets/expression_sheet_erroneous_data.xlsx +0 -0
  214. package/test-files/expression-data-test-sheets/expression_sheet_extra_gene_name.xlsx +0 -0
  215. package/test-files/expression-data-test-sheets/expression_sheet_incorrectly_ordered_time_points.xlsx +0 -0
  216. package/test-files/expression-data-test-sheets/expression_sheet_mismatched_case_gene_names.xlsx +0 -0
  217. package/test-files/expression-data-test-sheets/expression_sheet_mismatched_gene_names.xlsx +0 -0
  218. package/test-files/expression-data-test-sheets/expression_sheet_missing_column_header.xlsx +0 -0
  219. package/test-files/expression-data-test-sheets/expression_sheet_missing_data_error.xlsx +0 -0
  220. package/test-files/expression-data-test-sheets/expression_sheet_missing_data_ok.xlsx +0 -0
  221. package/test-files/expression-data-test-sheets/expression_sheet_missing_data_ok_export_exact.xlsx +0 -0
  222. package/test-files/expression-data-test-sheets/expression_sheet_missing_gene_name.xlsx +0 -0
  223. package/test-files/expression-data-test-sheets/expression_sheet_name_not_in_optparams.xlsx +0 -0
  224. package/test-files/expression-data-test-sheets/expression_sheet_name_not_present.xlsx +0 -0
  225. package/test-files/expression-data-test-sheets/expression_sheet_negative_time_points.xlsx +0 -0
  226. package/test-files/expression-data-test-sheets/expression_sheet_non_numerical_time_points.xlsx +0 -0
  227. package/test-files/expression-data-test-sheets/expression_sheet_not_existing.xlsx +0 -0
  228. package/test-files/expression-data-test-sheets/expression_sheet_wrong_id_label.xlsx +0 -0
  229. package/test-files/expression-data-test-sheets/expression_sheet_wrong_order_gene_names.xlsx +0 -0
  230. package/test-files/expression-data-test-sheets/expression_sheet_wrong_sheet_name_case.xlsx +0 -0
  231. package/test-files/expression-data-test-sheets/expression_sheet_wrong_sheet_name_convention.xlsx +0 -0
  232. package/test-files/gene-name-modifications/NaN-as-gene-name-input.xlsx +0 -0
  233. package/test-files/gene-name-modifications/NaN-as-gene-name-output.xlsx +0 -0
  234. package/test-files/gene-name-modifications/mismatched-case-related-input.xlsx +0 -0
  235. package/test-files/gene-name-modifications/mismatched-case-related-output.xlsx +0 -0
  236. package/test-files/gene-name-modifications/mismatched-case-unrelated-input.xlsx +0 -0
  237. package/test-files/gene-name-modifications/mismatched-case-unrelated-output.xlsx +0 -0
  238. package/test-files/graph-tests/different-sized-networks/{80-genes-0-edges.xlsx → 134-genes-0-edges.xlsx} +0 -0
  239. package/test-files/graph-tests/different-sized-networks/{45-genes-max-edges.xlsx → 44-source-genes-45-target-genes-max-edges.xlsx} +0 -0
  240. package/test-files/graph-tests/different-sized-networks/{1-gene-0-edges.xlsx → unused-files/1-gene-0-edges.xlsx} +0 -0
  241. package/test-files/graph-tests/different-sized-networks/{1-gene-1-edges.xlsx → unused-files/1-gene-1-edges.xlsx} +0 -0
  242. package/test-files/graph-tests/different-sized-networks/{10-genes-50-edges.xlsx → unused-files/10-genes-50-edges.xlsx} +0 -0
  243. package/test-files/graph-tests/different-sized-networks/{10-genes-90-edges.xlsx → unused-files/10-genes-90-edges.xlsx} +0 -0
  244. package/test-files/graph-tests/different-sized-networks/{100-genes-0-edges.xlsx → unused-files/100-genes-0-edges.xlsx} +0 -0
  245. package/test-files/graph-tests/different-sized-networks/{110-genes-0-edges.xlsx → unused-files/110-genes-0-edges.xlsx} +0 -0
  246. package/test-files/graph-tests/different-sized-networks/{120-genes-0-edges.xlsx → unused-files/120-genes-0-edges.xlsx} +0 -0
  247. package/test-files/graph-tests/different-sized-networks/{130-genes-0-edges.xlsx → unused-files/130-genes-0-edges.xlsx} +0 -0
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30
+ .scrollTable {
31
+ text-align: center;
32
+ table-layout: fixed;
33
+ margin-bottom: 10px;
34
+ }
35
+ .scrollTable td {
36
+ width: 40px;
37
+ height: 40px;
38
+ }
39
+ .scrollBtn {
40
+ border: 1px solid #aaa;
41
+ }
42
+ .movementArrow {
43
+ font-weight: bolder;
44
+ font-size: 24px;
45
+ }
46
+ .zoomTable {
47
+ margin-bottom: 5px;
48
+ text-align: center;
49
+ table-layout: fixed;
50
+ }
51
+ .zoomTable td {
52
+ height: 20px;
53
+ width: 120px;
54
+ }
55
+ .zoomCenter {
56
+ position: absolute;
57
+ width: 2px;
58
+ z-index: -1;
59
+ background-color: #aaa;
60
+ height: 25.5px;
61
+ left: 59.5px;
62
+ top: 148.5px;
63
+ }
64
+ .containerS {
65
+ width: 1104px;
66
+ height: 648px;
67
+ }
68
+ .containerM {
69
+ width: 1414px;
70
+ height: 840px;
71
+ }
72
+ .containerL {
73
+ width: 1920px;
74
+ height: 1080px;
75
+ }
76
+ .sidebar {
77
+ width: 225px;
78
+ margin-left: 10px;
79
+ }
80
+ #lockSlidersButton {
81
+ margin-bottom: 15px;
82
+ }
83
+ form label,
84
+ form span {
85
+ margin: 5px;
86
+ }
87
+ .navbar {
88
+ top: 1px;
89
+ margin-right: auto;
90
+ margin-bottom: 10px;
91
+ }
92
+ .glyphicon {
93
+ min-width: 22px;
94
+ }
95
+ .dropdown-menu > li > a.upload {
96
+ padding-left: 0;
97
+ padding-right: 0;
98
+ }
99
+ .dropdown-menu > li > a.upload > label {
100
+ font-weight: normal;
101
+ margin-bottom: 0;
102
+ padding-left: 20px;
103
+ padding-right: 20px;
104
+ width: 100%;
105
+ }
106
+ .dropdown-menu > li > a.upload > input[type=file] {
107
+ display: none;
108
+ }
109
+ #fileName {
110
+ color: #000;
111
+ cursor: text;
112
+ }
113
+ .not-yet-implemented,
114
+ .nav > li.not-yet-implemented {
115
+ display: none;
116
+ }
117
+ nav.navbar.navbar-default {
118
+ background-color: #dfebe5;
119
+ border-color: #dfebe5;
120
+ }
121
+ .navbar-default .navbar-nav>li>a {
122
+ color: #000;
123
+ }
124
+ .navbar-default .navbar-nav>li>a:hover {
125
+ color: #696969;
126
+ }
127
+ .navbar-default .navbar-nav>.open>a,
128
+ .navbar-default .navbar-nav>.open>a:hover,
129
+ .navbar-default .navbar-nav>.open>a:focus {
130
+ background-color: #16693f;
131
+ color: #fff;
132
+ }
133
+ .navbar-right.graph-metadata-container > li {
134
+ margin-top: 4px;
135
+ margin-bottom: 4px;
136
+ }
137
+ .info {
138
+ font-size: 13px;
139
+ }
140
+ .forceVal {
141
+ font-size: 12px;
142
+ display: inline-block;
143
+ }
144
+ .dropdown-menu > li > a:hover {
145
+ background-color: #dfebe5;
146
+ }
147
+ #undoResetButton {
148
+ margin-top: 5px;
149
+ }
150
+ #mouseOver {
151
+ margin-top: 10px;
152
+ text-align: center;
153
+ }
154
+ .btnSidebar {
155
+ width: 100%;
156
+ }
157
+ .buttonPairContainer {
158
+ display: flex;
159
+ justify-content: space-between;
160
+ margin-top: 0px;
161
+ }
162
+ .buttonPairContainer > input[type=button],
163
+ .buttonPairContainer > button {
164
+ padding: 6px 10px;
165
+ width: calc(50% - 2px);
166
+ }
167
+ .buttonPairContainer > input[type=button]:last-child,
168
+ .buttonPairContainer > button:last-child {
169
+ margin-left: 5px;
170
+ }
171
+ .panel-body {
172
+ padding: 0px 10px 10px;
173
+ }
174
+ .forceParameterContainer {
175
+ display: flex;
176
+ flex-direction: column;
177
+ margin-bottom: 5px;
178
+ }
179
+ .labelWithValueContainer {
180
+ align-items: baseline;
181
+ display: flex;
182
+ justify-content: flex-start;
183
+ margin-top: 10px;
184
+ }
185
+ .edgeControl {
186
+ align-items: center;
187
+ display: flex;
188
+ justify-content: flex-start;
189
+ }
190
+ .edgeControl > input[type=radio],
191
+ .edgeControl > input[type=checkbox] {
192
+ margin: 0;
193
+ }
194
+ .edgeControl > label {
195
+ font-size: 13px;
196
+ margin: 5px;
197
+ }
198
+ #grayThresholdInput {
199
+ margin-bottom: 5px;
200
+ }
201
+ #warningsModal #accordion {
202
+ margin-bottom: 0;
203
+ }
204
+ .dropdown-submenu {
205
+ position: relative;
206
+ }
207
+ .dropdown-submenu>.dropdown-menu {
208
+ top: 0;
209
+ left: 100%;
210
+ margin-top: -6px;
211
+ margin-left: -1px;
212
+ -webkit-border-radius: 0 6px 6px 6px;
213
+ -moz-border-radius: 0 6px 6px 6px;
214
+ border-radius: 0 6px 6px 6px;
215
+ }
216
+ .dropdown-submenu:hover>.dropdown-menu {
217
+ display: block;
218
+ }
219
+ .dropdown-submenu>a:after {
220
+ display: block;
221
+ content: " ";
222
+ float: right;
223
+ width: 0;
224
+ height: 0;
225
+ border-color: transparent;
226
+ border-style: solid;
227
+ border-width: 5px 0 5px 5px;
228
+ border-left-color: #ccc;
229
+ margin-top: 5px;
230
+ margin-right: -10px;
231
+ }
232
+ .dropdown-submenu:hover>a:after {
233
+ border-left-color: #fff;
234
+ }
235
+ .dropdown-submenu.pull-left {
236
+ float: none;
237
+ }
238
+ .dropdown-submenu.pull-left>.dropdown-menu {
239
+ left: -100%;
240
+ margin-left: 10px;
241
+ -webkit-border-radius: 6px 0 6px 6px;
242
+ -moz-border-radius: 6px 0 6px 6px;
243
+ border-radius: 6px 0 6px 6px;
244
+ }
245
+ .dropdown a.with-input {
246
+ display: flex;
247
+ align-items: center;
248
+ user-select: none;
249
+ }
250
+ .dropdown a.with-input>*:last-child {
251
+ margin-left: auto;
252
+ }
253
+ .graph-statistics-container {
254
+ margin-top: 256px;
255
+ margin-left: 15px;
256
+ width: 1335px;
257
+ }
258
+ text.weight {
259
+ cursor: default;
260
+ font-size: 20px;
261
+ font-weight: 900;
262
+ fill: #000;
263
+ opacity: 0;
264
+ stroke: #fff;
265
+ stroke-width: 0.5px;
266
+ transition: opacity 0.25s;
267
+ visibility: hidden;
268
+ }
269
+ text.weight.visible {
270
+ opacity: 1;
271
+ visibility: visible;
272
+ }
273
+ #weightsSideLabel {
274
+ line-height: 3px;
275
+ font-size: 13px;
276
+ }
277
+ .sidebarPanelHeader {
278
+ margin: 10px 10px 10px;
279
+ font-weight: bold;
280
+ font-size: 18px;
281
+ }
282
+ .sidebarPanelHeaderSpecies {
283
+ border-color: #ddd;
284
+ font-weight: bold;
285
+ font-size: 12px;
286
+ width: 100%;
287
+ }
288
+ .sidebarPanelHeaderID {
289
+ margin: 0px 5px 5px;
290
+ font-weight: bold;
291
+ font-size: 12px;
292
+ width: 100%;
293
+ }
294
+ .sideHeader {
295
+ font-weight: bold;
296
+ font-size: 13px;
297
+ margin-bottom: 4px;
298
+ margin-top: 6px;
299
+ }
300
+ .centered-sideHeader {
301
+ font-weight: normal;
302
+ font-size: 13px;
303
+ margin-bottom: 4px;
304
+ margin-top: 6px;
305
+ text-align: center;
306
+ }
307
+ .nodeColoringSidebarBody {
308
+ margin-top: 6px;
309
+ }
310
+ .node-coloring select {
311
+ width: 100%;
312
+ }
313
+ .node-coloring.disabled {
314
+ color: #aaa;
315
+ }
316
+ .data-sidebar select {
317
+ width: 100%;
318
+ }
319
+ .data-sidebar.disabled,
320
+ .species-display select {
321
+ width: 100%;
322
+ }
323
+ .speciesIdentifiedDropdown {
324
+ font-weight: normal;
325
+ }
326
+ .currentSpecies {
327
+ font-weight: bold;
328
+ }
329
+ label.sideLabel {
330
+ font-weight: normal;
331
+ }
332
+ path.mousezone {
333
+ opacity: 0;
334
+ }
335
+ .logFoldChangeControlContainer {
336
+ display: flex;
337
+ justify-content: space-between;
338
+ margin-top: 0px;
339
+ }
340
+ .logFoldChangeControlContainer > button:last-child {
341
+ margin-left: 5px;
342
+ padding-bottom: 0;
343
+ padding-top: 0;
344
+ }
345
+ .logFoldChangeMaxValue {
346
+ flex-grow: 1;
347
+ }
348
+ .normalization-form {
349
+ width: 100%;
350
+ margin-bottom: 5px;
351
+ }
352
+ .cursorGrab {
353
+ cursor: -webkit-grab;
354
+ cursor: grab;
355
+ }
356
+ .cursorGrabbing {
357
+ cursor: -webkit-grabbing;
358
+ cursor: grabbing;
359
+ }
360
+ .btn-norm {
361
+ display: inline-block;
362
+ width: 100px;
363
+ }
364
+ #grayLabel {
365
+ margin-top: 10px;
366
+ }
367
+ #normLabel {
368
+ margin-bottom: 5px;
369
+ margin-top: 10px;
370
+ }
371
+ #gray-edge-threshold-menu {
372
+ margin-right: 0.5ex;
373
+ }
374
+ .menu-subheader {
375
+ padding-left: 12px;
376
+ }
377
+ #force-graph input[type=range] {
378
+ box-shadow: none;
379
+ margin-top: -12px;
380
+ }
381
+ .minimum-zoom-display {
382
+ margin-right: 0.25rem;
383
+ }
384
+ .maximum-zoom-display {
385
+ margin-left: 0.25rem;
386
+ }
387
+ .edge-weight-sidebar.disabled {
388
+ color: #aaa;
389
+ }
390
+ #activateExpressionDBLabel {
391
+ text-align: center;
392
+ }
393
+ #expressionDBcheckbox {
394
+ text-align: center;
395
+ }
396
+ .expression-db-loader {
397
+ border: 12px solid #f3f3f3;
398
+ border-radius: 50%;
399
+ border-top: 10px solid #aeaeae;
400
+ width: 50px;
401
+ height: 50px;
402
+ animation: spin 2s linear infinite;
403
+ margin: auto;
404
+ display: none;
405
+ }
406
+ .expression-db-loader-text {
407
+ font-weight: bolder;
408
+ text-align: center;
409
+ margin-top: 15px;
410
+ display: none;
411
+ }
412
+ @-moz-keyframes spin {
413
+ 0% {
414
+ transform: rotate(0deg);
415
+ }
416
+ 100% {
417
+ transform: rotate(360deg);
418
+ }
419
+ }
420
+ @-webkit-keyframes spin {
421
+ 0% {
422
+ transform: rotate(0deg);
423
+ }
424
+ 100% {
425
+ transform: rotate(360deg);
426
+ }
427
+ }
428
+ @-o-keyframes spin {
429
+ 0% {
430
+ transform: rotate(0deg);
431
+ }
432
+ 100% {
433
+ transform: rotate(360deg);
434
+ }
435
+ }
436
+ @keyframes spin {
437
+ 0% {
438
+ transform: rotate(0deg);
439
+ }
440
+ 100% {
441
+ transform: rotate(360deg);
442
+ }
443
+ }