grnsight 3.0.0 → 5.1.0

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Files changed (489) hide show
  1. package/.eslintignore +1 -0
  2. package/.travis.yml +1 -1
  3. package/GRNsight - Beta.html +194 -0
  4. package/Gemfile.lock +259 -0
  5. package/README.md +1 -1
  6. package/_gh_pages/about.html +360 -45
  7. package/_gh_pages/assets/css/footer.css +3 -0
  8. package/_gh_pages/assets/css/main.css +28 -14
  9. package/_gh_pages/assets/images/21-genes_31-edges_Schade-data_estimation_output_binary-no-targetless-genes_sif.png +0 -0
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  25. 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
  26. 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
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  88. package/_gh_pages/documents/manuscripts/peerj-computerscience-2016/revisions/GRNsight_PeerJ-CS_manuscript_2016_text-only_revised-Dondi.docx +0 -0
  89. package/_gh_pages/encryption/server.cert +21 -0
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  109. package/coverage/coverage.json +1 -1
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  145. package/server/app.js +6 -2
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+ <a name='L110'></a><a href='#L110'>110</a>
159
+ <a name='L111'></a><a href='#L111'>111</a>
160
+ <a name='L112'></a><a href='#L112'>112</a>
161
+ <a name='L113'></a><a href='#L113'>113</a>
162
+ <a name='L114'></a><a href='#L114'>114</a>
163
+ <a name='L115'></a><a href='#L115'>115</a>
164
+ <a name='L116'></a><a href='#L116'>116</a>
165
+ <a name='L117'></a><a href='#L117'>117</a>
166
+ <a name='L118'></a><a href='#L118'>118</a>
167
+ <a name='L119'></a><a href='#L119'>119</a>
168
+ <a name='L120'></a><a href='#L120'>120</a>
169
+ <a name='L121'></a><a href='#L121'>121</a>
170
+ <a name='L122'></a><a href='#L122'>122</a>
171
+ <a name='L123'></a><a href='#L123'>123</a>
172
+ <a name='L124'></a><a href='#L124'>124</a>
173
+ <a name='L125'></a><a href='#L125'>125</a>
174
+ <a name='L126'></a><a href='#L126'>126</a>
175
+ <a name='L127'></a><a href='#L127'>127</a>
176
+ <a name='L128'></a><a href='#L128'>128</a>
177
+ <a name='L129'></a><a href='#L129'>129</a>
178
+ <a name='L130'></a><a href='#L130'>130</a>
179
+ <a name='L131'></a><a href='#L131'>131</a>
180
+ <a name='L132'></a><a href='#L132'>132</a>
181
+ <a name='L133'></a><a href='#L133'>133</a>
182
+ <a name='L134'></a><a href='#L134'>134</a>
183
+ <a name='L135'></a><a href='#L135'>135</a>
184
+ <a name='L136'></a><a href='#L136'>136</a>
185
+ <a name='L137'></a><a href='#L137'>137</a>
186
+ <a name='L138'></a><a href='#L138'>138</a>
187
+ <a name='L139'></a><a href='#L139'>139</a>
188
+ <a name='L140'></a><a href='#L140'>140</a>
189
+ <a name='L141'></a><a href='#L141'>141</a>
190
+ <a name='L142'></a><a href='#L142'>142</a>
191
+ <a name='L143'></a><a href='#L143'>143</a>
192
+ <a name='L144'></a><a href='#L144'>144</a>
193
+ <a name='L145'></a><a href='#L145'>145</a>
194
+ <a name='L146'></a><a href='#L146'>146</a>
195
+ <a name='L147'></a><a href='#L147'>147</a>
196
+ <a name='L148'></a><a href='#L148'>148</a>
197
+ <a name='L149'></a><a href='#L149'>149</a>
198
+ <a name='L150'></a><a href='#L150'>150</a>
199
+ <a name='L151'></a><a href='#L151'>151</a>
200
+ <a name='L152'></a><a href='#L152'>152</a>
201
+ <a name='L153'></a><a href='#L153'>153</a>
202
+ <a name='L154'></a><a href='#L154'>154</a>
203
+ <a name='L155'></a><a href='#L155'>155</a>
204
+ <a name='L156'></a><a href='#L156'>156</a>
205
+ <a name='L157'></a><a href='#L157'>157</a>
206
+ <a name='L158'></a><a href='#L158'>158</a>
207
+ <a name='L159'></a><a href='#L159'>159</a>
208
+ <a name='L160'></a><a href='#L160'>160</a>
209
+ <a name='L161'></a><a href='#L161'>161</a>
210
+ <a name='L162'></a><a href='#L162'>162</a>
211
+ <a name='L163'></a><a href='#L163'>163</a>
212
+ <a name='L164'></a><a href='#L164'>164</a>
213
+ <a name='L165'></a><a href='#L165'>165</a>
214
+ <a name='L166'></a><a href='#L166'>166</a>
215
+ <a name='L167'></a><a href='#L167'>167</a>
216
+ <a name='L168'></a><a href='#L168'>168</a>
217
+ <a name='L169'></a><a href='#L169'>169</a>
218
+ <a name='L170'></a><a href='#L170'>170</a>
219
+ <a name='L171'></a><a href='#L171'>171</a>
220
+ <a name='L172'></a><a href='#L172'>172</a>
221
+ <a name='L173'></a><a href='#L173'>173</a>
222
+ <a name='L174'></a><a href='#L174'>174</a>
223
+ <a name='L175'></a><a href='#L175'>175</a>
224
+ <a name='L176'></a><a href='#L176'>176</a>
225
+ <a name='L177'></a><a href='#L177'>177</a>
226
+ <a name='L178'></a><a href='#L178'>178</a>
227
+ <a name='L179'></a><a href='#L179'>179</a>
228
+ <a name='L180'></a><a href='#L180'>180</a>
229
+ <a name='L181'></a><a href='#L181'>181</a>
230
+ <a name='L182'></a><a href='#L182'>182</a>
231
+ <a name='L183'></a><a href='#L183'>183</a>
232
+ <a name='L184'></a><a href='#L184'>184</a>
233
+ <a name='L185'></a><a href='#L185'>185</a>
234
+ <a name='L186'></a><a href='#L186'>186</a>
235
+ <a name='L187'></a><a href='#L187'>187</a>
236
+ <a name='L188'></a><a href='#L188'>188</a>
237
+ <a name='L189'></a><a href='#L189'>189</a>
238
+ <a name='L190'></a><a href='#L190'>190</a>
239
+ <a name='L191'></a><a href='#L191'>191</a>
240
+ <a name='L192'></a><a href='#L192'>192</a>
241
+ <a name='L193'></a><a href='#L193'>193</a>
242
+ <a name='L194'></a><a href='#L194'>194</a>
243
+ <a name='L195'></a><a href='#L195'>195</a>
244
+ <a name='L196'></a><a href='#L196'>196</a>
245
+ <a name='L197'></a><a href='#L197'>197</a>
246
+ <a name='L198'></a><a href='#L198'>198</a>
247
+ <a name='L199'></a><a href='#L199'>199</a>
248
+ <a name='L200'></a><a href='#L200'>200</a>
249
+ <a name='L201'></a><a href='#L201'>201</a>
250
+ <a name='L202'></a><a href='#L202'>202</a>
251
+ <a name='L203'></a><a href='#L203'>203</a>
252
+ <a name='L204'></a><a href='#L204'>204</a>
253
+ <a name='L205'></a><a href='#L205'>205</a>
254
+ <a name='L206'></a><a href='#L206'>206</a>
255
+ <a name='L207'></a><a href='#L207'>207</a>
256
+ <a name='L208'></a><a href='#L208'>208</a>
257
+ <a name='L209'></a><a href='#L209'>209</a>
258
+ <a name='L210'></a><a href='#L210'>210</a>
259
+ <a name='L211'></a><a href='#L211'>211</a>
260
+ <a name='L212'></a><a href='#L212'>212</a>
261
+ <a name='L213'></a><a href='#L213'>213</a>
262
+ <a name='L214'></a><a href='#L214'>214</a>
263
+ <a name='L215'></a><a href='#L215'>215</a>
264
+ <a name='L216'></a><a href='#L216'>216</a>
265
+ <a name='L217'></a><a href='#L217'>217</a>
266
+ <a name='L218'></a><a href='#L218'>218</a>
267
+ <a name='L219'></a><a href='#L219'>219</a>
268
+ <a name='L220'></a><a href='#L220'>220</a>
269
+ <a name='L221'></a><a href='#L221'>221</a>
270
+ <a name='L222'></a><a href='#L222'>222</a>
271
+ <a name='L223'></a><a href='#L223'>223</a>
272
+ <a name='L224'></a><a href='#L224'>224</a>
273
+ <a name='L225'></a><a href='#L225'>225</a>
274
+ <a name='L226'></a><a href='#L226'>226</a>
275
+ <a name='L227'></a><a href='#L227'>227</a>
276
+ <a name='L228'></a><a href='#L228'>228</a>
277
+ <a name='L229'></a><a href='#L229'>229</a>
278
+ <a name='L230'></a><a href='#L230'>230</a>
279
+ <a name='L231'></a><a href='#L231'>231</a>
280
+ <a name='L232'></a><a href='#L232'>232</a>
281
+ <a name='L233'></a><a href='#L233'>233</a>
282
+ <a name='L234'></a><a href='#L234'>234</a>
283
+ <a name='L235'></a><a href='#L235'>235</a>
284
+ <a name='L236'></a><a href='#L236'>236</a>
285
+ <a name='L237'></a><a href='#L237'>237</a>
286
+ <a name='L238'></a><a href='#L238'>238</a>
287
+ <a name='L239'></a><a href='#L239'>239</a>
288
+ <a name='L240'></a><a href='#L240'>240</a>
289
+ <a name='L241'></a><a href='#L241'>241</a>
290
+ <a name='L242'></a><a href='#L242'>242</a>
291
+ <a name='L243'></a><a href='#L243'>243</a>
292
+ <a name='L244'></a><a href='#L244'>244</a>
293
+ <a name='L245'></a><a href='#L245'>245</a>
294
+ <a name='L246'></a><a href='#L246'>246</a>
295
+ <a name='L247'></a><a href='#L247'>247</a>
296
+ <a name='L248'></a><a href='#L248'>248</a>
297
+ <a name='L249'></a><a href='#L249'>249</a>
298
+ <a name='L250'></a><a href='#L250'>250</a>
299
+ <a name='L251'></a><a href='#L251'>251</a>
300
+ <a name='L252'></a><a href='#L252'>252</a>
301
+ <a name='L253'></a><a href='#L253'>253</a>
302
+ <a name='L254'></a><a href='#L254'>254</a>
303
+ <a name='L255'></a><a href='#L255'>255</a>
304
+ <a name='L256'></a><a href='#L256'>256</a>
305
+ <a name='L257'></a><a href='#L257'>257</a>
306
+ <a name='L258'></a><a href='#L258'>258</a>
307
+ <a name='L259'></a><a href='#L259'>259</a>
308
+ <a name='L260'></a><a href='#L260'>260</a>
309
+ <a name='L261'></a><a href='#L261'>261</a>
310
+ <a name='L262'></a><a href='#L262'>262</a>
311
+ <a name='L263'></a><a href='#L263'>263</a>
312
+ <a name='L264'></a><a href='#L264'>264</a>
313
+ <a name='L265'></a><a href='#L265'>265</a>
314
+ <a name='L266'></a><a href='#L266'>266</a>
315
+ <a name='L267'></a><a href='#L267'>267</a>
316
+ <a name='L268'></a><a href='#L268'>268</a>
317
+ <a name='L269'></a><a href='#L269'>269</a>
318
+ <a name='L270'></a><a href='#L270'>270</a>
319
+ <a name='L271'></a><a href='#L271'>271</a>
320
+ <a name='L272'></a><a href='#L272'>272</a>
321
+ <a name='L273'></a><a href='#L273'>273</a>
322
+ <a name='L274'></a><a href='#L274'>274</a>
323
+ <a name='L275'></a><a href='#L275'>275</a>
324
+ <a name='L276'></a><a href='#L276'>276</a>
325
+ <a name='L277'></a><a href='#L277'>277</a>
326
+ <a name='L278'></a><a href='#L278'>278</a>
327
+ <a name='L279'></a><a href='#L279'>279</a>
328
+ <a name='L280'></a><a href='#L280'>280</a>
329
+ <a name='L281'></a><a href='#L281'>281</a>
330
+ <a name='L282'></a><a href='#L282'>282</a>
331
+ <a name='L283'></a><a href='#L283'>283</a>
332
+ <a name='L284'></a><a href='#L284'>284</a>
333
+ <a name='L285'></a><a href='#L285'>285</a>
334
+ <a name='L286'></a><a href='#L286'>286</a>
335
+ <a name='L287'></a><a href='#L287'>287</a>
336
+ <a name='L288'></a><a href='#L288'>288</a>
337
+ <a name='L289'></a><a href='#L289'>289</a>
338
+ <a name='L290'></a><a href='#L290'>290</a>
339
+ <a name='L291'></a><a href='#L291'>291</a>
340
+ <a name='L292'></a><a href='#L292'>292</a>
341
+ <a name='L293'></a><a href='#L293'>293</a>
342
+ <a name='L294'></a><a href='#L294'>294</a>
343
+ <a name='L295'></a><a href='#L295'>295</a>
344
+ <a name='L296'></a><a href='#L296'>296</a>
345
+ <a name='L297'></a><a href='#L297'>297</a>
346
+ <a name='L298'></a><a href='#L298'>298</a>
347
+ <a name='L299'></a><a href='#L299'>299</a>
348
+ <a name='L300'></a><a href='#L300'>300</a>
349
+ <a name='L301'></a><a href='#L301'>301</a>
350
+ <a name='L302'></a><a href='#L302'>302</a>
351
+ <a name='L303'></a><a href='#L303'>303</a>
352
+ <a name='L304'></a><a href='#L304'>304</a>
353
+ <a name='L305'></a><a href='#L305'>305</a>
354
+ <a name='L306'></a><a href='#L306'>306</a>
355
+ <a name='L307'></a><a href='#L307'>307</a>
356
+ <a name='L308'></a><a href='#L308'>308</a>
357
+ <a name='L309'></a><a href='#L309'>309</a>
358
+ <a name='L310'></a><a href='#L310'>310</a>
359
+ <a name='L311'></a><a href='#L311'>311</a>
360
+ <a name='L312'></a><a href='#L312'>312</a>
361
+ <a name='L313'></a><a href='#L313'>313</a>
362
+ <a name='L314'></a><a href='#L314'>314</a>
363
+ <a name='L315'></a><a href='#L315'>315</a>
364
+ <a name='L316'></a><a href='#L316'>316</a>
365
+ <a name='L317'></a><a href='#L317'>317</a>
366
+ <a name='L318'></a><a href='#L318'>318</a>
367
+ <a name='L319'></a><a href='#L319'>319</a>
368
+ <a name='L320'></a><a href='#L320'>320</a>
369
+ <a name='L321'></a><a href='#L321'>321</a>
370
+ <a name='L322'></a><a href='#L322'>322</a>
371
+ <a name='L323'></a><a href='#L323'>323</a>
372
+ <a name='L324'></a><a href='#L324'>324</a>
373
+ <a name='L325'></a><a href='#L325'>325</a>
374
+ <a name='L326'></a><a href='#L326'>326</a>
375
+ <a name='L327'></a><a href='#L327'>327</a>
376
+ <a name='L328'></a><a href='#L328'>328</a>
377
+ <a name='L329'></a><a href='#L329'>329</a>
378
+ <a name='L330'></a><a href='#L330'>330</a>
379
+ <a name='L331'></a><a href='#L331'>331</a>
380
+ <a name='L332'></a><a href='#L332'>332</a>
381
+ <a name='L333'></a><a href='#L333'>333</a>
382
+ <a name='L334'></a><a href='#L334'>334</a>
383
+ <a name='L335'></a><a href='#L335'>335</a>
384
+ <a name='L336'></a><a href='#L336'>336</a>
385
+ <a name='L337'></a><a href='#L337'>337</a>
386
+ <a name='L338'></a><a href='#L338'>338</a>
387
+ <a name='L339'></a><a href='#L339'>339</a>
388
+ <a name='L340'></a><a href='#L340'>340</a>
389
+ <a name='L341'></a><a href='#L341'>341</a>
390
+ <a name='L342'></a><a href='#L342'>342</a>
391
+ <a name='L343'></a><a href='#L343'>343</a>
392
+ <a name='L344'></a><a href='#L344'>344</a>
393
+ <a name='L345'></a><a href='#L345'>345</a>
394
+ <a name='L346'></a><a href='#L346'>346</a>
395
+ <a name='L347'></a><a href='#L347'>347</a>
396
+ <a name='L348'></a><a href='#L348'>348</a>
397
+ <a name='L349'></a><a href='#L349'>349</a>
398
+ <a name='L350'></a><a href='#L350'>350</a>
399
+ <a name='L351'></a><a href='#L351'>351</a>
400
+ <a name='L352'></a><a href='#L352'>352</a>
401
+ <a name='L353'></a><a href='#L353'>353</a>
402
+ <a name='L354'></a><a href='#L354'>354</a>
403
+ <a name='L355'></a><a href='#L355'>355</a>
404
+ <a name='L356'></a><a href='#L356'>356</a>
405
+ <a name='L357'></a><a href='#L357'>357</a>
406
+ <a name='L358'></a><a href='#L358'>358</a>
407
+ <a name='L359'></a><a href='#L359'>359</a>
408
+ <a name='L360'></a><a href='#L360'>360</a>
409
+ <a name='L361'></a><a href='#L361'>361</a>
410
+ <a name='L362'></a><a href='#L362'>362</a>
411
+ <a name='L363'></a><a href='#L363'>363</a>
412
+ <a name='L364'></a><a href='#L364'>364</a>
413
+ <a name='L365'></a><a href='#L365'>365</a>
414
+ <a name='L366'></a><a href='#L366'>366</a>
415
+ <a name='L367'></a><a href='#L367'>367</a>
416
+ <a name='L368'></a><a href='#L368'>368</a>
417
+ <a name='L369'></a><a href='#L369'>369</a>
418
+ <a name='L370'></a><a href='#L370'>370</a>
419
+ <a name='L371'></a><a href='#L371'>371</a>
420
+ <a name='L372'></a><a href='#L372'>372</a>
421
+ <a name='L373'></a><a href='#L373'>373</a>
422
+ <a name='L374'></a><a href='#L374'>374</a>
423
+ <a name='L375'></a><a href='#L375'>375</a>
424
+ <a name='L376'></a><a href='#L376'>376</a>
425
+ <a name='L377'></a><a href='#L377'>377</a>
426
+ <a name='L378'></a><a href='#L378'>378</a>
427
+ <a name='L379'></a><a href='#L379'>379</a>
428
+ <a name='L380'></a><a href='#L380'>380</a>
429
+ <a name='L381'></a><a href='#L381'>381</a>
430
+ <a name='L382'></a><a href='#L382'>382</a>
431
+ <a name='L383'></a><a href='#L383'>383</a>
432
+ <a name='L384'></a><a href='#L384'>384</a>
433
+ <a name='L385'></a><a href='#L385'>385</a>
434
+ <a name='L386'></a><a href='#L386'>386</a>
435
+ <a name='L387'></a><a href='#L387'>387</a>
436
+ <a name='L388'></a><a href='#L388'>388</a>
437
+ <a name='L389'></a><a href='#L389'>389</a>
438
+ <a name='L390'></a><a href='#L390'>390</a>
439
+ <a name='L391'></a><a href='#L391'>391</a>
440
+ <a name='L392'></a><a href='#L392'>392</a>
441
+ <a name='L393'></a><a href='#L393'>393</a>
442
+ <a name='L394'></a><a href='#L394'>394</a>
443
+ <a name='L395'></a><a href='#L395'>395</a>
444
+ <a name='L396'></a><a href='#L396'>396</a>
445
+ <a name='L397'></a><a href='#L397'>397</a>
446
+ <a name='L398'></a><a href='#L398'>398</a>
447
+ <a name='L399'></a><a href='#L399'>399</a>
448
+ <a name='L400'></a><a href='#L400'>400</a>
449
+ <a name='L401'></a><a href='#L401'>401</a>
450
+ <a name='L402'></a><a href='#L402'>402</a>
451
+ <a name='L403'></a><a href='#L403'>403</a>
452
+ <a name='L404'></a><a href='#L404'>404</a>
453
+ <a name='L405'></a><a href='#L405'>405</a>
454
+ <a name='L406'></a><a href='#L406'>406</a>
455
+ <a name='L407'></a><a href='#L407'>407</a>
456
+ <a name='L408'></a><a href='#L408'>408</a>
457
+ <a name='L409'></a><a href='#L409'>409</a>
458
+ <a name='L410'></a><a href='#L410'>410</a>
459
+ <a name='L411'></a><a href='#L411'>411</a>
460
+ <a name='L412'></a><a href='#L412'>412</a>
461
+ <a name='L413'></a><a href='#L413'>413</a>
462
+ <a name='L414'></a><a href='#L414'>414</a>
463
+ <a name='L415'></a><a href='#L415'>415</a>
464
+ <a name='L416'></a><a href='#L416'>416</a>
465
+ <a name='L417'></a><a href='#L417'>417</a>
466
+ <a name='L418'></a><a href='#L418'>418</a>
467
+ <a name='L419'></a><a href='#L419'>419</a>
468
+ <a name='L420'></a><a href='#L420'>420</a>
469
+ <a name='L421'></a><a href='#L421'>421</a>
470
+ <a name='L422'></a><a href='#L422'>422</a>
471
+ <a name='L423'></a><a href='#L423'>423</a>
472
+ <a name='L424'></a><a href='#L424'>424</a>
473
+ <a name='L425'></a><a href='#L425'>425</a>
474
+ <a name='L426'></a><a href='#L426'>426</a>
475
+ <a name='L427'></a><a href='#L427'>427</a>
476
+ <a name='L428'></a><a href='#L428'>428</a>
477
+ <a name='L429'></a><a href='#L429'>429</a>
478
+ <a name='L430'></a><a href='#L430'>430</a>
479
+ <a name='L431'></a><a href='#L431'>431</a>
480
+ <a name='L432'></a><a href='#L432'>432</a>
481
+ <a name='L433'></a><a href='#L433'>433</a>
482
+ <a name='L434'></a><a href='#L434'>434</a>
483
+ <a name='L435'></a><a href='#L435'>435</a>
484
+ <a name='L436'></a><a href='#L436'>436</a>
485
+ <a name='L437'></a><a href='#L437'>437</a>
486
+ <a name='L438'></a><a href='#L438'>438</a>
487
+ <a name='L439'></a><a href='#L439'>439</a>
488
+ <a name='L440'></a><a href='#L440'>440</a>
489
+ <a name='L441'></a><a href='#L441'>441</a>
490
+ <a name='L442'></a><a href='#L442'>442</a>
491
+ <a name='L443'></a><a href='#L443'>443</a>
492
+ <a name='L444'></a><a href='#L444'>444</a>
493
+ <a name='L445'></a><a href='#L445'>445</a>
494
+ <a name='L446'></a><a href='#L446'>446</a>
495
+ <a name='L447'></a><a href='#L447'>447</a>
496
+ <a name='L448'></a><a href='#L448'>448</a>
497
+ <a name='L449'></a><a href='#L449'>449</a>
498
+ <a name='L450'></a><a href='#L450'>450</a>
499
+ <a name='L451'></a><a href='#L451'>451</a>
500
+ <a name='L452'></a><a href='#L452'>452</a>
501
+ <a name='L453'></a><a href='#L453'>453</a>
502
+ <a name='L454'></a><a href='#L454'>454</a>
503
+ <a name='L455'></a><a href='#L455'>455</a>
504
+ <a name='L456'></a><a href='#L456'>456</a>
505
+ <a name='L457'></a><a href='#L457'>457</a>
506
+ <a name='L458'></a><a href='#L458'>458</a>
507
+ <a name='L459'></a><a href='#L459'>459</a>
508
+ <a name='L460'></a><a href='#L460'>460</a>
509
+ <a name='L461'></a><a href='#L461'>461</a>
510
+ <a name='L462'></a><a href='#L462'>462</a>
511
+ <a name='L463'></a><a href='#L463'>463</a>
512
+ <a name='L464'></a><a href='#L464'>464</a>
513
+ <a name='L465'></a><a href='#L465'>465</a>
514
+ <a name='L466'></a><a href='#L466'>466</a>
515
+ <a name='L467'></a><a href='#L467'>467</a>
516
+ <a name='L468'></a><a href='#L468'>468</a>
517
+ <a name='L469'></a><a href='#L469'>469</a>
518
+ <a name='L470'></a><a href='#L470'>470</a>
519
+ <a name='L471'></a><a href='#L471'>471</a>
520
+ <a name='L472'></a><a href='#L472'>472</a>
521
+ <a name='L473'></a><a href='#L473'>473</a>
522
+ <a name='L474'></a><a href='#L474'>474</a>
523
+ <a name='L475'></a><a href='#L475'>475</a>
524
+ <a name='L476'></a><a href='#L476'>476</a>
525
+ <a name='L477'></a><a href='#L477'>477</a>
526
+ <a name='L478'></a><a href='#L478'>478</a>
527
+ <a name='L479'></a><a href='#L479'>479</a>
528
+ <a name='L480'></a><a href='#L480'>480</a>
529
+ <a name='L481'></a><a href='#L481'>481</a>
530
+ <a name='L482'></a><a href='#L482'>482</a>
531
+ <a name='L483'></a><a href='#L483'>483</a>
532
+ <a name='L484'></a><a href='#L484'>484</a>
533
+ <a name='L485'></a><a href='#L485'>485</a>
534
+ <a name='L486'></a><a href='#L486'>486</a>
535
+ <a name='L487'></a><a href='#L487'>487</a>
536
+ <a name='L488'></a><a href='#L488'>488</a>
537
+ <a name='L489'></a><a href='#L489'>489</a>
538
+ <a name='L490'></a><a href='#L490'>490</a>
539
+ <a name='L491'></a><a href='#L491'>491</a>
540
+ <a name='L492'></a><a href='#L492'>492</a>
541
+ <a name='L493'></a><a href='#L493'>493</a>
542
+ <a name='L494'></a><a href='#L494'>494</a>
543
+ <a name='L495'></a><a href='#L495'>495</a>
544
+ <a name='L496'></a><a href='#L496'>496</a>
545
+ <a name='L497'></a><a href='#L497'>497</a>
546
+ <a name='L498'></a><a href='#L498'>498</a>
547
+ <a name='L499'></a><a href='#L499'>499</a>
548
+ <a name='L500'></a><a href='#L500'>500</a>
549
+ <a name='L501'></a><a href='#L501'>501</a>
550
+ <a name='L502'></a><a href='#L502'>502</a>
551
+ <a name='L503'></a><a href='#L503'>503</a>
552
+ <a name='L504'></a><a href='#L504'>504</a>
553
+ <a name='L505'></a><a href='#L505'>505</a>
554
+ <a name='L506'></a><a href='#L506'>506</a>
555
+ <a name='L507'></a><a href='#L507'>507</a>
556
+ <a name='L508'></a><a href='#L508'>508</a>
557
+ <a name='L509'></a><a href='#L509'>509</a>
558
+ <a name='L510'></a><a href='#L510'>510</a>
559
+ <a name='L511'></a><a href='#L511'>511</a>
560
+ <a name='L512'></a><a href='#L512'>512</a>
561
+ <a name='L513'></a><a href='#L513'>513</a>
562
+ <a name='L514'></a><a href='#L514'>514</a>
563
+ <a name='L515'></a><a href='#L515'>515</a>
564
+ <a name='L516'></a><a href='#L516'>516</a>
565
+ <a name='L517'></a><a href='#L517'>517</a>
566
+ <a name='L518'></a><a href='#L518'>518</a>
567
+ <a name='L519'></a><a href='#L519'>519</a>
568
+ <a name='L520'></a><a href='#L520'>520</a>
569
+ <a name='L521'></a><a href='#L521'>521</a>
570
+ <a name='L522'></a><a href='#L522'>522</a>
571
+ <a name='L523'></a><a href='#L523'>523</a>
572
+ <a name='L524'></a><a href='#L524'>524</a>
573
+ <a name='L525'></a><a href='#L525'>525</a>
574
+ <a name='L526'></a><a href='#L526'>526</a>
575
+ <a name='L527'></a><a href='#L527'>527</a>
576
+ <a name='L528'></a><a href='#L528'>528</a>
577
+ <a name='L529'></a><a href='#L529'>529</a>
578
+ <a name='L530'></a><a href='#L530'>530</a>
579
+ <a name='L531'></a><a href='#L531'>531</a>
580
+ <a name='L532'></a><a href='#L532'>532</a>
581
+ <a name='L533'></a><a href='#L533'>533</a>
582
+ <a name='L534'></a><a href='#L534'>534</a>
583
+ <a name='L535'></a><a href='#L535'>535</a>
584
+ <a name='L536'></a><a href='#L536'>536</a>
585
+ <a name='L537'></a><a href='#L537'>537</a>
586
+ <a name='L538'></a><a href='#L538'>538</a>
587
+ <a name='L539'></a><a href='#L539'>539</a>
588
+ <a name='L540'></a><a href='#L540'>540</a>
589
+ <a name='L541'></a><a href='#L541'>541</a>
590
+ <a name='L542'></a><a href='#L542'>542</a>
591
+ <a name='L543'></a><a href='#L543'>543</a>
592
+ <a name='L544'></a><a href='#L544'>544</a>
593
+ <a name='L545'></a><a href='#L545'>545</a>
594
+ <a name='L546'></a><a href='#L546'>546</a>
595
+ <a name='L547'></a><a href='#L547'>547</a>
596
+ <a name='L548'></a><a href='#L548'>548</a>
597
+ <a name='L549'></a><a href='#L549'>549</a>
598
+ <a name='L550'></a><a href='#L550'>550</a>
599
+ <a name='L551'></a><a href='#L551'>551</a>
600
+ <a name='L552'></a><a href='#L552'>552</a>
601
+ <a name='L553'></a><a href='#L553'>553</a>
602
+ <a name='L554'></a><a href='#L554'>554</a>
603
+ <a name='L555'></a><a href='#L555'>555</a>
604
+ <a name='L556'></a><a href='#L556'>556</a>
605
+ <a name='L557'></a><a href='#L557'>557</a>
606
+ <a name='L558'></a><a href='#L558'>558</a>
607
+ <a name='L559'></a><a href='#L559'>559</a>
608
+ <a name='L560'></a><a href='#L560'>560</a>
609
+ <a name='L561'></a><a href='#L561'>561</a>
610
+ <a name='L562'></a><a href='#L562'>562</a>
611
+ <a name='L563'></a><a href='#L563'>563</a>
612
+ <a name='L564'></a><a href='#L564'>564</a>
613
+ <a name='L565'></a><a href='#L565'>565</a>
614
+ <a name='L566'></a><a href='#L566'>566</a>
615
+ <a name='L567'></a><a href='#L567'>567</a>
616
+ <a name='L568'></a><a href='#L568'>568</a>
617
+ <a name='L569'></a><a href='#L569'>569</a>
618
+ <a name='L570'></a><a href='#L570'>570</a>
619
+ <a name='L571'></a><a href='#L571'>571</a></td><td class="line-coverage quiet"><span class="cline-any cline-yes">1x</span>
620
+ <span class="cline-any cline-yes">1x</span>
621
+ <span class="cline-any cline-neutral">&nbsp;</span>
622
+ <span class="cline-any cline-yes">1x</span>
623
+ <span class="cline-any cline-yes">1x</span>
624
+ <span class="cline-any cline-neutral">&nbsp;</span>
625
+ <span class="cline-any cline-neutral">&nbsp;</span>
626
+ <span class="cline-any cline-yes">1x</span>
627
+ <span class="cline-any cline-neutral">&nbsp;</span>
628
+ <span class="cline-any cline-yes">1x</span>
629
+ <span class="cline-any cline-neutral">&nbsp;</span>
630
+ <span class="cline-any cline-neutral">&nbsp;</span>
631
+ <span class="cline-any cline-yes">1x</span>
632
+ <span class="cline-any cline-neutral">&nbsp;</span>
633
+ <span class="cline-any cline-neutral">&nbsp;</span>
634
+ <span class="cline-any cline-neutral">&nbsp;</span>
635
+ <span class="cline-any cline-neutral">&nbsp;</span>
636
+ <span class="cline-any cline-neutral">&nbsp;</span>
637
+ <span class="cline-any cline-neutral">&nbsp;</span>
638
+ <span class="cline-any cline-neutral">&nbsp;</span>
639
+ <span class="cline-any cline-neutral">&nbsp;</span>
640
+ <span class="cline-any cline-neutral">&nbsp;</span>
641
+ <span class="cline-any cline-neutral">&nbsp;</span>
642
+ <span class="cline-any cline-yes">1x</span>
588
643
  <span class="cline-any cline-neutral">&nbsp;</span>
589
- <span class="cline-any cline-yes">1×</span>
590
644
  <span class="cline-any cline-neutral">&nbsp;</span>
591
645
  <span class="cline-any cline-neutral">&nbsp;</span>
592
- <span class="cline-any cline-yes">1×</span>
593
646
  <span class="cline-any cline-neutral">&nbsp;</span>
594
- <span class="cline-any cline-yes">1×</span>
595
647
  <span class="cline-any cline-neutral">&nbsp;</span>
596
648
  <span class="cline-any cline-neutral">&nbsp;</span>
597
- <span class="cline-any cline-yes">1×</span>
598
649
  <span class="cline-any cline-neutral">&nbsp;</span>
599
650
  <span class="cline-any cline-neutral">&nbsp;</span>
600
651
  <span class="cline-any cline-neutral">&nbsp;</span>
652
+ <span class="cline-any cline-no">&nbsp;</span>
653
+ <span class="cline-any cline-no">&nbsp;</span>
654
+ <span class="cline-any cline-no">&nbsp;</span>
601
655
  <span class="cline-any cline-neutral">&nbsp;</span>
602
656
  <span class="cline-any cline-neutral">&nbsp;</span>
603
657
  <span class="cline-any cline-neutral">&nbsp;</span>
@@ -605,7 +659,9 @@
605
659
  <span class="cline-any cline-neutral">&nbsp;</span>
606
660
  <span class="cline-any cline-neutral">&nbsp;</span>
607
661
  <span class="cline-any cline-neutral">&nbsp;</span>
608
- <span class="cline-any cline-yes">1×</span>
662
+ <span class="cline-any cline-no">&nbsp;</span>
663
+ <span class="cline-any cline-no">&nbsp;</span>
664
+ <span class="cline-any cline-no">&nbsp;</span>
609
665
  <span class="cline-any cline-neutral">&nbsp;</span>
610
666
  <span class="cline-any cline-neutral">&nbsp;</span>
611
667
  <span class="cline-any cline-neutral">&nbsp;</span>
@@ -615,8 +671,6 @@
615
671
  <span class="cline-any cline-neutral">&nbsp;</span>
616
672
  <span class="cline-any cline-neutral">&nbsp;</span>
617
673
  <span class="cline-any cline-no">&nbsp;</span>
618
- <span class="cline-any cline-no">&nbsp;</span>
619
- <span class="cline-any cline-no">&nbsp;</span>
620
674
  <span class="cline-any cline-neutral">&nbsp;</span>
621
675
  <span class="cline-any cline-neutral">&nbsp;</span>
622
676
  <span class="cline-any cline-neutral">&nbsp;</span>
@@ -634,7 +688,8 @@
634
688
  <span class="cline-any cline-neutral">&nbsp;</span>
635
689
  <span class="cline-any cline-neutral">&nbsp;</span>
636
690
  <span class="cline-any cline-neutral">&nbsp;</span>
637
- <span class="cline-any cline-yes">16×</span>
691
+ <span class="cline-any cline-no">&nbsp;</span>
692
+ <span class="cline-any cline-no">&nbsp;</span>
638
693
  <span class="cline-any cline-neutral">&nbsp;</span>
639
694
  <span class="cline-any cline-neutral">&nbsp;</span>
640
695
  <span class="cline-any cline-neutral">&nbsp;</span>
@@ -642,18 +697,16 @@
642
697
  <span class="cline-any cline-neutral">&nbsp;</span>
643
698
  <span class="cline-any cline-neutral">&nbsp;</span>
644
699
  <span class="cline-any cline-neutral">&nbsp;</span>
645
- <span class="cline-any cline-yes">2×</span>
646
- <span class="cline-any cline-yes">2×</span>
647
- <span class="cline-any cline-yes">2×</span>
648
700
  <span class="cline-any cline-neutral">&nbsp;</span>
649
701
  <span class="cline-any cline-neutral">&nbsp;</span>
702
+ <span class="cline-any cline-no">&nbsp;</span>
703
+ <span class="cline-any cline-no">&nbsp;</span>
704
+ <span class="cline-any cline-no">&nbsp;</span>
650
705
  <span class="cline-any cline-neutral">&nbsp;</span>
651
706
  <span class="cline-any cline-neutral">&nbsp;</span>
652
707
  <span class="cline-any cline-neutral">&nbsp;</span>
653
708
  <span class="cline-any cline-neutral">&nbsp;</span>
654
709
  <span class="cline-any cline-neutral">&nbsp;</span>
655
- <span class="cline-any cline-yes">168×</span>
656
- <span class="cline-any cline-yes">168×</span>
657
710
  <span class="cline-any cline-neutral">&nbsp;</span>
658
711
  <span class="cline-any cline-neutral">&nbsp;</span>
659
712
  <span class="cline-any cline-neutral">&nbsp;</span>
@@ -663,9 +716,6 @@
663
716
  <span class="cline-any cline-neutral">&nbsp;</span>
664
717
  <span class="cline-any cline-neutral">&nbsp;</span>
665
718
  <span class="cline-any cline-neutral">&nbsp;</span>
666
- <span class="cline-any cline-no">&nbsp;</span>
667
- <span class="cline-any cline-no">&nbsp;</span>
668
- <span class="cline-any cline-no">&nbsp;</span>
669
719
  <span class="cline-any cline-neutral">&nbsp;</span>
670
720
  <span class="cline-any cline-neutral">&nbsp;</span>
671
721
  <span class="cline-any cline-neutral">&nbsp;</span>
@@ -689,51 +739,55 @@
689
739
  <span class="cline-any cline-neutral">&nbsp;</span>
690
740
  <span class="cline-any cline-neutral">&nbsp;</span>
691
741
  <span class="cline-any cline-neutral">&nbsp;</span>
742
+ <span class="cline-any cline-yes">1x</span>
692
743
  <span class="cline-any cline-neutral">&nbsp;</span>
744
+ <span class="cline-any cline-no">&nbsp;</span>
745
+ <span class="cline-any cline-no">&nbsp;</span>
746
+ <span class="cline-any cline-no">&nbsp;</span>
693
747
  <span class="cline-any cline-neutral">&nbsp;</span>
694
748
  <span class="cline-any cline-neutral">&nbsp;</span>
695
749
  <span class="cline-any cline-neutral">&nbsp;</span>
696
750
  <span class="cline-any cline-neutral">&nbsp;</span>
697
751
  <span class="cline-any cline-neutral">&nbsp;</span>
698
752
  <span class="cline-any cline-neutral">&nbsp;</span>
753
+ <span class="cline-any cline-no">&nbsp;</span>
754
+ <span class="cline-any cline-no">&nbsp;</span>
755
+ <span class="cline-any cline-no">&nbsp;</span>
756
+ <span class="cline-any cline-neutral">&nbsp;</span>
699
757
  <span class="cline-any cline-neutral">&nbsp;</span>
700
758
  <span class="cline-any cline-neutral">&nbsp;</span>
701
759
  <span class="cline-any cline-neutral">&nbsp;</span>
702
760
  <span class="cline-any cline-neutral">&nbsp;</span>
703
761
  <span class="cline-any cline-neutral">&nbsp;</span>
762
+ <span class="cline-any cline-no">&nbsp;</span>
763
+ <span class="cline-any cline-no">&nbsp;</span>
764
+ <span class="cline-any cline-no">&nbsp;</span>
704
765
  <span class="cline-any cline-neutral">&nbsp;</span>
705
- <span class="cline-any cline-yes">1×</span>
706
766
  <span class="cline-any cline-neutral">&nbsp;</span>
707
- <span class="cline-any cline-yes">20×</span>
708
- <span class="cline-any cline-yes">20×</span>
709
- <span class="cline-any cline-yes">20×</span>
710
767
  <span class="cline-any cline-neutral">&nbsp;</span>
711
768
  <span class="cline-any cline-neutral">&nbsp;</span>
712
769
  <span class="cline-any cline-neutral">&nbsp;</span>
713
770
  <span class="cline-any cline-neutral">&nbsp;</span>
771
+ <span class="cline-any cline-no">&nbsp;</span>
772
+ <span class="cline-any cline-no">&nbsp;</span>
773
+ <span class="cline-any cline-no">&nbsp;</span>
714
774
  <span class="cline-any cline-neutral">&nbsp;</span>
715
775
  <span class="cline-any cline-neutral">&nbsp;</span>
716
- <span class="cline-any cline-yes">28×</span>
717
- <span class="cline-any cline-yes">28×</span>
718
- <span class="cline-any cline-yes">28×</span>
719
776
  <span class="cline-any cline-neutral">&nbsp;</span>
720
777
  <span class="cline-any cline-neutral">&nbsp;</span>
721
778
  <span class="cline-any cline-neutral">&nbsp;</span>
722
779
  <span class="cline-any cline-neutral">&nbsp;</span>
723
780
  <span class="cline-any cline-neutral">&nbsp;</span>
781
+ <span class="cline-any cline-no">&nbsp;</span>
782
+ <span class="cline-any cline-no">&nbsp;</span>
724
783
  <span class="cline-any cline-neutral">&nbsp;</span>
725
- <span class="cline-any cline-yes">98398×</span>
726
- <span class="cline-any cline-yes">98398×</span>
727
- <span class="cline-any cline-yes">98398×</span>
728
784
  <span class="cline-any cline-neutral">&nbsp;</span>
729
785
  <span class="cline-any cline-neutral">&nbsp;</span>
730
786
  <span class="cline-any cline-neutral">&nbsp;</span>
731
787
  <span class="cline-any cline-neutral">&nbsp;</span>
732
788
  <span class="cline-any cline-neutral">&nbsp;</span>
789
+ <span class="cline-any cline-no">&nbsp;</span>
733
790
  <span class="cline-any cline-neutral">&nbsp;</span>
734
- <span class="cline-any cline-yes">43×</span>
735
- <span class="cline-any cline-yes">43×</span>
736
- <span class="cline-any cline-yes">43×</span>
737
791
  <span class="cline-any cline-neutral">&nbsp;</span>
738
792
  <span class="cline-any cline-neutral">&nbsp;</span>
739
793
  <span class="cline-any cline-neutral">&nbsp;</span>
@@ -741,256 +795,257 @@
741
795
  <span class="cline-any cline-neutral">&nbsp;</span>
742
796
  <span class="cline-any cline-neutral">&nbsp;</span>
743
797
  <span class="cline-any cline-no">&nbsp;</span>
744
- <span class="cline-any cline-no">&nbsp;</span>
745
798
  <span class="cline-any cline-neutral">&nbsp;</span>
746
799
  <span class="cline-any cline-neutral">&nbsp;</span>
747
800
  <span class="cline-any cline-neutral">&nbsp;</span>
748
801
  <span class="cline-any cline-neutral">&nbsp;</span>
749
802
  <span class="cline-any cline-neutral">&nbsp;</span>
750
803
  <span class="cline-any cline-neutral">&nbsp;</span>
751
- <span class="cline-any cline-no">&nbsp;</span>
752
804
  <span class="cline-any cline-neutral">&nbsp;</span>
753
805
  <span class="cline-any cline-neutral">&nbsp;</span>
754
806
  <span class="cline-any cline-neutral">&nbsp;</span>
807
+ <span class="cline-any cline-yes">1x</span>
808
+ <span class="cline-any cline-no">&nbsp;</span>
755
809
  <span class="cline-any cline-neutral">&nbsp;</span>
756
810
  <span class="cline-any cline-neutral">&nbsp;</span>
811
+ <span class="cline-any cline-yes">1x</span>
812
+ <span class="cline-any cline-no">&nbsp;</span>
813
+ <span class="cline-any cline-no">&nbsp;</span>
814
+ <span class="cline-any cline-no">&nbsp;</span>
815
+ <span class="cline-any cline-no">&nbsp;</span>
757
816
  <span class="cline-any cline-neutral">&nbsp;</span>
758
- <span class="cline-any cline-yes">63×</span>
817
+ <span class="cline-any cline-no">&nbsp;</span>
818
+ <span class="cline-any cline-no">&nbsp;</span>
759
819
  <span class="cline-any cline-neutral">&nbsp;</span>
760
820
  <span class="cline-any cline-neutral">&nbsp;</span>
761
821
  <span class="cline-any cline-neutral">&nbsp;</span>
822
+ <span class="cline-any cline-yes">1x</span>
823
+ <span class="cline-any cline-no">&nbsp;</span>
824
+ <span class="cline-any cline-no">&nbsp;</span>
825
+ <span class="cline-any cline-no">&nbsp;</span>
826
+ <span class="cline-any cline-no">&nbsp;</span>
762
827
  <span class="cline-any cline-neutral">&nbsp;</span>
828
+ <span class="cline-any cline-no">&nbsp;</span>
829
+ <span class="cline-any cline-no">&nbsp;</span>
763
830
  <span class="cline-any cline-neutral">&nbsp;</span>
764
831
  <span class="cline-any cline-neutral">&nbsp;</span>
765
- <span class="cline-any cline-yes">1×</span>
766
- <span class="cline-any cline-yes">98724×</span>
767
832
  <span class="cline-any cline-neutral">&nbsp;</span>
833
+ <span class="cline-any cline-yes">1x</span>
768
834
  <span class="cline-any cline-neutral">&nbsp;</span>
769
- <span class="cline-any cline-yes">1×</span>
770
- <span class="cline-any cline-yes">98552×</span>
771
- <span class="cline-any cline-yes">98552×</span>
772
- <span class="cline-any cline-yes">98552×</span>
773
- <span class="cline-any cline-yes">428×</span>
835
+ <span class="cline-any cline-no">&nbsp;</span>
836
+ <span class="cline-any cline-no">&nbsp;</span>
837
+ <span class="cline-any cline-no">&nbsp;</span>
774
838
  <span class="cline-any cline-neutral">&nbsp;</span>
775
- <span class="cline-any cline-yes">98124×</span>
776
- <span class="cline-any cline-yes">98124×</span>
777
839
  <span class="cline-any cline-neutral">&nbsp;</span>
778
840
  <span class="cline-any cline-neutral">&nbsp;</span>
841
+ <span class="cline-any cline-no">&nbsp;</span>
842
+ <span class="cline-any cline-no">&nbsp;</span>
843
+ <span class="cline-any cline-no">&nbsp;</span>
779
844
  <span class="cline-any cline-neutral">&nbsp;</span>
780
- <span class="cline-any cline-yes">1×</span>
781
- <span class="cline-any cline-yes">172×</span>
782
- <span class="cline-any cline-yes">172×</span>
783
- <span class="cline-any cline-yes">172×</span>
784
- <span class="cline-any cline-yes">168×</span>
785
845
  <span class="cline-any cline-neutral">&nbsp;</span>
786
- <span class="cline-any cline-yes">4×</span>
787
- <span class="cline-any cline-yes">4×</span>
788
846
  <span class="cline-any cline-neutral">&nbsp;</span>
789
847
  <span class="cline-any cline-neutral">&nbsp;</span>
848
+ <span class="cline-any cline-yes">1x</span>
790
849
  <span class="cline-any cline-neutral">&nbsp;</span>
791
- <span class="cline-any cline-yes">1×</span>
850
+ <span class="cline-any cline-no">&nbsp;</span>
792
851
  <span class="cline-any cline-neutral">&nbsp;</span>
793
- <span class="cline-any cline-yes">401×</span>
794
- <span class="cline-any cline-yes">5642×</span>
795
- <span class="cline-any cline-yes">8×</span>
796
852
  <span class="cline-any cline-neutral">&nbsp;</span>
797
853
  <span class="cline-any cline-neutral">&nbsp;</span>
798
854
  <span class="cline-any cline-neutral">&nbsp;</span>
799
- <span class="cline-any cline-yes">401×</span>
800
- <span class="cline-any cline-yes">5641×</span>
801
- <span class="cline-any cline-yes">8×</span>
802
855
  <span class="cline-any cline-neutral">&nbsp;</span>
803
856
  <span class="cline-any cline-neutral">&nbsp;</span>
804
857
  <span class="cline-any cline-neutral">&nbsp;</span>
805
858
  <span class="cline-any cline-neutral">&nbsp;</span>
806
- <span class="cline-any cline-yes">1×</span>
807
- <span class="cline-any cline-yes">409×</span>
808
- <span class="cline-any cline-yes">409×</span>
809
859
  <span class="cline-any cline-neutral">&nbsp;</span>
810
860
  <span class="cline-any cline-neutral">&nbsp;</span>
811
861
  <span class="cline-any cline-neutral">&nbsp;</span>
812
862
  <span class="cline-any cline-neutral">&nbsp;</span>
813
863
  <span class="cline-any cline-neutral">&nbsp;</span>
814
864
  <span class="cline-any cline-neutral">&nbsp;</span>
865
+ <span class="cline-any cline-no">&nbsp;</span>
866
+ <span class="cline-any cline-no">&nbsp;</span>
867
+ <span class="cline-any cline-no">&nbsp;</span>
815
868
  <span class="cline-any cline-neutral">&nbsp;</span>
816
869
  <span class="cline-any cline-neutral">&nbsp;</span>
817
- <span class="cline-any cline-yes">409×</span>
818
- <span class="cline-any cline-yes">409×</span>
819
- <span class="cline-any cline-yes">409×</span>
820
- <span class="cline-any cline-yes">409×</span>
821
- <span class="cline-any cline-yes">409×</span>
822
- <span class="cline-any cline-yes">409×</span>
823
- <span class="cline-any cline-yes">409×</span>
824
- <span class="cline-any cline-yes">409×</span>
825
- <span class="cline-any cline-yes">409×</span>
870
+ <span class="cline-any cline-no">&nbsp;</span>
871
+ <span class="cline-any cline-no">&nbsp;</span>
826
872
  <span class="cline-any cline-neutral">&nbsp;</span>
827
873
  <span class="cline-any cline-neutral">&nbsp;</span>
828
- <span class="cline-any cline-yes">409×</span>
829
- <span class="cline-any cline-yes">3028×</span>
874
+ <span class="cline-any cline-no">&nbsp;</span>
875
+ <span class="cline-any cline-no">&nbsp;</span>
830
876
  <span class="cline-any cline-neutral">&nbsp;</span>
831
877
  <span class="cline-any cline-neutral">&nbsp;</span>
832
- <span class="cline-any cline-yes">345×</span>
833
- <span class="cline-any cline-yes">2683×</span>
878
+ <span class="cline-any cline-no">&nbsp;</span>
879
+ <span class="cline-any cline-no">&nbsp;</span>
880
+ <span class="cline-any cline-no">&nbsp;</span>
881
+ <span class="cline-any cline-neutral">&nbsp;</span>
834
882
  <span class="cline-any cline-neutral">&nbsp;</span>
835
883
  <span class="cline-any cline-neutral">&nbsp;</span>
836
- <span class="cline-any cline-yes">202×</span>
837
- <span class="cline-any cline-yes">202×</span>
838
- <span class="cline-any cline-yes">202×</span>
839
884
  <span class="cline-any cline-neutral">&nbsp;</span>
840
885
  <span class="cline-any cline-neutral">&nbsp;</span>
841
886
  <span class="cline-any cline-neutral">&nbsp;</span>
887
+ <span class="cline-any cline-no">&nbsp;</span>
888
+ <span class="cline-any cline-no">&nbsp;</span>
889
+ <span class="cline-any cline-no">&nbsp;</span>
842
890
  <span class="cline-any cline-neutral">&nbsp;</span>
843
891
  <span class="cline-any cline-neutral">&nbsp;</span>
892
+ <span class="cline-any cline-no">&nbsp;</span>
893
+ <span class="cline-any cline-no">&nbsp;</span>
894
+ <span class="cline-any cline-no">&nbsp;</span>
895
+ <span class="cline-any cline-no">&nbsp;</span>
844
896
  <span class="cline-any cline-neutral">&nbsp;</span>
845
- <span class="cline-any cline-yes">409×</span>
846
- <span class="cline-any cline-yes">2×</span>
847
- <span class="cline-any cline-yes">2×</span>
848
897
  <span class="cline-any cline-neutral">&nbsp;</span>
849
898
  <span class="cline-any cline-neutral">&nbsp;</span>
850
- <span class="cline-any cline-yes">407×</span>
851
- <span class="cline-any cline-yes">6663×</span>
852
- <span class="cline-any cline-yes">168×</span>
853
- <span class="cline-any cline-yes">4×</span>
854
899
  <span class="cline-any cline-neutral">&nbsp;</span>
855
900
  <span class="cline-any cline-neutral">&nbsp;</span>
901
+ <span class="cline-any cline-no">&nbsp;</span>
902
+ <span class="cline-any cline-no">&nbsp;</span>
856
903
  <span class="cline-any cline-neutral">&nbsp;</span>
904
+ <span class="cline-any cline-no">&nbsp;</span>
857
905
  <span class="cline-any cline-neutral">&nbsp;</span>
906
+ <span class="cline-any cline-no">&nbsp;</span>
907
+ <span class="cline-any cline-no">&nbsp;</span>
858
908
  <span class="cline-any cline-neutral">&nbsp;</span>
859
- <span class="cline-any cline-yes">6495×</span>
860
- <span class="cline-any cline-yes">6495×</span>
861
- <span class="cline-any cline-yes">231319×</span>
909
+ <span class="cline-any cline-no">&nbsp;</span>
910
+ <span class="cline-any cline-no">&nbsp;</span>
911
+ <span class="cline-any cline-no">&nbsp;</span>
912
+ <span class="cline-any cline-no">&nbsp;</span>
862
913
  <span class="cline-any cline-neutral">&nbsp;</span>
863
- <span class="cline-any cline-yes">6117×</span>
864
- <span class="cline-any cline-yes">6117×</span>
865
914
  <span class="cline-any cline-neutral">&nbsp;</span>
866
- <span class="cline-any cline-yes">6117×</span>
867
- <span class="cline-any cline-yes">20×</span>
868
- <span class="cline-any cline-yes">6097×</span>
869
915
  <span class="cline-any cline-no">&nbsp;</span>
916
+ <span class="cline-any cline-no">&nbsp;</span>
917
+ <span class="cline-any cline-no">&nbsp;</span>
918
+ <span class="cline-any cline-no">&nbsp;</span>
919
+ <span class="cline-any cline-neutral">&nbsp;</span>
870
920
  <span class="cline-any cline-neutral">&nbsp;</span>
871
- <span class="cline-any cline-yes">6097×</span>
872
- <span class="cline-any cline-yes">6097×</span>
873
- <span class="cline-any cline-yes">6097×</span>
874
- <span class="cline-any cline-yes">6097×</span>
921
+ <span class="cline-any cline-no">&nbsp;</span>
922
+ <span class="cline-any cline-no">&nbsp;</span>
875
923
  <span class="cline-any cline-neutral">&nbsp;</span>
924
+ <span class="cline-any cline-no">&nbsp;</span>
876
925
  <span class="cline-any cline-neutral">&nbsp;</span>
877
926
  <span class="cline-any cline-no">&nbsp;</span>
878
927
  <span class="cline-any cline-no">&nbsp;</span>
928
+ <span class="cline-any cline-no">&nbsp;</span>
929
+ <span class="cline-any cline-no">&nbsp;</span>
930
+ <span class="cline-any cline-no">&nbsp;</span>
931
+ <span class="cline-any cline-no">&nbsp;</span>
879
932
  <span class="cline-any cline-neutral">&nbsp;</span>
880
- <span class="cline-any cline-yes">225202×</span>
881
933
  <span class="cline-any cline-neutral">&nbsp;</span>
882
- <span class="cline-any cline-yes">6088×</span>
883
- <span class="cline-any cline-yes">6088×</span>
884
- <span class="cline-any cline-yes">6088×</span>
885
- <span class="cline-any cline-yes">28×</span>
886
- <span class="cline-any cline-yes">6060×</span>
934
+ <span class="cline-any cline-no">&nbsp;</span>
887
935
  <span class="cline-any cline-no">&nbsp;</span>
888
936
  <span class="cline-any cline-neutral">&nbsp;</span>
889
- <span class="cline-any cline-yes">6060×</span>
890
937
  <span class="cline-any cline-neutral">&nbsp;</span>
891
938
  <span class="cline-any cline-neutral">&nbsp;</span>
892
939
  <span class="cline-any cline-neutral">&nbsp;</span>
940
+ <span class="cline-any cline-no">&nbsp;</span>
941
+ <span class="cline-any cline-no">&nbsp;</span>
942
+ <span class="cline-any cline-no">&nbsp;</span>
943
+ <span class="cline-any cline-neutral">&nbsp;</span>
893
944
  <span class="cline-any cline-neutral">&nbsp;</span>
894
- <span class="cline-any cline-yes">6060×</span>
895
- <span class="cline-any cline-yes">87×</span>
896
- <span class="cline-any cline-yes">87×</span>
897
- <span class="cline-any cline-yes">87×</span>
945
+ <span class="cline-any cline-neutral">&nbsp;</span>
946
+ <span class="cline-any cline-no">&nbsp;</span>
947
+ <span class="cline-any cline-no">&nbsp;</span>
948
+ <span class="cline-any cline-no">&nbsp;</span>
949
+ <span class="cline-any cline-no">&nbsp;</span>
898
950
  <span class="cline-any cline-neutral">&nbsp;</span>
899
951
  <span class="cline-any cline-neutral">&nbsp;</span>
952
+ <span class="cline-any cline-no">&nbsp;</span>
953
+ <span class="cline-any cline-no">&nbsp;</span>
900
954
  <span class="cline-any cline-neutral">&nbsp;</span>
901
955
  <span class="cline-any cline-no">&nbsp;</span>
902
956
  <span class="cline-any cline-no">&nbsp;</span>
957
+ <span class="cline-any cline-neutral">&nbsp;</span>
903
958
  <span class="cline-any cline-no">&nbsp;</span>
904
959
  <span class="cline-any cline-no">&nbsp;</span>
905
960
  <span class="cline-any cline-neutral">&nbsp;</span>
961
+ <span class="cline-any cline-no">&nbsp;</span>
906
962
  <span class="cline-any cline-neutral">&nbsp;</span>
907
- <span class="cline-any cline-yes">219114×</span>
908
- <span class="cline-any cline-yes">219114×</span>
963
+ <span class="cline-any cline-no">&nbsp;</span>
964
+ <span class="cline-any cline-no">&nbsp;</span>
965
+ <span class="cline-any cline-no">&nbsp;</span>
966
+ <span class="cline-any cline-no">&nbsp;</span>
967
+ <span class="cline-any cline-no">&nbsp;</span>
909
968
  <span class="cline-any cline-neutral">&nbsp;</span>
910
- <span class="cline-any cline-yes">98398×</span>
911
- <span class="cline-any cline-yes">120716×</span>
912
- <span class="cline-any cline-yes">2×</span>
913
- <span class="cline-any cline-yes">2×</span>
969
+ <span class="cline-any cline-no">&nbsp;</span>
914
970
  <span class="cline-any cline-neutral">&nbsp;</span>
915
- <span class="cline-any cline-yes">120714×</span>
916
971
  <span class="cline-any cline-neutral">&nbsp;</span>
917
- <span class="cline-any cline-yes">11264×</span>
918
- <span class="cline-any cline-yes">11264×</span>
919
- <span class="cline-any cline-yes">11264×</span>
920
- <span class="cline-any cline-yes">43×</span>
921
- <span class="cline-any cline-yes">11221×</span>
972
+ <span class="cline-any cline-no">&nbsp;</span>
973
+ <span class="cline-any cline-no">&nbsp;</span>
922
974
  <span class="cline-any cline-no">&nbsp;</span>
923
975
  <span class="cline-any cline-neutral">&nbsp;</span>
924
976
  <span class="cline-any cline-neutral">&nbsp;</span>
925
- <span class="cline-any cline-yes">11221×</span>
926
- <span class="cline-any cline-yes">11221×</span>
927
- <span class="cline-any cline-yes">11221×</span>
928
977
  <span class="cline-any cline-neutral">&nbsp;</span>
929
- <span class="cline-any cline-yes">11221×</span>
930
- <span class="cline-any cline-yes">4540×</span>
931
- <span class="cline-any cline-yes">2250×</span>
932
- <span class="cline-any cline-yes">2250×</span>
933
- <span class="cline-any cline-yes">2250×</span>
978
+ <span class="cline-any cline-no">&nbsp;</span>
979
+ <span class="cline-any cline-no">&nbsp;</span>
934
980
  <span class="cline-any cline-neutral">&nbsp;</span>
935
- <span class="cline-any cline-yes">2290×</span>
936
- <span class="cline-any cline-yes">2290×</span>
937
- <span class="cline-any cline-yes">2290×</span>
981
+ <span class="cline-any cline-no">&nbsp;</span>
938
982
  <span class="cline-any cline-neutral">&nbsp;</span>
939
- <span class="cline-any cline-yes">6681×</span>
940
- <span class="cline-any cline-yes">6681×</span>
941
- <span class="cline-any cline-yes">6681×</span>
942
- <span class="cline-any cline-yes">6681×</span>
943
- <span class="cline-any cline-yes">63×</span>
944
- <span class="cline-any cline-yes">63×</span>
945
983
  <span class="cline-any cline-neutral">&nbsp;</span>
946
- <span class="cline-any cline-yes">6681×</span>
947
984
  <span class="cline-any cline-neutral">&nbsp;</span>
948
- <span class="cline-any cline-yes">11221×</span>
985
+ <span class="cline-any cline-no">&nbsp;</span>
986
+ <span class="cline-any cline-no">&nbsp;</span>
949
987
  <span class="cline-any cline-neutral">&nbsp;</span>
988
+ <span class="cline-any cline-no">&nbsp;</span>
950
989
  <span class="cline-any cline-neutral">&nbsp;</span>
951
990
  <span class="cline-any cline-neutral">&nbsp;</span>
991
+ <span class="cline-any cline-no">&nbsp;</span>
992
+ <span class="cline-any cline-no">&nbsp;</span>
952
993
  <span class="cline-any cline-neutral">&nbsp;</span>
994
+ <span class="cline-any cline-no">&nbsp;</span>
995
+ <span class="cline-any cline-no">&nbsp;</span>
996
+ <span class="cline-any cline-no">&nbsp;</span>
997
+ <span class="cline-any cline-no">&nbsp;</span>
998
+ <span class="cline-any cline-no">&nbsp;</span>
999
+ <span class="cline-any cline-no">&nbsp;</span>
953
1000
  <span class="cline-any cline-neutral">&nbsp;</span>
954
1001
  <span class="cline-any cline-no">&nbsp;</span>
955
1002
  <span class="cline-any cline-neutral">&nbsp;</span>
956
1003
  <span class="cline-any cline-no">&nbsp;</span>
957
1004
  <span class="cline-any cline-neutral">&nbsp;</span>
958
1005
  <span class="cline-any cline-neutral">&nbsp;</span>
959
- <span class="cline-any cline-yes">231317×</span>
960
1006
  <span class="cline-any cline-neutral">&nbsp;</span>
961
- <span class="cline-any cline-yes">6493×</span>
962
1007
  <span class="cline-any cline-neutral">&nbsp;</span>
963
1008
  <span class="cline-any cline-neutral">&nbsp;</span>
964
1009
  <span class="cline-any cline-no">&nbsp;</span>
1010
+ <span class="cline-any cline-neutral">&nbsp;</span>
965
1011
  <span class="cline-any cline-no">&nbsp;</span>
966
1012
  <span class="cline-any cline-neutral">&nbsp;</span>
967
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1014
+ <span class="cline-any cline-no">&nbsp;</span>
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1016
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1019
+ <span class="cline-any cline-no">&nbsp;</span>
1020
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974
1024
  <span class="cline-any cline-neutral">&nbsp;</span>
975
- <span class="cline-any cline-yes">401×</span>
976
- <span class="cline-any cline-yes">401×</span>
977
1025
  <span class="cline-any cline-neutral">&nbsp;</span>
978
1026
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979
- <span class="cline-any cline-yes">401×</span>
980
1027
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981
1028
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982
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1030
+ <span class="cline-any cline-no">&nbsp;</span>
1031
+ <span class="cline-any cline-no">&nbsp;</span>
1032
+ <span class="cline-any cline-neutral">&nbsp;</span>
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+ <span class="cline-any cline-neutral">&nbsp;</span>
1034
+ <span class="cline-any cline-no">&nbsp;</span>
1035
+ <span class="cline-any cline-neutral">&nbsp;</span>
983
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984
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985
1038
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986
1039
  <span class="cline-any cline-neutral">&nbsp;</span>
987
- <span class="cline-any cline-yes">401×</span>
988
1040
  <span class="cline-any cline-neutral">&nbsp;</span>
989
1041
  <span class="cline-any cline-neutral">&nbsp;</span>
990
- <span class="cline-any cline-yes">1×</span>
991
- <span class="cline-any cline-no">&nbsp;</span>
992
1042
  <span class="cline-any cline-no">&nbsp;</span>
993
1043
  <span class="cline-any cline-neutral">&nbsp;</span>
1044
+ <span class="cline-any cline-neutral">&nbsp;</span>
1045
+ <span class="cline-any cline-yes">1x</span>
1046
+ <span class="cline-any cline-neutral">&nbsp;</span>
1047
+ <span class="cline-any cline-neutral">&nbsp;</span>
1048
+ <span class="cline-any cline-neutral">&nbsp;</span>
994
1049
  <span class="cline-any cline-no">&nbsp;</span>
995
1050
  <span class="cline-any cline-neutral">&nbsp;</span>
996
1051
  <span class="cline-any cline-no">&nbsp;</span>
@@ -1002,6 +1057,10 @@
1002
1057
  <span class="cline-any cline-no">&nbsp;</span>
1003
1058
  <span class="cline-any cline-no">&nbsp;</span>
1004
1059
  <span class="cline-any cline-neutral">&nbsp;</span>
1060
+ <span class="cline-any cline-neutral">&nbsp;</span>
1061
+ <span class="cline-any cline-no">&nbsp;</span>
1062
+ <span class="cline-any cline-no">&nbsp;</span>
1063
+ <span class="cline-any cline-neutral">&nbsp;</span>
1005
1064
  <span class="cline-any cline-no">&nbsp;</span>
1006
1065
  <span class="cline-any cline-neutral">&nbsp;</span>
1007
1066
  <span class="cline-any cline-neutral">&nbsp;</span>
@@ -1009,7 +1068,7 @@
1009
1068
  <span class="cline-any cline-neutral">&nbsp;</span>
1010
1069
  <span class="cline-any cline-neutral">&nbsp;</span>
1011
1070
  <span class="cline-any cline-neutral">&nbsp;</span>
1012
- <span class="cline-any cline-yes">1×</span>
1071
+ <span class="cline-any cline-yes">1x</span>
1013
1072
  <span class="cline-any cline-no">&nbsp;</span>
1014
1073
  <span class="cline-any cline-no">&nbsp;</span>
1015
1074
  <span class="cline-any cline-no">&nbsp;</span>
@@ -1071,8 +1130,8 @@
1071
1130
  <span class="cline-any cline-neutral">&nbsp;</span>
1072
1131
  <span class="cline-any cline-neutral">&nbsp;</span>
1073
1132
  <span class="cline-any cline-neutral">&nbsp;</span>
1074
- <span class="cline-any cline-yes">1×</span>
1075
- <span class="cline-any cline-yes">2×</span>
1133
+ <span class="cline-any cline-yes">1x</span>
1134
+ <span class="cline-any cline-yes">2x</span>
1076
1135
  <span class="cline-any cline-neutral">&nbsp;</span>
1077
1136
  <span class="cline-any cline-neutral">&nbsp;</span>
1078
1137
  <span class="cline-any cline-no">&nbsp;</span>
@@ -1095,6 +1154,8 @@
1095
1154
  <span class="cline-any cline-neutral">&nbsp;</span>
1096
1155
  <span class="cline-any cline-neutral">&nbsp;</span>
1097
1156
  <span class="cline-any cline-neutral">&nbsp;</span>
1157
+ <span class="cline-any cline-neutral">&nbsp;</span>
1158
+ <span class="cline-any cline-neutral">&nbsp;</span>
1098
1159
  <span class="cline-any cline-no">&nbsp;</span>
1099
1160
  <span class="cline-any cline-neutral">&nbsp;</span>
1100
1161
  <span class="cline-any cline-neutral">&nbsp;</span>
@@ -1108,6 +1169,7 @@
1108
1169
  <span class="cline-any cline-no">&nbsp;</span>
1109
1170
  <span class="cline-any cline-neutral">&nbsp;</span>
1110
1171
  <span class="cline-any cline-neutral">&nbsp;</span>
1172
+ <span class="cline-any cline-neutral">&nbsp;</span>
1111
1173
  <span class="cline-any cline-no">&nbsp;</span>
1112
1174
  <span class="cline-any cline-no">&nbsp;</span>
1113
1175
  <span class="cline-any cline-neutral">&nbsp;</span>
@@ -1118,7 +1180,8 @@
1118
1180
  <span class="cline-any cline-neutral">&nbsp;</span>
1119
1181
  <span class="cline-any cline-neutral">&nbsp;</span>
1120
1182
  <span class="cline-any cline-neutral">&nbsp;</span>
1121
- <span class="cline-any cline-yes">2×</span>
1183
+ <span class="cline-any cline-neutral">&nbsp;</span>
1184
+ <span class="cline-any cline-yes">2x</span>
1122
1185
  <span class="cline-any cline-neutral">&nbsp;</span>
1123
1186
  <span class="cline-any cline-neutral">&nbsp;</span>
1124
1187
  <span class="cline-any cline-neutral">&nbsp;</span>
@@ -1127,6 +1190,7 @@
1127
1190
  var xlsx = require("node-xlsx");
1128
1191
  // var util = require("util");
1129
1192
  var path = require("path");
1193
+ var parseAdditionalSheets = require(__dirname + "/additional-sheet-parser");
1130
1194
  // var cytoscape = require("cytoscape"); //NOTE: Commented out for issue #474
1131
1195
  &nbsp;
1132
1196
  var helpers = require(__dirname + "/helpers");
@@ -1149,13 +1213,14 @@ var errorList = {
1149
1213
  missingNetworkError: {
1150
1214
  errorCode: "MISSING_NETWORK",
1151
1215
  possibleCause: "This file does not have a 'network' sheet or a 'network_optimized_weights' sheet.",
1152
- suggestedFix: "Please select another file, or rename the sheet containing the adjacency matrix accordingly. Please refer to the " +
1153
- "&lt;a href='http://dondi.github.io/GRNsight/documentation.html#section1' target='_blank'&gt;Documentation page&lt;/a&gt; for more information."
1216
+ suggestedFix: "Please select another file, or rename the sheet containing the adjacency matrix accordingly. \
1217
+ Please refer to the " + "&lt;a href='http://dondi.github.io/GRNsight/documentation.html#section1' \
1218
+ target='_blank'&gt;Documentation page&lt;/a&gt; for more information."
1154
1219
  },
1155
1220
  &nbsp;
1156
- corruptGeneError: <span class="fstat-no" title="function not covered" >function (row, column) {</span>
1157
- <span class="cstat-no" title="statement not covered" > var colLetter = numbersToLetters[column];</span>
1158
- <span class="cstat-no" title="statement not covered" > var rowNum = row + 1;</span>
1221
+ corruptGeneError: <span class="fstat-no" title="function not covered" >fu</span>nction (row, column) {
1222
+ var colLetter = <span class="cstat-no" title="statement not covered" >numbersToLetters[column];</span>
1223
+ var rowNum = <span class="cstat-no" title="statement not covered" >row + 1;</span>
1159
1224
  <span class="cstat-no" title="statement not covered" > return {</span>
1160
1225
  errorCode: "CORRUPT_GENE",
1161
1226
  possibleCause: "The gene name in cell " + colLetter + rowNum + " appears to be invalid.",
@@ -1163,37 +1228,38 @@ var errorList = {
1163
1228
  };
1164
1229
  },
1165
1230
  &nbsp;
1166
- missingValueError: <span class="fstat-no" title="function not covered" >function (row, column) {</span>
1167
- <span class="cstat-no" title="statement not covered" > var colLetter = numbersToLetters[column];</span>
1168
- <span class="cstat-no" title="statement not covered" > var rowNum = row + 1;</span>
1231
+ missingValueError: <span class="fstat-no" title="function not covered" >fu</span>nction (row, column) {
1232
+ var colLetter = <span class="cstat-no" title="statement not covered" >numbersToLetters[column];</span>
1233
+ var rowNum = <span class="cstat-no" title="statement not covered" >row + 1;</span>
1169
1234
  <span class="cstat-no" title="statement not covered" > return {</span>
1170
1235
  errorCode: "MISSING_VALUE",
1171
- possibleCause: "The value in the cell " + colLetter + rowNum + " in the adjacency matrix appears to have a missing value.",
1236
+ possibleCause: "The value in the cell " + colLetter + rowNum +
1237
+ " in the adjacency matrix appears to have a missing value.",
1172
1238
  suggestedFix: "Please ensure that all cells have a value, then upload the file again."
1173
1239
  };
1174
1240
  },
1175
1241
  &nbsp;
1176
- duplicateGeneError: function(geneType, geneName) {
1177
- return {
1242
+ duplicateGeneError: <span class="fstat-no" title="function not covered" >fu</span>nction (geneType, geneName) {
1243
+ <span class="cstat-no" title="statement not covered" > return {</span>
1178
1244
  errorCode: "DUPLICATE_GENE",
1179
1245
  possibleCause: "There exists a duplicate for " + geneType + " gene " + geneName + ".",
1180
1246
  suggestedFix: "Please remove the duplicate gene and submit again."
1181
1247
  };
1182
1248
  },
1183
1249
  &nbsp;
1184
- dataTypeError: function (row, column) {
1185
- var colLetter = numbersToLetters[column];
1186
- var rowNum = row + 1;
1187
- return {
1250
+ dataTypeError: <span class="fstat-no" title="function not covered" >fu</span>nction (row, column) {
1251
+ var colLetter = <span class="cstat-no" title="statement not covered" >numbersToLetters[column];</span>
1252
+ var rowNum = <span class="cstat-no" title="statement not covered" >row + 1;</span>
1253
+ <span class="cstat-no" title="statement not covered" > return {</span>
1188
1254
  errorCode: "INVALID_CELL_DATA_TYPE",
1189
1255
  possibleCause: "The value in cell " + colLetter + rowNum + " is not a number.",
1190
1256
  suggestedFix: "Please ensure all values in the data matrix are numbers and try again."
1191
1257
  };
1192
1258
  },
1193
1259
  &nbsp;
1194
- emptyRowError: function (row) {
1195
- var rowNum = row + 1;
1196
- return {
1260
+ emptyRowError: <span class="fstat-no" title="function not covered" >fu</span>nction (row) {
1261
+ var rowNum = <span class="cstat-no" title="statement not covered" >row + 1;</span>
1262
+ <span class="cstat-no" title="statement not covered" > return {</span>
1197
1263
  errorCode: "EMPTY_ROW",
1198
1264
  possibleCause: "Row " + rowNum + " does not contain any data.",
1199
1265
  suggestedFix: "Please ensure all rows contain data and all empty rows are removed. " +
@@ -1202,9 +1268,9 @@ var errorList = {
1202
1268
  };
1203
1269
  },
1204
1270
  &nbsp;
1205
- outsideCellError: <span class="fstat-no" title="function not covered" >function (row, column) {</span>
1206
- <span class="cstat-no" title="statement not covered" > var colLetter = numbersToLetters[column];</span>
1207
- <span class="cstat-no" title="statement not covered" > var rowNum = row + 1;</span>
1271
+ outsideCellError: <span class="fstat-no" title="function not covered" >fu</span>nction (row, column) {
1272
+ var colLetter = <span class="cstat-no" title="statement not covered" >numbersToLetters[column];</span>
1273
+ var rowNum = <span class="cstat-no" title="statement not covered" >row + 1;</span>
1208
1274
  <span class="cstat-no" title="statement not covered" > return {</span>
1209
1275
  errorCode: "EMPTY_CELL",
1210
1276
  possibleCause: "The cell at " + colLetter + rowNum + " contains data that is outside the matrix.",
@@ -1234,7 +1300,8 @@ var errorList = {
1234
1300
  unknownError: {
1235
1301
  errorCode: "UNKNOWN_ERROR",
1236
1302
  possibleCause: "An unexpected error occurred.",
1237
- suggestedFix: "Please contact the GRNsight team at kdahlquist@lmu.edu, and attach the spreadsheet you attempted to upload."
1303
+ suggestedFix: "Please contact the GRNsight team at kdahlquist@lmu.edu, \
1304
+ and attach the spreadsheet you attempted to upload."
1238
1305
  }
1239
1306
  &nbsp;
1240
1307
  };
@@ -1243,109 +1310,114 @@ var errorList = {
1243
1310
  // This is the list of warnings.
1244
1311
  // The graph will still load if warnings are detected, but these will be reported to the user.
1245
1312
  var warningsList = {
1246
- missingSourceGeneWarning: function (row, column) {
1247
- var colLetter = numbersToLetters[column];
1248
- var rowNum = row + 1;
1249
- return {
1313
+ missingSourceGeneWarning: <span class="fstat-no" title="function not covered" >fu</span>nction (row, column) {
1314
+ var colLetter = <span class="cstat-no" title="statement not covered" >numbersToLetters[column];</span>
1315
+ var rowNum = <span class="cstat-no" title="statement not covered" >row + 1;</span>
1316
+ <span class="cstat-no" title="statement not covered" > return {</span>
1250
1317
  warningCode: "MISSING_SOURCE",
1251
1318
  errorDescription: "A source gene name is missing in cell " + colLetter + rowNum + "."
1252
1319
  };
1253
1320
  },
1254
1321
  &nbsp;
1255
- missingTargetGeneWarning: function (row, column) {
1256
- var colLetter = numbersToLetters[column];
1257
- var rowNum = row + 1;
1258
- return {
1322
+ missingTargetGeneWarning: <span class="fstat-no" title="function not covered" >fu</span>nction (row, column) {
1323
+ var colLetter = <span class="cstat-no" title="statement not covered" >numbersToLetters[column];</span>
1324
+ var rowNum = <span class="cstat-no" title="statement not covered" >row + 1;</span>
1325
+ <span class="cstat-no" title="statement not covered" > return {</span>
1259
1326
  warningCode: "MISSING_TARGET",
1260
1327
  errorDescription: "A target gene name is missing in cell " + colLetter + rowNum + "."
1261
1328
  };
1262
1329
  },
1263
1330
  &nbsp;
1264
- invalidMatrixDataWarning: function (row, column) {
1265
- var colLetter = numbersToLetters[column];
1266
- var rowNum = row + 1;
1267
- return {
1331
+ invalidMatrixDataWarning: <span class="fstat-no" title="function not covered" >fu</span>nction (row, column) {
1332
+ var colLetter = <span class="cstat-no" title="statement not covered" >numbersToLetters[column];</span>
1333
+ var rowNum = <span class="cstat-no" title="statement not covered" >row + 1;</span>
1334
+ <span class="cstat-no" title="statement not covered" > return {</span>
1268
1335
  warningCode: "INVALID_DATA",
1269
1336
  errorDescription: "The value in cell " + colLetter + rowNum + ", is undefined."
1270
1337
  };
1271
1338
  },
1272
1339
  &nbsp;
1273
- randomDataWarning: function (type, row, column) {
1274
- var colLetter = numbersToLetters[column];
1275
- var rowNum = row + 1;
1276
- return {
1340
+ randomDataWarning: <span class="fstat-no" title="function not covered" >fu</span>nction (type, row, column) {
1341
+ var colLetter = <span class="cstat-no" title="statement not covered" >numbersToLetters[column];</span>
1342
+ var rowNum = <span class="cstat-no" title="statement not covered" >row + 1;</span>
1343
+ <span class="cstat-no" title="statement not covered" > return {</span>
1277
1344
  warningCode: "RANDOM_DATA",
1278
- errorDescription: "The value in cell " + colLetter + rowNum + ", has a corresponding source and/or target gene that is detected as " + type + "."
1345
+ errorDescription: "The value in cell " + colLetter + rowNum +
1346
+ ", has a corresponding source and/or target gene that is detected as " + type + "."
1279
1347
  };
1280
1348
  },
1281
1349
  &nbsp;
1282
- emptyRowWarning: <span class="fstat-no" title="function not covered" >function (row) {</span>
1283
- <span class="cstat-no" title="statement not covered" > var rowNum = row + 1;</span>
1350
+ emptyRowWarning: <span class="fstat-no" title="function not covered" >fu</span>nction (row) {
1351
+ var rowNum = <span class="cstat-no" title="statement not covered" >row + 1;</span>
1284
1352
  <span class="cstat-no" title="statement not covered" > return {</span>
1285
1353
  warningCode: "EMPTY_ROW",
1286
1354
  errorDescription: "Row " + rowNum + " was found to contain no data."
1287
1355
  };
1288
1356
  },
1289
1357
  &nbsp;
1290
- networkSizeWarning: <span class="fstat-no" title="function not covered" >function (genesLength, edgesLength) {</span>
1358
+ networkSizeWarning: <span class="fstat-no" title="function not covered" >fu</span>nction (genesLength, edgesLength) {
1291
1359
  <span class="cstat-no" title="statement not covered" > return {</span>
1292
1360
  warningCode: "INVALID_NETWORK_SIZE",
1293
- errorDescription: "Your network has " + genesLength + " genes, and " + edgesLength + " edges. Please note that networks are recommended to have less than 50 genes and 100 edges."
1361
+ errorDescription: "Your network has " + genesLength + " genes, and " + edgesLength +
1362
+ " edges. Please note that networks are recommended to have less than 50 genes and 100 edges."
1294
1363
  };
1295
1364
  },
1296
1365
  &nbsp;
1297
- incorrectlyNamedSheetWarning: function() {
1298
- return {
1366
+ incorrectlyNamedSheetWarning: <span class="fstat-no" title="function not covered" >fu</span>nction () {
1367
+ <span class="cstat-no" title="statement not covered" > return {</span>
1299
1368
  warningCode: "INCORRECTLY_NAMED_SHEET",
1300
- errorDescription: "The uploaded file appears to contain a weighted network, but contains no 'network_optimized_weights' sheet. A weighted network must be contained in a sheet called 'network_optimized_weights' in order to be drawn as a weighted graph. Please check if the sheet(s) in the uploaded spreadsheet have been named properly."
1369
+ errorDescription: "The uploaded file appears to contain a weighted network, but contains no \
1370
+ 'network_optimized_weights' sheet. A weighted network must be contained in a sheet called \
1371
+ 'network_optimized_weights' in order to be drawn as a weighted graph. \
1372
+ Please check if the sheet(s) in the uploaded spreadsheet have been named properly."
1301
1373
  };
1302
1374
  }
1303
1375
  };
1304
1376
  &nbsp;
1305
- var addMessageToArray = function (messageArray, message) {
1306
- messageArray.push(message);
1377
+ var addMessageToArray = <span class="fstat-no" title="function not covered" >fu</span>nction (messageArray, message) {
1378
+ <span class="cstat-no" title="statement not covered" > messageArray.push(message);</span>
1307
1379
  };
1308
1380
  &nbsp;
1309
- var addWarning = function (network, message) {
1310
- var warningsCount = network.warnings.length;
1311
- var MAX_WARNINGS = 75;
1312
- if (warningsCount &lt; MAX_WARNINGS) {
1313
- addMessageToArray(network.warnings, message);
1381
+ var addWarning = <span class="fstat-no" title="function not covered" >fu</span>nction (network, message) {
1382
+ var warningsCount = <span class="cstat-no" title="statement not covered" >network.warnings.length;</span>
1383
+ var MAX_WARNINGS = <span class="cstat-no" title="statement not covered" >75;</span>
1384
+ <span class="cstat-no" title="statement not covered" > if (warningsCount &lt; MAX_WARNINGS) {</span>
1385
+ <span class="cstat-no" title="statement not covered" > addMessageToArray(network.warnings, message);</span>
1314
1386
  } else {
1315
- addMessageToArray(network.errors, errorList.warningsCountError);
1316
- return false;
1387
+ <span class="cstat-no" title="statement not covered" > addMessageToArray(network.errors, errorList.warningsCountError);</span>
1388
+ <span class="cstat-no" title="statement not covered" > return false;</span>
1317
1389
  }
1318
- }
1390
+ };
1319
1391
  &nbsp;
1320
- var addError = function (network, message) {
1321
- var errorsCount = network.errors.length;
1322
- var MAX_ERRORS = 20;
1323
- if (errorsCount &lt; MAX_ERRORS) {
1324
- addMessageToArray(network.errors, message);
1392
+ var addError = <span class="fstat-no" title="function not covered" >fu</span>nction (network, message) {
1393
+ var errorsCount = <span class="cstat-no" title="statement not covered" >network.errors.length;</span>
1394
+ var MAX_ERRORS = <span class="cstat-no" title="statement not covered" >20;</span>
1395
+ <span class="cstat-no" title="statement not covered" > if (errorsCount &lt; MAX_ERRORS) {</span>
1396
+ <span class="cstat-no" title="statement not covered" > addMessageToArray(network.errors, message);</span>
1325
1397
  } else {
1326
- addMessageToArray(network.errors, errorList.errorsCountError);
1327
- return false;
1398
+ <span class="cstat-no" title="statement not covered" > addMessageToArray(network.errors, errorList.errorsCountError);</span>
1399
+ <span class="cstat-no" title="statement not covered" > return false;</span>
1328
1400
  }
1329
1401
  };
1330
1402
  &nbsp;
1331
- var checkDuplicates = function(errorArray, sourceGenes, targetGenes) {
1403
+ var checkDuplicates = <span class="fstat-no" title="function not covered" >fu</span>nction (errorArray, sourceGenes, targetGenes) {
1332
1404
  // Run through the source genes and check if the gene in slot i is the same as the one next to it
1333
- for (var i = 0; i &lt; sourceGenes.length - 1; i++) {
1334
- if (sourceGenes[i] === sourceGenes[i + 1]) {
1335
- errorArray.push(errorList.duplicateGeneError("source", sourceGenes[i]));
1405
+ <span class="cstat-no" title="statement not covered" > for (var i = 0; i &lt; sourceGenes.length - 1; i++) {</span>
1406
+ <span class="cstat-no" title="statement not covered" > if (sourceGenes[i] === sourceGenes[i + 1]) {</span>
1407
+ <span class="cstat-no" title="statement not covered" > errorArray.push(errorList.duplicateGeneError("source", sourceGenes[i]));</span>
1336
1408
  }
1337
1409
  }
1338
1410
  // Run through the target genes and check if the gene in slot j is the same as the one next to it
1339
- for (var j = 0; j &lt; targetGenes.length - 1; j++) {
1340
- if (targetGenes[j] === targetGenes[j + 1]) {
1341
- errorArray.push(errorList.duplicateGeneError("target", targetGenes[j]));
1411
+ <span class="cstat-no" title="statement not covered" > for (var j = 0; j &lt; targetGenes.length - 1; j++) {</span>
1412
+ <span class="cstat-no" title="statement not covered" > if (targetGenes[j] === targetGenes[j + 1]) {</span>
1413
+ <span class="cstat-no" title="statement not covered" > errorArray.push(errorList.duplicateGeneError("target", targetGenes[j]));</span>
1342
1414
  }
1343
1415
  }
1344
1416
  };
1345
1417
  &nbsp;
1346
- var parseSheet = function(sheet) {
1418
+ var parseSheet = <span class="fstat-no" title="function not covered" >fu</span>nction (sheet) {
1347
1419
  var currentSheet;
1348
- var network = {
1420
+ var network = <span class="cstat-no" title="statement not covered" >{</span>
1349
1421
  genes: [],
1350
1422
  links: [],
1351
1423
  errors: [],
@@ -1360,81 +1432,84 @@ var parseSheet = function(sheet) {
1360
1432
  var targetGene;
1361
1433
  var sourceGeneNumber;
1362
1434
  var targetGeneNumber;
1363
- var genesList = []; // This will contain all of the genes in upper case for use in error checking
1364
- var sourceGenes = [];
1365
- var targetGenes = [];
1435
+ var genesList = <span class="cstat-no" title="statement not covered" >[];</span> // This will contain all of the genes in upper case for use in error checking
1436
+ var sourceGenes = <span class="cstat-no" title="statement not covered" >[];</span>
1437
+ var targetGenes = <span class="cstat-no" title="statement not covered" >[];</span>
1366
1438
  &nbsp;
1367
1439
  // Look for the worksheet containing the network data
1368
- for (var i = 0; i &lt; sheet.length; i++) {
1369
- if (sheet[i].name === "network") {
1440
+ <span class="cstat-no" title="statement not covered" > for (var i = 0; i &lt; sheet.length; i++) {</span>
1441
+ <span class="cstat-no" title="statement not covered" > if (sheet[i].name === "network") {</span>
1370
1442
  // Here we have found a sheet containing simple data. We keep looking
1371
1443
  // in case there is also a sheet with optimized weights
1372
- currentSheet = sheet[i];
1373
- } else if (sheet[i].name === "network_optimized_weights") {
1444
+ <span class="cstat-no" title="statement not covered" > currentSheet = sheet[i];</span>
1445
+ } else <span class="cstat-no" title="statement not covered" >if (sheet[i].name === "network_optimized_weights") {</span>
1374
1446
  // We found a sheet with optimized weights, which is the ideal data source.
1375
1447
  // So we stop looking.
1376
- currentSheet = sheet[i];
1377
- network.sheetType = "weighted";
1378
- break;
1448
+ <span class="cstat-no" title="statement not covered" > currentSheet = sheet[i];</span>
1449
+ <span class="cstat-no" title="statement not covered" > network.sheetType = "weighted";</span>
1450
+ <span class="cstat-no" title="statement not covered" > break;</span>
1379
1451
  }
1380
1452
  }
1381
1453
  &nbsp;
1382
1454
  // If it didn't find a network/network_optimized_weights sheet
1383
1455
  // TODO For expediency, we are wrapping every `return network` statement in `semanticChecker`.
1384
1456
  // Some refactoring may be desirable to prevent excessive repetition.
1385
- if (currentSheet === undefined) {
1386
- addError(network, errorList.missingNetworkError);
1387
- return network;
1457
+ <span class="cstat-no" title="statement not covered" > if (currentSheet === undefined) {</span>
1458
+ <span class="cstat-no" title="statement not covered" > addError(network, errorList.missingNetworkError);</span>
1459
+ <span class="cstat-no" title="statement not covered" > return network;</span>
1388
1460
  }
1389
1461
  &nbsp;
1390
- for (var row = 0, column = 1; row &lt; currentSheet.data.length; row++) {
1391
- if (currentSheet.data[row].length === 0) { // if the current row is empty
1392
- if (addError(network, errorList.emptyRowError(row)) === false) {
1393
- return network;
1462
+ <span class="cstat-no" title="statement not covered" > for (var row = 0, column = 1; row &lt; currentSheet.data.length; row++) {</span>
1463
+ <span class="cstat-no" title="statement not covered" > if (currentSheet.data[row].length === 0) { // if the current row is empty</span>
1464
+ <span class="cstat-no" title="statement not covered" > if (addError(network, errorList.emptyRowError(row)) === false) {</span>
1465
+ <span class="cstat-no" title="statement not covered" > return network;</span>
1394
1466
  }
1395
1467
  } else { // if the row has data...
1396
1468
  // Genes found when row = 0 are targets. Genes found when column = 0 are source genes.
1397
1469
  // We set column = 1 in the for loop so it skips row 0 column 0, since that contains no matrix data.
1398
1470
  // Yes, the rows and columns use array numbering. That is, they start at 0, not 1.
1399
- try { // This prevents the server from crashing if something goes wrong anywhere in here
1400
- while (column &lt; currentSheet.data[row].length) { // While we haven't gone through all of the columns in this row...
1401
- if (row === 0) { // If we are at the top of a new column...
1471
+ <span class="cstat-no" title="statement not covered" > try { // This prevents the server from crashing if something goes wrong anywhere in here</span>
1472
+ <span class="cstat-no" title="statement not covered" > while (column &lt; currentSheet.data[row].length) {</span>
1473
+ // While we haven't gone through all of the columns in this row...
1474
+ <span class="cstat-no" title="statement not covered" > if (row === 0) { // If we are at the top of a new column...</span>
1402
1475
  // These genes are the source genes
1403
- try {
1404
- currentGene = {name: currentSheet.data[0][column]};
1405
- // Set genes to upper case so case doesn't matter in error checking; ie: Cin5 is the same as cin5
1406
- if (currentGene.name === undefined) {
1407
- addWarning(network, warningsList.missingSourceGeneWarning(row, column));
1408
- } else <span class="missing-if-branch" title="if path not taken" >I</span>if (isNaN(currentGene.name) &amp;&amp; typeof currentGene.name !== "string") {
1476
+ <span class="cstat-no" title="statement not covered" > try {</span>
1477
+ <span class="cstat-no" title="statement not covered" > currentGene = {name: currentSheet.data[0][column]};</span>
1478
+ // ie: Cin5 is the same as cin5
1479
+ <span class="cstat-no" title="statement not covered" > if (currentGene.name === undefined) {</span>
1480
+ <span class="cstat-no" title="statement not covered" > addWarning(network, warningsList.missingSourceGeneWarning(row, column));</span>
1481
+ } else <span class="cstat-no" title="statement not covered" >if (isNaN(currentGene.name) &amp;&amp; typeof currentGene.name !== "string") {</span>
1409
1482
  <span class="cstat-no" title="statement not covered" > addWarning(network, warningsList.missingSourceGeneWarning(row, column));</span>
1410
1483
  } else {
1411
- sourceGenes.push(String(currentGene.name.toUpperCase()));
1412
- genesList.push(String(currentGene.name.toUpperCase()));
1413
- currentGene.name = currentGene.name;
1414
- network.genes.push(currentGene);
1484
+ // set currentGeneName to a String so toUpperCase doesn't mess up
1485
+ <span class="cstat-no" title="statement not covered" > currentGene.name = currentGene.name.toString();</span>
1486
+ <span class="cstat-no" title="statement not covered" > sourceGenes.push(String(currentGene.name.toUpperCase()));</span>
1487
+ <span class="cstat-no" title="statement not covered" > genesList.push(String(currentGene.name.toUpperCase()));</span>
1488
+ <span class="cstat-no" title="statement not covered" > network.genes.push(currentGene);</span>
1415
1489
  }
1416
1490
  } catch (err) {
1417
1491
  <span class="cstat-no" title="statement not covered" > addError(network, errorList.corruptGeneError(row, column));</span>
1418
1492
  <span class="cstat-no" title="statement not covered" > return network;</span>
1419
1493
  }
1420
- } else if (column === 0) { // If we are at the far left of a new row...
1494
+ } else <span class="cstat-no" title="statement not covered" >if (column === 0) { // If we are at the far left of a new row...</span>
1421
1495
  // These genes are the target genes
1422
- try {
1423
- currentGene = {name: currentSheet.data[row][0]};
1424
- if (currentGene.name === undefined) {
1425
- addWarning(network, warningsList.missingTargetGeneWarning(row, column));
1426
- } else <span class="missing-if-branch" title="if path not taken" >I</span>if (isNaN(currentGene.name) &amp;&amp; typeof currentGene.name !== "string") {
1496
+ <span class="cstat-no" title="statement not covered" > try {</span>
1497
+ <span class="cstat-no" title="statement not covered" > currentGene = {name: currentSheet.data[row][0]};</span>
1498
+ <span class="cstat-no" title="statement not covered" > if (currentGene.name === undefined) {</span>
1499
+ <span class="cstat-no" title="statement not covered" > addWarning(network, warningsList.missingTargetGeneWarning(row, column));</span>
1500
+ } else <span class="cstat-no" title="statement not covered" >if (isNaN(currentGene.name) &amp;&amp; typeof currentGene.name !== "string") {</span>
1427
1501
  <span class="cstat-no" title="statement not covered" > addWarning(network, warningsList.missingTargetGeneWarning(row, column));</span>
1428
1502
  } else {
1429
- targetGenes.push(String(currentGene.name.toUpperCase()));
1503
+ // set currentGeneName to a String so toUpperCase doesn't mess up
1504
+ <span class="cstat-no" title="statement not covered" > currentGene.name = currentGene.name.toString();</span>
1505
+ <span class="cstat-no" title="statement not covered" > targetGenes.push(String(currentGene.name.toUpperCase()));</span>
1430
1506
  // Here we check to see if we've already seen the gene name that we're about to store
1431
1507
  // Genes may or may not be present due to asymmetry or unorderedness
1432
1508
  // If it's in the genesList, it will return a number &gt; 0, so we won't store it
1433
1509
  // If it's not there, it will return -1, so we add it.
1434
- if (genesList.indexOf(String(currentGene.name.toUpperCase())) === -1) {
1435
- genesList.push(String(currentGene.name.toUpperCase()));
1436
- currentGene.name = currentGene.name;
1437
- network.genes.push(currentGene);
1510
+ <span class="cstat-no" title="statement not covered" > if (genesList.indexOf(String(currentGene.name.toUpperCase())) === -1) {</span>
1511
+ <span class="cstat-no" title="statement not covered" > genesList.push(String(currentGene.name.toUpperCase()));</span>
1512
+ <span class="cstat-no" title="statement not covered" > network.genes.push(currentGene);</span>
1438
1513
  }
1439
1514
  }
1440
1515
  } catch (err) {
@@ -1444,48 +1519,58 @@ var parseSheet = function(sheet) {
1444
1519
  <span class="cstat-no" title="statement not covered" > return network;</span>
1445
1520
  }
1446
1521
  } else { // If we're within the matrix and lookin' at the data...
1447
- try {
1448
- if (currentSheet.data[row][column] === undefined) {
1522
+ <span class="cstat-no" title="statement not covered" > try {</span>
1523
+ <span class="cstat-no" title="statement not covered" > if (currentSheet.data[row][column] === undefined) {</span>
1449
1524
  // SHOULD BE: addError(network, errorList.missingValueError(row, column));
1450
- addWarning(network, warningsList.invalidMatrixDataWarning(row, column));
1451
- } else if (isNaN(+("" + currentSheet.data[row][column])) || typeof currentSheet.data[row][column] !== "number") {
1452
- addError(network, errorList.dataTypeError(row, column));
1453
- return network;
1525
+ <span class="cstat-no" title="statement not covered" > addWarning(network, warningsList.invalidMatrixDataWarning(row, column));</span>
1526
+ } else <span class="cstat-no" title="statement not covered" >if (isNaN(+("" + currentSheet.data[row][column])) ||</span>
1527
+ typeof currentSheet.data[row][column] !== "number") {
1528
+ <span class="cstat-no" title="statement not covered" > addError(network, errorList.dataTypeError(row, column));</span>
1529
+ <span class="cstat-no" title="statement not covered" > return network;</span>
1454
1530
  } else {
1455
- if (currentSheet.data[row][column] !== 0) { // We only care about non-zero values
1531
+ <span class="cstat-no" title="statement not covered" > if (currentSheet.data[row][column] !== 0) { // We only care about non-zero values</span>
1456
1532
  // Grab the source and target genes' names
1457
- sourceGene = currentSheet.data[0][column];
1458
- targetGene = currentSheet.data[row][0];
1459
- if (sourceGene === undefined || targetGene === undefined) {
1460
- addWarning(network, warningsList.randomDataWarning("undefined", row, column));
1461
- } else <span class="missing-if-branch" title="if path not taken" >I</span>if ((isNaN(sourceGene) &amp;&amp; typeof sourceGene !== "string") || (isNaN(targetGene) &amp;&amp; typeof targetGene !== "string")) {
1533
+ <span class="cstat-no" title="statement not covered" > sourceGene = currentSheet.data[0][column];</span>
1534
+ <span class="cstat-no" title="statement not covered" > targetGene = currentSheet.data[row][0];</span>
1535
+ <span class="cstat-no" title="statement not covered" > if (sourceGene === undefined || targetGene === undefined) {</span>
1536
+ <span class="cstat-no" title="statement not covered" > addWarning(network, warningsList.randomDataWarning("undefined", row, column));</span>
1537
+ } else <span class="cstat-no" title="statement not covered" >if ((isNaN(sourceGene) &amp;&amp; typeof sourceGene !== "string") ||</span>
1538
+ (isNaN(targetGene) &amp;&amp; typeof targetGene !== "string")) {
1462
1539
  <span class="cstat-no" title="statement not covered" > addWarning(network, warningsList.randomDataWarning("NaN", row, column));</span>
1463
1540
  } else {
1464
1541
  // Grab the source and target genes' numbers
1465
- sourceGeneNumber = genesList.indexOf(sourceGene.toUpperCase());
1466
- targetGeneNumber = genesList.indexOf(targetGene.toUpperCase());
1467
- currentLink = {source: sourceGeneNumber, target: targetGeneNumber, value: currentSheet.data[row][column]};
1468
- // Here we set the properties of the current link before we push them to the network
1469
- if (network.sheetType === "weighted") {
1470
- if (currentLink.value &gt; 0) { // If it's a positive number, mark it as an activator
1471
- currentLink.type = "arrowhead";
1472
- currentLink.stroke = "MediumVioletRed";
1473
- network.positiveWeights.push(currentLink.value);
1542
+ <span class="cstat-no" title="statement not covered" > sourceGeneNumber = genesList.indexOf(sourceGene.toString().toUpperCase());</span>
1543
+ <span class="cstat-no" title="statement not covered" > targetGeneNumber = genesList.indexOf(targetGene.toString().toUpperCase());</span>
1544
+ <span class="cstat-no" title="statement not covered" > currentLink = {source: sourceGeneNumber, target: targetGeneNumber,</span>
1545
+ value: currentSheet.data[row][column]};
1546
+ // Here we set the properties of the current link
1547
+ // before we push them to the network
1548
+ <span class="cstat-no" title="statement not covered" > if (network.sheetType === "weighted") {</span>
1549
+ <span class="cstat-no" title="statement not covered" > if (currentLink.value &gt; 0) {</span>
1550
+ // If it's a positive number, mark it as an activator
1551
+ <span class="cstat-no" title="statement not covered" > currentLink.type = "arrowhead";</span>
1552
+ // GRNsight v1 magenta edge color
1553
+ // currentLink.stroke = "MediumVioletRed";
1554
+ // Node coloring-consistent red edge color
1555
+ <span class="cstat-no" title="statement not covered" > currentLink.stroke = "rgb(195, 61, 61)";</span>
1556
+ <span class="cstat-no" title="statement not covered" > network.positiveWeights.push(currentLink.value);</span>
1474
1557
  } else { // if it's a negative number, mark it as a repressor
1475
- currentLink.type = "repressor";
1476
- currentLink.stroke = "DarkTurquoise";
1477
- network.negativeWeights.push(currentLink.value);
1558
+ <span class="cstat-no" title="statement not covered" > currentLink.type = "repressor";</span>
1559
+ // currentLink.stroke = "DarkTurquoise"; // GRNsight v1 cyan edge color
1560
+ // Node coloring-consistent blue edge color
1561
+ <span class="cstat-no" title="statement not covered" > currentLink.stroke = "rgb(51, 124, 183)";</span>
1562
+ <span class="cstat-no" title="statement not covered" > network.negativeWeights.push(currentLink.value);</span>
1478
1563
  }
1479
- } else <span class="missing-if-branch" title="else path not taken" >E</span>if (network.sheetType === "unweighted") {
1480
- currentLink.type = "arrowhead";
1481
- currentLink.stroke = "black";
1482
- if (currentLink.value !== 1) {
1483
- addWarning(network, warningsList.incorrectlyNamedSheetWarning());
1484
- currentLink.value = 1;
1564
+ } else <span class="cstat-no" title="statement not covered" >if (network.sheetType === "unweighted") {</span>
1565
+ <span class="cstat-no" title="statement not covered" > currentLink.type = "arrowhead";</span>
1566
+ <span class="cstat-no" title="statement not covered" > currentLink.stroke = "black";</span>
1567
+ <span class="cstat-no" title="statement not covered" > if (currentLink.value !== 1) {</span>
1568
+ <span class="cstat-no" title="statement not covered" > addWarning(network, warningsList.incorrectlyNamedSheetWarning());</span>
1569
+ <span class="cstat-no" title="statement not covered" > currentLink.value = 1;</span>
1485
1570
  }
1486
- network.positiveWeights.push(currentLink.value);
1571
+ <span class="cstat-no" title="statement not covered" > network.positiveWeights.push(currentLink.value);</span>
1487
1572
  }
1488
- network.links.push(currentLink);
1573
+ <span class="cstat-no" title="statement not covered" > network.links.push(currentLink);</span>
1489
1574
  }
1490
1575
  }
1491
1576
  }
@@ -1496,9 +1581,9 @@ var parseSheet = function(sheet) {
1496
1581
  <span class="cstat-no" title="statement not covered" > return network;</span>
1497
1582
  }
1498
1583
  }
1499
- column++; // Let's move on to the next column!
1584
+ <span class="cstat-no" title="statement not covered" > column++; </span>// Let's move on to the next column!
1500
1585
  } // Once we finish with the current row...
1501
- column = 0; // let's go back to column 0 on the next row!
1586
+ <span class="cstat-no" title="statement not covered" > column = 0; </span>// let's go back to column 0 on the next row!
1502
1587
  } catch (err) {
1503
1588
  // We only get here if something goes drastically wrong. We don't want to get here.
1504
1589
  <span class="cstat-no" title="statement not covered" > addError(network, errorList.unknownError);</span>
@@ -1512,11 +1597,11 @@ var parseSheet = function(sheet) {
1512
1597
  &nbsp;
1513
1598
  // We sort them here because gene order is not relevant before this point
1514
1599
  // Sorting them now means duplicates will be right next to each other
1515
- sourceGenes.sort();
1516
- targetGenes.sort();
1600
+ <span class="cstat-no" title="statement not covered" > sourceGenes.sort();</span>
1601
+ <span class="cstat-no" title="statement not covered" > targetGenes.sort();</span>
1517
1602
  &nbsp;
1518
1603
  // syntactic duplicate checker for both columns and rows
1519
- checkDuplicates(network.errors, sourceGenes, targetGenes);
1604
+ <span class="cstat-no" title="statement not covered" > checkDuplicates(network.errors, sourceGenes, targetGenes);</span>
1520
1605
  &nbsp;
1521
1606
  // NOTE: Temporarily commented out pending resolution of #474, and other related issues
1522
1607
  // try {
@@ -1524,12 +1609,12 @@ var parseSheet = function(sheet) {
1524
1609
  // } catch (err) {
1525
1610
  // console.log ("Graph statistics report failed to be complete.");
1526
1611
  // }
1527
- return semanticChecker(network);
1612
+ <span class="cstat-no" title="statement not covered" > return semanticChecker(network);</span>
1528
1613
  };
1529
1614
  &nbsp;
1530
- var processGRNmap = <span class="fstat-no" title="function not covered" >function (path, res, app) {</span>
1531
- <span class="cstat-no" title="statement not covered" > var sheet;</span>
1532
- <span class="cstat-no" title="statement not covered" > var network;</span>
1615
+ var processGRNmap = <span class="fstat-no" title="function not covered" >fu</span>nction (path, res, app) {
1616
+ var sheet;
1617
+ var network;
1533
1618
  &nbsp;
1534
1619
  <span class="cstat-no" title="statement not covered" > helpers.attachCorsHeader(res, app);</span>
1535
1620
  &nbsp;
@@ -1541,17 +1626,21 @@ var processGRNmap = <span class="fstat-no" title="function not covered" >functio
1541
1626
  &nbsp;
1542
1627
  <span class="cstat-no" title="statement not covered" > helpers.attachFileHeaders(res, path);</span>
1543
1628
  <span class="cstat-no" title="statement not covered" > network = parseSheet(sheet);</span>
1629
+ &nbsp;
1630
+ // Parse expression and 2-column data, then add to network object
1631
+ var additionalData = <span class="cstat-no" title="statement not covered" >parseAdditionalSheets(sheet);</span>
1632
+ <span class="cstat-no" title="statement not covered" > Object.assign(network, additionalData);</span>
1544
1633
  &nbsp;
1545
1634
  <span class="cstat-no" title="statement not covered" > return (network.errors.length === 0) ?</span>
1546
- // If all looks well, return the network with an all clear
1547
- res.json(network) :
1548
- // If all does not look well, return the network with an error 400
1549
- res.json(400, network);
1635
+ // If all looks well, return the network with an all clear
1636
+ res.json(network) :
1637
+ // If all does not look well, return the network with an error 400
1638
+ res.status(400).json(network);
1550
1639
  };
1551
1640
  &nbsp;
1552
- var grnSightToCytoscape = <span class="fstat-no" title="function not covered" >function (network) {</span>
1553
- <span class="cstat-no" title="statement not covered" > var result = [];</span>
1554
- <span class="cstat-no" title="statement not covered" > network.genes.forEach(<span class="fstat-no" title="function not covered" >function (gene) {</span></span>
1641
+ var grnSightToCytoscape = <span class="fstat-no" title="function not covered" >fu</span>nction (network) {
1642
+ var result = <span class="cstat-no" title="statement not covered" >[];</span>
1643
+ <span class="cstat-no" title="statement not covered" > network.genes.forEach(<span class="fstat-no" title="function not covered" >fu</span>nction (gene) {</span>
1555
1644
  <span class="cstat-no" title="statement not covered" > result.push({</span>
1556
1645
  data: {
1557
1646
  id: gene.name
@@ -1559,9 +1648,9 @@ var grnSightToCytoscape = <span class="fstat-no" title="function not covered" >f
1559
1648
  });
1560
1649
  });
1561
1650
  &nbsp;
1562
- <span class="cstat-no" title="statement not covered" > network.links.forEach(<span class="fstat-no" title="function not covered" >function (link) {</span></span>
1563
- <span class="cstat-no" title="statement not covered" > var sourceGene = network.genes[link.source];</span>
1564
- <span class="cstat-no" title="statement not covered" > var targetGene = network.genes[link.target];</span>
1651
+ <span class="cstat-no" title="statement not covered" > network.links.forEach(<span class="fstat-no" title="function not covered" >fu</span>nction (link) {</span>
1652
+ var sourceGene = <span class="cstat-no" title="statement not covered" >network.genes[link.source];</span>
1653
+ var targetGene = <span class="cstat-no" title="statement not covered" >network.genes[link.target];</span>
1565
1654
  <span class="cstat-no" title="statement not covered" > result.push({</span>
1566
1655
  data: {
1567
1656
  id: sourceGene.name + targetGene.name,
@@ -1615,24 +1704,26 @@ module.exports = function (app) {
1615
1704
  <span class="missing-if-branch" title="if path not taken" >I</span>if (app) {
1616
1705
  &nbsp;
1617
1706
  // parse the incoming form data, then parse the spreadsheet. Finally, send back json.
1618
- <span class="cstat-no" title="statement not covered" > app.post("/upload", <span class="fstat-no" title="function not covered" >function (req, res) {</span></span>
1707
+ <span class="cstat-no" title="statement not covered" > app.post("/upload", <span class="fstat-no" title="function not covered" >fu</span>nction (req, res) {</span>
1619
1708
  // TODO: Add file validation
1620
- <span class="cstat-no" title="statement not covered" > (new multiparty.Form()).parse(req, <span class="fstat-no" title="function not covered" >function (err, fields, files) {</span></span>
1709
+ <span class="cstat-no" title="statement not covered" > (new multiparty.Form()).parse(req, <span class="fstat-no" title="function not covered" >fu</span>nction (err, fields, files) {</span>
1621
1710
  <span class="cstat-no" title="statement not covered" > if (err) {</span>
1622
1711
  <span class="cstat-no" title="statement not covered" > return res.json(400, "There was a problem uploading your file. Please try again.");</span>
1623
1712
  }
1624
- &nbsp;
1713
+ var input;
1625
1714
  <span class="cstat-no" title="statement not covered" > try {</span>
1626
- <span class="cstat-no" title="statement not covered" > var input = files.file[0].path;</span>
1715
+ <span class="cstat-no" title="statement not covered" > input = files.file[0].path;</span>
1627
1716
  } catch (err) {
1628
1717
  <span class="cstat-no" title="statement not covered" > return res.json(400, "No upload file selected.");</span>
1629
1718
  }
1630
1719
  &nbsp;
1631
1720
  <span class="cstat-no" title="statement not covered" > if (path.extname(input) !== ".xlsx") {</span>
1632
- <span class="cstat-no" title="statement not covered" > return res.json(400, "This file cannot be loaded because:&lt;br&gt;&lt;br&gt; The file is not in a format GRNsight can read." +</span>
1633
- "&lt;br&gt;Please select an Excel Workbook (.xlsx) file. Note that Excel 97-2003 Workbook (.xls) files are not " +
1634
- " able to be read by GRNsight. &lt;br&gt;&lt;br&gt;SIF and GraphML files can be loaded using the importer under File &gt; Import." +
1635
- " Additional information about file types that GRNsight supports is in the Documentation.");
1721
+ <span class="cstat-no" title="statement not covered" > return res.json(400, "This file cannot be loaded because:&lt;br&gt;&lt;br&gt; The file is \</span>
1722
+ not in a format GRNsight can read." + "&lt;br&gt;Please select an Excel Workbook \
1723
+ (.xlsx) file. Note that Excel 97-2003 Workbook (.xls) files are not " +
1724
+ " able to be read by GRNsight. &lt;br&gt;&lt;br&gt;SIF and GraphML files can be loaded \
1725
+ using the importer under File &gt; Import." + " Additional information about file \
1726
+ types that GRNsight supports is in the Documentation.");
1636
1727
  }
1637
1728
  &nbsp;
1638
1729
  <span class="cstat-no" title="statement not covered" > return processGRNmap(input, res, app);</span>
@@ -1640,20 +1731,22 @@ module.exports = function (app) {
1640
1731
  });
1641
1732
  &nbsp;
1642
1733
  // Load the demos
1643
- <span class="cstat-no" title="statement not covered" > app.get("/demo/unweighted", <span class="fstat-no" title="function not covered" >function (req, res) {</span></span>
1644
- <span class="cstat-no" title="statement not covered" > return processGRNmap("test-files/demo-files/21-genes_50-edges_Dahlquist-data_input.xlsx", res, app);</span>
1734
+ <span class="cstat-no" title="statement not covered" > app.get("/demo/unweighted", <span class="fstat-no" title="function not covered" >fu</span>nction (req, res) {</span>
1735
+ <span class="cstat-no" title="statement not covered" > return processGRNmap("test-files/demo-files/15-genes_28-edges_db5_Dahlquist-data_input.xlsx", res, app);</span>
1645
1736
  });
1646
1737
  &nbsp;
1647
- <span class="cstat-no" title="statement not covered" > app.get("/demo/weighted", <span class="fstat-no" title="function not covered" >function (req, res) {</span></span>
1648
- <span class="cstat-no" title="statement not covered" > return processGRNmap("test-files/demo-files/21-genes_50-edges_Dahlquist-data_estimation_output.xlsx", res, app);</span>
1738
+ <span class="cstat-no" title="statement not covered" > app.get("/demo/weighted", <span class="fstat-no" title="function not covered" >fu</span>nction (req, res) {</span>
1739
+ <span class="cstat-no" title="statement not covered" > return processGRNmap("test-files/demo-files/15-genes_28-edges_db5_Dahlquist-data_estimation_output.xlsx",</span>
1740
+ res, app);
1649
1741
  });
1650
1742
  &nbsp;
1651
- <span class="cstat-no" title="statement not covered" > app.get("/demo/schadeInput", <span class="fstat-no" title="function not covered" >function (req, res) {</span></span>
1743
+ <span class="cstat-no" title="statement not covered" > app.get("/demo/schadeInput", <span class="fstat-no" title="function not covered" >fu</span>nction (req, res) {</span>
1652
1744
  <span class="cstat-no" title="statement not covered" > return processGRNmap("test-files/demo-files/21-genes_31-edges_Schade-data_input.xlsx", res, app);</span>
1653
1745
  });
1654
1746
  &nbsp;
1655
- <span class="cstat-no" title="statement not covered" > app.get("/demo/schadeOutput", <span class="fstat-no" title="function not covered" >function (req, res) {</span></span>
1656
- <span class="cstat-no" title="statement not covered" > return processGRNmap("test-files/demo-files/21-genes_31-edges_Schade-data_estimation_output.xlsx", res, app);</span>
1747
+ <span class="cstat-no" title="statement not covered" > app.get("/demo/schadeOutput", <span class="fstat-no" title="function not covered" >fu</span>nction (req, res) {</span>
1748
+ <span class="cstat-no" title="statement not covered" > return processGRNmap("test-files/demo-files/21-genes_31-edges_Schade-data_estimation_output.xlsx",</span>
1749
+ res, app);
1657
1750
  });
1658
1751
  }
1659
1752
  &nbsp;
@@ -1669,7 +1762,7 @@ module.exports = function (app) {
1669
1762
  </div><!-- /wrapper -->
1670
1763
  <div class='footer quiet pad2 space-top1 center small'>
1671
1764
  Code coverage
1672
- generated by <a href="http://istanbul-js.org/" target="_blank">istanbul</a> at Fri Sep 29 2017 00:22:47 GMT-0700 (PDT)
1765
+ generated by <a href="https://istanbul.js.org/" target="_blank">istanbul</a> at Thu May 31 2018 15:29:17 GMT-0700 (PDT)
1673
1766
  </div>
1674
1767
  </div>
1675
1768
  <script src="../prettify.js"></script>
@@ -1681,5 +1774,6 @@ window.onload = function () {
1681
1774
  };
1682
1775
  </script>
1683
1776
  <script src="../sorter.js"></script>
1777
+ <script src="../block-navigation.js"></script>
1684
1778
  </body>
1685
1779
  </html>