diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs index 4be937d471..0d962082bc 100644 --- a/.git-blame-ignore-revs +++ b/.git-blame-ignore-revs @@ -3,3 +3,6 @@ # Scala Steward: Reformat with scalafmt 3.6.0 df858b0ea7cc4743ec9c78cee1486ad91de1dbd4 + +# Scala Steward: Reformat with scalafmt 3.9.9 +aa0891ef4a981f567bc7c8c827a934d5583e77ce diff --git a/.scalafmt.conf b/.scalafmt.conf index ace08b0c38..d666ac4cb7 100644 --- a/.scalafmt.conf +++ b/.scalafmt.conf @@ -13,5 +13,5 @@ optIn.breakChainOnFirstMethodDot = false align.openParenDefnSite = false project.git = true assumeStandardLibraryStripMargin = true -version = 3.6.1 +version = 3.9.9 runner.dialect = scala213 diff --git a/modules/auth/src/main/scala/de/proteinevolution/auth/dao/UserDao.scala b/modules/auth/src/main/scala/de/proteinevolution/auth/dao/UserDao.scala index ba681a4507..3715657963 100644 --- a/modules/auth/src/main/scala/de/proteinevolution/auth/dao/UserDao.scala +++ b/modules/auth/src/main/scala/de/proteinevolution/auth/dao/UserDao.scala @@ -108,7 +108,7 @@ class UserDao @Inject() ( User.ACCOUNT_TYPE -> AccountType.REGISTEREDUSER.toInt, User.DELETION_WARNING_SENT -> false, User.CONNECTED -> false, - User.DATE_LAST_LOGIN -> BSONDocument( + User.DATE_LAST_LOGIN -> BSONDocument( "$lt" -> BSONDateTime(warnRegistratedUserAfterLoginDate.toInstant.toEpochMilli) ) ) diff --git a/modules/auth/src/main/scala/de/proteinevolution/auth/services/UserSessionService.scala b/modules/auth/src/main/scala/de/proteinevolution/auth/services/UserSessionService.scala index a7ef651789..90daf9f7ce 100644 --- a/modules/auth/src/main/scala/de/proteinevolution/auth/services/UserSessionService.scala +++ b/modules/auth/src/main/scala/de/proteinevolution/auth/services/UserSessionService.scala @@ -53,7 +53,7 @@ class UserSessionService @Inject() ( // cache related stuff should remain in the project where the cache is bound userCache.get[User](sessionID) match { case Some(user) => fuccess(user) - case None => // session not known yet in cache + case None => // session not known yet in cache val newSessionData = SessionData( ip = MurmurHash3.stringHash(request.remoteAddress).toString, userAgent = request.headers.get(Http.HeaderNames.USER_AGENT).getOrElse("Not specified"), diff --git a/modules/backend/src/main/scala/de/proteinevolution/backend/controllers/BackendController.scala b/modules/backend/src/main/scala/de/proteinevolution/backend/controllers/BackendController.scala index 1fcb41e241..253400d8ba 100644 --- a/modules/backend/src/main/scala/de/proteinevolution/backend/controllers/BackendController.scala +++ b/modules/backend/src/main/scala/de/proteinevolution/backend/controllers/BackendController.scala @@ -101,7 +101,7 @@ final class BackendController @Inject() ( def setMaintenanceState(): Action[Json] = userAction(circe.json) { implicit request => if (request.user.isSuperuser) { request.body.asObject match { - case None => BadRequest + case None => BadRequest case Some(value) => maintenanceMessage = value("message").get.asString.orElse(Some("")).get maintenanceSubmitBlocked = value("submitBlocked").get.asBoolean.orElse(Some(false)).get diff --git a/modules/common/src/main/scala/de/proteinevolution/common/models/ConstantsV2.scala b/modules/common/src/main/scala/de/proteinevolution/common/models/ConstantsV2.scala index 260b15b0c4..c1a0017899 100644 --- a/modules/common/src/main/scala/de/proteinevolution/common/models/ConstantsV2.scala +++ b/modules/common/src/main/scala/de/proteinevolution/common/models/ConstantsV2.scala @@ -57,10 +57,10 @@ class ConstantsV2 @Inject() (config: Configuration) { // Job deletion settings /** Sweeps at this time after server start */ - final val jobDeletionDelay: FiniteDuration = 10 minutes + final val jobDeletionDelay: FiniteDuration = 10.minutes /** Sweeps in this interval */ - final val jobDeletionInterval: FiniteDuration = 3 hours + final val jobDeletionInterval: FiniteDuration = 3.hours /** all jobs of registered users that are older than the given number are permanently deleted everywhere */ final val jobDeletionRegistered: Int = 90 @@ -73,10 +73,10 @@ class ConstantsV2 @Inject() (config: Configuration) { // User Deletion settings /** Sweeps at this time after server start */ - final val userDeletionDelay: FiniteDuration = 70 minutes + final val userDeletionDelay: FiniteDuration = 70.minutes /** Sweeps in this interval */ - final val userDeletionInterval: FiniteDuration = 3 hours + final val userDeletionInterval: FiniteDuration = 3.hours /** Sending an eMail to the user this many days before the deletion */ final val userDeletionWarning: Int = 14 // days @@ -89,7 +89,7 @@ class ConstantsV2 @Inject() (config: Configuration) { // qstat long polling in order to detect zombie jobs, not used for cluster load calc anymore /** Interval of the qstat requests */ - final val pollingInterval: FiniteDuration = 5 minutes + final val pollingInterval: FiniteDuration = 5.minutes /** The marker for 100% load capacity */ final val loadPercentageMarker: Int = 32 // Jobs diff --git a/modules/common/src/main/scala/de/proteinevolution/common/models/util/ZonedDateTimeHelper.scala b/modules/common/src/main/scala/de/proteinevolution/common/models/util/ZonedDateTimeHelper.scala index 2e50718897..ef2496c4fb 100644 --- a/modules/common/src/main/scala/de/proteinevolution/common/models/util/ZonedDateTimeHelper.scala +++ b/modules/common/src/main/scala/de/proteinevolution/common/models/util/ZonedDateTimeHelper.scala @@ -23,8 +23,8 @@ import reactivemongo.api.bson.BSONDateTime object ZonedDateTimeHelper { - final val dateTimeFormatter: DateTimeFormatter = DateTimeFormatter.ofPattern("dd.MM.yyyy HH:mm:ss O") - final val defaultZoneID: ZoneId = ZoneId.systemDefault() + final val dateTimeFormatter: DateTimeFormatter = DateTimeFormatter.ofPattern("dd.MM.yyyy HH:mm:ss O") + final val defaultZoneID: ZoneId = ZoneId.systemDefault() def getZDT(bsonDateTime: BSONDateTime): ZonedDateTime = { Instant.ofEpochMilli(bsonDateTime.value).atZone(defaultZoneID) } diff --git a/modules/common/src/main/scala/de/proteinevolution/common/parsers/FASTA.scala b/modules/common/src/main/scala/de/proteinevolution/common/parsers/FASTA.scala index 89f07eca18..c5f01aae7e 100644 --- a/modules/common/src/main/scala/de/proteinevolution/common/parsers/FASTA.scala +++ b/modules/common/src/main/scala/de/proteinevolution/common/parsers/FASTA.scala @@ -140,7 +140,7 @@ object FASTA { private[FASTA] def parse(input: String): Option[FASTA] = { parseAll(sequence, input) match { case Success(es, _) => Some(FASTA(List(Entry("empty header", es)))) - case _ => + case _ => parseAll(entries, input) match { case Success(es, _) => Some(FASTA(es)) case _ => None diff --git a/modules/jobs/src/main/scala/de/proteinevolution/jobs/actors/JobActor.scala b/modules/jobs/src/main/scala/de/proteinevolution/jobs/actors/JobActor.scala index 9433b13e0a..590cad7e15 100644 --- a/modules/jobs/src/main/scala/de/proteinevolution/jobs/actors/JobActor.scala +++ b/modules/jobs/src/main/scala/de/proteinevolution/jobs/actors/JobActor.scala @@ -75,8 +75,8 @@ class JobActor @Inject() ( @volatile private var currentJobLogs: Map[String, JobEventLog] = Map.empty[String, JobEventLog] @volatile private var currentExecutionContexts: Map[String, ExecutionContext] = Map.empty[String, ExecutionContext] - private val fetchLatestInterval = 500 millis - private val Tick: Cancellable = { + private val fetchLatestInterval = 500.millis + private val Tick: Cancellable = { // scheduler should use the system dispatcher context.system.scheduler.scheduleWithFixedDelay(Duration.Zero, fetchLatestInterval, self, UpdateLog)( context.system.dispatcher @@ -109,7 +109,7 @@ class JobActor @Inject() ( private def getCurrentExecutionContext(jobID: String): Option[ExecutionContext] = { currentExecutionContexts.get(jobID) match { case Some(executionContext) => Some(executionContext) - case None => + case None => if ((constants.jobPath / jobID).exists) { val executionContext = ExecutionContext(constants.jobPath / jobID, reOpen = true) currentExecutionContexts = currentExecutionContexts.updated(jobID, executionContext) @@ -196,7 +196,7 @@ class JobActor @Inject() ( jobDao.updateJobStatus(job.jobID, job.status).map { _ => val jobLog = currentJobLogs.get(job.jobID) match { case Some(jobEventLog) => jobEventLog.addJobStateEvent(job.status) - case None => + case None => JobEventLog( jobID = job.jobID, toolName = job.tool, @@ -355,7 +355,7 @@ class JobActor @Inject() ( .getCurrentJob(jobID) .flatMap { case Some(job) => fuccess(Some(job)) - case None => + case None => if (verbose) log.info( s"[JobActor[$jobActorNumber].Delete] jobID $jobID not found in current jobs. Loading job from DB." diff --git a/modules/jobs/src/main/scala/de/proteinevolution/jobs/controllers/FileController.scala b/modules/jobs/src/main/scala/de/proteinevolution/jobs/controllers/FileController.scala index 5f3e836ad4..6ee75d6907 100644 --- a/modules/jobs/src/main/scala/de/proteinevolution/jobs/controllers/FileController.scala +++ b/modules/jobs/src/main/scala/de/proteinevolution/jobs/controllers/FileController.scala @@ -40,7 +40,7 @@ class FileController @Inject() ( with ContentTypes { def getStructureFile(accession: String): Action[AnyContent] = Action { implicit request => - val db = LinkUtil.identifyDatabase(accession) + val db = LinkUtil.identifyDatabase(accession) val ending = db match { case "scop" => "pdb" case "ecod" => "pdb" diff --git a/modules/jobs/src/main/scala/de/proteinevolution/jobs/controllers/JobGetController.scala b/modules/jobs/src/main/scala/de/proteinevolution/jobs/controllers/JobGetController.scala index fa284d9b3b..91158929fa 100644 --- a/modules/jobs/src/main/scala/de/proteinevolution/jobs/controllers/JobGetController.scala +++ b/modules/jobs/src/main/scala/de/proteinevolution/jobs/controllers/JobGetController.scala @@ -57,7 +57,7 @@ class JobGetController @Inject() ( def suggestJobsForQuery(queryString: String): Action[AnyContent] = userAction.async { implicit request => - val user = request.user + val user = request.user val tools: List[Tool] = toolConfig.values .unsafeRunSync() .values diff --git a/modules/jobs/src/main/scala/de/proteinevolution/jobs/controllers/ResultsController.scala b/modules/jobs/src/main/scala/de/proteinevolution/jobs/controllers/ResultsController.scala index 9d5a0d24bd..e237134429 100644 --- a/modules/jobs/src/main/scala/de/proteinevolution/jobs/controllers/ResultsController.scala +++ b/modules/jobs/src/main/scala/de/proteinevolution/jobs/controllers/ResultsController.scala @@ -71,8 +71,9 @@ final class ResultsController @Inject() ( // access allowed to job (for { json <- EitherT.liftF(resultFiles.getResults(jobID)) - r <- EitherT - .fromEither[Future](json.hcursor.downField(resultField.getOrElse("alignment")).as[AlignmentResult]) + r <- EitherT.fromEither[Future]( + json.hcursor.downField(resultField.getOrElse("alignment")).as[AlignmentResult] + ) } yield r).value.map { case Right(r) => val l = r.alignment.length diff --git a/modules/jobs/src/main/scala/de/proteinevolution/jobs/controllers/SubmissionController.scala b/modules/jobs/src/main/scala/de/proteinevolution/jobs/controllers/SubmissionController.scala index 09112c5d2d..06bb34f3a2 100644 --- a/modules/jobs/src/main/scala/de/proteinevolution/jobs/controllers/SubmissionController.scala +++ b/modules/jobs/src/main/scala/de/proteinevolution/jobs/controllers/SubmissionController.scala @@ -60,11 +60,13 @@ class SubmissionController @Inject() ( Unauthorized } else { request.body.asObject match { - case None => BadRequest + case None => BadRequest case Some(obj) => if (obj.contains("isPublic")) { - jobActorAccess - .sendToJobActor(jobID, SetJobPublic(jobID, obj("isPublic").get.asBoolean.getOrElse(false))) + jobActorAccess.sendToJobActor( + jobID, + SetJobPublic(jobID, obj("isPublic").get.asBoolean.getOrElse(false)) + ) } Ok } @@ -91,7 +93,7 @@ class SubmissionController @Inject() ( def submitJob(toolName: String): Action[Json] = userAction(circe.json).async { implicit request => request.body.asObject match { - case None => fuccess(BadRequest) + case None => fuccess(BadRequest) case Some(obj) => val parts: Iterable[(String, String)] = for { (key, json) <- obj.toIterable diff --git a/modules/jobs/src/main/scala/de/proteinevolution/jobs/results/HmmerHSP.scala b/modules/jobs/src/main/scala/de/proteinevolution/jobs/results/HmmerHSP.scala index 48221b220c..91a327bfff 100644 --- a/modules/jobs/src/main/scala/de/proteinevolution/jobs/results/HmmerHSP.scala +++ b/modules/jobs/src/main/scala/de/proteinevolution/jobs/results/HmmerHSP.scala @@ -62,7 +62,7 @@ case class HmmerHSP( "hitLen" -> hit_len.asJson, "observedDomains" -> domain_obs_num.asJson, "agree" -> midline.asJson, - "query" -> Map( + "query" -> Map( "start" -> query_start.asJson, "end" -> query_end.asJson, "seq" -> query_seq.asJson diff --git a/modules/jobs/src/main/scala/de/proteinevolution/jobs/results/LinkUtil.scala b/modules/jobs/src/main/scala/de/proteinevolution/jobs/results/LinkUtil.scala index 0cc1bcfc30..24a48f44a8 100644 --- a/modules/jobs/src/main/scala/de/proteinevolution/jobs/results/LinkUtil.scala +++ b/modules/jobs/src/main/scala/de/proteinevolution/jobs/results/LinkUtil.scala @@ -80,7 +80,7 @@ object LinkUtil { case "ecod" => val idEcod = id.slice(5, 14); generateLink(ecodBaseLink, idEcod, id) case "cath" => val idCath = id.slice(5, 12); generateLink(cathBaseLink, idCath, id) case "phrog" => val idPhrog = id.replaceAll("phrog_", ""); generateLink(phrogBaseLink, idPhrog, id) - case "keggoc" => + case "keggoc" => val idKeggoc = id.split("OC.").last; generateLink(keggocBaseLink, idKeggoc, id) case _ => id @@ -116,7 +116,7 @@ object LinkUtil { case prokaryoticProteasomeNameReg(_) => links += generateLink(ncbiProteinBaseLink, idNcbi, "NCBI Fasta") case pdbNameReg(_) => links += generateLink(pdbeBaseLink, idPdb, "PDBe") case pfamNameReg(_) => links += generateLink(cddBaseLink, idCDD, "CDD") - case alphafolddbNameReg(_) => + case alphafolddbNameReg(_) => links += generateLink(uniprotBaseLink, idAlphaFold, "UniProt") links += generateLink(uniprotBaseLink, idAlphaFold + ".fasta", "UniProt FASTA") case uniprotNameReg(_) => diff --git a/modules/jobs/src/main/scala/de/proteinevolution/jobs/results/PLMBlastHSP.scala b/modules/jobs/src/main/scala/de/proteinevolution/jobs/results/PLMBlastHSP.scala index 9cd0cbf7dc..3087f35a7c 100644 --- a/modules/jobs/src/main/scala/de/proteinevolution/jobs/results/PLMBlastHSP.scala +++ b/modules/jobs/src/main/scala/de/proteinevolution/jobs/results/PLMBlastHSP.scala @@ -53,7 +53,7 @@ case class PLMBlastHSP( "eval" -> eValue.asJson, "bitScore" -> (identScore * 100).round.asJson, "hitLen" -> hit_len.asJson, - "query" -> Map( + "query" -> Map( "start" -> query_start.asJson, "end" -> query_end.asJson ).asJson, diff --git a/modules/jobs/src/main/scala/de/proteinevolution/jobs/results/PSIBlastHSP.scala b/modules/jobs/src/main/scala/de/proteinevolution/jobs/results/PSIBlastHSP.scala index eee8ed4828..5b656c6760 100644 --- a/modules/jobs/src/main/scala/de/proteinevolution/jobs/results/PSIBlastHSP.scala +++ b/modules/jobs/src/main/scala/de/proteinevolution/jobs/results/PSIBlastHSP.scala @@ -71,7 +71,7 @@ case class PSIBlastHSP( "refLen" -> ref_len.asJson, "hitLen" -> hit_len.asJson, "agree" -> midLine.asJson, - "query" -> Map( + "query" -> Map( "start" -> query_start.asJson, "end" -> query_end.asJson, "seq" -> query_seq.asJson diff --git a/modules/jobs/src/main/scala/de/proteinevolution/jobs/services/HHService.scala b/modules/jobs/src/main/scala/de/proteinevolution/jobs/services/HHService.scala index 01703519e7..9961982a29 100644 --- a/modules/jobs/src/main/scala/de/proteinevolution/jobs/services/HHService.scala +++ b/modules/jobs/src/main/scala/de/proteinevolution/jobs/services/HHService.scala @@ -42,7 +42,7 @@ class HHService @Inject() ( tool <- toolFinder.getTool(jobID) } yield (json, tool)).map { case (json, tool) => resultFiles.parseResult(tool, json) - case _ => + case _ => val error = "parsing result json failed." logger.error(error) Left(DecodingFailure(error, Nil)) diff --git a/modules/jobs/src/main/scala/de/proteinevolution/jobs/services/JobDispatcher.scala b/modules/jobs/src/main/scala/de/proteinevolution/jobs/services/JobDispatcher.scala index 7f27286d7f..235fcdcbc3 100644 --- a/modules/jobs/src/main/scala/de/proteinevolution/jobs/services/JobDispatcher.scala +++ b/modules/jobs/src/main/scala/de/proteinevolution/jobs/services/JobDispatcher.scala @@ -54,10 +54,10 @@ final class JobDispatcher @Inject() ( EitherT.leftT(JobSubmitError.ModellerKeyInvalid) } else { for { - generatedId <- generateJobId(parts) - _ <- validateJobId(generatedId) - _ <- checkNotAlreadyTaken(generatedId) - job <- EitherT.pure[Future, JobSubmitError](generateJob(toolName, generatedId, parts, user)) + generatedId <- generateJobId(parts) + _ <- validateJobId(generatedId) + _ <- checkNotAlreadyTaken(generatedId) + job <- EitherT.pure[Future, JobSubmitError](generateJob(toolName, generatedId, parts, user)) isFromInstitute <- EitherT.pure[Future, JobSubmitError]( user.userData.map(_.eMail).getOrElse("").matches(".+@tuebingen.mpg.de") ) @@ -114,7 +114,7 @@ final class JobDispatcher @Inject() ( form: Map[String, String], user: User ): Job = { - val now = ZonedDateTime.now + val now = ZonedDateTime.now val dateDeletionOn = now.plusDays( if (user.isRegistered) constants.jobDeletionRegistered.toLong else constants.jobDeletion.toLong diff --git a/modules/jobs/src/main/scala/de/proteinevolution/jobs/services/ProcessService.scala b/modules/jobs/src/main/scala/de/proteinevolution/jobs/services/ProcessService.scala index dcab446f91..340ccd08cf 100644 --- a/modules/jobs/src/main/scala/de/proteinevolution/jobs/services/ProcessService.scala +++ b/modules/jobs/src/main/scala/de/proteinevolution/jobs/services/ProcessService.scala @@ -82,7 +82,7 @@ final class ProcessService @Inject() ( val generateAlignmentScript = (scriptPath + "/generateAlignment.sh").toFile // HHPRED, HHBLITS alnEval val retrieveFullSeq = (scriptPath + "/retrieveFullSeq.sh").toFile val retrieveAlnEval = (scriptPath + "/retrieveAlnEval.sh").toFile // Hmmer & PSIBLAST alnEval - val retrieveFullSeqHHblits = + val retrieveFullSeqHHblits = (scriptPath + "/retrieveFullSeqHHblits.sh").toFile // why so little abstractions ??? val fullEvalAccs: () => String = @@ -94,7 +94,7 @@ final class ProcessService @Inject() ( "%s ".format(result.HSPS(num - 1).accession) }.mkString - val tempFileName = UUID.randomUUID().toString + val tempFileName = UUID.randomUUID().toString val (script, params) = (tool, form.forwardHitsMode, form.sequenceLengthMode) match { case (HHBLITS, "eval", "aln") | (HHPRED, "eval", "aln") => ( @@ -102,7 +102,7 @@ final class ProcessService @Inject() ( List( "jobID" -> jobId, "filename" -> tempFileName, - "numList" -> + "numList" -> result.HSPS.filter(_.eValue <= form.eval).map { _.num }.mkString(" ") ) ) diff --git a/modules/statistics/src/main/scala/de/proteinevolution/statistics/UserStatistic.scala b/modules/statistics/src/main/scala/de/proteinevolution/statistics/UserStatistic.scala index e69de29bb2..8b13789179 100644 --- a/modules/statistics/src/main/scala/de/proteinevolution/statistics/UserStatistic.scala +++ b/modules/statistics/src/main/scala/de/proteinevolution/statistics/UserStatistic.scala @@ -0,0 +1 @@ + diff --git a/modules/tel/src/main/scala/de/proteinevolution/tel/runscripts/Runscript.scala b/modules/tel/src/main/scala/de/proteinevolution/tel/runscripts/Runscript.scala index 7b226e2300..f48ae59ce3 100644 --- a/modules/tel/src/main/scala/de/proteinevolution/tel/runscripts/Runscript.scala +++ b/modules/tel/src/main/scala/de/proteinevolution/tel/runscripts/Runscript.scala @@ -55,7 +55,7 @@ class Runscript(files: Seq[File]) extends TELRegex with Logging { // Special fields to put the runscript into a larger context private case class Replacer(arguments: Seq[(String, ValidArgument)]) { - private var counter = -1 + private var counter = -1 def apply(m: Regex.Match): String = { m.groupNames.foreach(s => logger.debug(s) diff --git a/modules/tools/src/main/scala/de/proteinevolution/tools/ToolConfig.scala b/modules/tools/src/main/scala/de/proteinevolution/tools/ToolConfig.scala index 3899628893..5e5aa46b3f 100644 --- a/modules/tools/src/main/scala/de/proteinevolution/tools/ToolConfig.scala +++ b/modules/tools/src/main/scala/de/proteinevolution/tools/ToolConfig.scala @@ -147,7 +147,7 @@ class ToolConfig @Inject() ( validationParams ) val inputGroup: Seq[String] = paramAccess.paramGroups("Input") - val toolParameterForm = ToolParameters( + val toolParameterForm = ToolParameters( Seq( ParameterSection( "Input", diff --git a/modules/tools/src/main/scala/de/proteinevolution/tools/parameters/ParamAccess.scala b/modules/tools/src/main/scala/de/proteinevolution/tools/parameters/ParamAccess.scala index 5d7215acb4..0574d25a54 100644 --- a/modules/tools/src/main/scala/de/proteinevolution/tools/parameters/ParamAccess.scala +++ b/modules/tools/src/main/scala/de/proteinevolution/tools/parameters/ParamAccess.scala @@ -84,7 +84,7 @@ class ParamAccess @Inject() (tel: TEL) { case "DIAMOND_MIN_ALN_COV" => select("diamond_min_aln_cov", default = Some("80")) // HHblits - case "HHBLITSDB" => select("hhblitsdb", default = Some("UniRef30")) + case "HHBLITSDB" => select("hhblitsdb", default = Some("UniRef30")) case "HHBLITS_INCL_EVAL" => select("hhblits_incl_eval", default = Some("1e-3")) @@ -93,14 +93,12 @@ class ParamAccess @Inject() (tel: TEL) { case "COSINE_PERCENTILE_CUTOFF" => select("cosine_percentile_cutoff", default = Some("70")) case "ALIGNMENT_CUTOFF" => select("alignment_cutoff", default = Some("0.30")) case "WIN_LEN" => select("win_len", default = Some("15")) - case "MERGE_HITS" => select("merge_hits", default = Some("1")) - case "PLM_ALN_MODE" => select("plm_aln_mode", default = Some("loc")) - case "SPAN" => select("span", default = Some("25")) - case "SIGMA_FACTOR" => select("sigma_factor", default = Some("2")) - case "BFACTOR" => select("bfactor", default = Some("2")) - case "PLM_GAP_EXT" => select("plm_gap_ext", default = Some("0.5")) - - + case "MERGE_HITS" => select("merge_hits", default = Some("1")) + case "PLM_ALN_MODE" => select("plm_aln_mode", default = Some("loc")) + case "SPAN" => select("span", default = Some("25")) + case "SIGMA_FACTOR" => select("sigma_factor", default = Some("2")) + case "BFACTOR" => select("bfactor", default = Some("2")) + case "PLM_GAP_EXT" => select("plm_gap_ext", default = Some("0.5")) // HHpred case "TWOTEXTALIGNMENT" => @@ -125,7 +123,7 @@ class ParamAccess @Inject() (tel: TEL) { case "MACTHRESHOLD" => select("macthreshold", default = Some("0.3")) // HMMER - case "HMMER_DB" => select("hmmerdb", default = Some("alphafold_uniprot50")) + case "HMMER_DB" => select("hmmerdb", default = Some("alphafold_uniprot50")) case "MAX_HHBLITS_ITER" => select("max_hhblits_iter", default = Some("1"), onDetectedMSA = Some("0")) @@ -139,7 +137,7 @@ class ParamAccess @Inject() (tel: TEL) { select("blast_incl_eval", default = Some("1e-3")) // Kalign - case "GAP_OPEN" => NumberParameter("gap_open", default = Some(11)) + case "GAP_OPEN" => NumberParameter("gap_open", default = Some(11)) case "GAP_EXT_KALN" => NumberParameter( "gap_ext_kaln", @@ -174,8 +172,8 @@ class ParamAccess @Inject() (tel: TEL) { // HHrepID case "MSA_GEN_MAX_ITER_HHREPID" => select("msa_gen_max_iter_hhrepid", default = Some("3"), onDetectedMSA = Some("0")) - case "SCORE_SS" => select("score_ss", default = Some("2")) - case "REP_PVAL_THRESHOLD" => select("rep_pval_threshold", default = Some("1e-2")) + case "SCORE_SS" => select("score_ss", default = Some("2")) + case "REP_PVAL_THRESHOLD" => select("rep_pval_threshold", default = Some("1e-2")) case "SELF_ALN_PVAL_THRESHOLD" => select("self_aln_pval_threshold", default = Some("1e-1")) case "MERGE_ITERS" => select("merge_iters", default = Some("3")) @@ -283,7 +281,7 @@ class ParamAccess @Inject() (tel: TEL) { case "OUT_FORMAT" => select("out_format", default = Some("fas")) // HHfilter - case "MAX_SEQID" => NumberParameter("max_seqid", default = Some(90)) + case "MAX_SEQID" => NumberParameter("max_seqid", default = Some(90)) case "MIN_QUERY_COV" => NumberParameter( "min_query_cov",