From 22bda6c64e1be99ee6c7d05724f8572934271e74 Mon Sep 17 00:00:00 2001 From: Vikram Alva Date: Wed, 26 Jun 2024 18:01:48 +0200 Subject: [PATCH] HHpred: update Pfam link --- conf/tools.conf | 2 +- .../de/proteinevolution/jobs/results/LinkUtil.scala | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/conf/tools.conf b/conf/tools.conf index c08da681e..6c99cd285 100644 --- a/conf/tools.conf +++ b/conf/tools.conf @@ -6,7 +6,7 @@ #Specify hardruntime in seconds # A new version indicates that the frontend should reload the configuration -version: "1.2.7" +version: "1.2.8" Tools { 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 c729d1a5b..0cc1bcfc3 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 @@ -49,7 +49,7 @@ object LinkUtil { "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?SUBMIT=y&db=structure&orig_db=structure&term=" private val ncbiProteinBaseLink = "https://www.ncbi.nlm.nih.gov/protein/" private val scopBaseLink = "http://scop.berkeley.edu/sid=" - private val pfamBaseLink = "http://pfam.xfam.org/family/" + private val pfamBaseLink = "https://www.ebi.ac.uk/interpro/entry/pfam/" private val cddBaseLink = "http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=" private val uniprotBaseLink = "http://www.uniprot.org/uniprot/" private val unirefBaseLink = "http://www.uniprot.org/uniref/" @@ -64,7 +64,7 @@ object LinkUtil { def getSingleLink(id: String): String = { val db = identifyDatabase(id) - val idPfam = id.replaceAll("am.*$||..*", "") + val idPfam = id.split("\\.").head val idPdb = id.replaceAll("_.*$", "") db match { case "scop" => val idScop = id.slice(5, 12); generateLink(scopBaseLink, idScop, id) @@ -73,7 +73,7 @@ object LinkUtil { case "ncbicd" => generateLink(cddBaseLink, id, id) case "cogkog" => generateLink(cddBaseLink, id, id) case "tigr" => generateLink(cddBaseLink, id, id) - case "pfam" => generateLink(pfamBaseLink, idPfam + "#tabview=tab0", id) + case "pfam" => generateLink(pfamBaseLink, idPfam, id) case "ncbi" => generateLink(ncbiProteinBaseLink, id, id) case "uniprot" => generateLink(uniprotBaseLink, id, id) case "smart" => generateLink(smartBaseLink, id, id) @@ -88,7 +88,7 @@ object LinkUtil { } def getSingleLinkDB(db: String, id: String): String = { - val idPfam = id.replaceAll("am.*$||..*", "") + val idPfam = id.split("\\.").head val idPdb = id.replaceAll("_.*$", "") val idAlphaFold = id.replaceAll("-.*$", "") @@ -98,7 +98,7 @@ object LinkUtil { case pdbNameReg(_) => generateLink(pdbBaseLink, idPdb, id) case uniprotNameReg(_) => generateLink(uniprotBaseLink, id, id) case unirefNameReg(_) => generateLink(unirefBaseLink, id, id) - case pfamNameReg(_) => generateLink(pfamBaseLink, idPfam + "#tabview=tab0", id) + case pfamNameReg(_) => generateLink(pfamBaseLink, idPfam, id) case alphafolddbNameReg(_) => generateLink(alphafoldBaseLink, idAlphaFold, id) case _ => id }