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HHpred: update Pfam link #1579

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merged 1 commit into from
Jun 26, 2024
Merged

HHpred: update Pfam link #1579

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2 changes: 1 addition & 1 deletion conf/tools.conf
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Original file line number Diff line number Diff line change
Expand Up @@ -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 {

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10 changes: 5 additions & 5 deletions modules/jobs/src/main/scala/de/proteinevolution/jobs/results/LinkUtil.scala
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Expand Up @@ -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/"
Expand All @@ -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)
Expand All @@ -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)
Expand All @@ -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("-.*$", "")

Expand All @@ -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
}
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