########################################################################################################
# InSilicoDicer configuration file
########################################################################################################

# 
miRNAregistry.miRNA.dat=file:share/databases/miRNA.dat.gz
#miRNAregistry.miRNA.dat=http://bibiserv.techfak.uni-bielefeld.de/insilicodicer/miRNAregistry/miRNA.dat.gz


#########################################################################################
#
# available Databases
db=cElegans,miRNAregistry,mMusculus
db.cElegans=file:share/databases/cElegans.vienna.gz
#db.cElegans=http://bibiserv.techfak.uni-bielefeld.de/insilicodicer/databases/cElegans.vienna.gz
db.miRNAregistry=file:share/databases/miRNAregistry.vienna.gz
#db.miRNAregistry=http://bibiserv.techfak.uni-bielefeld.de/insilicodicer/databases/miRNAregistry.vienna.gz
db.mMusculus=file:share/databases/mMusculus.vienna.gz
#db.mMusculus=http://bibiserv.techfak.uni-bielefeld.de/insilicodicer/databases/mMusculus.vienna.gz

########################################################################################################
#Available Action Classes to choose from (comma-separated list of class)
#
#Folding Action Classes:
folding=RNAfold(local),RNAfold(webservice)
folding.RNAfold(local)=de.unibi.techfak.InSilicoDicer.Actions.FoldPrecursor.Fold_Vienna
folding.RNAfold(local).conf=file:etc/Fold_Vienna.conf
folding.RNAfold(local).local=true
folding.RNAfold(webservice)=de.unibi.techfak.InSilicoDicer.Actions.FoldPrecursor.RNAfoldWS
folding.RNAfold(webservice).conf=http://bibiserv.techfak.uni-bielefeld.de/insilicodicer/conf/rnafold.conf
folding.RNAfold(webservice).local=false

#
#Calculation of Conservation Classes:
calccons=CalcCons_Entropy,CalcCons_Entropy_seed
calccons.CalcCons_Entropy=de.unibi.techfak.InSilicoDicer.Actions.CalcConservation.CalcCons_Entropy
calccons.CalcCons_Entropy.conf=
calccons.CalcCons_Entropy.local=internal
calccons.CalcCons_Entropy_seed=de.unibi.techfak.InSilicoDicer.Actions.CalcConservation.CalcCons_Entropy_seed
calccons.CalcCons_Entropy_seed.conf=
calccons.CalcCons_Entropy_seed.local=internal
#
#Multiple Alignment Classes:
ma=ClustalW(local),ClustalW(webservice)
ma.ClustalW(local)=de.unibi.techfak.InSilicoDicer.Actions.AlignPrecursors.MA_ClustalW
ma.ClustalW(local).conf=file:etc/MA_ClustalW.conf
ma.ClustalW(local).local=true
ma.ClustalW(webservice)=de.unibi.techfak.InSilicoDicer.Actions.AlignPrecursors.ClustalWWS
ma.ClustalW(webservice).conf=
ma.ClustalW(webservice).local=false

#
#Scoring Classes:
scoring=Gaasterland
scoring.Gaasterland=de.unibi.techfak.InSilicoDicer.Actions.ScorePrecursor.Score_Gaasterland
scoring.Gaasterland.conf=
scoring.Gaasterland.local=true
########################################################################################################