####example

#call all needed fuctions
source("EpicCapo.r")

#If the input file is text file format (must be ".txt" each row represented each nonapeptide)
Prototype = EpicCapoBasic("testlist.txt",allele="A6801")
print(Prototype)


#If the input file is a fasta file format
Prototype = EpicCapoFasta("testfasta.fasta",allele="A6801")
print(Prototype)
#filtering to get only predicted positive peptide
Positive_Prototype = getOnlyPositive(Prototype)
print(Positive_Prototype)


#If the input is just a vector of one nonapeptide
Prototype = EpicCapoBasic("AAFQSSMTK",allele="A6801")
print(Prototype)
#or
Prototype = EpicCapoBasic(c("AAFQSSMTK"),allele="A6801")
print(Prototype)


#If input a vector of two or more nonapeptides
Prototype = EpicCapoBasic(c("AAFQSSMTK","AAFQSSMRK","NAFQSSMTK","AAFQSTMTK"),allele="A6801")
print(Prototype)
#or
Prototype = EpicCapoBasic(c("AAFQSSMTK","AAFQSSMRK","NAFQSSMTK","AAFQSTMTK"),allele="A6801")
print(Prototype)

###############
