/usr/share/wise/methods is in wise-data 2.4.1-19.
This file is owned by root:root, with mode 0o644.
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real int
endtype
type codon
real int
endtype
#
# Stuff for PROTEIN
#
type PROTEIN
real ComplexSequence*
dbtype ProteinDB*
init init_ProteinDB
reload reload_ProteinDB
close close_ProteinDB
addentry dataentry_add_ProteinDB
name get_allocd_name_ComplexSequence
hardlink hard_link_ComplexSequence
free free_ComplexSequence
threadsafe
endtype
method AMINOACID
map CSEQ_PROTEIN_AMINOACID
arg PROTEIN
arg int
return aa
endmethod
#
# End of protein type and methods
#
type COMPMAT
real CompMat*
endtype
method AAMATCH
map CompMat_AAMATCH
arg COMPMAT
arg aa
arg aa
return int
endmethod
type DNACOMPMAT
real DnaMatrix*
endtype
method DNABASEMATCH
map DnaMatrix_MATCH
arg DNACOMPMAT
arg base
arg base
return int
endmethod
type CODONMATRIX
real CodonMatrixScore*
endtype
method CODON_MATCH
map CodonMatrix_MATCH
arg CODONMATRIX
arg codon
arg codon
return int
endmethod
#
# Genomic types and methods
#
type GENOMIC
real ComplexSequence*
dbtype GenomicDB*
init init_GenomicDB
reload reload_GenomicDB
close close_GenomicDB
addentry dataentry_add_GenomicDB
name get_allocd_name_ComplexSequence
hardlink hard_link_ComplexSequence
free free_ComplexSequence
threadsafe
endtype
method GENOMIC_CODON
map CSEQ_GENOMIC_CODON
arg GENOMIC
arg int
return codon
endmethod
method GENOMIC_BASE
map CSEQ_GENOMIC_BASE
arg GENOMIC
arg int
return base
endmethod
method GENOMIC_5SS
map CSEQ_GENOMIC_5SS
arg GENOMIC
arg int
return int
endmethod
method GENOMIC_3SS
map CSEQ_GENOMIC_3SS
arg GENOMIC
arg int
return int
endmethod
method GENOMIC_REPEAT
map CSEQ_GENOMIC_REPEAT
arg GENOMIC
arg int
return int
endmethod
method GENOMIC_CDS_POT
map CSEQ_GENOMIC_CDSPOT
arg GENOMIC
arg int
return int
endmethod
#
# Cdna Methods
#
type CDNA
real ComplexSequence*
dbtype cDNADB*
init init_cDNADB
reload reload_cDNADB
close close_cDNADB
addentry dataentry_add_cDNADB
hardlink hard_link_ComplexSequence
free free_ComplexSequence
threadsafe
endtype
method CDNA_CODON
map CSEQ_CDNA_CODON
arg CDNA
arg int
return codon
endmethod
method CDNA_BASE
map CSEQ_CDNA_BASE
arg CDNA
arg int
return base
endmethod
method CDNA_SEQ_POS
map CSEQ_SEQ
arg CDNA
arg int
return char*
endmethod
#
# Dna mehtods
#
type DNA
real ComplexSequence*
endtype
method DNA_BASE
map CSEQ_DNA_BASE
arg DNA
arg int
return base
endmethod
type DNAMAT
real DnaMatrix*
endtype
method DNAMATCH
map DnaMatrix_MATCH
arg DNAMAT
arg base
arg base
return int
endmethod
# genewise models
type CDNA_HMM
real GeneWiseScore*
dbtype GeneWiseDB*
init init_GeneWiseDB
reload reload_GeneWiseDB
close close_GeneWiseDB
addentry dataentry_add_GeneWiseDB
hardlink hard_link_GeneWiseScore
free free_GeneWiseScore
threadsafe
endtype
type GENEWISEMODEL
real GeneWiseScore*
dbtype GeneWiseDB*
init init_GeneWiseDB
reload reload_GeneWiseDB
close close_GeneWiseDB
addentry dataentry_add_GeneWiseDB
hardlink hard_link_GeneWiseScore
free free_GeneWiseScore
threadsafe
endtype
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