type aa
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