Mercurial > repos > ucsb-phylogenetics > osiris_phylogenetics
diff orthologs/ucsb_hamster/lib/wisecfg/methods @ 0:5b9a38ec4a39 draft default tip
First commit of old repositories
| author | osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> |
|---|---|
| date | Tue, 11 Mar 2014 12:19:13 -0700 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/orthologs/ucsb_hamster/lib/wisecfg/methods Tue Mar 11 12:19:13 2014 -0700 @@ -0,0 +1,236 @@ + +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 + +