1 2type aa 3real int 4endtype 5 6type codon 7real int 8endtype 9 10 11# 12# Stuff for PROTEIN 13# 14 15type PROTEIN 16real ComplexSequence* 17dbtype ProteinDB* 18init init_ProteinDB 19reload reload_ProteinDB 20close close_ProteinDB 21addentry dataentry_add_ProteinDB 22name get_allocd_name_ComplexSequence 23hardlink hard_link_ComplexSequence 24free free_ComplexSequence 25threadsafe 26endtype 27 28 29method AMINOACID 30map CSEQ_PROTEIN_AMINOACID 31arg PROTEIN 32arg int 33return aa 34endmethod 35 36 37# 38# End of protein type and methods 39# 40 41 42 43type COMPMAT 44real CompMat* 45endtype 46 47method AAMATCH 48map CompMat_AAMATCH 49arg COMPMAT 50arg aa 51arg aa 52return int 53endmethod 54 55 56type DNACOMPMAT 57real DnaMatrix* 58endtype 59 60method DNABASEMATCH 61map DnaMatrix_MATCH 62arg DNACOMPMAT 63arg base 64arg base 65return int 66endmethod 67 68type CODONMATRIX 69real CodonMatrixScore* 70endtype 71 72method CODON_MATCH 73map CodonMatrix_MATCH 74arg CODONMATRIX 75arg codon 76arg codon 77return int 78endmethod 79 80 81# 82# Genomic types and methods 83# 84 85 86type GENOMIC 87real ComplexSequence* 88dbtype GenomicDB* 89init init_GenomicDB 90reload reload_GenomicDB 91close close_GenomicDB 92addentry dataentry_add_GenomicDB 93name get_allocd_name_ComplexSequence 94hardlink hard_link_ComplexSequence 95free free_ComplexSequence 96threadsafe 97endtype 98 99method GENOMIC_CODON 100map CSEQ_GENOMIC_CODON 101arg GENOMIC 102arg int 103return codon 104endmethod 105 106method GENOMIC_BASE 107map CSEQ_GENOMIC_BASE 108arg GENOMIC 109arg int 110return base 111endmethod 112 113method GENOMIC_5SS 114map CSEQ_GENOMIC_5SS 115arg GENOMIC 116arg int 117return int 118endmethod 119 120method GENOMIC_3SS 121map CSEQ_GENOMIC_3SS 122arg GENOMIC 123arg int 124return int 125endmethod 126 127 128method GENOMIC_REPEAT 129map CSEQ_GENOMIC_REPEAT 130arg GENOMIC 131arg int 132return int 133endmethod 134 135method GENOMIC_CDS_POT 136map CSEQ_GENOMIC_CDSPOT 137arg GENOMIC 138arg int 139return int 140endmethod 141 142 143 144# 145# Cdna Methods 146# 147 148 149type CDNA 150real ComplexSequence* 151dbtype cDNADB* 152init init_cDNADB 153reload reload_cDNADB 154close close_cDNADB 155addentry dataentry_add_cDNADB 156hardlink hard_link_ComplexSequence 157free free_ComplexSequence 158threadsafe 159endtype 160 161method CDNA_CODON 162map CSEQ_CDNA_CODON 163arg CDNA 164arg int 165return codon 166endmethod 167 168method CDNA_BASE 169map CSEQ_CDNA_BASE 170arg CDNA 171arg int 172return base 173endmethod 174 175method CDNA_SEQ_POS 176map CSEQ_SEQ 177arg CDNA 178arg int 179return char* 180endmethod 181 182 183# 184# Dna mehtods 185# 186 187type DNA 188real ComplexSequence* 189endtype 190 191method DNA_BASE 192map CSEQ_DNA_BASE 193arg DNA 194arg int 195return base 196endmethod 197 198type DNAMAT 199real DnaMatrix* 200endtype 201 202method DNAMATCH 203map DnaMatrix_MATCH 204arg DNAMAT 205arg base 206arg base 207return int 208endmethod 209 210# genewise models 211 212type CDNA_HMM 213real GeneWiseScore* 214dbtype GeneWiseDB* 215init init_GeneWiseDB 216reload reload_GeneWiseDB 217close close_GeneWiseDB 218addentry dataentry_add_GeneWiseDB 219hardlink hard_link_GeneWiseScore 220free free_GeneWiseScore 221threadsafe 222endtype 223 224type GENEWISEMODEL 225real GeneWiseScore* 226dbtype GeneWiseDB* 227init init_GeneWiseDB 228reload reload_GeneWiseDB 229close close_GeneWiseDB 230addentry dataentry_add_GeneWiseDB 231hardlink hard_link_GeneWiseScore 232free free_GeneWiseScore 233threadsafe 234endtype 235 236 237