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comparison orthologs/ucsb_hamster/lib/wisecfg/methods @ 0:5b9a38ec4a39 draft default tip

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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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-1:000000000000 0:5b9a38ec4a39
1
2 type aa
3 real int
4 endtype
5
6 type codon
7 real int
8 endtype
9
10
11 #
12 # Stuff for PROTEIN
13 #
14
15 type PROTEIN
16 real ComplexSequence*
17 dbtype ProteinDB*
18 init init_ProteinDB
19 reload reload_ProteinDB
20 close close_ProteinDB
21 addentry dataentry_add_ProteinDB
22 name get_allocd_name_ComplexSequence
23 hardlink hard_link_ComplexSequence
24 free free_ComplexSequence
25 threadsafe
26 endtype
27
28
29 method AMINOACID
30 map CSEQ_PROTEIN_AMINOACID
31 arg PROTEIN
32 arg int
33 return aa
34 endmethod
35
36
37 #
38 # End of protein type and methods
39 #
40
41
42
43 type COMPMAT
44 real CompMat*
45 endtype
46
47 method AAMATCH
48 map CompMat_AAMATCH
49 arg COMPMAT
50 arg aa
51 arg aa
52 return int
53 endmethod
54
55
56 type DNACOMPMAT
57 real DnaMatrix*
58 endtype
59
60 method DNABASEMATCH
61 map DnaMatrix_MATCH
62 arg DNACOMPMAT
63 arg base
64 arg base
65 return int
66 endmethod
67
68 type CODONMATRIX
69 real CodonMatrixScore*
70 endtype
71
72 method CODON_MATCH
73 map CodonMatrix_MATCH
74 arg CODONMATRIX
75 arg codon
76 arg codon
77 return int
78 endmethod
79
80
81 #
82 # Genomic types and methods
83 #
84
85
86 type GENOMIC
87 real ComplexSequence*
88 dbtype GenomicDB*
89 init init_GenomicDB
90 reload reload_GenomicDB
91 close close_GenomicDB
92 addentry dataentry_add_GenomicDB
93 name get_allocd_name_ComplexSequence
94 hardlink hard_link_ComplexSequence
95 free free_ComplexSequence
96 threadsafe
97 endtype
98
99 method GENOMIC_CODON
100 map CSEQ_GENOMIC_CODON
101 arg GENOMIC
102 arg int
103 return codon
104 endmethod
105
106 method GENOMIC_BASE
107 map CSEQ_GENOMIC_BASE
108 arg GENOMIC
109 arg int
110 return base
111 endmethod
112
113 method GENOMIC_5SS
114 map CSEQ_GENOMIC_5SS
115 arg GENOMIC
116 arg int
117 return int
118 endmethod
119
120 method GENOMIC_3SS
121 map CSEQ_GENOMIC_3SS
122 arg GENOMIC
123 arg int
124 return int
125 endmethod
126
127
128 method GENOMIC_REPEAT
129 map CSEQ_GENOMIC_REPEAT
130 arg GENOMIC
131 arg int
132 return int
133 endmethod
134
135 method GENOMIC_CDS_POT
136 map CSEQ_GENOMIC_CDSPOT
137 arg GENOMIC
138 arg int
139 return int
140 endmethod
141
142
143
144 #
145 # Cdna Methods
146 #
147
148
149 type CDNA
150 real ComplexSequence*
151 dbtype cDNADB*
152 init init_cDNADB
153 reload reload_cDNADB
154 close close_cDNADB
155 addentry dataentry_add_cDNADB
156 hardlink hard_link_ComplexSequence
157 free free_ComplexSequence
158 threadsafe
159 endtype
160
161 method CDNA_CODON
162 map CSEQ_CDNA_CODON
163 arg CDNA
164 arg int
165 return codon
166 endmethod
167
168 method CDNA_BASE
169 map CSEQ_CDNA_BASE
170 arg CDNA
171 arg int
172 return base
173 endmethod
174
175 method CDNA_SEQ_POS
176 map CSEQ_SEQ
177 arg CDNA
178 arg int
179 return char*
180 endmethod
181
182
183 #
184 # Dna mehtods
185 #
186
187 type DNA
188 real ComplexSequence*
189 endtype
190
191 method DNA_BASE
192 map CSEQ_DNA_BASE
193 arg DNA
194 arg int
195 return base
196 endmethod
197
198 type DNAMAT
199 real DnaMatrix*
200 endtype
201
202 method DNAMATCH
203 map DnaMatrix_MATCH
204 arg DNAMAT
205 arg base
206 arg base
207 return int
208 endmethod
209
210 # genewise models
211
212 type CDNA_HMM
213 real GeneWiseScore*
214 dbtype GeneWiseDB*
215 init init_GeneWiseDB
216 reload reload_GeneWiseDB
217 close close_GeneWiseDB
218 addentry dataentry_add_GeneWiseDB
219 hardlink hard_link_GeneWiseScore
220 free free_GeneWiseScore
221 threadsafe
222 endtype
223
224 type GENEWISEMODEL
225 real GeneWiseScore*
226 dbtype GeneWiseDB*
227 init init_GeneWiseDB
228 reload reload_GeneWiseDB
229 close close_GeneWiseDB
230 addentry dataentry_add_GeneWiseDB
231 hardlink hard_link_GeneWiseScore
232 free free_GeneWiseScore
233 threadsafe
234 endtype
235
236