Mercurial > repos > ucsb-phylogenetics > osiris_phylogenetics

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