1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212
|
=head1 NAME
translation module - part of the Wise2 package
=head1 SYNOPSIS
This module contains the following objects
=over
=item Translation
=back
=head1 DESCRIPTION
=head2 Object Translation
=over
=item start
Type [int] Scalar No documentation
=item end
Type [int] Scalar No documentation
=item parent
Type [Transcript *] Scalar No documentation
=item protein
Type [Protein *] Scalar No documentation
=back
Translation represents a single translation from
a cDNA. Although most cDNAs will have one translation,
this does allow us to deal with alternative translation
points etc.
As with Transcript and Gene before it, the
translation does not necessarily have any
sequence in it. When sequence is asked for by
get_Protein_from_Translation() the cache is checked,
and if it is empty, then the transcript's DNA
is called for, and the converted into the translation
with appropiate start and stops.
Of course, get_Protein_from_Translation can
potentially trigger the construction of an entire
gene upstairs, but that need not worry you here
=head2 Member functions of Translation
=over
=item get_Protein_from_Translation
&Wise2::Translation::get_Protein_from_Translation(ts,ct)
Gets the protein
Argument ts [UNKN ] translation [Translation *]
Argument ct [UNKN ] codon table to use [CodonTable *]
Return [SOFT ] Protein sequence [Protein *]
=item hard_link_Translation
&Wise2::Translation::hard_link_Translation(obj)
Bumps up the reference count of the object
Meaning that multiple pointers can 'own' it
Argument obj [UNKN ] Object to be hard linked [Translation *]
Return [UNKN ] Undocumented return value [Translation *]
=item alloc
&Wise2::Translation::alloc(void)
Allocates structure: assigns defaults if given
Return [UNKN ] Undocumented return value [Translation *]
=item set_start
&Wise2::Translation::set_start(obj,start)
Replace member variable start
For use principly by API functions
Argument obj [UNKN ] Object holding the variable [Translation *]
Argument start [OWNER] New value of the variable [int]
Return [SOFT ] member variable start [boolean]
=item start
&Wise2::Translation::start(obj)
Access member variable start
For use principly by API functions
Argument obj [UNKN ] Object holding the variable [Translation *]
Return [SOFT ] member variable start [int]
=item set_end
&Wise2::Translation::set_end(obj,end)
Replace member variable end
For use principly by API functions
Argument obj [UNKN ] Object holding the variable [Translation *]
Argument end [OWNER] New value of the variable [int]
Return [SOFT ] member variable end [boolean]
=item end
&Wise2::Translation::end(obj)
Access member variable end
For use principly by API functions
Argument obj [UNKN ] Object holding the variable [Translation *]
Return [SOFT ] member variable end [int]
=item set_parent
&Wise2::Translation::set_parent(obj,parent)
Replace member variable parent
For use principly by API functions
Argument obj [UNKN ] Object holding the variable [Translation *]
Argument parent [OWNER] New value of the variable [Transcript *]
Return [SOFT ] member variable parent [boolean]
=item parent
&Wise2::Translation::parent(obj)
Access member variable parent
For use principly by API functions
Argument obj [UNKN ] Object holding the variable [Translation *]
Return [SOFT ] member variable parent [Transcript *]
=item set_protein
&Wise2::Translation::set_protein(obj,protein)
Replace member variable protein
For use principly by API functions
Argument obj [UNKN ] Object holding the variable [Translation *]
Argument protein [OWNER] New value of the variable [Protein *]
Return [SOFT ] member variable protein [boolean]
=item protein
&Wise2::Translation::protein(obj)
Access member variable protein
For use principly by API functions
Argument obj [UNKN ] Object holding the variable [Translation *]
Return [SOFT ] member variable protein [Protein *]
=back
|