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<div class="navpath"><a class="el" href="namespaceitk.html">itk</a>::<a class="el" href="namespaceitk_1_1bio.html">bio</a>::<a class="el" href="classitk_1_1bio_1_1Gene.html">Gene</a>
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<h1>itk::bio::Gene Class Reference</h1><!-- doxytag: class="itk::bio::Gene" -->This class implement the abstraction of a biological gene.
<a href="#_details">More...</a>
<p>
<code>#include <<a class="el" href="itkBioGene_8h_source.html">itkBioGene.h</a>></code>
<p>
<p>
<a href="classitk_1_1bio_1_1Gene-members.html">List of all members.</a><table border="0" cellpadding="0" cellspacing="0">
<tr><td></td></tr>
<tr><td colspan="2"><br><h2>Classes</h2></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">struct </td><td class="memItemRight" valign="bottom"><a class="el" href="structitk_1_1bio_1_1Gene_1_1ControlDomainType.html">ControlDomainType</a></td></tr>
<tr><td colspan="2"><br><h2>Public Types</h2></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">typedef double </td><td class="memItemRight" valign="bottom"><a class="el" href="classitk_1_1bio_1_1Gene.html#09fb7cb162fbbaa0aa7d73857048060e">AffinityType</a></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">typedef std::string </td><td class="memItemRight" valign="bottom"><a class="el" href="classitk_1_1bio_1_1Gene.html#639ce31b993d55990731dd4e8d7045c7">DomainType</a></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">typedef std::vector<br class="typebreak">
< <a class="el" href="structitk_1_1bio_1_1Gene_1_1ControlDomainType.html">ControlDomainType</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classitk_1_1bio_1_1Gene.html#982eb63aef2bc6938d664a784b18842f">GeneControlDomainsType</a></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">typedef std::string </td><td class="memItemRight" valign="bottom"><a class="el" href="classitk_1_1bio_1_1Gene.html#90b0e3ade8afc7b66e4c52b53b5bcd25">NameType</a></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">typedef std::map< <a class="el" href="classitk_1_1bio_1_1Gene.html#639ce31b993d55990731dd4e8d7045c7">DomainType</a>, <br class="typebreak">
<a class="el" href="classitk_1_1bio_1_1Gene.html#09fb7cb162fbbaa0aa7d73857048060e">AffinityType</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classitk_1_1bio_1_1Gene.html#d8872d8ac731be796678c2820eb9e8f9">ProteinDomainsType</a></td></tr>
<tr><td colspan="2"><br><h2>Public Member Functions</h2></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classitk_1_1bio_1_1Gene.html#bd130167ff2d28841e1555929053b92a">AddGeneControlDomain</a> (const <a class="el" href="classitk_1_1bio_1_1Gene.html#639ce31b993d55990731dd4e8d7045c7">DomainType</a> &domain, bool type)</td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classitk_1_1bio_1_1Gene.html#2b900e7c51f8330664c87b6aa8926236">AddProteinDomain</a> (const <a class="el" href="classitk_1_1bio_1_1Gene.html#639ce31b993d55990731dd4e8d7045c7">DomainType</a> &domain, <a class="el" href="classitk_1_1bio_1_1Gene.html#09fb7cb162fbbaa0aa7d73857048060e">AffinityType</a> affinity)</td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classitk_1_1bio_1_1Gene.html#6870219b5af8a552d869f8007c330183">Copy</a> (const <a class="el" href="classitk_1_1bio_1_1Gene.html">Gene</a> &genome)</td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classitk_1_1bio_1_1Gene.html#162c9d2c1a99d6e6933d621a79daa4a2">Gene</a> ()</td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">virtual </td><td class="memItemRight" valign="bottom"><a class="el" href="classitk_1_1bio_1_1Gene.html#f4fc9933d925b071a7972d5205bda5a3">~Gene</a> ()</td></tr>
<tr><td colspan="2"><div class="groupHeader"></div></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">const char * </td><td class="memItemRight" valign="bottom"><a class="el" href="classitk_1_1bio_1_1Gene.html#c8f88cfdf1243abcbd7c7a5d04558bc8">GetName</a> () const </td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classitk_1_1bio_1_1Gene.html#d2dafc525ee1b46b1b333df81f3898e1">SetName</a> (const char *name)</td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classitk_1_1bio_1_1Gene.html#f3d5f8e7b6c3257d18e6fae8e468b7d2">SetName</a> (const <a class="el" href="classitk_1_1bio_1_1Gene.html#90b0e3ade8afc7b66e4c52b53b5bcd25">NameType</a> &name)</td></tr>
</table>
<hr><a name="_details"></a><h2>Detailed Description</h2>
This class implement the abstraction of a biological gene.
<p>
The gene has a name and a specification of promoters and represor binding sites. Promoter and represors encode a boolean expression that allows to control the expression of the gene. These boolean expression will result in a polynome in a finite different equation determining the rate at which protein is syntethizied by this gene.
<p>Definition at line <a class="el" href="itkBioGene_8h_source.html#l00041">41</a> of file <a class="el" href="itkBioGene_8h_source.html">itkBioGene.h</a>.</p>
<hr><h2>Member Typedef Documentation</h2>
<a class="anchor" name="09fb7cb162fbbaa0aa7d73857048060e"></a><!-- doxytag: member="itk::bio::Gene::AffinityType" ref="09fb7cb162fbbaa0aa7d73857048060e" args="" -->
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<td class="memname">typedef double <a class="el" href="classitk_1_1bio_1_1Gene.html#09fb7cb162fbbaa0aa7d73857048060e">itk::bio::Gene::AffinityType</a> </td>
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<p>Definition at line <a class="el" href="itkBioGene_8h_source.html#l00046">46</a> of file <a class="el" href="itkBioGene_8h_source.html">itkBioGene.h</a>.</p>
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<a class="anchor" name="639ce31b993d55990731dd4e8d7045c7"></a><!-- doxytag: member="itk::bio::Gene::DomainType" ref="639ce31b993d55990731dd4e8d7045c7" args="" -->
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<td class="memname">typedef std::string <a class="el" href="classitk_1_1bio_1_1Gene.html#639ce31b993d55990731dd4e8d7045c7">itk::bio::Gene::DomainType</a> </td>
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<p>Definition at line <a class="el" href="itkBioGene_8h_source.html#l00045">45</a> of file <a class="el" href="itkBioGene_8h_source.html">itkBioGene.h</a>.</p>
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<a class="anchor" name="982eb63aef2bc6938d664a784b18842f"></a><!-- doxytag: member="itk::bio::Gene::GeneControlDomainsType" ref="982eb63aef2bc6938d664a784b18842f" args="" -->
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<td class="memname">typedef std::vector< <a class="el" href="structitk_1_1bio_1_1Gene_1_1ControlDomainType.html">ControlDomainType</a> > <a class="el" href="classitk_1_1bio_1_1Gene.html#982eb63aef2bc6938d664a784b18842f">itk::bio::Gene::GeneControlDomainsType</a> </td>
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<p>Definition at line <a class="el" href="itkBioGene_8h_source.html#l00050">50</a> of file <a class="el" href="itkBioGene_8h_source.html">itkBioGene.h</a>.</p>
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<a class="anchor" name="90b0e3ade8afc7b66e4c52b53b5bcd25"></a><!-- doxytag: member="itk::bio::Gene::NameType" ref="90b0e3ade8afc7b66e4c52b53b5bcd25" args="" -->
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<td class="memname">typedef std::string <a class="el" href="classitk_1_1bio_1_1Gene.html#90b0e3ade8afc7b66e4c52b53b5bcd25">itk::bio::Gene::NameType</a> </td>
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<p>Definition at line <a class="el" href="itkBioGene_8h_source.html#l00044">44</a> of file <a class="el" href="itkBioGene_8h_source.html">itkBioGene.h</a>.</p>
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<a class="anchor" name="d8872d8ac731be796678c2820eb9e8f9"></a><!-- doxytag: member="itk::bio::Gene::ProteinDomainsType" ref="d8872d8ac731be796678c2820eb9e8f9" args="" -->
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<td class="memname">typedef std::map< <a class="el" href="classitk_1_1bio_1_1Gene.html#639ce31b993d55990731dd4e8d7045c7">DomainType</a>, <a class="el" href="classitk_1_1bio_1_1Gene.html#09fb7cb162fbbaa0aa7d73857048060e">AffinityType</a> > <a class="el" href="classitk_1_1bio_1_1Gene.html#d8872d8ac731be796678c2820eb9e8f9">itk::bio::Gene::ProteinDomainsType</a> </td>
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<p>Definition at line <a class="el" href="itkBioGene_8h_source.html#l00047">47</a> of file <a class="el" href="itkBioGene_8h_source.html">itkBioGene.h</a>.</p>
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<hr><h2>Constructor & Destructor Documentation</h2>
<a class="anchor" name="162c9d2c1a99d6e6933d621a79daa4a2"></a><!-- doxytag: member="itk::bio::Gene::Gene" ref="162c9d2c1a99d6e6933d621a79daa4a2" args="()" -->
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<td class="memname">itk::bio::Gene::Gene </td>
<td>(</td>
<td class="paramname"> </td>
<td> ) </td>
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<a class="anchor" name="f4fc9933d925b071a7972d5205bda5a3"></a><!-- doxytag: member="itk::bio::Gene::~Gene" ref="f4fc9933d925b071a7972d5205bda5a3" args="()" -->
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<td class="memname">virtual itk::bio::Gene::~Gene </td>
<td>(</td>
<td class="paramname"> </td>
<td> ) </td>
<td><code> [virtual]</code></td>
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<hr><h2>Member Function Documentation</h2>
<a class="anchor" name="bd130167ff2d28841e1555929053b92a"></a><!-- doxytag: member="itk::bio::Gene::AddGeneControlDomain" ref="bd130167ff2d28841e1555929053b92a" args="(const DomainType &domain, bool type)" -->
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<td class="memname">void itk::bio::Gene::AddGeneControlDomain </td>
<td>(</td>
<td class="paramtype">const <a class="el" href="classitk_1_1bio_1_1Gene.html#639ce31b993d55990731dd4e8d7045c7">DomainType</a> & </td>
<td class="paramname"> <em>domain</em>, </td>
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<td class="paramtype">bool </td>
<td class="paramname"> <em>type</em></td><td> </td>
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<td>)</td>
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<p>
Add a control domain to the gene. <a class="el" href="classA.html">A</a> control domain is an enhancer or silencer. <a class="el" href="classA.html">A</a> gene can have any number of them. The type will indicate if they are enhancers or silencers.
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<a class="anchor" name="2b900e7c51f8330664c87b6aa8926236"></a><!-- doxytag: member="itk::bio::Gene::AddProteinDomain" ref="2b900e7c51f8330664c87b6aa8926236" args="(const DomainType &domain, AffinityType affinity)" -->
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<td class="memname">void itk::bio::Gene::AddProteinDomain </td>
<td>(</td>
<td class="paramtype">const <a class="el" href="classitk_1_1bio_1_1Gene.html#639ce31b993d55990731dd4e8d7045c7">DomainType</a> & </td>
<td class="paramname"> <em>domain</em>, </td>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="classitk_1_1bio_1_1Gene.html#09fb7cb162fbbaa0aa7d73857048060e">AffinityType</a> </td>
<td class="paramname"> <em>affinity</em></td><td> </td>
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<p>
Add a protein domain along with an affinity. The name of the domain here actually refers to the one for which this protein will have binding affinity. For example, adding "SH2" with affinity 0.05 will means that this gene will synthetize a proteing with a domain that has 0.05 affinity for a standard SH2 domain.
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<a class="anchor" name="6870219b5af8a552d869f8007c330183"></a><!-- doxytag: member="itk::bio::Gene::Copy" ref="6870219b5af8a552d869f8007c330183" args="(const Gene &genome)" -->
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<td class="memname">void itk::bio::Gene::Copy </td>
<td>(</td>
<td class="paramtype">const <a class="el" href="classitk_1_1bio_1_1Gene.html">Gene</a> & </td>
<td class="paramname"> <em>genome</em> </td>
<td> ) </td>
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<a class="anchor" name="c8f88cfdf1243abcbd7c7a5d04558bc8"></a><!-- doxytag: member="itk::bio::Gene::GetName" ref="c8f88cfdf1243abcbd7c7a5d04558bc8" args="() const " -->
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<td class="memname">const char* itk::bio::Gene::GetName </td>
<td>(</td>
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<td> const</td>
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Set/Get the name of the gene. This uses a std::string type.
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<a class="anchor" name="d2dafc525ee1b46b1b333df81f3898e1"></a><!-- doxytag: member="itk::bio::Gene::SetName" ref="d2dafc525ee1b46b1b333df81f3898e1" args="(const char *name)" -->
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<td class="memname">void itk::bio::Gene::SetName </td>
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<td class="paramtype">const char * </td>
<td class="paramname"> <em>name</em> </td>
<td> ) </td>
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Set/Get the name of the gene. This uses a std::string type.
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<a class="anchor" name="f3d5f8e7b6c3257d18e6fae8e468b7d2"></a><!-- doxytag: member="itk::bio::Gene::SetName" ref="f3d5f8e7b6c3257d18e6fae8e468b7d2" args="(const NameType &name)" -->
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<td class="memname">void itk::bio::Gene::SetName </td>
<td>(</td>
<td class="paramtype">const <a class="el" href="classitk_1_1bio_1_1Gene.html#90b0e3ade8afc7b66e4c52b53b5bcd25">NameType</a> & </td>
<td class="paramname"> <em>name</em> </td>
<td> ) </td>
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<p>
Set/Get the name of the gene. This uses a std::string type.
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<hr>The documentation for this class was generated from the following file:<ul>
<li><a class="el" href="itkBioGene_8h_source.html">itkBioGene.h</a></ul>
</div>
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