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<li class="navelem"><a class="el" href="namespaceOpenMS.html">OpenMS</a></li><li class="navelem"><a class="el" href="classOpenMS_1_1ControlledVocabulary.html">ControlledVocabulary</a></li> </ul>
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<div class="title">ControlledVocabulary Class Reference<div class="ingroups"><a class="el" href="group__Format.html">Format</a></div></div> </div>
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<p>Representation of a controlled vocabulary.
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<a href="classOpenMS_1_1ControlledVocabulary.html#details">More...</a></p>
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<p><code>#include <<a class="el" href="ControlledVocabulary_8h_source.html">OpenMS/FORMAT/ControlledVocabulary.h</a>></code></p>
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Classes</h2></td></tr>
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<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">struct  </td><td class="memItemRight" valign="bottom"><a class="el" href="structOpenMS_1_1ControlledVocabulary_1_1CVTerm.html">CVTerm</a></td></tr>
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<tr class="memdesc:"><td class="mdescLeft"> </td><td class="mdescRight">Representation of a CV term. <a href="structOpenMS_1_1ControlledVocabulary_1_1CVTerm.html#details">More...</a><br/></td></tr>
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<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a>
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Public Member Functions</h2></td></tr>
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<tr class="memitem:a0467af3c8247879181fe2e2930eeaabc"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ControlledVocabulary.html#a0467af3c8247879181fe2e2930eeaabc">ControlledVocabulary</a> ()</td></tr>
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<tr class="memdesc:a0467af3c8247879181fe2e2930eeaabc"><td class="mdescLeft"> </td><td class="mdescRight">Constructor. <a href="#a0467af3c8247879181fe2e2930eeaabc">More...</a><br/></td></tr>
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<tr class="memitem:a7f752f8524d194454a821cebac785b6f"><td class="memItemLeft" align="right" valign="top">virtual </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ControlledVocabulary.html#a7f752f8524d194454a821cebac785b6f">~ControlledVocabulary</a> ()</td></tr>
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<tr class="memdesc:a7f752f8524d194454a821cebac785b6f"><td class="mdescLeft"> </td><td class="mdescRight">Destructor. <a href="#a7f752f8524d194454a821cebac785b6f">More...</a><br/></td></tr>
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<tr class="memitem:ab31e7357671cfe484e3c3ed3cd6258e4"><td class="memItemLeft" align="right" valign="top">const <a class="el" href="classOpenMS_1_1String.html">String</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ControlledVocabulary.html#ab31e7357671cfe484e3c3ed3cd6258e4">name</a> () const </td></tr>
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<tr class="memdesc:ab31e7357671cfe484e3c3ed3cd6258e4"><td class="mdescLeft"> </td><td class="mdescRight">Returns the CV name (set in the load method) <a href="#ab31e7357671cfe484e3c3ed3cd6258e4">More...</a><br/></td></tr>
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<tr class="memitem:a3734f5236d43e8e2a3fade2f0d433428"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ControlledVocabulary.html#a3734f5236d43e8e2a3fade2f0d433428">loadFromOBO</a> (const <a class="el" href="classOpenMS_1_1String.html">String</a> &<a class="el" href="classOpenMS_1_1ControlledVocabulary.html#ab31e7357671cfe484e3c3ed3cd6258e4">name</a>, const <a class="el" href="classOpenMS_1_1String.html">String</a> &filename)</td></tr>
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<tr class="memdesc:a3734f5236d43e8e2a3fade2f0d433428"><td class="mdescLeft"> </td><td class="mdescRight">Loads the CV from an OBO file. <a href="#a3734f5236d43e8e2a3fade2f0d433428">More...</a><br/></td></tr>
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<tr class="memitem:a186f9c862f61f1563455af32660844c0"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ControlledVocabulary.html#a186f9c862f61f1563455af32660844c0">exists</a> (const <a class="el" href="classOpenMS_1_1String.html">String</a> &id) const </td></tr>
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<tr class="memdesc:a186f9c862f61f1563455af32660844c0"><td class="mdescLeft"> </td><td class="mdescRight">Returns true if the term is in the CV. Returns false otherwise. <a href="#a186f9c862f61f1563455af32660844c0">More...</a><br/></td></tr>
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<tr class="memitem:ad31829b95f825e205e05da9e4e8a4f96"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ControlledVocabulary.html#ad31829b95f825e205e05da9e4e8a4f96">hasTermWithName</a> (const <a class="el" href="classOpenMS_1_1String.html">String</a> &<a class="el" href="classOpenMS_1_1ControlledVocabulary.html#ab31e7357671cfe484e3c3ed3cd6258e4">name</a>) const </td></tr>
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<tr class="memdesc:ad31829b95f825e205e05da9e4e8a4f96"><td class="mdescLeft"> </td><td class="mdescRight">Returns true if a term with the given name is in the CV. Returns false otherwise. <a href="#ad31829b95f825e205e05da9e4e8a4f96">More...</a><br/></td></tr>
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<tr class="memitem:a29b00e2b3d45fa9f9a4428b33b58208f"><td class="memItemLeft" align="right" valign="top">const <a class="el" href="structOpenMS_1_1ControlledVocabulary_1_1CVTerm.html">CVTerm</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ControlledVocabulary.html#a29b00e2b3d45fa9f9a4428b33b58208f">getTerm</a> (const <a class="el" href="classOpenMS_1_1String.html">String</a> &id) const </td></tr>
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<tr class="memdesc:a29b00e2b3d45fa9f9a4428b33b58208f"><td class="mdescLeft"> </td><td class="mdescRight">Returns a term specified by ID. <a href="#a29b00e2b3d45fa9f9a4428b33b58208f">More...</a><br/></td></tr>
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<tr class="memitem:aeae0b56abf29c27d885b79b8a556acba"><td class="memItemLeft" align="right" valign="top">const <a class="el" href="structOpenMS_1_1ControlledVocabulary_1_1CVTerm.html">CVTerm</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ControlledVocabulary.html#aeae0b56abf29c27d885b79b8a556acba">getTermByName</a> (const <a class="el" href="classOpenMS_1_1String.html">String</a> &<a class="el" href="classOpenMS_1_1ControlledVocabulary.html#ab31e7357671cfe484e3c3ed3cd6258e4">name</a>, const <a class="el" href="classOpenMS_1_1String.html">String</a> &desc="") const </td></tr>
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<tr class="memdesc:aeae0b56abf29c27d885b79b8a556acba"><td class="mdescLeft"> </td><td class="mdescRight">Returns a term specified by name. <a href="#aeae0b56abf29c27d885b79b8a556acba">More...</a><br/></td></tr>
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<tr class="memitem:a79437580be56cbc464ac6130fd06b3a1"><td class="memItemLeft" align="right" valign="top">const <a class="el" href="classOpenMS_1_1Map.html">Map</a>< <a class="el" href="classOpenMS_1_1String.html">String</a>, <a class="el" href="structOpenMS_1_1ControlledVocabulary_1_1CVTerm.html">CVTerm</a> > & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ControlledVocabulary.html#a79437580be56cbc464ac6130fd06b3a1">getTerms</a> () const </td></tr>
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<tr class="memdesc:a79437580be56cbc464ac6130fd06b3a1"><td class="mdescLeft"> </td><td class="mdescRight">returns all the terms stored in the CV <a href="#a79437580be56cbc464ac6130fd06b3a1">More...</a><br/></td></tr>
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<tr class="memitem:aa3e1340b26625ec9a0051d4955f976da"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ControlledVocabulary.html#aa3e1340b26625ec9a0051d4955f976da">getAllChildTerms</a> (std::set< <a class="el" href="classOpenMS_1_1String.html">String</a> > &terms, const <a class="el" href="classOpenMS_1_1String.html">String</a> &parent) const </td></tr>
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<tr class="memdesc:aa3e1340b26625ec9a0051d4955f976da"><td class="mdescLeft"> </td><td class="mdescRight">Writes all child terms recursively into terms. <a href="#aa3e1340b26625ec9a0051d4955f976da">More...</a><br/></td></tr>
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<tr class="memitem:af770224e474f1b7f4d42b98bfc61a1ce"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ControlledVocabulary.html#af770224e474f1b7f4d42b98bfc61a1ce">isChildOf</a> (const <a class="el" href="classOpenMS_1_1String.html">String</a> &child, const <a class="el" href="classOpenMS_1_1String.html">String</a> &parent) const </td></tr>
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<tr class="memdesc:af770224e474f1b7f4d42b98bfc61a1ce"><td class="mdescLeft"> </td><td class="mdescRight">Returns if <code>child</code> is a child of <code>parent</code>. <a href="#af770224e474f1b7f4d42b98bfc61a1ce">More...</a><br/></td></tr>
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Protected Member Functions</h2></td></tr>
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<tr class="memitem:a7deacaa9770accdbf7fa60dff30a944b"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ControlledVocabulary.html#a7deacaa9770accdbf7fa60dff30a944b">checkName_</a> (const <a class="el" href="classOpenMS_1_1String.html">String</a> &id, const <a class="el" href="classOpenMS_1_1String.html">String</a> &<a class="el" href="classOpenMS_1_1ControlledVocabulary.html#ab31e7357671cfe484e3c3ed3cd6258e4">name</a>, bool ignore_case=true)</td></tr>
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<tr class="memdesc:a7deacaa9770accdbf7fa60dff30a944b"><td class="mdescLeft"> </td><td class="mdescRight">checks if a name corresponds to an id <a href="#a7deacaa9770accdbf7fa60dff30a944b">More...</a><br/></td></tr>
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Protected Attributes</h2></td></tr>
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<tr class="memitem:a7969e2be0e6e17d8e97a0ae1b50acda5"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1Map.html">Map</a>< <a class="el" href="classOpenMS_1_1String.html">String</a>, <a class="el" href="structOpenMS_1_1ControlledVocabulary_1_1CVTerm.html">CVTerm</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ControlledVocabulary.html#a7969e2be0e6e17d8e97a0ae1b50acda5">terms_</a></td></tr>
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<tr class="memdesc:a7969e2be0e6e17d8e97a0ae1b50acda5"><td class="mdescLeft"> </td><td class="mdescRight"><a class="el" href="classOpenMS_1_1Map.html" title="Map class based on the STL map (containing serveral convenience functions) ">Map</a> from ID to <a class="el" href="structOpenMS_1_1ControlledVocabulary_1_1CVTerm.html" title="Representation of a CV term. ">CVTerm</a>. <a href="#a7969e2be0e6e17d8e97a0ae1b50acda5">More...</a><br/></td></tr>
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<tr class="memitem:ac898dfba435913bb5f7e21625b67fc83"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1Map.html">Map</a>< <a class="el" href="classOpenMS_1_1String.html">String</a>, <a class="el" href="classOpenMS_1_1String.html">String</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ControlledVocabulary.html#ac898dfba435913bb5f7e21625b67fc83">namesToIds_</a></td></tr>
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<tr class="memdesc:ac898dfba435913bb5f7e21625b67fc83"><td class="mdescLeft"> </td><td class="mdescRight"><a class="el" href="classOpenMS_1_1Map.html" title="Map class based on the STL map (containing serveral convenience functions) ">Map</a> from name to id. <a href="#ac898dfba435913bb5f7e21625b67fc83">More...</a><br/></td></tr>
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<tr class="memitem:a46d25a1d56b8ab56e84b8bd0c7581e8f"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1String.html">String</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ControlledVocabulary.html#a46d25a1d56b8ab56e84b8bd0c7581e8f">name_</a></td></tr>
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<tr class="memdesc:a46d25a1d56b8ab56e84b8bd0c7581e8f"><td class="mdescLeft"> </td><td class="mdescRight">Name set in the load method. <a href="#a46d25a1d56b8ab56e84b8bd0c7581e8f">More...</a><br/></td></tr>
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Friends</h2></td></tr>
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<tr class="memitem:afaa6843e983fda7e77d49f7ea1475b7c"><td class="memItemLeft" align="right" valign="top">std::ostream & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ControlledVocabulary.html#afaa6843e983fda7e77d49f7ea1475b7c">operator<<</a> (std::ostream &os, const <a class="el" href="classOpenMS_1_1ControlledVocabulary.html">ControlledVocabulary</a> &cv)</td></tr>
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<tr class="memdesc:afaa6843e983fda7e77d49f7ea1475b7c"><td class="mdescLeft"> </td><td class="mdescRight">Print the contents to a stream. <a href="#afaa6843e983fda7e77d49f7ea1475b7c">More...</a><br/></td></tr>
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<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
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<div class="textblock"><p>Representation of a controlled vocabulary. </p>
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<p>This representation only contains the information used for parsing and validation. All other lines are stored in the <em>unparsed</em> member of the the <a class="el" href="structOpenMS_1_1ControlledVocabulary_1_1CVTerm.html" title="Representation of a CV term. ">CVTerm</a> struct. </p>
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</div><h2 class="groupheader">Constructor & Destructor Documentation</h2>
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<td class="paramname"></td><td>)</td>
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<td class="memname">virtual ~<a class="el" href="classOpenMS_1_1ControlledVocabulary.html">ControlledVocabulary</a> </td>
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<td class="paramname"></td><td>)</td>
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<h2 class="groupheader">Member Function Documentation</h2>
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<td class="memname">bool checkName_ </td>
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<td class="paramtype">const <a class="el" href="classOpenMS_1_1String.html">String</a> & </td>
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<td class="paramname"><em>id</em>, </td>
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<td class="paramname"><em>name</em>, </td>
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<td class="paramname"><em>ignore_case</em> = <code>true</code> </td>
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<p>checks if a name corresponds to an id </p>
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<p>If the term is not known, 'true' is returned! </p>
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<td class="memname">bool exists </td>
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<td class="paramtype">const <a class="el" href="classOpenMS_1_1String.html">String</a> & </td>
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<td class="paramname"><em>id</em></td><td>)</td>
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<p>Returns true if the term is in the CV. Returns false otherwise. </p>
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<td class="memname">void getAllChildTerms </td>
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<td class="paramtype">std::set< <a class="el" href="classOpenMS_1_1String.html">String</a> > & </td>
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<td class="paramname"><em>terms</em>, </td>
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<td class="paramtype">const <a class="el" href="classOpenMS_1_1String.html">String</a> & </td>
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<td class="paramname"><em>parent</em> </td>
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<td></td><td> const</td>
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<p>Writes all child terms recursively into terms. </p>
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<p>If parent has child this method writes them recursively into the term object</p>
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<dl class="exception"><dt>Exceptions</dt><dd>
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<tr><td class="paramname"><a class="el" href="classOpenMS_1_1Exception_1_1InvalidValue.html" title="Invalid value exception. ">Exception::InvalidValue</a></td><td>is thrown if the term is not present </td></tr>
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<td class="memname">const <a class="el" href="structOpenMS_1_1ControlledVocabulary_1_1CVTerm.html">CVTerm</a>& getTerm </td>
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<td class="paramtype">const <a class="el" href="classOpenMS_1_1String.html">String</a> & </td>
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<td class="paramname"><em>id</em></td><td>)</td>
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<p>Returns a term specified by ID. </p>
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<dl class="exception"><dt>Exceptions</dt><dd>
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<tr><td class="paramname"><a class="el" href="classOpenMS_1_1Exception_1_1InvalidValue.html" title="Invalid value exception. ">Exception::InvalidValue</a></td><td>is thrown if the term is not present </td></tr>
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<td class="memname">const <a class="el" href="structOpenMS_1_1ControlledVocabulary_1_1CVTerm.html">CVTerm</a>& getTermByName </td>
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<td class="paramtype">const <a class="el" href="classOpenMS_1_1String.html">String</a> & </td>
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<td class="paramname"><em>name</em>, </td>
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<td class="paramtype">const <a class="el" href="classOpenMS_1_1String.html">String</a> & </td>
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<td class="paramname"><em>desc</em> = <code>""</code> </td>
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<td></td><td> const</td>
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<p>Returns a term specified by name. </p>
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<dl class="exception"><dt>Exceptions</dt><dd>
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<tr><td class="paramname"><a class="el" href="classOpenMS_1_1Exception_1_1InvalidValue.html" title="Invalid value exception. ">Exception::InvalidValue</a></td><td>is thrown if the term is not present </td></tr>
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<td class="memname">const <a class="el" href="classOpenMS_1_1Map.html">Map</a><<a class="el" href="classOpenMS_1_1String.html">String</a>, <a class="el" href="structOpenMS_1_1ControlledVocabulary_1_1CVTerm.html">CVTerm</a>>& getTerms </td>
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<td class="paramname"></td><td>)</td>
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<p>returns all the terms stored in the CV </p>
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<td class="memname">bool hasTermWithName </td>
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<td class="paramname"><em>name</em></td><td>)</td>
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<p>Returns true if a term with the given name is in the CV. Returns false otherwise. </p>
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<td class="memname">bool isChildOf </td>
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<td class="paramname"><em>child</em>, </td>
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<td></td><td> const</td>
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<p>Returns if <code>child</code> is a child of <code>parent</code>. </p>
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<dl class="exception"><dt>Exceptions</dt><dd>
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<tr><td class="paramname"><a class="el" href="classOpenMS_1_1Exception_1_1InvalidValue.html" title="Invalid value exception. ">Exception::InvalidValue</a></td><td>is thrown if one of the terms is not present </td></tr>
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<td class="memname">void loadFromOBO </td>
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<td class="paramtype">const <a class="el" href="classOpenMS_1_1String.html">String</a> & </td>
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<td class="paramname"><em>name</em>, </td>
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<td class="paramtype">const <a class="el" href="classOpenMS_1_1String.html">String</a> & </td>
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<td class="paramname"><em>filename</em> </td>
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<p>Loads the CV from an OBO file. </p>
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<dl class="exception"><dt>Exceptions</dt><dd>
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<tr><td class="paramname"><a class="el" href="classOpenMS_1_1Exception_1_1ParseError.html" title="Parse Error exception. ">Exception::ParseError</a></td><td>is thrown if an error occurs during parsing </td></tr>
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<p>Referenced by <a class="el" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a0aaf41c383f973bf5a11f3a55022eda5">MzMLHandler< MapType >::MzMLHandler()</a>.</p>
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<td class="memname">const <a class="el" href="classOpenMS_1_1String.html">String</a>& name </td>
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<td class="paramname"></td><td>)</td>
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<p>Returns the CV name (set in the load method) </p>
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<h2 class="groupheader">Friends And Related Function Documentation</h2>
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<td class="memname">std::ostream& operator<< </td>
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<td class="paramname"><em>cv</em> </td>
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<span class="mlabels"><span class="mlabel">friend</span></span> </td>
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<p>Print the contents to a stream. </p>
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<h2 class="groupheader">Member Data Documentation</h2>
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<td class="memname"><a class="el" href="classOpenMS_1_1String.html">String</a> name_</td>
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<span class="mlabels"><span class="mlabel">protected</span></span> </td>
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<p>Name set in the load method. </p>
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<td class="memname"><a class="el" href="classOpenMS_1_1Map.html">Map</a><<a class="el" href="classOpenMS_1_1String.html">String</a>, <a class="el" href="classOpenMS_1_1String.html">String</a>> namesToIds_</td>
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<span class="mlabels"><span class="mlabel">protected</span></span> </td>
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<p><a class="el" href="classOpenMS_1_1Map.html" title="Map class based on the STL map (containing serveral convenience functions) ">Map</a> from name to id. </p>
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<td class="memname"><a class="el" href="classOpenMS_1_1Map.html">Map</a><<a class="el" href="classOpenMS_1_1String.html">String</a>, <a class="el" href="structOpenMS_1_1ControlledVocabulary_1_1CVTerm.html">CVTerm</a>> terms_</td>
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<span class="mlabels"><span class="mlabel">protected</span></span> </td>
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<p><a class="el" href="classOpenMS_1_1Map.html" title="Map class based on the STL map (containing serveral convenience functions) ">Map</a> from ID to <a class="el" href="structOpenMS_1_1ControlledVocabulary_1_1CVTerm.html" title="Representation of a CV term. ">CVTerm</a>. </p>
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<HR style="height:1px; border:none; border-top:1px solid #c0c0c0;">
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<TD><font color="#c0c0c0">OpenMS / TOPP release 1.11.1</font></TD>
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<TD align="right"><font color="#c0c0c0">Documentation generated on Thu Nov 14 2013 11:19:30 using doxygen 1.8.5</font></TD>
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