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<HTML>
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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_1ModifierRep.html">ModifierRep</a></li> </ul>
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<p>Implements modification for suffix arrays.
<a href="classOpenMS_1_1ModifierRep.html#details">More...</a></p>
<p><code>#include <<a class="el" href="ModifierRep_8h_source.html">OpenMS/CHEMISTRY/ModifierRep.h</a>></code></p>
<table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a>
Public Member Functions</h2></td></tr>
<tr class="memitem:a80f108db2ac232faed4aef168410c2ab"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ModifierRep.html#a80f108db2ac232faed4aef168410c2ab">ModifierRep</a> ()</td></tr>
<tr class="memdesc:a80f108db2ac232faed4aef168410c2ab"><td class="mdescLeft"> </td><td class="mdescRight">Constructor. <a href="#a80f108db2ac232faed4aef168410c2ab">More...</a><br/></td></tr>
<tr class="separator:a80f108db2ac232faed4aef168410c2ab"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a2996661d49fbd90c65102baed1ccad47"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ModifierRep.html#a2996661d49fbd90c65102baed1ccad47">ModifierRep</a> (const <a class="el" href="classOpenMS_1_1ModifierRep.html">ModifierRep</a> &source)</td></tr>
<tr class="memdesc:a2996661d49fbd90c65102baed1ccad47"><td class="mdescLeft"> </td><td class="mdescRight">copy constructor <a href="#a2996661d49fbd90c65102baed1ccad47">More...</a><br/></td></tr>
<tr class="separator:a2996661d49fbd90c65102baed1ccad47"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:aeff1417c524fb003cd266d2e33e7e872"><td class="memItemLeft" align="right" valign="top">virtual </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ModifierRep.html#aeff1417c524fb003cd266d2e33e7e872">~ModifierRep</a> ()</td></tr>
<tr class="memdesc:aeff1417c524fb003cd266d2e33e7e872"><td class="mdescLeft"> </td><td class="mdescRight">destructor <a href="#aeff1417c524fb003cd266d2e33e7e872">More...</a><br/></td></tr>
<tr class="separator:aeff1417c524fb003cd266d2e33e7e872"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a552dd945b87317962e726bc1c5c73411"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ModifierRep.html#a552dd945b87317962e726bc1c5c73411">setNumberOfModifications</a> (<a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i)</td></tr>
<tr class="memdesc:a552dd945b87317962e726bc1c5c73411"><td class="mdescLeft"> </td><td class="mdescRight">setter for number of modifications <a href="#a552dd945b87317962e726bc1c5c73411">More...</a><br/></td></tr>
<tr class="separator:a552dd945b87317962e726bc1c5c73411"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a9093aa103751307fb7fc728347d6606e"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ModifierRep.html#a9093aa103751307fb7fc728347d6606e">getNumberOfModifications</a> () const </td></tr>
<tr class="memdesc:a9093aa103751307fb7fc728347d6606e"><td class="mdescLeft"> </td><td class="mdescRight">getter for number of modifications <a href="#a9093aa103751307fb7fc728347d6606e">More...</a><br/></td></tr>
<tr class="separator:a9093aa103751307fb7fc728347d6606e"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a1bbf02c08dda16fc7fd94ade1e45bc47"><td class="memItemLeft" align="right" valign="top">const std::vector< std::vector<br class="typebreak"/>
< <a class="el" href="classdouble.html">double</a> > > & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ModifierRep.html#a1bbf02c08dda16fc7fd94ade1e45bc47">getModificationTable</a> ()</td></tr>
<tr class="memdesc:a1bbf02c08dda16fc7fd94ade1e45bc47"><td class="mdescLeft"> </td><td class="mdescRight">getter for the modification table <a href="#a1bbf02c08dda16fc7fd94ade1e45bc47">More...</a><br/></td></tr>
<tr class="separator:a1bbf02c08dda16fc7fd94ade1e45bc47"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a4116322e6cba135c6bb4f48a3f5177f7"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ModifierRep.html#a4116322e6cba135c6bb4f48a3f5177f7">refreshModificationList</a> (std::map< <a class="el" href="classdouble.html">double</a>, <a class="el" href="group__Concept.html#gae113cb41304c6692c7bf5d0624dc6f0f">SignedSize</a> > &mod_map, const char &c)</td></tr>
<tr class="memdesc:a4116322e6cba135c6bb4f48a3f5177f7"><td class="mdescLeft"> </td><td class="mdescRight">updates the modifications list if with the modifications of a new amino acid <a href="#a4116322e6cba135c6bb4f48a3f5177f7">More...</a><br/></td></tr>
<tr class="separator:a4116322e6cba135c6bb4f48a3f5177f7"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ad6ee839d30f5b8af728878ceb5a35115"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ModifierRep.html#ad6ee839d30f5b8af728878ceb5a35115">getMaxModificationMasses</a> ()</td></tr>
<tr class="memdesc:ad6ee839d30f5b8af728878ceb5a35115"><td class="mdescLeft"> </td><td class="mdescRight">calculates the maximal number unique masses of combinations of modifications (maximal possible size of the modification map) <a href="#ad6ee839d30f5b8af728878ceb5a35115">More...</a><br/></td></tr>
<tr class="separator:ad6ee839d30f5b8af728878ceb5a35115"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a296adf1639c62fda2661bd74e9821f16"><td class="memItemLeft" align="right" valign="top">std::vector< <a class="el" href="classOpenMS_1_1String.html">String</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ModifierRep.html#a296adf1639c62fda2661bd74e9821f16">getModificationsForMass</a> (<a class="el" href="classdouble.html">double</a> &m)</td></tr>
<tr class="memdesc:a296adf1639c62fda2661bd74e9821f16"><td class="mdescLeft"> </td><td class="mdescRight">gets all modification possibilities for a given mass <a href="#a296adf1639c62fda2661bd74e9821f16">More...</a><br/></td></tr>
<tr class="separator:a296adf1639c62fda2661bd74e9821f16"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a6b830b5859e44ac6101ee5063aa7babb"><td class="memItemLeft" align="right" valign="top">std::vector< <a class="el" href="classOpenMS_1_1String.html">String</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ModifierRep.html#a6b830b5859e44ac6101ee5063aa7babb">getModificationsForMass</a> (<a class="el" href="classdouble.html">double</a> &m, const <a class="el" href="classOpenMS_1_1String.html">String</a> &seq)</td></tr>
<tr class="memdesc:a6b830b5859e44ac6101ee5063aa7babb"><td class="mdescLeft"> </td><td class="mdescRight">gets all modification possibilities for a given mass and for the given peptide <a href="#a6b830b5859e44ac6101ee5063aa7babb">More...</a><br/></td></tr>
<tr class="separator:a6b830b5859e44ac6101ee5063aa7babb"><td class="memSeparator" colspan="2"> </td></tr>
</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pro-attribs"></a>
Protected Attributes</h2></td></tr>
<tr class="memitem:a32b1bbbf4ab7468d7baeae2f2afdb364"><td class="memItemLeft" align="right" valign="top">std::vector< std::vector<br class="typebreak"/>
< <a class="el" href="classdouble.html">double</a> > > </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ModifierRep.html#a32b1bbbf4ab7468d7baeae2f2afdb364">modification_table_</a></td></tr>
<tr class="memdesc:a32b1bbbf4ab7468d7baeae2f2afdb364"><td class="mdescLeft"> </td><td class="mdescRight">all possible modifications <a href="#a32b1bbbf4ab7468d7baeae2f2afdb364">More...</a><br/></td></tr>
<tr class="separator:a32b1bbbf4ab7468d7baeae2f2afdb364"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a5609ab550eb96c106ca2be458a149fcc"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ModifierRep.html#a5609ab550eb96c106ca2be458a149fcc">number_of_modifications_</a></td></tr>
<tr class="memdesc:a5609ab550eb96c106ca2be458a149fcc"><td class="mdescLeft"> </td><td class="mdescRight">number of maximal modifications <a href="#a5609ab550eb96c106ca2be458a149fcc">More...</a><br/></td></tr>
<tr class="separator:a5609ab550eb96c106ca2be458a149fcc"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a6dfda100b47c61a93075d5a42ecbb1c5"><td class="memItemLeft" align="right" valign="top">std::map< <a class="el" href="classOpenMS_1_1String.html">String</a>, std::vector<br class="typebreak"/>
< <a class="el" href="classOpenMS_1_1String.html">String</a> > > </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ModifierRep.html#a6dfda100b47c61a93075d5a42ecbb1c5">mass_mapping_</a></td></tr>
<tr class="memdesc:a6dfda100b47c61a93075d5a42ecbb1c5"><td class="mdescLeft"> </td><td class="mdescRight">maps a mass to the combination of modifications <a href="#a6dfda100b47c61a93075d5a42ecbb1c5">More...</a><br/></td></tr>
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<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
<div class="textblock"><p>Implements modification for suffix arrays. </p>
</div><h2 class="groupheader">Constructor & Destructor Documentation</h2>
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<td class="memname"><a class="el" href="classOpenMS_1_1ModifierRep.html">ModifierRep</a> </td>
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<p>Constructor. </p>
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<td class="memname"><a class="el" href="classOpenMS_1_1ModifierRep.html">ModifierRep</a> </td>
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<td class="paramtype">const <a class="el" href="classOpenMS_1_1ModifierRep.html">ModifierRep</a> & </td>
<td class="paramname"><em>source</em></td><td>)</td>
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<p>copy constructor </p>
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<td class="memname">virtual ~<a class="el" href="classOpenMS_1_1ModifierRep.html">ModifierRep</a> </td>
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<td class="paramname"></td><td>)</td>
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<span class="mlabels"><span class="mlabel">virtual</span></span> </td>
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<p>destructor </p>
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<h2 class="groupheader">Member Function Documentation</h2>
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<td class="memname"><a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> getMaxModificationMasses </td>
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<p>calculates the maximal number unique masses of combinations of modifications (maximal possible size of the modification map) </p>
<dl class="section return"><dt>Returns</dt><dd>Size </dd></dl>
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<td class="memname">std::vector<<a class="el" href="classOpenMS_1_1String.html">String</a>> getModificationsForMass </td>
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<td class="paramtype"><a class="el" href="classdouble.html">double</a> & </td>
<td class="paramname"><em>m</em></td><td>)</td>
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<p>gets all modification possibilities for a given mass </p>
<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramname">m</td><td>masse </td></tr>
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<dl class="section return"><dt>Returns</dt><dd>vector of strings therefor at first the massmapping is calculated. This massmapping will be saved as private member mass_mapping_ so that it has to be calculated only once. </dd></dl>
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<td class="memname">std::vector<<a class="el" href="classOpenMS_1_1String.html">String</a>> getModificationsForMass </td>
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<td class="paramtype">const <a class="el" href="classOpenMS_1_1String.html">String</a> & </td>
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<p>gets all modification possibilities for a given mass and for the given peptide </p>
<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramname">m</td><td>masse </td></tr>
<tr><td class="paramname">seq</td><td>peptide sequence </td></tr>
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<dl class="section return"><dt>Returns</dt><dd>vector of strings the getModificationsForMass (double & m) will be used. then a chacater histogramm of the sequence is created as well as for every possible combination of modifications. Then only modifications that are possible are returned. </dd></dl>
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<td class="memname">const std::vector<std::vector<<a class="el" href="classdouble.html">double</a>> >& getModificationTable </td>
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<p>getter for the modification table </p>
<dl class="section return"><dt>Returns</dt><dd>const reference to the modofication table </dd></dl>
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<td class="memname"><a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> getNumberOfModifications </td>
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<p>getter for number of modifications </p>
<dl class="section return"><dt>Returns</dt><dd>number of modifications </dd></dl>
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<td class="memname">void refreshModificationList </td>
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<td class="paramtype">std::map< <a class="el" href="classdouble.html">double</a>, <a class="el" href="group__Concept.html#gae113cb41304c6692c7bf5d0624dc6f0f">SignedSize</a> > & </td>
<td class="paramname"><em>mod_map</em>, </td>
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<p>updates the modifications list if with the modifications of a new amino acid </p>
<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramname">mod_map</td><td>reference to the map holding the possible modifications </td></tr>
<tr><td class="paramname">c</td><td>const character for the amino acid</td></tr>
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<p>all modification for the given amino acid are added to the map. The key is the mass, the value is the number of modifications for that mass. So the advantage of using a map is that a value will occure only once. the mass of the modification is added to all elements in the map whose number of modifications is smaller than the maximal number of modifications. </p>
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<td class="memname">void setNumberOfModifications </td>
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<p>setter for number of modifications </p>
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<tr><td class="paramname">i</td><td>number of modifications </td></tr>
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<h2 class="groupheader">Member Data Documentation</h2>
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<td class="memname">std::map<<a class="el" href="classOpenMS_1_1String.html">String</a>, std::vector<<a class="el" href="classOpenMS_1_1String.html">String</a>> > mass_mapping_</td>
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<p>maps a mass to the combination of modifications </p>
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<td class="memname">std::vector<std::vector<<a class="el" href="classdouble.html">double</a>> > modification_table_</td>
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<p>all possible modifications </p>
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<td class="memname"><a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> number_of_modifications_</td>
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<p>number of maximal modifications </p>
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<TD><font color="#c0c0c0">OpenMS / TOPP release 1.11.1</font></TD>
<TD align="right"><font color="#c0c0c0">Documentation generated on Thu Nov 14 2013 11:19:27 using doxygen 1.8.5</font></TD>
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