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<TITLE>PepNovoInfile Class Reference</TITLE>
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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_1PepNovoInfile.html">PepNovoInfile</a></li> </ul>
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<a href="#pub-methods">Public Member Functions</a> |
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<a href="#pri-methods">Private Member Functions</a> |
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<a href="#pri-attribs">Private Attributes</a> |
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<a href="classOpenMS_1_1PepNovoInfile-members.html">List of all members</a> </div>
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<div class="title">PepNovoInfile Class Reference<div class="ingroups"><a class="el" href="group__FileIO.html">File IO</a></div></div> </div>
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<div class="contents">
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<p>PepNovo input file adapter.
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<a href="classOpenMS_1_1PepNovoInfile.html#details">More...</a></p>
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<p><code>#include <<a class="el" href="PepNovoInfile_8h_source.html">OpenMS/FORMAT/PepNovoInfile.h</a>></code></p>
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<table class="memberdecls">
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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:a513f3e33f07e148a9ee904c341d25bcb"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1PepNovoInfile.html#a513f3e33f07e148a9ee904c341d25bcb">PepNovoInfile</a> ()</td></tr>
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<tr class="memdesc:a513f3e33f07e148a9ee904c341d25bcb"><td class="mdescLeft"> </td><td class="mdescRight">default constructor <a href="#a513f3e33f07e148a9ee904c341d25bcb">More...</a><br/></td></tr>
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<tr class="separator:a513f3e33f07e148a9ee904c341d25bcb"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a192d37aa9e1d497150a6a2a0b1a5c5fa"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1PepNovoInfile.html#a192d37aa9e1d497150a6a2a0b1a5c5fa">PepNovoInfile</a> (const <a class="el" href="classOpenMS_1_1PepNovoInfile.html">PepNovoInfile</a> &pepnovo_infile)</td></tr>
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<tr class="memdesc:a192d37aa9e1d497150a6a2a0b1a5c5fa"><td class="mdescLeft"> </td><td class="mdescRight">copy constructor <a href="#a192d37aa9e1d497150a6a2a0b1a5c5fa">More...</a><br/></td></tr>
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<tr class="separator:a192d37aa9e1d497150a6a2a0b1a5c5fa"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a7a3f9795b99e509efbbf2a96e4f37d76"><td class="memItemLeft" align="right" valign="top">virtual </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1PepNovoInfile.html#a7a3f9795b99e509efbbf2a96e4f37d76">~PepNovoInfile</a> ()</td></tr>
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<tr class="memdesc:a7a3f9795b99e509efbbf2a96e4f37d76"><td class="mdescLeft"> </td><td class="mdescRight">destructor <a href="#a7a3f9795b99e509efbbf2a96e4f37d76">More...</a><br/></td></tr>
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<tr class="separator:a7a3f9795b99e509efbbf2a96e4f37d76"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a07c033ab1288a35cb5e945d4e59ff325"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1PepNovoInfile.html">PepNovoInfile</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1PepNovoInfile.html#a07c033ab1288a35cb5e945d4e59ff325">operator=</a> (const <a class="el" href="classOpenMS_1_1PepNovoInfile.html">PepNovoInfile</a> &pepnovo_infile)</td></tr>
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<tr class="memdesc:a07c033ab1288a35cb5e945d4e59ff325"><td class="mdescLeft"> </td><td class="mdescRight">assignment operator <a href="#a07c033ab1288a35cb5e945d4e59ff325">More...</a><br/></td></tr>
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<tr class="separator:a07c033ab1288a35cb5e945d4e59ff325"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a21f7c1772f42881256c3a90f92afb508"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1PepNovoInfile.html#a21f7c1772f42881256c3a90f92afb508">operator==</a> (const <a class="el" href="classOpenMS_1_1PepNovoInfile.html">PepNovoInfile</a> &pepnovo_infile) const </td></tr>
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<tr class="memdesc:a21f7c1772f42881256c3a90f92afb508"><td class="mdescLeft"> </td><td class="mdescRight">equality operator <a href="#a21f7c1772f42881256c3a90f92afb508">More...</a><br/></td></tr>
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<tr class="memitem:a4fb93f999151e70a0f506c4c36f63fd7"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1PepNovoInfile.html#a4fb93f999151e70a0f506c4c36f63fd7">store</a> (const <a class="el" href="classOpenMS_1_1String.html">String</a> &filename)</td></tr>
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<tr class="memitem:a55368814c05cafb6718ee3a7e76402f8"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1PepNovoInfile.html#a55368814c05cafb6718ee3a7e76402f8">setModifications</a> (const <a class="el" href="classOpenMS_1_1StringList.html">StringList</a> &fixed_mods, const <a class="el" href="classOpenMS_1_1StringList.html">StringList</a> &variable_mods)</td></tr>
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<tr class="memdesc:a55368814c05cafb6718ee3a7e76402f8"><td class="mdescLeft"> </td><td class="mdescRight">generates the PepNovo Infile for given fixed and variable modifications * <a href="#a55368814c05cafb6718ee3a7e76402f8">More...</a><br/></td></tr>
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<tr class="memitem:a9321818c2e263c084ad4210c59544099"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1PepNovoInfile.html#a9321818c2e263c084ad4210c59544099">getModifications</a> (std::map< <a class="el" href="classOpenMS_1_1String.html">String</a>, <a class="el" href="classOpenMS_1_1String.html">String</a> > &modification_key_map) const </td></tr>
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<tr class="memdesc:a9321818c2e263c084ad4210c59544099"><td class="mdescLeft"> </td><td class="mdescRight">return the modifications. <a href="#a9321818c2e263c084ad4210c59544099">More...</a><br/></td></tr>
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</table><table class="memberdecls">
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Private Member Functions</h2></td></tr>
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<tr class="memitem:a5fefc01f9e478eeea2669c4b9e28765c"><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_1PepNovoInfile.html#a5fefc01f9e478eeea2669c4b9e28765c">handlePTMs_</a> (const <a class="el" href="classOpenMS_1_1String.html">String</a> &modification, const bool variable)</td></tr>
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Private Attributes</h2></td></tr>
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<tr class="memitem:a3791aa8b4e64703f5a5539ecec8bc85d"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1ModificationDefinitionsSet.html">ModificationDefinitionsSet</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1PepNovoInfile.html#a3791aa8b4e64703f5a5539ecec8bc85d">mods_</a></td></tr>
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<tr class="memitem:aaba85fef662ba21702803a609c98b2de"><td class="memItemLeft" align="right" valign="top">std::map< <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_1PepNovoInfile.html#aaba85fef662ba21702803a609c98b2de">mods_and_keys_</a></td></tr>
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<tr class="memitem:a4dbfe56272a3df11439d7e3dc804b75c"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1TextFile.html">TextFile</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1PepNovoInfile.html#a4dbfe56272a3df11439d7e3dc804b75c">ptm_file_</a></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>PepNovo input file adapter. </p>
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<p>Creates a PepNovo_PTMs.txt file for PepNovo search. </p>
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</div><h2 class="groupheader">Constructor & Destructor Documentation</h2>
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<td class="memname"><a class="el" href="classOpenMS_1_1PepNovoInfile.html">PepNovoInfile</a> </td>
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<td class="paramname"></td><td>)</td>
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<p>default constructor </p>
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<td class="memname"><a class="el" href="classOpenMS_1_1PepNovoInfile.html">PepNovoInfile</a> </td>
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<td class="paramtype">const <a class="el" href="classOpenMS_1_1PepNovoInfile.html">PepNovoInfile</a> & </td>
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<td class="paramname"><em>pepnovo_infile</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_1PepNovoInfile.html">PepNovoInfile</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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<h2 class="groupheader">Member Function Documentation</h2>
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<td class="memname">void getModifications </td>
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<td class="paramtype">std::map< <a class="el" href="classOpenMS_1_1String.html">String</a>, <a class="el" href="classOpenMS_1_1String.html">String</a> > & </td>
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<td class="paramname"><em>modification_key_map</em></td><td>)</td>
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<p>return the modifications. </p>
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<p>the modification unique identifiers are mapped to the keys used in the PepNovo Infile (origin+rounded monoisotopic mass of modification ). (e.g. modification_key_map["K+16"]=="Oxidation (K)" ) </p>
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<td class="memname"><a class="el" href="classOpenMS_1_1String.html">String</a> handlePTMs_ </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>modification</em>, </td>
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<td class="paramtype">const bool </td>
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<td class="paramname"><em>variable</em> </td>
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<p>retrieves the name of modification, and generates the corresponding line for the PepNovo infile. </p>
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<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramname">modification</td><td>the modification </td></tr>
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<tr><td class="paramname">variable</td><td>should be set to true if it variable </td></tr>
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<td class="memname"><a class="el" href="classOpenMS_1_1PepNovoInfile.html">PepNovoInfile</a>& operator= </td>
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<td class="paramtype">const <a class="el" href="classOpenMS_1_1PepNovoInfile.html">PepNovoInfile</a> & </td>
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<td class="paramname"><em>pepnovo_infile</em></td><td>)</td>
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<p>assignment operator </p>
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<td class="memname">bool operator== </td>
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<td class="paramtype">const <a class="el" href="classOpenMS_1_1PepNovoInfile.html">PepNovoInfile</a> & </td>
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<td class="paramname"><em>pepnovo_infile</em></td><td>)</td>
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<p>equality operator </p>
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<td class="memname">void setModifications </td>
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<td class="paramtype">const <a class="el" href="classOpenMS_1_1StringList.html">StringList</a> & </td>
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<td class="paramname"><em>fixed_mods</em>, </td>
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<td class="paramtype">const <a class="el" href="classOpenMS_1_1StringList.html">StringList</a> & </td>
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<td class="paramname"><em>variable_mods</em> </td>
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<p>generates the PepNovo Infile for given fixed and variable modifications * </p>
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<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramname">fixed_mods</td><td><a class="el" href="classOpenMS_1_1StringList.html" title="String list. ">StringList</a> of fixed modifications unique identifiers </td></tr>
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<tr><td class="paramname">variable_mods</td><td><a class="el" href="classOpenMS_1_1StringList.html" title="String list. ">StringList</a> of variable modifications unique identifiers </td></tr>
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<td class="memname">void store </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><td>)</td>
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<p>stores the experiment data in a PepNovo input file that can be used as input for PepNovo shell execution</p>
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<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramname">filename</td><td>the file which the input file is stored into </td></tr>
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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_1UnableToCreateFile.html" title="Unable to create file exception. ">Exception::UnableToCreateFile</a></td><td>is thrown if the given file could not be created </td></tr>
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<h2 class="groupheader">Member Data Documentation</h2>
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<td class="memname"><a class="el" href="classOpenMS_1_1ModificationDefinitionsSet.html">ModificationDefinitionsSet</a> mods_</td>
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<td class="memname">std::map<<a class="el" href="classOpenMS_1_1String.html">String</a>, <a class="el" href="classOpenMS_1_1String.html">String</a>> mods_and_keys_</td>
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<td class="memname"><a class="el" href="classOpenMS_1_1TextFile.html">TextFile</a> ptm_file_</td>
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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 11:19:31 using doxygen 1.8.5</font></TD>
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