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<HTML>
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<TITLE>Member List</TITLE>
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<A href="index.html">Home</A> &nbsp;&middot;
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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_1PepXMLFile.html">PepXMLFile</a></li>  </ul>
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<div class="title">PepXMLFile Member List</div>  </div>
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<p>This is the complete list of members for <a class="el" href="classOpenMS_1_1PepXMLFile.html">PepXMLFile</a>, including all inherited members.</p>
<table class="directory">
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLHandler.html#a6cc566e3bbfdcb8a5a9d85941238cef5">ActionMode</a> enum name</td><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLHandler.html">XMLHandler</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLHandler.html#a5dc26987442a8a81af7bbd43e2e48f4a">asBool_</a>(const String &amp;in)</td><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLHandler.html">XMLHandler</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">protected</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLHandler.html#ae9988608535348608067112395e56562">asDateTime_</a>(String date_string)</td><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLHandler.html">XMLHandler</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">protected</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLHandler.html#a48e8be8cff3d25b265c4f3b6a1c446b0">asDouble_</a>(const String &amp;in)</td><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLHandler.html">XMLHandler</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">protected</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLHandler.html#aa6a2e65ba3dc9581e4cb5a719ddace92">asFloat_</a>(const String &amp;in)</td><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLHandler.html">XMLHandler</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">protected</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLHandler.html#a666aacffa457b641218b98fa7b47071e">asInt_</a>(const String &amp;in)</td><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLHandler.html">XMLHandler</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">protected</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLHandler.html#acce0b8fbe7a5a90972407cc4ec2ae742">asInt_</a>(const XMLCh *in)</td><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLHandler.html">XMLHandler</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">protected</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLHandler.html#a8cec7757132342e4d52771f09113378b">asUInt_</a>(const String &amp;in)</td><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLHandler.html">XMLHandler</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">protected</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLHandler.html#a8b86d61a994bea8fc963fb5ba58b53cc">attributeAsDouble_</a>(const xercesc::Attributes &amp;a, const char *name) const </td><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLHandler.html">XMLHandler</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">protected</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLHandler.html#a1b66b54ff53c138638bebea5bea36cf9">attributeAsDouble_</a>(const xercesc::Attributes &amp;a, const XMLCh *name) const </td><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLHandler.html">XMLHandler</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">protected</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLHandler.html#a6e998b95ac924dce7c79c389e0c7515a">attributeAsDoubleList_</a>(const xercesc::Attributes &amp;a, const char *name) const </td><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLHandler.html">XMLHandler</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">protected</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLHandler.html#a54f3fb485e059c3cb16afc2235635fc0">attributeAsDoubleList_</a>(const xercesc::Attributes &amp;a, const XMLCh *name) const </td><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLHandler.html">XMLHandler</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">protected</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLHandler.html#a72fc926d019cece725e2acca29ba6bd7">attributeAsInt_</a>(const xercesc::Attributes &amp;a, const char *name) const </td><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLHandler.html">XMLHandler</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">protected</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLHandler.html#af1c6de5bf11e4cb7ec9aa007da5c163f">attributeAsInt_</a>(const xercesc::Attributes &amp;a, const XMLCh *name) const </td><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLHandler.html">XMLHandler</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">protected</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLHandler.html#abc312cc6190151275be5f511d36ca8d4">attributeAsIntList_</a>(const xercesc::Attributes &amp;a, const char *name) const </td><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLHandler.html">XMLHandler</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">protected</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLHandler.html#a5dc4ddd6685eb948019e1537d6fe9034">attributeAsIntList_</a>(const xercesc::Attributes &amp;a, const XMLCh *name) const </td><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLHandler.html">XMLHandler</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">protected</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLHandler.html#a9e474cc66784ceba31591381c45a7fda">attributeAsString_</a>(const xercesc::Attributes &amp;a, const char *name) const </td><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLHandler.html">XMLHandler</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">protected</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLHandler.html#ad63dfd11e1161067d1634f7b92bee573">attributeAsString_</a>(const xercesc::Attributes &amp;a, const XMLCh *name) const </td><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLHandler.html">XMLHandler</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">protected</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLHandler.html#aa4b445d152e82df2f8c8254d16f6215b">attributeAsStringList_</a>(const xercesc::Attributes &amp;a, const char *name) const </td><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLHandler.html">XMLHandler</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">protected</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLHandler.html#ac65e3edffffcaee33d18d735b8295661">attributeAsStringList_</a>(const xercesc::Attributes &amp;a, const XMLCh *name) const </td><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLHandler.html">XMLHandler</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">protected</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLHandler.html#ad14063bc858ff5ef2f218f9ec3efa1a6">characters</a>(const XMLCh *const chars, const XMLSize_t length)</td><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLHandler.html">XMLHandler</a></td><td class="entry"><span class="mlabel">protected</span><span class="mlabel">virtual</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1PepXMLFile.html#af71274961d8487036283991f2ba652a1">charge_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1PepXMLFile.html">PepXMLFile</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1PepXMLFile.html#a689c9221bfb5ffea61465aa5018d421c">checked_base_name_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1PepXMLFile.html">PepXMLFile</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1PepXMLFile.html#a93a2d66d67637792143b1b2bc2b65b3d">current_modifications_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1PepXMLFile.html">PepXMLFile</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1PepXMLFile.html#a4e96a9037f26680129f5f1b128ec71d0">current_peptide_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1PepXMLFile.html">PepXMLFile</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1PepXMLFile.html#a6ecfd3d5770da70f19ca938d6f71d804">current_proteins_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1PepXMLFile.html">PepXMLFile</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1PepXMLFile.html#a3e597f3665d43b306ba043ca6913d706">current_sequence_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1PepXMLFile.html">PepXMLFile</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLHandler.html#a6476bfc5285236c19e7f731e43d05cdd">cv_terms_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLHandler.html">XMLHandler</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLHandler.html#ab42b06789e80b05f0b754201cb1deccc">cvStringToEnum_</a>(const Size section, const String &amp;term, const char *message, const SignedSize result_on_error=0)</td><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLHandler.html">XMLHandler</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">protected</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1PepXMLFile.html#ab11b7dd5f2f6ffc800af0152f5c2e69a">date_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1PepXMLFile.html">PepXMLFile</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1PepXMLFile.html#a66e33712cdc523d0d7a516c760933174">endElement</a>(const XMLCh *const , const XMLCh *const , const XMLCh *const qname)</td><td class="entry"><a class="el" href="classOpenMS_1_1PepXMLFile.html">PepXMLFile</a></td><td class="entry"><span class="mlabel">protected</span><span class="mlabel">virtual</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLFile.html#a6b0159bfc4bc3062d47825cccfeec9cd">enforced_encoding_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLFile.html">XMLFile</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLFile.html#a97478c2a7b5ed960dae2ac5da0c03045">enforceEncoding_</a>(const String &amp;encoding)</td><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLFile.html">XMLFile</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1PepXMLFile.html#a59a0e004888af308552b44e57832a5a9">enzyme_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1PepXMLFile.html">PepXMLFile</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLHandler.html#afa42ec5acb52289d25d125a69ca28611">equal_</a>(const XMLCh *a, const XMLCh *b)</td><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLHandler.html">XMLHandler</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">protected</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLHandler.html#ae4ec481066391f85153ac035f3184178">error</a>(const xercesc::SAXParseException &amp;exception)</td><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLHandler.html">XMLHandler</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLHandler.html#a9d340a52e4146988835f8f1ac9efab07">error</a>(ActionMode mode, const String &amp;msg, UInt line=0, UInt column=0) const </td><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLHandler.html">XMLHandler</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLHandler.html#a51b11736a292f64a76f20729bb699879">error_message_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLHandler.html">XMLHandler</a></td><td class="entry"><span class="mlabel">mutable</span><span class="mlabel">protected</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLHandler.html#a0bc03d238ded5afdd53da91dbec5a9a4">errorString</a>()</td><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLHandler.html">XMLHandler</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1PepXMLFile.html#a20485bae7a3bd7b2fcd5d491b4cf51c9">exp_name_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1PepXMLFile.html">PepXMLFile</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1PepXMLFile.html#a911a12c1b01a39d866ca2df63ebe71c2">experiment_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1PepXMLFile.html">PepXMLFile</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLHandler.html#a479fa8182f39759e3b6c800419b7fe35">fatalError</a>(const xercesc::SAXParseException &amp;exception)</td><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLHandler.html">XMLHandler</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLHandler.html#a8b468975f6696641be7ef3c4de304cf9">fatalError</a>(ActionMode mode, const String &amp;msg, UInt line=0, UInt column=0) const </td><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLHandler.html">XMLHandler</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLHandler.html#a45e9455fa6290f5c2d1f179902bae53a">file_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLHandler.html">XMLHandler</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1PepXMLFile.html#ab15bace4e9b1d69bcbb4c123bd679c9c">fixed_modifications_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1PepXMLFile.html">PepXMLFile</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLFile.html#ae6b3b4b6857bc1987282e2f29611dd41">getVersion</a>() const </td><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLFile.html">XMLFile</a></td><td class="entry"></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1PepXMLFile.html#aba244924723289b66a604a9826e8dcd5">hydrogen_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1PepXMLFile.html">PepXMLFile</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1PepXMLFile.html#ac47b1fa6e7b9aaab7558c6887cdcf497">hydrogen_mass_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1PepXMLFile.html">PepXMLFile</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLFile.html#a2f3216da86d8ced03f1b102a5c2e886c">isValid</a>(const String &amp;filename, std::ostream &amp;os=std::cerr)</td><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLFile.html">XMLFile</a></td><td class="entry"></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1PepXMLFile.html#a333fccc0e63f82c206894908b86d8a37">load</a>(const String &amp;filename, std::vector&lt; ProteinIdentification &gt; &amp;proteins, std::vector&lt; PeptideIdentification &gt; &amp;peptides, const String &amp;experiment_name, const MSExperiment&lt;&gt; &amp;experiment, bool use_precursor_data=false)</td><td class="entry"><a class="el" href="classOpenMS_1_1PepXMLFile.html">PepXMLFile</a></td><td class="entry"></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1PepXMLFile.html#a3c79d8ce20923773151e99accb626c0b">load</a>(const String &amp;filename, std::vector&lt; ProteinIdentification &gt; &amp;proteins, std::vector&lt; PeptideIdentification &gt; &amp;peptides, const String &amp;experiment_name=&quot;&quot;)</td><td class="entry"><a class="el" href="classOpenMS_1_1PepXMLFile.html">PepXMLFile</a></td><td class="entry"></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLHandler.html#a6cc566e3bbfdcb8a5a9d85941238cef5a972dbcdf74cff71e20bdcfb53be9c391">LOAD</a> enum value</td><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLHandler.html">XMLHandler</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1PepXMLFile.html#af4a9b4b9d69fadae6470d845d5ac3bd2">makeScanMap_</a>()</td><td class="entry"><a class="el" href="classOpenMS_1_1PepXMLFile.html">PepXMLFile</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1PepXMLFile.html#a9b6d0c4ae8cce639565dd13e42489ffe">matchModification_</a>(const DoubleReal mass, const String &amp;origin, String &amp;modification_description)</td><td class="entry"><a class="el" href="classOpenMS_1_1PepXMLFile.html">PepXMLFile</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1PepXMLFile.html#ae23f3c856a76faaa8a37015bd7fef8bc">mz_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1PepXMLFile.html">PepXMLFile</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1PepXMLFile.html#a377dded88a3397ad33ef3e403ab60671">mz_tol_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1PepXMLFile.html">PepXMLFile</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLHandler.html#a11019255364568a4576df012500da50c">open_tags_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLHandler.html">XMLHandler</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLHandler.html#a958ee97861f22f49d562abce6e258aa1">optionalAttributeAsDouble_</a>(DoubleReal &amp;value, const xercesc::Attributes &amp;a, const char *name) const </td><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLHandler.html">XMLHandler</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">protected</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLHandler.html#acc6bb4fc8db1bf5653be91ad6ffa92d7">optionalAttributeAsDouble_</a>(DoubleReal &amp;value, const xercesc::Attributes &amp;a, const XMLCh *name) const </td><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLHandler.html">XMLHandler</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">protected</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLHandler.html#a50fb629d6e3a9db12a5858916616edfa">optionalAttributeAsDoubleList_</a>(DoubleList &amp;value, const xercesc::Attributes &amp;a, const char *name) const </td><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLHandler.html">XMLHandler</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">protected</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLHandler.html#a2363e021cb7d1b71e437f3e0e90160de">optionalAttributeAsDoubleList_</a>(DoubleList &amp;value, const xercesc::Attributes &amp;a, const XMLCh *name) const </td><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLHandler.html">XMLHandler</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">protected</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLHandler.html#abad7c51846f619044d97dcd4b2dc1a58">optionalAttributeAsInt_</a>(Int &amp;value, const xercesc::Attributes &amp;a, const char *name) const </td><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLHandler.html">XMLHandler</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">protected</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLHandler.html#a2e667f2db91d4711dc89e63d61fbc42d">optionalAttributeAsInt_</a>(Int &amp;value, const xercesc::Attributes &amp;a, const XMLCh *name) const </td><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLHandler.html">XMLHandler</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">protected</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLHandler.html#ab39e3f1ff99a6e677b0c918266645673">optionalAttributeAsIntList_</a>(IntList &amp;value, const xercesc::Attributes &amp;a, const char *name) const </td><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLHandler.html">XMLHandler</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">protected</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLHandler.html#a54465788da22f2da8b11a237e470a27e">optionalAttributeAsIntList_</a>(IntList &amp;value, const xercesc::Attributes &amp;a, const XMLCh *name) const </td><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLHandler.html">XMLHandler</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">protected</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLHandler.html#a7c08febb7e7f52f2be01217ab2560178">optionalAttributeAsString_</a>(String &amp;value, const xercesc::Attributes &amp;a, const char *name) const </td><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLHandler.html">XMLHandler</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">protected</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLHandler.html#a8faacc5e743fd40965b5088409b2c22b">optionalAttributeAsString_</a>(String &amp;value, const xercesc::Attributes &amp;a, const XMLCh *name) const </td><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLHandler.html">XMLHandler</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">protected</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLHandler.html#a05c8ac2143fb0e36774bd0973326c4f1">optionalAttributeAsStringList_</a>(StringList &amp;value, const xercesc::Attributes &amp;a, const char *name) const </td><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLHandler.html">XMLHandler</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">protected</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLHandler.html#af1084b998ce1559ff34c1febcd8193fb">optionalAttributeAsStringList_</a>(StringList &amp;value, const xercesc::Attributes &amp;a, const XMLCh *name) const </td><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLHandler.html">XMLHandler</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">protected</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLHandler.html#aba139b5879b8b0fe8e67d0630592c092">optionalAttributeAsUInt_</a>(UInt &amp;value, const xercesc::Attributes &amp;a, const char *name) const </td><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLHandler.html">XMLHandler</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">protected</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLHandler.html#af1216a9eaddc5ea6a5aec32a2f63f42d">optionalAttributeAsUInt_</a>(UInt &amp;value, const xercesc::Attributes &amp;a, const XMLCh *name) const </td><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLHandler.html">XMLHandler</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">protected</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1PepXMLFile.html#ac3d586e03dbf806c042823615bb112d7">params_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1PepXMLFile.html">PepXMLFile</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLFile.html#ab08cc6e67bde4d478045ece950deb32b">parse_</a>(const String &amp;filename, XMLHandler *handler)</td><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLFile.html">XMLFile</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1PepXMLFile.html#a43a54f0e9678737ac75292aad6e394a6">peptide_hit_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1PepXMLFile.html">PepXMLFile</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1PepXMLFile.html#a6f28b892172fe0ec098cb6781e58c7f4">peptides_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1PepXMLFile.html">PepXMLFile</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1PepXMLFile.html#a9b8d5746b2caf95804846c058c7cb062">PepXMLFile</a>()</td><td class="entry"><a class="el" href="classOpenMS_1_1PepXMLFile.html">PepXMLFile</a></td><td class="entry"></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1PepXMLFile.html#a9e325af3cdc9e77753f1042b18c6676f">prot_id_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1PepXMLFile.html">PepXMLFile</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1PepXMLFile.html#aaecddb731d6a7b2f86d458429a6a8529">proteins_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1PepXMLFile.html">PepXMLFile</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1PepXMLFile.html#acfc197c87ac22f118934868bf394292e">readRTMZCharge_</a>(const xercesc::Attributes &amp;attributes)</td><td class="entry"><a class="el" href="classOpenMS_1_1PepXMLFile.html">PepXMLFile</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLHandler.html#ad20897c5c8bd47f5d4005989bead0e55">reset</a>()</td><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLHandler.html">XMLHandler</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1PepXMLFile.html#a51db91c41ce0919dd864710eb01a99aa">rt_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1PepXMLFile.html">PepXMLFile</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1PepXMLFile.html#a4b56759c1db4a79eb15d182c26752227">rt_tol_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1PepXMLFile.html">PepXMLFile</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLFile.html#aa99a8fa1726ecc3b865167eea1c17db7">save_</a>(const String &amp;filename, XMLHandler *handler) const </td><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLFile.html">XMLFile</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1PepXMLFile.html#add5c0d058e0cee825f46ec0aeeec89da">scan_map_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1PepXMLFile.html">PepXMLFile</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLFile.html#aea8dd5b28e6057c3e2b3f296966431c3">schema_location_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLFile.html">XMLFile</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLFile.html#a5a33231ac1616a429e6533af15231951">schema_version_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLFile.html">XMLFile</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1PepXMLFile.html#a5025f2dee8f88a7632f01b5cea7043d9">search_engine_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1PepXMLFile.html">PepXMLFile</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1PepXMLFile.html#af03ad2b8299753b5d1e1b88dde2d7188">search_id_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1PepXMLFile.html">PepXMLFile</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1PepXMLFile.html#a27d0704c17599647c1ebd10fe406f69c">seen_experiment_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1PepXMLFile.html">PepXMLFile</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLHandler.html#a9baa4a46e0c6855a03e6263782e3fe8c">sm_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLHandler.html">XMLHandler</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1PepXMLFile.html#a40f650be05ac6391244e5aabda5fc682">startElement</a>(const XMLCh *const , const XMLCh *const , const XMLCh *const qname, const xercesc::Attributes &amp;attributes)</td><td class="entry"><a class="el" href="classOpenMS_1_1PepXMLFile.html">PepXMLFile</a></td><td class="entry"><span class="mlabel">protected</span><span class="mlabel">virtual</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1PepXMLFile.html#a86c356a2707e219e7201b3c593d95df8">store</a>(const String &amp;filename, std::vector&lt; ProteinIdentification &gt; &amp;protein_ids, std::vector&lt; PeptideIdentification &gt; &amp;peptide_ids)</td><td class="entry"><a class="el" href="classOpenMS_1_1PepXMLFile.html">PepXMLFile</a></td><td class="entry"></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLHandler.html#a6cc566e3bbfdcb8a5a9d85941238cef5afeb01cb4572ba190cd7932e49446c480">STORE</a> enum value</td><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLHandler.html">XMLHandler</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1PepXMLFile.html#ab727f118bb1450b2204ed4b5bf2d1ab6">use_precursor_data_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1PepXMLFile.html">PepXMLFile</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1PepXMLFile.html#a44cdb39bffdb662fe69039cb91a72c9c">variable_modifications_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1PepXMLFile.html">PepXMLFile</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLHandler.html#a4e87a8f69bbc06cd56776556dc1680ed">version_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLHandler.html">XMLHandler</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLHandler.html#af86a807dd4b1ed6f4ba006b9bcd24763">warning</a>(const xercesc::SAXParseException &amp;exception)</td><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLHandler.html">XMLHandler</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLHandler.html#a02ac5e91757ddd89078f7a04386b95f1">warning</a>(ActionMode mode, const String &amp;msg, UInt line=0, UInt column=0) const </td><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLHandler.html">XMLHandler</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLHandler.html#ac758e589cc142657a0ff748a49038298">writeTo</a>(std::ostream &amp;)</td><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLHandler.html">XMLHandler</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">protected</span><span class="mlabel">virtual</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLHandler.html#a2036f384f9e7f1259f0c147d24100a37">writeUserParam_</a>(const String &amp;tag_name, std::ostream &amp;os, const MetaInfoInterface &amp;meta, UInt indent) const </td><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLHandler.html">XMLHandler</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1PepXMLFile.html#ae16b642f67c5b8385bb2d967257129ed">wrong_experiment_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1PepXMLFile.html">PepXMLFile</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLFile.html#a5288a663fb130ba112c205bd7c556fd4">XMLFile</a>()</td><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLFile.html">XMLFile</a></td><td class="entry"></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLFile.html#ab6a2f018df297124fba778512994282a">XMLFile</a>(const String &amp;schema_location, const String &amp;version)</td><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLFile.html">XMLFile</a></td><td class="entry"></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLHandler.html#a1f2a4ba30e2b659550286b460e842503">XMLHandler</a>(const String &amp;filename, const String &amp;version)</td><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLHandler.html">XMLHandler</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1PepXMLFile.html#a79e276a8412d6c02338c5bb999814f25">~PepXMLFile</a>()</td><td class="entry"><a class="el" href="classOpenMS_1_1PepXMLFile.html">PepXMLFile</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLFile.html#ae64064342fc97bdd2008c5a91cd6d9de">~XMLFile</a>()</td><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLFile.html">XMLFile</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLHandler.html#ae466820b5ac9b008d33937e7dc7a180b">~XMLHandler</a>()</td><td class="entry"><a class="el" href="classOpenMS_1_1Internal_1_1XMLHandler.html">XMLHandler</a></td><td class="entry"><span class="mlabel">protected</span><span class="mlabel">virtual</span></td></tr>
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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 11:19:31 using doxygen 1.8.5</font></TD>
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