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<HTML>
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<TITLE>ProteinIdentification 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_1ProteinIdentification.html">ProteinIdentification</a></li> </ul>
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<div class="title">ProteinIdentification Class Reference<div class="ingroups"><a class="el" href="group__Metadata.html">Metadata</a></div></div> </div>
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<div class="contents">
<p>Representation of a protein identification run.
<a href="classOpenMS_1_1ProteinIdentification.html#details">More...</a></p>
<p><code>#include <<a class="el" href="ProteinIdentification_8h_source.html">OpenMS/METADATA/ProteinIdentification.h</a>></code></p>
<div class="dynheader">
Inheritance diagram for ProteinIdentification:</div>
<div class="dyncontent">
<div class="center">
<img src="classOpenMS_1_1ProteinIdentification.png" usemap="#ProteinIdentification_map" alt=""/>
<map id="ProteinIdentification_map" name="ProteinIdentification_map">
<area href="classOpenMS_1_1MetaInfoInterface.html" title="Interface for classes that can store arbitrary meta information (Type-Name-Value tuples). " alt="MetaInfoInterface" shape="rect" coords="0,0,123,24"/>
</map>
</div></div>
<table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="nested-classes"></a>
Classes</h2></td></tr>
<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">struct  </td><td class="memItemRight" valign="bottom"><a class="el" href="structOpenMS_1_1ProteinIdentification_1_1ProteinGroup.html">ProteinGroup</a></td></tr>
<tr class="memdesc:"><td class="mdescLeft"> </td><td class="mdescRight">Bundles multiple (e.g. indistinguishable) proteins in a group. <a href="structOpenMS_1_1ProteinIdentification_1_1ProteinGroup.html#details">More...</a><br/></td></tr>
<tr class="separator:"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">struct  </td><td class="memItemRight" valign="bottom"><a class="el" href="structOpenMS_1_1ProteinIdentification_1_1SearchParameters.html">SearchParameters</a></td></tr>
<tr class="memdesc:"><td class="mdescLeft"> </td><td class="mdescRight">Search parameters of the DB search. <a href="structOpenMS_1_1ProteinIdentification_1_1SearchParameters.html#details">More...</a><br/></td></tr>
<tr class="separator:"><td class="memSeparator" colspan="2"> </td></tr>
</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-types"></a>
Public Types</h2></td></tr>
<tr class="memitem:a5431b65220b7ad71b5e8768876ee3e53"><td class="memItemLeft" align="right" valign="top">enum  </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProteinIdentification.html#a5431b65220b7ad71b5e8768876ee3e53">PeakMassType</a> { <a class="el" href="classOpenMS_1_1ProteinIdentification.html#a5431b65220b7ad71b5e8768876ee3e53aba27416c974c26497ea0f4aa59fcf669">MONOISOTOPIC</a>,
<a class="el" href="classOpenMS_1_1ProteinIdentification.html#a5431b65220b7ad71b5e8768876ee3e53ab6f2220659ddcb84a0622d4aa4e0b112">AVERAGE</a>,
<a class="el" href="classOpenMS_1_1ProteinIdentification.html#a5431b65220b7ad71b5e8768876ee3e53a2989e7c6c70923c0941b34c64517d012">SIZE_OF_PEAKMASSTYPE</a>
}</td></tr>
<tr class="memdesc:a5431b65220b7ad71b5e8768876ee3e53"><td class="mdescLeft"> </td><td class="mdescRight">Peak mass type. <a href="classOpenMS_1_1ProteinIdentification.html#a5431b65220b7ad71b5e8768876ee3e53">More...</a><br/></td></tr>
<tr class="separator:a5431b65220b7ad71b5e8768876ee3e53"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ac1976fd756a09ae4e26fe6b32fcb396c"><td class="memItemLeft" align="right" valign="top">enum  </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProteinIdentification.html#ac1976fd756a09ae4e26fe6b32fcb396c">DigestionEnzyme</a> { <br/>
  <a class="el" href="classOpenMS_1_1ProteinIdentification.html#ac1976fd756a09ae4e26fe6b32fcb396caa87783975563314a167c39f08f065bfd">TRYPSIN</a>,
<a class="el" href="classOpenMS_1_1ProteinIdentification.html#ac1976fd756a09ae4e26fe6b32fcb396ca9cf5aedb487753ed0440ab34d94e1b33">PEPSIN_A</a>,
<a class="el" href="classOpenMS_1_1ProteinIdentification.html#ac1976fd756a09ae4e26fe6b32fcb396ca3b5e4efa6ca1ae00905ead21fe2c1e73">PROTEASE_K</a>,
<a class="el" href="classOpenMS_1_1ProteinIdentification.html#ac1976fd756a09ae4e26fe6b32fcb396ca240cc037883891d0eb859a89530893ba">CHYMOTRYPSIN</a>,
<br/>
  <a class="el" href="classOpenMS_1_1ProteinIdentification.html#ac1976fd756a09ae4e26fe6b32fcb396ca8013b03f6b7f2d27796adf371a715a81">NO_ENZYME</a>,
<a class="el" href="classOpenMS_1_1ProteinIdentification.html#ac1976fd756a09ae4e26fe6b32fcb396ca36a56e667bdbe75daa08c655e85ec49a">UNKNOWN_ENZYME</a>,
<a class="el" href="classOpenMS_1_1ProteinIdentification.html#ac1976fd756a09ae4e26fe6b32fcb396ca59ffc2972d48cca58d73eb79e40edf9f">SIZE_OF_DIGESTIONENZYME</a>
<br/>
}</td></tr>
<tr class="separator:ac1976fd756a09ae4e26fe6b32fcb396c"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a81790367e26e192b9eb9c7cad5f1730d"><td class="memItemLeft" align="right" valign="top">typedef <a class="el" href="classOpenMS_1_1ProteinHit.html">ProteinHit</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProteinIdentification.html#a81790367e26e192b9eb9c7cad5f1730d">HitType</a></td></tr>
<tr class="memdesc:a81790367e26e192b9eb9c7cad5f1730d"><td class="mdescLeft"> </td><td class="mdescRight">Hit type definition. <a href="#a81790367e26e192b9eb9c7cad5f1730d">More...</a><br/></td></tr>
<tr class="separator:a81790367e26e192b9eb9c7cad5f1730d"><td class="memSeparator" colspan="2"> </td></tr>
</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a>
Public Member Functions</h2></td></tr>
<tr><td colspan="2"><div class="groupHeader">Constructors, destructors, assignment operator <br></div></td></tr>
<tr class="memitem:a55950a0a644349138b409ad87528d016"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProteinIdentification.html#a55950a0a644349138b409ad87528d016">ProteinIdentification</a> ()</td></tr>
<tr class="memdesc:a55950a0a644349138b409ad87528d016"><td class="mdescLeft"> </td><td class="mdescRight">Default constructor. <a href="#a55950a0a644349138b409ad87528d016">More...</a><br/></td></tr>
<tr class="separator:a55950a0a644349138b409ad87528d016"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:addb98a31adc7bac884352bf0c41bd93b"><td class="memItemLeft" align="right" valign="top">virtual </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProteinIdentification.html#addb98a31adc7bac884352bf0c41bd93b">~ProteinIdentification</a> ()</td></tr>
<tr class="memdesc:addb98a31adc7bac884352bf0c41bd93b"><td class="mdescLeft"> </td><td class="mdescRight">Destructor. <a href="#addb98a31adc7bac884352bf0c41bd93b">More...</a><br/></td></tr>
<tr class="separator:addb98a31adc7bac884352bf0c41bd93b"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a8dc19ab7d7f7494764003a7084e5e08a"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProteinIdentification.html#a8dc19ab7d7f7494764003a7084e5e08a">ProteinIdentification</a> (const <a class="el" href="classOpenMS_1_1ProteinIdentification.html">ProteinIdentification</a> &source)</td></tr>
<tr class="memdesc:a8dc19ab7d7f7494764003a7084e5e08a"><td class="mdescLeft"> </td><td class="mdescRight">Copy constructor. <a href="#a8dc19ab7d7f7494764003a7084e5e08a">More...</a><br/></td></tr>
<tr class="separator:a8dc19ab7d7f7494764003a7084e5e08a"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:aa6f91f4434cf5df06855463df8cac3a4"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1ProteinIdentification.html">ProteinIdentification</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProteinIdentification.html#aa6f91f4434cf5df06855463df8cac3a4">operator=</a> (const <a class="el" href="classOpenMS_1_1ProteinIdentification.html">ProteinIdentification</a> &source)</td></tr>
<tr class="memdesc:aa6f91f4434cf5df06855463df8cac3a4"><td class="mdescLeft"> </td><td class="mdescRight">Assignment operator. <a href="#aa6f91f4434cf5df06855463df8cac3a4">More...</a><br/></td></tr>
<tr class="separator:aa6f91f4434cf5df06855463df8cac3a4"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ac132c368b397df3fce49aebc03233d78"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProteinIdentification.html#ac132c368b397df3fce49aebc03233d78">operator==</a> (const <a class="el" href="classOpenMS_1_1ProteinIdentification.html">ProteinIdentification</a> &rhs) const </td></tr>
<tr class="memdesc:ac132c368b397df3fce49aebc03233d78"><td class="mdescLeft"> </td><td class="mdescRight">Equality operator. <a href="#ac132c368b397df3fce49aebc03233d78">More...</a><br/></td></tr>
<tr class="separator:ac132c368b397df3fce49aebc03233d78"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ab44928b3c11da52e66a6c885b9df5019"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProteinIdentification.html#ab44928b3c11da52e66a6c885b9df5019">operator!=</a> (const <a class="el" href="classOpenMS_1_1ProteinIdentification.html">ProteinIdentification</a> &rhs) const </td></tr>
<tr class="memdesc:ab44928b3c11da52e66a6c885b9df5019"><td class="mdescLeft"> </td><td class="mdescRight">Inequality operator. <a href="#ab44928b3c11da52e66a6c885b9df5019">More...</a><br/></td></tr>
<tr class="separator:ab44928b3c11da52e66a6c885b9df5019"><td class="memSeparator" colspan="2"> </td></tr>
<tr><td colspan="2"><div class="groupHeader">Protein hit information (public members)</div></td></tr>
<tr class="memitem:a69a3da6373dcd1505ea046971251023b"><td class="memItemLeft" align="right" valign="top">const std::vector< <a class="el" href="classOpenMS_1_1ProteinHit.html">ProteinHit</a> > & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProteinIdentification.html#a69a3da6373dcd1505ea046971251023b">getHits</a> () const </td></tr>
<tr class="memdesc:a69a3da6373dcd1505ea046971251023b"><td class="mdescLeft"> </td><td class="mdescRight">Returns the protein hits. <a href="#a69a3da6373dcd1505ea046971251023b">More...</a><br/></td></tr>
<tr class="separator:a69a3da6373dcd1505ea046971251023b"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:abe95b905e951a7ca86fd24e47455132d"><td class="memItemLeft" align="right" valign="top">std::vector< <a class="el" href="classOpenMS_1_1ProteinHit.html">ProteinHit</a> > & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProteinIdentification.html#abe95b905e951a7ca86fd24e47455132d">getHits</a> ()</td></tr>
<tr class="memdesc:abe95b905e951a7ca86fd24e47455132d"><td class="mdescLeft"> </td><td class="mdescRight">Returns the protein hits (mutable) <a href="#abe95b905e951a7ca86fd24e47455132d">More...</a><br/></td></tr>
<tr class="separator:abe95b905e951a7ca86fd24e47455132d"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a10cda19a10520916989653260846e62c"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProteinIdentification.html#a10cda19a10520916989653260846e62c">insertHit</a> (const <a class="el" href="classOpenMS_1_1ProteinHit.html">ProteinHit</a> &input)</td></tr>
<tr class="memdesc:a10cda19a10520916989653260846e62c"><td class="mdescLeft"> </td><td class="mdescRight">Appends a protein hit. <a href="#a10cda19a10520916989653260846e62c">More...</a><br/></td></tr>
<tr class="separator:a10cda19a10520916989653260846e62c"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a86f5c6d7c17c3aa94ec734e2a4fb50fa"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProteinIdentification.html#a86f5c6d7c17c3aa94ec734e2a4fb50fa">setHits</a> (const std::vector< <a class="el" href="classOpenMS_1_1ProteinHit.html">ProteinHit</a> > &hits)</td></tr>
<tr class="memdesc:a86f5c6d7c17c3aa94ec734e2a4fb50fa"><td class="mdescLeft"> </td><td class="mdescRight">Sets the protein hits. <a href="#a86f5c6d7c17c3aa94ec734e2a4fb50fa">More...</a><br/></td></tr>
<tr class="separator:a86f5c6d7c17c3aa94ec734e2a4fb50fa"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ab16748f562f2a75f13a7e902529781fc"><td class="memItemLeft" align="right" valign="top">std::vector< <a class="el" href="classOpenMS_1_1ProteinHit.html">ProteinHit</a> >::iterator </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProteinIdentification.html#ab16748f562f2a75f13a7e902529781fc">findHit</a> (const <a class="el" href="classOpenMS_1_1String.html">String</a> &accession)</td></tr>
<tr class="memdesc:ab16748f562f2a75f13a7e902529781fc"><td class="mdescLeft"> </td><td class="mdescRight">Finds a protein hit by accession (returns past-the-end iterator if not found) <a href="#ab16748f562f2a75f13a7e902529781fc">More...</a><br/></td></tr>
<tr class="separator:ab16748f562f2a75f13a7e902529781fc"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a7dd433346d59c74fd50f0b9ef3337421"><td class="memItemLeft" align="right" valign="top">const std::vector< <a class="el" href="structOpenMS_1_1ProteinIdentification_1_1ProteinGroup.html">ProteinGroup</a> > & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProteinIdentification.html#a7dd433346d59c74fd50f0b9ef3337421">getProteinGroups</a> () const </td></tr>
<tr class="memdesc:a7dd433346d59c74fd50f0b9ef3337421"><td class="mdescLeft"> </td><td class="mdescRight">Returns the protein groups. <a href="#a7dd433346d59c74fd50f0b9ef3337421">More...</a><br/></td></tr>
<tr class="separator:a7dd433346d59c74fd50f0b9ef3337421"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:afd581b5b93d50641655b6a9e5664f951"><td class="memItemLeft" align="right" valign="top">std::vector< <a class="el" href="structOpenMS_1_1ProteinIdentification_1_1ProteinGroup.html">ProteinGroup</a> > & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProteinIdentification.html#afd581b5b93d50641655b6a9e5664f951">getProteinGroups</a> ()</td></tr>
<tr class="memdesc:afd581b5b93d50641655b6a9e5664f951"><td class="mdescLeft"> </td><td class="mdescRight">Returns the protein groups (mutable) <a href="#afd581b5b93d50641655b6a9e5664f951">More...</a><br/></td></tr>
<tr class="separator:afd581b5b93d50641655b6a9e5664f951"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a0d889a239a08902ffeae4fa9e9b943ee"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProteinIdentification.html#a0d889a239a08902ffeae4fa9e9b943ee">insertProteinGroup</a> (const <a class="el" href="structOpenMS_1_1ProteinIdentification_1_1ProteinGroup.html">ProteinGroup</a> &group)</td></tr>
<tr class="memdesc:a0d889a239a08902ffeae4fa9e9b943ee"><td class="mdescLeft"> </td><td class="mdescRight">Appends a new protein group. <a href="#a0d889a239a08902ffeae4fa9e9b943ee">More...</a><br/></td></tr>
<tr class="separator:a0d889a239a08902ffeae4fa9e9b943ee"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a10cda78eb5e80735212810f84612c716"><td class="memItemLeft" align="right" valign="top">const std::vector< <a class="el" href="structOpenMS_1_1ProteinIdentification_1_1ProteinGroup.html">ProteinGroup</a> > & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProteinIdentification.html#a10cda78eb5e80735212810f84612c716">getIndistinguishableProteins</a> () const </td></tr>
<tr class="memdesc:a10cda78eb5e80735212810f84612c716"><td class="mdescLeft"> </td><td class="mdescRight">Returns the indistinguishable proteins. <a href="#a10cda78eb5e80735212810f84612c716">More...</a><br/></td></tr>
<tr class="separator:a10cda78eb5e80735212810f84612c716"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:aa166b4774e6ba66bffd9cc1aefec6e25"><td class="memItemLeft" align="right" valign="top">std::vector< <a class="el" href="structOpenMS_1_1ProteinIdentification_1_1ProteinGroup.html">ProteinGroup</a> > & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProteinIdentification.html#aa166b4774e6ba66bffd9cc1aefec6e25">getIndistinguishableProteins</a> ()</td></tr>
<tr class="memdesc:aa166b4774e6ba66bffd9cc1aefec6e25"><td class="mdescLeft"> </td><td class="mdescRight">Returns the indistinguishable proteins (mutable) <a href="#aa166b4774e6ba66bffd9cc1aefec6e25">More...</a><br/></td></tr>
<tr class="separator:aa166b4774e6ba66bffd9cc1aefec6e25"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a4bd3b158c7786828b89af834891f2ce7"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProteinIdentification.html#a4bd3b158c7786828b89af834891f2ce7">insertIndistinguishableProteins</a> (const <a class="el" href="structOpenMS_1_1ProteinIdentification_1_1ProteinGroup.html">ProteinGroup</a> &group)</td></tr>
<tr class="memdesc:a4bd3b158c7786828b89af834891f2ce7"><td class="mdescLeft"> </td><td class="mdescRight">Appends new indistinguishable proteins. <a href="#a4bd3b158c7786828b89af834891f2ce7">More...</a><br/></td></tr>
<tr class="separator:a4bd3b158c7786828b89af834891f2ce7"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ae4816d8a2a93d47bb52174f16eaf9bed"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProteinIdentification.html#ae4816d8a2a93d47bb52174f16eaf9bed">getSignificanceThreshold</a> () const </td></tr>
<tr class="memdesc:ae4816d8a2a93d47bb52174f16eaf9bed"><td class="mdescLeft"> </td><td class="mdescRight">Returns the protein significance threshold value. <a href="#ae4816d8a2a93d47bb52174f16eaf9bed">More...</a><br/></td></tr>
<tr class="separator:ae4816d8a2a93d47bb52174f16eaf9bed"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a8abccfc6fb1eceb2a2c43f17055a9360"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProteinIdentification.html#a8abccfc6fb1eceb2a2c43f17055a9360">setSignificanceThreshold</a> (<a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> value)</td></tr>
<tr class="memdesc:a8abccfc6fb1eceb2a2c43f17055a9360"><td class="mdescLeft"> </td><td class="mdescRight">Sets the protein significance threshold value. <a href="#a8abccfc6fb1eceb2a2c43f17055a9360">More...</a><br/></td></tr>
<tr class="separator:a8abccfc6fb1eceb2a2c43f17055a9360"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a0fcbbc096bc75375f17b08f3b99e36e7"><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_1ProteinIdentification.html#a0fcbbc096bc75375f17b08f3b99e36e7">getScoreType</a> () const </td></tr>
<tr class="memdesc:a0fcbbc096bc75375f17b08f3b99e36e7"><td class="mdescLeft"> </td><td class="mdescRight">Returns the protein score type. <a href="#a0fcbbc096bc75375f17b08f3b99e36e7">More...</a><br/></td></tr>
<tr class="separator:a0fcbbc096bc75375f17b08f3b99e36e7"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a915462ec4a7a731fdd71f28e8a3463b1"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProteinIdentification.html#a915462ec4a7a731fdd71f28e8a3463b1">setScoreType</a> (const <a class="el" href="classOpenMS_1_1String.html">String</a> &type)</td></tr>
<tr class="memdesc:a915462ec4a7a731fdd71f28e8a3463b1"><td class="mdescLeft"> </td><td class="mdescRight">Sets the protein score type. <a href="#a915462ec4a7a731fdd71f28e8a3463b1">More...</a><br/></td></tr>
<tr class="separator:a915462ec4a7a731fdd71f28e8a3463b1"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a7ae34a5d293424fbf091a3fa7218ccfb"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProteinIdentification.html#a7ae34a5d293424fbf091a3fa7218ccfb">isHigherScoreBetter</a> () const </td></tr>
<tr class="memdesc:a7ae34a5d293424fbf091a3fa7218ccfb"><td class="mdescLeft"> </td><td class="mdescRight">Returns true if a higher score represents a better score. <a href="#a7ae34a5d293424fbf091a3fa7218ccfb">More...</a><br/></td></tr>
<tr class="separator:a7ae34a5d293424fbf091a3fa7218ccfb"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a2b12b0259c1b9a843a11013ea4097899"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProteinIdentification.html#a2b12b0259c1b9a843a11013ea4097899">setHigherScoreBetter</a> (bool higher_is_better)</td></tr>
<tr class="memdesc:a2b12b0259c1b9a843a11013ea4097899"><td class="mdescLeft"> </td><td class="mdescRight">Sets the orientation of the score (is higher better?) <a href="#a2b12b0259c1b9a843a11013ea4097899">More...</a><br/></td></tr>
<tr class="separator:a2b12b0259c1b9a843a11013ea4097899"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a47fdc9eea42b6975cdc835bb2e08810e"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProteinIdentification.html#a47fdc9eea42b6975cdc835bb2e08810e">sort</a> ()</td></tr>
<tr class="memdesc:a47fdc9eea42b6975cdc835bb2e08810e"><td class="mdescLeft"> </td><td class="mdescRight">Sorts the protein hits according to their score. <a href="#a47fdc9eea42b6975cdc835bb2e08810e">More...</a><br/></td></tr>
<tr class="separator:a47fdc9eea42b6975cdc835bb2e08810e"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:aa79958ac1cf2cb1fc4b9ae1cd766cfcb"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProteinIdentification.html#aa79958ac1cf2cb1fc4b9ae1cd766cfcb">assignRanks</a> ()</td></tr>
<tr class="memdesc:aa79958ac1cf2cb1fc4b9ae1cd766cfcb"><td class="mdescLeft"> </td><td class="mdescRight">Sorts the protein hits by score and assigns ranks (best score has rank 1) <a href="#aa79958ac1cf2cb1fc4b9ae1cd766cfcb">More...</a><br/></td></tr>
<tr class="separator:aa79958ac1cf2cb1fc4b9ae1cd766cfcb"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a23ffbf566068fc9558bf0496a6338ac8"><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_1ProteinIdentification.html#a23ffbf566068fc9558bf0496a6338ac8">computeCoverage</a> (const std::vector< <a class="el" href="classOpenMS_1_1PeptideIdentification.html">PeptideIdentification</a> > &pep_ids)</td></tr>
<tr class="memdesc:a23ffbf566068fc9558bf0496a6338ac8"><td class="mdescLeft"> </td><td class="mdescRight">Compute the coverage (in percent) of all ProteinHits given PeptideHits. <a href="#a23ffbf566068fc9558bf0496a6338ac8">More...</a><br/></td></tr>
<tr class="separator:a23ffbf566068fc9558bf0496a6338ac8"><td class="memSeparator" colspan="2"> </td></tr>
<tr><td colspan="2"><div class="groupHeader">General information</div></td></tr>
<tr class="memitem:ae2c8ff7196c08b1ff00e8f80d6293135"><td class="memItemLeft" align="right" valign="top">const <a class="el" href="classOpenMS_1_1DateTime.html">DateTime</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProteinIdentification.html#ae2c8ff7196c08b1ff00e8f80d6293135">getDateTime</a> () const </td></tr>
<tr class="memdesc:ae2c8ff7196c08b1ff00e8f80d6293135"><td class="mdescLeft"> </td><td class="mdescRight">Returns the date of the protein identification run. <a href="#ae2c8ff7196c08b1ff00e8f80d6293135">More...</a><br/></td></tr>
<tr class="separator:ae2c8ff7196c08b1ff00e8f80d6293135"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ae0728c54c04bcc99a4c6ebfa961ed2c5"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProteinIdentification.html#ae0728c54c04bcc99a4c6ebfa961ed2c5">setDateTime</a> (const <a class="el" href="classOpenMS_1_1DateTime.html">DateTime</a> &date)</td></tr>
<tr class="memdesc:ae0728c54c04bcc99a4c6ebfa961ed2c5"><td class="mdescLeft"> </td><td class="mdescRight">Sets the date of the protein identification run. <a href="#ae0728c54c04bcc99a4c6ebfa961ed2c5">More...</a><br/></td></tr>
<tr class="separator:ae0728c54c04bcc99a4c6ebfa961ed2c5"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a15a14866884b8b4dea8950b2151a0963"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProteinIdentification.html#a15a14866884b8b4dea8950b2151a0963">setSearchEngine</a> (const <a class="el" href="classOpenMS_1_1String.html">String</a> &search_engine)</td></tr>
<tr class="memdesc:a15a14866884b8b4dea8950b2151a0963"><td class="mdescLeft"> </td><td class="mdescRight">Sets the search engine type. <a href="#a15a14866884b8b4dea8950b2151a0963">More...</a><br/></td></tr>
<tr class="separator:a15a14866884b8b4dea8950b2151a0963"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a00f317e7e119f34ef02743f594e5d232"><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_1ProteinIdentification.html#a00f317e7e119f34ef02743f594e5d232">getSearchEngine</a> () const </td></tr>
<tr class="memdesc:a00f317e7e119f34ef02743f594e5d232"><td class="mdescLeft"> </td><td class="mdescRight">Returns the type of search engine used. <a href="#a00f317e7e119f34ef02743f594e5d232">More...</a><br/></td></tr>
<tr class="separator:a00f317e7e119f34ef02743f594e5d232"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a82e595befae76c1f7c22918420d2d9e8"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProteinIdentification.html#a82e595befae76c1f7c22918420d2d9e8">setSearchEngineVersion</a> (const <a class="el" href="classOpenMS_1_1String.html">String</a> &search_engine_version)</td></tr>
<tr class="memdesc:a82e595befae76c1f7c22918420d2d9e8"><td class="mdescLeft"> </td><td class="mdescRight">Sets the search engine version. <a href="#a82e595befae76c1f7c22918420d2d9e8">More...</a><br/></td></tr>
<tr class="separator:a82e595befae76c1f7c22918420d2d9e8"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:af3a348db6191709eff7d1cb9429db28d"><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_1ProteinIdentification.html#af3a348db6191709eff7d1cb9429db28d">getSearchEngineVersion</a> () const </td></tr>
<tr class="memdesc:af3a348db6191709eff7d1cb9429db28d"><td class="mdescLeft"> </td><td class="mdescRight">Returns the search engine version. <a href="#af3a348db6191709eff7d1cb9429db28d">More...</a><br/></td></tr>
<tr class="separator:af3a348db6191709eff7d1cb9429db28d"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:afb0f58ddeea0e6f58da132fae1421563"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProteinIdentification.html#afb0f58ddeea0e6f58da132fae1421563">setSearchParameters</a> (const <a class="el" href="structOpenMS_1_1ProteinIdentification_1_1SearchParameters.html">SearchParameters</a> &search_parameters)</td></tr>
<tr class="memdesc:afb0f58ddeea0e6f58da132fae1421563"><td class="mdescLeft"> </td><td class="mdescRight">Sets the search parameters. <a href="#afb0f58ddeea0e6f58da132fae1421563">More...</a><br/></td></tr>
<tr class="separator:afb0f58ddeea0e6f58da132fae1421563"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:af7e8f29d109ed9627598d2f8a6bb28a9"><td class="memItemLeft" align="right" valign="top">const <a class="el" href="structOpenMS_1_1ProteinIdentification_1_1SearchParameters.html">SearchParameters</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProteinIdentification.html#af7e8f29d109ed9627598d2f8a6bb28a9">getSearchParameters</a> () const </td></tr>
<tr class="memdesc:af7e8f29d109ed9627598d2f8a6bb28a9"><td class="mdescLeft"> </td><td class="mdescRight">Returns the search parameters. <a href="#af7e8f29d109ed9627598d2f8a6bb28a9">More...</a><br/></td></tr>
<tr class="separator:af7e8f29d109ed9627598d2f8a6bb28a9"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a4eb8ec8636a89f575db95a370fd480b6"><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_1ProteinIdentification.html#a4eb8ec8636a89f575db95a370fd480b6">getIdentifier</a> () const </td></tr>
<tr class="memdesc:a4eb8ec8636a89f575db95a370fd480b6"><td class="mdescLeft"> </td><td class="mdescRight">Returns the identifier. <a href="#a4eb8ec8636a89f575db95a370fd480b6">More...</a><br/></td></tr>
<tr class="separator:a4eb8ec8636a89f575db95a370fd480b6"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a00f1456779f764c2738c35be2c04f6e8"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProteinIdentification.html#a00f1456779f764c2738c35be2c04f6e8">setIdentifier</a> (const <a class="el" href="classOpenMS_1_1String.html">String</a> &id)</td></tr>
<tr class="memdesc:a00f1456779f764c2738c35be2c04f6e8"><td class="mdescLeft"> </td><td class="mdescRight">Sets the identifier. <a href="#a00f1456779f764c2738c35be2c04f6e8">More...</a><br/></td></tr>
<tr class="separator:a00f1456779f764c2738c35be2c04f6e8"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="inherit_header pub_methods_classOpenMS_1_1MetaInfoInterface"><td colspan="2" onclick="javascript:toggleInherit('pub_methods_classOpenMS_1_1MetaInfoInterface')"><img src="closed.png" alt="-"/> Public Member Functions inherited from <a class="el" href="classOpenMS_1_1MetaInfoInterface.html">MetaInfoInterface</a></td></tr>
<tr class="memitem:a4adf02f403d7b972e7e6a58e938ecb6c inherit pub_methods_classOpenMS_1_1MetaInfoInterface"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MetaInfoInterface.html#a4adf02f403d7b972e7e6a58e938ecb6c">MetaInfoInterface</a> ()</td></tr>
<tr class="memdesc:a4adf02f403d7b972e7e6a58e938ecb6c inherit pub_methods_classOpenMS_1_1MetaInfoInterface"><td class="mdescLeft"> </td><td class="mdescRight">constructor <a href="#a4adf02f403d7b972e7e6a58e938ecb6c">More...</a><br/></td></tr>
<tr class="separator:a4adf02f403d7b972e7e6a58e938ecb6c inherit pub_methods_classOpenMS_1_1MetaInfoInterface"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ae216eb0aa3192b67d70da8c461583256 inherit pub_methods_classOpenMS_1_1MetaInfoInterface"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MetaInfoInterface.html#ae216eb0aa3192b67d70da8c461583256">MetaInfoInterface</a> (const <a class="el" href="classOpenMS_1_1MetaInfoInterface.html">MetaInfoInterface</a> &rhs)</td></tr>
<tr class="memdesc:ae216eb0aa3192b67d70da8c461583256 inherit pub_methods_classOpenMS_1_1MetaInfoInterface"><td class="mdescLeft"> </td><td class="mdescRight">copy constructor <a href="#ae216eb0aa3192b67d70da8c461583256">More...</a><br/></td></tr>
<tr class="separator:ae216eb0aa3192b67d70da8c461583256 inherit pub_methods_classOpenMS_1_1MetaInfoInterface"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a30c6469ab28a1ae578b23109f8b931c6 inherit pub_methods_classOpenMS_1_1MetaInfoInterface"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MetaInfoInterface.html#a30c6469ab28a1ae578b23109f8b931c6">~MetaInfoInterface</a> ()</td></tr>
<tr class="memdesc:a30c6469ab28a1ae578b23109f8b931c6 inherit pub_methods_classOpenMS_1_1MetaInfoInterface"><td class="mdescLeft"> </td><td class="mdescRight">destructor <a href="#a30c6469ab28a1ae578b23109f8b931c6">More...</a><br/></td></tr>
<tr class="separator:a30c6469ab28a1ae578b23109f8b931c6 inherit pub_methods_classOpenMS_1_1MetaInfoInterface"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a0b7e858982ccb9d37b01971e6cd43596 inherit pub_methods_classOpenMS_1_1MetaInfoInterface"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1MetaInfoInterface.html">MetaInfoInterface</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MetaInfoInterface.html#a0b7e858982ccb9d37b01971e6cd43596">operator=</a> (const <a class="el" href="classOpenMS_1_1MetaInfoInterface.html">MetaInfoInterface</a> &rhs)</td></tr>
<tr class="memdesc:a0b7e858982ccb9d37b01971e6cd43596 inherit pub_methods_classOpenMS_1_1MetaInfoInterface"><td class="mdescLeft"> </td><td class="mdescRight">assignment operator <a href="#a0b7e858982ccb9d37b01971e6cd43596">More...</a><br/></td></tr>
<tr class="separator:a0b7e858982ccb9d37b01971e6cd43596 inherit pub_methods_classOpenMS_1_1MetaInfoInterface"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ae1233471a3265a00a5edef4017ee8f20 inherit pub_methods_classOpenMS_1_1MetaInfoInterface"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MetaInfoInterface.html#ae1233471a3265a00a5edef4017ee8f20">operator==</a> (const <a class="el" href="classOpenMS_1_1MetaInfoInterface.html">MetaInfoInterface</a> &rhs) const </td></tr>
<tr class="memdesc:ae1233471a3265a00a5edef4017ee8f20 inherit pub_methods_classOpenMS_1_1MetaInfoInterface"><td class="mdescLeft"> </td><td class="mdescRight">Equality operator. <a href="#ae1233471a3265a00a5edef4017ee8f20">More...</a><br/></td></tr>
<tr class="separator:ae1233471a3265a00a5edef4017ee8f20 inherit pub_methods_classOpenMS_1_1MetaInfoInterface"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:aabdb6bf51d554dba98617e3f7609c6cf inherit pub_methods_classOpenMS_1_1MetaInfoInterface"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MetaInfoInterface.html#aabdb6bf51d554dba98617e3f7609c6cf">operator!=</a> (const <a class="el" href="classOpenMS_1_1MetaInfoInterface.html">MetaInfoInterface</a> &rhs) const </td></tr>
<tr class="memdesc:aabdb6bf51d554dba98617e3f7609c6cf inherit pub_methods_classOpenMS_1_1MetaInfoInterface"><td class="mdescLeft"> </td><td class="mdescRight">Equality operator. <a href="#aabdb6bf51d554dba98617e3f7609c6cf">More...</a><br/></td></tr>
<tr class="separator:aabdb6bf51d554dba98617e3f7609c6cf inherit pub_methods_classOpenMS_1_1MetaInfoInterface"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:aae35ae2dfad88d673b03c787aafca83d inherit pub_methods_classOpenMS_1_1MetaInfoInterface"><td class="memItemLeft" align="right" valign="top">const <a class="el" href="classOpenMS_1_1DataValue.html">DataValue</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MetaInfoInterface.html#aae35ae2dfad88d673b03c787aafca83d">getMetaValue</a> (const <a class="el" href="classOpenMS_1_1String.html">String</a> &name) const </td></tr>
<tr class="memdesc:aae35ae2dfad88d673b03c787aafca83d inherit pub_methods_classOpenMS_1_1MetaInfoInterface"><td class="mdescLeft"> </td><td class="mdescRight">returns the value corresponding to a string <a href="#aae35ae2dfad88d673b03c787aafca83d">More...</a><br/></td></tr>
<tr class="separator:aae35ae2dfad88d673b03c787aafca83d inherit pub_methods_classOpenMS_1_1MetaInfoInterface"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ae9b2516ea1331df63e4fc098c16b50e3 inherit pub_methods_classOpenMS_1_1MetaInfoInterface"><td class="memItemLeft" align="right" valign="top">const <a class="el" href="classOpenMS_1_1DataValue.html">DataValue</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MetaInfoInterface.html#ae9b2516ea1331df63e4fc098c16b50e3">getMetaValue</a> (<a class="el" href="group__Concept.html#gaba0996d26f7be2572973245b51852757">UInt</a> index) const </td></tr>
<tr class="memdesc:ae9b2516ea1331df63e4fc098c16b50e3 inherit pub_methods_classOpenMS_1_1MetaInfoInterface"><td class="mdescLeft"> </td><td class="mdescRight">returns the value corresponding to an index <a href="#ae9b2516ea1331df63e4fc098c16b50e3">More...</a><br/></td></tr>
<tr class="separator:ae9b2516ea1331df63e4fc098c16b50e3 inherit pub_methods_classOpenMS_1_1MetaInfoInterface"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:acabf8a0e3c40224df62b282a5ce0318f inherit pub_methods_classOpenMS_1_1MetaInfoInterface"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MetaInfoInterface.html#acabf8a0e3c40224df62b282a5ce0318f">metaValueExists</a> (const <a class="el" href="classOpenMS_1_1String.html">String</a> &name) const </td></tr>
<tr class="memdesc:acabf8a0e3c40224df62b282a5ce0318f inherit pub_methods_classOpenMS_1_1MetaInfoInterface"><td class="mdescLeft"> </td><td class="mdescRight">returns if this <a class="el" href="classOpenMS_1_1MetaInfo.html" title="A Type-Name-Value tuple class. ">MetaInfo</a> is set <a href="#acabf8a0e3c40224df62b282a5ce0318f">More...</a><br/></td></tr>
<tr class="separator:acabf8a0e3c40224df62b282a5ce0318f inherit pub_methods_classOpenMS_1_1MetaInfoInterface"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:aabf87daa46e081dd9584d4987d2206f6 inherit pub_methods_classOpenMS_1_1MetaInfoInterface"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MetaInfoInterface.html#aabf87daa46e081dd9584d4987d2206f6">metaValueExists</a> (<a class="el" href="group__Concept.html#gaba0996d26f7be2572973245b51852757">UInt</a> index) const </td></tr>
<tr class="memdesc:aabf87daa46e081dd9584d4987d2206f6 inherit pub_methods_classOpenMS_1_1MetaInfoInterface"><td class="mdescLeft"> </td><td class="mdescRight">returns if this <a class="el" href="classOpenMS_1_1MetaInfo.html" title="A Type-Name-Value tuple class. ">MetaInfo</a> is set <a href="#aabf87daa46e081dd9584d4987d2206f6">More...</a><br/></td></tr>
<tr class="separator:aabf87daa46e081dd9584d4987d2206f6 inherit pub_methods_classOpenMS_1_1MetaInfoInterface"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a135a7e818125b31198a8a65d9ac7a3d1 inherit pub_methods_classOpenMS_1_1MetaInfoInterface"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MetaInfoInterface.html#a135a7e818125b31198a8a65d9ac7a3d1">setMetaValue</a> (const <a class="el" href="classOpenMS_1_1String.html">String</a> &name, const <a class="el" href="classOpenMS_1_1DataValue.html">DataValue</a> &value)</td></tr>
<tr class="memdesc:a135a7e818125b31198a8a65d9ac7a3d1 inherit pub_methods_classOpenMS_1_1MetaInfoInterface"><td class="mdescLeft"> </td><td class="mdescRight">sets the <a class="el" href="classOpenMS_1_1DataValue.html" title="Class to hold strings, numeric values, lists of strings and lists of numeric values. ">DataValue</a> corresponding to a name <a href="#a135a7e818125b31198a8a65d9ac7a3d1">More...</a><br/></td></tr>
<tr class="separator:a135a7e818125b31198a8a65d9ac7a3d1 inherit pub_methods_classOpenMS_1_1MetaInfoInterface"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:abbb9d3ebe8c7c3f6a9ed131faa8cf2c9 inherit pub_methods_classOpenMS_1_1MetaInfoInterface"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MetaInfoInterface.html#abbb9d3ebe8c7c3f6a9ed131faa8cf2c9">setMetaValue</a> (<a class="el" href="group__Concept.html#gaba0996d26f7be2572973245b51852757">UInt</a> index, const <a class="el" href="classOpenMS_1_1DataValue.html">DataValue</a> &value)</td></tr>
<tr class="memdesc:abbb9d3ebe8c7c3f6a9ed131faa8cf2c9 inherit pub_methods_classOpenMS_1_1MetaInfoInterface"><td class="mdescLeft"> </td><td class="mdescRight">sets the <a class="el" href="classOpenMS_1_1DataValue.html" title="Class to hold strings, numeric values, lists of strings and lists of numeric values. ">DataValue</a> corresponding to an index <a href="#abbb9d3ebe8c7c3f6a9ed131faa8cf2c9">More...</a><br/></td></tr>
<tr class="separator:abbb9d3ebe8c7c3f6a9ed131faa8cf2c9 inherit pub_methods_classOpenMS_1_1MetaInfoInterface"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:aac68103b8336fa854cf4c59f8bd6cff8 inherit pub_methods_classOpenMS_1_1MetaInfoInterface"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MetaInfoInterface.html#aac68103b8336fa854cf4c59f8bd6cff8">removeMetaValue</a> (const <a class="el" href="classOpenMS_1_1String.html">String</a> &name)</td></tr>
<tr class="memdesc:aac68103b8336fa854cf4c59f8bd6cff8 inherit pub_methods_classOpenMS_1_1MetaInfoInterface"><td class="mdescLeft"> </td><td class="mdescRight">Removes the <a class="el" href="classOpenMS_1_1DataValue.html" title="Class to hold strings, numeric values, lists of strings and lists of numeric values. ">DataValue</a> corresponding to <code>name</code> if it exists. <a href="#aac68103b8336fa854cf4c59f8bd6cff8">More...</a><br/></td></tr>
<tr class="separator:aac68103b8336fa854cf4c59f8bd6cff8 inherit pub_methods_classOpenMS_1_1MetaInfoInterface"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a3a8a7da0f5e71d3b96ea902c29bcf632 inherit pub_methods_classOpenMS_1_1MetaInfoInterface"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MetaInfoInterface.html#a3a8a7da0f5e71d3b96ea902c29bcf632">removeMetaValue</a> (<a class="el" href="group__Concept.html#gaba0996d26f7be2572973245b51852757">UInt</a> index)</td></tr>
<tr class="memdesc:a3a8a7da0f5e71d3b96ea902c29bcf632 inherit pub_methods_classOpenMS_1_1MetaInfoInterface"><td class="mdescLeft"> </td><td class="mdescRight">Removes the <a class="el" href="classOpenMS_1_1DataValue.html" title="Class to hold strings, numeric values, lists of strings and lists of numeric values. ">DataValue</a> corresponding to <code>index</code> if it exists. <a href="#a3a8a7da0f5e71d3b96ea902c29bcf632">More...</a><br/></td></tr>
<tr class="separator:a3a8a7da0f5e71d3b96ea902c29bcf632 inherit pub_methods_classOpenMS_1_1MetaInfoInterface"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:aaefa2a4a5d50f899cdd82d686104d164 inherit pub_methods_classOpenMS_1_1MetaInfoInterface"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MetaInfoInterface.html#aaefa2a4a5d50f899cdd82d686104d164">getKeys</a> (std::vector< <a class="el" href="classOpenMS_1_1String.html">String</a> > &keys) const </td></tr>
<tr class="memdesc:aaefa2a4a5d50f899cdd82d686104d164 inherit pub_methods_classOpenMS_1_1MetaInfoInterface"><td class="mdescLeft"> </td><td class="mdescRight">fills the given vector with a list of all keys for which a value is set <a href="#aaefa2a4a5d50f899cdd82d686104d164">More...</a><br/></td></tr>
<tr class="separator:aaefa2a4a5d50f899cdd82d686104d164 inherit pub_methods_classOpenMS_1_1MetaInfoInterface"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a121b22fe4dd05ef9fc4160bd52e9bd0b inherit pub_methods_classOpenMS_1_1MetaInfoInterface"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MetaInfoInterface.html#a121b22fe4dd05ef9fc4160bd52e9bd0b">getKeys</a> (std::vector< <a class="el" href="group__Concept.html#gaba0996d26f7be2572973245b51852757">UInt</a> > &keys) const </td></tr>
<tr class="memdesc:a121b22fe4dd05ef9fc4160bd52e9bd0b inherit pub_methods_classOpenMS_1_1MetaInfoInterface"><td class="mdescLeft"> </td><td class="mdescRight">fills the given vector with a list of all keys for which a value is set <a href="#a121b22fe4dd05ef9fc4160bd52e9bd0b">More...</a><br/></td></tr>
<tr class="separator:a121b22fe4dd05ef9fc4160bd52e9bd0b inherit pub_methods_classOpenMS_1_1MetaInfoInterface"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a001483d1f67f068e585f10d9abcc487d inherit pub_methods_classOpenMS_1_1MetaInfoInterface"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MetaInfoInterface.html#a001483d1f67f068e585f10d9abcc487d">isMetaEmpty</a> () const </td></tr>
<tr class="memdesc:a001483d1f67f068e585f10d9abcc487d inherit pub_methods_classOpenMS_1_1MetaInfoInterface"><td class="mdescLeft"> </td><td class="mdescRight">returns if the <a class="el" href="classOpenMS_1_1MetaInfo.html" title="A Type-Name-Value tuple class. ">MetaInfo</a> is empty <a href="#a001483d1f67f068e585f10d9abcc487d">More...</a><br/></td></tr>
<tr class="separator:a001483d1f67f068e585f10d9abcc487d inherit pub_methods_classOpenMS_1_1MetaInfoInterface"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ae5b77ecfe9182ebd648d54ca1137eba0 inherit pub_methods_classOpenMS_1_1MetaInfoInterface"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MetaInfoInterface.html#ae5b77ecfe9182ebd648d54ca1137eba0">clearMetaInfo</a> ()</td></tr>
<tr class="memdesc:ae5b77ecfe9182ebd648d54ca1137eba0 inherit pub_methods_classOpenMS_1_1MetaInfoInterface"><td class="mdescLeft"> </td><td class="mdescRight">removes all meta values <a href="#ae5b77ecfe9182ebd648d54ca1137eba0">More...</a><br/></td></tr>
<tr class="separator:ae5b77ecfe9182ebd648d54ca1137eba0 inherit pub_methods_classOpenMS_1_1MetaInfoInterface"><td class="memSeparator" colspan="2"> </td></tr>
</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-static-attribs"></a>
Static Public Attributes</h2></td></tr>
<tr class="memitem:a4dbe2d19835aa05a1c9c672fa254ef66"><td class="memItemLeft" align="right" valign="top">static const std::string </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProteinIdentification.html#a4dbe2d19835aa05a1c9c672fa254ef66">NamesOfPeakMassType</a> [<a class="el" href="classOpenMS_1_1ProteinIdentification.html#a5431b65220b7ad71b5e8768876ee3e53a2989e7c6c70923c0941b34c64517d012">SIZE_OF_PEAKMASSTYPE</a>]</td></tr>
<tr class="memdesc:a4dbe2d19835aa05a1c9c672fa254ef66"><td class="mdescLeft"> </td><td class="mdescRight">Names corresponding to peak mass types. <a href="#a4dbe2d19835aa05a1c9c672fa254ef66">More...</a><br/></td></tr>
<tr class="separator:a4dbe2d19835aa05a1c9c672fa254ef66"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a5712ee000feacb9e63b879136a658c57"><td class="memItemLeft" align="right" valign="top">static const std::string </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProteinIdentification.html#a5712ee000feacb9e63b879136a658c57">NamesOfDigestionEnzyme</a> [<a class="el" href="classOpenMS_1_1ProteinIdentification.html#ac1976fd756a09ae4e26fe6b32fcb396ca59ffc2972d48cca58d73eb79e40edf9f">SIZE_OF_DIGESTIONENZYME</a>]</td></tr>
<tr class="memdesc:a5712ee000feacb9e63b879136a658c57"><td class="mdescLeft"> </td><td class="mdescRight">Names corresponding to digestion enzymes. <a href="#a5712ee000feacb9e63b879136a658c57">More...</a><br/></td></tr>
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<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pro-attribs"></a>
Protected Attributes</h2></td></tr>
<tr><td colspan="2"><div class="groupHeader">General information (search engine, parameters and database)</div></td></tr>
<tr class="memitem:ae1d43a6f8bee9f364bea98c12662e966"><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_1ProteinIdentification.html#ae1d43a6f8bee9f364bea98c12662e966">id_</a></td></tr>
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<tr class="memitem:a5025f2dee8f88a7632f01b5cea7043d9"><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_1ProteinIdentification.html#a5025f2dee8f88a7632f01b5cea7043d9">search_engine_</a></td></tr>
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<tr class="memitem:a82c64193b7343b0080e0b59d51f462b9"><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_1ProteinIdentification.html#a82c64193b7343b0080e0b59d51f462b9">search_engine_version_</a></td></tr>
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<tr class="memitem:a8d4d0ec9e43eeec30776ae8db269c8c8"><td class="memItemLeft" align="right" valign="top"><a class="el" href="structOpenMS_1_1ProteinIdentification_1_1SearchParameters.html">SearchParameters</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProteinIdentification.html#a8d4d0ec9e43eeec30776ae8db269c8c8">search_parameters_</a></td></tr>
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<tr class="memitem:ab11b7dd5f2f6ffc800af0152f5c2e69a"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1DateTime.html">DateTime</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProteinIdentification.html#ab11b7dd5f2f6ffc800af0152f5c2e69a">date_</a></td></tr>
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<tr><td colspan="2"><div class="groupHeader">Protein hit information (protected members)</div></td></tr>
<tr class="memitem:a940dace1dddca4443da1921a15603575"><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_1ProteinIdentification.html#a940dace1dddca4443da1921a15603575">protein_score_type_</a></td></tr>
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<tr class="memitem:a9e5d348a14e5fe639d88db39f0ff7ada"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProteinIdentification.html#a9e5d348a14e5fe639d88db39f0ff7ada">higher_score_better_</a></td></tr>
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<tr class="memitem:a5a059567f3e766f14ee245d880454e7c"><td class="memItemLeft" align="right" valign="top">std::vector< <a class="el" href="classOpenMS_1_1ProteinHit.html">ProteinHit</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProteinIdentification.html#a5a059567f3e766f14ee245d880454e7c">protein_hits_</a></td></tr>
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<tr class="memitem:ad8740a5936ee7eecd38542b9130f4b93"><td class="memItemLeft" align="right" valign="top">std::vector< <a class="el" href="structOpenMS_1_1ProteinIdentification_1_1ProteinGroup.html">ProteinGroup</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProteinIdentification.html#ad8740a5936ee7eecd38542b9130f4b93">protein_groups_</a></td></tr>
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<tr class="memitem:ad134aae1077cd7c582d367e8fe890609"><td class="memItemLeft" align="right" valign="top">std::vector< <a class="el" href="structOpenMS_1_1ProteinIdentification_1_1ProteinGroup.html">ProteinGroup</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProteinIdentification.html#ad134aae1077cd7c582d367e8fe890609">indistinguishable_proteins_</a></td></tr>
<tr class="memdesc:ad134aae1077cd7c582d367e8fe890609"><td class="mdescLeft"> </td><td class="mdescRight">Indistinguishable proteins: <code>accessions</code>[0] is "group leader", <code>probability</code> is meaningless. <a href="#ad134aae1077cd7c582d367e8fe890609">More...</a><br/></td></tr>
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<tr class="memitem:a47f7aa8465f37243ff2b9cca5b8cd0b4"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProteinIdentification.html#a47f7aa8465f37243ff2b9cca5b8cd0b4">protein_significance_threshold_</a></td></tr>
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<tr class="inherit_header pro_attribs_classOpenMS_1_1MetaInfoInterface"><td colspan="2" onclick="javascript:toggleInherit('pro_attribs_classOpenMS_1_1MetaInfoInterface')"><img src="closed.png" alt="-"/> Protected Attributes inherited from <a class="el" href="classOpenMS_1_1MetaInfoInterface.html">MetaInfoInterface</a></td></tr>
<tr class="memitem:a07ce72f4d24f650fcdbba3801e1b8f59 inherit pro_attribs_classOpenMS_1_1MetaInfoInterface"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1MetaInfo.html">MetaInfo</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MetaInfoInterface.html#a07ce72f4d24f650fcdbba3801e1b8f59">meta_</a></td></tr>
<tr class="memdesc:a07ce72f4d24f650fcdbba3801e1b8f59 inherit pro_attribs_classOpenMS_1_1MetaInfoInterface"><td class="mdescLeft"> </td><td class="mdescRight">pointer to the <a class="el" href="classOpenMS_1_1MetaInfo.html" title="A Type-Name-Value tuple class. ">MetaInfo</a> object. 0 by default <a href="#a07ce72f4d24f650fcdbba3801e1b8f59">More...</a><br/></td></tr>
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Additional Inherited Members</h2></td></tr>
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<tr class="memitem:adc0992991f912788ed14e72b6f62b2dd inherit pub_static_methods_classOpenMS_1_1MetaInfoInterface"><td class="memItemLeft" align="right" valign="top">static <a class="el" href="classOpenMS_1_1MetaInfoRegistry.html">MetaInfoRegistry</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MetaInfoInterface.html#adc0992991f912788ed14e72b6f62b2dd">metaRegistry</a> ()</td></tr>
<tr class="memdesc:adc0992991f912788ed14e72b6f62b2dd inherit pub_static_methods_classOpenMS_1_1MetaInfoInterface"><td class="mdescLeft"> </td><td class="mdescRight">retuns a reference to the <a class="el" href="classOpenMS_1_1MetaInfoRegistry.html" title="Registry which assigns unique integer indices to strings. ">MetaInfoRegistry</a> <a href="#adc0992991f912788ed14e72b6f62b2dd">More...</a><br/></td></tr>
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<tr class="inherit_header pro_methods_classOpenMS_1_1MetaInfoInterface"><td colspan="2" onclick="javascript:toggleInherit('pro_methods_classOpenMS_1_1MetaInfoInterface')"><img src="closed.png" alt="-"/> Protected Member Functions inherited from <a class="el" href="classOpenMS_1_1MetaInfoInterface.html">MetaInfoInterface</a></td></tr>
<tr class="memitem:a23bcf7d2c2357d11e1363dfe44057037 inherit pro_methods_classOpenMS_1_1MetaInfoInterface"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MetaInfoInterface.html#a23bcf7d2c2357d11e1363dfe44057037">createIfNotExists_</a> ()</td></tr>
<tr class="memdesc:a23bcf7d2c2357d11e1363dfe44057037 inherit pro_methods_classOpenMS_1_1MetaInfoInterface"><td class="mdescLeft"> </td><td class="mdescRight">creates the <a class="el" href="classOpenMS_1_1MetaInfo.html" title="A Type-Name-Value tuple class. ">MetaInfo</a> object if it does not exist <a href="#a23bcf7d2c2357d11e1363dfe44057037">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>Representation of a protein identification run. </p>
<p>This class stores the general information and the protein hits of a protein identification run.</p>
<p>The actual peptide hits are stored in <a class="el" href="classOpenMS_1_1PeptideIdentification.html" title="Represents the peptide hits for a spectrum. ">PeptideIdentification</a> instances that are part of spectra or features.</p>
<p>In order to be able to connect the <a class="el" href="classOpenMS_1_1ProteinIdentification.html" title="Representation of a protein identification run. ">ProteinIdentification</a> and the corresponding peptide identifications, both classes have a string identifier. We recommend using the search engine name and the date as identifier. Setting this identifier is especially important when there are several protein identification runs for a map, i.e. several <a class="el" href="classOpenMS_1_1ProteinIdentification.html" title="Representation of a protein identification run. ">ProteinIdentification</a> instances.</p>
<dl class="todo"><dt><b><a class="el" href="todo.html#_todo000017">Todo:</a></b></dt><dd>Add <a class="el" href="classOpenMS_1_1MetaInfoInterface.html" title="Interface for classes that can store arbitrary meta information (Type-Name-Value tuples). ">MetaInfoInterface</a> to modifications => update <a class="el" href="classOpenMS_1_1IdXMLFile.html" title="Used to load and store idXML files. ">IdXMLFile</a> and <a class="el" href="classOpenMS_1_1ProteinIdentificationVisualizer.html" title="Class that displays all meta information for ProteinIdentification objects. ">ProteinIdentificationVisualizer</a> (Andreas)</dd></dl>
</div><h2 class="groupheader">Member Typedef Documentation</h2>
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<td class="memname">typedef <a class="el" href="classOpenMS_1_1ProteinHit.html">ProteinHit</a> <a class="el" href="classOpenMS_1_1ProteinIdentification.html#a81790367e26e192b9eb9c7cad5f1730d">HitType</a></td>
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<p>Hit type definition. </p>
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<h2 class="groupheader">Member Enumeration Documentation</h2>
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<td class="memname">enum <a class="el" href="classOpenMS_1_1ProteinIdentification.html#ac1976fd756a09ae4e26fe6b32fcb396c">DigestionEnzyme</a></td>
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<tr><th colspan="2">Enumerator</th></tr><tr><td class="fieldname"><em><a class="anchor" id="ac1976fd756a09ae4e26fe6b32fcb396caa87783975563314a167c39f08f065bfd"></a>TRYPSIN</em> </td><td class="fielddoc">
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<tr><td class="fieldname"><em><a class="anchor" id="ac1976fd756a09ae4e26fe6b32fcb396ca9cf5aedb487753ed0440ab34d94e1b33"></a>PEPSIN_A</em> </td><td class="fielddoc">
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<tr><td class="fieldname"><em><a class="anchor" id="ac1976fd756a09ae4e26fe6b32fcb396ca3b5e4efa6ca1ae00905ead21fe2c1e73"></a>PROTEASE_K</em> </td><td class="fielddoc">
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<tr><td class="fieldname"><em><a class="anchor" id="ac1976fd756a09ae4e26fe6b32fcb396ca240cc037883891d0eb859a89530893ba"></a>CHYMOTRYPSIN</em> </td><td class="fielddoc">
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<tr><td class="fieldname"><em><a class="anchor" id="ac1976fd756a09ae4e26fe6b32fcb396ca8013b03f6b7f2d27796adf371a715a81"></a>NO_ENZYME</em> </td><td class="fielddoc">
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<tr><td class="fieldname"><em><a class="anchor" id="ac1976fd756a09ae4e26fe6b32fcb396ca36a56e667bdbe75daa08c655e85ec49a"></a>UNKNOWN_ENZYME</em> </td><td class="fielddoc">
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<tr><td class="fieldname"><em><a class="anchor" id="ac1976fd756a09ae4e26fe6b32fcb396ca59ffc2972d48cca58d73eb79e40edf9f"></a>SIZE_OF_DIGESTIONENZYME</em> </td><td class="fielddoc">
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<td class="memname">enum <a class="el" href="classOpenMS_1_1ProteinIdentification.html#a5431b65220b7ad71b5e8768876ee3e53">PeakMassType</a></td>
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<p>Peak mass type. </p>
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<tr><th colspan="2">Enumerator</th></tr><tr><td class="fieldname"><em><a class="anchor" id="a5431b65220b7ad71b5e8768876ee3e53aba27416c974c26497ea0f4aa59fcf669"></a>MONOISOTOPIC</em> </td><td class="fielddoc">
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<tr><td class="fieldname"><em><a class="anchor" id="a5431b65220b7ad71b5e8768876ee3e53ab6f2220659ddcb84a0622d4aa4e0b112"></a>AVERAGE</em> </td><td class="fielddoc">
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<tr><td class="fieldname"><em><a class="anchor" id="a5431b65220b7ad71b5e8768876ee3e53a2989e7c6c70923c0941b34c64517d012"></a>SIZE_OF_PEAKMASSTYPE</em> </td><td class="fielddoc">
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<h2 class="groupheader">Constructor & Destructor Documentation</h2>
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<td class="memname"><a class="el" href="classOpenMS_1_1ProteinIdentification.html">ProteinIdentification</a> </td>
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<p>Default constructor. </p>
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<td class="memname">virtual ~<a class="el" href="classOpenMS_1_1ProteinIdentification.html">ProteinIdentification</a> </td>
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<p>Destructor. </p>
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<td class="memname"><a class="el" href="classOpenMS_1_1ProteinIdentification.html">ProteinIdentification</a> </td>
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<td class="paramtype">const <a class="el" href="classOpenMS_1_1ProteinIdentification.html">ProteinIdentification</a> & </td>
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<p>Copy constructor. </p>
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<h2 class="groupheader">Member Function Documentation</h2>
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<td class="memname">void assignRanks </td>
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<p>Sorts the protein hits by score and assigns ranks (best score has rank 1) </p>
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<td class="memname"><a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> computeCoverage </td>
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<td class="paramtype">const std::vector< <a class="el" href="classOpenMS_1_1PeptideIdentification.html">PeptideIdentification</a> > & </td>
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<p>Compute the coverage (in percent) of all ProteinHits given PeptideHits. </p>
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<tr><td class="paramname"><a class="el" href="classOpenMS_1_1Exception_1_1MissingInformation.html" title="Not all required information provided. ">Exception::MissingInformation</a></td><td>if ProteinsHits do not have sequence information</td></tr>
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<dl class="section return"><dt>Returns</dt><dd>The number of Proteins referenced by the <code>pep_ids</code> that are not contained in this <a class="el" href="classOpenMS_1_1ProteinIdentification.html" title="Representation of a protein identification run. ">ProteinIdentification</a> set (should be 0) </dd></dl>
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<td class="memname">std::vector<<a class="el" href="classOpenMS_1_1ProteinHit.html">ProteinHit</a>>::iterator findHit </td>
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<p>Finds a protein hit by accession (returns past-the-end iterator if not found) </p>
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<p>Returns the date of the protein identification run. </p>
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<td class="memname">const std::vector<<a class="el" href="classOpenMS_1_1ProteinHit.html">ProteinHit</a>>& getHits </td>
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<p>Returns the protein hits. </p>
<p>Referenced by <a class="el" href="classOpenMS_1_1IDFilter.html#adbddef78d7fcfbd5a87e19762fd1cc7b">IDFilter::filterIdentificationsByBestNHits()</a>, <a class="el" href="classOpenMS_1_1IDFilter.html#aeb523c70d4d0f6e8cabd7b8db02cf638">IDFilter::filterIdentificationsByScores()</a>, and <a class="el" href="classOpenMS_1_1IDFilter.html#a5317f48e0a2b44028ade11faa175dc12">IDFilter::filterIdentificationsByThresholds()</a>.</p>
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<p>Returns the protein hits (mutable) </p>
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<p>Returns the identifier. </p>
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<td class="memname">const std::vector<<a class="el" href="structOpenMS_1_1ProteinIdentification_1_1ProteinGroup.html">ProteinGroup</a>>& getIndistinguishableProteins </td>
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<p>Returns the indistinguishable proteins. </p>
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<td class="memname">std::vector<<a class="el" href="structOpenMS_1_1ProteinIdentification_1_1ProteinGroup.html">ProteinGroup</a>>& getIndistinguishableProteins </td>
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<p>Returns the indistinguishable proteins (mutable) </p>
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<td class="memname">const std::vector<<a class="el" href="structOpenMS_1_1ProteinIdentification_1_1ProteinGroup.html">ProteinGroup</a>>& getProteinGroups </td>
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<p>Returns the protein groups. </p>
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<p>Returns the protein groups (mutable) </p>
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<td class="memname">const <a class="el" href="classOpenMS_1_1String.html">String</a>& getScoreType </td>
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<p>Returns the protein score type. </p>
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<p>Returns the type of search engine used. </p>
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<td class="memname">const <a class="el" href="classOpenMS_1_1String.html">String</a>& getSearchEngineVersion </td>
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<p>Returns the search engine version. </p>
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<td class="memname">const <a class="el" href="structOpenMS_1_1ProteinIdentification_1_1SearchParameters.html">SearchParameters</a>& getSearchParameters </td>
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<p>Returns the search parameters. </p>
<p>Referenced by <a class="el" href="classOpenMS_1_1DBAdapter.html#ad1664f90cd894f0713284a213733afb8">DBAdapter::loadExperiment()</a>.</p>
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<td class="memname"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> getSignificanceThreshold </td>
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<p>Returns the protein significance threshold value. </p>
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<td class="memname">void insertHit </td>
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<p>Appends a protein hit. </p>
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<td class="memname">void insertIndistinguishableProteins </td>
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<p>Appends new indistinguishable proteins. </p>
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<td class="memname">void insertProteinGroup </td>
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<p>Appends a new protein group. </p>
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<p>Returns true if a higher score represents a better score. </p>
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<td class="memname">bool operator!= </td>
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<td class="paramname"><em>rhs</em></td><td>)</td>
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<p>Inequality operator. </p>
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<td class="memname"><a class="el" href="classOpenMS_1_1ProteinIdentification.html">ProteinIdentification</a>& operator= </td>
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<p>Assignment operator. </p>
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<td class="paramname"><em>rhs</em></td><td>)</td>
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<p>Equality operator. </p>
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<td class="memname">void setDateTime </td>
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<p>Sets the date of the protein identification run. </p>
<p>Referenced by <a class="el" href="classOpenMS_1_1DBAdapter.html#ad1664f90cd894f0713284a213733afb8">DBAdapter::loadExperiment()</a>.</p>
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<td class="memname">void setHigherScoreBetter </td>
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<p>Sets the orientation of the score (is higher better?) </p>
<p>Referenced by <a class="el" href="classOpenMS_1_1DBAdapter.html#ad1664f90cd894f0713284a213733afb8">DBAdapter::loadExperiment()</a>.</p>
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<td class="memname">void setHits </td>
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<p>Sets the protein hits. </p>
<p>Referenced by <a class="el" href="classOpenMS_1_1DBAdapter.html#ad1664f90cd894f0713284a213733afb8">DBAdapter::loadExperiment()</a>, and <a class="el" href="classOpenMS_1_1MRMFeatureFinderScoring.html#a21e38df433d05118f343c33af60816e9">MRMFeatureFinderScoring::pickExperiment()</a>.</p>
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<td class="memname">void setIdentifier </td>
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<p>Sets the identifier. </p>
<p>Referenced by <a class="el" href="classOpenMS_1_1MRMFeatureFinderScoring.html#a21e38df433d05118f343c33af60816e9">MRMFeatureFinderScoring::pickExperiment()</a>.</p>
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<td class="memname">void setScoreType </td>
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<p>Sets the protein score type. </p>
<p>Referenced by <a class="el" href="classOpenMS_1_1DBAdapter.html#ad1664f90cd894f0713284a213733afb8">DBAdapter::loadExperiment()</a>.</p>
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<td class="memname">void setSearchEngine </td>
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<p>Sets the search engine type. </p>
<p>Referenced by <a class="el" href="classOpenMS_1_1DBAdapter.html#ad1664f90cd894f0713284a213733afb8">DBAdapter::loadExperiment()</a>.</p>
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<td class="memname">void setSearchEngineVersion </td>
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<p>Sets the search engine version. </p>
<p>Referenced by <a class="el" href="classOpenMS_1_1DBAdapter.html#ad1664f90cd894f0713284a213733afb8">DBAdapter::loadExperiment()</a>.</p>
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<td class="memname">void setSearchParameters </td>
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<td class="paramtype">const <a class="el" href="structOpenMS_1_1ProteinIdentification_1_1SearchParameters.html">SearchParameters</a> & </td>
<td class="paramname"><em>search_parameters</em></td><td>)</td>
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<p>Sets the search parameters. </p>
<p>Referenced by <a class="el" href="classOpenMS_1_1DBAdapter.html#ad1664f90cd894f0713284a213733afb8">DBAdapter::loadExperiment()</a>.</p>
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<td class="memname">void setSignificanceThreshold </td>
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<td class="paramtype"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> </td>
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<p>Sets the protein significance threshold value. </p>
<p>Referenced by <a class="el" href="classOpenMS_1_1DBAdapter.html#ad1664f90cd894f0713284a213733afb8">DBAdapter::loadExperiment()</a>.</p>
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<td class="memname">void sort </td>
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<p>Sorts the protein hits according to their score. </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_1DateTime.html">DateTime</a> date_</td>
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<td class="memname"><a class="el" href="classOpenMS_1_1String.html">String</a> id_</td>
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<td class="memname">std::vector<<a class="el" href="structOpenMS_1_1ProteinIdentification_1_1ProteinGroup.html">ProteinGroup</a>> indistinguishable_proteins_</td>
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<p>Indistinguishable proteins: <code>accessions</code>[0] is "group leader", <code>probability</code> is meaningless. </p>
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<td class="memname">const std::string NamesOfDigestionEnzyme[<a class="el" href="classOpenMS_1_1ProteinIdentification.html#ac1976fd756a09ae4e26fe6b32fcb396ca59ffc2972d48cca58d73eb79e40edf9f">SIZE_OF_DIGESTIONENZYME</a>]</td>
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<p>Names corresponding to digestion enzymes. </p>
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<td class="memname">const std::string NamesOfPeakMassType[<a class="el" href="classOpenMS_1_1ProteinIdentification.html#a5431b65220b7ad71b5e8768876ee3e53a2989e7c6c70923c0941b34c64517d012">SIZE_OF_PEAKMASSTYPE</a>]</td>
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<p>Names corresponding to peak mass types. </p>
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<td class="memname">std::vector<<a class="el" href="structOpenMS_1_1ProteinIdentification_1_1ProteinGroup.html">ProteinGroup</a>> protein_groups_</td>
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<td class="memname">std::vector<<a class="el" href="classOpenMS_1_1ProteinHit.html">ProteinHit</a>> protein_hits_</td>
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<td class="memname"><a class="el" href="classOpenMS_1_1String.html">String</a> protein_score_type_</td>
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<td class="memname"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> protein_significance_threshold_</td>
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<td class="memname"><a class="el" href="classOpenMS_1_1String.html">String</a> search_engine_</td>
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<td class="memname"><a class="el" href="classOpenMS_1_1String.html">String</a> search_engine_version_</td>
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<td class="memname"><a class="el" href="structOpenMS_1_1ProteinIdentification_1_1SearchParameters.html">SearchParameters</a> search_parameters_</td>
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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 11:19:33 using doxygen 1.8.5</font></TD>
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