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  • Committer: Package Import Robot
  • Author(s): Filippo Rusconi
  • Date: 2013-12-20 11:30:16 UTC
  • mfrom: (5.1.2 sid)
  • Revision ID: package-import@ubuntu.com-20131220113016-wre5g9bteeheq6he
Tags: 1.11.1-3
* remove version number from libbost development package names;
* ensure that AUTHORS is correctly shipped in all packages.

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doc/html/classOpenMS_1_1MS2File.html
 
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<HTML>
 
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<HEAD>
 
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<TITLE>MS2File Class Reference</TITLE>
 
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<LINK HREF="doxygen.css" REL="stylesheet" TYPE="text/css">
 
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<LINK HREF="style_ini.css" REL="stylesheet" TYPE="text/css">
 
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</HEAD>
 
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<BODY BGCOLOR="#FFFFFF">
 
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<A href="index.html">Home</A> &nbsp;&middot;
 
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<A href="classes.html">Classes</A> &nbsp;&middot;
 
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<A href="annotated.html">Annotated Classes</A> &nbsp;&middot;
 
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<A href="modules.html">Modules</A> &nbsp;&middot;
 
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<A href="functions_func.html">Members</A> &nbsp;&middot;
 
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<A href="namespaces.html">Namespaces</A> &nbsp;&middot;
 
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<A href="pages.html">Related Pages</A>
 
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<HR style="height:1px; border:none; border-top:1px solid #c0c0c0;">
 
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<!-- Generated by Doxygen 1.8.5 -->
 
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<div id="nav-path" class="navpath">
 
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  <ul>
 
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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_1MS2File.html">MS2File</a></li>  </ul>
 
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</div>
 
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</div><!-- top -->
 
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<div class="header">
 
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  <div class="summary">
 
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<a href="#pub-methods">Public Member Functions</a> &#124;
 
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<a href="classOpenMS_1_1MS2File-members.html">List of all members</a>  </div>
 
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  <div class="headertitle">
 
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<div class="title">MS2File Class Reference<div class="ingroups"><a class="el" href="group__FileIO.html">File IO</a></div></div>  </div>
 
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</div><!--header-->
 
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<div class="contents">
 
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<p>MS2 input file adapter.  
 
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 <a href="classOpenMS_1_1MS2File.html#details">More...</a></p>
 
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<p><code>#include &lt;<a class="el" href="MS2File_8h_source.html">OpenMS/FORMAT/MS2File.h</a>&gt;</code></p>
 
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<div class="dynheader">
 
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Inheritance diagram for MS2File:</div>
 
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<div class="dyncontent">
 
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 <div class="center">
 
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  <img src="classOpenMS_1_1MS2File.png" usemap="#MS2File_map" alt=""/>
 
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  <map id="MS2File_map" name="MS2File_map">
 
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<area href="classOpenMS_1_1ProgressLogger.html" title="Base class for all classes that want to report their progess. " alt="ProgressLogger" shape="rect" coords="0,0,103,24"/>
 
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</map>
 
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 </div></div>
 
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<table class="memberdecls">
 
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<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a>
 
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Public Member Functions</h2></td></tr>
 
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<tr class="memitem:a1c2b9bfed175faff9fff1b8f7b847fc4"><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MS2File.html#a1c2b9bfed175faff9fff1b8f7b847fc4">MS2File</a> ()</td></tr>
 
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<tr class="memdesc:a1c2b9bfed175faff9fff1b8f7b847fc4"><td class="mdescLeft">&#160;</td><td class="mdescRight">constructor  <a href="#a1c2b9bfed175faff9fff1b8f7b847fc4">More...</a><br/></td></tr>
 
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<tr class="separator:a1c2b9bfed175faff9fff1b8f7b847fc4"><td class="memSeparator" colspan="2">&#160;</td></tr>
 
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<tr class="memitem:afce38ea59fb9864edc8d0703cbd6a223"><td class="memItemLeft" align="right" valign="top">virtual&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MS2File.html#afce38ea59fb9864edc8d0703cbd6a223">~MS2File</a> ()</td></tr>
 
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<tr class="memdesc:afce38ea59fb9864edc8d0703cbd6a223"><td class="mdescLeft">&#160;</td><td class="mdescRight">constructor  <a href="#afce38ea59fb9864edc8d0703cbd6a223">More...</a><br/></td></tr>
 
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<tr class="separator:afce38ea59fb9864edc8d0703cbd6a223"><td class="memSeparator" colspan="2">&#160;</td></tr>
 
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<tr class="memitem:a98bebe67b8b06a9a67a3654d631355b4"><td class="memTemplParams" colspan="2">template&lt;typename MapType &gt; </td></tr>
 
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<tr class="memitem:a98bebe67b8b06a9a67a3654d631355b4"><td class="memTemplItemLeft" align="right" valign="top">void&#160;</td><td class="memTemplItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MS2File.html#a98bebe67b8b06a9a67a3654d631355b4">load</a> (const <a class="el" href="classOpenMS_1_1String.html">String</a> &amp;filename, MapType &amp;exp)</td></tr>
 
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<tr class="separator:a98bebe67b8b06a9a67a3654d631355b4"><td class="memSeparator" colspan="2">&#160;</td></tr>
 
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<tr class="inherit_header pub_methods_classOpenMS_1_1ProgressLogger"><td colspan="2" onclick="javascript:toggleInherit('pub_methods_classOpenMS_1_1ProgressLogger')"><img src="closed.png" alt="-"/>&#160;Public Member Functions inherited from <a class="el" href="classOpenMS_1_1ProgressLogger.html">ProgressLogger</a></td></tr>
 
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<tr class="memitem:a2a106011aec95b2013d7a545f2063d01 inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProgressLogger.html#a2a106011aec95b2013d7a545f2063d01">ProgressLogger</a> ()</td></tr>
 
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<tr class="memdesc:a2a106011aec95b2013d7a545f2063d01 inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="mdescLeft">&#160;</td><td class="mdescRight">Constructor.  <a href="#a2a106011aec95b2013d7a545f2063d01">More...</a><br/></td></tr>
 
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<tr class="separator:a2a106011aec95b2013d7a545f2063d01 inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="memSeparator" colspan="2">&#160;</td></tr>
 
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<tr class="memitem:a19c882d907f90f7f88c7436d82cd2a13 inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProgressLogger.html#a19c882d907f90f7f88c7436d82cd2a13">~ProgressLogger</a> ()</td></tr>
 
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<tr class="memdesc:a19c882d907f90f7f88c7436d82cd2a13 inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="mdescLeft">&#160;</td><td class="mdescRight">Destructor.  <a href="#a19c882d907f90f7f88c7436d82cd2a13">More...</a><br/></td></tr>
 
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<tr class="separator:a19c882d907f90f7f88c7436d82cd2a13 inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="memSeparator" colspan="2">&#160;</td></tr>
 
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<tr class="memitem:acc3538c5284777d8702ccaefeb61e74c inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProgressLogger.html#acc3538c5284777d8702ccaefeb61e74c">setLogType</a> (<a class="el" href="classOpenMS_1_1ProgressLogger.html#af67907baa897e9fb84df0cb89795b87c">LogType</a> type) const </td></tr>
 
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<tr class="memdesc:acc3538c5284777d8702ccaefeb61e74c inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="mdescLeft">&#160;</td><td class="mdescRight">Sets the progress log that should be used. The default type is NONE!  <a href="#acc3538c5284777d8702ccaefeb61e74c">More...</a><br/></td></tr>
 
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<tr class="separator:acc3538c5284777d8702ccaefeb61e74c inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="memSeparator" colspan="2">&#160;</td></tr>
 
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<tr class="memitem:a67024cdd5c34ec571baecabd8f783310 inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1ProgressLogger.html#af67907baa897e9fb84df0cb89795b87c">LogType</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProgressLogger.html#a67024cdd5c34ec571baecabd8f783310">getLogType</a> () const </td></tr>
 
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<tr class="memdesc:a67024cdd5c34ec571baecabd8f783310 inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="mdescLeft">&#160;</td><td class="mdescRight">Returns the type of progress log being used.  <a href="#a67024cdd5c34ec571baecabd8f783310">More...</a><br/></td></tr>
 
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<tr class="separator:a67024cdd5c34ec571baecabd8f783310 inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="memSeparator" colspan="2">&#160;</td></tr>
 
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<tr class="memitem:af1c45ecd71b5041b70319249e8e73591 inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProgressLogger.html#af1c45ecd71b5041b70319249e8e73591">startProgress</a> (<a class="el" href="group__Concept.html#gae113cb41304c6692c7bf5d0624dc6f0f">SignedSize</a> begin, <a class="el" href="group__Concept.html#gae113cb41304c6692c7bf5d0624dc6f0f">SignedSize</a> end, const <a class="el" href="classOpenMS_1_1String.html">String</a> &amp;label) const </td></tr>
 
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<tr class="memdesc:af1c45ecd71b5041b70319249e8e73591 inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="mdescLeft">&#160;</td><td class="mdescRight">Initializes the progress display.  <a href="#af1c45ecd71b5041b70319249e8e73591">More...</a><br/></td></tr>
 
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<tr class="separator:af1c45ecd71b5041b70319249e8e73591 inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="memSeparator" colspan="2">&#160;</td></tr>
 
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<tr class="memitem:a8852277abd03220cc7b80d6c1bed6fed inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProgressLogger.html#a8852277abd03220cc7b80d6c1bed6fed">setProgress</a> (<a class="el" href="group__Concept.html#gae113cb41304c6692c7bf5d0624dc6f0f">SignedSize</a> value) const </td></tr>
 
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<tr class="memdesc:a8852277abd03220cc7b80d6c1bed6fed inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="mdescLeft">&#160;</td><td class="mdescRight">Sets the current progress.  <a href="#a8852277abd03220cc7b80d6c1bed6fed">More...</a><br/></td></tr>
 
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<tr class="separator:a8852277abd03220cc7b80d6c1bed6fed inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="memSeparator" colspan="2">&#160;</td></tr>
 
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<tr class="memitem:a1cc1012b0cdaea97f58d571af1ff45de inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProgressLogger.html#a1cc1012b0cdaea97f58d571af1ff45de">endProgress</a> () const </td></tr>
 
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<tr class="memdesc:a1cc1012b0cdaea97f58d571af1ff45de inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="mdescLeft">&#160;</td><td class="mdescRight">Ends the progress display.  <a href="#a1cc1012b0cdaea97f58d571af1ff45de">More...</a><br/></td></tr>
 
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<tr class="separator:a1cc1012b0cdaea97f58d571af1ff45de inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="memSeparator" colspan="2">&#160;</td></tr>
 
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</table><table class="memberdecls">
 
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<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="inherited"></a>
 
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Additional Inherited Members</h2></td></tr>
 
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<tr class="inherit_header pub_types_classOpenMS_1_1ProgressLogger"><td colspan="2" onclick="javascript:toggleInherit('pub_types_classOpenMS_1_1ProgressLogger')"><img src="closed.png" alt="-"/>&#160;Public Types inherited from <a class="el" href="classOpenMS_1_1ProgressLogger.html">ProgressLogger</a></td></tr>
 
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<tr class="memitem:af67907baa897e9fb84df0cb89795b87c inherit pub_types_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top">enum &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProgressLogger.html#af67907baa897e9fb84df0cb89795b87c">LogType</a> { <a class="el" href="classOpenMS_1_1ProgressLogger.html#af67907baa897e9fb84df0cb89795b87ca3ab34dd50405af2d5a62627d572f7860">CMD</a>, 
 
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<a class="el" href="classOpenMS_1_1ProgressLogger.html#af67907baa897e9fb84df0cb89795b87ca73c6901c7c648a6a735770bc038bb26a">GUI</a>, 
 
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<a class="el" href="classOpenMS_1_1ProgressLogger.html#af67907baa897e9fb84df0cb89795b87cac157bdf0b85a40d2619cbc8bc1ae5fe2">NONE</a>
 
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 }</td></tr>
 
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<tr class="memdesc:af67907baa897e9fb84df0cb89795b87c"><td class="mdescLeft">&#160;</td><td class="mdescRight">Possible log types.  <a href="classOpenMS_1_1ProgressLogger.html#af67907baa897e9fb84df0cb89795b87c">More...</a><br/></td></tr>
 
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<tr class="separator:af67907baa897e9fb84df0cb89795b87c inherit pub_types_classOpenMS_1_1ProgressLogger"><td class="memSeparator" colspan="2">&#160;</td></tr>
 
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<tr class="inherit_header pro_attribs_classOpenMS_1_1ProgressLogger"><td colspan="2" onclick="javascript:toggleInherit('pro_attribs_classOpenMS_1_1ProgressLogger')"><img src="closed.png" alt="-"/>&#160;Protected Attributes inherited from <a class="el" href="classOpenMS_1_1ProgressLogger.html">ProgressLogger</a></td></tr>
 
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<tr class="memitem:a7c691d7de2a43bc5606e96cb15da3641 inherit pro_attribs_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1ProgressLogger.html#af67907baa897e9fb84df0cb89795b87c">LogType</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProgressLogger.html#a7c691d7de2a43bc5606e96cb15da3641">type_</a></td></tr>
 
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<tr class="separator:a7c691d7de2a43bc5606e96cb15da3641 inherit pro_attribs_classOpenMS_1_1ProgressLogger"><td class="memSeparator" colspan="2">&#160;</td></tr>
 
91
<tr class="memitem:a56589612e0e4164bf80c3918a087d05a inherit pro_attribs_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__Concept.html#gae113cb41304c6692c7bf5d0624dc6f0f">SignedSize</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProgressLogger.html#a56589612e0e4164bf80c3918a087d05a">begin_</a></td></tr>
 
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<tr class="separator:a56589612e0e4164bf80c3918a087d05a inherit pro_attribs_classOpenMS_1_1ProgressLogger"><td class="memSeparator" colspan="2">&#160;</td></tr>
 
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<tr class="memitem:a0c749bf4e621699b7a5c45ae22c2fa90 inherit pro_attribs_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__Concept.html#gae113cb41304c6692c7bf5d0624dc6f0f">SignedSize</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProgressLogger.html#a0c749bf4e621699b7a5c45ae22c2fa90">end_</a></td></tr>
 
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<tr class="separator:a0c749bf4e621699b7a5c45ae22c2fa90 inherit pro_attribs_classOpenMS_1_1ProgressLogger"><td class="memSeparator" colspan="2">&#160;</td></tr>
 
95
<tr class="memitem:aec57b26e143202dc119a41592e075932 inherit pro_attribs_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__Concept.html#gae113cb41304c6692c7bf5d0624dc6f0f">SignedSize</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProgressLogger.html#aec57b26e143202dc119a41592e075932">value_</a></td></tr>
 
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<tr class="separator:aec57b26e143202dc119a41592e075932 inherit pro_attribs_classOpenMS_1_1ProgressLogger"><td class="memSeparator" colspan="2">&#160;</td></tr>
 
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<tr class="memitem:a76072b3919abcf01141ba68da8a001fd inherit pro_attribs_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top">QProgressDialog *&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProgressLogger.html#a76072b3919abcf01141ba68da8a001fd">dlg_</a></td></tr>
 
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<tr class="separator:a76072b3919abcf01141ba68da8a001fd inherit pro_attribs_classOpenMS_1_1ProgressLogger"><td class="memSeparator" colspan="2">&#160;</td></tr>
 
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<tr class="memitem:a6d9750520313ea7f843d7a49cb2e9e5f inherit pro_attribs_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1StopWatch.html">StopWatch</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProgressLogger.html#a6d9750520313ea7f843d7a49cb2e9e5f">stop_watch_</a></td></tr>
 
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<tr class="separator:a6d9750520313ea7f843d7a49cb2e9e5f inherit pro_attribs_classOpenMS_1_1ProgressLogger"><td class="memSeparator" colspan="2">&#160;</td></tr>
 
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<tr class="memitem:a79bacf60c4109d7517590441c7f85f9c inherit pro_attribs_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top">time_t&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProgressLogger.html#a79bacf60c4109d7517590441c7f85f9c">last_invoke_</a></td></tr>
 
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<tr class="separator:a79bacf60c4109d7517590441c7f85f9c inherit pro_attribs_classOpenMS_1_1ProgressLogger"><td class="memSeparator" colspan="2">&#160;</td></tr>
 
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<tr class="inherit_header pro_static_attribs_classOpenMS_1_1ProgressLogger"><td colspan="2" onclick="javascript:toggleInherit('pro_static_attribs_classOpenMS_1_1ProgressLogger')"><img src="closed.png" alt="-"/>&#160;Static Protected Attributes inherited from <a class="el" href="classOpenMS_1_1ProgressLogger.html">ProgressLogger</a></td></tr>
 
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<tr class="memitem:a94eb3ef5ef94b83eb348dd00a2b53119 inherit pro_static_attribs_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top">static int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProgressLogger.html#a94eb3ef5ef94b83eb348dd00a2b53119">recursion_depth_</a></td></tr>
 
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<tr class="separator:a94eb3ef5ef94b83eb348dd00a2b53119 inherit pro_static_attribs_classOpenMS_1_1ProgressLogger"><td class="memSeparator" colspan="2">&#160;</td></tr>
 
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</table>
 
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<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
 
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<div class="textblock"><p>MS2 input file adapter. </p>
 
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<p>For the format description take a look at: Rapid Commun Mass Spectrom. 2004;18(18):2162-8.</p>
 
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<p>MS1, MS2, and SQT-three unified, compact, and easily parsed file formats for the storage of shotgun proteomic spectra and identifications.</p>
 
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<p>McDonald WH, Tabb DL, Sadygov RG, MacCoss MJ, Venable J, Graumann J, Johnson JR, Cociorva D, Yates JR 3rd.</p>
 
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<p>PMID: 15317041 </p>
 
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</div><h2 class="groupheader">Constructor &amp; Destructor Documentation</h2>
 
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          <td class="memname"><a class="el" href="classOpenMS_1_1MS2File.html">MS2File</a> </td>
 
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          <td>(</td>
 
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<p>constructor </p>
 
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          <td class="memname">virtual ~<a class="el" href="classOpenMS_1_1MS2File.html">MS2File</a> </td>
 
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<p>constructor </p>
 
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<h2 class="groupheader">Member Function Documentation</h2>
 
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          <td class="memname">void load </td>
 
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          <td class="paramtype">const <a class="el" href="classOpenMS_1_1String.html">String</a> &amp;&#160;</td>
 
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          <td class="paramname"><em>filename</em>, </td>
 
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          <td class="paramname"><em>exp</em>&#160;</td>
 
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          <td>)</td>
 
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<p>References <a class="el" href="classOpenMS_1_1File.html#a103bc592f26fed81f56f2f92b7ab5063">File::exists()</a>, <a class="el" href="classOpenMS_1_1File.html#abd34aea245381ce44044c36ce1895470">File::readable()</a>, <a class="el" href="classOpenMS_1_1String.html#a23eb8a9a84f24127e87e0fb41076254c">String::simplify()</a>, <a class="el" href="classOpenMS_1_1String.html#ae580d960e12c7f0ebc5c95931cf39ad5">String::split()</a>, and <a class="el" href="classOpenMS_1_1String.html#a86864c88ee12eb322f1645f238c1dbe5">String::trim()</a>.</p>
 
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<p>Referenced by <a class="el" href="classOpenMS_1_1FileHandler.html#a408091416e0e1f6019abd59bdb6a9269">FileHandler::loadExperiment()</a>.</p>
 
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<TD><font color="#c0c0c0">OpenMS / TOPP release 1.11.1</font></TD>
 
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<TD align="right"><font color="#c0c0c0">Documentation generated on Thu Nov 14 2013 11:19:31 using doxygen 1.8.5</font></TD>
 
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