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<HTML>
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<TITLE>BigString 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_1BigString.html">BigString</a></li> </ul>
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<a href="#pub-types">Public Types</a> |
<a href="#pub-methods">Public Member Functions</a> |
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<div class="title">BigString Class Reference</div> </div>
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<p>concatenates Proteins given as FASTAEntry to one big string separated by a unique character (by default $)
<a href="classOpenMS_1_1BigString.html#details">More...</a></p>
<p><code>#include <<a class="el" href="BigString_8h_source.html">OpenMS/DATASTRUCTURES/BigString.h</a>></code></p>
<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:a21b87598c52cebe4ab2ebc0bb1655e89"><td class="memItemLeft" align="right" valign="top">typedef std::pair< <a class="el" href="classOpenMS_1_1String.html">String</a>, <a class="el" href="classOpenMS_1_1String.html">String</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1BigString.html#a21b87598c52cebe4ab2ebc0bb1655e89">FASTAEntry</a></td></tr>
<tr class="separator:a21b87598c52cebe4ab2ebc0bb1655e89"><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 class="memitem:a90091edb5109cfc1629b95ac8fbf5d26"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1BigString.html#a90091edb5109cfc1629b95ac8fbf5d26">BigString</a> ()</td></tr>
<tr class="memdesc:a90091edb5109cfc1629b95ac8fbf5d26"><td class="mdescLeft"> </td><td class="mdescRight">constructor <a href="#a90091edb5109cfc1629b95ac8fbf5d26">More...</a><br/></td></tr>
<tr class="separator:a90091edb5109cfc1629b95ac8fbf5d26"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:aa472367803bdae6faadef5c5004e8630"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1BigString.html#aa472367803bdae6faadef5c5004e8630">BigString</a> (const <a class="el" href="classOpenMS_1_1BigString.html">BigString</a> &bs)</td></tr>
<tr class="memdesc:aa472367803bdae6faadef5c5004e8630"><td class="mdescLeft"> </td><td class="mdescRight">copy constructor <a href="#aa472367803bdae6faadef5c5004e8630">More...</a><br/></td></tr>
<tr class="separator:aa472367803bdae6faadef5c5004e8630"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a6d70cc4299fdd490b4c5586a97e0a330"><td class="memItemLeft" align="right" valign="top">virtual </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1BigString.html#a6d70cc4299fdd490b4c5586a97e0a330">~BigString</a> ()</td></tr>
<tr class="memdesc:a6d70cc4299fdd490b4c5586a97e0a330"><td class="mdescLeft"> </td><td class="mdescRight">desctructor <a href="#a6d70cc4299fdd490b4c5586a97e0a330">More...</a><br/></td></tr>
<tr class="separator:a6d70cc4299fdd490b4c5586a97e0a330"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a0018fbf09ab94596b2a0dac01709102f"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1BigString.html#a0018fbf09ab94596b2a0dac01709102f">add</a> (<a class="el" href="classOpenMS_1_1BigString.html#a21b87598c52cebe4ab2ebc0bb1655e89">FASTAEntry</a> const &new_entry)</td></tr>
<tr class="memdesc:a0018fbf09ab94596b2a0dac01709102f"><td class="mdescLeft"> </td><td class="mdescRight">add new string to bigString <a href="#a0018fbf09ab94596b2a0dac01709102f">More...</a><br/></td></tr>
<tr class="separator:a0018fbf09ab94596b2a0dac01709102f"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a182ba12137dcc8b4b249d7b6abda433d"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1BigString.html#a182ba12137dcc8b4b249d7b6abda433d">setSeparator</a> (const char sep)</td></tr>
<tr class="memdesc:a182ba12137dcc8b4b249d7b6abda433d"><td class="mdescLeft"> </td><td class="mdescRight">setter for separator character by default $ <a href="#a182ba12137dcc8b4b249d7b6abda433d">More...</a><br/></td></tr>
<tr class="separator:a182ba12137dcc8b4b249d7b6abda433d"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ae7b0bd97cdb5896fd2731f2d856f525a"><td class="memItemLeft" align="right" valign="top">char </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1BigString.html#ae7b0bd97cdb5896fd2731f2d856f525a">getSeparator</a> ()</td></tr>
<tr class="memdesc:ae7b0bd97cdb5896fd2731f2d856f525a"><td class="mdescLeft"> </td><td class="mdescRight">getter for separator character <a href="#ae7b0bd97cdb5896fd2731f2d856f525a">More...</a><br/></td></tr>
<tr class="separator:ae7b0bd97cdb5896fd2731f2d856f525a"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a9a4c32403766cd16ca4e3a5479f075bd"><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_1BigString.html#a9a4c32403766cd16ca4e3a5479f075bd">size</a> ()</td></tr>
<tr class="memdesc:a9a4c32403766cd16ca4e3a5479f075bd"><td class="mdescLeft"> </td><td class="mdescRight">returns the number of strings <a href="#a9a4c32403766cd16ca4e3a5479f075bd">More...</a><br/></td></tr>
<tr class="separator:a9a4c32403766cd16ca4e3a5479f075bd"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:aaaf1aca45bfc66af6bc0a5673108d38a"><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_1BigString.html#aaaf1aca45bfc66af6bc0a5673108d38a">length</a> ()</td></tr>
<tr class="memdesc:aaaf1aca45bfc66af6bc0a5673108d38a"><td class="mdescLeft"> </td><td class="mdescRight">length of bigString <a href="#aaaf1aca45bfc66af6bc0a5673108d38a">More...</a><br/></td></tr>
<tr class="separator:aaaf1aca45bfc66af6bc0a5673108d38a"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a7c981a0ec604e11d0f0dd97bdeb56b01"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1BigString.html#a7c981a0ec604e11d0f0dd97bdeb56b01">getPeptide</a> (<a class="el" href="classOpenMS_1_1BigString.html#a21b87598c52cebe4ab2ebc0bb1655e89">FASTAEntry</a> &entry, <a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> start, <a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> <a class="el" href="classOpenMS_1_1BigString.html#aaaf1aca45bfc66af6bc0a5673108d38a">length</a>)</td></tr>
<tr class="memdesc:a7c981a0ec604e11d0f0dd97bdeb56b01"><td class="mdescLeft"> </td><td class="mdescRight">getPeptide from start position with given length this includes FASTAHeader <a href="#a7c981a0ec604e11d0f0dd97bdeb56b01">More...</a><br/></td></tr>
<tr class="separator:a7c981a0ec604e11d0f0dd97bdeb56b01"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a124636f680cd9fc2b1b42d4372fca1b8"><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_1BigString.html#a124636f680cd9fc2b1b42d4372fca1b8">getBigString</a> () const </td></tr>
<tr class="memdesc:a124636f680cd9fc2b1b42d4372fca1b8"><td class="mdescLeft"> </td><td class="mdescRight">returns bigString <a href="#a124636f680cd9fc2b1b42d4372fca1b8">More...</a><br/></td></tr>
<tr class="separator:a124636f680cd9fc2b1b42d4372fca1b8"><td class="memSeparator" colspan="2"> </td></tr>
</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pro-methods"></a>
Protected Member Functions</h2></td></tr>
<tr class="memitem:abdd570405d1825af242caa8c0c859cda"><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_1BigString.html#abdd570405d1825af242caa8c0c859cda">getIndex_</a> (<a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> index, <a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> start, <a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> end)</td></tr>
<tr class="memdesc:abdd570405d1825af242caa8c0c859cda"><td class="mdescLeft"> </td><td class="mdescRight">private function to implement binary search <a href="#abdd570405d1825af242caa8c0c859cda">More...</a><br/></td></tr>
<tr class="separator:abdd570405d1825af242caa8c0c859cda"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a8a53ba506ac69731eb94aab9658668c9"><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_1BigString.html#a8a53ba506ac69731eb94aab9658668c9">getIndex_</a> (<a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> index)</td></tr>
<tr class="memdesc:a8a53ba506ac69731eb94aab9658668c9"><td class="mdescLeft"> </td><td class="mdescRight">retrieves index of inserted protein by bigStringPosition <a href="#a8a53ba506ac69731eb94aab9658668c9">More...</a><br/></td></tr>
<tr class="separator:a8a53ba506ac69731eb94aab9658668c9"><td class="memSeparator" colspan="2"> </td></tr>
</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pro-attribs"></a>
Protected Attributes</h2></td></tr>
<tr class="memitem:a8a65075c9d200cc5027f0e9cbe040c5d"><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_1BigString.html#a8a65075c9d200cc5027f0e9cbe040c5d">big_string_</a></td></tr>
<tr class="memdesc:a8a65075c9d200cc5027f0e9cbe040c5d"><td class="mdescLeft"> </td><td class="mdescRight">concatenated <a class="el" href="classOpenMS_1_1String.html" title="A more convenient string class. ">String</a> <a href="#a8a65075c9d200cc5027f0e9cbe040c5d">More...</a><br/></td></tr>
<tr class="separator:a8a65075c9d200cc5027f0e9cbe040c5d"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a650afe260de7540becd03fd198dd1a59"><td class="memItemLeft" align="right" valign="top">char </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1BigString.html#a650afe260de7540becd03fd198dd1a59">separator_</a></td></tr>
<tr class="memdesc:a650afe260de7540becd03fd198dd1a59"><td class="mdescLeft"> </td><td class="mdescRight">separator sign <a href="#a650afe260de7540becd03fd198dd1a59">More...</a><br/></td></tr>
<tr class="separator:a650afe260de7540becd03fd198dd1a59"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:aeb9e2c7a944dffe88a8ea94209ae917b"><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_1BigString.html#aeb9e2c7a944dffe88a8ea94209ae917b">count_</a></td></tr>
<tr class="memdesc:aeb9e2c7a944dffe88a8ea94209ae917b"><td class="mdescLeft"> </td><td class="mdescRight">number of Strings added to big_string <a href="#aeb9e2c7a944dffe88a8ea94209ae917b">More...</a><br/></td></tr>
<tr class="separator:aeb9e2c7a944dffe88a8ea94209ae917b"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a5509b33ed5551a07f18978662c83be95"><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_1BigString.html#a5509b33ed5551a07f18978662c83be95">len_</a></td></tr>
<tr class="memdesc:a5509b33ed5551a07f18978662c83be95"><td class="mdescLeft"> </td><td class="mdescRight">length of the big_string <a href="#a5509b33ed5551a07f18978662c83be95">More...</a><br/></td></tr>
<tr class="separator:a5509b33ed5551a07f18978662c83be95"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a38d9a314ab260c979f84008adb21e988"><td class="memItemLeft" align="right" valign="top">std::vector< <a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1BigString.html#a38d9a314ab260c979f84008adb21e988">sep_indices_</a></td></tr>
<tr class="memdesc:a38d9a314ab260c979f84008adb21e988"><td class="mdescLeft"> </td><td class="mdescRight">indices of separators <a href="#a38d9a314ab260c979f84008adb21e988">More...</a><br/></td></tr>
<tr class="separator:a38d9a314ab260c979f84008adb21e988"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:aa213011c3043f6dc5f5431374702f417"><td class="memItemLeft" align="right" valign="top">std::vector< <a class="el" href="classOpenMS_1_1String.html">String</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1BigString.html#aa213011c3043f6dc5f5431374702f417">FASTA_header_</a></td></tr>
<tr class="memdesc:aa213011c3043f6dc5f5431374702f417"><td class="mdescLeft"> </td><td class="mdescRight">vector with headers of FASTAEntry <a href="#aa213011c3043f6dc5f5431374702f417">More...</a><br/></td></tr>
<tr class="separator:aa213011c3043f6dc5f5431374702f417"><td class="memSeparator" colspan="2"> </td></tr>
</table>
<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
<div class="textblock"><p>concatenates Proteins given as FASTAEntry to one big string separated by a unique character (by default $) </p>
<p>Concatenates the strings given as FASTAEntry separating them with a unique character and storing the headers of FASTAEntry as well as the position of separator characters. So a substring can be accessed easily and the corresponding header can be found fast by using bineary search. </p>
</div><h2 class="groupheader">Member Typedef Documentation</h2>
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<td class="memname">typedef std::pair<<a class="el" href="classOpenMS_1_1String.html">String</a>, <a class="el" href="classOpenMS_1_1String.html">String</a>> <a class="el" href="classOpenMS_1_1BigString.html#a21b87598c52cebe4ab2ebc0bb1655e89">FASTAEntry</a></td>
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<h2 class="groupheader">Constructor & Destructor Documentation</h2>
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<td class="memname"><a class="el" href="classOpenMS_1_1BigString.html">BigString</a> </td>
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<p>constructor </p>
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<td class="memname"><a class="el" href="classOpenMS_1_1BigString.html">BigString</a> </td>
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<td class="paramtype">const <a class="el" href="classOpenMS_1_1BigString.html">BigString</a> & </td>
<td class="paramname"><em>bs</em></td><td>)</td>
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<p>copy constructor </p>
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<td class="memname">virtual ~<a class="el" href="classOpenMS_1_1BigString.html">BigString</a> </td>
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<p>desctructor </p>
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<h2 class="groupheader">Member Function Documentation</h2>
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<td class="memname">void add </td>
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<p>add new string to bigString </p>
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<tr><td class="paramname">new_entry</td><td>FASTAEntry to be added to big_string </td></tr>
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<td class="memname">const <a class="el" href="classOpenMS_1_1String.html">String</a>& getBigString </td>
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<p>returns bigString </p>
<dl class="section return"><dt>Returns</dt><dd>const reference to bigString </dd></dl>
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<td class="memname"><a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> getIndex_ </td>
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<p>private function to implement binary search </p>
<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramname">index</td><td></td></tr>
<tr><td class="paramname">start</td><td>start index </td></tr>
<tr><td class="paramname">end</td><td>end inxed </td></tr>
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<dl class="section return"><dt>Returns</dt><dd>int with index </dd></dl>
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<td class="memname"><a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> getIndex_ </td>
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<p>retrieves index of inserted protein by bigStringPosition </p>
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<dl class="section return"><dt>Returns</dt><dd>int with index </dd></dl>
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<td class="memname">void getPeptide </td>
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<td class="paramname"><em>entry</em>, </td>
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<p>getPeptide from start position with given length this includes FASTAHeader </p>
<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramname">entry</td><td>contains the entry of the given range after calling </td></tr>
<tr><td class="paramname">start</td><td>start index </td></tr>
<tr><td class="paramname">length</td><td>length of desired substring </td></tr>
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<dl class="section return"><dt>Returns</dt><dd>FASTAEntry describing the protein </dd></dl>
<dl class="exception"><dt>Exceptions</dt><dd>
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<tr><td class="paramname">InvalidValue</td><td>if a peptide is part of two different fasta entrys </td></tr>
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<td class="memname">char getSeparator </td>
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<p>getter for separator character </p>
<dl class="section return"><dt>Returns</dt><dd>separator character </dd></dl>
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<td class="memname"><a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> length </td>
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<p>length of bigString </p>
<dl class="section return"><dt>Returns</dt><dd>int with length of the created bigString </dd></dl>
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<td class="memname">void setSeparator </td>
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<p>setter for separator character by default $ </p>
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<tr><td class="paramname">sep</td><td>separator character </td></tr>
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<td class="memname"><a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> size </td>
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<p>returns the number of strings </p>
<dl class="section return"><dt>Returns</dt><dd>int with number of strings </dd></dl>
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<h2 class="groupheader">Member Data Documentation</h2>
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<td class="memname"><a class="el" href="classOpenMS_1_1String.html">String</a> big_string_</td>
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<p>concatenated <a class="el" href="classOpenMS_1_1String.html" title="A more convenient string class. ">String</a> </p>
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<td class="memname"><a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> count_</td>
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<p>number of Strings added to big_string </p>
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<td class="memname">std::vector<<a class="el" href="classOpenMS_1_1String.html">String</a>> FASTA_header_</td>
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<p>vector with headers of FASTAEntry </p>
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<td class="memname"><a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> len_</td>
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<p>length of the big_string </p>
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<td class="memname">std::vector<<a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a>> sep_indices_</td>
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<p>indices of separators </p>
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<td class="memname">char separator_</td>
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<p>separator sign </p>
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<TD><font color="#c0c0c0">OpenMS / TOPP release 1.11.1</font></TD>
<TD align="right"><font color="#c0c0c0">Documentation generated on Thu Nov 14 2013 11:19:28 using doxygen 1.8.5</font></TD>
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