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<TITLE>SuffixArrayTrypticSeqan 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_1SuffixArrayTrypticSeqan.html">SuffixArrayTrypticSeqan</a></li> </ul>
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<a href="#pub-methods">Public Member Functions</a> |
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<a href="classOpenMS_1_1SuffixArrayTrypticSeqan-members.html">List of all members</a> </div>
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<div class="title">SuffixArrayTrypticSeqan Class Reference</div> </div>
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<p>Class that uses SEQAN library for a suffix array. It can be used to find peptide Candidates for a MS spectrum.
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<a href="classOpenMS_1_1SuffixArrayTrypticSeqan.html#details">More...</a></p>
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<p><code>#include <<a class="el" href="SuffixArrayTrypticSeqan_8h_source.html">OpenMS/DATASTRUCTURES/SuffixArrayTrypticSeqan.h</a>></code></p>
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<div class="dynheader">
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Inheritance diagram for SuffixArrayTrypticSeqan:</div>
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<div class="dyncontent">
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<img src="classOpenMS_1_1SuffixArrayTrypticSeqan.png" usemap="#SuffixArrayTrypticSeqan_map" alt=""/>
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<map id="SuffixArrayTrypticSeqan_map" name="SuffixArrayTrypticSeqan_map">
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<area href="classOpenMS_1_1SuffixArraySeqan.html" title="Class that uses SEQAN library for a suffix array. It can be used to find peptide Candidates for a MS ..." alt="SuffixArraySeqan" shape="rect" coords="80,56,231,80"/>
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<area href="classOpenMS_1_1SuffixArray.html" title="abstract class for suffix array " alt="SuffixArray" shape="rect" coords="0,0,151,24"/>
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<area href="classOpenMS_1_1WeightWrapper.html" title="Encapsulated weight queries to simplify mono vs average weight computation. " alt="WeightWrapper" shape="rect" coords="161,0,312,24"/>
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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:a10119b1df48bec175a8f4811b02bed25"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SuffixArrayTrypticSeqan.html#a10119b1df48bec175a8f4811b02bed25">SuffixArrayTrypticSeqan</a> (const <a class="el" href="classOpenMS_1_1String.html">String</a> &st, const <a class="el" href="classOpenMS_1_1String.html">String</a> &filename, const <a class="el" href="classOpenMS_1_1WeightWrapper.html#aa0e0675e46f34052468f523f1c8aff2b">WeightWrapper::WEIGHTMODE</a> weight_mode=<a class="el" href="classOpenMS_1_1WeightWrapper.html#aa0e0675e46f34052468f523f1c8aff2ba3828195437a1112429b5c7a3e8780570">WeightWrapper::MONO</a>)</td></tr>
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<tr class="memdesc:a10119b1df48bec175a8f4811b02bed25"><td class="mdescLeft"> </td><td class="mdescRight">constructor for tryptic seqan array with a specially optimized implementation <a href="#a10119b1df48bec175a8f4811b02bed25">More...</a><br/></td></tr>
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<tr class="separator:a10119b1df48bec175a8f4811b02bed25"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a9eedb3b9aa20ef87f387b54c9e7813d7"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SuffixArrayTrypticSeqan.html#a9eedb3b9aa20ef87f387b54c9e7813d7">isDigestingEnd</a> (const char aa1, const char aa2) const </td></tr>
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<tr class="memdesc:a9eedb3b9aa20ef87f387b54c9e7813d7"><td class="mdescLeft"> </td><td class="mdescRight">returns if an enzyme will cut after first character <a href="#a9eedb3b9aa20ef87f387b54c9e7813d7">More...</a><br/></td></tr>
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<tr class="separator:a9eedb3b9aa20ef87f387b54c9e7813d7"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="inherit_header pub_methods_classOpenMS_1_1SuffixArraySeqan"><td colspan="2" onclick="javascript:toggleInherit('pub_methods_classOpenMS_1_1SuffixArraySeqan')"><img src="closed.png" alt="-"/> Public Member Functions inherited from <a class="el" href="classOpenMS_1_1SuffixArraySeqan.html">SuffixArraySeqan</a></td></tr>
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<tr class="memitem:a35a04b37e5b3a31a6bd2eab2596403c2 inherit pub_methods_classOpenMS_1_1SuffixArraySeqan"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SuffixArraySeqan.html#a35a04b37e5b3a31a6bd2eab2596403c2">SuffixArraySeqan</a> (const <a class="el" href="classOpenMS_1_1String.html">String</a> &st, const <a class="el" href="classOpenMS_1_1String.html">String</a> &filename, const <a class="el" href="classOpenMS_1_1WeightWrapper.html#aa0e0675e46f34052468f523f1c8aff2b">WeightWrapper::WEIGHTMODE</a> weight_mode=<a class="el" href="classOpenMS_1_1WeightWrapper.html#aa0e0675e46f34052468f523f1c8aff2ba3828195437a1112429b5c7a3e8780570">WeightWrapper::MONO</a>)</td></tr>
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<tr class="memdesc:a35a04b37e5b3a31a6bd2eab2596403c2 inherit pub_methods_classOpenMS_1_1SuffixArraySeqan"><td class="mdescLeft"> </td><td class="mdescRight">constructor <a href="#a35a04b37e5b3a31a6bd2eab2596403c2">More...</a><br/></td></tr>
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<tr class="separator:a35a04b37e5b3a31a6bd2eab2596403c2 inherit pub_methods_classOpenMS_1_1SuffixArraySeqan"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a26dc50bfb537bb5cc0082a1481f54ff3 inherit pub_methods_classOpenMS_1_1SuffixArraySeqan"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SuffixArraySeqan.html#a26dc50bfb537bb5cc0082a1481f54ff3">SuffixArraySeqan</a> (const <a class="el" href="classOpenMS_1_1SuffixArraySeqan.html">SuffixArraySeqan</a> &source)</td></tr>
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<tr class="memdesc:a26dc50bfb537bb5cc0082a1481f54ff3 inherit pub_methods_classOpenMS_1_1SuffixArraySeqan"><td class="mdescLeft"> </td><td class="mdescRight">copy constructor <a href="#a26dc50bfb537bb5cc0082a1481f54ff3">More...</a><br/></td></tr>
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<tr class="separator:a26dc50bfb537bb5cc0082a1481f54ff3 inherit pub_methods_classOpenMS_1_1SuffixArraySeqan"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a4b0a33b865746aaefac892cf22de5832 inherit pub_methods_classOpenMS_1_1SuffixArraySeqan"><td class="memItemLeft" align="right" valign="top">virtual </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SuffixArraySeqan.html#a4b0a33b865746aaefac892cf22de5832">~SuffixArraySeqan</a> ()</td></tr>
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<tr class="memdesc:a4b0a33b865746aaefac892cf22de5832 inherit pub_methods_classOpenMS_1_1SuffixArraySeqan"><td class="mdescLeft"> </td><td class="mdescRight">destructor <a href="#a4b0a33b865746aaefac892cf22de5832">More...</a><br/></td></tr>
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<tr class="separator:a4b0a33b865746aaefac892cf22de5832 inherit pub_methods_classOpenMS_1_1SuffixArraySeqan"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:ad146fa8579a5f8a876c4688cc5a68520 inherit pub_methods_classOpenMS_1_1SuffixArraySeqan"><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_1SuffixArraySeqan.html#ad146fa8579a5f8a876c4688cc5a68520">toString</a> ()</td></tr>
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<tr class="memdesc:ad146fa8579a5f8a876c4688cc5a68520 inherit pub_methods_classOpenMS_1_1SuffixArraySeqan"><td class="mdescLeft"> </td><td class="mdescRight">converts suffix array to a printable string <a href="#ad146fa8579a5f8a876c4688cc5a68520">More...</a><br/></td></tr>
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<tr class="separator:ad146fa8579a5f8a876c4688cc5a68520 inherit pub_methods_classOpenMS_1_1SuffixArraySeqan"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:aa78cc1ec6532c467e25f892d1a649e1d inherit pub_methods_classOpenMS_1_1SuffixArraySeqan"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SuffixArraySeqan.html#aa78cc1ec6532c467e25f892d1a649e1d">findSpec</a> (std::vector< std::vector< std::pair< std::pair< <a class="el" href="group__Concept.html#gae113cb41304c6692c7bf5d0624dc6f0f">SignedSize</a>, <a class="el" href="group__Concept.html#gae113cb41304c6692c7bf5d0624dc6f0f">SignedSize</a> >, <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> > > > &candidates, const std::vector< <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> > &spec)</td></tr>
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<tr class="memdesc:aa78cc1ec6532c467e25f892d1a649e1d inherit pub_methods_classOpenMS_1_1SuffixArraySeqan"><td class="mdescLeft"> </td><td class="mdescRight">the function that will find all peptide candidates for a given spectrum <a href="#aa78cc1ec6532c467e25f892d1a649e1d">More...</a><br/></td></tr>
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<tr class="separator:aa78cc1ec6532c467e25f892d1a649e1d inherit pub_methods_classOpenMS_1_1SuffixArraySeqan"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:af055ab1935e7aa87eb45534e2d26115c inherit pub_methods_classOpenMS_1_1SuffixArraySeqan"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SuffixArraySeqan.html#af055ab1935e7aa87eb45534e2d26115c">save</a> (const <a class="el" href="classOpenMS_1_1String.html">String</a> &filename)</td></tr>
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<tr class="memdesc:af055ab1935e7aa87eb45534e2d26115c inherit pub_methods_classOpenMS_1_1SuffixArraySeqan"><td class="mdescLeft"> </td><td class="mdescRight">saves the suffix array to disc <a href="#af055ab1935e7aa87eb45534e2d26115c">More...</a><br/></td></tr>
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<tr class="separator:af055ab1935e7aa87eb45534e2d26115c inherit pub_methods_classOpenMS_1_1SuffixArraySeqan"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a439f6d35e3fe7db057e9bf13f42a2485 inherit pub_methods_classOpenMS_1_1SuffixArraySeqan"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SuffixArraySeqan.html#a439f6d35e3fe7db057e9bf13f42a2485">open</a> (const <a class="el" href="classOpenMS_1_1String.html">String</a> &filename)</td></tr>
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<tr class="memdesc:a439f6d35e3fe7db057e9bf13f42a2485 inherit pub_methods_classOpenMS_1_1SuffixArraySeqan"><td class="mdescLeft"> </td><td class="mdescRight">opens the suffix array <a href="#a439f6d35e3fe7db057e9bf13f42a2485">More...</a><br/></td></tr>
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<tr class="separator:a439f6d35e3fe7db057e9bf13f42a2485 inherit pub_methods_classOpenMS_1_1SuffixArraySeqan"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a946a09425e78f45c9cc2b921d72e8409 inherit pub_methods_classOpenMS_1_1SuffixArraySeqan"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SuffixArraySeqan.html#a946a09425e78f45c9cc2b921d72e8409">setTolerance</a> (<a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> t)</td></tr>
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<tr class="memdesc:a946a09425e78f45c9cc2b921d72e8409 inherit pub_methods_classOpenMS_1_1SuffixArraySeqan"><td class="mdescLeft"> </td><td class="mdescRight">setter for tolerance <a href="#a946a09425e78f45c9cc2b921d72e8409">More...</a><br/></td></tr>
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<tr class="separator:a946a09425e78f45c9cc2b921d72e8409 inherit pub_methods_classOpenMS_1_1SuffixArraySeqan"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a8a62378185408f6af2e4349e6037b32a inherit pub_methods_classOpenMS_1_1SuffixArraySeqan"><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_1SuffixArraySeqan.html#a8a62378185408f6af2e4349e6037b32a">getTolerance</a> () const </td></tr>
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<tr class="memdesc:a8a62378185408f6af2e4349e6037b32a inherit pub_methods_classOpenMS_1_1SuffixArraySeqan"><td class="mdescLeft"> </td><td class="mdescRight">getter for tolerance <a href="#a8a62378185408f6af2e4349e6037b32a">More...</a><br/></td></tr>
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<tr class="separator:a8a62378185408f6af2e4349e6037b32a inherit pub_methods_classOpenMS_1_1SuffixArraySeqan"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a89089f1b7138b71dfa5096c51367632b inherit pub_methods_classOpenMS_1_1SuffixArraySeqan"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SuffixArraySeqan.html#a89089f1b7138b71dfa5096c51367632b">setTags</a> (const std::vector< <a class="el" href="classOpenMS_1_1String.html">OpenMS::String</a> > &tags)</td></tr>
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<tr class="memdesc:a89089f1b7138b71dfa5096c51367632b inherit pub_methods_classOpenMS_1_1SuffixArraySeqan"><td class="mdescLeft"> </td><td class="mdescRight">setter for tags <a href="#a89089f1b7138b71dfa5096c51367632b">More...</a><br/></td></tr>
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<tr class="separator:a89089f1b7138b71dfa5096c51367632b inherit pub_methods_classOpenMS_1_1SuffixArraySeqan"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a35995e158ba0a000e682986f2ab57160 inherit pub_methods_classOpenMS_1_1SuffixArraySeqan"><td class="memItemLeft" align="right" valign="top">const std::vector<br class="typebreak"/>
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< <a class="el" href="classOpenMS_1_1String.html">OpenMS::String</a> > & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SuffixArraySeqan.html#a35995e158ba0a000e682986f2ab57160">getTags</a> ()</td></tr>
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<tr class="memdesc:a35995e158ba0a000e682986f2ab57160 inherit pub_methods_classOpenMS_1_1SuffixArraySeqan"><td class="mdescLeft"> </td><td class="mdescRight">getter for tags <a href="#a35995e158ba0a000e682986f2ab57160">More...</a><br/></td></tr>
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<tr class="separator:a35995e158ba0a000e682986f2ab57160 inherit pub_methods_classOpenMS_1_1SuffixArraySeqan"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:ab2650d016b9e7eaf4574d44817868f3d inherit pub_methods_classOpenMS_1_1SuffixArraySeqan"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SuffixArraySeqan.html#ab2650d016b9e7eaf4574d44817868f3d">setUseTags</a> (bool use_tags)</td></tr>
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<tr class="memdesc:ab2650d016b9e7eaf4574d44817868f3d inherit pub_methods_classOpenMS_1_1SuffixArraySeqan"><td class="mdescLeft"> </td><td class="mdescRight">setter for use_tags <a href="#ab2650d016b9e7eaf4574d44817868f3d">More...</a><br/></td></tr>
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<tr class="separator:ab2650d016b9e7eaf4574d44817868f3d inherit pub_methods_classOpenMS_1_1SuffixArraySeqan"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a65ab7ffcdc877e66b410aa4bc92935fb inherit pub_methods_classOpenMS_1_1SuffixArraySeqan"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SuffixArraySeqan.html#a65ab7ffcdc877e66b410aa4bc92935fb">getUseTags</a> ()</td></tr>
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<tr class="memdesc:a65ab7ffcdc877e66b410aa4bc92935fb inherit pub_methods_classOpenMS_1_1SuffixArraySeqan"><td class="mdescLeft"> </td><td class="mdescRight">getter for use_tags <a href="#a65ab7ffcdc877e66b410aa4bc92935fb">More...</a><br/></td></tr>
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<tr class="separator:a65ab7ffcdc877e66b410aa4bc92935fb inherit pub_methods_classOpenMS_1_1SuffixArraySeqan"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a04c30ff2f4f8f35549000277592c9e8d inherit pub_methods_classOpenMS_1_1SuffixArraySeqan"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SuffixArraySeqan.html#a04c30ff2f4f8f35549000277592c9e8d">setNumberOfModifications</a> (<a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> number_of_mods)</td></tr>
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<tr class="memdesc:a04c30ff2f4f8f35549000277592c9e8d inherit pub_methods_classOpenMS_1_1SuffixArraySeqan"><td class="mdescLeft"> </td><td class="mdescRight">setter for number of modifications <a href="#a04c30ff2f4f8f35549000277592c9e8d">More...</a><br/></td></tr>
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<tr class="separator:a04c30ff2f4f8f35549000277592c9e8d inherit pub_methods_classOpenMS_1_1SuffixArraySeqan"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a30dec5fbc364fa6168ef5c28d2ce988f inherit pub_methods_classOpenMS_1_1SuffixArraySeqan"><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_1SuffixArraySeqan.html#a30dec5fbc364fa6168ef5c28d2ce988f">getNumberOfModifications</a> ()</td></tr>
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<tr class="memdesc:a30dec5fbc364fa6168ef5c28d2ce988f inherit pub_methods_classOpenMS_1_1SuffixArraySeqan"><td class="mdescLeft"> </td><td class="mdescRight">getter for number of modifications <a href="#a30dec5fbc364fa6168ef5c28d2ce988f">More...</a><br/></td></tr>
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<tr class="separator:a30dec5fbc364fa6168ef5c28d2ce988f inherit pub_methods_classOpenMS_1_1SuffixArraySeqan"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:af51327da313f22aa8cb1abebb11cebe5 inherit pub_methods_classOpenMS_1_1SuffixArraySeqan"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SuffixArraySeqan.html#af51327da313f22aa8cb1abebb11cebe5">printStatistic</a> ()</td></tr>
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<tr class="memdesc:af51327da313f22aa8cb1abebb11cebe5 inherit pub_methods_classOpenMS_1_1SuffixArraySeqan"><td class="mdescLeft"> </td><td class="mdescRight">output for statistic <a href="#af51327da313f22aa8cb1abebb11cebe5">More...</a><br/></td></tr>
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<tr class="inherit_header pub_methods_classOpenMS_1_1SuffixArray"><td colspan="2" onclick="javascript:toggleInherit('pub_methods_classOpenMS_1_1SuffixArray')"><img src="closed.png" alt="-"/> Public Member Functions inherited from <a class="el" href="classOpenMS_1_1SuffixArray.html">SuffixArray</a></td></tr>
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<tr class="memitem:abfdabd2b559c341d60a3a3979e81daaa inherit pub_methods_classOpenMS_1_1SuffixArray"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SuffixArray.html#abfdabd2b559c341d60a3a3979e81daaa">SuffixArray</a> (const <a class="el" href="classOpenMS_1_1String.html">String</a> &st, const <a class="el" href="classOpenMS_1_1String.html">String</a> &filename)</td></tr>
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<tr class="memdesc:abfdabd2b559c341d60a3a3979e81daaa inherit pub_methods_classOpenMS_1_1SuffixArray"><td class="mdescLeft"> </td><td class="mdescRight">constructor taking the string and the filename for writing or reading <a href="#abfdabd2b559c341d60a3a3979e81daaa">More...</a><br/></td></tr>
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<tr class="separator:abfdabd2b559c341d60a3a3979e81daaa inherit pub_methods_classOpenMS_1_1SuffixArray"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a4b1b30caafcf911c9e5b53d454fc3d42 inherit pub_methods_classOpenMS_1_1SuffixArray"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SuffixArray.html#a4b1b30caafcf911c9e5b53d454fc3d42">SuffixArray</a> (const <a class="el" href="classOpenMS_1_1SuffixArray.html">SuffixArray</a> &sa)</td></tr>
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<tr class="memdesc:a4b1b30caafcf911c9e5b53d454fc3d42 inherit pub_methods_classOpenMS_1_1SuffixArray"><td class="mdescLeft"> </td><td class="mdescRight">copy constructor <a href="#a4b1b30caafcf911c9e5b53d454fc3d42">More...</a><br/></td></tr>
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<tr class="separator:a4b1b30caafcf911c9e5b53d454fc3d42 inherit pub_methods_classOpenMS_1_1SuffixArray"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:afa4acc59f254c5cb91963806dd8d9757 inherit pub_methods_classOpenMS_1_1SuffixArray"><td class="memItemLeft" align="right" valign="top">virtual </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SuffixArray.html#afa4acc59f254c5cb91963806dd8d9757">~SuffixArray</a> ()=0</td></tr>
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<tr class="memdesc:afa4acc59f254c5cb91963806dd8d9757 inherit pub_methods_classOpenMS_1_1SuffixArray"><td class="mdescLeft"> </td><td class="mdescRight">destructor <a href="#afa4acc59f254c5cb91963806dd8d9757">More...</a><br/></td></tr>
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<tr class="separator:afa4acc59f254c5cb91963806dd8d9757 inherit pub_methods_classOpenMS_1_1SuffixArray"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a7d57710f630ba50753236ec1860bc096 inherit pub_methods_classOpenMS_1_1SuffixArray"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SuffixArray.html#a7d57710f630ba50753236ec1860bc096">SuffixArray</a> ()</td></tr>
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<tr class="memdesc:a7d57710f630ba50753236ec1860bc096 inherit pub_methods_classOpenMS_1_1SuffixArray"><td class="mdescLeft"> </td><td class="mdescRight">constructor <a href="#a7d57710f630ba50753236ec1860bc096">More...</a><br/></td></tr>
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<tr class="separator:a7d57710f630ba50753236ec1860bc096 inherit pub_methods_classOpenMS_1_1SuffixArray"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="inherit_header pub_methods_classOpenMS_1_1WeightWrapper"><td colspan="2" onclick="javascript:toggleInherit('pub_methods_classOpenMS_1_1WeightWrapper')"><img src="closed.png" alt="-"/> Public Member Functions inherited from <a class="el" href="classOpenMS_1_1WeightWrapper.html">WeightWrapper</a></td></tr>
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<tr class="memitem:ad17dfc0067cbade3b4862477bb535c83 inherit pub_methods_classOpenMS_1_1WeightWrapper"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1WeightWrapper.html#ad17dfc0067cbade3b4862477bb535c83">WeightWrapper</a> ()</td></tr>
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<tr class="memdesc:ad17dfc0067cbade3b4862477bb535c83 inherit pub_methods_classOpenMS_1_1WeightWrapper"><td class="mdescLeft"> </td><td class="mdescRight">constructor <a href="#ad17dfc0067cbade3b4862477bb535c83">More...</a><br/></td></tr>
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<tr class="separator:ad17dfc0067cbade3b4862477bb535c83 inherit pub_methods_classOpenMS_1_1WeightWrapper"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a60ffdc2b9c2147851399c529b1a1fd51 inherit pub_methods_classOpenMS_1_1WeightWrapper"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1WeightWrapper.html#a60ffdc2b9c2147851399c529b1a1fd51">WeightWrapper</a> (const <a class="el" href="classOpenMS_1_1WeightWrapper.html#aa0e0675e46f34052468f523f1c8aff2b">WEIGHTMODE</a> weight_mode)</td></tr>
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<tr class="memdesc:a60ffdc2b9c2147851399c529b1a1fd51 inherit pub_methods_classOpenMS_1_1WeightWrapper"><td class="mdescLeft"> </td><td class="mdescRight">constructor <a href="#a60ffdc2b9c2147851399c529b1a1fd51">More...</a><br/></td></tr>
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<tr class="separator:a60ffdc2b9c2147851399c529b1a1fd51 inherit pub_methods_classOpenMS_1_1WeightWrapper"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a0f2c08d0cebb514fee6ba050bb17aa0f inherit pub_methods_classOpenMS_1_1WeightWrapper"><td class="memItemLeft" align="right" valign="top">virtual </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1WeightWrapper.html#a0f2c08d0cebb514fee6ba050bb17aa0f">~WeightWrapper</a> ()</td></tr>
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<tr class="memdesc:a0f2c08d0cebb514fee6ba050bb17aa0f inherit pub_methods_classOpenMS_1_1WeightWrapper"><td class="mdescLeft"> </td><td class="mdescRight">destructor <a href="#a0f2c08d0cebb514fee6ba050bb17aa0f">More...</a><br/></td></tr>
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<tr class="separator:a0f2c08d0cebb514fee6ba050bb17aa0f inherit pub_methods_classOpenMS_1_1WeightWrapper"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:acf810b578f701801ea752d534d7fcbe9 inherit pub_methods_classOpenMS_1_1WeightWrapper"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1WeightWrapper.html#acf810b578f701801ea752d534d7fcbe9">WeightWrapper</a> (const <a class="el" href="classOpenMS_1_1WeightWrapper.html">WeightWrapper</a> &source)</td></tr>
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<tr class="memdesc:acf810b578f701801ea752d534d7fcbe9 inherit pub_methods_classOpenMS_1_1WeightWrapper"><td class="mdescLeft"> </td><td class="mdescRight">copy constructor <a href="#acf810b578f701801ea752d534d7fcbe9">More...</a><br/></td></tr>
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<tr class="separator:acf810b578f701801ea752d534d7fcbe9 inherit pub_methods_classOpenMS_1_1WeightWrapper"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a86f49dcf25cd06d439db0390ae5604b5 inherit pub_methods_classOpenMS_1_1WeightWrapper"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1WeightWrapper.html#a86f49dcf25cd06d439db0390ae5604b5">setWeightMode</a> (const <a class="el" href="classOpenMS_1_1WeightWrapper.html#aa0e0675e46f34052468f523f1c8aff2b">WEIGHTMODE</a> mode)</td></tr>
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<tr class="memdesc:a86f49dcf25cd06d439db0390ae5604b5 inherit pub_methods_classOpenMS_1_1WeightWrapper"><td class="mdescLeft"> </td><td class="mdescRight">Sets the weight mode (MONO or AVERAGE) <a href="#a86f49dcf25cd06d439db0390ae5604b5">More...</a><br/></td></tr>
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<tr class="separator:a86f49dcf25cd06d439db0390ae5604b5 inherit pub_methods_classOpenMS_1_1WeightWrapper"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a12c0a3ef8cbe7321db6724f92ba07730 inherit pub_methods_classOpenMS_1_1WeightWrapper"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1WeightWrapper.html#aa0e0675e46f34052468f523f1c8aff2b">WEIGHTMODE</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1WeightWrapper.html#a12c0a3ef8cbe7321db6724f92ba07730">getWeightMode</a> () const </td></tr>
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<tr class="memdesc:a12c0a3ef8cbe7321db6724f92ba07730 inherit pub_methods_classOpenMS_1_1WeightWrapper"><td class="mdescLeft"> </td><td class="mdescRight">Gets the weight mode (MONO or AVERAGE) <a href="#a12c0a3ef8cbe7321db6724f92ba07730">More...</a><br/></td></tr>
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<tr class="separator:a12c0a3ef8cbe7321db6724f92ba07730 inherit pub_methods_classOpenMS_1_1WeightWrapper"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:af26fbe119eda2461447f2312786531f6 inherit pub_methods_classOpenMS_1_1WeightWrapper"><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_1WeightWrapper.html#af26fbe119eda2461447f2312786531f6">getWeight</a> (const <a class="el" href="classOpenMS_1_1AASequence.html">AASequence</a> &aa) const </td></tr>
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<tr class="memdesc:af26fbe119eda2461447f2312786531f6 inherit pub_methods_classOpenMS_1_1WeightWrapper"><td class="mdescLeft"> </td><td class="mdescRight">returns the weight of either mono or average value <a href="#af26fbe119eda2461447f2312786531f6">More...</a><br/></td></tr>
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<tr class="separator:af26fbe119eda2461447f2312786531f6 inherit pub_methods_classOpenMS_1_1WeightWrapper"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a83b54901c7aa15994c0c665b8249e0f7 inherit pub_methods_classOpenMS_1_1WeightWrapper"><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_1WeightWrapper.html#a83b54901c7aa15994c0c665b8249e0f7">getWeight</a> (const <a class="el" href="classOpenMS_1_1EmpiricalFormula.html">EmpiricalFormula</a> &ef) const </td></tr>
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<tr class="memdesc:a83b54901c7aa15994c0c665b8249e0f7 inherit pub_methods_classOpenMS_1_1WeightWrapper"><td class="mdescLeft"> </td><td class="mdescRight">returns the weight of either mono or average value <a href="#a83b54901c7aa15994c0c665b8249e0f7">More...</a><br/></td></tr>
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<tr class="separator:a83b54901c7aa15994c0c665b8249e0f7 inherit pub_methods_classOpenMS_1_1WeightWrapper"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:acf259e90e6852e4baab243bd5eff44e5 inherit pub_methods_classOpenMS_1_1WeightWrapper"><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_1WeightWrapper.html#acf259e90e6852e4baab243bd5eff44e5">getWeight</a> (const <a class="el" href="classOpenMS_1_1Residue.html">Residue</a> &r, <a class="el" href="classOpenMS_1_1Residue.html#a7651af21f9cf8ed6445415903fc6cb48">Residue::ResidueType</a> res_type=<a class="el" href="classOpenMS_1_1Residue.html#a7651af21f9cf8ed6445415903fc6cb48a8b7c5cd8bd8eb51ee6d3fd0eac584679">Residue::Full</a>) const </td></tr>
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<tr class="memdesc:acf259e90e6852e4baab243bd5eff44e5 inherit pub_methods_classOpenMS_1_1WeightWrapper"><td class="mdescLeft"> </td><td class="mdescRight">returns the weight of either mono or average value <a href="#acf259e90e6852e4baab243bd5eff44e5">More...</a><br/></td></tr>
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<tr class="separator:acf259e90e6852e4baab243bd5eff44e5 inherit pub_methods_classOpenMS_1_1WeightWrapper"><td class="memSeparator" colspan="2"> </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_1WeightWrapper"><td colspan="2" onclick="javascript:toggleInherit('pub_types_classOpenMS_1_1WeightWrapper')"><img src="closed.png" alt="-"/> Public Types inherited from <a class="el" href="classOpenMS_1_1WeightWrapper.html">WeightWrapper</a></td></tr>
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<tr class="memitem:aa0e0675e46f34052468f523f1c8aff2b inherit pub_types_classOpenMS_1_1WeightWrapper"><td class="memItemLeft" align="right" valign="top">enum  </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1WeightWrapper.html#aa0e0675e46f34052468f523f1c8aff2b">WEIGHTMODE</a> { <a class="el" href="classOpenMS_1_1WeightWrapper.html#aa0e0675e46f34052468f523f1c8aff2bab6f2220659ddcb84a0622d4aa4e0b112">AVERAGE</a> = 0,
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<a class="el" href="classOpenMS_1_1WeightWrapper.html#aa0e0675e46f34052468f523f1c8aff2ba3828195437a1112429b5c7a3e8780570">MONO</a>,
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<a class="el" href="classOpenMS_1_1WeightWrapper.html#aa0e0675e46f34052468f523f1c8aff2ba4226c2437cbb49f44511f47e1bde3109">SIZE_OF_WEIGHTMODE</a>
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<tr class="separator:aa0e0675e46f34052468f523f1c8aff2b inherit pub_types_classOpenMS_1_1WeightWrapper"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="inherit_header pro_methods_classOpenMS_1_1SuffixArraySeqan"><td colspan="2" onclick="javascript:toggleInherit('pro_methods_classOpenMS_1_1SuffixArraySeqan')"><img src="closed.png" alt="-"/> Protected Member Functions inherited from <a class="el" href="classOpenMS_1_1SuffixArraySeqan.html">SuffixArraySeqan</a></td></tr>
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<tr class="memitem:a8d5af4ff6cc3b745d142d15950196917 inherit pro_methods_classOpenMS_1_1SuffixArraySeqan"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SuffixArraySeqan.html#a8d5af4ff6cc3b745d142d15950196917">goNextSubTree_</a> (<a class="el" href="classOpenMS_1_1SuffixArraySeqan.html#ac252e4ae3b28e15b76e9c79be16971b5">TIter</a> &it, <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> &m, std::stack< <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> > &allm, std::stack< std::map< <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a>, <a class="el" href="group__Concept.html#gae113cb41304c6692c7bf5d0624dc6f0f">SignedSize</a> > > &mod_map)</td></tr>
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<tr class="memdesc:a8d5af4ff6cc3b745d142d15950196917 inherit pro_methods_classOpenMS_1_1SuffixArraySeqan"><td class="mdescLeft"> </td><td class="mdescRight">overwriting goNextSubTree_ from seqan index_esa_stree.h for mass update during suffix array traversal <a href="#a8d5af4ff6cc3b745d142d15950196917">More...</a><br/></td></tr>
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<tr class="separator:a8d5af4ff6cc3b745d142d15950196917 inherit pro_methods_classOpenMS_1_1SuffixArraySeqan"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:aab7a3c8279f06017689bc067db553866 inherit pro_methods_classOpenMS_1_1SuffixArraySeqan"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SuffixArraySeqan.html#aab7a3c8279f06017689bc067db553866">goNextSubTree_</a> (<a class="el" href="classOpenMS_1_1SuffixArraySeqan.html#ac252e4ae3b28e15b76e9c79be16971b5">TIter</a> &it)</td></tr>
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<tr class="memdesc:aab7a3c8279f06017689bc067db553866 inherit pro_methods_classOpenMS_1_1SuffixArraySeqan"><td class="mdescLeft"> </td><td class="mdescRight">goes to the next sub tree <a href="#aab7a3c8279f06017689bc067db553866">More...</a><br/></td></tr>
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<tr class="separator:aab7a3c8279f06017689bc067db553866 inherit pro_methods_classOpenMS_1_1SuffixArraySeqan"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:abc7e9c615867171906af75f497ac65f6 inherit pro_methods_classOpenMS_1_1SuffixArraySeqan"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SuffixArraySeqan.html#abc7e9c615867171906af75f497ac65f6">goNext_</a> (<a class="el" href="classOpenMS_1_1SuffixArraySeqan.html#ac252e4ae3b28e15b76e9c79be16971b5">TIter</a> &it, <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> &m, std::stack< <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> > &allm, std::stack< std::map< <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a>, <a class="el" href="group__Concept.html#gae113cb41304c6692c7bf5d0624dc6f0f">SignedSize</a> > > &mod_map)</td></tr>
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<tr class="memdesc:abc7e9c615867171906af75f497ac65f6 inherit pro_methods_classOpenMS_1_1SuffixArraySeqan"><td class="mdescLeft"> </td><td class="mdescRight">overwriting goNext from seqan index_esa_stree.h for mass update during suffix array traversal <a href="#abc7e9c615867171906af75f497ac65f6">More...</a><br/></td></tr>
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<tr class="separator:abc7e9c615867171906af75f497ac65f6 inherit pro_methods_classOpenMS_1_1SuffixArraySeqan"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:af401425e4fadc7f9dae12bde81ed2ba4 inherit pro_methods_classOpenMS_1_1SuffixArraySeqan"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SuffixArraySeqan.html#af401425e4fadc7f9dae12bde81ed2ba4">parseTree_</a> (<a class="el" href="classOpenMS_1_1SuffixArraySeqan.html#ac252e4ae3b28e15b76e9c79be16971b5">TIter</a> &it, std::vector< std::pair< <a class="el" href="group__Concept.html#gae113cb41304c6692c7bf5d0624dc6f0f">SignedSize</a>, <a class="el" href="group__Concept.html#gae113cb41304c6692c7bf5d0624dc6f0f">SignedSize</a> > > &out_number, std::vector< std::pair< <a class="el" href="group__Concept.html#gae113cb41304c6692c7bf5d0624dc6f0f">SignedSize</a>, <a class="el" href="group__Concept.html#gae113cb41304c6692c7bf5d0624dc6f0f">SignedSize</a> > > &edge_length, std::vector< <a class="el" href="group__Concept.html#gae113cb41304c6692c7bf5d0624dc6f0f">SignedSize</a> > &leafe_depth)</td></tr>
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<tr class="separator:af401425e4fadc7f9dae12bde81ed2ba4 inherit pro_methods_classOpenMS_1_1SuffixArraySeqan"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:af827429c64446f0d89d8d53f4029c63c inherit pro_methods_classOpenMS_1_1SuffixArraySeqan"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__Concept.html#gae113cb41304c6692c7bf5d0624dc6f0f">SignedSize</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SuffixArraySeqan.html#af827429c64446f0d89d8d53f4029c63c">findFirst_</a> (const std::vector< <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> > &spec, <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> &m)</td></tr>
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<tr class="memdesc:af827429c64446f0d89d8d53f4029c63c inherit pro_methods_classOpenMS_1_1SuffixArraySeqan"><td class="mdescLeft"> </td><td class="mdescRight">binary search for finding the index of the first element of the spectrum that matches the desired mass within the tolerance. <a href="#af827429c64446f0d89d8d53f4029c63c">More...</a><br/></td></tr>
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<tr class="separator:af827429c64446f0d89d8d53f4029c63c inherit pro_methods_classOpenMS_1_1SuffixArraySeqan"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:aceab577fe4e204ba7f9d260591c13b43 inherit pro_methods_classOpenMS_1_1SuffixArraySeqan"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__Concept.html#gae113cb41304c6692c7bf5d0624dc6f0f">SignedSize</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SuffixArraySeqan.html#aceab577fe4e204ba7f9d260591c13b43">findFirst_</a> (const std::vector< <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> > &spec, <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> &m, <a class="el" href="group__Concept.html#gae113cb41304c6692c7bf5d0624dc6f0f">SignedSize</a> start, <a class="el" href="group__Concept.html#gae113cb41304c6692c7bf5d0624dc6f0f">SignedSize</a> end)</td></tr>
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<tr class="memdesc:aceab577fe4e204ba7f9d260591c13b43 inherit pro_methods_classOpenMS_1_1SuffixArraySeqan"><td class="mdescLeft"> </td><td class="mdescRight">binary search for finding the index of the first element of the spectrum that matches the desired mass within the tolerance. it searches recursivly. <a href="#aceab577fe4e204ba7f9d260591c13b43">More...</a><br/></td></tr>
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<tr class="separator:aceab577fe4e204ba7f9d260591c13b43 inherit pro_methods_classOpenMS_1_1SuffixArraySeqan"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="inherit_header pro_attribs_classOpenMS_1_1SuffixArraySeqan"><td colspan="2" onclick="javascript:toggleInherit('pro_attribs_classOpenMS_1_1SuffixArraySeqan')"><img src="closed.png" alt="-"/> Protected Attributes inherited from <a class="el" href="classOpenMS_1_1SuffixArraySeqan.html">SuffixArraySeqan</a></td></tr>
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<tr class="memitem:a4bcd335dc7db2067a36e380cc36e69db inherit pro_attribs_classOpenMS_1_1SuffixArraySeqan"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1SuffixArraySeqan.html#a2401ebe0488d209f33c011173b4067c0">TIndex</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SuffixArraySeqan.html#a4bcd335dc7db2067a36e380cc36e69db">index_</a></td></tr>
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<tr class="memdesc:a4bcd335dc7db2067a36e380cc36e69db inherit pro_attribs_classOpenMS_1_1SuffixArraySeqan"><td class="mdescLeft"> </td><td class="mdescRight">seqan suffix array <a href="#a4bcd335dc7db2067a36e380cc36e69db">More...</a><br/></td></tr>
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<tr class="separator:a4bcd335dc7db2067a36e380cc36e69db inherit pro_attribs_classOpenMS_1_1SuffixArraySeqan"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a7f643787a8ddf761d7f96cc7890643d6 inherit pro_attribs_classOpenMS_1_1SuffixArraySeqan"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1SuffixArraySeqan.html#ac252e4ae3b28e15b76e9c79be16971b5">TIter</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SuffixArraySeqan.html#a7f643787a8ddf761d7f96cc7890643d6">it_</a></td></tr>
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<tr class="memdesc:a7f643787a8ddf761d7f96cc7890643d6 inherit pro_attribs_classOpenMS_1_1SuffixArraySeqan"><td class="mdescLeft"> </td><td class="mdescRight">seqan suffix array iterator <a href="#a7f643787a8ddf761d7f96cc7890643d6">More...</a><br/></td></tr>
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<tr class="separator:a7f643787a8ddf761d7f96cc7890643d6 inherit pro_attribs_classOpenMS_1_1SuffixArraySeqan"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a28d5fa0a5f589e44cd18c30b6b6dbf63 inherit pro_attribs_classOpenMS_1_1SuffixArraySeqan"><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_1SuffixArraySeqan.html#a28d5fa0a5f589e44cd18c30b6b6dbf63">s_</a></td></tr>
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<tr class="memdesc:a28d5fa0a5f589e44cd18c30b6b6dbf63 inherit pro_attribs_classOpenMS_1_1SuffixArraySeqan"><td class="mdescLeft"> </td><td class="mdescRight">reference to strings for which the suffix array is build <a href="#a28d5fa0a5f589e44cd18c30b6b6dbf63">More...</a><br/></td></tr>
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<tr class="separator:a28d5fa0a5f589e44cd18c30b6b6dbf63 inherit pro_attribs_classOpenMS_1_1SuffixArraySeqan"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a82b500a04e1c860859dea2a5de81d486 inherit pro_attribs_classOpenMS_1_1SuffixArraySeqan"><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_1SuffixArraySeqan.html#a82b500a04e1c860859dea2a5de81d486">masse_</a> [255]</td></tr>
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<tr class="memdesc:a82b500a04e1c860859dea2a5de81d486 inherit pro_attribs_classOpenMS_1_1SuffixArraySeqan"><td class="mdescLeft"> </td><td class="mdescRight">amino acid masses <a href="#a82b500a04e1c860859dea2a5de81d486">More...</a><br/></td></tr>
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<tr class="separator:a82b500a04e1c860859dea2a5de81d486 inherit pro_attribs_classOpenMS_1_1SuffixArraySeqan"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:afb270f403ee1906142ed086faddd9579 inherit pro_attribs_classOpenMS_1_1SuffixArraySeqan"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__Concept.html#gae113cb41304c6692c7bf5d0624dc6f0f">SignedSize</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SuffixArraySeqan.html#afb270f403ee1906142ed086faddd9579">number_of_modifications_</a></td></tr>
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<tr class="memdesc:afb270f403ee1906142ed086faddd9579 inherit pro_attribs_classOpenMS_1_1SuffixArraySeqan"><td class="mdescLeft"> </td><td class="mdescRight">number of allowed modifications <a href="#afb270f403ee1906142ed086faddd9579">More...</a><br/></td></tr>
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<tr class="separator:afb270f403ee1906142ed086faddd9579 inherit pro_attribs_classOpenMS_1_1SuffixArraySeqan"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a26d1215083518387975aecec042c0fc0 inherit pro_attribs_classOpenMS_1_1SuffixArraySeqan"><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_1SuffixArraySeqan.html#a26d1215083518387975aecec042c0fc0">tags_</a></td></tr>
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<tr class="memdesc:a26d1215083518387975aecec042c0fc0 inherit pro_attribs_classOpenMS_1_1SuffixArraySeqan"><td class="mdescLeft"> </td><td class="mdescRight">all tags <a href="#a26d1215083518387975aecec042c0fc0">More...</a><br/></td></tr>
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<tr class="memitem:a0a7158b249ff8c267b98581e56a584e3 inherit pro_attribs_classOpenMS_1_1SuffixArraySeqan"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SuffixArraySeqan.html#a0a7158b249ff8c267b98581e56a584e3">use_tags_</a></td></tr>
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<tr class="memdesc:a0a7158b249ff8c267b98581e56a584e3 inherit pro_attribs_classOpenMS_1_1SuffixArraySeqan"><td class="mdescLeft"> </td><td class="mdescRight">if tags are used <a href="#a0a7158b249ff8c267b98581e56a584e3">More...</a><br/></td></tr>
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<tr class="separator:a0a7158b249ff8c267b98581e56a584e3 inherit pro_attribs_classOpenMS_1_1SuffixArraySeqan"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:ad71c965ded7781aca71019c3873bc535 inherit pro_attribs_classOpenMS_1_1SuffixArraySeqan"><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_1SuffixArraySeqan.html#ad71c965ded7781aca71019c3873bc535">tol_</a></td></tr>
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<tr class="memdesc:ad71c965ded7781aca71019c3873bc535 inherit pro_attribs_classOpenMS_1_1SuffixArraySeqan"><td class="mdescLeft"> </td><td class="mdescRight">tolerance <a href="#ad71c965ded7781aca71019c3873bc535">More...</a><br/></td></tr>
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<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
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<div class="textblock"><p>Class that uses SEQAN library for a suffix array. It can be used to find peptide Candidates for a MS spectrum. </p>
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<p>This class uses SEQAN suffix array. It can just be used for finding peptide Candidates for a given MS Spectrum within a certain mass tolerance. The suffix array can be saved to disc for reused so it has to be build just once. </p>
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</div><h2 class="groupheader">Constructor & Destructor Documentation</h2>
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<a class="anchor" id="a10119b1df48bec175a8f4811b02bed25"></a>
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<div class="memitem">
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<td class="memname"><a class="el" href="classOpenMS_1_1SuffixArrayTrypticSeqan.html">SuffixArrayTrypticSeqan</a> </td>
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<td class="paramtype">const <a class="el" href="classOpenMS_1_1String.html">String</a> & </td>
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<td class="paramname"><em>st</em>, </td>
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<td class="paramkey"></td>
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<td class="paramtype">const <a class="el" href="classOpenMS_1_1String.html">String</a> & </td>
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<td class="paramname"><em>filename</em>, </td>
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<td class="paramkey"></td>
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<td class="paramtype">const <a class="el" href="classOpenMS_1_1WeightWrapper.html#aa0e0675e46f34052468f523f1c8aff2b">WeightWrapper::WEIGHTMODE</a> </td>
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<td class="paramname"><em>weight_mode</em> = <code><a class="el" href="classOpenMS_1_1WeightWrapper.html#aa0e0675e46f34052468f523f1c8aff2ba3828195437a1112429b5c7a3e8780570">WeightWrapper::MONO</a></code> </td>
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</div><div class="memdoc">
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<p>constructor for tryptic seqan array with a specially optimized implementation </p>
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<dl class="params"><dt>Parameters</dt><dd>
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<table class="params">
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<tr><td class="paramname">st</td><td>the suffix array string, which is used to build the suffix array </td></tr>
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<tr><td class="paramname">filename</td><td>filename of fasta file </td></tr>
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<tr><td class="paramname">weight_mode</td><td>if not monoistopic weight should be used, this parameters can be set to AVERAGE </td></tr>
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<dl class="exception"><dt>Exceptions</dt><dd>
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<table class="exception">
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<tr><td class="paramname">InvalidValue</td><td>is thrown if string st if invalid </td></tr>
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<tr><td class="paramname">FileNotFound</td><td>is thrown if given file is not found </td></tr>
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<h2 class="groupheader">Member Function Documentation</h2>
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<a class="anchor" id="a9eedb3b9aa20ef87f387b54c9e7813d7"></a>
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<div class="memitem">
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<div class="memproto">
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<table class="mlabels">
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<td class="mlabels-left">
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<table class="memname">
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<td class="memname">bool isDigestingEnd </td>
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<td class="paramtype">const char </td>
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<td class="paramname"><em>aa1</em>, </td>
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<td class="paramkey"></td>
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<td class="paramtype">const char </td>
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<td class="paramname"><em>aa2</em> </td>
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<td></td><td> const</td>
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<td class="mlabels-right">
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<span class="mlabels"><span class="mlabel">virtual</span></span> </td>
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<p>returns if an enzyme will cut after first character </p>
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<dl class="params"><dt>Parameters</dt><dd>
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<table class="params">
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<tr><td class="paramname">aa1</td><td>const char as first aminoacid </td></tr>
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<tr><td class="paramname">aa2</td><td>const char as second aminoacid </td></tr>
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<dl class="section return"><dt>Returns</dt><dd>bool descibing if it is a digesting site </dd></dl>
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<p>Reimplemented from <a class="el" href="classOpenMS_1_1SuffixArraySeqan.html#a9eedb3b9aa20ef87f387b54c9e7813d7">SuffixArraySeqan</a>.</p>
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</div><!-- contents -->
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<HR style="height:1px; border:none; border-top:1px solid #c0c0c0;">
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<TABLE width="100%" border="0">
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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 11:19:29 using doxygen 1.8.5</font></TD>
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