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<HTML>
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<TITLE>SuffixArray 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_1SuffixArray.html">SuffixArray</a></li> </ul>
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<p>abstract class for suffix array
<a href="classOpenMS_1_1SuffixArray.html#details">More...</a></p>
<p><code>#include <<a class="el" href="SuffixArray_8h_source.html">OpenMS/DATASTRUCTURES/SuffixArray.h</a>></code></p>
<div class="dynheader">
Inheritance diagram for SuffixArray:</div>
<div class="dyncontent">
<div class="center">
<img src="classOpenMS_1_1SuffixArray.png" usemap="#SuffixArray_map" alt=""/>
<map id="SuffixArray_map" name="SuffixArray_map">
<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="0,56,186,80"/>
<area href="classOpenMS_1_1SuffixArrayTrypticCompressed.html" title="Class that implements a suffix array for a String. It can be used to find peptide Candidates for a MS..." alt="SuffixArrayTrypticCompressed" shape="rect" coords="196,56,382,80"/>
<area href="classOpenMS_1_1SuffixArrayTrypticSeqan.html" title="Class that uses SEQAN library for a suffix array. It can be used to find peptide Candidates for a MS ..." alt="SuffixArrayTrypticSeqan" shape="rect" coords="0,112,186,136"/>
</map>
</div></div>
<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:abfdabd2b559c341d60a3a3979e81daaa"><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>
<tr class="memdesc:abfdabd2b559c341d60a3a3979e81daaa"><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>
<tr class="separator:abfdabd2b559c341d60a3a3979e81daaa"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a4b1b30caafcf911c9e5b53d454fc3d42"><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>
<tr class="memdesc:a4b1b30caafcf911c9e5b53d454fc3d42"><td class="mdescLeft"> </td><td class="mdescRight">copy constructor <a href="#a4b1b30caafcf911c9e5b53d454fc3d42">More...</a><br/></td></tr>
<tr class="separator:a4b1b30caafcf911c9e5b53d454fc3d42"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:afa4acc59f254c5cb91963806dd8d9757"><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>
<tr class="memdesc:afa4acc59f254c5cb91963806dd8d9757"><td class="mdescLeft"> </td><td class="mdescRight">destructor <a href="#afa4acc59f254c5cb91963806dd8d9757">More...</a><br/></td></tr>
<tr class="separator:afa4acc59f254c5cb91963806dd8d9757"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:afdaf3cb169ec00377bee2cd175d8e1f8"><td class="memItemLeft" align="right" valign="top">virtual <a class="el" href="classOpenMS_1_1String.html">String</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SuffixArray.html#afdaf3cb169ec00377bee2cd175d8e1f8">toString</a> ()=0</td></tr>
<tr class="memdesc:afdaf3cb169ec00377bee2cd175d8e1f8"><td class="mdescLeft"> </td><td class="mdescRight">transforms suffix array to a printable <a class="el" href="classOpenMS_1_1String.html" title="A more convenient string class. ">String</a> <a href="#afdaf3cb169ec00377bee2cd175d8e1f8">More...</a><br/></td></tr>
<tr class="separator:afdaf3cb169ec00377bee2cd175d8e1f8"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a0affa38cc125d13f708da436e1f4e6d6"><td class="memItemLeft" align="right" valign="top">virtual void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SuffixArray.html#a0affa38cc125d13f708da436e1f4e6d6">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)=0</td></tr>
<tr class="memdesc:a0affa38cc125d13f708da436e1f4e6d6"><td class="mdescLeft"> </td><td class="mdescRight">the function that will find all peptide candidates for a given spectrum <a href="#a0affa38cc125d13f708da436e1f4e6d6">More...</a><br/></td></tr>
<tr class="separator:a0affa38cc125d13f708da436e1f4e6d6"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ac089570bb6a9e2fe55702ca4401588d6"><td class="memItemLeft" align="right" valign="top">virtual bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SuffixArray.html#ac089570bb6a9e2fe55702ca4401588d6">save</a> (const <a class="el" href="classOpenMS_1_1String.html">String</a> &filename)=0</td></tr>
<tr class="memdesc:ac089570bb6a9e2fe55702ca4401588d6"><td class="mdescLeft"> </td><td class="mdescRight">saves the suffix array to disc <a href="#ac089570bb6a9e2fe55702ca4401588d6">More...</a><br/></td></tr>
<tr class="separator:ac089570bb6a9e2fe55702ca4401588d6"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ab02477e3a21855a2103a9f23e1d8043e"><td class="memItemLeft" align="right" valign="top">virtual bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SuffixArray.html#ab02477e3a21855a2103a9f23e1d8043e">open</a> (const <a class="el" href="classOpenMS_1_1String.html">String</a> &filename)=0</td></tr>
<tr class="memdesc:ab02477e3a21855a2103a9f23e1d8043e"><td class="mdescLeft"> </td><td class="mdescRight">opens the suffix array <a href="#ab02477e3a21855a2103a9f23e1d8043e">More...</a><br/></td></tr>
<tr class="separator:ab02477e3a21855a2103a9f23e1d8043e"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a398690ada878a7dc5e01d57929ef2363"><td class="memItemLeft" align="right" valign="top">virtual void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SuffixArray.html#a398690ada878a7dc5e01d57929ef2363">setTolerance</a> (<a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> t)=0</td></tr>
<tr class="memdesc:a398690ada878a7dc5e01d57929ef2363"><td class="mdescLeft"> </td><td class="mdescRight">setter for tolerance <a href="#a398690ada878a7dc5e01d57929ef2363">More...</a><br/></td></tr>
<tr class="separator:a398690ada878a7dc5e01d57929ef2363"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a98bd68f109f31bed227c8ee46d5ab6bc"><td class="memItemLeft" align="right" valign="top">virtual <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SuffixArray.html#a98bd68f109f31bed227c8ee46d5ab6bc">getTolerance</a> () const =0</td></tr>
<tr class="memdesc:a98bd68f109f31bed227c8ee46d5ab6bc"><td class="mdescLeft"> </td><td class="mdescRight">getter for tolerance <a href="#a98bd68f109f31bed227c8ee46d5ab6bc">More...</a><br/></td></tr>
<tr class="separator:a98bd68f109f31bed227c8ee46d5ab6bc"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:af622ecda02a91322b72d7de10ae9a6f6"><td class="memItemLeft" align="right" valign="top">virtual bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SuffixArray.html#af622ecda02a91322b72d7de10ae9a6f6">isDigestingEnd</a> (const char aa1, const char aa2) const =0</td></tr>
<tr class="memdesc:af622ecda02a91322b72d7de10ae9a6f6"><td class="mdescLeft"> </td><td class="mdescRight">returns if an enzyme will cut after first character <a href="#af622ecda02a91322b72d7de10ae9a6f6">More...</a><br/></td></tr>
<tr class="separator:af622ecda02a91322b72d7de10ae9a6f6"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:af1b40afd1ef4b811c37612cd4ced7d8e"><td class="memItemLeft" align="right" valign="top">virtual void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SuffixArray.html#af1b40afd1ef4b811c37612cd4ced7d8e">setTags</a> (const std::vector< <a class="el" href="classOpenMS_1_1String.html">String</a> > &tags)=0</td></tr>
<tr class="memdesc:af1b40afd1ef4b811c37612cd4ced7d8e"><td class="mdescLeft"> </td><td class="mdescRight">setter for tags <a href="#af1b40afd1ef4b811c37612cd4ced7d8e">More...</a><br/></td></tr>
<tr class="separator:af1b40afd1ef4b811c37612cd4ced7d8e"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a181d0d02184726d599f9039570c61305"><td class="memItemLeft" align="right" valign="top">virtual const std::vector<br class="typebreak"/>
< <a class="el" href="classOpenMS_1_1String.html">String</a> > & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SuffixArray.html#a181d0d02184726d599f9039570c61305">getTags</a> ()=0</td></tr>
<tr class="memdesc:a181d0d02184726d599f9039570c61305"><td class="mdescLeft"> </td><td class="mdescRight">getter for tags <a href="#a181d0d02184726d599f9039570c61305">More...</a><br/></td></tr>
<tr class="separator:a181d0d02184726d599f9039570c61305"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a10824f8f112c42e00795592f7ddba6b3"><td class="memItemLeft" align="right" valign="top">virtual void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SuffixArray.html#a10824f8f112c42e00795592f7ddba6b3">setUseTags</a> (bool use_tags)=0</td></tr>
<tr class="memdesc:a10824f8f112c42e00795592f7ddba6b3"><td class="mdescLeft"> </td><td class="mdescRight">setter for use_tags <a href="#a10824f8f112c42e00795592f7ddba6b3">More...</a><br/></td></tr>
<tr class="separator:a10824f8f112c42e00795592f7ddba6b3"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a65af38a9cc6ff114c7f509cd3f0f607b"><td class="memItemLeft" align="right" valign="top">virtual bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SuffixArray.html#a65af38a9cc6ff114c7f509cd3f0f607b">getUseTags</a> ()=0</td></tr>
<tr class="memdesc:a65af38a9cc6ff114c7f509cd3f0f607b"><td class="mdescLeft"> </td><td class="mdescRight">getter for use_tags <a href="#a65af38a9cc6ff114c7f509cd3f0f607b">More...</a><br/></td></tr>
<tr class="separator:a65af38a9cc6ff114c7f509cd3f0f607b"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a42afad5b2df41f737839ebf8e31d6cb1"><td class="memItemLeft" align="right" valign="top">virtual void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SuffixArray.html#a42afad5b2df41f737839ebf8e31d6cb1">setNumberOfModifications</a> (<a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> number_of_mods)=0</td></tr>
<tr class="memdesc:a42afad5b2df41f737839ebf8e31d6cb1"><td class="mdescLeft"> </td><td class="mdescRight">setter for number of modifications <a href="#a42afad5b2df41f737839ebf8e31d6cb1">More...</a><br/></td></tr>
<tr class="separator:a42afad5b2df41f737839ebf8e31d6cb1"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a758e89b9a3f517a9a496a354b7e2f86e"><td class="memItemLeft" align="right" valign="top">virtual <a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SuffixArray.html#a758e89b9a3f517a9a496a354b7e2f86e">getNumberOfModifications</a> ()=0</td></tr>
<tr class="memdesc:a758e89b9a3f517a9a496a354b7e2f86e"><td class="mdescLeft"> </td><td class="mdescRight">getter for number of modifications <a href="#a758e89b9a3f517a9a496a354b7e2f86e">More...</a><br/></td></tr>
<tr class="separator:a758e89b9a3f517a9a496a354b7e2f86e"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a85e900bc7d60e593b51054ae7ebf72ea"><td class="memItemLeft" align="right" valign="top">virtual void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SuffixArray.html#a85e900bc7d60e593b51054ae7ebf72ea">printStatistic</a> ()=0</td></tr>
<tr class="memdesc:a85e900bc7d60e593b51054ae7ebf72ea"><td class="mdescLeft"> </td><td class="mdescRight">output for statistic <a href="#a85e900bc7d60e593b51054ae7ebf72ea">More...</a><br/></td></tr>
<tr class="separator:a85e900bc7d60e593b51054ae7ebf72ea"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a7d57710f630ba50753236ec1860bc096"><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>
<tr class="memdesc:a7d57710f630ba50753236ec1860bc096"><td class="mdescLeft"> </td><td class="mdescRight">constructor <a href="#a7d57710f630ba50753236ec1860bc096">More...</a><br/></td></tr>
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<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
<div class="textblock"><p>abstract class for suffix array </p>
</div><h2 class="groupheader">Constructor & Destructor Documentation</h2>
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<td class="memname"><a class="el" href="classOpenMS_1_1SuffixArray.html">SuffixArray</a> </td>
<td>(</td>
<td class="paramtype">const <a class="el" href="classOpenMS_1_1String.html">String</a> & </td>
<td class="paramname"><em>st</em>, </td>
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<td class="paramtype">const <a class="el" href="classOpenMS_1_1String.html">String</a> & </td>
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<p>constructor taking the string and the filename for writing or reading </p>
<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramname">st</td><td>the string as const reference with which the suffix array will be build </td></tr>
<tr><td class="paramname">filename</td><td>the filename for writing or reading the suffix array </td></tr>
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</dd>
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<dl class="exception"><dt>Exceptions</dt><dd>
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<tr><td class="paramname"><a class="el" href="classOpenMS_1_1Exception_1_1InvalidValue.html" title="Invalid value exception. ">Exception::InvalidValue</a></td><td>if string does not start with empty string ($) </td></tr>
<tr><td class="paramname"><a class="el" href="classOpenMS_1_1Exception_1_1FileNotFound.html" title="File not found exception. ">Exception::FileNotFound</a></td><td>is thrown if the given filename is not found </td></tr>
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<td class="memname"><a class="el" href="classOpenMS_1_1SuffixArray.html">SuffixArray</a> </td>
<td>(</td>
<td class="paramtype">const <a class="el" href="classOpenMS_1_1SuffixArray.html">SuffixArray</a> & </td>
<td class="paramname"><em>sa</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_1SuffixArray.html">SuffixArray</a> </td>
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<span class="mlabels"><span class="mlabel">pure virtual</span></span> </td>
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<p>destructor </p>
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<td class="memname"><a class="el" href="classOpenMS_1_1SuffixArray.html">SuffixArray</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">virtual void findSpec </td>
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<td class="paramtype">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> > > > & </td>
<td class="paramname"><em>candidates</em>, </td>
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<td class="paramtype">const std::vector< <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> > & </td>
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<p>the function that will find all peptide candidates for a given spectrum </p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">spec</td><td>const reference of DoubleReal vector describing the spectrum </td></tr>
<tr><td class="paramname">candidates</td><td>the candidates which are returned for the masses given in spec </td></tr>
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</dd>
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<dl class="section return"><dt>Returns</dt><dd>a vector of SignedSize pairs. </dd></dl>
<dl class="exception"><dt>Exceptions</dt><dd>
<table class="exception">
<tr><td class="paramname">InvalidValue</td><td>if the spectrum is not sorted ascendingly </td></tr>
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</dd>
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<p>Implemented in <a class="el" href="classOpenMS_1_1SuffixArraySeqan.html#aa78cc1ec6532c467e25f892d1a649e1d">SuffixArraySeqan</a>, and <a class="el" href="classOpenMS_1_1SuffixArrayTrypticCompressed.html#aa78cc1ec6532c467e25f892d1a649e1d">SuffixArrayTrypticCompressed</a>.</p>
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<td class="memname">virtual <a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> getNumberOfModifications </td>
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<p>getter for number of modifications </p>
<dl class="section return"><dt>Returns</dt><dd>Size describing number of modifications </dd></dl>
<p>Implemented in <a class="el" href="classOpenMS_1_1SuffixArraySeqan.html#a30dec5fbc364fa6168ef5c28d2ce988f">SuffixArraySeqan</a>, and <a class="el" href="classOpenMS_1_1SuffixArrayTrypticCompressed.html#a30dec5fbc364fa6168ef5c28d2ce988f">SuffixArrayTrypticCompressed</a>.</p>
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<td class="memname">virtual const std::vector<<a class="el" href="classOpenMS_1_1String.html">String</a>>& getTags </td>
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<p>getter for tags </p>
<dl class="section return"><dt>Returns</dt><dd>const vector of string with tags </dd></dl>
<p>Implemented in <a class="el" href="classOpenMS_1_1SuffixArraySeqan.html#a35995e158ba0a000e682986f2ab57160">SuffixArraySeqan</a>, and <a class="el" href="classOpenMS_1_1SuffixArrayTrypticCompressed.html#ad8e969d3476318682e49a4e03ec5ca80">SuffixArrayTrypticCompressed</a>.</p>
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<td class="memname">virtual <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> getTolerance </td>
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<p>getter for tolerance </p>
<dl class="section return"><dt>Returns</dt><dd>DoubleReal with tolerance </dd></dl>
<p>Implemented in <a class="el" href="classOpenMS_1_1SuffixArraySeqan.html#a8a62378185408f6af2e4349e6037b32a">SuffixArraySeqan</a>, and <a class="el" href="classOpenMS_1_1SuffixArrayTrypticCompressed.html#a8a62378185408f6af2e4349e6037b32a">SuffixArrayTrypticCompressed</a>.</p>
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<td class="memname">virtual bool getUseTags </td>
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<p>getter for use_tags </p>
<dl class="section return"><dt>Returns</dt><dd>bool indicating whether tags are used or not </dd></dl>
<p>Implemented in <a class="el" href="classOpenMS_1_1SuffixArraySeqan.html#a65ab7ffcdc877e66b410aa4bc92935fb">SuffixArraySeqan</a>, and <a class="el" href="classOpenMS_1_1SuffixArrayTrypticCompressed.html#a65ab7ffcdc877e66b410aa4bc92935fb">SuffixArrayTrypticCompressed</a>.</p>
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<td class="memname">virtual bool isDigestingEnd </td>
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<p>returns if an enzyme will cut after first character </p>
<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramname">aa1</td><td>const char as first aminoacid </td></tr>
<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 describing if it is a digesting site </dd></dl>
<p>Implemented in <a class="el" href="classOpenMS_1_1SuffixArraySeqan.html#a9eedb3b9aa20ef87f387b54c9e7813d7">SuffixArraySeqan</a>, <a class="el" href="classOpenMS_1_1SuffixArrayTrypticCompressed.html#a9eedb3b9aa20ef87f387b54c9e7813d7">SuffixArrayTrypticCompressed</a>, and <a class="el" href="classOpenMS_1_1SuffixArrayTrypticSeqan.html#a9eedb3b9aa20ef87f387b54c9e7813d7">SuffixArrayTrypticSeqan</a>.</p>
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<td class="memname">virtual bool open </td>
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<td class="paramtype">const <a class="el" href="classOpenMS_1_1String.html">String</a> & </td>
<td class="paramname"><em>filename</em></td><td>)</td>
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<p>opens the suffix array </p>
<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramname">filename</td><td>const reference string describing the filename </td></tr>
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</dd>
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<dl class="section return"><dt>Returns</dt><dd>bool if operation was succesful </dd></dl>
<dl class="exception"><dt>Exceptions</dt><dd>
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<tr><td class="paramname">FileNotFound</td><td></td></tr>
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</dd>
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<p>Implemented in <a class="el" href="classOpenMS_1_1SuffixArraySeqan.html#a439f6d35e3fe7db057e9bf13f42a2485">SuffixArraySeqan</a>, and <a class="el" href="classOpenMS_1_1SuffixArrayTrypticCompressed.html#aae96c10617e1b87cb5a1960aa9855a49">SuffixArrayTrypticCompressed</a>.</p>
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<td class="memname">virtual void printStatistic </td>
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<p>output for statistic </p>
<p>Implemented in <a class="el" href="classOpenMS_1_1SuffixArraySeqan.html#af51327da313f22aa8cb1abebb11cebe5">SuffixArraySeqan</a>, and <a class="el" href="classOpenMS_1_1SuffixArrayTrypticCompressed.html#af51327da313f22aa8cb1abebb11cebe5">SuffixArrayTrypticCompressed</a>.</p>
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<td class="memname">virtual bool save </td>
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<p>saves the suffix array to disc </p>
<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramname">filename</td><td>const reference string describing the filename </td></tr>
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<dl class="section return"><dt>Returns</dt><dd>bool if operation was succesful </dd></dl>
<dl class="exception"><dt>Exceptions</dt><dd>
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<tr><td class="paramname">UnableToCreateFile</td><td>if file could not be created (e.x. if you have no rigths) </td></tr>
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<p>Implemented in <a class="el" href="classOpenMS_1_1SuffixArraySeqan.html#af055ab1935e7aa87eb45534e2d26115c">SuffixArraySeqan</a>, and <a class="el" href="classOpenMS_1_1SuffixArrayTrypticCompressed.html#a1c7203771149727e897bac6c1ce88a7f">SuffixArrayTrypticCompressed</a>.</p>
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<td class="memname">virtual void setNumberOfModifications </td>
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<td class="paramtype"><a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> </td>
<td class="paramname"><em>number_of_mods</em></td><td>)</td>
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<p>setter for number of modifications </p>
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<p>Implemented in <a class="el" href="classOpenMS_1_1SuffixArraySeqan.html#a04c30ff2f4f8f35549000277592c9e8d">SuffixArraySeqan</a>, and <a class="el" href="classOpenMS_1_1SuffixArrayTrypticCompressed.html#a04c30ff2f4f8f35549000277592c9e8d">SuffixArrayTrypticCompressed</a>.</p>
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<td class="memname">virtual void setTags </td>
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<td class="paramtype">const std::vector< <a class="el" href="classOpenMS_1_1String.html">String</a> > & </td>
<td class="paramname"><em>tags</em></td><td>)</td>
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<p>setter for tags </p>
<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramname">tags</td><td>const vector of strings with tags with length 3 each </td></tr>
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<dl class="exception"><dt>Exceptions</dt><dd>
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<tr><td class="paramname"><a class="el" href="classOpenMS_1_1Exception_1_1InvalidValue.html" title="Invalid value exception. ">Exception::InvalidValue</a></td><td>if at least one tag does not have size of 3 </td></tr>
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<p>Implemented in <a class="el" href="classOpenMS_1_1SuffixArraySeqan.html#a89089f1b7138b71dfa5096c51367632b">SuffixArraySeqan</a>, and <a class="el" href="classOpenMS_1_1SuffixArrayTrypticCompressed.html#a516052dbb7b4b3769779821175153957">SuffixArrayTrypticCompressed</a>.</p>
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<td class="memname">virtual void setTolerance </td>
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<td class="paramname"><em>t</em></td><td>)</td>
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<p>setter for tolerance </p>
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<tr><td class="paramname">t</td><td>DoubleReal with tolerance </td></tr>
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<dl class="exception"><dt>Exceptions</dt><dd>
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<tr><td class="paramname">InvalidValue</td><td>if tolerance is negative </td></tr>
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<p>Implemented in <a class="el" href="classOpenMS_1_1SuffixArraySeqan.html#a946a09425e78f45c9cc2b921d72e8409">SuffixArraySeqan</a>, and <a class="el" href="classOpenMS_1_1SuffixArrayTrypticCompressed.html#a946a09425e78f45c9cc2b921d72e8409">SuffixArrayTrypticCompressed</a>.</p>
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<td class="memname">virtual void setUseTags </td>
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<td class="paramname"><em>use_tags</em></td><td>)</td>
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<p>setter for use_tags </p>
<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramname">use_tags</td><td>indicating whether tags should be used or not </td></tr>
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<p>Implemented in <a class="el" href="classOpenMS_1_1SuffixArraySeqan.html#ab2650d016b9e7eaf4574d44817868f3d">SuffixArraySeqan</a>, and <a class="el" href="classOpenMS_1_1SuffixArrayTrypticCompressed.html#ab2650d016b9e7eaf4574d44817868f3d">SuffixArrayTrypticCompressed</a>.</p>
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<td class="memname">virtual <a class="el" href="classOpenMS_1_1String.html">String</a> toString </td>
<td>(</td>
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<span class="mlabels"><span class="mlabel">pure virtual</span></span> </td>
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<p>transforms suffix array to a printable <a class="el" href="classOpenMS_1_1String.html" title="A more convenient string class. ">String</a> </p>
<p>Implemented in <a class="el" href="classOpenMS_1_1SuffixArraySeqan.html#ad146fa8579a5f8a876c4688cc5a68520">SuffixArraySeqan</a>, and <a class="el" href="classOpenMS_1_1SuffixArrayTrypticCompressed.html#ad146fa8579a5f8a876c4688cc5a68520">SuffixArrayTrypticCompressed</a>.</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 11:19:29 using doxygen 1.8.5</font></TD>
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