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<HTML>
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<TITLE>SuffixArrayPeptideFinder 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_1SuffixArrayPeptideFinder.html">SuffixArrayPeptideFinder</a></li> </ul>
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<a href="#pub-types">Public Types</a> |
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<div class="title">SuffixArrayPeptideFinder Class Reference</div> </div>
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<p>wrapper for easy use of sufArray
<a href="classOpenMS_1_1SuffixArrayPeptideFinder.html#details">More...</a></p>
<p><code>#include <<a class="el" href="SuffixArrayPeptideFinder_8h_source.html">OpenMS/DATASTRUCTURES/SuffixArrayPeptideFinder.h</a>></code></p>
<div class="dynheader">
Inheritance diagram for SuffixArrayPeptideFinder:</div>
<div class="dyncontent">
<div class="center">
<img src="classOpenMS_1_1SuffixArrayPeptideFinder.png" usemap="#SuffixArrayPeptideFinder_map" alt=""/>
<map id="SuffixArrayPeptideFinder_map" name="SuffixArrayPeptideFinder_map">
<area href="classOpenMS_1_1WeightWrapper.html" title="Encapsulated weight queries to simplify mono vs average weight computation. " alt="WeightWrapper" shape="rect" coords="0,0,156,24"/>
</map>
</div></div>
<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_1SuffixArrayPeptideFinder.html#a21b87598c52cebe4ab2ebc0bb1655e89">FASTAEntry</a></td></tr>
<tr class="separator:a21b87598c52cebe4ab2ebc0bb1655e89"><td class="memSeparator" colspan="2"> </td></tr>
<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>
<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,
<a class="el" href="classOpenMS_1_1WeightWrapper.html#aa0e0675e46f34052468f523f1c8aff2ba3828195437a1112429b5c7a3e8780570">MONO</a>,
<a class="el" href="classOpenMS_1_1WeightWrapper.html#aa0e0675e46f34052468f523f1c8aff2ba4226c2437cbb49f44511f47e1bde3109">SIZE_OF_WEIGHTMODE</a>
}</td></tr>
<tr class="separator:aa0e0675e46f34052468f523f1c8aff2b inherit pub_types_classOpenMS_1_1WeightWrapper"><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:aa94cda92b39e823c650d667a1ada6f32"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SuffixArrayPeptideFinder.html#aa94cda92b39e823c650d667a1ada6f32">SuffixArrayPeptideFinder</a> (const <a class="el" href="classOpenMS_1_1String.html">String</a> &filename, const <a class="el" href="classOpenMS_1_1String.html">String</a> &method, 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>
<tr class="memdesc:aa94cda92b39e823c650d667a1ada6f32"><td class="mdescLeft"> </td><td class="mdescRight">constructor <a href="#aa94cda92b39e823c650d667a1ada6f32">More...</a><br/></td></tr>
<tr class="separator:aa94cda92b39e823c650d667a1ada6f32"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a4cfe93f01ea66eb8adc71135b21d1ce8"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SuffixArrayPeptideFinder.html#a4cfe93f01ea66eb8adc71135b21d1ce8">SuffixArrayPeptideFinder</a> (const <a class="el" href="classOpenMS_1_1SuffixArrayPeptideFinder.html">SuffixArrayPeptideFinder</a> &source)</td></tr>
<tr class="memdesc:a4cfe93f01ea66eb8adc71135b21d1ce8"><td class="mdescLeft"> </td><td class="mdescRight">copy constructor <a href="#a4cfe93f01ea66eb8adc71135b21d1ce8">More...</a><br/></td></tr>
<tr class="separator:a4cfe93f01ea66eb8adc71135b21d1ce8"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a6c106052fd680e3d0705c24c36923108"><td class="memItemLeft" align="right" valign="top">virtual </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SuffixArrayPeptideFinder.html#a6c106052fd680e3d0705c24c36923108">~SuffixArrayPeptideFinder</a> ()</td></tr>
<tr class="memdesc:a6c106052fd680e3d0705c24c36923108"><td class="mdescLeft"> </td><td class="mdescRight">destructor <a href="#a6c106052fd680e3d0705c24c36923108">More...</a><br/></td></tr>
<tr class="separator:a6c106052fd680e3d0705c24c36923108"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a4a5d3bc1a017931bc09e109ab94eb42b"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SuffixArrayPeptideFinder.html#a4a5d3bc1a017931bc09e109ab94eb42b">getCandidates</a> (std::vector< std::vector< std::pair< <a class="el" href="classOpenMS_1_1SuffixArrayPeptideFinder.html#a21b87598c52cebe4ab2ebc0bb1655e89">FASTAEntry</a>, <a class="el" href="classOpenMS_1_1String.html">String</a> > > > &candidates, const std::vector< <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> > &spec)</td></tr>
<tr class="memdesc:a4a5d3bc1a017931bc09e109ab94eb42b"><td class="mdescLeft"> </td><td class="mdescRight">finds all candidates for given spectrum in the suffix array <a href="#a4a5d3bc1a017931bc09e109ab94eb42b">More...</a><br/></td></tr>
<tr class="separator:a4a5d3bc1a017931bc09e109ab94eb42b"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a0d6683cf91e5041c65b1150100e1e6af"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SuffixArrayPeptideFinder.html#a0d6683cf91e5041c65b1150100e1e6af">getCandidates</a> (std::vector< std::vector< std::pair< <a class="el" href="classOpenMS_1_1SuffixArrayPeptideFinder.html#a21b87598c52cebe4ab2ebc0bb1655e89">FASTAEntry</a>, <a class="el" href="classOpenMS_1_1String.html">String</a> > > > &candidates, const <a class="el" href="classOpenMS_1_1String.html">String</a> &DTA_file)</td></tr>
<tr class="memdesc:a0d6683cf91e5041c65b1150100e1e6af"><td class="mdescLeft"> </td><td class="mdescRight">finds all candidate for given DTA file <a href="#a0d6683cf91e5041c65b1150100e1e6af">More...</a><br/></td></tr>
<tr class="separator:a0d6683cf91e5041c65b1150100e1e6af"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a3876c1a05342180cf155b3ec0f3c759b"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SuffixArrayPeptideFinder.html#a3876c1a05342180cf155b3ec0f3c759b">setTolerance</a> (const <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> t)</td></tr>
<tr class="memdesc:a3876c1a05342180cf155b3ec0f3c759b"><td class="mdescLeft"> </td><td class="mdescRight">allowed tolerance for mass match <a href="#a3876c1a05342180cf155b3ec0f3c759b">More...</a><br/></td></tr>
<tr class="separator:a3876c1a05342180cf155b3ec0f3c759b"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a8a62378185408f6af2e4349e6037b32a"><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_1SuffixArrayPeptideFinder.html#a8a62378185408f6af2e4349e6037b32a">getTolerance</a> () const </td></tr>
<tr class="memdesc:a8a62378185408f6af2e4349e6037b32a"><td class="mdescLeft"> </td><td class="mdescRight">allowed tolerance for mass match <a href="#a8a62378185408f6af2e4349e6037b32a">More...</a><br/></td></tr>
<tr class="separator:a8a62378185408f6af2e4349e6037b32a"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a923f68e74c7b952fc7acb4f4aa3f4dcc"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SuffixArrayPeptideFinder.html#a923f68e74c7b952fc7acb4f4aa3f4dcc">setNumberOfModifications</a> (<a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> number_of_mods) const </td></tr>
<tr class="memdesc:a923f68e74c7b952fc7acb4f4aa3f4dcc"><td class="mdescLeft"> </td><td class="mdescRight">setter for number of modifications <a href="#a923f68e74c7b952fc7acb4f4aa3f4dcc">More...</a><br/></td></tr>
<tr class="separator:a923f68e74c7b952fc7acb4f4aa3f4dcc"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a9093aa103751307fb7fc728347d6606e"><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_1SuffixArrayPeptideFinder.html#a9093aa103751307fb7fc728347d6606e">getNumberOfModifications</a> () const </td></tr>
<tr class="memdesc:a9093aa103751307fb7fc728347d6606e"><td class="mdescLeft"> </td><td class="mdescRight">getter for number of modifications <a href="#a9093aa103751307fb7fc728347d6606e">More...</a><br/></td></tr>
<tr class="separator:a9093aa103751307fb7fc728347d6606e"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a516052dbb7b4b3769779821175153957"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SuffixArrayPeptideFinder.html#a516052dbb7b4b3769779821175153957">setTags</a> (const std::vector< <a class="el" href="classOpenMS_1_1String.html">String</a> > &tags)</td></tr>
<tr class="memdesc:a516052dbb7b4b3769779821175153957"><td class="mdescLeft"> </td><td class="mdescRight">setter for tags <a href="#a516052dbb7b4b3769779821175153957">More...</a><br/></td></tr>
<tr class="separator:a516052dbb7b4b3769779821175153957"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ad8e969d3476318682e49a4e03ec5ca80"><td class="memItemLeft" align="right" valign="top">const std::vector< <a class="el" href="classOpenMS_1_1String.html">String</a> > & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SuffixArrayPeptideFinder.html#ad8e969d3476318682e49a4e03ec5ca80">getTags</a> ()</td></tr>
<tr class="memdesc:ad8e969d3476318682e49a4e03ec5ca80"><td class="mdescLeft"> </td><td class="mdescRight">getter for tags <a href="#ad8e969d3476318682e49a4e03ec5ca80">More...</a><br/></td></tr>
<tr class="separator:ad8e969d3476318682e49a4e03ec5ca80"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ab2650d016b9e7eaf4574d44817868f3d"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SuffixArrayPeptideFinder.html#ab2650d016b9e7eaf4574d44817868f3d">setUseTags</a> (bool use_tags)</td></tr>
<tr class="memdesc:ab2650d016b9e7eaf4574d44817868f3d"><td class="mdescLeft"> </td><td class="mdescRight">setter for use_tags <a href="#ab2650d016b9e7eaf4574d44817868f3d">More...</a><br/></td></tr>
<tr class="separator:ab2650d016b9e7eaf4574d44817868f3d"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a65ab7ffcdc877e66b410aa4bc92935fb"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SuffixArrayPeptideFinder.html#a65ab7ffcdc877e66b410aa4bc92935fb">getUseTags</a> ()</td></tr>
<tr class="memdesc:a65ab7ffcdc877e66b410aa4bc92935fb"><td class="mdescLeft"> </td><td class="mdescRight">getter for use_tags <a href="#a65ab7ffcdc877e66b410aa4bc92935fb">More...</a><br/></td></tr>
<tr class="separator:a65ab7ffcdc877e66b410aa4bc92935fb"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ab4636faec99f9a1d895e440b69b54a91"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SuffixArrayPeptideFinder.html#ab4636faec99f9a1d895e440b69b54a91">setModificationOutputMethod</a> (const <a class="el" href="classOpenMS_1_1String.html">String</a> &s)</td></tr>
<tr class="memdesc:ab4636faec99f9a1d895e440b69b54a91"><td class="mdescLeft"> </td><td class="mdescRight">set modification output method (valid are: "mass", "stringUnchecked", "stringChecked") <a href="#ab4636faec99f9a1d895e440b69b54a91">More...</a><br/></td></tr>
<tr class="separator:ab4636faec99f9a1d895e440b69b54a91"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a38060c5d1f3cd095bc4cbdfdea1f3b4b"><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_1SuffixArrayPeptideFinder.html#a38060c5d1f3cd095bc4cbdfdea1f3b4b">getModificationOutputMethod</a> ()</td></tr>
<tr class="memdesc:a38060c5d1f3cd095bc4cbdfdea1f3b4b"><td class="mdescLeft"> </td><td class="mdescRight">getter for modification output method <a href="#a38060c5d1f3cd095bc4cbdfdea1f3b4b">More...</a><br/></td></tr>
<tr class="separator:a38060c5d1f3cd095bc4cbdfdea1f3b4b"><td class="memSeparator" colspan="2"> </td></tr>
<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>
<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>
<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>
<tr class="separator:ad17dfc0067cbade3b4862477bb535c83 inherit pub_methods_classOpenMS_1_1WeightWrapper"><td class="memSeparator" colspan="2"> </td></tr>
<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>
<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>
<tr class="separator:a60ffdc2b9c2147851399c529b1a1fd51 inherit pub_methods_classOpenMS_1_1WeightWrapper"><td class="memSeparator" colspan="2"> </td></tr>
<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>
<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>
<tr class="separator:a0f2c08d0cebb514fee6ba050bb17aa0f inherit pub_methods_classOpenMS_1_1WeightWrapper"><td class="memSeparator" colspan="2"> </td></tr>
<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>
<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>
<tr class="separator:acf810b578f701801ea752d534d7fcbe9 inherit pub_methods_classOpenMS_1_1WeightWrapper"><td class="memSeparator" colspan="2"> </td></tr>
<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>
<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>
<tr class="separator:a86f49dcf25cd06d439db0390ae5604b5 inherit pub_methods_classOpenMS_1_1WeightWrapper"><td class="memSeparator" colspan="2"> </td></tr>
<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>
<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>
<tr class="separator:a12c0a3ef8cbe7321db6724f92ba07730 inherit pub_methods_classOpenMS_1_1WeightWrapper"><td class="memSeparator" colspan="2"> </td></tr>
<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>
<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>
<tr class="separator:af26fbe119eda2461447f2312786531f6 inherit pub_methods_classOpenMS_1_1WeightWrapper"><td class="memSeparator" colspan="2"> </td></tr>
<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>
<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="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>
<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="heading"><td colspan="2"><h2 class="groupheader"><a name="pro-methods"></a>
Protected Member Functions</h2></td></tr>
<tr class="memitem:a13e8c30f5dc4bc18299c97769c45838e"><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_1SuffixArrayPeptideFinder.html#a13e8c30f5dc4bc18299c97769c45838e">vToString_</a> (std::vector< <a class="el" href="classOpenMS_1_1String.html">String</a> > v)</td></tr>
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<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pro-attribs"></a>
Protected Attributes</h2></td></tr>
<tr class="memitem:a884def75ab638a8e8b30783f9193a9cd"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1BigString.html">BigString</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SuffixArrayPeptideFinder.html#a884def75ab638a8e8b30783f9193a9cd">big_string_</a></td></tr>
<tr class="memdesc:a884def75ab638a8e8b30783f9193a9cd"><td class="mdescLeft"> </td><td class="mdescRight">bigString object holding all peptides of fasta file <a href="#a884def75ab638a8e8b30783f9193a9cd">More...</a><br/></td></tr>
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<tr class="memitem:ae86d4c23eec1ed13295ae0b1c8261631"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1SuffixArray.html">SuffixArray</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SuffixArrayPeptideFinder.html#ae86d4c23eec1ed13295ae0b1c8261631">sa_</a></td></tr>
<tr class="memdesc:ae86d4c23eec1ed13295ae0b1c8261631"><td class="mdescLeft"> </td><td class="mdescRight">pointer to suffixarray <a href="#ae86d4c23eec1ed13295ae0b1c8261631">More...</a><br/></td></tr>
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<tr class="memitem:a1fc49a7a70a5d955ff3bdb43b52cab5b"><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_1SuffixArrayPeptideFinder.html#a1fc49a7a70a5d955ff3bdb43b52cab5b">modification_output_method_</a></td></tr>
<tr class="memdesc:a1fc49a7a70a5d955ff3bdb43b52cab5b"><td class="mdescLeft"> </td><td class="mdescRight">output method for modifications <a href="#a1fc49a7a70a5d955ff3bdb43b52cab5b">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>wrapper for easy use of sufArray </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_1SuffixArrayPeptideFinder.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_1SuffixArrayPeptideFinder.html">SuffixArrayPeptideFinder</a> </td>
<td>(</td>
<td class="paramtype">const <a class="el" href="classOpenMS_1_1String.html">String</a> & </td>
<td class="paramname"><em>filename</em>, </td>
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<td class="paramtype">const <a class="el" href="classOpenMS_1_1String.html">String</a> & </td>
<td class="paramname"><em>method</em>, </td>
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<td class="paramtype">const <a class="el" href="classOpenMS_1_1WeightWrapper.html#aa0e0675e46f34052468f523f1c8aff2b">WeightWrapper::WEIGHTMODE</a> </td>
<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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<p>constructor </p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">filename</td><td>FASTA <a class="el" href="classOpenMS_1_1File.html" title="Basic file handling operations. ">File</a> name </td></tr>
<tr><td class="paramname">method</td><td>Name of the method used (trypticCompressed, seqan, trypticSeqan) </td></tr>
<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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<tr><td class="paramname">FileNotFound</td><td>is thrown if the filename is not found </td></tr>
<tr><td class="paramname">ParseError</td><td>is thrown if a error in parsing of the fasta file occurs </td></tr>
<tr><td class="paramname">InvalidValue</td><td>is thrown if an unknown method is supplied </td></tr>
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<td class="memname"><a class="el" href="classOpenMS_1_1SuffixArrayPeptideFinder.html">SuffixArrayPeptideFinder</a> </td>
<td>(</td>
<td class="paramtype">const <a class="el" href="classOpenMS_1_1SuffixArrayPeptideFinder.html">SuffixArrayPeptideFinder</a> & </td>
<td class="paramname"><em>source</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_1SuffixArrayPeptideFinder.html">SuffixArrayPeptideFinder</a> </td>
<td>(</td>
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<span class="mlabels"><span class="mlabel">virtual</span></span> </td>
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<p>destructor </p>
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<h2 class="groupheader">Member Function Documentation</h2>
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<td class="memname">void getCandidates </td>
<td>(</td>
<td class="paramtype">std::vector< std::vector< std::pair< <a class="el" href="classOpenMS_1_1SuffixArrayPeptideFinder.html#a21b87598c52cebe4ab2ebc0bb1655e89">FASTAEntry</a>, <a class="el" href="classOpenMS_1_1String.html">String</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>
<td class="paramname"><em>spec</em> </td>
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<p>finds all candidates for given spectrum in the suffix array </p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">spec</td><td>vector holding the mass values to query </td></tr>
<tr><td class="paramname">candidates</td><td>Output holding the candidates for input masses (one vector per mass) FASTAEntry contains the FASTA header and the peptide sequence The <a class="el" href="classOpenMS_1_1String.html" title="A more convenient string class. ">String</a> contains the modification (if any) in the format specified by <a class="el" href="classOpenMS_1_1SuffixArrayPeptideFinder.html#a38060c5d1f3cd095bc4cbdfdea1f3b4b" title="getter for modification output method ">getModificationOutputMethod()</a> </td></tr>
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<dl class="section see"><dt>See Also</dt><dd>sufArray.h </dd></dl>
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<td class="memname">void getCandidates </td>
<td>(</td>
<td class="paramtype">std::vector< std::vector< std::pair< <a class="el" href="classOpenMS_1_1SuffixArrayPeptideFinder.html#a21b87598c52cebe4ab2ebc0bb1655e89">FASTAEntry</a>, <a class="el" href="classOpenMS_1_1String.html">String</a> > > > & </td>
<td class="paramname"><em>candidates</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>
<td class="paramname"><em>DTA_file</em> </td>
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<p>finds all candidate for given DTA file </p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">DTA_file</td><td>DTA file location </td></tr>
<tr><td class="paramname">candidates</td><td>Output parameters which holds the candidates suitable for the mass given in the dta file FASTAEntry contains the FASTA header and the peptide sequence The <a class="el" href="classOpenMS_1_1String.html" title="A more convenient string class. ">String</a> contains the modification (if any) in the format specified by <a class="el" href="classOpenMS_1_1SuffixArrayPeptideFinder.html#a38060c5d1f3cd095bc4cbdfdea1f3b4b" title="getter for modification output method ">getModificationOutputMethod()</a> </td></tr>
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<dl class="exception"><dt>Exceptions</dt><dd>
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<tr><td class="paramname">FileNotFound</td><td>if DTA file does not exists </td></tr>
<tr><td class="paramname">ParseError</td><td>is thrown if the dta file could not be parsed </td></tr>
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<dl class="section see"><dt>See Also</dt><dd>sufArray.h </dd></dl>
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<td class="memname"><a class="el" href="classOpenMS_1_1String.html">String</a> getModificationOutputMethod </td>
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<p>getter for modification output method </p>
<dl class="section return"><dt>Returns</dt><dd><a class="el" href="classOpenMS_1_1String.html" title="A more convenient string class. ">String</a> </dd></dl>
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<td class="memname"><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>number of modifications </dd></dl>
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<td class="memname">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 reference to vector of strings </dd></dl>
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<td class="memname"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> getTolerance </td>
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<p>allowed tolerance for mass match </p>
<dl class="section return"><dt>Returns</dt><dd>Tolerance in u </dd></dl>
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<td class="memname">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>
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<td class="memname">void setModificationOutputMethod </td>
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<p>set modification output method (valid are: "mass", "stringUnchecked", "stringChecked") </p>
<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramname">s</td><td>describing how modifications sould be given back </td></tr>
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<td class="memname">void setNumberOfModifications </td>
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<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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<td class="memname">void setTags </td>
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<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>reference to vector of strings with tags </td></tr>
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<dl class="section note"><dt>Note</dt><dd>sets use_tags = true </dd></dl>
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<td class="memname">void setTolerance </td>
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<p>allowed tolerance for mass match </p>
<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramname">t</td><td>Tolerance in u </td></tr>
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<td class="memname">void setUseTags </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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<td class="memname"><a class="el" href="classOpenMS_1_1String.html">String</a> vToString_ </td>
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<td class="paramname"><em>v</em></td><td>)</td>
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<h2 class="groupheader">Member Data Documentation</h2>
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<td class="memname"><a class="el" href="classOpenMS_1_1BigString.html">BigString</a> big_string_</td>
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<p>bigString object holding all peptides of fasta file </p>
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<td class="memname"><a class="el" href="classOpenMS_1_1String.html">String</a> modification_output_method_</td>
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<p>output method for modifications </p>
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<td class="memname"><a class="el" href="classOpenMS_1_1SuffixArray.html">SuffixArray</a>* sa_</td>
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<p>pointer to suffixarray </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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