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<TITLE>EdwardsLippertIterator 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_1EdwardsLippertIterator.html">EdwardsLippertIterator</a></li> </ul>
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<a href="#pub-types">Public Types</a> |
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<a href="#pub-methods">Public Member Functions</a> |
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<a href="#pub-static-methods">Static Public Member Functions</a> |
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<a href="#pro-methods">Protected Member Functions</a> |
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<a href="#pro-attribs">Protected Attributes</a> |
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<a href="classOpenMS_1_1EdwardsLippertIterator-members.html">List of all members</a> </div>
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<div class="title">EdwardsLippertIterator Class Reference</div> </div>
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<p>finds all Peptide Candidates with given masses and given fasta file
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<a href="classOpenMS_1_1EdwardsLippertIterator.html#details">More...</a></p>
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<p><code>#include <<a class="el" href="EdwardsLippertIterator_8h_source.html">OpenMS/CHEMISTRY/EdwardsLippertIterator.h</a>></code></p>
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<div class="dynheader">
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Inheritance diagram for EdwardsLippertIterator:</div>
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<div class="dyncontent">
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<img src="classOpenMS_1_1EdwardsLippertIterator.png" usemap="#EdwardsLippertIterator_map" alt=""/>
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<map id="EdwardsLippertIterator_map" name="EdwardsLippertIterator_map">
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<area href="classOpenMS_1_1PepIterator.html" title="Abstract base class for different peptide iterators. " alt="PepIterator" shape="rect" coords="0,0,179,24"/>
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<area href="classOpenMS_1_1EdwardsLippertIteratorTryptic.html" title="EdwardsLippertIterator that only retrieves tryptic seqences. " alt="EdwardsLippertIteratorTryptic" shape="rect" coords="0,112,179,136"/>
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<table class="memberdecls">
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<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-types"></a>
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Public Types</h2></td></tr>
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<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_1EdwardsLippertIterator.html#a21b87598c52cebe4ab2ebc0bb1655e89">FASTAEntry</a></td></tr>
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<tr class="separator:a21b87598c52cebe4ab2ebc0bb1655e89"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="inherit_header pub_types_classOpenMS_1_1PepIterator"><td colspan="2" onclick="javascript:toggleInherit('pub_types_classOpenMS_1_1PepIterator')"><img src="closed.png" alt="-"/> Public Types inherited from <a class="el" href="classOpenMS_1_1PepIterator.html">PepIterator</a></td></tr>
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<tr class="memitem:a21b87598c52cebe4ab2ebc0bb1655e89 inherit pub_types_classOpenMS_1_1PepIterator"><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_1PepIterator.html#a21b87598c52cebe4ab2ebc0bb1655e89">FASTAEntry</a></td></tr>
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<tr class="separator:a21b87598c52cebe4ab2ebc0bb1655e89 inherit pub_types_classOpenMS_1_1PepIterator"><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="pub-methods"></a>
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Public Member Functions</h2></td></tr>
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<tr class="memitem:add167f2dfba4790474721a1cbd586d59"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1EdwardsLippertIterator.html#add167f2dfba4790474721a1cbd586d59">EdwardsLippertIterator</a> ()</td></tr>
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<tr class="memdesc:add167f2dfba4790474721a1cbd586d59"><td class="mdescLeft"> </td><td class="mdescRight">Constructor. <a href="#add167f2dfba4790474721a1cbd586d59">More...</a><br/></td></tr>
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<tr class="separator:add167f2dfba4790474721a1cbd586d59"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a44c1f7957c78b5559702d9be4b5408ac"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1EdwardsLippertIterator.html#a44c1f7957c78b5559702d9be4b5408ac">EdwardsLippertIterator</a> (const <a class="el" href="classOpenMS_1_1EdwardsLippertIterator.html">EdwardsLippertIterator</a> &)</td></tr>
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<tr class="memdesc:a44c1f7957c78b5559702d9be4b5408ac"><td class="mdescLeft"> </td><td class="mdescRight">Copy Constructor. <a href="#a44c1f7957c78b5559702d9be4b5408ac">More...</a><br/></td></tr>
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<tr class="separator:a44c1f7957c78b5559702d9be4b5408ac"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a71f30695b983ddc3f82e6ff760406a6b"><td class="memItemLeft" align="right" valign="top">virtual </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1EdwardsLippertIterator.html#a71f30695b983ddc3f82e6ff760406a6b">~EdwardsLippertIterator</a> ()</td></tr>
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<tr class="memdesc:a71f30695b983ddc3f82e6ff760406a6b"><td class="mdescLeft"> </td><td class="mdescRight">Destructor. <a href="#a71f30695b983ddc3f82e6ff760406a6b">More...</a><br/></td></tr>
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<tr class="separator:a71f30695b983ddc3f82e6ff760406a6b"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a2468d86d946f361d96ea90bb8e6e28da"><td class="memItemLeft" align="right" valign="top">virtual <a class="el" href="classOpenMS_1_1EdwardsLippertIterator.html#a21b87598c52cebe4ab2ebc0bb1655e89">FASTAEntry</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1EdwardsLippertIterator.html#a2468d86d946f361d96ea90bb8e6e28da">operator*</a> ()</td></tr>
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<tr class="memdesc:a2468d86d946f361d96ea90bb8e6e28da"><td class="mdescLeft"> </td><td class="mdescRight">* operator for getting the value of the iterator <a href="#a2468d86d946f361d96ea90bb8e6e28da">More...</a><br/></td></tr>
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<tr class="separator:a2468d86d946f361d96ea90bb8e6e28da"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a55f6d71bc104d273092993e29f301e72"><td class="memItemLeft" align="right" valign="top">virtual <a class="el" href="classOpenMS_1_1PepIterator.html">PepIterator</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1EdwardsLippertIterator.html#a55f6d71bc104d273092993e29f301e72">operator++</a> ()</td></tr>
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<tr class="memdesc:a55f6d71bc104d273092993e29f301e72"><td class="mdescLeft"> </td><td class="mdescRight">opperator ++ for postincrement <a href="#a55f6d71bc104d273092993e29f301e72">More...</a><br/></td></tr>
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<tr class="separator:a55f6d71bc104d273092993e29f301e72"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a72227229d40a649a89bde5f60d48782e"><td class="memItemLeft" align="right" valign="top">virtual <a class="el" href="classOpenMS_1_1PepIterator.html">PepIterator</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1EdwardsLippertIterator.html#a72227229d40a649a89bde5f60d48782e">operator++</a> (int i)</td></tr>
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<tr class="memdesc:a72227229d40a649a89bde5f60d48782e"><td class="mdescLeft"> </td><td class="mdescRight">opperator ++ for preincrement <a href="#a72227229d40a649a89bde5f60d48782e">More...</a><br/></td></tr>
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<tr class="separator:a72227229d40a649a89bde5f60d48782e"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a7d238aef71f460f8ebe0c267b7b7792b"><td class="memItemLeft" align="right" valign="top">virtual void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1EdwardsLippertIterator.html#a7d238aef71f460f8ebe0c267b7b7792b">setFastaFile</a> (const <a class="el" href="classOpenMS_1_1String.html">String</a> &f)</td></tr>
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<tr class="memdesc:a7d238aef71f460f8ebe0c267b7b7792b"><td class="mdescLeft"> </td><td class="mdescRight">setter for fasta file <a href="#a7d238aef71f460f8ebe0c267b7b7792b">More...</a><br/></td></tr>
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<tr class="separator:a7d238aef71f460f8ebe0c267b7b7792b"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a5bac16112a17e0b3b01ba5e5468e744f"><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_1EdwardsLippertIterator.html#a5bac16112a17e0b3b01ba5e5468e744f">getFastaFile</a> ()</td></tr>
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<tr class="memdesc:a5bac16112a17e0b3b01ba5e5468e744f"><td class="mdescLeft"> </td><td class="mdescRight">getter for FASTA file <a href="#a5bac16112a17e0b3b01ba5e5468e744f">More...</a><br/></td></tr>
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<tr class="separator:a5bac16112a17e0b3b01ba5e5468e744f"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a0b331f554495174d4e957af367a22425"><td class="memItemLeft" align="right" valign="top">virtual void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1EdwardsLippertIterator.html#a0b331f554495174d4e957af367a22425">setTolerance</a> (<a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> t)</td></tr>
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<tr class="memdesc:a0b331f554495174d4e957af367a22425"><td class="mdescLeft"> </td><td class="mdescRight">setter for tolerance <a href="#a0b331f554495174d4e957af367a22425">More...</a><br/></td></tr>
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<tr class="separator:a0b331f554495174d4e957af367a22425"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a3cf6b0a9ead1e00ecdf43310820955e7"><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_1EdwardsLippertIterator.html#a3cf6b0a9ead1e00ecdf43310820955e7">getTolerance</a> ()</td></tr>
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<tr class="memdesc:a3cf6b0a9ead1e00ecdf43310820955e7"><td class="mdescLeft"> </td><td class="mdescRight">getter for tolerance <a href="#a3cf6b0a9ead1e00ecdf43310820955e7">More...</a><br/></td></tr>
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<tr class="separator:a3cf6b0a9ead1e00ecdf43310820955e7"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:abed3a62ee31d0d1add508b20d932fae5"><td class="memItemLeft" align="right" valign="top">virtual void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1EdwardsLippertIterator.html#abed3a62ee31d0d1add508b20d932fae5">setSpectrum</a> (const std::vector< <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> > &s)</td></tr>
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<tr class="memdesc:abed3a62ee31d0d1add508b20d932fae5"><td class="mdescLeft"> </td><td class="mdescRight">setter for spectrum <a href="#abed3a62ee31d0d1add508b20d932fae5">More...</a><br/></td></tr>
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<tr class="separator:abed3a62ee31d0d1add508b20d932fae5"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:ae5d8ae6a47625445018d8a7e416aec1b"><td class="memItemLeft" align="right" valign="top">virtual const std::vector<br class="typebreak"/>
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< <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> > & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1EdwardsLippertIterator.html#ae5d8ae6a47625445018d8a7e416aec1b">getSpectrum</a> ()</td></tr>
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<tr class="memdesc:ae5d8ae6a47625445018d8a7e416aec1b"><td class="mdescLeft"> </td><td class="mdescRight">getter for spectrum <a href="#ae5d8ae6a47625445018d8a7e416aec1b">More...</a><br/></td></tr>
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<tr class="separator:ae5d8ae6a47625445018d8a7e416aec1b"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a50f45551c10ca30a0bc7f447e70188b1"><td class="memItemLeft" align="right" valign="top">virtual bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1EdwardsLippertIterator.html#a50f45551c10ca30a0bc7f447e70188b1">begin</a> ()</td></tr>
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<tr class="memdesc:a50f45551c10ca30a0bc7f447e70188b1"><td class="mdescLeft"> </td><td class="mdescRight">initializing iterator <a href="#a50f45551c10ca30a0bc7f447e70188b1">More...</a><br/></td></tr>
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<tr class="separator:a50f45551c10ca30a0bc7f447e70188b1"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:ae078b21926e77272e3cc2792e8176e33"><td class="memItemLeft" align="right" valign="top">virtual bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1EdwardsLippertIterator.html#ae078b21926e77272e3cc2792e8176e33">isAtEnd</a> ()</td></tr>
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<tr class="memdesc:ae078b21926e77272e3cc2792e8176e33"><td class="mdescLeft"> </td><td class="mdescRight">indicates whether iterator is at end <a href="#ae078b21926e77272e3cc2792e8176e33">More...</a><br/></td></tr>
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<tr class="separator:ae078b21926e77272e3cc2792e8176e33"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a47df1538f6e1b2ae27db5fe98a0b67aa"><td class="memItemLeft" align="right" valign="top">virtual bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1EdwardsLippertIterator.html#a47df1538f6e1b2ae27db5fe98a0b67aa">isDigestingEnd</a> (char, char)</td></tr>
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<tr class="memdesc:a47df1538f6e1b2ae27db5fe98a0b67aa"><td class="mdescLeft"> </td><td class="mdescRight">indicated if a digesting enzyme will cut at this position <a href="#a47df1538f6e1b2ae27db5fe98a0b67aa">More...</a><br/></td></tr>
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<tr class="separator:a47df1538f6e1b2ae27db5fe98a0b67aa"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="inherit_header pub_methods_classOpenMS_1_1PepIterator"><td colspan="2" onclick="javascript:toggleInherit('pub_methods_classOpenMS_1_1PepIterator')"><img src="closed.png" alt="-"/> Public Member Functions inherited from <a class="el" href="classOpenMS_1_1PepIterator.html">PepIterator</a></td></tr>
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<tr class="memitem:aebe4326baeb556ac80ae9429d5037956 inherit pub_methods_classOpenMS_1_1PepIterator"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1PepIterator.html#aebe4326baeb556ac80ae9429d5037956">PepIterator</a> ()</td></tr>
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<tr class="memdesc:aebe4326baeb556ac80ae9429d5037956 inherit pub_methods_classOpenMS_1_1PepIterator"><td class="mdescLeft"> </td><td class="mdescRight">constructor <a href="#aebe4326baeb556ac80ae9429d5037956">More...</a><br/></td></tr>
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<tr class="separator:aebe4326baeb556ac80ae9429d5037956 inherit pub_methods_classOpenMS_1_1PepIterator"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a89afd5646a25e6d814456741c4687e31 inherit pub_methods_classOpenMS_1_1PepIterator"><td class="memItemLeft" align="right" valign="top">virtual </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1PepIterator.html#a89afd5646a25e6d814456741c4687e31">~PepIterator</a> ()</td></tr>
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<tr class="memdesc:a89afd5646a25e6d814456741c4687e31 inherit pub_methods_classOpenMS_1_1PepIterator"><td class="mdescLeft"> </td><td class="mdescRight">destructor <a href="#a89afd5646a25e6d814456741c4687e31">More...</a><br/></td></tr>
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<tr class="separator:a89afd5646a25e6d814456741c4687e31 inherit pub_methods_classOpenMS_1_1PepIterator"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:aa5ee57c068ee8f610d0bf9f231421760 inherit pub_methods_classOpenMS_1_1PepIterator"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1PepIterator.html#aa5ee57c068ee8f610d0bf9f231421760">PepIterator</a> (const <a class="el" href="classOpenMS_1_1PepIterator.html">PepIterator</a> &source)</td></tr>
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<tr class="memdesc:aa5ee57c068ee8f610d0bf9f231421760 inherit pub_methods_classOpenMS_1_1PepIterator"><td class="mdescLeft"> </td><td class="mdescRight">copy constructor <a href="#aa5ee57c068ee8f610d0bf9f231421760">More...</a><br/></td></tr>
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<tr class="separator:aa5ee57c068ee8f610d0bf9f231421760 inherit pub_methods_classOpenMS_1_1PepIterator"><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="pub-static-methods"></a>
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Static Public Member Functions</h2></td></tr>
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<tr class="memitem:af73fd15708e50e77665070023a09cc87"><td class="memItemLeft" align="right" valign="top">static const <a class="el" href="classOpenMS_1_1String.html">String</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1EdwardsLippertIterator.html#af73fd15708e50e77665070023a09cc87">getProductName</a> ()</td></tr>
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<tr class="memdesc:af73fd15708e50e77665070023a09cc87"><td class="mdescLeft"> </td><td class="mdescRight">needed by <a class="el" href="classOpenMS_1_1Factory.html" title="Returns FactoryProduct* based on the name of the desired concrete FactoryProduct. ...">Factory</a> <a href="#af73fd15708e50e77665070023a09cc87">More...</a><br/></td></tr>
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<tr class="separator:af73fd15708e50e77665070023a09cc87"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a8655641304d0f901ffb687edca0b59f8"><td class="memItemLeft" align="right" valign="top">static <a class="el" href="classOpenMS_1_1PepIterator.html">PepIterator</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1EdwardsLippertIterator.html#a8655641304d0f901ffb687edca0b59f8">create</a> ()</td></tr>
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<tr class="memdesc:a8655641304d0f901ffb687edca0b59f8"><td class="mdescLeft"> </td><td class="mdescRight">needed by <a class="el" href="classOpenMS_1_1Factory.html" title="Returns FactoryProduct* based on the name of the desired concrete FactoryProduct. ...">Factory</a> <a href="#a8655641304d0f901ffb687edca0b59f8">More...</a><br/></td></tr>
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<tr class="separator:a8655641304d0f901ffb687edca0b59f8"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="inherit_header pub_static_methods_classOpenMS_1_1PepIterator"><td colspan="2" onclick="javascript:toggleInherit('pub_static_methods_classOpenMS_1_1PepIterator')"><img src="closed.png" alt="-"/> Static Public Member Functions inherited from <a class="el" href="classOpenMS_1_1PepIterator.html">PepIterator</a></td></tr>
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<tr class="memitem:a7899dbe105534dc1f81971dd71a26ff0 inherit pub_static_methods_classOpenMS_1_1PepIterator"><td class="memItemLeft" align="right" valign="top">static void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1PepIterator.html#a7899dbe105534dc1f81971dd71a26ff0">registerChildren</a> ()</td></tr>
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<tr class="memdesc:a7899dbe105534dc1f81971dd71a26ff0 inherit pub_static_methods_classOpenMS_1_1PepIterator"><td class="mdescLeft"> </td><td class="mdescRight">all children has to be registered here <a href="#a7899dbe105534dc1f81971dd71a26ff0">More...</a><br/></td></tr>
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<tr class="separator:a7899dbe105534dc1f81971dd71a26ff0 inherit pub_static_methods_classOpenMS_1_1PepIterator"><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="pro-methods"></a>
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Protected Member Functions</h2></td></tr>
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<tr class="memitem:a63173babfe4e8063832f2ed405f80d91"><td class="memItemLeft" align="right" valign="top">virtual std::string </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1EdwardsLippertIterator.html#a63173babfe4e8063832f2ed405f80d91">next_</a> ()</td></tr>
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<tr class="memdesc:a63173babfe4e8063832f2ed405f80d91"><td class="mdescLeft"> </td><td class="mdescRight">getting the next candidate <a href="#a63173babfe4e8063832f2ed405f80d91">More...</a><br/></td></tr>
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<tr class="memitem:a468aa064b555d0fd15e072ac6fd84d20"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1EdwardsLippertIterator.html#a468aa064b555d0fd15e072ac6fd84d20">hasNext_</a> ()</td></tr>
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<tr class="memdesc:a468aa064b555d0fd15e072ac6fd84d20"><td class="mdescLeft"> </td><td class="mdescRight">indicates if there will be a next element <a href="#a468aa064b555d0fd15e072ac6fd84d20">More...</a><br/></td></tr>
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<tr class="memitem:ae798f8264b42bdbf0830121570a09a09"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1EdwardsLippertIterator.html#ae798f8264b42bdbf0830121570a09a09">goToNextAA_</a> ()</td></tr>
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<tr class="memdesc:ae798f8264b42bdbf0830121570a09a09"><td class="mdescLeft"> </td><td class="mdescRight">finds the next starting position where a digesting enzyme will cut the sequence <a href="#ae798f8264b42bdbf0830121570a09a09">More...</a><br/></td></tr>
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<tr class="memitem:a0a6931a2f0abccd42cf54022538a4026"><td class="memItemLeft" align="right" valign="top">virtual bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1EdwardsLippertIterator.html#a0a6931a2f0abccd42cf54022538a4026">isInSpectrum_</a> (<a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> &mass)</td></tr>
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<tr class="memdesc:a0a6931a2f0abccd42cf54022538a4026"><td class="mdescLeft"> </td><td class="mdescRight">indicates if a mass is in spectrum <a href="#a0a6931a2f0abccd42cf54022538a4026">More...</a><br/></td></tr>
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<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pro-attribs"></a>
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Protected Attributes</h2></td></tr>
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<tr class="memitem:a77bf7467eb8490b89bc16a4565bfb210"><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_1EdwardsLippertIterator.html#a77bf7467eb8490b89bc16a4565bfb210">f_file_</a></td></tr>
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<tr class="memdesc:a77bf7467eb8490b89bc16a4565bfb210"><td class="mdescLeft"> </td><td class="mdescRight">fasta file location <a href="#a77bf7467eb8490b89bc16a4565bfb210">More...</a><br/></td></tr>
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<tr class="memitem:ac721cab8a1772a2739c5ad71f307685b"><td class="memItemLeft" align="right" valign="top">std::string </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1EdwardsLippertIterator.html#ac721cab8a1772a2739c5ad71f307685b">actual_pep_</a></td></tr>
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<tr class="memdesc:ac721cab8a1772a2739c5ad71f307685b"><td class="mdescLeft"> </td><td class="mdescRight">actual peptide <a href="#ac721cab8a1772a2739c5ad71f307685b">More...</a><br/></td></tr>
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<tr class="memitem:a54610da679df141855bfa1eb4be9a8f1"><td class="memItemLeft" align="right" valign="top">std::vector< <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1EdwardsLippertIterator.html#a54610da679df141855bfa1eb4be9a8f1">spec_</a></td></tr>
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<tr class="memdesc:a54610da679df141855bfa1eb4be9a8f1"><td class="mdescLeft"> </td><td class="mdescRight">given spectrum <a href="#a54610da679df141855bfa1eb4be9a8f1">More...</a><br/></td></tr>
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<tr class="memitem:ad71c965ded7781aca71019c3873bc535"><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_1EdwardsLippertIterator.html#ad71c965ded7781aca71019c3873bc535">tol_</a></td></tr>
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<tr class="memdesc:ad71c965ded7781aca71019c3873bc535"><td class="mdescLeft"> </td><td class="mdescRight">tolerance <a href="#ad71c965ded7781aca71019c3873bc535">More...</a><br/></td></tr>
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<tr class="memitem:a82b500a04e1c860859dea2a5de81d486"><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_1EdwardsLippertIterator.html#a82b500a04e1c860859dea2a5de81d486">masse_</a> [255]</td></tr>
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<tr class="memdesc:a82b500a04e1c860859dea2a5de81d486"><td class="mdescLeft"> </td><td class="mdescRight">mass table <a href="#a82b500a04e1c860859dea2a5de81d486">More...</a><br/></td></tr>
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<tr class="memitem:aa90b7cf7d5e734dbd7edd788d8cd77be"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1EdwardsLippertIterator.html#aa90b7cf7d5e734dbd7edd788d8cd77be">is_at_end_</a></td></tr>
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<tr class="memdesc:aa90b7cf7d5e734dbd7edd788d8cd77be"><td class="mdescLeft"> </td><td class="mdescRight">indicates if iterator is at end <a href="#aa90b7cf7d5e734dbd7edd788d8cd77be">More...</a><br/></td></tr>
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<tr class="memitem:a1b2f85409e3ffcb4916d74dd7f542684"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1PepIterator.html">PepIterator</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1EdwardsLippertIterator.html#a1b2f85409e3ffcb4916d74dd7f542684">f_iterator_</a></td></tr>
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<tr class="memdesc:a1b2f85409e3ffcb4916d74dd7f542684"><td class="mdescLeft"> </td><td class="mdescRight"><a class="el" href="classOpenMS_1_1FastaIterator.html" title="Iterator over FASTA file. ">FastaIterator</a>. <a href="#a1b2f85409e3ffcb4916d74dd7f542684">More...</a><br/></td></tr>
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<tr class="memitem:a89f7f9e14ec978a5f12c40dd7a21ee56"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1EdwardsLippertIterator.html#a21b87598c52cebe4ab2ebc0bb1655e89">FASTAEntry</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1EdwardsLippertIterator.html#a89f7f9e14ec978a5f12c40dd7a21ee56">f_entry_</a></td></tr>
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<tr class="memdesc:a89f7f9e14ec978a5f12c40dd7a21ee56"><td class="mdescLeft"> </td><td class="mdescRight">actual fasta entry <a href="#a89f7f9e14ec978a5f12c40dd7a21ee56">More...</a><br/></td></tr>
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<tr class="memitem:ae2847b8c4992d9d40699554a6255d696"><td class="memItemLeft" align="right" valign="top">unsigned int </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1EdwardsLippertIterator.html#ae2847b8c4992d9d40699554a6255d696">b_</a></td></tr>
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<tr class="memitem:a773d402b3a881e53092a4aa0647883c4"><td class="memItemLeft" align="right" valign="top">unsigned int </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1EdwardsLippertIterator.html#a773d402b3a881e53092a4aa0647883c4">e_</a></td></tr>
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<tr class="memdesc:a773d402b3a881e53092a4aa0647883c4"><td class="mdescLeft"> </td><td class="mdescRight">to ints representing a position within the actual string (b = begin, e = end) <a href="#a773d402b3a881e53092a4aa0647883c4">More...</a><br/></td></tr>
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<tr class="memitem:a0b4cb059c8429516b5c1e3623db4e619"><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_1EdwardsLippertIterator.html#a0b4cb059c8429516b5c1e3623db4e619">m_</a></td></tr>
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<tr class="memitem:ae23b695d905d82e0469e08265608f96c"><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_1EdwardsLippertIterator.html#ae23b695d905d82e0469e08265608f96c">massMax_</a></td></tr>
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<tr class="memdesc:ae23b695d905d82e0469e08265608f96c"><td class="mdescLeft"> </td><td class="mdescRight">mass and maximum masse <a href="#ae23b695d905d82e0469e08265608f96c">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>finds all Peptide Candidates with given masses and given fasta file </p>
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<p>The used algorithm was described by Edwards and Lippert. The algorithm uses two pointers to iterator over a sequence. One pointer represents the start the other the end. </p>
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</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_1EdwardsLippertIterator.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_1EdwardsLippertIterator.html">EdwardsLippertIterator</a> </td>
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<td class="paramname"></td><td>)</td>
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<td class="memname"><a class="el" href="classOpenMS_1_1EdwardsLippertIterator.html">EdwardsLippertIterator</a> </td>
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<td class="paramtype">const <a class="el" href="classOpenMS_1_1EdwardsLippertIterator.html">EdwardsLippertIterator</a> & </td>
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<td class="paramname"></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_1EdwardsLippertIterator.html">EdwardsLippertIterator</a> </td>
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<td class="paramname"></td><td>)</td>
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<span class="mlabels"><span class="mlabel">virtual</span></span> </td>
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<h2 class="groupheader">Member Function Documentation</h2>
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<td class="memname">virtual bool begin </td>
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<p>initializing iterator </p>
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<dl class="section return"><dt>Returns</dt><dd>true if everything was ok </dd></dl>
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<dl class="exception"><dt>Exceptions</dt><dd>
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<tr><td class="paramname">InvalidIterator</td><td>is thrown if the begin iterator is invalid </td></tr>
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<p>Implements <a class="el" href="classOpenMS_1_1PepIterator.html#ae8a0d9ca63f8bb3de100e347c3f3bca4">PepIterator</a>.</p>
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<td class="memname">static <a class="el" href="classOpenMS_1_1PepIterator.html">PepIterator</a>* create </td>
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<p>needed by <a class="el" href="classOpenMS_1_1Factory.html" title="Returns FactoryProduct* based on the name of the desired concrete FactoryProduct. ...">Factory</a> </p>
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<dl class="section return"><dt>Returns</dt><dd>poiter to new object </dd></dl>
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<td class="memname">virtual <a class="el" href="classOpenMS_1_1String.html">String</a> getFastaFile </td>
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<p>getter for FASTA file </p>
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<dl class="section return"><dt>Returns</dt><dd><a class="el" href="classOpenMS_1_1String.html" title="A more convenient string class. ">String</a> with file location </dd></dl>
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<p>Implements <a class="el" href="classOpenMS_1_1PepIterator.html#a9b9d24053affd496e54afedfed47f3e0">PepIterator</a>.</p>
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<p>needed by <a class="el" href="classOpenMS_1_1Factory.html" title="Returns FactoryProduct* based on the name of the desired concrete FactoryProduct. ...">Factory</a> </p>
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<dl class="section return"><dt>Returns</dt><dd>const string name of class </dd></dl>
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<td class="memname">virtual const std::vector<<a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a>>& getSpectrum </td>
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<p>getter for spectrum </p>
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<dl class="section return"><dt>Returns</dt><dd>the used spectrum </dd></dl>
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<p>Implements <a class="el" href="classOpenMS_1_1PepIterator.html#a76ac9563a3dd40f2f02790bdb1e00fd9">PepIterator</a>.</p>
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<p>getter for tolerance </p>
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<dl class="section return"><dt>Returns</dt><dd>tolerance </dd></dl>
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<p>Implements <a class="el" href="classOpenMS_1_1PepIterator.html#a8b733898cb0fedb36fa2ca2c149c202e">PepIterator</a>.</p>
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<td class="memname">void goToNextAA_ </td>
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<p>finds the next starting position where a digesting enzyme will cut the sequence </p>
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<p>indicates if there will be a next element </p>
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<dl class="section return"><dt>Returns</dt><dd>true if iterator has more elements </dd></dl>
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<p>indicates whether iterator is at end </p>
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<dl class="section return"><dt>Returns</dt><dd>true if iterator is at end </dd></dl>
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<dl class="section see"><dt>See Also</dt><dd>hasNext </dd></dl>
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<p>Implements <a class="el" href="classOpenMS_1_1PepIterator.html#a2c60e21a5b7f6f394e0151ac242aff5d">PepIterator</a>.</p>
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<a class="anchor" id="a47df1538f6e1b2ae27db5fe98a0b67aa"></a>
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<div class="memitem">
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<td class="mlabels-left">
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<td class="memname">virtual bool isDigestingEnd </td>
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<td class="paramtype">char </td>
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<td class="paramname">, </td>
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<td class="paramkey"></td>
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<td class="paramtype">char </td>
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<td class="paramname"> </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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</div><div class="memdoc">
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<p>indicated if a digesting enzyme will cut at this position </p>
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<dl class="section return"><dt>Returns</dt><dd>true if digenting enzym cuts the sequence </dd></dl>
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<p>Reimplemented in <a class="el" href="classOpenMS_1_1EdwardsLippertIteratorTryptic.html#aaf772e5ec6d5592a9fb7eae11bf945a1">EdwardsLippertIteratorTryptic</a>.</p>
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<a class="anchor" id="a0a6931a2f0abccd42cf54022538a4026"></a>
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<td class="memname">virtual bool isInSpectrum_ </td>
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<td class="paramtype"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> & </td>
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<td class="paramname"><em>mass</em></td><td>)</td>
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<td class="mlabels-right">
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<span class="mlabels"><span class="mlabel">protected</span><span class="mlabel">virtual</span></span> </td>
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</div><div class="memdoc">
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<p>indicates if a mass is in spectrum </p>
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<dl class="section return"><dt>Returns</dt><dd>true if a given mass is in spectrum </dd></dl>
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<a class="anchor" id="a63173babfe4e8063832f2ed405f80d91"></a>
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<td class="memname">virtual std::string next_ </td>
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<td class="paramname"></td><td>)</td>
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<span class="mlabels"><span class="mlabel">protected</span><span class="mlabel">virtual</span></span> </td>
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<p>getting the next candidate </p>
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<dl class="section return"><dt>Returns</dt><dd>string with next sequence </dd></dl>
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<a class="anchor" id="a2468d86d946f361d96ea90bb8e6e28da"></a>
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<td class="memname">virtual <a class="el" href="classOpenMS_1_1EdwardsLippertIterator.html#a21b87598c52cebe4ab2ebc0bb1655e89">FASTAEntry</a> operator* </td>
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<td class="paramname"></td><td>)</td>
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<span class="mlabels"><span class="mlabel">virtual</span></span> </td>
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<p>* operator for getting the value of the iterator </p>
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<dl class="section return"><dt>Returns</dt><dd>FASTAEntry with specific candidate </dd></dl>
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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">InvalidIterator</td><td>if iterator has not been initialized </td></tr>
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<p>Implements <a class="el" href="classOpenMS_1_1PepIterator.html#a1e97ffb93531c2360ae0bb63ab0a62c6">PepIterator</a>.</p>
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<a class="anchor" id="a55f6d71bc104d273092993e29f301e72"></a>
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<div class="memitem">
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<td class="memname">virtual <a class="el" href="classOpenMS_1_1PepIterator.html">PepIterator</a>& operator++ </td>
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<td class="paramname"></td><td>)</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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</div><div class="memdoc">
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<p>opperator ++ for postincrement </p>
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<dl class="section return"><dt>Returns</dt><dd>Reference to <a class="el" href="classOpenMS_1_1PepIterator.html" title="Abstract base class for different peptide iterators. ">PepIterator</a> </dd></dl>
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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">InvalidIterator</td><td>if iterator has not been initialized </td></tr>
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<p>Implements <a class="el" href="classOpenMS_1_1PepIterator.html#a6db496644ee00c57075340072ad1d3b8">PepIterator</a>.</p>
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<a class="anchor" id="a72227229d40a649a89bde5f60d48782e"></a>
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<div class="memitem">
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<td class="memname">virtual <a class="el" href="classOpenMS_1_1PepIterator.html">PepIterator</a>* operator++ </td>
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<td class="paramtype">int </td>
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<td class="paramname"><em>i</em></td><td>)</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>opperator ++ for preincrement </p>
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<dl class="section return"><dt>Returns</dt><dd>pointer to <a class="el" href="classOpenMS_1_1PepIterator.html" title="Abstract base class for different peptide iterators. ">PepIterator</a> </dd></dl>
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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">InvalidIterator</td><td>if iterator has not been initialized </td></tr>
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<p>Implements <a class="el" href="classOpenMS_1_1PepIterator.html#aa4e696669eb33d163d65ec9d3b343b09">PepIterator</a>.</p>
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<a class="anchor" id="a7d238aef71f460f8ebe0c267b7b7792b"></a>
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<td class="memname">virtual void setFastaFile </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>f</em></td><td>)</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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</div><div class="memdoc">
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<p>setter for fasta file </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">f</td><td><a class="el" href="classOpenMS_1_1String.html" title="A more convenient string class. ">String</a> with fasta file location </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">FileNotFound</td><td>if file could not be found </td></tr>
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<p>Implements <a class="el" href="classOpenMS_1_1PepIterator.html#ae4e709e523353cfb85943b8813fdef0f">PepIterator</a>.</p>
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<a class="anchor" id="abed3a62ee31d0d1add508b20d932fae5"></a>
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<td class="memname">virtual void setSpectrum </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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<td class="paramname"><em>s</em></td><td>)</td>
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<span class="mlabels"><span class="mlabel">virtual</span></span> </td>
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<p>setter for spectrum </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">s</td><td>spectrum as a vector of DoubleReals </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>if spectrum is not sorted </td></tr>
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<p>Implements <a class="el" href="classOpenMS_1_1PepIterator.html#aa3d9038f341c4e7693684bc4608d6ed4">PepIterator</a>.</p>
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<a class="anchor" id="a0b331f554495174d4e957af367a22425"></a>
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<td class="memname">virtual void setTolerance </td>
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<td class="paramtype"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> </td>
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<td class="paramname"><em>t</em></td><td>)</td>
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<span class="mlabels"><span class="mlabel">virtual</span></span> </td>
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<p>setter for tolerance </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">t</td><td>tolerance </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>if tolerance is negative </td></tr>
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<p>Implements <a class="el" href="classOpenMS_1_1PepIterator.html#a398690ada878a7dc5e01d57929ef2363">PepIterator</a>.</p>
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<h2 class="groupheader">Member Data Documentation</h2>
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<td class="memname">std::string actual_pep_</td>
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<span class="mlabels"><span class="mlabel">protected</span></span> </td>
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<p>actual peptide </p>
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<td class="memname">unsigned int b_</td>
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<td class="memname">unsigned int e_</td>
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<p>to ints representing a position within the actual string (b = begin, e = end) </p>
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<td class="memname"><a class="el" href="classOpenMS_1_1EdwardsLippertIterator.html#a21b87598c52cebe4ab2ebc0bb1655e89">FASTAEntry</a> f_entry_</td>
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<td class="mlabels-right">
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<span class="mlabels"><span class="mlabel">protected</span></span> </td>
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<p>actual fasta entry </p>
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<td class="memname"><a class="el" href="classOpenMS_1_1String.html">String</a> f_file_</td>
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<span class="mlabels"><span class="mlabel">protected</span></span> </td>
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<p>fasta file location </p>
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<td class="memname"><a class="el" href="classOpenMS_1_1PepIterator.html">PepIterator</a>* f_iterator_</td>
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<span class="mlabels"><span class="mlabel">protected</span></span> </td>
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<p><a class="el" href="classOpenMS_1_1FastaIterator.html" title="Iterator over FASTA file. ">FastaIterator</a>. </p>
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<td class="memname">bool is_at_end_</td>
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<p>indicates if iterator is at end </p>
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<td class="memname"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> m_</td>
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<span class="mlabels"><span class="mlabel">protected</span></span> </td>
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</div><div class="memdoc">
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<a class="anchor" id="a82b500a04e1c860859dea2a5de81d486"></a>
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<td class="memname"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> masse_[255]</td>
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<span class="mlabels"><span class="mlabel">protected</span></span> </td>
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<td class="memname"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> massMax_</td>
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<p>mass and maximum masse </p>
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<td class="memname">std::vector<<a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a>> spec_</td>
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<p>given spectrum </p>
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<td class="memname"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> tol_</td>
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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 11:19:27 using doxygen 1.8.5</font></TD>
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