1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
|
<HTML>
<HEAD>
<TITLE>DIAHelper.h Source File</TITLE>
<LINK HREF="doxygen.css" REL="stylesheet" TYPE="text/css">
<LINK HREF="style_ini.css" REL="stylesheet" TYPE="text/css">
</HEAD>
<BODY BGCOLOR="#FFFFFF">
<A href="index.html">Home</A> ·
<A href="classes.html">Classes</A> ·
<A href="annotated.html">Annotated Classes</A> ·
<A href="modules.html">Modules</A> ·
<A href="functions_func.html">Members</A> ·
<A href="namespaces.html">Namespaces</A> ·
<A href="pages.html">Related Pages</A>
<HR style="height:1px; border:none; border-top:1px solid #c0c0c0;">
<!-- Generated by Doxygen 1.8.5 -->
<div id="nav-path" class="navpath">
<ul>
<li class="navelem"><a class="el" href="dir_e770f0cf77e550adde3f44739ef529fe.html">include</a></li><li class="navelem"><a class="el" href="dir_6a63c4937d4da007e55fff5dcf71e0f8.html">OpenMS</a></li><li class="navelem"><a class="el" href="dir_330fe73d44ce641f33dd6036f80161a5.html">ANALYSIS</a></li><li class="navelem"><a class="el" href="dir_cebea83b16d377be32dcb02fb88342dd.html">OPENSWATH</a></li> </ul>
</div>
</div><!-- top -->
<div class="header">
<div class="headertitle">
<div class="title">DIAHelper.h</div> </div>
</div><!--header-->
<div class="contents">
<a href="DIAHelper_8h.html">Go to the documentation of this file.</a><div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno"> 1</span> <span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00002"></a><span class="lineno"> 2</span> <span class="comment">// OpenMS -- Open-Source Mass Spectrometry</span></div>
<div class="line"><a name="l00003"></a><span class="lineno"> 3</span> <span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00004"></a><span class="lineno"> 4</span> <span class="comment">// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,</span></div>
<div class="line"><a name="l00005"></a><span class="lineno"> 5</span> <span class="comment">// ETH Zurich, and Freie Universitaet Berlin 2002-2013.</span></div>
<div class="line"><a name="l00006"></a><span class="lineno"> 6</span> <span class="comment">//</span></div>
<div class="line"><a name="l00007"></a><span class="lineno"> 7</span> <span class="comment">// This software is released under a three-clause BSD license:</span></div>
<div class="line"><a name="l00008"></a><span class="lineno"> 8</span> <span class="comment">// * Redistributions of source code must retain the above copyright</span></div>
<div class="line"><a name="l00009"></a><span class="lineno"> 9</span> <span class="comment">// notice, this list of conditions and the following disclaimer.</span></div>
<div class="line"><a name="l00010"></a><span class="lineno"> 10</span> <span class="comment">// * Redistributions in binary form must reproduce the above copyright</span></div>
<div class="line"><a name="l00011"></a><span class="lineno"> 11</span> <span class="comment">// notice, this list of conditions and the following disclaimer in the</span></div>
<div class="line"><a name="l00012"></a><span class="lineno"> 12</span> <span class="comment">// documentation and/or other materials provided with the distribution.</span></div>
<div class="line"><a name="l00013"></a><span class="lineno"> 13</span> <span class="comment">// * Neither the name of any author or any participating institution</span></div>
<div class="line"><a name="l00014"></a><span class="lineno"> 14</span> <span class="comment">// may be used to endorse or promote products derived from this software</span></div>
<div class="line"><a name="l00015"></a><span class="lineno"> 15</span> <span class="comment">// without specific prior written permission.</span></div>
<div class="line"><a name="l00016"></a><span class="lineno"> 16</span> <span class="comment">// For a full list of authors, refer to the file AUTHORS.</span></div>
<div class="line"><a name="l00017"></a><span class="lineno"> 17</span> <span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00018"></a><span class="lineno"> 18</span> <span class="comment">// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"</span></div>
<div class="line"><a name="l00019"></a><span class="lineno"> 19</span> <span class="comment">// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE</span></div>
<div class="line"><a name="l00020"></a><span class="lineno"> 20</span> <span class="comment">// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE</span></div>
<div class="line"><a name="l00021"></a><span class="lineno"> 21</span> <span class="comment">// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING</span></div>
<div class="line"><a name="l00022"></a><span class="lineno"> 22</span> <span class="comment">// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,</span></div>
<div class="line"><a name="l00023"></a><span class="lineno"> 23</span> <span class="comment">// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,</span></div>
<div class="line"><a name="l00024"></a><span class="lineno"> 24</span> <span class="comment">// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;</span></div>
<div class="line"><a name="l00025"></a><span class="lineno"> 25</span> <span class="comment">// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,</span></div>
<div class="line"><a name="l00026"></a><span class="lineno"> 26</span> <span class="comment">// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR</span></div>
<div class="line"><a name="l00027"></a><span class="lineno"> 27</span> <span class="comment">// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF</span></div>
<div class="line"><a name="l00028"></a><span class="lineno"> 28</span> <span class="comment">// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.</span></div>
<div class="line"><a name="l00029"></a><span class="lineno"> 29</span> <span class="comment">//</span></div>
<div class="line"><a name="l00030"></a><span class="lineno"> 30</span> <span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00031"></a><span class="lineno"> 31</span> <span class="comment">// $Maintainer: Witold Wolski, Hannes Roest $</span></div>
<div class="line"><a name="l00032"></a><span class="lineno"> 32</span> <span class="comment">// $Authors: Witold Wolski, Hannes Roest $</span></div>
<div class="line"><a name="l00033"></a><span class="lineno"> 33</span> <span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00034"></a><span class="lineno"> 34</span> </div>
<div class="line"><a name="l00035"></a><span class="lineno"> 35</span> <span class="preprocessor">#ifndef OPENMS_ANALYSIS_OPENSWATH_DIAHELPER_H</span></div>
<div class="line"><a name="l00036"></a><span class="lineno"> 36</span> <span class="preprocessor"></span><span class="preprocessor">#define OPENMS_ANALYSIS_OPENSWATH_DIAHELPER_H</span></div>
<div class="line"><a name="l00037"></a><span class="lineno"> 37</span> <span class="preprocessor"></span></div>
<div class="line"><a name="l00038"></a><span class="lineno"> 38</span> <span class="preprocessor">#include <vector></span></div>
<div class="line"><a name="l00039"></a><span class="lineno"> 39</span> <span class="preprocessor">#include <<a class="code" href="AASequence_8h.html">OpenMS/CHEMISTRY/AASequence.h</a>></span></div>
<div class="line"><a name="l00040"></a><span class="lineno"> 40</span> </div>
<div class="line"><a name="l00041"></a><span class="lineno"> 41</span> <span class="keyword">namespace </span>OpenMS</div>
<div class="line"><a name="l00042"></a><span class="lineno"> 42</span> {</div>
<div class="line"><a name="l00043"></a><span class="lineno"><a class="line" href="namespaceOpenMS_1_1DIAHelpers.html"> 43</a></span>  <span class="keyword">namespace </span>DIAHelpers</div>
<div class="line"><a name="l00044"></a><span class="lineno"> 44</span>  {</div>
<div class="line"><a name="l00048"></a><span class="lineno"> 48</span>  OPENMS_DLLAPI <span class="keywordtype">void</span> <a class="code" href="namespaceOpenMS_1_1DIAHelpers.html#a9769de62a2263a1d37c14cc36a4c7991">getBYSeries</a>(<a class="code" href="classOpenMS_1_1AASequence.html">AASequence</a>& a,</div>
<div class="line"><a name="l00051"></a><span class="lineno"> 51</span>  std::vector<double>& bseries, std::vector<double>& yseries, <a class="code" href="classunsigned_01int.html">UInt</a> charge = 1u);</div>
<div class="line"><a name="l00052"></a><span class="lineno"> 52</span> </div>
<div class="line"><a name="l00054"></a><span class="lineno"> 54</span>  OPENMS_DLLAPI <span class="keywordtype">void</span> <a class="code" href="namespaceOpenMS_1_1DIAHelpers.html#a85cd7b412a7bf9bffdb490e0008a4372">getTheorMasses</a>(<a class="code" href="classOpenMS_1_1AASequence.html">AASequence</a>& a, std::vector<double>& masses, <a class="code" href="classunsigned_01int.html">UInt</a> charge = 1u);</div>
<div class="line"><a name="l00055"></a><span class="lineno"> 55</span> </div>
<div class="line"><a name="l00057"></a><span class="lineno"> 57</span>  OPENMS_DLLAPI <span class="keywordtype">void</span> <a class="code" href="namespaceOpenMS_1_1DIAHelpers.html#a9cdad8f5d8f328c29985eedc697c0480">getAveragineIsotopeDistribution</a>(<span class="keywordtype">double</span> product_mz,</div>
<div class="line"><a name="l00058"></a><span class="lineno"> 58</span>  std::vector<std::pair<double, double> >& isotopesSpec, </div>
<div class="line"><a name="l00059"></a><span class="lineno"> 59</span>  <span class="keywordtype">double</span> charge = 1.,</div>
<div class="line"><a name="l00060"></a><span class="lineno"> 60</span>  <span class="keywordtype">int</span> nr_isotopes = 4,</div>
<div class="line"><a name="l00061"></a><span class="lineno"> 61</span>  <span class="keywordtype">double</span> mannmass = 1.00048);</div>
<div class="line"><a name="l00062"></a><span class="lineno"> 62</span> </div>
<div class="line"><a name="l00064"></a><span class="lineno"> 64</span>  OPENMS_DLLAPI <span class="keywordtype">void</span> <a class="code" href="namespaceOpenMS_1_1DIAHelpers.html#aa13ca80bab92c96f1ba50e48d11c221f">simulateSpectrumFromAASequence</a>(<a class="code" href="classOpenMS_1_1AASequence.html">AASequence</a>& aa,</div>
<div class="line"><a name="l00065"></a><span class="lineno"> 65</span>  std::vector<double>& firstIsotopeMasses, <span class="comment">//[out]</span></div>
<div class="line"><a name="l00066"></a><span class="lineno"> 66</span>  std::vector<std::pair<double, double> >& isotopeMasses, <span class="comment">//[out]</span></div>
<div class="line"><a name="l00067"></a><span class="lineno"> 67</span>  <span class="keywordtype">double</span> charge = 1.);</div>
<div class="line"><a name="l00068"></a><span class="lineno"> 68</span> </div>
<div class="line"><a name="l00070"></a><span class="lineno"> 70</span>  OPENMS_DLLAPI <span class="keywordtype">void</span> <a class="code" href="namespaceOpenMS_1_1DIAHelpers.html#aca5b206b4fc842041245da352d4bb7d7">modifyMassesByCharge</a>(<span class="keyword">const</span> std::vector<std::pair<double, double> >& masses, </div>
<div class="line"><a name="l00071"></a><span class="lineno"> 71</span>  std::vector<std::pair<double, double> >& modmass, </div>
<div class="line"><a name="l00072"></a><span class="lineno"> 72</span>  <span class="keywordtype">double</span> charge = 1.);</div>
<div class="line"><a name="l00073"></a><span class="lineno"> 73</span> </div>
<div class="line"><a name="l00075"></a><span class="lineno"> 75</span>  OPENMS_DLLAPI <span class="keywordtype">void</span> <a class="code" href="namespaceOpenMS_1_1DIAHelpers.html#a1511d296413984e80255da29ef7c9018">addPreisotopeWeights</a>(<span class="keyword">const</span> std::vector<double>& firstIsotopeMasses,</div>
<div class="line"><a name="l00076"></a><span class="lineno"> 76</span>  std::vector<std::pair<double, double> >& isotopeSpec, <span class="comment">// output</span></div>
<div class="line"><a name="l00077"></a><span class="lineno"> 77</span>  <a class="code" href="classunsigned_01int.html">UInt</a> nrpeaks = 2, <span class="comment">//nr of preisotope peaks</span></div>
<div class="line"><a name="l00078"></a><span class="lineno"> 78</span>  <span class="keywordtype">double</span> preIsotopePeaksWeight = -0.5, <span class="comment">// weight of preisotope peaks</span></div>
<div class="line"><a name="l00079"></a><span class="lineno"> 79</span>  <span class="keywordtype">double</span> mannmass = 1.000482, <span class="comment">//</span></div>
<div class="line"><a name="l00080"></a><span class="lineno"> 80</span>  <span class="keywordtype">double</span> charge = 1.);</div>
<div class="line"><a name="l00081"></a><span class="lineno"> 81</span> </div>
<div class="line"><a name="l00083"></a><span class="lineno"> 83</span>  OPENMS_DLLAPI <span class="keywordtype">void</span> <a class="code" href="namespaceOpenMS_1_1DIAHelpers.html#a3fcc07b9c14df0a334853c7a807c45fd">addIsotopes2Spec</a>(<span class="keyword">const</span> std::vector<std::pair<double, double> >& spec,</div>
<div class="line"><a name="l00084"></a><span class="lineno"> 84</span>  std::vector<std::pair<double, double> >& isotopeMasses, <span class="comment">//[out]</span></div>
<div class="line"><a name="l00085"></a><span class="lineno"> 85</span>  <span class="keywordtype">double</span> charge = 1.);</div>
<div class="line"><a name="l00086"></a><span class="lineno"> 86</span> </div>
<div class="line"><a name="l00088"></a><span class="lineno"> 88</span>  OPENMS_DLLAPI <span class="keywordtype">void</span> <a class="code" href="namespaceOpenMS_1_1DIAHelpers.html#a531c55d1403b0c55e44d153bac38c2d9">sortByFirst</a>(std::vector<std::pair<double, double> >& tmp);</div>
<div class="line"><a name="l00090"></a><span class="lineno"> 90</span>  OPENMS_DLLAPI <span class="keywordtype">void</span> <a class="code" href="namespaceOpenMS_1_1DIAHelpers.html#ab60b132f6575b79c2f6c9d4227ef7872">extractFirst</a>(<span class="keyword">const</span> std::vector<std::pair<double, double> >& peaks, std::vector<double>& mass);</div>
<div class="line"><a name="l00092"></a><span class="lineno"> 92</span>  OPENMS_DLLAPI <span class="keywordtype">void</span> <a class="code" href="namespaceOpenMS_1_1DIAHelpers.html#a358a796392a847b5835d94252a9e7a81">extractSecond</a>(<span class="keyword">const</span> std::vector<std::pair<double, double> >& peaks, std::vector<double>& mass);</div>
<div class="line"><a name="l00093"></a><span class="lineno"> 93</span>  </div>
<div class="line"><a name="l00095"></a><span class="lineno"> 95</span>  }</div>
<div class="line"><a name="l00096"></a><span class="lineno"> 96</span> }</div>
<div class="line"><a name="l00097"></a><span class="lineno"> 97</span> <span class="preprocessor">#endif</span></div>
<div class="ttc" id="classunsigned_01int_html"><div class="ttname"><a href="classunsigned_01int.html">unsigned int</a></div></div>
<div class="ttc" id="namespaceOpenMS_1_1DIAHelpers_html_ab60b132f6575b79c2f6c9d4227ef7872"><div class="ttname"><a href="namespaceOpenMS_1_1DIAHelpers.html#ab60b132f6575b79c2f6c9d4227ef7872">OpenMS::DIAHelpers::extractFirst</a></div><div class="ttdeci">void extractFirst(const std::vector< std::pair< double, double > > &peaks, std::vector< double > &mass)</div><div class="ttdoc">extract first from vector of pairs </div></div>
<div class="ttc" id="AASequence_8h_html"><div class="ttname"><a href="AASequence_8h.html">AASequence.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1AASequence_html"><div class="ttname"><a href="classOpenMS_1_1AASequence.html">OpenMS::AASequence</a></div><div class="ttdoc">Representation of a peptide/protein sequence. </div><div class="ttdef"><b>Definition:</b> AASequence.h:84</div></div>
<div class="ttc" id="namespaceOpenMS_1_1DIAHelpers_html_a85cd7b412a7bf9bffdb490e0008a4372"><div class="ttname"><a href="namespaceOpenMS_1_1DIAHelpers.html#a85cd7b412a7bf9bffdb490e0008a4372">OpenMS::DIAHelpers::getTheorMasses</a></div><div class="ttdeci">void getTheorMasses(AASequence &a, std::vector< double > &masses, UInt charge=1u)</div><div class="ttdoc">for SWATH – get the theoretical b and y series masses for a sequence </div></div>
<div class="ttc" id="namespaceOpenMS_1_1DIAHelpers_html_aca5b206b4fc842041245da352d4bb7d7"><div class="ttname"><a href="namespaceOpenMS_1_1DIAHelpers.html#aca5b206b4fc842041245da352d4bb7d7">OpenMS::DIAHelpers::modifyMassesByCharge</a></div><div class="ttdeci">void modifyMassesByCharge(const std::vector< std::pair< double, double > > &masses, std::vector< std::pair< double, double > > &modmass, double charge=1.)</div><div class="ttdoc">modify masses by charge </div></div>
<div class="ttc" id="namespaceOpenMS_1_1DIAHelpers_html_a9cdad8f5d8f328c29985eedc697c0480"><div class="ttname"><a href="namespaceOpenMS_1_1DIAHelpers.html#a9cdad8f5d8f328c29985eedc697c0480">OpenMS::DIAHelpers::getAveragineIsotopeDistribution</a></div><div class="ttdeci">void getAveragineIsotopeDistribution(double product_mz, std::vector< std::pair< double, double > > &isotopesSpec, double charge=1., int nr_isotopes=4, double mannmass=1.00048)</div><div class="ttdoc">get averagine distribution given mass </div></div>
<div class="ttc" id="namespaceOpenMS_1_1DIAHelpers_html_a531c55d1403b0c55e44d153bac38c2d9"><div class="ttname"><a href="namespaceOpenMS_1_1DIAHelpers.html#a531c55d1403b0c55e44d153bac38c2d9">OpenMS::DIAHelpers::sortByFirst</a></div><div class="ttdeci">void sortByFirst(std::vector< std::pair< double, double > > &tmp)</div><div class="ttdoc">sorts vector of pairs by first </div></div>
<div class="ttc" id="namespaceOpenMS_1_1DIAHelpers_html_a3fcc07b9c14df0a334853c7a807c45fd"><div class="ttname"><a href="namespaceOpenMS_1_1DIAHelpers.html#a3fcc07b9c14df0a334853c7a807c45fd">OpenMS::DIAHelpers::addIsotopes2Spec</a></div><div class="ttdeci">void addIsotopes2Spec(const std::vector< std::pair< double, double > > &spec, std::vector< std::pair< double, double > > &isotopeMasses, double charge=1.)</div><div class="ttdoc">given an experimental spectrum add isotope pattern. </div></div>
<div class="ttc" id="namespaceOpenMS_1_1DIAHelpers_html_a358a796392a847b5835d94252a9e7a81"><div class="ttname"><a href="namespaceOpenMS_1_1DIAHelpers.html#a358a796392a847b5835d94252a9e7a81">OpenMS::DIAHelpers::extractSecond</a></div><div class="ttdeci">void extractSecond(const std::vector< std::pair< double, double > > &peaks, std::vector< double > &mass)</div><div class="ttdoc">extract second from vector of pairs </div></div>
<div class="ttc" id="namespaceOpenMS_1_1DIAHelpers_html_a1511d296413984e80255da29ef7c9018"><div class="ttname"><a href="namespaceOpenMS_1_1DIAHelpers.html#a1511d296413984e80255da29ef7c9018">OpenMS::DIAHelpers::addPreisotopeWeights</a></div><div class="ttdeci">void addPreisotopeWeights(const std::vector< double > &firstIsotopeMasses, std::vector< std::pair< double, double > > &isotopeSpec, UInt nrpeaks=2, double preIsotopePeaksWeight=-0.5, double mannmass=1.000482, double charge=1.)</div><div class="ttdoc">add negative preisotope weights to spectrum </div></div>
<div class="ttc" id="namespaceOpenMS_1_1DIAHelpers_html_a9769de62a2263a1d37c14cc36a4c7991"><div class="ttname"><a href="namespaceOpenMS_1_1DIAHelpers.html#a9769de62a2263a1d37c14cc36a4c7991">OpenMS::DIAHelpers::getBYSeries</a></div><div class="ttdeci">void getBYSeries(AASequence &a, std::vector< double > &bseries, std::vector< double > &yseries, UInt charge=1u)</div><div class="ttdoc">Helper functions for the DIA scoring of OpenSWATH. </div></div>
<div class="ttc" id="namespaceOpenMS_1_1DIAHelpers_html_aa13ca80bab92c96f1ba50e48d11c221f"><div class="ttname"><a href="namespaceOpenMS_1_1DIAHelpers.html#aa13ca80bab92c96f1ba50e48d11c221f">OpenMS::DIAHelpers::simulateSpectrumFromAASequence</a></div><div class="ttdeci">void simulateSpectrumFromAASequence(AASequence &aa, std::vector< double > &firstIsotopeMasses, std::vector< std::pair< double, double > > &isotopeMasses, double charge=1.)</div><div class="ttdoc">simulate spectrum from AASequence </div></div>
</div><!-- fragment --></div><!-- contents -->
<HR style="height:1px; border:none; border-top:1px solid #c0c0c0;">
<TABLE width="100%" border="0">
<TR>
<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 11:19:12 using doxygen 1.8.5</font></TD>
</TR>
</TABLE>
</BODY>
</HTML>
|
