File: Scoring_8h_source.html

package info (click to toggle)
openms 1.11.1-5
  • links: PTS, VCS
  • area: main
  • in suites: jessie, jessie-kfreebsd
  • size: 436,688 kB
  • ctags: 150,907
  • sloc: cpp: 387,126; xml: 71,547; python: 7,764; ansic: 2,626; php: 2,499; sql: 737; ruby: 342; sh: 325; makefile: 128
file content (121 lines) | stat: -rw-r--r-- 19,423 bytes parent folder | download 
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
 
<HTML>
<HEAD>
<TITLE>Scoring.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> &nbsp;&middot;
<A href="classes.html">Classes</A> &nbsp;&middot;
<A href="annotated.html">Annotated Classes</A> &nbsp;&middot;
<A href="modules.html">Modules</A> &nbsp;&middot;
<A href="functions_func.html">Members</A> &nbsp;&middot;
<A href="namespaces.html">Namespaces</A> &nbsp;&middot;
<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><li class="navelem"><a class="el" href="dir_196520b3448eb06b41492b7c96611130.html">OPENSWATHALGO</a></li><li class="navelem"><a class="el" href="dir_0003f9d042246912df87a6259aa0261b.html">ALGO</a></li>  </ul>
</div>
</div><!-- top -->
<div class="header">
  <div class="headertitle">
<div class="title">Scoring.h</div>  </div>
</div><!--header-->
<div class="contents">
<a href="Scoring_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>&#160;<span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00002"></a><span class="lineno">    2</span>&#160;<span class="comment">//                   OpenMS -- Open-Source Mass Spectrometry</span></div>
<div class="line"><a name="l00003"></a><span class="lineno">    3</span>&#160;<span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00004"></a><span class="lineno">    4</span>&#160;<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>&#160;<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>&#160;<span class="comment">//</span></div>
<div class="line"><a name="l00007"></a><span class="lineno">    7</span>&#160;<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>&#160;<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>&#160;<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>&#160;<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>&#160;<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>&#160;<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>&#160;<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>&#160;<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>&#160;<span class="comment">//    without specific prior written permission.</span></div>
<div class="line"><a name="l00016"></a><span class="lineno">   16</span>&#160;<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>&#160;<span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00018"></a><span class="lineno">   18</span>&#160;<span class="comment">// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS &quot;AS IS&quot;</span></div>
<div class="line"><a name="l00019"></a><span class="lineno">   19</span>&#160;<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>&#160;<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>&#160;<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>&#160;<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>&#160;<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>&#160;<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>&#160;<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>&#160;<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>&#160;<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>&#160;<span class="comment">// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.</span></div>
<div class="line"><a name="l00029"></a><span class="lineno">   29</span>&#160;<span class="comment">//</span></div>
<div class="line"><a name="l00030"></a><span class="lineno">   30</span>&#160;<span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00031"></a><span class="lineno">   31</span>&#160;<span class="comment">// $Maintainer: Hannes Roest$</span></div>
<div class="line"><a name="l00032"></a><span class="lineno">   32</span>&#160;<span class="comment">// $Authors: Hannes Roest$</span></div>
<div class="line"><a name="l00033"></a><span class="lineno">   33</span>&#160;<span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00034"></a><span class="lineno">   34</span>&#160;</div>
<div class="line"><a name="l00035"></a><span class="lineno">   35</span>&#160;<span class="preprocessor">#ifndef OPENMS_ANALYSIS_OPENSWATH_OPENSWATHALGO_ALGO_SCORING_H</span></div>
<div class="line"><a name="l00036"></a><span class="lineno">   36</span>&#160;<span class="preprocessor"></span><span class="preprocessor">#define OPENMS_ANALYSIS_OPENSWATH_OPENSWATHALGO_ALGO_SCORING_H</span></div>
<div class="line"><a name="l00037"></a><span class="lineno">   37</span>&#160;<span class="preprocessor"></span></div>
<div class="line"><a name="l00038"></a><span class="lineno">   38</span>&#160;<span class="preprocessor">#include &lt;numeric&gt;</span></div>
<div class="line"><a name="l00039"></a><span class="lineno">   39</span>&#160;<span class="preprocessor">#include &lt;map&gt;</span></div>
<div class="line"><a name="l00040"></a><span class="lineno">   40</span>&#160;<span class="preprocessor">#include &lt;vector&gt;</span></div>
<div class="line"><a name="l00041"></a><span class="lineno">   41</span>&#160;</div>
<div class="line"><a name="l00042"></a><span class="lineno">   42</span>&#160;<span class="preprocessor">#include &lt;OpenMS/ANALYSIS/OPENSWATH/OPENSWATHALGO/OpenSwathAlgoConfig.h&gt;</span></div>
<div class="line"><a name="l00043"></a><span class="lineno">   43</span>&#160;</div>
<div class="line"><a name="l00044"></a><span class="lineno">   44</span>&#160;<span class="keyword">namespace </span>OpenSwath</div>
<div class="line"><a name="l00045"></a><span class="lineno">   45</span>&#160;{</div>
<div class="line"><a name="l00046"></a><span class="lineno">   46</span>&#160;</div>
<div class="line"><a name="l00052"></a><span class="lineno"><a class="line" href="namespaceOpenSwath_1_1Scoring.html">   52</a></span>&#160;  <span class="keyword">namespace </span>Scoring</div>
<div class="line"><a name="l00053"></a><span class="lineno">   53</span>&#160;  {</div>
<div class="line"><a name="l00056"></a><span class="lineno">   56</span>&#160;    <span class="keyword">typedef</span> std::map&lt;int, double&gt; <a class="code" href="namespaceOpenSwath_1_1Scoring.html#a531d297e28f364cbc5ebad37d5d85881">XCorrArrayType</a>;</div>
<div class="line"><a name="l00059"></a><span class="lineno">   59</span>&#160;</div>
<div class="line"><a name="l00062"></a><span class="lineno">   62</span>&#160;    OPENSWATHALGO_DLLAPI <span class="keywordtype">double</span> <a class="code" href="namespaceOpenSwath_1_1Scoring.html#a82baea39716c7d127c506e3343372d7b">RMSD</a>(<span class="keywordtype">double</span> x[], <span class="keywordtype">double</span> y[], <span class="keywordtype">int</span> n);</div>
<div class="line"><a name="l00064"></a><span class="lineno">   64</span>&#160;</div>
<div class="line"><a name="l00066"></a><span class="lineno">   66</span>&#160;    OPENSWATHALGO_DLLAPI <a class="code" href="namespaceOpenSwath_1_1Scoring.html#a531d297e28f364cbc5ebad37d5d85881">XCorrArrayType</a> <a class="code" href="namespaceOpenSwath_1_1Scoring.html#ab44fd5104dcced8e12efeb08599697de">calcxcorr</a>(std::vector&lt;double&gt;&amp; data1,</div>
<div class="line"><a name="l00067"></a><span class="lineno">   67</span>&#160;                                                  std::vector&lt;double&gt;&amp; data2, <span class="keywordtype">bool</span> <a class="code" href="namespaceOpenSwath.html#a546b9a9117f4207e3cfc9ef2ea4aad3d">normalize</a>);</div>
<div class="line"><a name="l00068"></a><span class="lineno">   68</span>&#160;</div>
<div class="line"><a name="l00070"></a><span class="lineno">   70</span>&#160;    OPENSWATHALGO_DLLAPI <a class="code" href="namespaceOpenSwath_1_1Scoring.html#a531d297e28f364cbc5ebad37d5d85881">XCorrArrayType</a> <a class="code" href="namespaceOpenSwath_1_1Scoring.html#a6d275d97fb154967e3b3d668f33704c5">normalizedCalcxcorr</a>(std::vector&lt;double&gt;&amp; data1,</div>
<div class="line"><a name="l00071"></a><span class="lineno">   71</span>&#160;                                                            std::vector&lt;double&gt;&amp; data2, <span class="keywordtype">int</span> maxdelay, <span class="keywordtype">int</span> lag);</div>
<div class="line"><a name="l00072"></a><span class="lineno">   72</span>&#160;</div>
<div class="line"><a name="l00074"></a><span class="lineno">   74</span>&#160;    OPENSWATHALGO_DLLAPI <a class="code" href="namespaceOpenSwath_1_1Scoring.html#a531d297e28f364cbc5ebad37d5d85881">XCorrArrayType</a> <a class="code" href="namespaceOpenSwath_1_1Scoring.html#a0d4b9442fba883288afffc8333653017">calcxcorr_new</a>(std::vector&lt;double&gt;&amp; data1,</div>
<div class="line"><a name="l00075"></a><span class="lineno">   75</span>&#160;                                                      std::vector&lt;double&gt;&amp; data2, <span class="keywordtype">int</span> maxdelay, <span class="keywordtype">int</span> lag);</div>
<div class="line"><a name="l00076"></a><span class="lineno">   76</span>&#160;</div>
<div class="line"><a name="l00077"></a><span class="lineno">   77</span>&#160;    <span class="comment">/*</span></div>
<div class="line"><a name="l00078"></a><span class="lineno">   78</span>&#160;<span class="comment">    XCorrArrayType calcxcorr_lag1(std::vector&lt;double&gt; &amp; data1,</span></div>
<div class="line"><a name="l00079"></a><span class="lineno">   79</span>&#160;<span class="comment">        std::vector&lt;double&gt; &amp; data2, int maxdelay);</span></div>
<div class="line"><a name="l00080"></a><span class="lineno">   80</span>&#160;<span class="comment">    */</span></div>
<div class="line"><a name="l00081"></a><span class="lineno">   81</span>&#160;</div>
<div class="line"><a name="l00083"></a><span class="lineno">   83</span>&#160;    OPENSWATHALGO_DLLAPI XCorrArrayType::iterator <a class="code" href="namespaceOpenSwath_1_1Scoring.html#ae63ae5fe7d891f478a4f4262dd160b80">xcorrArrayGetMaxPeak</a>(<a class="code" href="namespaceOpenSwath_1_1Scoring.html#a531d297e28f364cbc5ebad37d5d85881">XCorrArrayType</a> &amp; array);</div>
<div class="line"><a name="l00084"></a><span class="lineno">   84</span>&#160;</div>
<div class="line"><a name="l00086"></a><span class="lineno">   86</span>&#160;    OPENSWATHALGO_DLLAPI <span class="keywordtype">void</span> <a class="code" href="namespaceOpenSwath_1_1Scoring.html#aa755534eb4feae3d28ef3f5c065f97fc">standardize_data</a>(std::vector&lt;double&gt;&amp; data);</div>
<div class="line"><a name="l00087"></a><span class="lineno">   87</span>&#160;</div>
<div class="line"><a name="l00089"></a><span class="lineno">   89</span>&#160;    OPENSWATHALGO_DLLAPI <span class="keywordtype">void</span> <a class="code" href="namespaceOpenSwath_1_1Scoring.html#afa39e794c622d1fdfc2d702517fffc80">normalize_sum</a>(<span class="keywordtype">double</span> x[], <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> n);</div>
<div class="line"><a name="l00091"></a><span class="lineno">   91</span>&#160;</div>
<div class="line"><a name="l00092"></a><span class="lineno">   92</span>&#160;  }</div>
<div class="line"><a name="l00093"></a><span class="lineno">   93</span>&#160;}</div>
<div class="line"><a name="l00094"></a><span class="lineno">   94</span>&#160;</div>
<div class="line"><a name="l00095"></a><span class="lineno">   95</span>&#160;<span class="preprocessor">#endif // OPENMS_ANALYSIS_OPENSWATH_OPENSWATHALGO_ALGO_SCORING_H</span></div>
<div class="ttc" id="namespaceOpenSwath_1_1Scoring_html_a531d297e28f364cbc5ebad37d5d85881"><div class="ttname"><a href="namespaceOpenSwath_1_1Scoring.html#a531d297e28f364cbc5ebad37d5d85881">OpenSwath::Scoring::XCorrArrayType</a></div><div class="ttdeci">std::map&lt; int, double &gt; XCorrArrayType</div><div class="ttdoc">Cross Correlation array. </div><div class="ttdef"><b>Definition:</b> Scoring.h:57</div></div>
<div class="ttc" id="namespaceOpenSwath_html_a546b9a9117f4207e3cfc9ef2ea4aad3d"><div class="ttname"><a href="namespaceOpenSwath.html#a546b9a9117f4207e3cfc9ef2ea4aad3d">OpenSwath::normalize</a></div><div class="ttdeci">OPENSWATHALGO_DLLAPI void normalize(const std::vector&lt; double &gt; &amp;intensities, double normalization_factor, std::vector&lt; double &gt; &amp;normalized_intensities)</div><div class="ttdoc">Normalize intensities in vector by normalization_factor. </div></div>
<div class="ttc" id="namespaceOpenSwath_1_1Scoring_html_aa755534eb4feae3d28ef3f5c065f97fc"><div class="ttname"><a href="namespaceOpenSwath_1_1Scoring.html#aa755534eb4feae3d28ef3f5c065f97fc">OpenSwath::Scoring::standardize_data</a></div><div class="ttdeci">OPENSWATHALGO_DLLAPI void standardize_data(std::vector&lt; double &gt; &amp;data)</div><div class="ttdoc">Standardize a vector (subtract mean, divide by standard deviation) </div></div>
<div class="ttc" id="namespaceOpenSwath_1_1Scoring_html_afa39e794c622d1fdfc2d702517fffc80"><div class="ttname"><a href="namespaceOpenSwath_1_1Scoring.html#afa39e794c622d1fdfc2d702517fffc80">OpenSwath::Scoring::normalize_sum</a></div><div class="ttdeci">OPENSWATHALGO_DLLAPI void normalize_sum(double x[], unsigned int n)</div><div class="ttdoc">divide each element of x by the sum of the vector </div></div>
<div class="ttc" id="namespaceOpenSwath_1_1Scoring_html_a82baea39716c7d127c506e3343372d7b"><div class="ttname"><a href="namespaceOpenSwath_1_1Scoring.html#a82baea39716c7d127c506e3343372d7b">OpenSwath::Scoring::RMSD</a></div><div class="ttdeci">OPENSWATHALGO_DLLAPI double RMSD(double x[], double y[], int n)</div><div class="ttdoc">Fxn &amp;quot;deltaRatioSum&amp;quot; from mQuest to calculate similarity between library intensity and experimental on...</div></div>
<div class="ttc" id="namespaceOpenSwath_1_1Scoring_html_a0d4b9442fba883288afffc8333653017"><div class="ttname"><a href="namespaceOpenSwath_1_1Scoring.html#a0d4b9442fba883288afffc8333653017">OpenSwath::Scoring::calcxcorr_new</a></div><div class="ttdeci">OPENSWATHALGO_DLLAPI XCorrArrayType calcxcorr_new(std::vector&lt; double &gt; &amp;data1, std::vector&lt; double &gt; &amp;data2, int maxdelay, int lag)</div><div class="ttdoc">Calculate crosscorrelation on std::vector data without normalization. </div></div>
<div class="ttc" id="namespaceOpenSwath_1_1Scoring_html_a6d275d97fb154967e3b3d668f33704c5"><div class="ttname"><a href="namespaceOpenSwath_1_1Scoring.html#a6d275d97fb154967e3b3d668f33704c5">OpenSwath::Scoring::normalizedCalcxcorr</a></div><div class="ttdeci">OPENSWATHALGO_DLLAPI XCorrArrayType normalizedCalcxcorr(std::vector&lt; double &gt; &amp;data1, std::vector&lt; double &gt; &amp;data2, int maxdelay, int lag)</div><div class="ttdoc">Calculate crosscorrelation on std::vector data (which is first normalized) </div></div>
<div class="ttc" id="namespaceOpenSwath_1_1Scoring_html_ab44fd5104dcced8e12efeb08599697de"><div class="ttname"><a href="namespaceOpenSwath_1_1Scoring.html#ab44fd5104dcced8e12efeb08599697de">OpenSwath::Scoring::calcxcorr</a></div><div class="ttdeci">OPENSWATHALGO_DLLAPI XCorrArrayType calcxcorr(std::vector&lt; double &gt; &amp;data1, std::vector&lt; double &gt; &amp;data2, bool normalize)</div><div class="ttdoc">Calculate crosscorrelation on std::vector data. </div></div>
<div class="ttc" id="namespaceOpenSwath_1_1Scoring_html_ae63ae5fe7d891f478a4f4262dd160b80"><div class="ttname"><a href="namespaceOpenSwath_1_1Scoring.html#ae63ae5fe7d891f478a4f4262dd160b80">OpenSwath::Scoring::xcorrArrayGetMaxPeak</a></div><div class="ttdeci">OPENSWATHALGO_DLLAPI XCorrArrayType::iterator xcorrArrayGetMaxPeak(XCorrArrayType &amp;array)</div><div class="ttdoc">Find best peak in an cross-correlation (highest apex) </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 11:19:20 using doxygen 1.8.5</font></TD>
</TR>
</TABLE>
</BODY>
</HTML>