3
<TITLE>OpenSwathDataAccessHelper Class Reference</TITLE>
4
<LINK HREF="doxygen.css" REL="stylesheet" TYPE="text/css">
5
<LINK HREF="style_ini.css" REL="stylesheet" TYPE="text/css">
7
<BODY BGCOLOR="#FFFFFF">
8
<A href="index.html">Home</A> ·
9
<A href="classes.html">Classes</A> ·
10
<A href="annotated.html">Annotated Classes</A> ·
11
<A href="modules.html">Modules</A> ·
12
<A href="functions_func.html">Members</A> ·
13
<A href="namespaces.html">Namespaces</A> ·
14
<A href="pages.html">Related Pages</A>
15
<HR style="height:1px; border:none; border-top:1px solid #c0c0c0;">
16
<!-- Generated by Doxygen 1.8.5 -->
17
<div id="nav-path" class="navpath">
19
<li class="navelem"><a class="el" href="namespaceOpenMS.html">OpenMS</a></li><li class="navelem"><a class="el" href="classOpenMS_1_1OpenSwathDataAccessHelper.html">OpenSwathDataAccessHelper</a></li> </ul>
24
<a href="#pub-static-methods">Static Public Member Functions</a> |
25
<a href="classOpenMS_1_1OpenSwathDataAccessHelper-members.html">List of all members</a> </div>
26
<div class="headertitle">
27
<div class="title">OpenSwathDataAccessHelper Class Reference</div> </div>
29
<div class="contents">
31
<p>Several helpers to convert <a class="el" href="namespaceOpenMS.html" title="Main OpenMS namespace. ">OpenMS</a> datastructures to structures that implement the OpenSWATH interfaces.
32
<a href="classOpenMS_1_1OpenSwathDataAccessHelper.html#details">More...</a></p>
34
<p><code>#include <<a class="el" href="DataAccessHelper_8h_source.html">OpenMS/ANALYSIS/OPENSWATH/DATAACCESS/DataAccessHelper.h</a>></code></p>
35
<table class="memberdecls">
36
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-static-methods"></a>
37
Static Public Member Functions</h2></td></tr>
38
<tr class="memitem:abdfea944b47657cb07679cb723bb7d1e"><td class="memItemLeft" align="right" valign="top">static void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1OpenSwathDataAccessHelper.html#abdfea944b47657cb07679cb723bb7d1e">convertToOpenMSSpectrum</a> (const <a class="el" href="namespaceOpenSwath.html#a93e7d6a13eb66ccae0357dbae6f33523">OpenSwath::SpectrumPtr</a> sptr, <a class="el" href="classOpenMS_1_1MSSpectrum.html">OpenMS::MSSpectrum</a><> &spectrum)</td></tr>
39
<tr class="memdesc:abdfea944b47657cb07679cb723bb7d1e"><td class="mdescLeft"> </td><td class="mdescRight">Convert a SpectrumPtr to an <a class="el" href="namespaceOpenMS.html" title="Main OpenMS namespace. ">OpenMS</a> Spectrum. <a href="#abdfea944b47657cb07679cb723bb7d1e">More...</a><br/></td></tr>
40
<tr class="separator:abdfea944b47657cb07679cb723bb7d1e"><td class="memSeparator" colspan="2"> </td></tr>
41
<tr class="memitem:a13d17d1899b239966950b8124acb38ae"><td class="memItemLeft" align="right" valign="top">static <a class="el" href="namespaceOpenSwath.html#a93e7d6a13eb66ccae0357dbae6f33523">OpenSwath::SpectrumPtr</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1OpenSwathDataAccessHelper.html#a13d17d1899b239966950b8124acb38ae">convertToSpectrumPtr</a> (const <a class="el" href="classOpenMS_1_1MSSpectrum.html">OpenMS::MSSpectrum</a><> &spectrum)</td></tr>
42
<tr class="memdesc:a13d17d1899b239966950b8124acb38ae"><td class="mdescLeft"> </td><td class="mdescRight">Convert an <a class="el" href="namespaceOpenMS.html" title="Main OpenMS namespace. ">OpenMS</a> Spectrum to an SpectrumPtr. <a href="#a13d17d1899b239966950b8124acb38ae">More...</a><br/></td></tr>
43
<tr class="separator:a13d17d1899b239966950b8124acb38ae"><td class="memSeparator" colspan="2"> </td></tr>
44
<tr class="memitem:a64343e3d648cde97d9d7970c08eea3f7"><td class="memItemLeft" align="right" valign="top">static void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1OpenSwathDataAccessHelper.html#a64343e3d648cde97d9d7970c08eea3f7">convertToOpenMSChromatogram</a> (<a class="el" href="classOpenMS_1_1MSChromatogram.html">OpenMS::MSChromatogram</a><> &chromatogram, const <a class="el" href="namespaceOpenSwath.html#a159d76e81a041373752ffca5f953a5ca">OpenSwath::ChromatogramPtr</a> cptr)</td></tr>
45
<tr class="memdesc:a64343e3d648cde97d9d7970c08eea3f7"><td class="mdescLeft"> </td><td class="mdescRight">Convert a ChromatogramPtr to an <a class="el" href="namespaceOpenMS.html" title="Main OpenMS namespace. ">OpenMS</a> Chromatogram. <a href="#a64343e3d648cde97d9d7970c08eea3f7">More...</a><br/></td></tr>
46
<tr class="separator:a64343e3d648cde97d9d7970c08eea3f7"><td class="memSeparator" colspan="2"> </td></tr>
47
<tr class="memitem:a0476f3ea925f584d9064efee48c7db6a"><td class="memItemLeft" align="right" valign="top">static void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1OpenSwathDataAccessHelper.html#a0476f3ea925f584d9064efee48c7db6a">convertTargetedExp</a> (const <a class="el" href="classOpenMS_1_1TargetedExperiment.html">OpenMS::TargetedExperiment</a> &transition_exp_, <a class="el" href="structOpenSwath_1_1LightTargetedExperiment.html">OpenSwath::LightTargetedExperiment</a> &transition_exp)</td></tr>
48
<tr class="memdesc:a0476f3ea925f584d9064efee48c7db6a"><td class="mdescLeft"> </td><td class="mdescRight">convert from the <a class="el" href="namespaceOpenMS.html" title="Main OpenMS namespace. ">OpenMS</a> Targeted experiment to the light Targeted Experiment <a href="#a0476f3ea925f584d9064efee48c7db6a">More...</a><br/></td></tr>
49
<tr class="separator:a0476f3ea925f584d9064efee48c7db6a"><td class="memSeparator" colspan="2"> </td></tr>
50
<tr class="memitem:a8ae154a5964d69f913d864b169b7310e"><td class="memItemLeft" align="right" valign="top">static void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1OpenSwathDataAccessHelper.html#a8ae154a5964d69f913d864b169b7310e">convertPeptideToAASequence</a> (const <a class="el" href="structOpenSwath_1_1LightPeptide.html">OpenSwath::LightPeptide</a> &peptide, <a class="el" href="classOpenMS_1_1AASequence.html">AASequence</a> &aa_sequence)</td></tr>
51
<tr class="memdesc:a8ae154a5964d69f913d864b169b7310e"><td class="mdescLeft"> </td><td class="mdescRight">convert from the LightPeptide to an <a class="el" href="namespaceOpenMS.html" title="Main OpenMS namespace. ">OpenMS</a> <a class="el" href="classOpenMS_1_1AASequence.html" title="Representation of a peptide/protein sequence. ">AASequence</a> (with correct modifications) <a href="#a8ae154a5964d69f913d864b169b7310e">More...</a><br/></td></tr>
52
<tr class="separator:a8ae154a5964d69f913d864b169b7310e"><td class="memSeparator" colspan="2"> </td></tr>
54
<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
55
<div class="textblock"><p>Several helpers to convert <a class="el" href="namespaceOpenMS.html" title="Main OpenMS namespace. ">OpenMS</a> datastructures to structures that implement the OpenSWATH interfaces. </p>
56
</div><h2 class="groupheader">Member Function Documentation</h2>
57
<a class="anchor" id="a8ae154a5964d69f913d864b169b7310e"></a>
59
<div class="memproto">
60
<table class="mlabels">
62
<td class="mlabels-left">
63
<table class="memname">
65
<td class="memname">static void convertPeptideToAASequence </td>
67
<td class="paramtype">const <a class="el" href="structOpenSwath_1_1LightPeptide.html">OpenSwath::LightPeptide</a> & </td>
68
<td class="paramname"><em>peptide</em>, </td>
71
<td class="paramkey"></td>
73
<td class="paramtype"><a class="el" href="classOpenMS_1_1AASequence.html">AASequence</a> & </td>
74
<td class="paramname"><em>aa_sequence</em> </td>
83
<td class="mlabels-right">
84
<span class="mlabels"><span class="mlabel">static</span></span> </td>
87
</div><div class="memdoc">
89
<p>convert from the LightPeptide to an <a class="el" href="namespaceOpenMS.html" title="Main OpenMS namespace. ">OpenMS</a> <a class="el" href="classOpenMS_1_1AASequence.html" title="Representation of a peptide/protein sequence. ">AASequence</a> (with correct modifications) </p>
91
<p>Referenced by <a class="el" href="classOpenMS_1_1MRMFeatureFinderScoring.html#a7aa7123edb723725ec69f259c69d46d0">MRMFeatureFinderScoring::calculateSwathScores_()</a>.</p>
95
<a class="anchor" id="a0476f3ea925f584d9064efee48c7db6a"></a>
97
<div class="memproto">
98
<table class="mlabels">
100
<td class="mlabels-left">
101
<table class="memname">
103
<td class="memname">static void convertTargetedExp </td>
105
<td class="paramtype">const <a class="el" href="classOpenMS_1_1TargetedExperiment.html">OpenMS::TargetedExperiment</a> & </td>
106
<td class="paramname"><em>transition_exp_</em>, </td>
109
<td class="paramkey"></td>
111
<td class="paramtype"><a class="el" href="structOpenSwath_1_1LightTargetedExperiment.html">OpenSwath::LightTargetedExperiment</a> & </td>
112
<td class="paramname"><em>transition_exp</em> </td>
121
<td class="mlabels-right">
122
<span class="mlabels"><span class="mlabel">static</span></span> </td>
125
</div><div class="memdoc">
127
<p>convert from the <a class="el" href="namespaceOpenMS.html" title="Main OpenMS namespace. ">OpenMS</a> Targeted experiment to the light Targeted Experiment </p>
129
<p>Referenced by <a class="el" href="classOpenMS_1_1MRMFeatureFinderScoring.html#af879ba2bc9bcc83bed021af39c24e9d6">MRMFeatureFinderScoring::pickExperiment()</a>.</p>
133
<a class="anchor" id="a64343e3d648cde97d9d7970c08eea3f7"></a>
134
<div class="memitem">
135
<div class="memproto">
136
<table class="mlabels">
138
<td class="mlabels-left">
139
<table class="memname">
141
<td class="memname">static void convertToOpenMSChromatogram </td>
143
<td class="paramtype"><a class="el" href="classOpenMS_1_1MSChromatogram.html">OpenMS::MSChromatogram</a><> & </td>
144
<td class="paramname"><em>chromatogram</em>, </td>
147
<td class="paramkey"></td>
149
<td class="paramtype">const <a class="el" href="namespaceOpenSwath.html#a159d76e81a041373752ffca5f953a5ca">OpenSwath::ChromatogramPtr</a> </td>
150
<td class="paramname"><em>cptr</em> </td>
159
<td class="mlabels-right">
160
<span class="mlabels"><span class="mlabel">static</span></span> </td>
163
</div><div class="memdoc">
165
<p>Convert a ChromatogramPtr to an <a class="el" href="namespaceOpenMS.html" title="Main OpenMS namespace. ">OpenMS</a> Chromatogram. </p>
169
<a class="anchor" id="abdfea944b47657cb07679cb723bb7d1e"></a>
170
<div class="memitem">
171
<div class="memproto">
172
<table class="mlabels">
174
<td class="mlabels-left">
175
<table class="memname">
177
<td class="memname">static void convertToOpenMSSpectrum </td>
179
<td class="paramtype">const <a class="el" href="namespaceOpenSwath.html#a93e7d6a13eb66ccae0357dbae6f33523">OpenSwath::SpectrumPtr</a> </td>
180
<td class="paramname"><em>sptr</em>, </td>
183
<td class="paramkey"></td>
185
<td class="paramtype"><a class="el" href="classOpenMS_1_1MSSpectrum.html">OpenMS::MSSpectrum</a><> & </td>
186
<td class="paramname"><em>spectrum</em> </td>
195
<td class="mlabels-right">
196
<span class="mlabels"><span class="mlabel">static</span></span> </td>
199
</div><div class="memdoc">
201
<p>Convert a SpectrumPtr to an <a class="el" href="namespaceOpenMS.html" title="Main OpenMS namespace. ">OpenMS</a> Spectrum. </p>
205
<a class="anchor" id="a13d17d1899b239966950b8124acb38ae"></a>
206
<div class="memitem">
207
<div class="memproto">
208
<table class="mlabels">
210
<td class="mlabels-left">
211
<table class="memname">
213
<td class="memname">static <a class="el" href="namespaceOpenSwath.html#a93e7d6a13eb66ccae0357dbae6f33523">OpenSwath::SpectrumPtr</a> convertToSpectrumPtr </td>
215
<td class="paramtype">const <a class="el" href="classOpenMS_1_1MSSpectrum.html">OpenMS::MSSpectrum</a><> & </td>
216
<td class="paramname"><em>spectrum</em></td><td>)</td>
221
<td class="mlabels-right">
222
<span class="mlabels"><span class="mlabel">static</span></span> </td>
225
</div><div class="memdoc">
227
<p>Convert an <a class="el" href="namespaceOpenMS.html" title="Main OpenMS namespace. ">OpenMS</a> Spectrum to an SpectrumPtr. </p>
231
</div><!-- contents -->
232
<HR style="height:1px; border:none; border-top:1px solid #c0c0c0;">
233
<TABLE width="100%" border="0">
235
<TD><font color="#c0c0c0">OpenMS / TOPP release 1.11.1</font></TD>
236
<TD align="right"><font color="#c0c0c0">Documentation generated on Thu Nov 14 2013 11:19:26 using doxygen 1.8.5</font></TD>