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<HTML>
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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_1TransformationDescription.html">TransformationDescription</a></li> </ul>
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<a href="#pub-types">Public Types</a> |
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<div class="title">TransformationDescription Class Reference<div class="ingroups"><a class="el" href="group__MapAlignment.html">MapAlignment</a></div></div> </div>
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<p>Generic description of a coordinate transformation.
<a href="classOpenMS_1_1TransformationDescription.html#details">More...</a></p>
<p><code>#include <<a class="el" href="TransformationDescription_8h_source.html">OpenMS/ANALYSIS/MAPMATCHING/TransformationDescription.h</a>></code></p>
<table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-types"></a>
Public Types</h2></td></tr>
<tr class="memitem:a8e6cd3d7f43ee94f3bd39d2a1ebf9c2e"><td class="memItemLeft" align="right" valign="top">typedef <br class="typebreak"/>
<a class="el" href="classOpenMS_1_1TransformationModel.html#ac93bbaab8952124bfb6a32870b773ac1">TransformationModel::DataPoint</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TransformationDescription.html#a8e6cd3d7f43ee94f3bd39d2a1ebf9c2e">DataPoint</a></td></tr>
<tr class="memdesc:a8e6cd3d7f43ee94f3bd39d2a1ebf9c2e"><td class="mdescLeft"> </td><td class="mdescRight">Coordinate pair. <a href="#a8e6cd3d7f43ee94f3bd39d2a1ebf9c2e">More...</a><br/></td></tr>
<tr class="separator:a8e6cd3d7f43ee94f3bd39d2a1ebf9c2e"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:acfd5876dc642e1f35afc2f32dcc65d25"><td class="memItemLeft" align="right" valign="top">typedef <br class="typebreak"/>
<a class="el" href="classOpenMS_1_1TransformationModel.html#a4067970d097e9b2f62de2058276b0c24">TransformationModel::DataPoints</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TransformationDescription.html#acfd5876dc642e1f35afc2f32dcc65d25">DataPoints</a></td></tr>
<tr class="memdesc:acfd5876dc642e1f35afc2f32dcc65d25"><td class="mdescLeft"> </td><td class="mdescRight">Vector of coordinate pairs. <a href="#acfd5876dc642e1f35afc2f32dcc65d25">More...</a><br/></td></tr>
<tr class="separator:acfd5876dc642e1f35afc2f32dcc65d25"><td class="memSeparator" colspan="2"> </td></tr>
</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a>
Public Member Functions</h2></td></tr>
<tr class="memitem:a144a0b0d701b1720a1727fc3cf277ae8"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TransformationDescription.html#a144a0b0d701b1720a1727fc3cf277ae8">TransformationDescription</a> ()</td></tr>
<tr class="memdesc:a144a0b0d701b1720a1727fc3cf277ae8"><td class="mdescLeft"> </td><td class="mdescRight">Default constructor. <a href="#a144a0b0d701b1720a1727fc3cf277ae8">More...</a><br/></td></tr>
<tr class="separator:a144a0b0d701b1720a1727fc3cf277ae8"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a6c6c5a1fe722a064d6cf2f560dd77276"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TransformationDescription.html#a6c6c5a1fe722a064d6cf2f560dd77276">TransformationDescription</a> (const <a class="el" href="classOpenMS_1_1TransformationDescription.html#acfd5876dc642e1f35afc2f32dcc65d25">DataPoints</a> &data)</td></tr>
<tr class="memdesc:a6c6c5a1fe722a064d6cf2f560dd77276"><td class="mdescLeft"> </td><td class="mdescRight">Constructor from data. <a href="#a6c6c5a1fe722a064d6cf2f560dd77276">More...</a><br/></td></tr>
<tr class="separator:a6c6c5a1fe722a064d6cf2f560dd77276"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a05a93476218e4da0afaa212474e97885"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TransformationDescription.html#a05a93476218e4da0afaa212474e97885">~TransformationDescription</a> ()</td></tr>
<tr class="memdesc:a05a93476218e4da0afaa212474e97885"><td class="mdescLeft"> </td><td class="mdescRight">Destructor. <a href="#a05a93476218e4da0afaa212474e97885">More...</a><br/></td></tr>
<tr class="separator:a05a93476218e4da0afaa212474e97885"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a98ec2d156b10679d84b4c2751697ca19"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TransformationDescription.html#a98ec2d156b10679d84b4c2751697ca19">TransformationDescription</a> (const <a class="el" href="classOpenMS_1_1TransformationDescription.html">TransformationDescription</a> &rhs)</td></tr>
<tr class="memdesc:a98ec2d156b10679d84b4c2751697ca19"><td class="mdescLeft"> </td><td class="mdescRight">Copy constructor. <a href="#a98ec2d156b10679d84b4c2751697ca19">More...</a><br/></td></tr>
<tr class="separator:a98ec2d156b10679d84b4c2751697ca19"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a6777b882f67ef2433cc298e6a851f267"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1TransformationDescription.html">TransformationDescription</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TransformationDescription.html#a6777b882f67ef2433cc298e6a851f267">operator=</a> (const <a class="el" href="classOpenMS_1_1TransformationDescription.html">TransformationDescription</a> &rhs)</td></tr>
<tr class="memdesc:a6777b882f67ef2433cc298e6a851f267"><td class="mdescLeft"> </td><td class="mdescRight">Assignment operator. <a href="#a6777b882f67ef2433cc298e6a851f267">More...</a><br/></td></tr>
<tr class="separator:a6777b882f67ef2433cc298e6a851f267"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a7703888e680ea25672baf4e831987ed3"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TransformationDescription.html#a7703888e680ea25672baf4e831987ed3">fitModel</a> (const <a class="el" href="classOpenMS_1_1String.html">String</a> &model_type, const <a class="el" href="classOpenMS_1_1Param.html">Param</a> &params=<a class="el" href="classOpenMS_1_1Param.html">Param</a>())</td></tr>
<tr class="memdesc:a7703888e680ea25672baf4e831987ed3"><td class="mdescLeft"> </td><td class="mdescRight">Fits a model to the data. <a href="#a7703888e680ea25672baf4e831987ed3">More...</a><br/></td></tr>
<tr class="separator:a7703888e680ea25672baf4e831987ed3"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:aa280f8d4730c216c58a3edd091b99767"><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_1TransformationDescription.html#aa280f8d4730c216c58a3edd091b99767">apply</a> (<a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> value) const </td></tr>
<tr class="memdesc:aa280f8d4730c216c58a3edd091b99767"><td class="mdescLeft"> </td><td class="mdescRight">Applies the transformation to <code>value</code>. <a href="#aa280f8d4730c216c58a3edd091b99767">More...</a><br/></td></tr>
<tr class="separator:aa280f8d4730c216c58a3edd091b99767"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:af2111f3d29fe3ba10b75dc9594c4729c"><td class="memItemLeft" align="right" valign="top">const <a class="el" href="classOpenMS_1_1String.html">String</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TransformationDescription.html#af2111f3d29fe3ba10b75dc9594c4729c">getModelType</a> () const </td></tr>
<tr class="memdesc:af2111f3d29fe3ba10b75dc9594c4729c"><td class="mdescLeft"> </td><td class="mdescRight">Gets the type of the fitted model. <a href="#af2111f3d29fe3ba10b75dc9594c4729c">More...</a><br/></td></tr>
<tr class="separator:af2111f3d29fe3ba10b75dc9594c4729c"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a080a7748a0f5bd19412f8ceffbcc56c1"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TransformationDescription.html#a080a7748a0f5bd19412f8ceffbcc56c1">setDataPoints</a> (const <a class="el" href="classOpenMS_1_1TransformationDescription.html#acfd5876dc642e1f35afc2f32dcc65d25">DataPoints</a> &data)</td></tr>
<tr class="memdesc:a080a7748a0f5bd19412f8ceffbcc56c1"><td class="mdescLeft"> </td><td class="mdescRight">Sets the data points. <a href="#a080a7748a0f5bd19412f8ceffbcc56c1">More...</a><br/></td></tr>
<tr class="separator:a080a7748a0f5bd19412f8ceffbcc56c1"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ab46b6593d300724af3e58e120c16817b"><td class="memItemLeft" align="right" valign="top">const <a class="el" href="classOpenMS_1_1TransformationDescription.html#acfd5876dc642e1f35afc2f32dcc65d25">DataPoints</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TransformationDescription.html#ab46b6593d300724af3e58e120c16817b">getDataPoints</a> () const </td></tr>
<tr class="memdesc:ab46b6593d300724af3e58e120c16817b"><td class="mdescLeft"> </td><td class="mdescRight">Returns the data points. <a href="#ab46b6593d300724af3e58e120c16817b">More...</a><br/></td></tr>
<tr class="separator:ab46b6593d300724af3e58e120c16817b"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:aab3ccb8350de2c9bf4f123033bc1239e"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TransformationDescription.html#aab3ccb8350de2c9bf4f123033bc1239e">getModelParameters</a> (<a class="el" href="classOpenMS_1_1Param.html">Param</a> &params) const </td></tr>
<tr class="memdesc:aab3ccb8350de2c9bf4f123033bc1239e"><td class="mdescLeft"> </td><td class="mdescRight">Non-mutable access to the model parameters. <a href="#aab3ccb8350de2c9bf4f123033bc1239e">More...</a><br/></td></tr>
<tr class="separator:aab3ccb8350de2c9bf4f123033bc1239e"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a7fa1616cc61c19a5efcc863c950f7f30"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TransformationDescription.html#a7fa1616cc61c19a5efcc863c950f7f30">invert</a> ()</td></tr>
<tr class="memdesc:a7fa1616cc61c19a5efcc863c950f7f30"><td class="mdescLeft"> </td><td class="mdescRight">Computes an (approximate) inverse of the transformation. <a href="#a7fa1616cc61c19a5efcc863c950f7f30">More...</a><br/></td></tr>
<tr class="separator:a7fa1616cc61c19a5efcc863c950f7f30"><td class="memSeparator" colspan="2"> </td></tr>
</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-static-methods"></a>
Static Public Member Functions</h2></td></tr>
<tr class="memitem:a58918dddba0fd309a5be6d353a077419"><td class="memItemLeft" align="right" valign="top">static void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TransformationDescription.html#a58918dddba0fd309a5be6d353a077419">getModelTypes</a> (<a class="el" href="classOpenMS_1_1StringList.html">StringList</a> &result)</td></tr>
<tr class="memdesc:a58918dddba0fd309a5be6d353a077419"><td class="mdescLeft"> </td><td class="mdescRight">Gets the possible types of models. <a href="#a58918dddba0fd309a5be6d353a077419">More...</a><br/></td></tr>
<tr class="separator:a58918dddba0fd309a5be6d353a077419"><td class="memSeparator" colspan="2"> </td></tr>
</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pro-attribs"></a>
Protected Attributes</h2></td></tr>
<tr class="memitem:a50cb06485f4046e357f7750176d51783"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1TransformationDescription.html#acfd5876dc642e1f35afc2f32dcc65d25">DataPoints</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TransformationDescription.html#a50cb06485f4046e357f7750176d51783">data_</a></td></tr>
<tr class="memdesc:a50cb06485f4046e357f7750176d51783"><td class="mdescLeft"> </td><td class="mdescRight">Data points. <a href="#a50cb06485f4046e357f7750176d51783">More...</a><br/></td></tr>
<tr class="separator:a50cb06485f4046e357f7750176d51783"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a4bc1aa3db307203e7719a96808120858"><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_1TransformationDescription.html#a4bc1aa3db307203e7719a96808120858">model_type_</a></td></tr>
<tr class="memdesc:a4bc1aa3db307203e7719a96808120858"><td class="mdescLeft"> </td><td class="mdescRight">Type of model. <a href="#a4bc1aa3db307203e7719a96808120858">More...</a><br/></td></tr>
<tr class="separator:a4bc1aa3db307203e7719a96808120858"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ae709da349f14f3559e5c038809a0e625"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1TransformationModel.html">TransformationModel</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TransformationDescription.html#ae709da349f14f3559e5c038809a0e625">model_</a></td></tr>
<tr class="memdesc:ae709da349f14f3559e5c038809a0e625"><td class="mdescLeft"> </td><td class="mdescRight">Pointer to model. <a href="#ae709da349f14f3559e5c038809a0e625">More...</a><br/></td></tr>
<tr class="separator:ae709da349f14f3559e5c038809a0e625"><td class="memSeparator" colspan="2"> </td></tr>
</table>
<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
<div class="textblock"><p>Generic description of a coordinate transformation. </p>
<p>This description primarily stores data points (coordinate pairs) from which a <a class="el" href="classOpenMS_1_1TransformationModel.html">transformation model</a> can be estimated. Applying the transformation to a coordinate (via <code>apply</code>) then means evaluating the model at that coordinate.</p>
<p>The following models are available:</p>
<ul>
<li><code>none</code> (<a class="el" href="classOpenMS_1_1TransformationModel.html" title="Base class for transformation models. ">TransformationModel</a>): <img class="formulaInl" alt="$ f(x) = x $" src="form_26.png"/> (identity)</li>
<li><code>identity:</code> Same as <code>none</code>, but intended for reference files (used to indicate that no other model should be fit, because the identity is already optimal).</li>
<li><code>linear</code> (<a class="el" href="classOpenMS_1_1TransformationModelLinear.html" title="Linear model for transformations. ">TransformationModelLinear</a>): <img class="formulaInl" alt="$ f(x) = slope * x + intercept $" src="form_27.png"/></li>
<li><code>interpolated</code> (<a class="el" href="classOpenMS_1_1TransformationModelInterpolated.html" title="Interpolation model for transformations. ">TransformationModelInterpolated</a>): Interpolation between pairs, extrapolation using first and last pair. Supports different interpolation types.</li>
<li><code>b_spline</code> (<a class="el" href="classOpenMS_1_1TransformationModelBSpline.html" title="B-spline model for transformations. ">TransformationModelBSpline</a>): Smoothing cubic B-spline.</li>
</ul>
<dl class="section remark"><dt>Remarks</dt><dd><a class="el" href="classOpenMS_1_1TransformationDescription.html" title="Generic description of a coordinate transformation. ">TransformationDescription</a> stores data points, <a class="el" href="classOpenMS_1_1TransformationModel.html" title="Base class for transformation models. ">TransformationModel</a> stores parameters. That way, data can be modeled using different models/parameters, and models can still keep a representation of the data in the format they need (if at all). </dd></dl>
</div><h2 class="groupheader">Member Typedef Documentation</h2>
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<td class="memname">typedef <a class="el" href="classOpenMS_1_1TransformationModel.html#ac93bbaab8952124bfb6a32870b773ac1">TransformationModel::DataPoint</a> <a class="el" href="classOpenMS_1_1TransformationDescription.html#a8e6cd3d7f43ee94f3bd39d2a1ebf9c2e">DataPoint</a></td>
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<p>Coordinate pair. </p>
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<td class="memname">typedef <a class="el" href="classOpenMS_1_1TransformationModel.html#a4067970d097e9b2f62de2058276b0c24">TransformationModel::DataPoints</a> <a class="el" href="classOpenMS_1_1TransformationDescription.html#acfd5876dc642e1f35afc2f32dcc65d25">DataPoints</a></td>
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<p>Vector of coordinate pairs. </p>
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<td class="memname"><a class="el" href="classOpenMS_1_1TransformationDescription.html">TransformationDescription</a> </td>
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<p>Default constructor. </p>
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<td class="memname"><a class="el" href="classOpenMS_1_1TransformationDescription.html">TransformationDescription</a> </td>
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<td class="paramtype">const <a class="el" href="classOpenMS_1_1TransformationDescription.html#acfd5876dc642e1f35afc2f32dcc65d25">DataPoints</a> & </td>
<td class="paramname"><em>data</em></td><td>)</td>
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<p>Constructor from data. </p>
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<td class="memname">~<a class="el" href="classOpenMS_1_1TransformationDescription.html">TransformationDescription</a> </td>
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<p>Destructor. </p>
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<td class="memname"><a class="el" href="classOpenMS_1_1TransformationDescription.html">TransformationDescription</a> </td>
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<p>Copy constructor. </p>
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<h2 class="groupheader">Member Function Documentation</h2>
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<td class="memname"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> apply </td>
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<p>Applies the transformation to <code>value</code>. </p>
<p>Returns the result of evaluating the fitted model at <code>value</code>. Returns <code>value</code> unchanged if no model was fitted. </p>
<p>Referenced by <a class="el" href="classOpenMS_1_1InternalCalibration.html#a2157a7fbbba00561b9bf8b26b469786d">InternalCalibration::calibrateMapGlobally()</a>, <a class="el" href="classOpenMS_1_1InternalCalibration.html#a1651981607d6c86252b9ab64e5f7996c">InternalCalibration::calibrateMapSpectrumwise()</a>, <a class="el" href="classOpenMS_1_1ChromatogramExtractor.html#acee142f4f394a06534b33c828b42f7ec">ChromatogramExtractor::outsideExtractionWindow_()</a>, and <a class="el" href="classOpenMS_1_1MRMFeatureFinderScoring.html#a1d7f11c2be93f8140f508487ba0ae718">MRMFeatureFinderScoring::scorePeakgroups_()</a>.</p>
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<td class="memname">void fitModel </td>
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<p>Fits a model to the data. </p>
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<td class="memname">const <a class="el" href="classOpenMS_1_1TransformationDescription.html#acfd5876dc642e1f35afc2f32dcc65d25">DataPoints</a>& getDataPoints </td>
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<p>Returns the data points. </p>
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<td class="memname">void getModelParameters </td>
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<p>Non-mutable access to the model parameters. </p>
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<td class="memname">const <a class="el" href="classOpenMS_1_1String.html">String</a>& getModelType </td>
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<p>Gets the type of the fitted model. </p>
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<td class="memname">static void getModelTypes </td>
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<td class="paramtype"><a class="el" href="classOpenMS_1_1StringList.html">StringList</a> & </td>
<td class="paramname"><em>result</em></td><td>)</td>
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<p>Gets the possible types of models. </p>
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<td class="memname">void invert </td>
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<p>Computes an (approximate) inverse of the transformation. </p>
<p>Referenced by <a class="el" href="classOpenMS_1_1ChromatogramExtractor.html#ab8e5068d0d5799146b80ea6282ff0a6c">ChromatogramExtractor::extractChromatograms()</a>, and <a class="el" href="classOpenMS_1_1MRMFeatureFinderScoring.html#a1d7f11c2be93f8140f508487ba0ae718">MRMFeatureFinderScoring::scorePeakgroups_()</a>.</p>
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<td class="memname"><a class="el" href="classOpenMS_1_1TransformationDescription.html">TransformationDescription</a>& operator= </td>
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<p>Assignment operator. </p>
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<td class="memname">void setDataPoints </td>
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<td class="paramtype">const <a class="el" href="classOpenMS_1_1TransformationDescription.html#acfd5876dc642e1f35afc2f32dcc65d25">DataPoints</a> & </td>
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<p>Sets the data points. </p>
<p>Removes the model that was previously fitted to the data (if any). </p>
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<h2 class="groupheader">Member Data Documentation</h2>
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<td class="memname"><a class="el" href="classOpenMS_1_1TransformationDescription.html#acfd5876dc642e1f35afc2f32dcc65d25">DataPoints</a> data_</td>
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<p>Data points. </p>
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<td class="memname"><a class="el" href="classOpenMS_1_1TransformationModel.html">TransformationModel</a>* model_</td>
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<p>Pointer to model. </p>
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<td class="memname"><a class="el" href="classOpenMS_1_1String.html">String</a> model_type_</td>
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<p>Type of model. </p>
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<TD><font color="#c0c0c0">OpenMS / TOPP release 1.11.1</font></TD>
<TD align="right"><font color="#c0c0c0">Documentation generated on Thu Nov 14 2013 11:19:26 using doxygen 1.8.5</font></TD>
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