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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_1FileHandler.html">FileHandler</a></li> </ul>
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<a href="#pub-methods">Public Member Functions</a> |
<a href="#pub-static-methods">Static Public Member Functions</a> |
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<div class="title">FileHandler Class Reference<div class="ingroups"><a class="el" href="group__FileIO.html">File IO</a></div></div> </div>
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<p>Facilitates file handling by file type recognition.
<a href="classOpenMS_1_1FileHandler.html#details">More...</a></p>
<p><code>#include <<a class="el" href="FileHandler_8h_source.html">OpenMS/FORMAT/FileHandler.h</a>></code></p>
<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:a819235ed2844f03df53f4983a7008f28"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1PeakFileOptions.html">PeakFileOptions</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FileHandler.html#a819235ed2844f03df53f4983a7008f28">getOptions</a> ()</td></tr>
<tr class="memdesc:a819235ed2844f03df53f4983a7008f28"><td class="mdescLeft"> </td><td class="mdescRight">Mutable access to the options for loading/storing. <a href="#a819235ed2844f03df53f4983a7008f28">More...</a><br/></td></tr>
<tr class="separator:a819235ed2844f03df53f4983a7008f28"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a5fa0d33e72b9dc6624eeb42c2ca6955a"><td class="memItemLeft" align="right" valign="top">const <a class="el" href="classOpenMS_1_1PeakFileOptions.html">PeakFileOptions</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FileHandler.html#a5fa0d33e72b9dc6624eeb42c2ca6955a">getOptions</a> () const </td></tr>
<tr class="memdesc:a5fa0d33e72b9dc6624eeb42c2ca6955a"><td class="mdescLeft"> </td><td class="mdescRight">Non-mutable access to the options for loading/storing. <a href="#a5fa0d33e72b9dc6624eeb42c2ca6955a">More...</a><br/></td></tr>
<tr class="separator:a5fa0d33e72b9dc6624eeb42c2ca6955a"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a408091416e0e1f6019abd59bdb6a9269"><td class="memTemplParams" colspan="2">template<class PeakType > </td></tr>
<tr class="memitem:a408091416e0e1f6019abd59bdb6a9269"><td class="memTemplItemLeft" align="right" valign="top">bool </td><td class="memTemplItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FileHandler.html#a408091416e0e1f6019abd59bdb6a9269">loadExperiment</a> (const <a class="el" href="classOpenMS_1_1String.html">String</a> &filename, <a class="el" href="classOpenMS_1_1MSExperiment.html">MSExperiment</a>< <a class="el" href="namespaceOpenMS.html#a013338b7bdbb5c3b4c78666656070e23">PeakType</a> > &exp, <a class="el" href="structOpenMS_1_1FileTypes.html#a1d1cfd8ffb84e947f82999c682b666a7">FileTypes::Type</a> force_type=<a class="el" href="structOpenMS_1_1FileTypes.html#a1d1cfd8ffb84e947f82999c682b666a7a6ce26a62afab55d7606ad4e92428b30c">FileTypes::UNKNOWN</a>, <a class="el" href="classOpenMS_1_1ProgressLogger.html#af67907baa897e9fb84df0cb89795b87c">ProgressLogger::LogType</a> log=<a class="el" href="classOpenMS_1_1ProgressLogger.html#af67907baa897e9fb84df0cb89795b87cac157bdf0b85a40d2619cbc8bc1ae5fe2">ProgressLogger::NONE</a>, const bool compute_hash=true)</td></tr>
<tr class="memdesc:a408091416e0e1f6019abd59bdb6a9269"><td class="mdescLeft"> </td><td class="mdescRight">Loads a file into an <a class="el" href="classOpenMS_1_1MSExperiment.html" title="Representation of a mass spectrometry experiment. ">MSExperiment</a>. <a href="#a408091416e0e1f6019abd59bdb6a9269">More...</a><br/></td></tr>
<tr class="separator:a408091416e0e1f6019abd59bdb6a9269"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a4a8354ef45f8a0eac5a5038b3a025f37"><td class="memTemplParams" colspan="2">template<class PeakType > </td></tr>
<tr class="memitem:a4a8354ef45f8a0eac5a5038b3a025f37"><td class="memTemplItemLeft" align="right" valign="top">void </td><td class="memTemplItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FileHandler.html#a4a8354ef45f8a0eac5a5038b3a025f37">storeExperiment</a> (const <a class="el" href="classOpenMS_1_1String.html">String</a> &filename, const <a class="el" href="classOpenMS_1_1MSExperiment.html">MSExperiment</a>< <a class="el" href="namespaceOpenMS.html#a013338b7bdbb5c3b4c78666656070e23">PeakType</a> > &exp, <a class="el" href="classOpenMS_1_1ProgressLogger.html#af67907baa897e9fb84df0cb89795b87c">ProgressLogger::LogType</a> log=<a class="el" href="classOpenMS_1_1ProgressLogger.html#af67907baa897e9fb84df0cb89795b87cac157bdf0b85a40d2619cbc8bc1ae5fe2">ProgressLogger::NONE</a>)</td></tr>
<tr class="memdesc:a4a8354ef45f8a0eac5a5038b3a025f37"><td class="mdescLeft"> </td><td class="mdescRight">Stores an <a class="el" href="classOpenMS_1_1MSExperiment.html" title="Representation of a mass spectrometry experiment. ">MSExperiment</a> to a file. <a href="#a4a8354ef45f8a0eac5a5038b3a025f37">More...</a><br/></td></tr>
<tr class="separator:a4a8354ef45f8a0eac5a5038b3a025f37"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a5bc5a0452855c2d30d125261783b55cf"><td class="memTemplParams" colspan="2">template<class FeatureType > </td></tr>
<tr class="memitem:a5bc5a0452855c2d30d125261783b55cf"><td class="memTemplItemLeft" align="right" valign="top">bool </td><td class="memTemplItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FileHandler.html#a5bc5a0452855c2d30d125261783b55cf">loadFeatures</a> (const <a class="el" href="classOpenMS_1_1String.html">String</a> &filename, <a class="el" href="classOpenMS_1_1FeatureMap.html">FeatureMap</a>< FeatureType > &map, <a class="el" href="structOpenMS_1_1FileTypes.html#a1d1cfd8ffb84e947f82999c682b666a7">FileTypes::Type</a> force_type=<a class="el" href="structOpenMS_1_1FileTypes.html#a1d1cfd8ffb84e947f82999c682b666a7a6ce26a62afab55d7606ad4e92428b30c">FileTypes::UNKNOWN</a>)</td></tr>
<tr class="memdesc:a5bc5a0452855c2d30d125261783b55cf"><td class="mdescLeft"> </td><td class="mdescRight">Loads a file into a <a class="el" href="classOpenMS_1_1FeatureMap.html" title="A container for features. ">FeatureMap</a>. <a href="#a5bc5a0452855c2d30d125261783b55cf">More...</a><br/></td></tr>
<tr class="separator:a5bc5a0452855c2d30d125261783b55cf"><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:a851b569c3e65a4eeabdd10425f2e6402"><td class="memItemLeft" align="right" valign="top">static <a class="el" href="structOpenMS_1_1FileTypes.html#a1d1cfd8ffb84e947f82999c682b666a7">FileTypes::Type</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FileHandler.html#a851b569c3e65a4eeabdd10425f2e6402">getType</a> (const <a class="el" href="classOpenMS_1_1String.html">String</a> &filename)</td></tr>
<tr class="memdesc:a851b569c3e65a4eeabdd10425f2e6402"><td class="mdescLeft"> </td><td class="mdescRight">Tries to determine the file type (by name or content) <a href="#a851b569c3e65a4eeabdd10425f2e6402">More...</a><br/></td></tr>
<tr class="separator:a851b569c3e65a4eeabdd10425f2e6402"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a86452aafcfba244e1bdf058e2b3b8475"><td class="memItemLeft" align="right" valign="top">static <a class="el" href="structOpenMS_1_1FileTypes.html#a1d1cfd8ffb84e947f82999c682b666a7">FileTypes::Type</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FileHandler.html#a86452aafcfba244e1bdf058e2b3b8475">getTypeByFileName</a> (const <a class="el" href="classOpenMS_1_1String.html">String</a> &filename)</td></tr>
<tr class="memdesc:a86452aafcfba244e1bdf058e2b3b8475"><td class="mdescLeft"> </td><td class="mdescRight">Determines the file type from a file name. <a href="#a86452aafcfba244e1bdf058e2b3b8475">More...</a><br/></td></tr>
<tr class="separator:a86452aafcfba244e1bdf058e2b3b8475"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a6189bfbef8639c71f3ef2dfa55c4fad7"><td class="memItemLeft" align="right" valign="top">static <a class="el" href="structOpenMS_1_1FileTypes.html#a1d1cfd8ffb84e947f82999c682b666a7">FileTypes::Type</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FileHandler.html#a6189bfbef8639c71f3ef2dfa55c4fad7">getTypeByContent</a> (const <a class="el" href="classOpenMS_1_1String.html">String</a> &filename)</td></tr>
<tr class="memdesc:a6189bfbef8639c71f3ef2dfa55c4fad7"><td class="mdescLeft"> </td><td class="mdescRight">Determines the file type of a file by parsing the first few lines. <a href="#a6189bfbef8639c71f3ef2dfa55c4fad7">More...</a><br/></td></tr>
<tr class="separator:a6189bfbef8639c71f3ef2dfa55c4fad7"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a0c93b278d8c65098eab2c5de485b22f0"><td class="memItemLeft" align="right" valign="top">static bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FileHandler.html#a0c93b278d8c65098eab2c5de485b22f0">isSupported</a> (<a class="el" href="structOpenMS_1_1FileTypes.html#a1d1cfd8ffb84e947f82999c682b666a7">FileTypes::Type</a> type)</td></tr>
<tr class="memdesc:a0c93b278d8c65098eab2c5de485b22f0"><td class="mdescLeft"> </td><td class="mdescRight">Returns if the file type is supported in this build of the library. <a href="#a0c93b278d8c65098eab2c5de485b22f0">More...</a><br/></td></tr>
<tr class="separator:a0c93b278d8c65098eab2c5de485b22f0"><td class="memSeparator" colspan="2"> </td></tr>
</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pri-methods"></a>
Private Member Functions</h2></td></tr>
<tr class="memitem:a8c1cb2878ce0dfad77312c964962ff30"><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_1FileHandler.html#a8c1cb2878ce0dfad77312c964962ff30">computeFileHash_</a> (const <a class="el" href="classOpenMS_1_1String.html">String</a> &filename) const </td></tr>
<tr class="memdesc:a8c1cb2878ce0dfad77312c964962ff30"><td class="mdescLeft"> </td><td class="mdescRight">Computes a SHA-1 hash value for the content of the given file. <a href="#a8c1cb2878ce0dfad77312c964962ff30">More...</a><br/></td></tr>
<tr class="separator:a8c1cb2878ce0dfad77312c964962ff30"><td class="memSeparator" colspan="2"> </td></tr>
</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pri-attribs"></a>
Private Attributes</h2></td></tr>
<tr class="memitem:a654a0b5941d937e303c64bc9e732baec"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1PeakFileOptions.html">PeakFileOptions</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FileHandler.html#a654a0b5941d937e303c64bc9e732baec">options_</a></td></tr>
<tr class="separator:a654a0b5941d937e303c64bc9e732baec"><td class="memSeparator" colspan="2"> </td></tr>
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<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
<div class="textblock"><p>Facilitates file handling by file type recognition. </p>
<p>This class provides file type recognition from the file name and from the file content.</p>
<p>It also offer a common interface to load <a class="el" href="classOpenMS_1_1MSExperiment.html" title="Representation of a mass spectrometry experiment. ">MSExperiment</a> data and allows querying for supported file types.</p>
<dl class="section see"><dt>See Also</dt><dd><a class="el" href="structOpenMS_1_1FileTypes.html" title="Centralizes the file types recognized by FileHandler. ">FileTypes</a> </dd></dl>
</div><h2 class="groupheader">Member Function Documentation</h2>
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<td class="memname"><a class="el" href="classOpenMS_1_1String.html">String</a> computeFileHash_ </td>
<td>(</td>
<td class="paramtype">const <a class="el" href="classOpenMS_1_1String.html">String</a> & </td>
<td class="paramname"><em>filename</em></td><td>)</td>
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<p>Computes a SHA-1 hash value for the content of the given file. </p>
<dl class="section return"><dt>Returns</dt><dd>The SHA-1 hash of the given file. </dd></dl>
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<td class="memname"><a class="el" href="classOpenMS_1_1PeakFileOptions.html">PeakFileOptions</a>& getOptions </td>
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<p>Mutable access to the options for loading/storing. </p>
<p>Referenced by <a class="el" href="classOpenMS_1_1TOPPViewBase.html#a78af6f231fd21f56ca7b167c51bdbb00">TOPPViewBase::metadataFileDialog()</a>.</p>
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<td class="memname">const <a class="el" href="classOpenMS_1_1PeakFileOptions.html">PeakFileOptions</a>& getOptions </td>
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<p>Non-mutable access to the options for loading/storing. </p>
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<td class="memname">static <a class="el" href="structOpenMS_1_1FileTypes.html#a1d1cfd8ffb84e947f82999c682b666a7">FileTypes::Type</a> getType </td>
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<p>Tries to determine the file type (by name or content) </p>
<p>First the type is determined from the file name. If this fails, the type is determined from the file content.</p>
<dl class="exception"><dt>Exceptions</dt><dd>
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<tr><td class="paramname"><a class="el" href="classOpenMS_1_1Exception_1_1FileNotFound.html" title="File not found exception. ">Exception::FileNotFound</a></td><td>is thrown if the file is not present </td></tr>
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<p>Referenced by <a class="el" href="classOpenMS_1_1TOPPViewBase.html#a1c92b33d10330879ab9d4bc2bb888d07">TOPPViewBase::addDataFile()</a>, and <a class="el" href="classOpenMS_1_1IDEvaluationBase.html#aa95be3d53de372161a9acfd90a6f7fe1">IDEvaluationBase::loadCurve()</a>.</p>
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<td class="memname">static <a class="el" href="structOpenMS_1_1FileTypes.html#a1d1cfd8ffb84e947f82999c682b666a7">FileTypes::Type</a> getTypeByContent </td>
<td>(</td>
<td class="paramtype">const <a class="el" href="classOpenMS_1_1String.html">String</a> & </td>
<td class="paramname"><em>filename</em></td><td>)</td>
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<p>Determines the file type of a file by parsing the first few lines. </p>
<dl class="exception"><dt>Exceptions</dt><dd>
<table class="exception">
<tr><td class="paramname"><a class="el" href="classOpenMS_1_1Exception_1_1FileNotFound.html" title="File not found exception. ">Exception::FileNotFound</a></td><td>is thrown if the file is not present </td></tr>
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</dd>
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<p>Referenced by <a class="el" href="classOpenMS_1_1InspectOutfile.html#a94fe62a5040d77b84878d091f0eb8686">InspectOutfile::getExperiment()</a>.</p>
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<td class="memname">static <a class="el" href="structOpenMS_1_1FileTypes.html#a1d1cfd8ffb84e947f82999c682b666a7">FileTypes::Type</a> getTypeByFileName </td>
<td>(</td>
<td class="paramtype">const <a class="el" href="classOpenMS_1_1String.html">String</a> & </td>
<td class="paramname"><em>filename</em></td><td>)</td>
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<p>Determines the file type from a file name. </p>
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<td class="memname">static bool isSupported </td>
<td>(</td>
<td class="paramtype"><a class="el" href="structOpenMS_1_1FileTypes.html#a1d1cfd8ffb84e947f82999c682b666a7">FileTypes::Type</a> </td>
<td class="paramname"><em>type</em></td><td>)</td>
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<p>Returns if the file type is supported in this build of the library. </p>
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<td class="memname">bool loadExperiment </td>
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<td class="paramtype">const <a class="el" href="classOpenMS_1_1String.html">String</a> & </td>
<td class="paramname"><em>filename</em>, </td>
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<td class="paramkey"></td>
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<td class="paramtype"><a class="el" href="classOpenMS_1_1MSExperiment.html">MSExperiment</a>< <a class="el" href="namespaceOpenMS.html#a013338b7bdbb5c3b4c78666656070e23">PeakType</a> > & </td>
<td class="paramname"><em>exp</em>, </td>
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<td class="paramtype"><a class="el" href="structOpenMS_1_1FileTypes.html#a1d1cfd8ffb84e947f82999c682b666a7">FileTypes::Type</a> </td>
<td class="paramname"><em>force_type</em> = <code><a class="el" href="structOpenMS_1_1FileTypes.html#a1d1cfd8ffb84e947f82999c682b666a7a6ce26a62afab55d7606ad4e92428b30c">FileTypes::UNKNOWN</a></code>, </td>
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<td class="paramkey"></td>
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<td class="paramtype"><a class="el" href="classOpenMS_1_1ProgressLogger.html#af67907baa897e9fb84df0cb89795b87c">ProgressLogger::LogType</a> </td>
<td class="paramname"><em>log</em> = <code><a class="el" href="classOpenMS_1_1ProgressLogger.html#af67907baa897e9fb84df0cb89795b87cac157bdf0b85a40d2619cbc8bc1ae5fe2">ProgressLogger::NONE</a></code>, </td>
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<td class="paramtype">const bool </td>
<td class="paramname"><em>compute_hash</em> = <code>true</code> </td>
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<td>)</td>
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<p>Loads a file into an <a class="el" href="classOpenMS_1_1MSExperiment.html" title="Representation of a mass spectrometry experiment. ">MSExperiment</a>. </p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">filename</td><td>The file name of the file to load. </td></tr>
<tr><td class="paramname">exp</td><td>The experiment to load the data into. </td></tr>
<tr><td class="paramname">force_type</td><td>Forces to load the file with that file type. If no type is forced, it is determined from the extention ( or from the content if that fails). </td></tr>
<tr><td class="paramname">log</td><td>Progress logging mode </td></tr>
<tr><td class="paramname">compute_hash</td><td>Computes a hash value for the loaded file and stores it in the <a class="el" href="classOpenMS_1_1SourceFile.html" title="Description of a file location, used to store the origin of (meta) data. ">SourceFile</a></td></tr>
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<dl class="section return"><dt>Returns</dt><dd>true if the file could be loaded, false otherwise</dd></dl>
<dl class="exception"><dt>Exceptions</dt><dd>
<table class="exception">
<tr><td class="paramname"><a class="el" href="classOpenMS_1_1Exception_1_1FileNotFound.html" title="File not found exception. ">Exception::FileNotFound</a></td><td>is thrown if the file could not be opened </td></tr>
<tr><td class="paramname"><a class="el" href="classOpenMS_1_1Exception_1_1ParseError.html" title="Parse Error exception. ">Exception::ParseError</a></td><td>is thrown if an error occurs during parsing </td></tr>
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<p>References <a class="el" href="classOpenMS_1_1File.html#a6487771c96fec9db032960c91864884e">File::basename()</a>, <a class="el" href="classOpenMS_1_1ChromatogramTools.html#af3ff28dcfb8f80c33a57605672ebb0b1">ChromatogramTools::convertSpectraToChromatograms()</a>, <a class="el" href="structOpenMS_1_1FileTypes.html#a1d1cfd8ffb84e947f82999c682b666a7ad8654d9b2a9c38ece897bfbdd8152214">FileTypes::DTA</a>, <a class="el" href="structOpenMS_1_1FileTypes.html#a1d1cfd8ffb84e947f82999c682b666a7a66c2f5cd90913752f565186657e85d84">FileTypes::DTA2D</a>, <a class="el" href="classOpenMS_1_1MzXMLFile.html#a819235ed2844f03df53f4983a7008f28">MzXMLFile::getOptions()</a>, <a class="el" href="classOpenMS_1_1MzDataFile.html#a819235ed2844f03df53f4983a7008f28">MzDataFile::getOptions()</a>, <a class="el" href="classOpenMS_1_1MzMLFile.html#a819235ed2844f03df53f4983a7008f28">MzMLFile::getOptions()</a>, <a class="el" href="classOpenMS_1_1DTA2DFile.html#a819235ed2844f03df53f4983a7008f28">DTA2DFile::getOptions()</a>, <a class="el" href="classOpenMS_1_1ExperimentalSettings.html#a9b357a65e5ec19027b8fa94379439f8c">ExperimentalSettings::getSourceFiles()</a>, <a class="el" href="classOpenMS_1_1XMassFile.html#a43556a513eaa5395c068a7c9874cc6d1">XMassFile::importExperimentalSettings()</a>, <a class="el" href="classOpenMS_1_1DTAFile.html#a583280bb0e47a5d57b337d6440c96b73">DTAFile::load()</a>, <a class="el" href="classOpenMS_1_1MS2File.html#a98bebe67b8b06a9a67a3654d631355b4">MS2File::load()</a>, <a class="el" href="classOpenMS_1_1MzXMLFile.html#aed378b9a389ec00fa2b559bf7d3b710b">MzXMLFile::load()</a>, <a class="el" href="classOpenMS_1_1MzDataFile.html#aed378b9a389ec00fa2b559bf7d3b710b">MzDataFile::load()</a>, <a class="el" href="classOpenMS_1_1XMassFile.html#a865164e026ef00fa12377c1d63613613">XMassFile::load()</a>, <a class="el" href="classOpenMS_1_1MzMLFile.html#aed378b9a389ec00fa2b559bf7d3b710b">MzMLFile::load()</a>, <a class="el" href="classOpenMS_1_1MascotGenericFile.html#a98bebe67b8b06a9a67a3654d631355b4">MascotGenericFile::load()</a>, <a class="el" href="classOpenMS_1_1DTA2DFile.html#aed378b9a389ec00fa2b559bf7d3b710b">DTA2DFile::load()</a>, <a class="el" href="structOpenMS_1_1FileTypes.html#a1d1cfd8ffb84e947f82999c682b666a7a29bb13323f25136faf82e418da451b26">FileTypes::MGF</a>, <a class="el" href="structOpenMS_1_1FileTypes.html#a1d1cfd8ffb84e947f82999c682b666a7ac59ebe001fb1923baf25b050436a5f15">FileTypes::MS2</a>, <a class="el" href="structOpenMS_1_1FileTypes.html#a1d1cfd8ffb84e947f82999c682b666a7ae5b2d8f7eb59b2fc050e6bc3c1cba802">FileTypes::MZDATA</a>, <a class="el" href="structOpenMS_1_1FileTypes.html#a1d1cfd8ffb84e947f82999c682b666a7ab5518cc16bd1f60ebbb47e681a56b75f">FileTypes::MZML</a>, <a class="el" href="structOpenMS_1_1FileTypes.html#a1d1cfd8ffb84e947f82999c682b666a7af8a53519bd415aacd429c4239bbfd66e">FileTypes::MZXML</a>, <a class="el" href="classOpenMS_1_1File.html#a43bdcb2e5cb18da64e25b2467c8fdcaa">File::path()</a>, <a class="el" href="classOpenMS_1_1MSExperiment.html#ad20897c5c8bd47f5d4005989bead0e55">MSExperiment< PeakT, ChromatogramPeakT >::reset()</a>, <a class="el" href="classOpenMS_1_1MSExperiment.html#ac2bc824d6ff2633ec34793c9e918d479">MSExperiment< PeakT, ChromatogramPeakT >::resize()</a>, <a class="el" href="classOpenMS_1_1SourceFile.html#affa32793fdd4f1526a6c34c17626a60a">SourceFile::setChecksum()</a>, <a class="el" href="classOpenMS_1_1SourceFile.html#a2d47bfad02d5ce05dcfab38bc1b21400">SourceFile::setFileType()</a>, <a class="el" href="classOpenMS_1_1ProgressLogger.html#acc3538c5284777d8702ccaefeb61e74c">ProgressLogger::setLogType()</a>, <a class="el" href="classOpenMS_1_1SourceFile.html#af0a7eddbacf20c4f4045b671df6b0fe7">SourceFile::setNameOfFile()</a>, <a class="el" href="classOpenMS_1_1SourceFile.html#a2edd9a092842480801a9738a3a514fb3">SourceFile::setPathToFile()</a>, <a class="el" href="classOpenMS_1_1SourceFile.html#a6440df7f4dbfc4c3370e2b6781bc74e5a27028cc8b5d6f0a1cb3030c180019abc">SourceFile::SHA1</a>, <a class="el" href="structOpenMS_1_1FileTypes.html#a854df315fb804a3fba0232334a7f1d0f">FileTypes::typeToMZML()</a>, <a class="el" href="structOpenMS_1_1FileTypes.html#a1d1cfd8ffb84e947f82999c682b666a7a6ce26a62afab55d7606ad4e92428b30c">FileTypes::UNKNOWN</a>, and <a class="el" href="structOpenMS_1_1FileTypes.html#a1d1cfd8ffb84e947f82999c682b666a7a87b48e9729223183349bdfb171076285">FileTypes::XMASS</a>.</p>
<p>Referenced by <a class="el" href="classOpenMS_1_1TOPPViewBase.html#a1c92b33d10330879ab9d4bc2bb888d07">TOPPViewBase::addDataFile()</a>, <a class="el" href="classOpenMS_1_1TOPPViewBase.html#a26fb52355d1e3f483d9e9cf9d1cf6e25">TOPPViewBase::fileChanged_()</a>, <a class="el" href="classOpenMS_1_1InspectOutfile.html#a94fe62a5040d77b84878d091f0eb8686">InspectOutfile::getExperiment()</a>, and <a class="el" href="classOpenMS_1_1TOPPViewBase.html#a78af6f231fd21f56ca7b167c51bdbb00">TOPPViewBase::metadataFileDialog()</a>.</p>
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<td class="memname">bool loadFeatures </td>
<td>(</td>
<td class="paramtype">const <a class="el" href="classOpenMS_1_1String.html">String</a> & </td>
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<td class="paramtype"><a class="el" href="classOpenMS_1_1FeatureMap.html">FeatureMap</a>< FeatureType > & </td>
<td class="paramname"><em>map</em>, </td>
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<td class="paramtype"><a class="el" href="structOpenMS_1_1FileTypes.html#a1d1cfd8ffb84e947f82999c682b666a7">FileTypes::Type</a> </td>
<td class="paramname"><em>force_type</em> = <code><a class="el" href="structOpenMS_1_1FileTypes.html#a1d1cfd8ffb84e947f82999c682b666a7a6ce26a62afab55d7606ad4e92428b30c">FileTypes::UNKNOWN</a></code> </td>
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<p>Loads a file into a <a class="el" href="classOpenMS_1_1FeatureMap.html" title="A container for features. ">FeatureMap</a>. </p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">filename</td><td>the file name of the file to load. </td></tr>
<tr><td class="paramname">map</td><td>The <a class="el" href="classOpenMS_1_1FeatureMap.html" title="A container for features. ">FeatureMap</a> to load the data into. </td></tr>
<tr><td class="paramname">force_type</td><td>Forces to load the file with that file type. If no type is forced, it is determined from the extention (or from the content if that fails).</td></tr>
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<dl class="section return"><dt>Returns</dt><dd>true if the file could be loaded, false otherwise</dd></dl>
<dl class="exception"><dt>Exceptions</dt><dd>
<table class="exception">
<tr><td class="paramname"><a class="el" href="classOpenMS_1_1Exception_1_1FileNotFound.html" title="File not found exception. ">Exception::FileNotFound</a></td><td>is thrown if the file could not be opened </td></tr>
<tr><td class="paramname"><a class="el" href="classOpenMS_1_1Exception_1_1ParseError.html" title="Parse Error exception. ">Exception::ParseError</a></td><td>is thrown if an error occurs during parsing </td></tr>
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<p>References <a class="el" href="structOpenMS_1_1FileTypes.html#a1d1cfd8ffb84e947f82999c682b666a7a753b825a63c99787d10e05f7d65a87a6">FileTypes::FEATUREXML</a>, <a class="el" href="structOpenMS_1_1FileTypes.html#a1d1cfd8ffb84e947f82999c682b666a7a55c4004ffd908d6e6ec96028e90916d0">FileTypes::KROENIK</a>, <a class="el" href="classOpenMS_1_1MsInspectFile.html#aa4e73ca60efa3ca29e203f46b5187c6c">MsInspectFile::load()</a>, <a class="el" href="classOpenMS_1_1SpecArrayFile.html#aa4e73ca60efa3ca29e203f46b5187c6c">SpecArrayFile::load()</a>, <a class="el" href="classOpenMS_1_1FeatureXMLFile.html#a7315500f55fb5cae883f0b1f2024c5b7">FeatureXMLFile::load()</a>, <a class="el" href="classOpenMS_1_1KroenikFile.html#aa4e73ca60efa3ca29e203f46b5187c6c">KroenikFile::load()</a>, <a class="el" href="structOpenMS_1_1FileTypes.html#a1d1cfd8ffb84e947f82999c682b666a7a87ac627b0f0c019e05a735e1a00b861d">FileTypes::PEPLIST</a>, <a class="el" href="structOpenMS_1_1FileTypes.html#a1d1cfd8ffb84e947f82999c682b666a7a9ceeac5c1982a8aeeb7518cb4a488935">FileTypes::TSV</a>, and <a class="el" href="structOpenMS_1_1FileTypes.html#a1d1cfd8ffb84e947f82999c682b666a7a6ce26a62afab55d7606ad4e92428b30c">FileTypes::UNKNOWN</a>.</p>
<p>Referenced by <a class="el" href="classOpenMS_1_1TOPPViewBase.html#a26fb52355d1e3f483d9e9cf9d1cf6e25">TOPPViewBase::fileChanged_()</a>.</p>
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<td class="memname">void storeExperiment </td>
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<td class="paramtype">const <a class="el" href="classOpenMS_1_1MSExperiment.html">MSExperiment</a>< <a class="el" href="namespaceOpenMS.html#a013338b7bdbb5c3b4c78666656070e23">PeakType</a> > & </td>
<td class="paramname"><em>exp</em>, </td>
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<td class="paramtype"><a class="el" href="classOpenMS_1_1ProgressLogger.html#af67907baa897e9fb84df0cb89795b87c">ProgressLogger::LogType</a> </td>
<td class="paramname"><em>log</em> = <code><a class="el" href="classOpenMS_1_1ProgressLogger.html#af67907baa897e9fb84df0cb89795b87cac157bdf0b85a40d2619cbc8bc1ae5fe2">ProgressLogger::NONE</a></code> </td>
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<p>Stores an <a class="el" href="classOpenMS_1_1MSExperiment.html" title="Representation of a mass spectrometry experiment. ">MSExperiment</a> to a file. </p>
<p>The file type to store the data in is determined by the file name. Supported formats for storing are mzML, mzXML, mzData and DTA2D. If the file format cannot be determined from the file name, the mzML format is used.</p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">filename</td><td>The name of the file to store the data in. </td></tr>
<tr><td class="paramname">exp</td><td>The experiment to store. </td></tr>
<tr><td class="paramname">log</td><td>Progress logging mode</td></tr>
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<dl class="exception"><dt>Exceptions</dt><dd>
<table class="exception">
<tr><td class="paramname"><a class="el" href="classOpenMS_1_1Exception_1_1UnableToCreateFile.html" title="Unable to create file exception. ">Exception::UnableToCreateFile</a></td><td>is thrown if the file could not be written </td></tr>
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<p>References <a class="el" href="classOpenMS_1_1ChromatogramTools.html#a180cb4974eaf3d4dea0de5326b132951">ChromatogramTools::convertChromatogramsToSpectra()</a>, <a class="el" href="structOpenMS_1_1FileTypes.html#a1d1cfd8ffb84e947f82999c682b666a7a66c2f5cd90913752f565186657e85d84">FileTypes::DTA2D</a>, <a class="el" href="classOpenMS_1_1MSExperiment.html#a02fccfed86a20f8bd0f6b98c23fadb2e">MSExperiment< PeakT, ChromatogramPeakT >::getChromatograms()</a>, <a class="el" href="classOpenMS_1_1MzXMLFile.html#a819235ed2844f03df53f4983a7008f28">MzXMLFile::getOptions()</a>, <a class="el" href="classOpenMS_1_1MzDataFile.html#a819235ed2844f03df53f4983a7008f28">MzDataFile::getOptions()</a>, <a class="el" href="classOpenMS_1_1MzMLFile.html#a819235ed2844f03df53f4983a7008f28">MzMLFile::getOptions()</a>, <a class="el" href="classOpenMS_1_1DTA2DFile.html#a819235ed2844f03df53f4983a7008f28">DTA2DFile::getOptions()</a>, <a class="el" href="structOpenMS_1_1FileTypes.html#a1d1cfd8ffb84e947f82999c682b666a7ae5b2d8f7eb59b2fc050e6bc3c1cba802">FileTypes::MZDATA</a>, <a class="el" href="structOpenMS_1_1FileTypes.html#a1d1cfd8ffb84e947f82999c682b666a7af8a53519bd415aacd429c4239bbfd66e">FileTypes::MZXML</a>, <a class="el" href="classOpenMS_1_1ProgressLogger.html#acc3538c5284777d8702ccaefeb61e74c">ProgressLogger::setLogType()</a>, <a class="el" href="classOpenMS_1_1MzXMLFile.html#adb795d215478320be7c6130ff7ddf853">MzXMLFile::store()</a>, <a class="el" href="classOpenMS_1_1MzDataFile.html#adb795d215478320be7c6130ff7ddf853">MzDataFile::store()</a>, <a class="el" href="classOpenMS_1_1MzMLFile.html#adb795d215478320be7c6130ff7ddf853">MzMLFile::store()</a>, and <a class="el" href="classOpenMS_1_1DTA2DFile.html#adb795d215478320be7c6130ff7ddf853">DTA2DFile::store()</a>.</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 11:19:30 using doxygen 1.8.5</font></TD>
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