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MzMLFile.h
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31 // $Maintainer: Andreas Bertsch $
32 // $Authors: Marc Sturm $
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34 
35 #ifndef OPENMS_FORMAT_MZMLFILE_H
36 #define OPENMS_FORMAT_MZMLFILE_H
37 
38 #include <OpenMS/FORMAT/XMLFile.h>
44 
45 namespace OpenMS
46 {
58  class OPENMS_DLLAPI MzMLFile :
59  public Internal::XMLFile,
60  public ProgressLogger
61  {
62 public:
64  MzMLFile();
66  ~MzMLFile();
67 
69  PeakFileOptions& getOptions();
70 
72  const PeakFileOptions& getOptions() const;
73 
75  void setOptions(const PeakFileOptions &);
76 
85  template <typename MapType>
86  void load(const String& filename, MapType& map)
87  {
88  map.reset();
89 
90  //set DocumentIdentifier
91  map.setLoadedFileType(filename);
92  map.setLoadedFilePath(filename);
93 
94  Internal::MzMLHandler<MapType> handler(map, filename, getVersion(), *this);
95  handler.setOptions(options_);
96  //handler can throw parse error and other errors - catch those here - they are the cause for a parse error - report accordingly
97  try
98  {
99  parse_(filename, &handler);
100  }
101  catch (Exception::BaseException& e)
102  {
103  std::string expr;
104  expr.append(e.getFile());
105  expr.append("@");
106  std::stringstream ss;
107  ss << e.getLine(); // we need c++11!! maybe in 2012?
108  expr.append(ss.str());
109  expr.append("-");
110  expr.append(e.getFunction());
111  std::string mess = "- due to that error of type ";
112  mess.append(e.getName());
113  throw Exception::ParseError(__FILE__, __LINE__, __PRETTY_FUNCTION__, expr, mess);
114  }
115 
116  }
117 
125  template <typename MapType>
126  void store(const String& filename, const MapType& map) const
127  {
128  Internal::MzMLHandler<MapType> handler(map, filename, getVersion(), *this);
129  handler.setOptions(options_);
130  save_(filename, &handler);
131  }
132 
138  bool isValid(const String& filename, std::ostream& os = std::cerr);
139 
149  bool isSemanticallyValid(const String& filename, StringList& errors, StringList& warnings);
150 
151 private:
152 
155 
158  };
159 
160 } // namespace OpenMS
161 
162 #endif // OPENMS_FOMAT_MZMLFILE_H
A more convenient string class.
Definition: String.h:56
int getLine() const
Returns the line number where it occured.
PeakFileOptions options_
Options for loading / storing.
Definition: MzMLFile.h:154
const char * getFile() const
Returns the file where it occured.
File adapter for MzML files.
Definition: MzMLFile.h:58
XML handler for MzMLFile.
Definition: MzMLHandler.h:94
const char * getName() const
Returns the name of the exception.
void load(const String &filename, MapType &map)
Loads a map from a MzML file.
Definition: MzMLFile.h:86
void store(const String &filename, const MapType &map) const
Stores a map in a MzML file.
Definition: MzMLFile.h:126
Exception base class.
Definition: Exception.h:90
const char * getFunction() const
Returns the function where it occured.
String list.
Definition: StringList.h:56
Base class for all classes that want to report their progess.
Definition: ProgressLogger.h:56
void setOptions(const PeakFileOptions &opt)
Definition: MzMLHandler.h:184
Base class for loading/storing XML files that have a handler derived from XMLHandler.
Definition: XMLFile.h:51
Options for loading files containing peak data.
Definition: PeakFileOptions.h:47
String indexed_schema_location_
Location of indexed mzML schema.
Definition: MzMLFile.h:157
Parse Error exception.
Definition: Exception.h:608

OpenMS / TOPP release 1.11.1 Documentation generated on Thu Nov 14 2013 11:19:18 using doxygen 1.8.5