OpenMS  2.6.0
XMLHandler.h
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31 // $Maintainer: Chris Bielow $
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34 
35 #pragma once
36 
37 #include <OpenMS/CONCEPT/Types.h>
38 #include <OpenMS/CONCEPT/Macros.h>
39 
40 #include <OpenMS/DATASTRUCTURES/ListUtils.h> // StringList
44 
45 #include <xercesc/util/XMLString.hpp>
46 #include <xercesc/sax2/DefaultHandler.hpp>
47 #include <xercesc/sax/Locator.hpp>
48 #include <xercesc/sax2/Attributes.hpp>
49 
50 #include <algorithm>
51 #include <iosfwd>
52 #include <string>
53 
54 namespace OpenMS
55 {
56  class ProteinIdentification;
57 
58 
59  namespace Internal
60  {
61 
62  /*
63  * @brief Helper class for XML parsing that handles the conversions of Xerces strings
64  *
65  * It provides the convert() function which internally calls
66  * XMLString::transcode and ensures that the memory is released properly
67  * through XMLString::release internally. It returns a std::string or
68  * std::basic_string<XMLCh> to the caller who takes ownership of the data.
69  *
70  */
71  class OPENMS_DLLAPI StringManager
72  {
73 
74  typedef std::basic_string<XMLCh> XercesString;
75 
76  // Converts from a narrow-character string to a wide-character string.
77  inline XercesString fromNative_(const char* str) const
78  {
79  XMLCh* ptr(xercesc::XMLString::transcode(str));
80  XercesString result(ptr);
81  xercesc::XMLString::release(&ptr);
82  return result;
83  }
84 
85  // Converts from a narrow-character string to a wide-character string.
86  inline XercesString fromNative_(const String& str) const
87  {
88  return fromNative_(str.c_str());
89  }
90 
91  // Converts from a wide-character string to a narrow-character string.
92  inline String toNative_(const XMLCh* str) const
93  {
94  char* ptr(xercesc::XMLString::transcode(str));
95  String result(ptr);
96  xercesc::XMLString::release(&ptr);
97  return result;
98  }
99 
100  // Converts from a wide-character string to a narrow-character string.
101  inline String toNative_(const XercesString& str) const
102  {
103  return toNative_(str.c_str());
104  }
105 
106 
107 public:
109  StringManager();
110 
112  ~StringManager();
113 
115  inline XercesString convert(const char * str) const
116  {
117  return fromNative_(str);
118  }
119 
121  inline XercesString convert(const std::string & str) const
122  {
123  return fromNative_(str.c_str());
124  }
125 
127  inline XercesString convert(const String & str) const
128  {
129  return fromNative_(str.c_str());
130  }
131 
133  inline String convert(const XMLCh * str) const
134  {
135  return toNative_(str);
136  }
137 
144  static void appendASCII(const XMLCh * str, const XMLSize_t length, String & result);
145 
146  };
147 
151  class OPENMS_DLLAPI XMLHandler :
152  public xercesc::DefaultHandler
153  {
154 public:
155 
157  class OPENMS_DLLAPI EndParsingSoftly :
159  {
160  public:
161  EndParsingSoftly(const char * file, int line, const char * function) :
162  Exception::BaseException(file, line, function)
163  {
164  }
165 
166  };
167 
170  {
172  STORE
173  };
174 
176  {
177  LD_ALLDATA, // default; load all data
178  LD_RAWCOUNTS, // only count the total number of spectra and chromatograms (usually very fast)
179  LD_COUNTS_WITHOPTIONS // count the number of spectra, while respecting PeakFileOptions (msLevel and RTRange) and chromatograms (fast)
180  };
181 
182 
184  XMLHandler(const String & filename, const String & version);
186  ~XMLHandler() override;
187 
189  void reset();
190 
191 
198  void fatalError(const xercesc::SAXParseException & exception) override;
199  void error(const xercesc::SAXParseException & exception) override;
200  void warning(const xercesc::SAXParseException & exception) override;
202 
204  void fatalError(ActionMode mode, const String & msg, UInt line = 0, UInt column = 0) const;
206  void error(ActionMode mode, const String & msg, UInt line = 0, UInt column = 0) const;
208  void warning(ActionMode mode, const String & msg, UInt line = 0, UInt column = 0) const;
209 
211  void characters(const XMLCh * const chars, const XMLSize_t length) override;
213  void startElement(const XMLCh * const uri, const XMLCh * const localname, const XMLCh * const qname, const xercesc::Attributes & attrs) override;
215  void endElement(const XMLCh * const uri, const XMLCh * const localname, const XMLCh * const qname) override;
216 
218  virtual void writeTo(std::ostream & /*os*/);
219 
221  String errorString();
222 
224  virtual LOADDETAIL getLoadDetail() const;
225 
227  virtual void setLoadDetail(const LOADDETAIL d);
228 
236  static String writeXMLEscape(const String& to_escape)
237  {
238  String _copy = to_escape;
239  // has() is cheap, so check before calling substitute(), since substitute() will usually happen rarely
240  if (_copy.has('&')) _copy.substitute("&","&amp;");
241  if (_copy.has('>')) _copy.substitute(">","&gt;");
242  if (_copy.has('"')) _copy.substitute("\"","&quot;");
243  if (_copy.has('<')) _copy.substitute("<","&lt;");
244  if (_copy.has('\'')) _copy.substitute("'","&apos;");
245 
246  return _copy;
247  }
248 
251  void checkUniqueIdentifiers_(const std::vector<ProteinIdentification>& prot_ids);
252 
253 protected:
256 
259 
262 
265 
271  std::vector<String> open_tags_;
272 
275 
276 
278  inline bool equal_(const XMLCh * a, const XMLCh * b) const
279  {
280  return xercesc::XMLString::compareString(a, b) == 0;
281  }
282 
284 
285 
287  void writeUserParam_(const String & tag_name, std::ostream & os, const MetaInfoInterface & meta, UInt indent) const;
288 
290 
292 
293 
295  std::vector<std::vector<String> > cv_terms_;
296 
299  inline SignedSize cvStringToEnum_(const Size section, const String & term, const char * message, const SignedSize result_on_error = 0)
300  {
301  OPENMS_PRECONDITION(section < cv_terms_.size(), "cvStringToEnum_: Index overflow (section number too large)");
302 
303  std::vector<String>::const_iterator it = std::find(cv_terms_[section].begin(), cv_terms_[section].end(), term);
304  if (it != cv_terms_[section].end())
305  {
306  return it - cv_terms_[section].begin();
307  }
308  else
309  {
310  warning(LOAD, String("Unexpected CV entry '") + message + "'='" + term + "'");
311  return result_on_error;
312  }
313  }
314 
316 
318 
319 
321  inline Int asInt_(const String & in)
322  {
323  Int res = 0;
324  try
325  {
326  res = in.toInt();
327  }
329  {
330  error(LOAD, String("Int conversion error of \"") + in + "\"");
331  }
332  return res;
333  }
334 
336  inline Int asInt_(const XMLCh * in)
337  {
338  return xercesc::XMLString::parseInt(in);
339  }
340 
342  inline UInt asUInt_(const String & in)
343  {
344  UInt res = 0;
345  try
346  {
347  Int tmp = in.toInt();
348  if (tmp < 0)
349  {
350  throw Exception::ConversionError(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, "");
351  }
352  res = UInt(tmp);
353  }
355  {
356  error(LOAD, String("UInt conversion error of \"") + in + "\"");
357  }
358  return res;
359  }
360 
362  inline double asDouble_(const String & in)
363  {
364  double res = 0.0;
365  try
366  {
367  res = in.toDouble();
368  }
370  {
371  error(LOAD, String("Double conversion error of \"") + in + "\"");
372  }
373  return res;
374  }
375 
377  inline float asFloat_(const String & in)
378  {
379  float res = 0.0;
380  try
381  {
382  res = in.toFloat();
383  }
385  {
386  error(LOAD, String("Float conversion error of \"") + in + "\"");
387  }
388  return res;
389  }
390 
398  inline bool asBool_(const String & in)
399  {
400  if (in == "true" || in == "TRUE" || in == "True" || in == "1")
401  {
402  return true;
403  }
404  else if (in == "false" || in == "FALSE" || in == "False" || in == "0")
405  {
406  return false;
407  }
408  else
409  {
410  error(LOAD, String("Boolean conversion error of \"") + in + "\"");
411  }
412  return false;
413  }
414 
416  inline DateTime asDateTime_(String date_string)
417  {
418  DateTime date_time;
419  if (date_string != "")
420  {
421  try
422  {
423  //strip away milliseconds
424  date_string.trim();
425  date_string = date_string.substr(0, 19);
426  date_time.set(date_string);
427  }
428  catch (Exception::ParseError& /*err*/ )
429  {
430  error(LOAD, String("DateTime conversion error of \"") + date_string + "\"");
431  }
432  }
433  return date_time;
434  }
435 
437 
439 
440 
442  inline String attributeAsString_(const xercesc::Attributes & a, const char * name) const
443  {
444  const XMLCh * val = a.getValue(sm_.convert(name).c_str());
445  if (val == nullptr) fatalError(LOAD, String("Required attribute '") + name + "' not present!");
446  return sm_.convert(val);
447  }
448 
450  inline Int attributeAsInt_(const xercesc::Attributes & a, const char * name) const
451  {
452  const XMLCh * val = a.getValue(sm_.convert(name).c_str());
453  if (val == nullptr) fatalError(LOAD, String("Required attribute '") + name + "' not present!");
454  return xercesc::XMLString::parseInt(val);
455  }
456 
458  inline double attributeAsDouble_(const xercesc::Attributes & a, const char * name) const
459  {
460  const XMLCh * val = a.getValue(sm_.convert(name).c_str());
461  if (val == nullptr) fatalError(LOAD, String("Required attribute '") + name + "' not present!");
462  return String(sm_.convert(val)).toDouble();
463  }
464 
466  inline DoubleList attributeAsDoubleList_(const xercesc::Attributes & a, const char * name) const
467  {
468  String tmp(expectList_(attributeAsString_(a, name)));
469  return ListUtils::create<double>(tmp.substr(1, tmp.size() - 2));
470  }
471 
473  inline IntList attributeAsIntList_(const xercesc::Attributes & a, const char * name) const
474  {
475  String tmp(expectList_(attributeAsString_(a, name)));
476  return ListUtils::create<Int>(tmp.substr(1, tmp.size() - 2));
477  }
478 
480  inline StringList attributeAsStringList_(const xercesc::Attributes & a, const char * name) const
481  {
482  String tmp(expectList_(attributeAsString_(a, name)));
483  return ListUtils::create<String>(tmp.substr(1, tmp.size() - 2));
484  }
485 
491  inline bool optionalAttributeAsString_(String & value, const xercesc::Attributes & a, const char * name) const
492  {
493  const XMLCh * val = a.getValue(sm_.convert(name).c_str());
494  if (val != nullptr)
495  {
496  value = sm_.convert(val);
497  return true;
498  }
499  return false;
500  }
501 
507  inline bool optionalAttributeAsInt_(Int & value, const xercesc::Attributes & a, const char * name) const
508  {
509  const XMLCh * val = a.getValue(sm_.convert(name).c_str());
510  if (val != nullptr)
511  {
512  value = xercesc::XMLString::parseInt(val);
513  return true;
514  }
515  return false;
516  }
517 
523  inline bool optionalAttributeAsUInt_(UInt & value, const xercesc::Attributes & a, const char * name) const
524  {
525  const XMLCh * val = a.getValue(sm_.convert(name).c_str());
526  if (val != nullptr)
527  {
528  value = xercesc::XMLString::parseInt(val);
529  return true;
530  }
531  return false;
532  }
533 
539  inline bool optionalAttributeAsDouble_(double & value, const xercesc::Attributes & a, const char * name) const
540  {
541  const XMLCh * val = a.getValue(sm_.convert(name).c_str());
542  if (val != nullptr)
543  {
544  value = String(sm_.convert(val)).toDouble();
545  return true;
546  }
547  return false;
548  }
549 
555  inline bool optionalAttributeAsDoubleList_(DoubleList & value, const xercesc::Attributes & a, const char * name) const
556  {
557  const XMLCh * val = a.getValue(sm_.convert(name).c_str());
558  if (val != nullptr)
559  {
560  value = attributeAsDoubleList_(a, name);
561  return true;
562  }
563  return false;
564  }
565 
571  inline bool optionalAttributeAsStringList_(StringList & value, const xercesc::Attributes & a, const char * name) const
572  {
573  const XMLCh * val = a.getValue(sm_.convert(name).c_str());
574  if (val != nullptr)
575  {
576  value = attributeAsStringList_(a, name);
577  return true;
578  }
579  return false;
580  }
581 
587  inline bool optionalAttributeAsIntList_(IntList & value, const xercesc::Attributes & a, const char * name) const
588  {
589  const XMLCh * val = a.getValue(sm_.convert(name).c_str());
590  if (val != nullptr)
591  {
592  value = attributeAsIntList_(a, name);
593  return true;
594  }
595  return false;
596  }
597 
599  inline String attributeAsString_(const xercesc::Attributes & a, const XMLCh * name) const
600  {
601  const XMLCh * val = a.getValue(name);
602  if (val == nullptr) fatalError(LOAD, String("Required attribute '") + sm_.convert(name) + "' not present!");
603  return sm_.convert(val);
604  }
605 
607  inline Int attributeAsInt_(const xercesc::Attributes & a, const XMLCh * name) const
608  {
609  const XMLCh * val = a.getValue(name);
610  if (val == nullptr) fatalError(LOAD, String("Required attribute '") + sm_.convert(name) + "' not present!");
611  return xercesc::XMLString::parseInt(val);
612  }
613 
615  inline double attributeAsDouble_(const xercesc::Attributes & a, const XMLCh * name) const
616  {
617  const XMLCh * val = a.getValue(name);
618  if (val == nullptr) fatalError(LOAD, String("Required attribute '") + sm_.convert(name) + "' not present!");
619  return sm_.convert(val).toDouble();
620  }
621 
623  inline DoubleList attributeAsDoubleList_(const xercesc::Attributes & a, const XMLCh * name) const
624  {
625  String tmp(expectList_(attributeAsString_(a, name)));
626  return ListUtils::create<double>(tmp.substr(1, tmp.size() - 2));
627  }
628 
630  inline IntList attributeAsIntList_(const xercesc::Attributes & a, const XMLCh * name) const
631  {
632  String tmp(expectList_(attributeAsString_(a, name)));
633  return ListUtils::create<Int>(tmp.substr(1, tmp.size() - 2));
634  }
635 
637  inline StringList attributeAsStringList_(const xercesc::Attributes & a, const XMLCh * name) const
638  {
639  String tmp(expectList_(attributeAsString_(a, name)));
640  return ListUtils::create<String>(tmp.substr(1, tmp.size() - 2));
641  }
642 
644  inline bool optionalAttributeAsString_(String& value, const xercesc::Attributes & a, const XMLCh * name) const
645  {
646  const XMLCh * val = a.getValue(name);
647  if (val != nullptr)
648  {
649  value = sm_.convert(val);
650  return !value.empty();
651  }
652  return false;
653  }
654 
656  inline bool optionalAttributeAsInt_(Int & value, const xercesc::Attributes & a, const XMLCh * name) const
657  {
658  const XMLCh * val = a.getValue(name);
659  if (val != nullptr)
660  {
661  value = xercesc::XMLString::parseInt(val);
662  return true;
663  }
664  return false;
665  }
666 
668  inline bool optionalAttributeAsUInt_(UInt & value, const xercesc::Attributes & a, const XMLCh * name) const
669  {
670  const XMLCh * val = a.getValue(name);
671  if (val != nullptr)
672  {
673  value = xercesc::XMLString::parseInt(val);
674  return true;
675  }
676  return false;
677  }
678 
680  inline bool optionalAttributeAsDouble_(double & value, const xercesc::Attributes & a, const XMLCh * name) const
681  {
682  const XMLCh * val = a.getValue(name);
683  if (val != nullptr)
684  {
685  value = sm_.convert(val).toDouble();
686  return true;
687  }
688  return false;
689  }
690 
696  inline bool optionalAttributeAsDoubleList_(DoubleList & value, const xercesc::Attributes & a, const XMLCh * name) const
697  {
698  const XMLCh * val = a.getValue(name);
699  if (val != nullptr)
700  {
701  value = attributeAsDoubleList_(a, name);
702  return true;
703  }
704  return false;
705  }
706 
712  inline bool optionalAttributeAsIntList_(IntList & value, const xercesc::Attributes & a, const XMLCh * name) const
713  {
714  const XMLCh * val = a.getValue(name);
715  if (val != nullptr)
716  {
717  value = attributeAsIntList_(a, name);
718  return true;
719  }
720  return false;
721  }
722 
728  inline bool optionalAttributeAsStringList_(StringList & value, const xercesc::Attributes & a, const XMLCh * name) const
729  {
730  const XMLCh * val = a.getValue(name);
731  if (val != nullptr)
732  {
733  value = attributeAsStringList_(a, name);
734  return true;
735  }
736  return false;
737  }
738 
740 
741 private:
743  XMLHandler();
744 
745  inline const String& expectList_(const String& str) const
746  {
747  if (!(str.hasPrefix('[') && str.hasSuffix(']')))
748  {
749  fatalError(LOAD, String("List argument is not a string representation of a list!"));
750  }
751  return str;
752  }
753 
754  };
755 
756  } // namespace Internal
757 } // namespace OpenMS
758 
759 
OpenMS::Internal::XMLHandler::attributeAsStringList_
StringList attributeAsStringList_(const xercesc::Attributes &a, const char *name) const
Converts an attribute to an StringList.
Definition: XMLHandler.h:480
OpenMS::Internal::XMLHandler::LD_ALLDATA
Definition: XMLHandler.h:177
OpenMS::Internal::XMLHandler::version_
String version_
Schema version.
Definition: XMLHandler.h:261
OpenMS::Internal::XMLHandler::attributeAsInt_
Int attributeAsInt_(const xercesc::Attributes &a, const char *name) const
Converts an attribute to a Int.
Definition: XMLHandler.h:450
OpenMS::Internal::XMLHandler::attributeAsString_
String attributeAsString_(const xercesc::Attributes &a, const XMLCh *name) const
Converts an attribute to a String.
Definition: XMLHandler.h:599
OpenMS::Internal::XMLHandler::LOAD
Loading a file.
Definition: XMLHandler.h:171
OpenMS::Internal::XMLHandler::attributeAsStringList_
StringList attributeAsStringList_(const xercesc::Attributes &a, const XMLCh *name) const
Converts an attribute to a StringList.
Definition: XMLHandler.h:637
OpenMS::Internal::StringManager::convert
XercesString convert(const char *str) const
Transcode the supplied C string to a xerces string.
Definition: XMLHandler.h:115
OpenMS::Internal::XMLHandler::asFloat_
float asFloat_(const String &in)
Conversion of a String to a float value.
Definition: XMLHandler.h:377
OpenMS::Internal::StringManager::convert
String convert(const XMLCh *str) const
Transcode the supplied XMLCh* to a String.
Definition: XMLHandler.h:133
Types.h
OpenMS::Internal::XMLHandler
Base class for XML handlers.
Definition: XMLHandler.h:151
OpenMS::Internal::XMLHandler::optionalAttributeAsIntList_
bool optionalAttributeAsIntList_(IntList &value, const xercesc::Attributes &a, const char *name) const
Assigns the attribute content to the IntList value if the attribute is present.
Definition: XMLHandler.h:587
OpenMS::String::substitute
String & substitute(char from, char to)
Replaces all occurrences of the character from by the character to.
OpenMS::Internal::XMLHandler::optionalAttributeAsDouble_
bool optionalAttributeAsDouble_(double &value, const xercesc::Attributes &a, const char *name) const
Assigns the attribute content to the double value if the attribute is present.
Definition: XMLHandler.h:539
OpenMS::String::toDouble
double toDouble() const
Conversion to double.
OpenMS::Internal::XMLHandler::attributeAsDouble_
double attributeAsDouble_(const xercesc::Attributes &a, const XMLCh *name) const
Converts an attribute to a double.
Definition: XMLHandler.h:615
OpenMS::Internal::XMLHandler::optionalAttributeAsUInt_
bool optionalAttributeAsUInt_(UInt &value, const xercesc::Attributes &a, const char *name) const
Assigns the attribute content to the UInt value if the attribute is present.
Definition: XMLHandler.h:523
DateTime.h
OpenMS::Internal::XMLHandler::cvStringToEnum_
SignedSize cvStringToEnum_(const Size section, const String &term, const char *message, const SignedSize result_on_error=0)
Definition: XMLHandler.h:299
OpenMS::String
A more convenient string class.
Definition: String.h:59
OpenMS::Internal::StringManager::toNative_
String toNative_(const XercesString &str) const
Definition: XMLHandler.h:101
OpenMS::String::trim
String & trim()
removes whitespaces (space, tab, line feed, carriage return) at the beginning and the end of the stri...
OpenMS::Internal::XMLHandler::attributeAsDoubleList_
DoubleList attributeAsDoubleList_(const xercesc::Attributes &a, const XMLCh *name) const
Converts an attribute to a DoubleList.
Definition: XMLHandler.h:623
OpenMS::DoubleList
std::vector< double > DoubleList
Vector of double precision real types.
Definition: ListUtils.h:62
OpenMS::Exception::ConversionError
Invalid conversion exception.
Definition: Exception.h:362
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
OpenMS::Internal::XMLHandler::asDateTime_
DateTime asDateTime_(String date_string)
Conversion of a xs:datetime string to a DateTime value.
Definition: XMLHandler.h:416
OpenMS::Internal::XMLHandler::optionalAttributeAsIntList_
bool optionalAttributeAsIntList_(IntList &value, const xercesc::Attributes &a, const XMLCh *name) const
Assigns the attribute content to the IntList value if the attribute is present.
Definition: XMLHandler.h:712
OpenMS::Internal::XMLHandler::LD_RAWCOUNTS
Definition: XMLHandler.h:178
OpenMS::Internal::StringManager::XercesString
std::basic_string< XMLCh > XercesString
Definition: XMLHandler.h:74
OpenMS::Internal::ClassTest::exception
int exception
(Used by various macros. Indicates a rough category of the exception being caught....
OpenMS::Internal::XMLHandler::writeXMLEscape
static String writeXMLEscape(const String &to_escape)
Escapes a string and returns the escaped string.
Definition: XMLHandler.h:236
OpenMS::IntList
std::vector< Int > IntList
Vector of signed integers.
Definition: ListUtils.h:55
OPENMS_PRECONDITION
#define OPENMS_PRECONDITION(condition, message)
Precondition macro.
Definition: openms/include/OpenMS/CONCEPT/Macros.h:136
OpenMS::Internal::XMLHandler::LOADDETAIL
LOADDETAIL
Definition: XMLHandler.h:175
OpenMS::String::hasPrefix
bool hasPrefix(const String &string) const
true if String begins with string, false otherwise
ListUtils.h
OpenMS::Internal::StringManager
Definition: XMLHandler.h:71
OpenMS::Internal::XMLHandler::optionalAttributeAsStringList_
bool optionalAttributeAsStringList_(StringList &value, const xercesc::Attributes &a, const XMLCh *name) const
Assigns the attribute content to the StringList value if the attribute is present.
Definition: XMLHandler.h:728
Macros.h
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::Internal::XMLHandler::expectList_
const String & expectList_(const String &str) const
Definition: XMLHandler.h:745
OpenMS::Internal::XMLHandler::error_message_
String error_message_
Error message of the last error.
Definition: XMLHandler.h:255
OpenMS::Internal::XMLHandler::optionalAttributeAsDouble_
bool optionalAttributeAsDouble_(double &value, const xercesc::Attributes &a, const XMLCh *name) const
Assigns the attribute content to the double value if the attribute is present.
Definition: XMLHandler.h:680
OpenMS::Internal::XMLHandler::cv_terms_
std::vector< std::vector< String > > cv_terms_
Array of CV term lists (one sublist denotes one term and it's children)
Definition: XMLHandler.h:295
OpenMS::Internal::XMLHandler::equal_
bool equal_(const XMLCh *a, const XMLCh *b) const
Returns if two Xerces strings are equal.
Definition: XMLHandler.h:278
OpenMS::Internal::XMLHandler::optionalAttributeAsInt_
bool optionalAttributeAsInt_(Int &value, const xercesc::Attributes &a, const XMLCh *name) const
Assigns the attribute content to the Int value if the attribute is present.
Definition: XMLHandler.h:656
OpenMS::Internal::StringManager::toNative_
String toNative_(const XMLCh *str) const
Definition: XMLHandler.h:92
OpenMS::MetaInfoInterface
Interface for classes that can store arbitrary meta information (Type-Name-Value tuples).
Definition: MetaInfoInterface.h:60
int
OpenMS::Internal::StringManager::fromNative_
XercesString fromNative_(const char *str) const
Definition: XMLHandler.h:77
OpenMS::Internal::XMLHandler::asUInt_
UInt asUInt_(const String &in)
Conversion of a String to an unsigned integer value.
Definition: XMLHandler.h:342
OpenMS::String::has
bool has(Byte byte) const
true if String contains the byte, false otherwise
OpenMS::Internal::XMLHandler::optionalAttributeAsDoubleList_
bool optionalAttributeAsDoubleList_(DoubleList &value, const xercesc::Attributes &a, const char *name) const
Assigns the attribute content to the DoubleList value if the attribute is present.
Definition: XMLHandler.h:555
OpenMS::Internal::XMLHandler::open_tags_
std::vector< String > open_tags_
Stack of open XML tags.
Definition: XMLHandler.h:271
OpenMS::Internal::XMLHandler::attributeAsIntList_
IntList attributeAsIntList_(const xercesc::Attributes &a, const XMLCh *name) const
Converts an attribute to a IntList.
Definition: XMLHandler.h:630
OpenMS::Internal::StringManager::fromNative_
XercesString fromNative_(const String &str) const
Definition: XMLHandler.h:86
OpenMS::Exception::BaseException
Exception base class.
Definition: Exception.h:89
OpenMS::String::hasSuffix
bool hasSuffix(const String &string) const
true if String ends with string, false otherwise
OpenMS::Internal::XMLHandler::asInt_
Int asInt_(const String &in)
Conversion of a String to an integer value.
Definition: XMLHandler.h:321
OpenMS::Internal::XMLHandler::optionalAttributeAsUInt_
bool optionalAttributeAsUInt_(UInt &value, const xercesc::Attributes &a, const XMLCh *name) const
Assigns the attribute content to the UInt value if the attribute is present.
Definition: XMLHandler.h:668
OpenMS::DateTime::set
void set(UInt month, UInt day, UInt year, UInt hour, UInt minute, UInt second)
sets data from six integers
seqan::find
bool find(TFinder &finder, const Pattern< TNeedle, FuzzyAC > &me, PatternAuxData< TNeedle > &dh)
Definition: AhoCorasickAmbiguous.h:884
OpenMS::Internal::XMLHandler::attributeAsDouble_
double attributeAsDouble_(const xercesc::Attributes &a, const char *name) const
Converts an attribute to a double.
Definition: XMLHandler.h:458
OpenMS::StringList
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:70
OpenMS::UInt
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
OpenMS::Internal::XMLHandler::attributeAsString_
String attributeAsString_(const xercesc::Attributes &a, const char *name) const
Converts an attribute to a String.
Definition: XMLHandler.h:442
OpenMS::Internal::XMLHandler::optionalAttributeAsStringList_
bool optionalAttributeAsStringList_(StringList &value, const xercesc::Attributes &a, const char *name) const
Assigns the attribute content to the StringList value if the attribute is present.
Definition: XMLHandler.h:571
OpenMS::Internal::XMLHandler::asDouble_
double asDouble_(const String &in)
Conversion of a String to a double value.
Definition: XMLHandler.h:362
OpenMS::SignedSize
ptrdiff_t SignedSize
Signed Size type e.g. used as pointer difference.
Definition: Types.h:134
OpenMS::Exception::ParseError
Parse Error exception.
Definition: Exception.h:622
OpenMS::String::substr
String substr(size_t pos=0, size_t n=npos) const
Wrapper for the STL substr() method. Returns a String object with its contents initialized to a subst...
OpenMS::Internal::XMLHandler::ActionMode
ActionMode
Action to set the current mode (for error messages)
Definition: XMLHandler.h:169
OpenMS::Internal::XMLHandler::asInt_
Int asInt_(const XMLCh *in)
Conversion of a Xerces string to an integer value.
Definition: XMLHandler.h:336
OpenMS::Internal::XMLHandler::attributeAsInt_
Int attributeAsInt_(const xercesc::Attributes &a, const XMLCh *name) const
Converts an attribute to a Int.
Definition: XMLHandler.h:607
OpenMS::Internal::StringManager::convert
XercesString convert(const String &str) const
Transcode the supplied OpenMS string to a xerces string.
Definition: XMLHandler.h:127
OpenMS::Internal::StringManager::convert
XercesString convert(const std::string &str) const
Transcode the supplied C++ string to a xerces string.
Definition: XMLHandler.h:121
OpenMS::Internal::XMLHandler::attributeAsDoubleList_
DoubleList attributeAsDoubleList_(const xercesc::Attributes &a, const char *name) const
Converts an attribute to a DoubleList.
Definition: XMLHandler.h:466
MetaInfoInterface.h
OpenMS::Internal::XMLHandler::optionalAttributeAsString_
bool optionalAttributeAsString_(String &value, const xercesc::Attributes &a, const char *name) const
Assigns the attribute content to the String value if the attribute is present.
Definition: XMLHandler.h:491
OpenMS::Internal::XMLHandler::attributeAsIntList_
IntList attributeAsIntList_(const xercesc::Attributes &a, const char *name) const
Converts an attribute to an IntList.
Definition: XMLHandler.h:473
OpenMS::Internal::XMLHandler::sm_
StringManager sm_
Helper class for string conversion.
Definition: XMLHandler.h:264
OpenMS::Internal::XMLHandler::asBool_
bool asBool_(const String &in)
Conversion of a string to a boolean value.
Definition: XMLHandler.h:398
OpenMS::Internal::XMLHandler::EndParsingSoftly
Exception that is thrown if the parsing is ended by some event (e.g. if only a prefix of the XML file...
Definition: XMLHandler.h:157
OpenMS::Internal::XMLHandler::file_
String file_
File name.
Definition: XMLHandler.h:258
OpenMS::Internal::XMLHandler::optionalAttributeAsString_
bool optionalAttributeAsString_(String &value, const xercesc::Attributes &a, const XMLCh *name) const
Assigns the attribute content to the String value if the attribute is present.
Definition: XMLHandler.h:644
OpenMS::Internal::XMLHandler::optionalAttributeAsDoubleList_
bool optionalAttributeAsDoubleList_(DoubleList &value, const xercesc::Attributes &a, const XMLCh *name) const
Assigns the attribute content to the DoubleList value if the attribute is present.
Definition: XMLHandler.h:696
OpenMS::Internal::XMLHandler::EndParsingSoftly::EndParsingSoftly
EndParsingSoftly(const char *file, int line, const char *function)
Definition: XMLHandler.h:161
OpenMS::String::toInt
Int toInt() const
Conversion to int.
OpenMS::DateTime
DateTime Class.
Definition: DateTime.h:54
OpenMS::String::toFloat
float toFloat() const
Conversion to float.
OpenMS::Internal::XMLHandler::optionalAttributeAsInt_
bool optionalAttributeAsInt_(Int &value, const xercesc::Attributes &a, const char *name) const
Assigns the attribute content to the Int value if the attribute is present.
Definition: XMLHandler.h:507
OpenMS::Internal::XMLHandler::load_detail_
LOADDETAIL load_detail_
parse only until total number of scans and chroms have been determined from attributes
Definition: XMLHandler.h:274