| OpenMS 2.5.0

Public Member Functions | Protected Types | Protected Member Functions | Protected Attributes | Private Member Functions | List of all members
MzDataHandler Class Reference

`#include <OpenMS/FORMAT/HANDLERS/MzDataHandler.h>`

Inheritance diagram for MzDataHandler:

## Public Member Functions

void | endElement (const XMLCh *const, const XMLCh *const, const XMLCh *const qname) override
void | startElement (const XMLCh *const, const XMLCh *const, const XMLCh *const qname, const xercesc::Attributes &attributes) override
void | characters (const XMLCh *const chars, const XMLSize_t length) override
void | writeTo (std::ostream &os) override
| Writes the contents to a stream. More...
void | setOptions (const PeakFileOptions &options)
| Sets the options. More...
Constructors and destructor
| MzDataHandler (MapType &exp, const String &filename, const String &version, ProgressLogger &logger)
| Constructor for a write-only handler. More...
| MzDataHandler (const MapType &exp, const String &filename, const String &version, const ProgressLogger &logger)
| Constructor for a read-only handler. More...
| ~MzDataHandler () override
| Destructor. More...
Public Member Functions inherited from XMLHandler
| XMLHandler (const String &filename, const String &version)
| Default constructor. More...
| ~XMLHandler () override
| Destructor. More...
void | reset ()
| Release internal memory used for parsing (call. More...
void | fatalError (ActionMode mode, const String &msg, UInt line=0, UInt column=0) const
| Fatal error handler. Throws a ParseError exception. More...
void | error (ActionMode mode, const String &msg, UInt line=0, UInt column=0) const
| Error handler for recoverable errors. More...
void | warning (ActionMode mode, const String &msg, UInt line=0, UInt column=0) const
| Warning handler. More...
void | characters (const XMLCh *const chars, const XMLSize_t length) override
| Parsing method for character data. More...
void | startElement (const XMLCh *const uri, const XMLCh *const localname, const XMLCh *const qname, const xercesc::Attributes &attrs) override
| Parsing method for opening tags. More...
void | endElement (const XMLCh *const uri, const XMLCh *const localname, const XMLCh *const qname) override
| Parsing method for closing tags. More...
String | errorString ()
| Returns the last error description. More...
virtual LOADDETAIL | getLoadDetail () const
| handler which support partial loading, implement this method More...
virtual void | setLoadDetail (const LOADDETAIL d)
| handler which support partial loading, implement this method More...
void | checkUniqueIdentifiers_ (const std::vector< ProteinIdentification > &prot_ids)
void | fatalError (const xercesc::SAXParseException &exception) override
void | error (const xercesc::SAXParseException &exception) override
void | warning (const xercesc::SAXParseException &exception) override

## Protected Types

typedef MapType::PeakType | PeakType
| Peak type. More...
typedef MSSpectrum | SpectrumType
| Spectrum type. More...

## Protected Member Functions

void | fillData_ ()
| fills the current spectrum with peaks and meta data More...
void | writeBinary_ (std::ostream &os, Size size, const String &tag, const String &name="", SignedSize id=-1)
| write binary data to stream (first one) More...
cvParam and userParam handling methods (for mzData and featureXML)
void | writeCVS_ (std::ostream &os, double value, const String &acc, const String &name, UInt indent=4) const
| write cvParam containing strings to stream More...
void | writeCVS_ (std::ostream &os, const String &value, const String &acc, const String &name, UInt indent=4) const
| write cvParam containing strings to stream More...
void | writeCVS_ (std::ostream &os, UInt value, UInt map, const String &acc, const String &name, UInt indent=4)
| write cvParam element to stream More...
void | writeUserParam_ (std::ostream &os, const MetaInfoInterface &meta, UInt indent=4)
| Writing the MetaInfo as UserParam to the file. More...
void | cvParam_ (const String &name, const String &value)
| read attributes of MzData's cvParamType More...
Protected Member Functions inherited from XMLHandler
bool | equal_ (const XMLCh *a, const XMLCh *b) const
| Returns if two Xerces strings are equal. More...
void | writeUserParam_ (const String &tag_name, std::ostream &os, const MetaInfoInterface &meta, UInt indent) const
| Writes the content of MetaInfoInterface to the file. More...
Int | asInt_ (const String &in)
| Conversion of a String to an integer value. More...
Int | asInt_ (const XMLCh *in)
| Conversion of a Xerces string to an integer value. More...
UInt | asUInt_ (const String &in)
| Conversion of a String to an unsigned integer value. More...
double | asDouble_ (const String &in)
| Conversion of a String to a double value. More...
float | asFloat_ (const String &in)
| Conversion of a String to a float value. More...
bool | asBool_ (const String &in)
| Conversion of a string to a boolean value. More...
DateTime | asDateTime_ (String date_string)
| Conversion of a xs:datetime string to a DateTime value. More...
String | attributeAsString_ (const xercesc::Attributes &a, const char *name) const
| Converts an attribute to a String. More...
Int | attributeAsInt_ (const xercesc::Attributes &a, const char *name) const
| Converts an attribute to a Int. More...
double | attributeAsDouble_ (const xercesc::Attributes &a, const char *name) const
| Converts an attribute to a double. More...
DoubleList | attributeAsDoubleList_ (const xercesc::Attributes &a, const char *name) const
| Converts an attribute to a DoubleList. More...
IntList | attributeAsIntList_ (const xercesc::Attributes &a, const char *name) const
| Converts an attribute to an IntList. More...
StringList | attributeAsStringList_ (const xercesc::Attributes &a, const char *name) const
| Converts an attribute to an StringList. More...
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. More...
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. More...
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. More...
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. More...
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. More...
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. More...
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. More...
String | attributeAsString_ (const xercesc::Attributes &a, const XMLCh *name) const
| Converts an attribute to a String. More...
Int | attributeAsInt_ (const xercesc::Attributes &a, const XMLCh *name) const
| Converts an attribute to a Int. More...
double | attributeAsDouble_ (const xercesc::Attributes &a, const XMLCh *name) const
| Converts an attribute to a double. More...
DoubleList | attributeAsDoubleList_ (const xercesc::Attributes &a, const XMLCh *name) const
| Converts an attribute to a DoubleList. More...
IntList | attributeAsIntList_ (const xercesc::Attributes &a, const XMLCh *name) const
| Converts an attribute to a IntList. More...
StringList | attributeAsStringList_ (const xercesc::Attributes &a, const XMLCh *name) const
| Converts an attribute to a StringList. More...
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. More...
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. More...
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. More...
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. More...
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. More...
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. More...
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. More...
SignedSize | cvStringToEnum_ (const Size section, const String &term, const char *message, const SignedSize result_on_error=0)

## Protected Attributes

MapType * | exp_
| map pointer for reading More...
const MapType * | cexp_
| map pointer for writing More...
PeakFileOptions | options_
| Options that can be set for loading/storing. More...
bool | skip_spectrum_
| Flag that indicates whether this spectrum should be skipped (due to options) More...
const ProgressLogger & | logger_
| Progress logger. More...
boost::shared_ptr< DataProcessing > | data_processing_
temporary datastructures to hold parsed data
UInt | peak_count_
| The number of peaks in the current spectrum. More...
SpectrumType | spec_
| The current spectrum. More...
std::vector< std::pair< String, MetaInfoDescription > > | meta_id_descs_
| An array of pairs MetaInfodescriptions and their ids. More...
std::vector< String > | data_to_decode_
| encoded data which is read and has to be decoded More...
std::vector< float > | data_to_encode_
| floating point numbers which have to be encoded and written More...
std::vector< std::vector< float > > | decoded_list_
std::vector< std::vector< double > > | decoded_double_list_
std::vector< String > | precisions_
std::vector< String > | endians_
Protected Attributes inherited from XMLHandler
String | error_message_
| Error message of the last error. More...
String | file_
| File name. More...
String | version_
| Schema version. More...
StringManager | sm_
| Helper class for string conversion. More...
std::vector< String > | open_tags_
| Stack of open XML tags. More...
LOADDETAIL | load_detail_
| parse only until total number of scans and chroms have been determined from attributes More...
std::vector< std::vector< String > > | cv_terms_
| Array of CV term lists (one sublist denotes one term and it's children) More...

## Private Member Functions

void | init_ ()

## Additional Inherited Members

Public Types inherited from XMLHandler
enum | ActionMode { LOAD, STORE }
| Action to set the current mode (for error messages) More...
enum | LOADDETAIL { LD_ALLDATA, LD_RAWCOUNTS, LD_COUNTS_WITHOPTIONS }
Static Public Member Functions inherited from XMLHandler
static String | writeXMLEscape (const String &to_escape)
| Escapes a string and returns the escaped string. More...

## Member Typedef Documentation

## ◆ PeakType

typedef MapType::PeakType PeakType

protected

Peak type.

## ◆ SpectrumType

typedef MSSpectrum SpectrumType

protected

Spectrum type.

## Constructor & Destructor Documentation

## ◆ MzDataHandler() [1/2]

MzDataHandler | ( | MapType & | exp,
|  | const String & | filename,
|  | const String & | version,
|  | ProgressLogger & | logger
| ) |  |

Constructor for a write-only handler.

## ◆ MzDataHandler() [2/2]

MzDataHandler | ( | const MapType & | exp,
|  | const String & | filename,
|  | const String & | version,
|  | const ProgressLogger & | logger
| ) |  |

Constructor for a read-only handler.

## ◆ ~MzDataHandler()

~MzDataHandler | ( |  | ) |

inline override

Destructor.

## Member Function Documentation

## ◆ characters()

void characters | ( | const XMLCh *const | chars,
|  | const XMLSize_t | length
| ) |  |

override

## ◆ cvParam_()

void cvParam_ | ( | const String & | name,
|  | const String & | value
| ) |  |

protected

read attributes of MzData's cvParamType

Example: <cvParam cvLabel="psi" accession="PSI:1000001" name="@p name" value="@p value"/> `name` and sometimes `value` are defined in the MzData ontology.

## ◆ endElement()

void endElement | ( | const XMLCh * | const,
|  | const XMLCh * | const,
|  | const XMLCh *const | qname
| ) |  |

override

## ◆ fillData_()

void fillData_ | ( |  | ) |

protected

fills the current spectrum with peaks and meta data

## ◆ init_()

void init_ | ( |  | ) |

private

## ◆ setOptions()

void setOptions | ( | const PeakFileOptions & | options | ) |

inline

Sets the options.

## ◆ startElement()

void startElement | ( | const XMLCh * | const,
|  | const XMLCh * | const,
|  | const XMLCh *const | qname,
|  | const xercesc::Attributes & | attributes
| ) |  |

override

## ◆ writeBinary_()

void writeBinary_ | ( | std::ostream & | os,
|  | Size | size,
|  | const String & | tag,
|  | const String & | name = `""`,
|  | SignedSize | id = `-1`
| ) |  |

inline protected

write binary data to stream (first one)

The `name` and `id` are only used if the `tag` is supDataArrayBinary or supDataArray.

## ◆ writeCVS_() [1/3]

void writeCVS_ | ( | std::ostream & | os,
|  | double | value,
|  | const String & | acc,
|  | const String & | name,
|  | UInt | indent = `4`
| ) |  | const

inline protected

write cvParam containing strings to stream

`value` string value `acc` accession number defined by ontology `name` term defined by ontology `indent` number of tabs used in front of tag

Example: <cvParam cvLabel="psi" accession="PSI:@p acc" name="@p name" value="@p value"/>

## ◆ writeCVS_() [2/3]

void writeCVS_ | ( | std::ostream & | os,
|  | const String & | value,
|  | const String & | acc,
|  | const String & | name,
|  | UInt | indent = `4`
| ) |  | const

inline protected

write cvParam containing strings to stream

`value` string value `acc` accession number defined by ontology `name` term defined by ontology `indent` number of tabs used in front of tag

Example: <cvParam cvLabel="psi" accession="PSI:@p acc" name="@p name" value="@p value"/>

## ◆ writeCVS_() [3/3]

void writeCVS_ | ( | std::ostream & | os,
|  | UInt | value,
|  | UInt | map,
|  | const String & | acc,
|  | const String & | name,
|  | UInt | indent = `4`
| ) |  |

inline protected

write cvParam element to stream

`os` Output stream `value` enumeration value `map` index if the terms in cv_terms_ `acc` accession number defined by ontology `name` term defined by ontology `indent` number of tabs used in front of tag

Example: <cvParam cvLabel="psi" accession="PSI:@p acc" name="@p name" value=""/>

## ◆ writeTo()

void writeTo | ( | std::ostream & | os | ) |

override virtual

Writes the contents to a stream.

Reimplemented from XMLHandler.

## ◆ writeUserParam_()

void writeUserParam_ | ( | std::ostream & | os,
|  | const MetaInfoInterface & | meta,
|  | UInt | indent = `4`
| ) |  |

inline protected

Writing the MetaInfo as UserParam to the file.

## Member Data Documentation

## ◆ cexp_

const MapType* cexp_

protected

map pointer for writing

## ◆ data_processing_

boost::shared_ptr< DataProcessing > data_processing_

protected

## ◆ data_to_decode_

std::vector<String> data_to_decode_

protected

encoded data which is read and has to be decoded

## ◆ data_to_encode_

std::vector<float> data_to_encode_

protected

floating point numbers which have to be encoded and written

## ◆ decoded_double_list_

std::vector<std::vector<double> > decoded_double_list_

protected

## ◆ decoded_list_

std::vector<std::vector<float> > decoded_list_

protected

## ◆ endians_

std::vector<String> endians_

protected

## ◆ exp_

MapType* exp_

protected

map pointer for reading

## ◆ logger_

const ProgressLogger& logger_

protected

Progress logger.

## ◆ meta_id_descs_

std::vector<std::pair<String, MetaInfoDescription> > meta_id_descs_

protected

An array of pairs MetaInfodescriptions and their ids.

## ◆ options_

PeakFileOptions options_

protected

Options that can be set for loading/storing.

## ◆ peak_count_

UInt peak_count_

protected

The number of peaks in the current spectrum.

## ◆ precisions_

std::vector<String> precisions_

protected

## ◆ skip_spectrum_

bool skip_spectrum_

protected

Flag that indicates whether this spectrum should be skipped (due to options)

## ◆ spec_

SpectrumType spec_

protected

The current spectrum.