Used to load and store PepXML files. More...
#include <OpenMS/FORMAT/PepXMLFile.h>
 
  
 | Classes | |
| struct | AminoAcidModification | 
| Public Member Functions | |
| PepXMLFile () | |
| Constructor.  More... | |
| virtual | ~PepXMLFile () | 
| Destructor.  More... | |
| void | load (const String &filename, std::vector< ProteinIdentification > &proteins, std::vector< PeptideIdentification > &peptides, const String &experiment_name, const MSExperiment<> &experiment, bool use_precursor_data=false) | 
| Loads peptide sequences with modifications out of a PepXML file.  More... | |
| void | load (const String &filename, std::vector< ProteinIdentification > &proteins, std::vector< PeptideIdentification > &peptides, const String &experiment_name="") | 
| load function with empty defaults for some parameters (see above)  More... | |
| void | store (const String &filename, std::vector< ProteinIdentification > &protein_ids, std::vector< PeptideIdentification > &peptide_ids) | 
| Stores idXML as PepXML file.  More... | |
|  Public Member Functions inherited from XMLFile | |
| XMLFile () | |
| Default constructor.  More... | |
| XMLFile (const String &schema_location, const String &version) | |
| Constructor that sets the schema location.  More... | |
| virtual | ~XMLFile () | 
| Destructor.  More... | |
| bool | isValid (const String &filename, std::ostream &os=std::cerr) | 
| Checks if a file validates against the XML schema.  More... | |
| const String & | getVersion () const | 
| return the version of the schema  More... | |
| Protected Member Functions | |
| virtual void | endElement (const XMLCh *const , const XMLCh *const , const XMLCh *const qname) | 
| Docu in base class.  More... | |
| virtual void | startElement (const XMLCh *const , const XMLCh *const , const XMLCh *const qname, const xercesc::Attributes &attributes) | 
| Docu in base class.  More... | |
|  Protected Member Functions inherited from XMLHandler | |
| bool | equal_ (const XMLCh *a, const XMLCh *b) | 
| 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 DataTime value.  More... | |
| char * | 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... | |
| DoubleReal | attributeAsDouble_ (const xercesc::Attributes &a, const char *name) const | 
| Converts an attribute to a DoubleReal.  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_ (DoubleReal &value, const xercesc::Attributes &a, const char *name) const | 
| Assigns the attribute content to the DoubleReal 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... | |
| char * | 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... | |
| DoubleReal | attributeAsDouble_ (const xercesc::Attributes &a, const XMLCh *name) const | 
| Converts an attribute to a DoubleReal.  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_ (DoubleReal &value, const xercesc::Attributes &a, const XMLCh *name) const | 
| Assigns the attribute content to the DoubleReal 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) | 
| XMLHandler (const String &filename, const String &version) | |
| Default constructor.  More... | |
| virtual | ~XMLHandler () | 
| 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... | |
| virtual void | characters (const XMLCh *const chars, const XMLSize_t length) | 
| Parsing method for character data.  More... | |
| virtual void | writeTo (std::ostream &) | 
| Writes the contents to a stream.  More... | |
| String | errorString () | 
| Returns the last error description.  More... | |
| void | fatalError (const xercesc::SAXParseException &exception) | 
| void | error (const xercesc::SAXParseException &exception) | 
| void | warning (const xercesc::SAXParseException &exception) | 
|  Protected Member Functions inherited from XMLFile | |
| void | parse_ (const String &filename, XMLHandler *handler) | 
| Parses the XML file given by filenameusing the handler given byhandler.  More... | |
| void | save_ (const String &filename, XMLHandler *handler) const | 
| Stores the contents of the XML handler given by handlerin the file given byfilename.  More... | |
| void | enforceEncoding_ (const String &encoding) | 
| XMLFile () | |
| Default constructor.  More... | |
| XMLFile (const String &schema_location, const String &version) | |
| Constructor that sets the schema location.  More... | |
| virtual | ~XMLFile () | 
| Destructor.  More... | |
| bool | isValid (const String &filename, std::ostream &os=std::cerr) | 
| Checks if a file validates against the XML schema.  More... | |
| const String & | getVersion () const | 
| return the version of the schema  More... | |
| Private Member Functions | |
| void | makeScanMap_ () | 
| Fill scan_map_.  More... | |
| void | readRTMZCharge_ (const xercesc::Attributes &attributes) | 
| Read RT, m/z, charge information from attributes of "spectrum_query".  More... | |
| void | matchModification_ (const DoubleReal mass, const String &origin, String &modification_description) | 
| find modification name given a modified AA mass  More... | |
| Private Attributes | |
| std::vector < ProteinIdentification > * | proteins_ | 
| Pointer to the list of identified proteins.  More... | |
| std::vector < PeptideIdentification > * | peptides_ | 
| Pointer to the list of identified peptides.  More... | |
| const MSExperiment * | experiment_ | 
| Pointer to the experiment from which the pepXML file was generated.  More... | |
| String | exp_name_ | 
| Name of the associated experiment (filename of the data file, extension will be removed)  More... | |
| String | search_engine_ | 
| Set name of search engine.  More... | |
| bool | use_precursor_data_ | 
| Get RT and m/z for peptide ID from precursor scan (should only matter for RT)?  More... | |
| std::map< Size, Size > | scan_map_ | 
| Mapping between scan number in the pepXML file and index in the corresponding MSExperiment.  More... | |
| DoubleReal | rt_tol_ | 
| Retention time and mass-to-charge tolerance.  More... | |
| DoubleReal | mz_tol_ | 
| Element | hydrogen_ | 
| Hydrogen data (for mass types)  More... | |
| bool | wrong_experiment_ | 
| Do current entries belong to the experiment of interest (for pepXML files that bundle results from different experiments)?  More... | |
| bool | seen_experiment_ | 
| Have we seen the experiment of interest at all?  More... | |
| bool | checked_base_name_ | 
| Have we checked the "base_name" attribute in the "msms_run_summary" element?  More... | |
| std::vector< std::vector < ProteinIdentification > ::iterator > | current_proteins_ | 
| References to currently active ProteinIdentifications.  More... | |
| ProteinIdentification::SearchParameters | params_ | 
| Search parameters of the current identification run.  More... | |
| ProteinIdentification::DigestionEnzyme | enzyme_ | 
| Enyzme associated with the current identification run.  More... | |
| PeptideIdentification | current_peptide_ | 
| PeptideIdentification instance currently being processed.  More... | |
| PeptideHit | peptide_hit_ | 
| PeptideHit instance currently being processed.  More... | |
| String | current_sequence_ | 
| Sequence of the current peptide hit.  More... | |
| DoubleReal | rt_ | 
| RT and m/z of current PeptideIdentification.  More... | |
| DoubleReal | mz_ | 
| Int | charge_ | 
| Precursor ion charge.  More... | |
| UInt | search_id_ | 
| ID of current search result.  More... | |
| String | prot_id_ | 
| Identifier linking PeptideIdentifications and ProteinIdentifications.  More... | |
| DateTime | date_ | 
| Date the pepXML file was generated.  More... | |
| DoubleReal | hydrogen_mass_ | 
| Mass of a hydrogen atom (monoisotopic/average depending on case)  More... | |
| std::vector< std::pair< String, Size > > | current_modifications_ | 
| The modifications of the current peptide hit (position is 1-based)  More... | |
| std::vector < AminoAcidModification > | fixed_modifications_ | 
| Fixed aminoacid modifications.  More... | |
| std::vector < AminoAcidModification > | variable_modifications_ | 
| Variable aminoacid modifications.  More... | |
| Additional Inherited Members | |
|  Protected Types inherited from XMLHandler | |
| enum | ActionMode { LOAD, STORE } | 
| Action to set the current mode (for error messages)  More... | |
|  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... | |
| std::vector< std::vector < String > > | cv_terms_ | 
| Array of CV term lists (one sublist denotes one term and it's children)  More... | |
|  Protected Attributes inherited from XMLFile | |
| String | schema_location_ | 
| XML schema file location.  More... | |
| String | schema_version_ | 
| Version string.  More... | |
| String | enforced_encoding_ | 
| Encoding string that replaces the encoding (system dependend or specified in the XML). Disabled if empty. Used as a workaround for XTandem output xml.  More... | |
Used to load and store PepXML files.
This class is used to load and store documents that implement the schema of PepXML files.
| PepXMLFile | ( | ) | 
Constructor.
| 
 | virtual | 
Destructor.
| 
 | protectedvirtual | 
Docu in base class.
Reimplemented from XMLHandler.
| void load | ( | const String & | filename, | 
| std::vector< ProteinIdentification > & | proteins, | ||
| std::vector< PeptideIdentification > & | peptides, | ||
| const String & | experiment_name, | ||
| const MSExperiment<> & | experiment, | ||
| bool | use_precursor_data = false | ||
| ) | 
Loads peptide sequences with modifications out of a PepXML file.
| filename | PepXML file to load | 
| proteins | Protein identification output | 
| peptides | Peptide identification output | 
| experiment_name | Experiment file name, which is used to extract the corresponding search results from the PepXML file. | 
| experiment | MS run to extract the retention times from (PepXML may contain only scan numbers). | 
| use_precursor_data | Use m/z and RT of the precursor (instead of the RT of the MS2 spectrum) for the peptide? | 
| Exception::FileNotFound | is thrown if the file could not be opened | 
| Exception::ParseError | is thrown if an error occurs during parsing | 
| void load | ( | const String & | filename, | 
| std::vector< ProteinIdentification > & | proteins, | ||
| std::vector< PeptideIdentification > & | peptides, | ||
| const String & | experiment_name = "" | ||
| ) | 
load function with empty defaults for some parameters (see above)
| Exception::FileNotFound | is thrown if the file could not be opened | 
| Exception::ParseError | is thrown if an error occurs during parsing | 
| 
 | private | 
Fill scan_map_. 
| 
 | private | 
find modification name given a modified AA mass
Matches a mass of a modified AA to a mod in our modification db For ambigious mods, the first (arbitrary) is returned If no mod is found an error is issued and the return string is empty
| mass | Modified AA's mass | 
| origin | AA one letter code | 
| modification_description | [out] Name of the modification, e.g. 'Carboxymethyl (C)' | 
| 
 | private | 
Read RT, m/z, charge information from attributes of "spectrum_query".
| 
 | protectedvirtual | 
Docu in base class.
Reimplemented from XMLHandler.
| void store | ( | const String & | filename, | 
| std::vector< ProteinIdentification > & | protein_ids, | ||
| std::vector< PeptideIdentification > & | peptide_ids | ||
| ) | 
Stores idXML as PepXML file.
| Exception::UnableToCreateFile | is thrown if the file could not be opened for writing | 
| 
 | private | 
Have we checked the "base_name" attribute in the "msms_run_summary" element?
The modifications of the current peptide hit (position is 1-based)
| 
 | private | 
PeptideIdentification instance currently being processed.
| 
 | private | 
References to currently active ProteinIdentifications.
| 
 | private | 
Sequence of the current peptide hit.
| 
 | private | 
Enyzme associated with the current identification run.
| 
 | private | 
Name of the associated experiment (filename of the data file, extension will be removed)
| 
 | private | 
Pointer to the experiment from which the pepXML file was generated.
| 
 | private | 
Fixed aminoacid modifications.
| 
 | private | 
Hydrogen data (for mass types)
| 
 | private | 
Mass of a hydrogen atom (monoisotopic/average depending on case)
| 
 | private | 
| 
 | private | 
| 
 | private | 
Search parameters of the current identification run.
| 
 | private | 
PeptideHit instance currently being processed.
| 
 | private | 
Pointer to the list of identified peptides.
| 
 | private | 
Identifier linking PeptideIdentifications and ProteinIdentifications.
| 
 | private | 
Pointer to the list of identified proteins.
| 
 | private | 
RT and m/z of current PeptideIdentification.
| 
 | private | 
Retention time and mass-to-charge tolerance.
Mapping between scan number in the pepXML file and index in the corresponding MSExperiment.
| 
 | private | 
Set name of search engine.
| 
 | private | 
ID of current search result.
| 
 | private | 
Have we seen the experiment of interest at all?
| 
 | private | 
Get RT and m/z for peptide ID from precursor scan (should only matter for RT)?
| 
 | private | 
Variable aminoacid modifications.
| 
 | private | 
Do current entries belong to the experiment of interest (for pepXML files that bundle results from different experiments)?
| OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:31 using doxygen 1.8.5 |