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 filename using the handler given by handler. More... | |
| void | save_ (const String &filename, XMLHandler *handler) const |
Stores the contents of the XML handler given by handler in the file given by filename. 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)
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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 |