OpenMS
2.5.0
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XMLHandler for the result files of XQuest. More...
#include <OpenMS/FORMAT/HANDLERS/XQuestResultXMLHandler.h>
Public Member Functions | |
XQuestResultXMLHandler (const String &filename, std::vector< PeptideIdentification > &pep_ids, std::vector< ProteinIdentification > &prot_ids) | |
Constructor for a read-only handler for internal identification structures. More... | |
XQuestResultXMLHandler (const std::vector< ProteinIdentification > &pro_id, const std::vector< PeptideIdentification > &pep_id, const String &filename, const String &version) | |
Constructor for a write-only handler for internal identification structures. More... | |
~XQuestResultXMLHandler () override | |
void | endElement (const XMLCh *const uri, const XMLCh *const local_name, const XMLCh *const qname) override |
void | startElement (const XMLCh *const uri, const XMLCh *const local_name, const XMLCh *const qname, const xercesc::Attributes &attributes) override |
double | getMinScore () const |
Returns the minimum score encountered in the file. More... | |
double | getMaxScore () const |
Returns the maximum score encountered in the file. More... | |
UInt | getNumberOfHits () const |
Returns the total number of hits in the file. More... | |
virtual void | writeTo (std::ostream &os) override |
Writes the contents to a stream. 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 (const xercesc::SAXParseException &exception) override |
void | error (const xercesc::SAXParseException &exception) override |
void | warning (const xercesc::SAXParseException &exception) override |
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) |
Static Public Member Functions | |
static StringList | splitByNth (const String &input, const char separator, const Size n) |
splits the @input string at the nth occurrence of the @separator More... | |
static StringList | splitByMiddle (const String &input, const char separator) |
counts occurrences of the @separator and splits the @input string into two at the middle More... | |
Static Public Member Functions inherited from XMLHandler | |
static String | writeXMLEscape (const String &to_escape) |
Escapes a string and returns the escaped string. More... | |
Static Public Attributes | |
static std::map< Size, String > | enzymes |
Maps enzyme_num in xQuest result file to the enzyme name used by OpenMS. More... | |
static std::map< String, UInt > | months |
Maps String encoding month to the numeric value. More... | |
Private Member Functions | |
void | extractDateTime_ (const String &xquest_datetime_string, DateTime &date_time) |
Extracts the DateTime from datetime string from xQuest. More... | |
void | addMetaValues_ (MetaInfoInterface &meta_info_interface) |
Assigns all meta values stored in the peptide_id_attributes member to an meta info interface. More... | |
void | getLinkPosition_ (const xercesc::Attributes &attributes, std::pair< SignedSize, SignedSize > &pair) |
Gets the link location of a xQuest xlinkPositionString. More... | |
void | setPeptideEvidence_ (const String &prot_string, PeptideHit &pep_hit) |
Sets the peptide evidence for Alpha and Beta. More... | |
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 } |
Protected Member Functions inherited from XMLHandler | |
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... | |
bool | equal_ (const XMLCh *a, const XMLCh *b) const |
Returns if two Xerces strings are equal. More... | |
SignedSize | cvStringToEnum_ (const Size section, const String &term, const char *message, const SignedSize result_on_error=0) |
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... | |
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... | |
XMLHandler for the result files of XQuest.
XQuestResultXMLHandler | ( | const String & | filename, |
std::vector< PeptideIdentification > & | pep_ids, | ||
std::vector< ProteinIdentification > & | prot_ids | ||
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Constructor for a read-only handler for internal identification structures.
XQuestResultXMLHandler | ( | const std::vector< ProteinIdentification > & | pro_id, |
const std::vector< PeptideIdentification > & | pep_id, | ||
const String & | filename, | ||
const String & | version | ||
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Constructor for a write-only handler for internal identification structures.
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Assigns all meta values stored in the peptide_id_attributes member to an meta info interface.
meta_info_interface | Where the meta values from the peptide_id_attributes member should be assigned to |
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Gets the link location of a xQuest xlinkPositionString.
attributes | XML attributes of Xerces. |
pair | Pair to be populated with the xlinkposition in xQuest. |
double getMaxScore | ( | ) | const |
Returns the maximum score encountered in the file.
double getMinScore | ( | ) | const |
Returns the minimum score encountered in the file.
UInt getNumberOfHits | ( | ) | const |
Returns the total number of hits in the file.
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Sets the peptide evidence for Alpha and Beta.
prot_string | Protein string of the xquest file the peptide evidence should be populated from. |
pep_hit | For which peptide hit the peptide evidence should be set. |
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counts occurrences of the @separator and splits the @input string into two at the middle
If the separator occurs 5 times in the input string, the string will be split at the 3rd occurrence. If 7 times, then at the 4th. The separator has to occur in the string an uneven number of times. If the separator occurs once, the string will be split at this one instance. If this one occurrence is at the beginning or end, one of the result strings will be empty.
Exception::IllegalArgument | is thrown if the @separator does not occur in the @input string an uneven number of times and at least once |
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splits the @input string at the nth occurrence of the @separator
If the separator does not occur in the input string n times, then the first output string will be the entire input string and the second one will be empty.
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Writes the contents to a stream.
Reimplemented from XMLHandler.
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Set of all protein accessions that are within the ProteinHits.
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Keeps track of the charges of the hits.
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The current spectrum search.
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Maps enzyme_num in xQuest result file to the enzyme name used by OpenMS.
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The enzyme database for enzyme lookup.
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Whether or not current xquest result tag comes from OpenPepXL (xQuest otherwise)
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Total no. of hits found in the result XML file.
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Stores the attributes of a record (peptide identification)
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