QcMLFile

class pyopenms.QcMLFile

Bases: object

Cython implementation of _QcMLFile

Documentation is available at http://www.openms.de/current_doxygen/html/classOpenMS_1_1QcMLFile.html

– Inherits from [‘XMLHandler’, ‘XMLFile’, ‘ProgressLogger’]

__init__()

Cython signature: void QcMLFile()

Methods

__init__	Cython signature: void QcMLFile()
addRunAttachment	Cython signature: void addRunAttachment(String r, Attachment at) Adds a attachment to run by the name r
addRunQualityParameter	Cython signature: void addRunQualityParameter(String r, QualityParameter qp) Adds a QualityParameter to run by the name r
addSetAttachment	Cython signature: void addSetAttachment(String r, Attachment at) Adds a attachment to set by the name r
addSetQualityParameter	Cython signature: void addSetQualityParameter(String r, QualityParameter qp) Adds a QualityParameter to set by the name r
collectSetParameter	Cython signature: void collectSetParameter(String setname, String qp, libcpp_vector[String] & ret) Collects the values of given QPs (as CVid) of the given set
endProgress	Cython signature: void endProgress() Ends the progress display
error	Cython signature: void error(ActionMode mode, const String & msg, unsigned int line, unsigned int column)
errorString	Cython signature: String errorString()
existsRun	Cython signature: bool existsRun(String filename) Returns true if the given run id is present in this file, if checkname is true it also checks the names
existsRunQualityParameter	Cython signature: void existsRunQualityParameter(String filename, String qpname, libcpp_vector[String] & ids) Returns the ids of the parameter name given if found in given run empty else
existsSet	Cython signature: bool existsSet(String filename) Returns true if the given set id is present in this file, if checkname is true it also checks the names
existsSetQualityParameter	Cython signature: void existsSetQualityParameter(String filename, String qpname, libcpp_vector[String] & ids) Returns the ids of the parameter name given if found in given set, empty else
exportAttachment	Cython signature: String exportAttachment(String filename, String qpname) Returns a String of a tab separated rows if found empty string else from run/set by the name filename of the qualityparameter by the name qpname
exportIDstats	Cython signature: String exportIDstats(const String & filename)
exportQP	Cython signature: String exportQP(String filename, String qpname) Returns a String value in quotation of a QualityParameter by the name qpname in run/set by the name filename
exportQPs	Cython signature: String exportQPs(String filename, StringList qpnames) Returns a String of a tab separated QualityParameter by the name qpname in run/set by the name filename
getLogType	Cython signature: LogType getLogType() Returns the type of progress log being used
getRunIDs	Cython signature: void getRunIDs(libcpp_vector[String] & ids) Gives the ids of the registered runs in the vector ids
getRunNames	Cython signature: void getRunNames(libcpp_vector[String] & ids) Gives the names of the registered runs in the vector ids
getVersion	Cython signature: String getVersion() Return the version of the schema
load	Cython signature: void load(const String & filename) Load a QCFile
map2csv
merge	Cython signature: void merge(QcMLFile & addendum, String setname) Merges the given QCFile into this one
nextProgress	Cython signature: void nextProgress() Increment progress by 1 (according to range begin-end)
registerRun	Cython signature: void registerRun(String id_, String name) Registers a run in the qcml file with the respective mappings
registerSet	Cython signature: void registerSet(String id_, String name, libcpp_set[String] & names) Registers a set in the qcml file with the respective mappings
removeAllAttachments	Cython signature: void removeAllAttachments(String at) Removes attachment with cv accession at from all runs/sets
removeAttachment	Cython signature: void removeAttachment(String r, libcpp_vector[String] & ids, String at)
removeQualityParameter	Cython signature: void removeQualityParameter(String r, libcpp_vector[String] & ids) Removes QualityParameter going by one of the ID attributes given in ids
reset	Cython signature: void reset()
setLogType	Cython signature: void setLogType(LogType) Sets the progress log that should be used.
setProgress	Cython signature: void setProgress(ptrdiff_t value) Sets the current progress
startProgress	Cython signature: void startProgress(ptrdiff_t begin, ptrdiff_t end, String label)
store	Cython signature: void store(const String & filename) Store the qcML file
warning	Cython signature: void warning(ActionMode mode, const String & msg, unsigned int line, unsigned int column)

addRunAttachment()

Cython signature: void addRunAttachment(String r, Attachment at) Adds a attachment to run by the name r

addRunQualityParameter()

Cython signature: void addRunQualityParameter(String r, QualityParameter qp) Adds a QualityParameter to run by the name r

addSetAttachment()

Cython signature: void addSetAttachment(String r, Attachment at) Adds a attachment to set by the name r

addSetQualityParameter()

Cython signature: void addSetQualityParameter(String r, QualityParameter qp) Adds a QualityParameter to set by the name r

collectSetParameter()

Cython signature: void collectSetParameter(String setname, String qp, libcpp_vector[String] & ret) Collects the values of given QPs (as CVid) of the given set

endProgress()

Cython signature: void endProgress() Ends the progress display

error()

Cython signature: void error(ActionMode mode, const String & msg, unsigned int line, unsigned int column)

errorString()

Cython signature: String errorString()

existsRun()

Cython signature: bool existsRun(String filename) Returns true if the given run id is present in this file, if checkname is true it also checks the names

existsRunQualityParameter()

Cython signature: void existsRunQualityParameter(String filename, String qpname, libcpp_vector[String] & ids) Returns the ids of the parameter name given if found in given run empty else

existsSet()

Cython signature: bool existsSet(String filename) Returns true if the given set id is present in this file, if checkname is true it also checks the names

existsSetQualityParameter()

Cython signature: void existsSetQualityParameter(String filename, String qpname, libcpp_vector[String] & ids) Returns the ids of the parameter name given if found in given set, empty else

exportAttachment()

Cython signature: String exportAttachment(String filename, String qpname) Returns a String of a tab separated rows if found empty string else from run/set by the name filename of the qualityparameter by the name qpname

exportIDstats()

Cython signature: String exportIDstats(const String & filename)

exportQP()

Cython signature: String exportQP(String filename, String qpname) Returns a String value in quotation of a QualityParameter by the name qpname in run/set by the name filename

exportQPs()

Cython signature: String exportQPs(String filename, StringList qpnames) Returns a String of a tab separated QualityParameter by the name qpname in run/set by the name filename

getLogType()

Cython signature: LogType getLogType() Returns the type of progress log being used

getRunIDs()

Cython signature: void getRunIDs(libcpp_vector[String] & ids) Gives the ids of the registered runs in the vector ids

getRunNames()

Cython signature: void getRunNames(libcpp_vector[String] & ids) Gives the names of the registered runs in the vector ids

getVersion()

Cython signature: String getVersion() Return the version of the schema

load()

Cython signature: void load(const String & filename) Load a QCFile

map2csv()

merge()

Cython signature: void merge(QcMLFile & addendum, String setname) Merges the given QCFile into this one

nextProgress()

Cython signature: void nextProgress() Increment progress by 1 (according to range begin-end)

registerRun()

Cython signature: void registerRun(String id_, String name) Registers a run in the qcml file with the respective mappings

registerSet()

Cython signature: void registerSet(String id_, String name, libcpp_set[String] & names) Registers a set in the qcml file with the respective mappings

removeAllAttachments()

Cython signature: void removeAllAttachments(String at) Removes attachment with cv accession at from all runs/sets

removeAttachment()

• Cython signature: void removeAttachment(String r, libcpp_vector[String] & ids, String at) Removes attachments referencing an id given in ids, from run/set r. All attachments if no attachment name is given with at

• Cython signature: void removeAttachment(String r, String at) Removes attachment with cv accession at from run/set r

removeQualityParameter()

Cython signature: void removeQualityParameter(String r, libcpp_vector[String] & ids) Removes QualityParameter going by one of the ID attributes given in ids

reset()

Cython signature: void reset()

setLogType()

Cython signature: void setLogType(LogType) Sets the progress log that should be used. The default type is NONE!

setProgress()

Cython signature: void setProgress(ptrdiff_t value) Sets the current progress

startProgress()

Cython signature: void startProgress(ptrdiff_t begin, ptrdiff_t end, String label)

store()

Cython signature: void store(const String & filename) Store the qcML file

warning()

Cython signature: void warning(ActionMode mode, const String & msg, unsigned int line, unsigned int column)