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)