QcMLFile#

class pyopenms.QcMLFile#

Bases: object

Cython implementation of _QcMLFile

Original C++ documentation is available here: – Inherits from [‘XMLHandler’, ‘XMLFile’, ‘ProgressLogger’]

__init__(self) → None#

Methods

`__init__`(self)
`addRunAttachment`(self, r, at)	Adds a attachment to run by the name r
`addRunQualityParameter`(self, r, qp)	Adds a QualityParameter to run by the name r
`addSetAttachment`(self, r, at)	Adds a attachment to set by the name r
`addSetQualityParameter`(self, r, qp)	Adds a QualityParameter to set by the name r
`collectSetParameter`(self, setname, qp, ret)	Collects the values of given QPs (as CVid) of the given set
`endProgress`(self)	Ends the progress display
`error`(self, mode, msg, line, column)
`errorString`(self)
`existsRun`(self, filename)	Returns true if the given run id is present in this file, if checkname is true it also checks the names
`existsRunQualityParameter`(self, filename, ...)	Returns the ids of the parameter name given if found in given run empty else
`existsSet`(self, filename)	Returns true if the given set id is present in this file, if checkname is true it also checks the names
`existsSetQualityParameter`(self, filename, ...)	Returns the ids of the parameter name given if found in given set, empty else
`exportAttachment`(self, filename, 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`(self, filename)
`exportQP`(self, filename, qpname)	Returns a String value in quotation of a QualityParameter by the name qpname in run/set by the name filename
`exportQPs`(self, filename, qpnames)	Returns a String of a tab separated QualityParameter by the name qpname in run/set by the name filename
`getLogType`(self)	Returns the type of progress log being used
`getRunIDs`(self, ids)	Gives the ids of the registered runs in the vector ids
`getRunNames`(self, ids)	Gives the names of the registered runs in the vector ids
`getVersion`(self)	Return the version of the schema
`load`(self, filename)	Load a QCFile
`map2csv`
`merge`(self, addendum, setname)	Merges the given QCFile into this one
`nextProgress`(self)	Increment progress by 1 (according to range begin-end)
`registerRun`(self, id_, name)	Registers a run in the qcml file with the respective mappings
`registerSet`(self, id_, name, names)	Registers a set in the qcml file with the respective mappings
`removeAllAttachments`(self, at)	Removes attachment with cv accession at from all runs/sets
`removeAttachment`	Overload:
`removeQualityParameter`(self, r, ids)	Removes QualityParameter going by one of the ID attributes given in ids
`reset`(self)
`setLogType`(self, in_0)	Sets the progress log that should be used.
`setProgress`(self, value)	Sets the current progress
`startProgress`(self, begin, end, label)
`store`(self, filename)	Store the qcML file
`warning`(self, mode, msg, line, column)

addRunAttachment(self, r: bytes | str | String, at: Attachment) → None#: Adds a attachment to run by the name r

addRunQualityParameter(self, r: bytes | str | String, qp: QualityParameter) → None#: Adds a QualityParameter to run by the name r

addSetAttachment(self, r: bytes | str | String, at: Attachment) → None#: Adds a attachment to set by the name r

addSetQualityParameter(self, r: bytes | str | String, qp: QualityParameter) → None#: Adds a QualityParameter to set by the name r

collectSetParameter(self, setname: bytes | str | String, qp: bytes | str | String, ret: List[bytes]) → None#: Collects the values of given QPs (as CVid) of the given set

endProgress(self) → None#: Ends the progress display

error(self, mode: int, msg: bytes | str | String, line: int, column: int) → None#

errorString(self) → bytes | str | String#

existsRun(self, filename: bytes | str | String) → bool#: Returns true if the given run id is present in this file, if checkname is true it also checks the names

existsRunQualityParameter(self, filename: bytes | str | String, qpname: bytes | str | String, ids: List[bytes]) → None#: Returns the ids of the parameter name given if found in given run empty else

existsSet(self, filename: bytes | str | String) → bool#: Returns true if the given set id is present in this file, if checkname is true it also checks the names

existsSetQualityParameter(self, filename: bytes | str | String, qpname: bytes | str | String, ids: List[bytes]) → None#: Returns the ids of the parameter name given if found in given set, empty else

exportAttachment(self, filename: bytes | str | String, qpname: bytes | str | String) → bytes | str | String#: 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(self, filename: bytes | str | String) → bytes | str | String#

exportQP(self, filename: bytes | str | String, qpname: bytes | str | String) → bytes | str | String#: Returns a String value in quotation of a QualityParameter by the name qpname in run/set by the name filename

exportQPs(self, filename: bytes | str | String, qpnames: List[bytes]) → bytes | str | String#: Returns a String of a tab separated QualityParameter by the name qpname in run/set by the name filename

getLogType(self) → int#: Returns the type of progress log being used

getRunIDs(self, ids: List[bytes]) → None#: Gives the ids of the registered runs in the vector ids

getRunNames(self, ids: List[bytes]) → None#: Gives the names of the registered runs in the vector ids

getVersion(self) → bytes | str | String#: Return the version of the schema

load(self, filename: bytes | str | String) → None#: Load a QCFile

map2csv()#

merge(self, addendum: QcMLFile, setname: bytes | str | String) → None#: Merges the given QCFile into this one

nextProgress(self) → None#: Increment progress by 1 (according to range begin-end)

registerRun(self, id_: bytes | str | String, name: bytes | str | String) → None#: Registers a run in the qcml file with the respective mappings

registerSet(self, id_: bytes | str | String, name: bytes | str | String, names: Set[bytes]) → None#: Registers a set in the qcml file with the respective mappings

removeAllAttachments(self, at: bytes | str | String) → None#: Removes attachment with cv accession at from all runs/sets

removeAttachment()#

Overload:

removeAttachment(self, r: bytes | str | String, ids: List[bytes], at: bytes | str | String) → None

Removes attachments referencing an id given in ids, from run/set r. All attachments if no attachment name is given with at

Overload:

removeAttachment(self, r: bytes | str | String, at: bytes | str | String) → None

Removes attachment with cv accession at from run/set r

removeQualityParameter(self, r: bytes | str | String, ids: List[bytes]) → None#: Removes QualityParameter going by one of the ID attributes given in ids

reset(self) → None#

setLogType(self, in_0: int) → None#: Sets the progress log that should be used. The default type is NONE!

setProgress(self, value: int) → None#: Sets the current progress

startProgress(self, begin: int, end: int, label: bytes | str | String) → None#

store(self, filename: bytes | str | String) → None#: Store the qcML file

warning(self, mode: int, msg: bytes | str | String, line: int, column: int) → None#