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Software

mzmlpy.elems.software.Software dataclass 

Software(element: ElementTree.Element)

Bases: _ParamGroup

Software used to acquire or process the data, identified by id and version.

ns cached property 

ns: str

Get XML namespace from the element tag.

cv_params cached property 

cv_params: list[CvParam]

Parse cvParams from the XML element.

accessions cached property 

accessions: set[str]

Get a set of all accession numbers from the cvParams.

names cached property 

names: set[str]

Get a set of all names from the cvParams.

user_params property 

user_params: list[UserParam]

Parse userParams from the XML element.

ref_params property 

ref_params: list[ReferenceableParamGroupRef]

Get a list of all referenceable parameters from the XML element.

serialize 

serialize() -> dict

return the full element content

Source code in src/mzmlpy/elems/dtree_wrapper.py 
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def serialize(self) -> dict:
    """return the full element content"""
    return {
        "tag": self.element.tag,
        "attributes": self.element.attrib,
        "text": self.element.text,
        "children": [_DataTreeWrapper(child).serialize() for child in self.element],
    }

get_attribute 

get_attribute(attr_name: str) -> str | None

Get an attribute value from the element.

Source code in src/mzmlpy/elems/dtree_wrapper.py 
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def get_attribute(self, attr_name: str) -> str | None:
    """Get an attribute value from the element."""
    return self.element.attrib.get(attr_name)

get_cvparm 

get_cvparm(id: str) -> CvParam | None

Get a cvParam by accession or name.

Source code in src/mzmlpy/elems/dtree_wrapper.py 
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def get_cvparm(self, id: str) -> CvParam | None:
    """Get a cvParam by accession or name."""
    for cv_param in self.cv_params:
        if cv_param.accession == id or cv_param.name == id:
            return cv_param
    return None

has_cvparm 

has_cvparm(id: str) -> bool

Check if a cvParam with the given accession or name exists.

Source code in src/mzmlpy/elems/dtree_wrapper.py 
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def has_cvparm(self, id: str) -> bool:
    """Check if a cvParam with the given accession or name exists."""
    return any(cv_param.accession == id or cv_param.name == id for cv_param in self.cv_params)

get_user_param 

get_user_param(name: str) -> UserParam | None

Get a userParam by name.

Source code in src/mzmlpy/elems/dtree_wrapper.py 
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def get_user_param(self, name: str) -> UserParam | None:
    """Get a userParam by name."""
    for user_param in self.user_params:
        if user_param.name == name:
            return user_param
    return None

has_user_param 

has_user_param(name: str) -> bool

Check if a userParam with the given name exists.

Source code in src/mzmlpy/elems/dtree_wrapper.py 
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def has_user_param(self, name: str) -> bool:
    """Check if a userParam with the given name exists."""
    return any(user_param.name == name for user_param in self.user_params)

get_ref_param 

get_ref_param(
    ref: str,
) -> ReferenceableParamGroupRef | None

Get a referenceable parameter by ref.

Source code in src/mzmlpy/elems/dtree_wrapper.py 
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def get_ref_param(self, ref: str) -> ReferenceableParamGroupRef | None:
    """Get a referenceable parameter by ref."""
    for ref_param in self.ref_params:
        if ref_param.ref == ref:
            return ref_param
    return None

has_ref_param 

has_ref_param(ref: str) -> bool

Check if a referenceable parameter with the given ref exists.

Source code in src/mzmlpy/elems/dtree_wrapper.py 
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def has_ref_param(self, ref: str) -> bool:
    """Check if a referenceable parameter with the given ref exists."""
    return any(ref_param.ref == ref for ref_param in self.ref_params)

Sample

mzmlpy.elems.sample.Sample dataclass 

Sample(element: ElementTree.Element)

Bases: _ParamGroup

A sample analyzed in the experiment, described by id, optional name, and CV parameters.

ns cached property 

ns: str

Get XML namespace from the element tag.

cv_params cached property 

cv_params: list[CvParam]

Parse cvParams from the XML element.

accessions cached property 

accessions: set[str]

Get a set of all accession numbers from the cvParams.

names cached property 

names: set[str]

Get a set of all names from the cvParams.

user_params property 

user_params: list[UserParam]

Parse userParams from the XML element.

ref_params property 

ref_params: list[ReferenceableParamGroupRef]

Get a list of all referenceable parameters from the XML element.

serialize 

serialize() -> dict

return the full element content

Source code in src/mzmlpy/elems/dtree_wrapper.py 
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def serialize(self) -> dict:
    """return the full element content"""
    return {
        "tag": self.element.tag,
        "attributes": self.element.attrib,
        "text": self.element.text,
        "children": [_DataTreeWrapper(child).serialize() for child in self.element],
    }

get_attribute 

get_attribute(attr_name: str) -> str | None

Get an attribute value from the element.

Source code in src/mzmlpy/elems/dtree_wrapper.py 
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def get_attribute(self, attr_name: str) -> str | None:
    """Get an attribute value from the element."""
    return self.element.attrib.get(attr_name)

get_cvparm 

get_cvparm(id: str) -> CvParam | None

Get a cvParam by accession or name.

Source code in src/mzmlpy/elems/dtree_wrapper.py 
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def get_cvparm(self, id: str) -> CvParam | None:
    """Get a cvParam by accession or name."""
    for cv_param in self.cv_params:
        if cv_param.accession == id or cv_param.name == id:
            return cv_param
    return None

has_cvparm 

has_cvparm(id: str) -> bool

Check if a cvParam with the given accession or name exists.

Source code in src/mzmlpy/elems/dtree_wrapper.py 
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def has_cvparm(self, id: str) -> bool:
    """Check if a cvParam with the given accession or name exists."""
    return any(cv_param.accession == id or cv_param.name == id for cv_param in self.cv_params)

get_user_param 

get_user_param(name: str) -> UserParam | None

Get a userParam by name.

Source code in src/mzmlpy/elems/dtree_wrapper.py 
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def get_user_param(self, name: str) -> UserParam | None:
    """Get a userParam by name."""
    for user_param in self.user_params:
        if user_param.name == name:
            return user_param
    return None

has_user_param 

has_user_param(name: str) -> bool

Check if a userParam with the given name exists.

Source code in src/mzmlpy/elems/dtree_wrapper.py 
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def has_user_param(self, name: str) -> bool:
    """Check if a userParam with the given name exists."""
    return any(user_param.name == name for user_param in self.user_params)

get_ref_param 

get_ref_param(
    ref: str,
) -> ReferenceableParamGroupRef | None

Get a referenceable parameter by ref.

Source code in src/mzmlpy/elems/dtree_wrapper.py 
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def get_ref_param(self, ref: str) -> ReferenceableParamGroupRef | None:
    """Get a referenceable parameter by ref."""
    for ref_param in self.ref_params:
        if ref_param.ref == ref:
            return ref_param
    return None

has_ref_param 

has_ref_param(ref: str) -> bool

Check if a referenceable parameter with the given ref exists.

Source code in src/mzmlpy/elems/dtree_wrapper.py 
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def has_ref_param(self, ref: str) -> bool:
    """Check if a referenceable parameter with the given ref exists."""
    return any(ref_param.ref == ref for ref_param in self.ref_params)

Run

mzmlpy.elems.run.Run dataclass 

Run(element: ElementTree.Element)

Bases: _ParamGroup

The mzML run element containing instrument configuration, sample, and acquisition timestamp references.

ns cached property 

ns: str

Get XML namespace from the element tag.

cv_params cached property 

cv_params: list[CvParam]

Parse cvParams from the XML element.

accessions cached property 

accessions: set[str]

Get a set of all accession numbers from the cvParams.

names cached property 

names: set[str]

Get a set of all names from the cvParams.

user_params property 

user_params: list[UserParam]

Parse userParams from the XML element.

ref_params property 

ref_params: list[ReferenceableParamGroupRef]

Get a list of all referenceable parameters from the XML element.

serialize 

serialize() -> dict

return the full element content

Source code in src/mzmlpy/elems/dtree_wrapper.py 
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def serialize(self) -> dict:
    """return the full element content"""
    return {
        "tag": self.element.tag,
        "attributes": self.element.attrib,
        "text": self.element.text,
        "children": [_DataTreeWrapper(child).serialize() for child in self.element],
    }

get_attribute 

get_attribute(attr_name: str) -> str | None

Get an attribute value from the element.

Source code in src/mzmlpy/elems/dtree_wrapper.py 
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def get_attribute(self, attr_name: str) -> str | None:
    """Get an attribute value from the element."""
    return self.element.attrib.get(attr_name)

get_cvparm 

get_cvparm(id: str) -> CvParam | None

Get a cvParam by accession or name.

Source code in src/mzmlpy/elems/dtree_wrapper.py 
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def get_cvparm(self, id: str) -> CvParam | None:
    """Get a cvParam by accession or name."""
    for cv_param in self.cv_params:
        if cv_param.accession == id or cv_param.name == id:
            return cv_param
    return None

has_cvparm 

has_cvparm(id: str) -> bool

Check if a cvParam with the given accession or name exists.

Source code in src/mzmlpy/elems/dtree_wrapper.py 
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def has_cvparm(self, id: str) -> bool:
    """Check if a cvParam with the given accession or name exists."""
    return any(cv_param.accession == id or cv_param.name == id for cv_param in self.cv_params)

get_user_param 

get_user_param(name: str) -> UserParam | None

Get a userParam by name.

Source code in src/mzmlpy/elems/dtree_wrapper.py 
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def get_user_param(self, name: str) -> UserParam | None:
    """Get a userParam by name."""
    for user_param in self.user_params:
        if user_param.name == name:
            return user_param
    return None

has_user_param 

has_user_param(name: str) -> bool

Check if a userParam with the given name exists.

Source code in src/mzmlpy/elems/dtree_wrapper.py 
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def has_user_param(self, name: str) -> bool:
    """Check if a userParam with the given name exists."""
    return any(user_param.name == name for user_param in self.user_params)

get_ref_param 

get_ref_param(
    ref: str,
) -> ReferenceableParamGroupRef | None

Get a referenceable parameter by ref.

Source code in src/mzmlpy/elems/dtree_wrapper.py 
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def get_ref_param(self, ref: str) -> ReferenceableParamGroupRef | None:
    """Get a referenceable parameter by ref."""
    for ref_param in self.ref_params:
        if ref_param.ref == ref:
            return ref_param
    return None

has_ref_param 

has_ref_param(ref: str) -> bool

Check if a referenceable parameter with the given ref exists.

Source code in src/mzmlpy/elems/dtree_wrapper.py 
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def has_ref_param(self, ref: str) -> bool:
    """Check if a referenceable parameter with the given ref exists."""
    return any(ref_param.ref == ref for ref_param in self.ref_params)

ScanSetting

mzmlpy.elems.scan_setting.ScanSetting dataclass 

ScanSetting(element: ElementTree.Element)

Bases: _ParamGroup

Scan acquisition settings including source file references and target m/z lists.

ns cached property 

ns: str

Get XML namespace from the element tag.

cv_params cached property 

cv_params: list[CvParam]

Parse cvParams from the XML element.

accessions cached property 

accessions: set[str]

Get a set of all accession numbers from the cvParams.

names cached property 

names: set[str]

Get a set of all names from the cvParams.

user_params property 

user_params: list[UserParam]

Parse userParams from the XML element.

ref_params property 

ref_params: list[ReferenceableParamGroupRef]

Get a list of all referenceable parameters from the XML element.

serialize 

serialize() -> dict

return the full element content

Source code in src/mzmlpy/elems/dtree_wrapper.py 
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def serialize(self) -> dict:
    """return the full element content"""
    return {
        "tag": self.element.tag,
        "attributes": self.element.attrib,
        "text": self.element.text,
        "children": [_DataTreeWrapper(child).serialize() for child in self.element],
    }

get_attribute 

get_attribute(attr_name: str) -> str | None

Get an attribute value from the element.

Source code in src/mzmlpy/elems/dtree_wrapper.py 
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def get_attribute(self, attr_name: str) -> str | None:
    """Get an attribute value from the element."""
    return self.element.attrib.get(attr_name)

get_cvparm 

get_cvparm(id: str) -> CvParam | None

Get a cvParam by accession or name.

Source code in src/mzmlpy/elems/dtree_wrapper.py 
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def get_cvparm(self, id: str) -> CvParam | None:
    """Get a cvParam by accession or name."""
    for cv_param in self.cv_params:
        if cv_param.accession == id or cv_param.name == id:
            return cv_param
    return None

has_cvparm 

has_cvparm(id: str) -> bool

Check if a cvParam with the given accession or name exists.

Source code in src/mzmlpy/elems/dtree_wrapper.py 
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def has_cvparm(self, id: str) -> bool:
    """Check if a cvParam with the given accession or name exists."""
    return any(cv_param.accession == id or cv_param.name == id for cv_param in self.cv_params)

get_user_param 

get_user_param(name: str) -> UserParam | None

Get a userParam by name.

Source code in src/mzmlpy/elems/dtree_wrapper.py 
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def get_user_param(self, name: str) -> UserParam | None:
    """Get a userParam by name."""
    for user_param in self.user_params:
        if user_param.name == name:
            return user_param
    return None

has_user_param 

has_user_param(name: str) -> bool

Check if a userParam with the given name exists.

Source code in src/mzmlpy/elems/dtree_wrapper.py 
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def has_user_param(self, name: str) -> bool:
    """Check if a userParam with the given name exists."""
    return any(user_param.name == name for user_param in self.user_params)

get_ref_param 

get_ref_param(
    ref: str,
) -> ReferenceableParamGroupRef | None

Get a referenceable parameter by ref.

Source code in src/mzmlpy/elems/dtree_wrapper.py 
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def get_ref_param(self, ref: str) -> ReferenceableParamGroupRef | None:
    """Get a referenceable parameter by ref."""
    for ref_param in self.ref_params:
        if ref_param.ref == ref:
            return ref_param
    return None

has_ref_param 

has_ref_param(ref: str) -> bool

Check if a referenceable parameter with the given ref exists.

Source code in src/mzmlpy/elems/dtree_wrapper.py 
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def has_ref_param(self, ref: str) -> bool:
    """Check if a referenceable parameter with the given ref exists."""
    return any(ref_param.ref == ref for ref_param in self.ref_params)

Target

mzmlpy.elems.scan_setting.Target dataclass 

Target(element: ElementTree.Element)

Bases: _ParamGroup

A targeted m/z entry within a scan settings target list.

ns cached property 

ns: str

Get XML namespace from the element tag.

cv_params cached property 

cv_params: list[CvParam]

Parse cvParams from the XML element.

accessions cached property 

accessions: set[str]

Get a set of all accession numbers from the cvParams.

names cached property 

names: set[str]

Get a set of all names from the cvParams.

user_params property 

user_params: list[UserParam]

Parse userParams from the XML element.

ref_params property 

ref_params: list[ReferenceableParamGroupRef]

Get a list of all referenceable parameters from the XML element.

serialize 

serialize() -> dict

return the full element content

Source code in src/mzmlpy/elems/dtree_wrapper.py 
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def serialize(self) -> dict:
    """return the full element content"""
    return {
        "tag": self.element.tag,
        "attributes": self.element.attrib,
        "text": self.element.text,
        "children": [_DataTreeWrapper(child).serialize() for child in self.element],
    }

get_attribute 

get_attribute(attr_name: str) -> str | None

Get an attribute value from the element.

Source code in src/mzmlpy/elems/dtree_wrapper.py 
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def get_attribute(self, attr_name: str) -> str | None:
    """Get an attribute value from the element."""
    return self.element.attrib.get(attr_name)

get_cvparm 

get_cvparm(id: str) -> CvParam | None

Get a cvParam by accession or name.

Source code in src/mzmlpy/elems/dtree_wrapper.py 
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def get_cvparm(self, id: str) -> CvParam | None:
    """Get a cvParam by accession or name."""
    for cv_param in self.cv_params:
        if cv_param.accession == id or cv_param.name == id:
            return cv_param
    return None

has_cvparm 

has_cvparm(id: str) -> bool

Check if a cvParam with the given accession or name exists.

Source code in src/mzmlpy/elems/dtree_wrapper.py 
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def has_cvparm(self, id: str) -> bool:
    """Check if a cvParam with the given accession or name exists."""
    return any(cv_param.accession == id or cv_param.name == id for cv_param in self.cv_params)

get_user_param 

get_user_param(name: str) -> UserParam | None

Get a userParam by name.

Source code in src/mzmlpy/elems/dtree_wrapper.py 
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def get_user_param(self, name: str) -> UserParam | None:
    """Get a userParam by name."""
    for user_param in self.user_params:
        if user_param.name == name:
            return user_param
    return None

has_user_param 

has_user_param(name: str) -> bool

Check if a userParam with the given name exists.

Source code in src/mzmlpy/elems/dtree_wrapper.py 
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def has_user_param(self, name: str) -> bool:
    """Check if a userParam with the given name exists."""
    return any(user_param.name == name for user_param in self.user_params)

get_ref_param 

get_ref_param(
    ref: str,
) -> ReferenceableParamGroupRef | None

Get a referenceable parameter by ref.

Source code in src/mzmlpy/elems/dtree_wrapper.py 
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def get_ref_param(self, ref: str) -> ReferenceableParamGroupRef | None:
    """Get a referenceable parameter by ref."""
    for ref_param in self.ref_params:
        if ref_param.ref == ref:
            return ref_param
    return None

has_ref_param 

has_ref_param(ref: str) -> bool

Check if a referenceable parameter with the given ref exists.

Source code in src/mzmlpy/elems/dtree_wrapper.py 
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def has_ref_param(self, ref: str) -> bool:
    """Check if a referenceable parameter with the given ref exists."""
    return any(ref_param.ref == ref for ref_param in self.ref_params)

SourceFileRef

mzmlpy.elems.scan_setting.SourceFileRef dataclass 

SourceFileRef(ref: str)

A reference to a source file by its id string.

ReferenceableParamGroup

mzmlpy.elems.referenceable_param_group.ReferenceableParamGroup dataclass 

ReferenceableParamGroup(element: ElementTree.Element)

Bases: _ParamGroup

A named group of CV and user parameters that can be referenced by other elements to avoid repetition.

ns cached property 

ns: str

Get XML namespace from the element tag.

cv_params cached property 

cv_params: list[CvParam]

Parse cvParams from the XML element.

accessions cached property 

accessions: set[str]

Get a set of all accession numbers from the cvParams.

names cached property 

names: set[str]

Get a set of all names from the cvParams.

user_params property 

user_params: list[UserParam]

Parse userParams from the XML element.

ref_params property 

ref_params: list[ReferenceableParamGroupRef]

Get a list of all referenceable parameters from the XML element.

serialize 

serialize() -> dict

return the full element content

Source code in src/mzmlpy/elems/dtree_wrapper.py 
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def serialize(self) -> dict:
    """return the full element content"""
    return {
        "tag": self.element.tag,
        "attributes": self.element.attrib,
        "text": self.element.text,
        "children": [_DataTreeWrapper(child).serialize() for child in self.element],
    }

get_attribute 

get_attribute(attr_name: str) -> str | None

Get an attribute value from the element.

Source code in src/mzmlpy/elems/dtree_wrapper.py 
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def get_attribute(self, attr_name: str) -> str | None:
    """Get an attribute value from the element."""
    return self.element.attrib.get(attr_name)

get_cvparm 

get_cvparm(id: str) -> CvParam | None

Get a cvParam by accession or name.

Source code in src/mzmlpy/elems/dtree_wrapper.py 
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def get_cvparm(self, id: str) -> CvParam | None:
    """Get a cvParam by accession or name."""
    for cv_param in self.cv_params:
        if cv_param.accession == id or cv_param.name == id:
            return cv_param
    return None

has_cvparm 

has_cvparm(id: str) -> bool

Check if a cvParam with the given accession or name exists.

Source code in src/mzmlpy/elems/dtree_wrapper.py 
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def has_cvparm(self, id: str) -> bool:
    """Check if a cvParam with the given accession or name exists."""
    return any(cv_param.accession == id or cv_param.name == id for cv_param in self.cv_params)

get_user_param 

get_user_param(name: str) -> UserParam | None

Get a userParam by name.

Source code in src/mzmlpy/elems/dtree_wrapper.py 
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def get_user_param(self, name: str) -> UserParam | None:
    """Get a userParam by name."""
    for user_param in self.user_params:
        if user_param.name == name:
            return user_param
    return None

has_user_param 

has_user_param(name: str) -> bool

Check if a userParam with the given name exists.

Source code in src/mzmlpy/elems/dtree_wrapper.py 
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def has_user_param(self, name: str) -> bool:
    """Check if a userParam with the given name exists."""
    return any(user_param.name == name for user_param in self.user_params)

get_ref_param 

get_ref_param(
    ref: str,
) -> ReferenceableParamGroupRef | None

Get a referenceable parameter by ref.

Source code in src/mzmlpy/elems/dtree_wrapper.py 
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def get_ref_param(self, ref: str) -> ReferenceableParamGroupRef | None:
    """Get a referenceable parameter by ref."""
    for ref_param in self.ref_params:
        if ref_param.ref == ref:
            return ref_param
    return None

has_ref_param 

has_ref_param(ref: str) -> bool

Check if a referenceable parameter with the given ref exists.

Source code in src/mzmlpy/elems/dtree_wrapper.py 
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def has_ref_param(self, ref: str) -> bool:
    """Check if a referenceable parameter with the given ref exists."""
    return any(ref_param.ref == ref for ref_param in self.ref_params)

ReferenceableParamGroupRef

mzmlpy.elems.params.ReferenceableParamGroupRef dataclass 

ReferenceableParamGroupRef(ref: str)

A reference to a referenceable parameter group by its id string.