masster 0.2.4__py3-none-any.whl → 0.3.0__py3-none-any.whl

masster/sample/defaults/find_ms2_def.py

@@ -1,285 +1,285 @@
-"""
-Find MS2 Parameters Module
-
-This module defines parameters for MS2 spectrum linking in mass spectrometry data.
-It consolidates all parameters used in the find_ms2() method with type checking,
-validation, and comprehensive descriptions.
-
-Classes:
-    find_ms2_defaults: Configuration parameters for the find_ms2() method.
-"""
-
-from __future__ import annotations
-
-from dataclasses import dataclass, field
-from typing import Any
-
-
-@dataclass
-class find_ms2_defaults:
-    """
-    Parameters for MS2 spectrum linking functionality.
-
-    This class consolidates all parameters used in the find_ms2() method including
-    m/z tolerance, centroiding options, and processing flags.
-    It provides type checking, validation, and comprehensive parameter descriptions.
-
-    MS2 Linking Parameters:
-        mz_tol: m/z tolerance for MS2 precursor matching.
-        centroid: Whether to centroid the returned spectrum.
-        deisotope: Whether to deisotope the returned spectrum.
-        dia_stats: Whether to collect DIA-related statistics.
-        features: Specific feature UID(s) to process, or None for all.
-        mz_tol_ztscan: m/z tolerance for ztscan/DIA file types.
-
-    Available Methods:
-        - validate(param_name, value): Validate a single parameter value
-        - validate_all(): Validate all parameters at once
-        - to_dict(): Convert parameters to dictionary
-        - set_from_dict(param_dict, validate=True): Update multiple parameters from dict
-        - set(param_name, value, validate=True): Set parameter value with validation
-        - get(param_name): Get parameter value
-        - get_description(param_name): Get parameter description
-        - get_info(param_name): Get full parameter metadata
-        - list_parameters(): Get list of all parameter names
-        - get_mz_tolerance(file_type): Get appropriate m/z tolerance based on file type
-    """
-
-    # Core MS2 linking parameters
-    mz_tol: float = 0.5
-    centroid: bool = True
-    deisotope: bool = False
-    dia_stats: bool = False
-
-    # Feature selection parameters - can be None, int, or list of ints
-    features: int | list[int] | None = field(default_factory=list)
-
-    # File type specific adjustments
-    mz_tol_ztscan: float = 4.0
-
-    # Parameter metadata for validation and description
-    _param_metadata: dict[str, dict[str, Any]] = field(
-        default_factory=lambda: {
-            "mz_tol": {
-                "dtype": float,
-                "description": "m/z tolerance for MS2 precursor matching",
-                "min_value": 0.01,
-                "max_value": 10.0,
-            },
-            "centroid": {
-                "dtype": bool,
-                "description": "Whether to centroid the returned spectrum",
-            },
-            "deisotope": {
-                "dtype": bool,
-                "description": "Whether to deisotope the returned spectrum",
-            },
-            "dia_stats": {
-                "dtype": bool,
-                "description": "Whether to collect DIA-related statistics",
-            },
-            "features": {
-                "dtype": "Union[int, List[int], None]",
-                "description": "Specific feature UID(s) to process, or None for all",
-            },
-            "mz_tol_ztscan": {
-                "dtype": float,
-                "description": "m/z tolerance for ztscan/DIA file types",
-                "min_value": 0.1,
-                "max_value": 20.0,
-            },
-        },
-    )
-
-    def get_info(self, param_name: str) -> dict[str, Any]:
-        """
-        Get information about a specific parameter.
-
-        Args:
-            param_name: Name of the parameter
-
-        Returns:
-            Dictionary containing parameter metadata
-
-        Raises:
-            KeyError: If parameter name is not found
-        """
-        if param_name not in self._param_metadata:
-            raise KeyError(f"Parameter '{param_name}' not found")
-        return self._param_metadata[param_name]
-
-    def get_description(self, param_name: str) -> str:
-        """
-        Get description for a specific parameter.
-
-        Args:
-            param_name: Name of the parameter
-
-        Returns:
-            Parameter description string
-        """
-        return str(self.get_info(param_name)["description"])
-
-    def validate(self, param_name: str, value: Any) -> bool:
-        """
-        Validate a parameter value against its constraints.
-
-        Args:
-            param_name: Name of the parameter
-            value: Value to validate
-
-        Returns:
-            True if value is valid, False otherwise
-        """
-        if param_name not in self._param_metadata:
-            return False
-
-        metadata = self._param_metadata[param_name]
-        expected_dtype = metadata["dtype"]
-
-        # Handle Union types for features parameter
-        if param_name == "features":
-            if value is None or isinstance(value, (int, list)):
-                if isinstance(value, list):
-                    return all(isinstance(item, int) for item in value)
-                return True
-            return False
-
-        # Type checking for non-Union types
-        if expected_dtype is float:
-            if not isinstance(value, (int, float)):
-                try:
-                    value = float(value)
-                except (ValueError, TypeError):
-                    return False
-        elif expected_dtype is bool:
-            if not isinstance(value, bool):
-                return False
-
-        # Range checking for numeric values
-        if isinstance(value, (int, float)) and value is not None:
-            if "min_value" in metadata and value < metadata["min_value"]:
-                return False
-            if "max_value" in metadata and value > metadata["max_value"]:
-                return False
-
-        return True
-
-    def set(self, param_name: str, value: Any, validate: bool = True) -> bool:
-        """
-        Set a parameter value with optional validation.
-
-        Args:
-            param_name: Name of the parameter
-            value: New value for the parameter
-            validate: Whether to validate the value before setting
-
-        Returns:
-            True if parameter was set successfully, False otherwise
-        """
-        if not hasattr(self, param_name):
-            return False
-
-        if validate and not self.validate(param_name, value):
-            return False
-
-        # Convert to expected type if needed
-        if param_name in self._param_metadata:
-            expected_dtype = self._param_metadata[param_name]["dtype"]
-            if expected_dtype is float and not isinstance(value, float):
-                try:
-                    value = float(value)
-                except (ValueError, TypeError):
-                    if validate:
-                        return False
-
-        setattr(self, param_name, value)
-        return True
-
-    def get(self, param_name: str) -> Any:
-        """
-        Get the value of a parameter by name.
-
-        Args:
-            param_name: Name of the parameter
-
-        Returns:
-            Current value of the parameter
-        """
-        if not hasattr(self, param_name):
-            raise KeyError(f"Parameter '{param_name}' not found")
-        return getattr(self, param_name)
-
-    def set_from_dict(
-        self,
-        param_dict: dict[str, Any],
-        validate: bool = True,
-    ) -> list[str]:
-        """
-        Update multiple parameters from a dictionary.
-
-        Args:
-            param_dict: Dictionary of parameter names and values
-            validate: Whether to validate values before setting
-
-        Returns:
-            List of parameter names that could not be set
-        """
-        failed_params = []
-
-        for param_name, value in param_dict.items():
-            if not self.set(param_name, value, validate):
-                failed_params.append(param_name)
-
-        return failed_params
-
-    def to_dict(self) -> dict[str, Any]:
-        """
-        Convert parameters to dictionary, excluding metadata.
-
-        Returns:
-            Dictionary of parameter names and values
-        """
-        return {k: v for k, v in self.__dict__.items() if not k.startswith("_")}
-
-    def list_parameters(self) -> list[str]:
-        """
-        Get list of all parameter names.
-
-        Returns:
-            List of parameter names
-        """
-        return [k for k in self.__dict__.keys() if not k.startswith("_")]
-
-    def validate_all(self) -> tuple[bool, list[str]]:
-        """
-        Validate all parameters in the instance.
-
-        Returns:
-            Tuple of (all_valid, list_of_invalid_params)
-            - all_valid: True if all parameters are valid, False otherwise
-            - list_of_invalid_params: List of parameter names that failed validation
-        """
-        invalid_params = []
-
-        for param_name in self.list_parameters():
-            if param_name in self._param_metadata:
-                current_value = getattr(self, param_name)
-                if not self.validate(param_name, current_value):
-                    invalid_params.append(param_name)
-
-        return len(invalid_params) == 0, invalid_params
-
-    def get_mz_tolerance(self, file_type=None):
-        """
-        Get the appropriate m/z tolerance based on file type.
-
-        Args:
-            file_type (str, optional): File type ('ztscan', 'dia', or other)
-
-        Returns:
-            float: Appropriate m/z tolerance value
-        """
-        if file_type is not None and file_type.lower() in ["ztscan", "dia"]:
-            return self.get("mz_tol_ztscan")
-        return self.get("mz_tol")
+"""
+Find MS2 Parameters Module
+
+This module defines parameters for MS2 spectrum linking in mass spectrometry data.
+It consolidates all parameters used in the find_ms2() method with type checking,
+validation, and comprehensive descriptions.
+
+Classes:
+    find_ms2_defaults: Configuration parameters for the find_ms2() method.
+"""
+
+from __future__ import annotations
+
+from dataclasses import dataclass, field
+from typing import Any
+
+
+@dataclass
+class find_ms2_defaults:
+    """
+    Parameters for MS2 spectrum linking functionality.
+
+    This class consolidates all parameters used in the find_ms2() method including
+    m/z tolerance, centroiding options, and processing flags.
+    It provides type checking, validation, and comprehensive parameter descriptions.
+
+    MS2 Linking Parameters:
+        mz_tol: m/z tolerance for MS2 precursor matching.
+        centroid: Whether to centroid the returned spectrum.
+        deisotope: Whether to deisotope the returned spectrum.
+        dia_stats: Whether to collect DIA-related statistics.
+        features: Specific feature UID(s) to process, or None for all.
+        mz_tol_ztscan: m/z tolerance for ztscan/DIA file types.
+
+    Available Methods:
+        - validate(param_name, value): Validate a single parameter value
+        - validate_all(): Validate all parameters at once
+        - to_dict(): Convert parameters to dictionary
+        - set_from_dict(param_dict, validate=True): Update multiple parameters from dict
+        - set(param_name, value, validate=True): Set parameter value with validation
+        - get(param_name): Get parameter value
+        - get_description(param_name): Get parameter description
+        - get_info(param_name): Get full parameter metadata
+        - list_parameters(): Get list of all parameter names
+        - get_mz_tolerance(file_type): Get appropriate m/z tolerance based on file type
+    """
+
+    # Core MS2 linking parameters
+    mz_tol: float = 0.5
+    centroid: bool = True
+    deisotope: bool = False
+    dia_stats: bool = False
+
+    # Feature selection parameters - can be None, int, or list of ints
+    features: int | list[int] | None = field(default_factory=list)
+
+    # File type specific adjustments
+    mz_tol_ztscan: float = 4.0
+
+    # Parameter metadata for validation and description
+    _param_metadata: dict[str, dict[str, Any]] = field(
+        default_factory=lambda: {
+            "mz_tol": {
+                "dtype": float,
+                "description": "m/z tolerance for MS2 precursor matching",
+                "min_value": 0.01,
+                "max_value": 10.0,
+            },
+            "centroid": {
+                "dtype": bool,
+                "description": "Whether to centroid the returned spectrum",
+            },
+            "deisotope": {
+                "dtype": bool,
+                "description": "Whether to deisotope the returned spectrum",
+            },
+            "dia_stats": {
+                "dtype": bool,
+                "description": "Whether to collect DIA-related statistics",
+            },
+            "features": {
+                "dtype": "Union[int, List[int], None]",
+                "description": "Specific feature UID(s) to process, or None for all",
+            },
+            "mz_tol_ztscan": {
+                "dtype": float,
+                "description": "m/z tolerance for ztscan/DIA file types",
+                "min_value": 0.1,
+                "max_value": 20.0,
+            },
+        },
+    )
+
+    def get_info(self, param_name: str) -> dict[str, Any]:
+        """
+        Get information about a specific parameter.
+
+        Args:
+            param_name: Name of the parameter
+
+        Returns:
+            Dictionary containing parameter metadata
+
+        Raises:
+            KeyError: If parameter name is not found
+        """
+        if param_name not in self._param_metadata:
+            raise KeyError(f"Parameter '{param_name}' not found")
+        return self._param_metadata[param_name]
+
+    def get_description(self, param_name: str) -> str:
+        """
+        Get description for a specific parameter.
+
+        Args:
+            param_name: Name of the parameter
+
+        Returns:
+            Parameter description string
+        """
+        return str(self.get_info(param_name)["description"])
+
+    def validate(self, param_name: str, value: Any) -> bool:
+        """
+        Validate a parameter value against its constraints.
+
+        Args:
+            param_name: Name of the parameter
+            value: Value to validate
+
+        Returns:
+            True if value is valid, False otherwise
+        """
+        if param_name not in self._param_metadata:
+            return False
+
+        metadata = self._param_metadata[param_name]
+        expected_dtype = metadata["dtype"]
+
+        # Handle Union types for features parameter
+        if param_name == "features":
+            if value is None or isinstance(value, (int, list)):
+                if isinstance(value, list):
+                    return all(isinstance(item, int) for item in value)
+                return True
+            return False
+
+        # Type checking for non-Union types
+        if expected_dtype is float:
+            if not isinstance(value, (int, float)):
+                try:
+                    value = float(value)
+                except (ValueError, TypeError):
+                    return False
+        elif expected_dtype is bool:
+            if not isinstance(value, bool):
+                return False
+
+        # Range checking for numeric values
+        if isinstance(value, (int, float)) and value is not None:
+            if "min_value" in metadata and value < metadata["min_value"]:
+                return False
+            if "max_value" in metadata and value > metadata["max_value"]:
+                return False
+
+        return True
+
+    def set(self, param_name: str, value: Any, validate: bool = True) -> bool:
+        """
+        Set a parameter value with optional validation.
+
+        Args:
+            param_name: Name of the parameter
+            value: New value for the parameter
+            validate: Whether to validate the value before setting
+
+        Returns:
+            True if parameter was set successfully, False otherwise
+        """
+        if not hasattr(self, param_name):
+            return False
+
+        if validate and not self.validate(param_name, value):
+            return False
+
+        # Convert to expected type if needed
+        if param_name in self._param_metadata:
+            expected_dtype = self._param_metadata[param_name]["dtype"]
+            if expected_dtype is float and not isinstance(value, float):
+                try:
+                    value = float(value)
+                except (ValueError, TypeError):
+                    if validate:
+                        return False
+
+        setattr(self, param_name, value)
+        return True
+
+    def get(self, param_name: str) -> Any:
+        """
+        Get the value of a parameter by name.
+
+        Args:
+            param_name: Name of the parameter
+
+        Returns:
+            Current value of the parameter
+        """
+        if not hasattr(self, param_name):
+            raise KeyError(f"Parameter '{param_name}' not found")
+        return getattr(self, param_name)
+
+    def set_from_dict(
+        self,
+        param_dict: dict[str, Any],
+        validate: bool = True,
+    ) -> list[str]:
+        """
+        Update multiple parameters from a dictionary.
+
+        Args:
+            param_dict: Dictionary of parameter names and values
+            validate: Whether to validate values before setting
+
+        Returns:
+            List of parameter names that could not be set
+        """
+        failed_params = []
+
+        for param_name, value in param_dict.items():
+            if not self.set(param_name, value, validate):
+                failed_params.append(param_name)
+
+        return failed_params
+
+    def to_dict(self) -> dict[str, Any]:
+        """
+        Convert parameters to dictionary, excluding metadata.
+
+        Returns:
+            Dictionary of parameter names and values
+        """
+        return {k: v for k, v in self.__dict__.items() if not k.startswith("_")}
+
+    def list_parameters(self) -> list[str]:
+        """
+        Get list of all parameter names.
+
+        Returns:
+            List of parameter names
+        """
+        return [k for k in self.__dict__.keys() if not k.startswith("_")]
+
+    def validate_all(self) -> tuple[bool, list[str]]:
+        """
+        Validate all parameters in the instance.
+
+        Returns:
+            Tuple of (all_valid, list_of_invalid_params)
+            - all_valid: True if all parameters are valid, False otherwise
+            - list_of_invalid_params: List of parameter names that failed validation
+        """
+        invalid_params = []
+
+        for param_name in self.list_parameters():
+            if param_name in self._param_metadata:
+                current_value = getattr(self, param_name)
+                if not self.validate(param_name, current_value):
+                    invalid_params.append(param_name)
+
+        return len(invalid_params) == 0, invalid_params
+
+    def get_mz_tolerance(self, file_type=None):
+        """
+        Get the appropriate m/z tolerance based on file type.
+
+        Args:
+            file_type (str, optional): File type ('ztscan', 'dia', or other)
+
+        Returns:
+            float: Appropriate m/z tolerance value
+        """
+        if file_type is not None and file_type.lower() in ["ztscan", "dia"]:
+            return self.get("mz_tol_ztscan")
+        return self.get("mz_tol")