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

masster/sample/defaults/find_adducts_def.py

@@ -1,325 +1,325 @@
-"""
-Find Adducts Parameters Module
-
-This module defines parameters for adduct detection in mass spectrometry data.
-It consolidates all parameters used in the find_adducts() method with type checking,
-validation, and comprehensive descriptions.
-
-Classes:
-    find_adducts_defaults: Configuration parameters for the find_adducts() method.
-"""
-
-from __future__ import annotations
-
-from dataclasses import dataclass, field
-from typing import Any
-
-
-@dataclass
-class find_adducts_defaults:
-    """
-    Parameters for mass spectrometry adduct detection using OpenMS MetaboliteFeatureDeconvolution.
-
-    This class consolidates all parameters used in the find_adducts() method including
-    potential adducts, charge constraints, and retention time tolerances.
-    It provides type checking, validation, and comprehensive parameter descriptions.
-
-    Adduct Detection Parameters:
-        adducts: List of potential adducts or ionization mode string.
-        charge_min: Minimal possible charge state.
-        charge_max: Maximal possible charge state.
-        charge_span_max: Maximum span between different charge states.
-        retention_max_diff: Maximum retention time difference for adduct grouping.
-        retention_max_diff_local: Maximum local retention time difference.
-
-    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_openms_adducts(): Get processed adducts list for OpenMS
-    """
-
-    # Adduct specification
-    adducts: list[str] | str | None = None
-
-    # Charge constraints
-    charge_min: int = 1
-    charge_max: int = 2
-    charge_span_max: int = 2
-
-    # Retention time constraints
-    retention_max_diff: float = 1.0
-    retention_max_diff_local: float = 1.0
-
-    # Parameter metadata for validation and description
-    _param_metadata: dict[str, dict[str, Any]] = field(
-        default_factory=lambda: {
-            "adducts": {
-                "dtype": "Union[List[str], str, None]",
-                "description": "List of potential adducts or ionization mode ('pos', 'neg', 'positive', 'negative')",
-                "allowed_values": ["pos", "neg", "positive", "negative"],
-            },
-            "charge_min": {
-                "dtype": int,
-                "description": "Minimal possible charge state for adduct detection",
-                "min_value": 1,
-                "max_value": 10,
-            },
-            "charge_max": {
-                "dtype": int,
-                "description": "Maximal possible charge state for adduct detection",
-                "min_value": 1,
-                "max_value": 10,
-            },
-            "charge_span_max": {
-                "dtype": int,
-                "description": "Maximum span between different charge states in the same adduct group",
-                "min_value": 1,
-                "max_value": 5,
-            },
-            "retention_max_diff": {
-                "dtype": float,
-                "description": "Maximum retention time difference (in minutes) for global adduct grouping",
-                "min_value": 0.1,
-                "max_value": 10.0,
-            },
-            "retention_max_diff_local": {
-                "dtype": float,
-                "description": "Maximum local retention time difference (in minutes) for adduct grouping",
-                "min_value": 0.1,
-                "max_value": 10.0,
-            },
-        },
-    )
-
-    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 adducts parameter
-        if param_name == "adducts":
-            if value is None:
-                return True
-            if isinstance(value, str):
-                # Check if it's a valid ionization mode
-                allowed_values = metadata.get("allowed_values", [])
-                return value in allowed_values
-            elif isinstance(value, list):
-                # Check if all elements are strings
-                return all(isinstance(item, str) for item in value)
-            else:
-                return False
-
-        # Type checking for non-Union types
-        if expected_dtype is int:
-            if not isinstance(value, int):
-                try:
-                    value = int(value)
-                except (ValueError, TypeError):
-                    return False
-        elif expected_dtype is float:
-            if not isinstance(value, (int, float)):
-                try:
-                    value = float(value)
-                except (ValueError, TypeError):
-                    return False
-
-        # Range validation for numeric types
-        if expected_dtype in (int, float):
-            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 int and not isinstance(value, int):
-                try:
-                    value = int(value)
-                except (ValueError, TypeError):
-                    if validate:
-                        return False
-            elif 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)
-
-        # Trigger dynamic calculation if this is the adducts parameter
-        if param_name == "adducts":
-            self._update_openms_adducts()
-
-        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 _update_openms_adducts(self) -> None:
-        """
-        Update the internal OpenMS adducts list when adducts parameter changes.
-        This is called automatically when the adducts parameter is set.
-        """
-        # This will update the internal state that get_openms_adducts() uses
-        pass
-
-    def get_openms_adducts(self) -> list[str]:
-        """
-        Get the processed adducts list for OpenMS MetaboliteFeatureDeconvolution.
-
-        Returns:
-            List of adduct strings formatted for OpenMS
-        """
-        adducts = self.adducts
-
-        if adducts is None or adducts in ["pos", "positive"]:
-            return ["H:+:0.4", "Na:+:0.3", "NH4:+:0.3"]
-        elif adducts in ["neg", "negative"]:
-            return ["H-1:-:1", "CH2O2:0:0.5"]
-        elif isinstance(adducts, list):
-            return adducts
-        else:
-            # Fallback to positive mode if unexpected format
-            return ["H:+:0.4", "Na:+:0.3", "NH4:+:0.3"]
+"""
+Find Adducts Parameters Module
+
+This module defines parameters for adduct detection in mass spectrometry data.
+It consolidates all parameters used in the find_adducts() method with type checking,
+validation, and comprehensive descriptions.
+
+Classes:
+    find_adducts_defaults: Configuration parameters for the find_adducts() method.
+"""
+
+from __future__ import annotations
+
+from dataclasses import dataclass, field
+from typing import Any
+
+
+@dataclass
+class find_adducts_defaults:
+    """
+    Parameters for mass spectrometry adduct detection using OpenMS MetaboliteFeatureDeconvolution.
+
+    This class consolidates all parameters used in the find_adducts() method including
+    potential adducts, charge constraints, and retention time tolerances.
+    It provides type checking, validation, and comprehensive parameter descriptions.
+
+    Adduct Detection Parameters:
+        adducts: List of potential adducts or ionization mode string.
+        charge_min: Minimal possible charge state.
+        charge_max: Maximal possible charge state.
+        charge_span_max: Maximum span between different charge states.
+        retention_max_diff: Maximum retention time difference for adduct grouping.
+        retention_max_diff_local: Maximum local retention time difference.
+
+    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_openms_adducts(): Get processed adducts list for OpenMS
+    """
+
+    # Adduct specification
+    adducts: list[str] | str | None = None
+
+    # Charge constraints
+    charge_min: int = 1
+    charge_max: int = 2
+    charge_span_max: int = 2
+
+    # Retention time constraints
+    retention_max_diff: float = 1.0
+    retention_max_diff_local: float = 1.0
+
+    # Parameter metadata for validation and description
+    _param_metadata: dict[str, dict[str, Any]] = field(
+        default_factory=lambda: {
+            "adducts": {
+                "dtype": "Union[List[str], str, None]",
+                "description": "List of potential adducts or ionization mode ('pos', 'neg', 'positive', 'negative')",
+                "allowed_values": ["pos", "neg", "positive", "negative"],
+            },
+            "charge_min": {
+                "dtype": int,
+                "description": "Minimal possible charge state for adduct detection",
+                "min_value": 1,
+                "max_value": 10,
+            },
+            "charge_max": {
+                "dtype": int,
+                "description": "Maximal possible charge state for adduct detection",
+                "min_value": 1,
+                "max_value": 10,
+            },
+            "charge_span_max": {
+                "dtype": int,
+                "description": "Maximum span between different charge states in the same adduct group",
+                "min_value": 1,
+                "max_value": 5,
+            },
+            "retention_max_diff": {
+                "dtype": float,
+                "description": "Maximum retention time difference (in minutes) for global adduct grouping",
+                "min_value": 0.1,
+                "max_value": 10.0,
+            },
+            "retention_max_diff_local": {
+                "dtype": float,
+                "description": "Maximum local retention time difference (in minutes) for adduct grouping",
+                "min_value": 0.1,
+                "max_value": 10.0,
+            },
+        },
+    )
+
+    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 adducts parameter
+        if param_name == "adducts":
+            if value is None:
+                return True
+            if isinstance(value, str):
+                # Check if it's a valid ionization mode
+                allowed_values = metadata.get("allowed_values", [])
+                return value in allowed_values
+            elif isinstance(value, list):
+                # Check if all elements are strings
+                return all(isinstance(item, str) for item in value)
+            else:
+                return False
+
+        # Type checking for non-Union types
+        if expected_dtype is int:
+            if not isinstance(value, int):
+                try:
+                    value = int(value)
+                except (ValueError, TypeError):
+                    return False
+        elif expected_dtype is float:
+            if not isinstance(value, (int, float)):
+                try:
+                    value = float(value)
+                except (ValueError, TypeError):
+                    return False
+
+        # Range validation for numeric types
+        if expected_dtype in (int, float):
+            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 int and not isinstance(value, int):
+                try:
+                    value = int(value)
+                except (ValueError, TypeError):
+                    if validate:
+                        return False
+            elif 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)
+
+        # Trigger dynamic calculation if this is the adducts parameter
+        if param_name == "adducts":
+            self._update_openms_adducts()
+
+        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 _update_openms_adducts(self) -> None:
+        """
+        Update the internal OpenMS adducts list when adducts parameter changes.
+        This is called automatically when the adducts parameter is set.
+        """
+        # This will update the internal state that get_openms_adducts() uses
+        pass
+
+    def get_openms_adducts(self) -> list[str]:
+        """
+        Get the processed adducts list for OpenMS MetaboliteFeatureDeconvolution.
+
+        Returns:
+            List of adduct strings formatted for OpenMS
+        """
+        adducts = self.adducts
+
+        if adducts is None or adducts in ["pos", "positive"]:
+            return ["H:+:0.4", "Na:+:0.3", "NH4:+:0.3"]
+        elif adducts in ["neg", "negative"]:
+            return ["H-1:-:1", "CH2O2:0:0.5"]
+        elif isinstance(adducts, list):
+            return adducts
+        else:
+            # Fallback to positive mode if unexpected format
+            return ["H:+:0.4", "Na:+:0.3", "NH4:+:0.3"]