masster 0.2.5__py3-none-any.whl → 0.3.1__py3-none-any.whl

masster/sample/defaults/get_spectrum_def.py

@@ -1,318 +1,314 @@
-"""
-Get Spectrum Parameters Module
-
-This module defines parameters for spectrum retrieval and processing in mass spectrometry data.
-It consolidates all parameters used in the get_spectrum() method with type checking,
-validation, and comprehensive descriptions.
-
-Classes:
-    get_spectrum_defaults: Configuration parameters for the get_spectrum() method.
-"""
-
-from __future__ import annotations
-
-from dataclasses import dataclass, field
-from typing import Any
-
-
-@dataclass
-class get_spectrum_defaults:
-    """
-    Parameters for spectrum retrieval and processing.
-
-    This class consolidates all parameters used in the get_spectrum() method including
-    scan identification, spectrum processing options, and optional parameters.
-    It provides type checking, validation, and comprehensive parameter descriptions.
-
-    Spectrum Processing Parameters:
-        scan: Unique identifier of the scan to retrieve.
-        precursor_trim: Value used to trim the precursor m/z for MS2 spectra.
-        max_peaks: Maximum number of peaks to retain in the spectrum.
-        centroid: Flag indicating whether the spectrum should be centroided.
-        deisotope: Flag indicating whether deisotoping should be performed.
-        dia_stats: Flag for processing DIA (data-independent acquisition) statistics.
-        feature: An optional identifier used when computing DIA statistics.
-        label: Optional label to assign to the spectrum.
-        centroid_algo: Algorithm to use for centroiding.
-
-    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
-    """
-
-    scan: list[int] = field(default_factory=lambda: [0])
-    precursor_trim: int = -10
-    max_peaks: int | None = 50000
-    centroid: bool = True
-    deisotope: bool = True
-    dia_stats: bool | None = False
-    feature: int | None = None
-    label: str | None = None
-    centroid_algo: str | None = "lmp"
-
-    # Parameter metadata for validation and description
-    _param_metadata: dict[str, dict[str, Any]] = field(
-        default_factory=lambda: {
-            "scan": {
-                "dtype": list,
-                "description": "List of scan identifiers to retrieve",
-            },
-            "precursor_trim": {
-                "dtype": int,
-                "description": "Value used to trim the precursor m/z for MS2 spectra",
-                "min_value": -50,
-                "max_value": 50,
-            },
-            "max_peaks": {
-                "dtype": "Optional[int]",
-                "description": "Maximum number of peaks to retain in the spectrum",
-                "min_value": 1,
-                "max_value": 100000,
-            },
-            "centroid": {
-                "dtype": bool,
-                "description": "Flag indicating whether the spectrum should be centroided",
-            },
-            "deisotope": {
-                "dtype": bool,
-                "description": "Flag indicating whether deisotoping should be performed",
-            },
-            "dia_stats": {
-                "dtype": "Optional[bool]",
-                "description": "Flag for processing DIA (data-independent acquisition) statistics",
-            },
-            "feature": {
-                "dtype": "Optional[int]",
-                "description": "An optional identifier used when computing DIA statistics",
-            },
-            "label": {
-                "dtype": "Optional[str]",
-                "description": "Optional label to assign to the spectrum",
-            },
-            "centroid_algo": {
-                "dtype": "Optional[str]",
-                "description": "Algorithm to use for centroiding",
-                "allowed_values": ["lmp", "cwt", "gaussian"],
-            },
-        },
-    )
-
-    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 optional types
-        if isinstance(expected_dtype, str) and expected_dtype.startswith("Optional"):
-            if value is None:
-                return True
-            # Extract the inner type for validation
-            if "int" in expected_dtype:
-                expected_dtype = int
-            elif "str" in expected_dtype:
-                expected_dtype = str
-            elif "bool" in expected_dtype:
-                expected_dtype = bool
-
-        # Type checking
-        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
-        elif expected_dtype is bool:
-            if not isinstance(value, bool):
-                return False
-        elif expected_dtype is str:
-            if not isinstance(value, str):
-                return False
-        elif expected_dtype is list:
-            if not isinstance(value, list):
-                return False
-
-        # Range validation for numeric types
-        if expected_dtype in (int, float) and isinstance(value, (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
-
-        # Allowed values validation for strings
-        if expected_dtype is str and "allowed_values" in metadata:
-            if value not in metadata["allowed_values"]:
-                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"]
-
-            # Handle optional types
-            if (
-                isinstance(expected_dtype, str)
-                and expected_dtype.startswith("Optional")
-                and value is not None
-            ):
-                if "int" in expected_dtype and not isinstance(value, int):
-                    try:
-                        value = int(value)
-                    except (ValueError, TypeError):
-                        if validate:
-                            return False
-                elif "float" in expected_dtype 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
+"""
+Get Spectrum Parameters Module
+
+This module defines parameters for spectrum retrieval and processing in mass spectrometry data.
+It consolidates all parameters used in the get_spectrum() method with type checking,
+validation, and comprehensive descriptions.
+
+Classes:
+    get_spectrum_defaults: Configuration parameters for the get_spectrum() method.
+"""
+
+from __future__ import annotations
+
+from dataclasses import dataclass, field
+from typing import Any
+
+
+@dataclass
+class get_spectrum_defaults:
+    """
+    Parameters for spectrum retrieval and processing.
+
+    This class consolidates all parameters used in the get_spectrum() method including
+    scan identification, spectrum processing options, and optional parameters.
+    It provides type checking, validation, and comprehensive parameter descriptions.
+
+    Spectrum Processing Parameters:
+        scan: Unique identifier of the scan to retrieve.
+        precursor_trim: Value used to trim the precursor m/z for MS2 spectra.
+        max_peaks: Maximum number of peaks to retain in the spectrum.
+        centroid: Flag indicating whether the spectrum should be centroided.
+        deisotope: Flag indicating whether deisotoping should be performed.
+        dia_stats: Flag for processing DIA (data-independent acquisition) statistics.
+        feature: An optional identifier used when computing DIA statistics.
+        label: Optional label to assign to the spectrum.
+        centroid_algo: Algorithm to use for centroiding.
+
+    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
+    """
+
+    scan: list[int] = field(default_factory=lambda: [0])
+    precursor_trim: int = -10
+    max_peaks: int | None = 50000
+    centroid: bool = True
+    deisotope: bool = True
+    dia_stats: bool | None = False
+    feature: int | None = None
+    label: str | None = None
+    centroid_algo: str | None = "lmp"
+
+    # Parameter metadata for validation and description
+    _param_metadata: dict[str, dict[str, Any]] = field(
+        default_factory=lambda: {
+            "scan": {
+                "dtype": list,
+                "description": "List of scan identifiers to retrieve",
+            },
+            "precursor_trim": {
+                "dtype": int,
+                "description": "Value used to trim the precursor m/z for MS2 spectra",
+                "min_value": -50,
+                "max_value": 50,
+            },
+            "max_peaks": {
+                "dtype": "Optional[int]",
+                "description": "Maximum number of peaks to retain in the spectrum",
+                "min_value": 1,
+                "max_value": 100000,
+            },
+            "centroid": {
+                "dtype": bool,
+                "description": "Flag indicating whether the spectrum should be centroided",
+            },
+            "deisotope": {
+                "dtype": bool,
+                "description": "Flag indicating whether deisotoping should be performed",
+            },
+            "dia_stats": {
+                "dtype": "Optional[bool]",
+                "description": "Flag for processing DIA (data-independent acquisition) statistics",
+            },
+            "feature": {
+                "dtype": "Optional[int]",
+                "description": "An optional identifier used when computing DIA statistics",
+            },
+            "label": {
+                "dtype": "Optional[str]",
+                "description": "Optional label to assign to the spectrum",
+            },
+            "centroid_algo": {
+                "dtype": "Optional[str]",
+                "description": "Algorithm to use for centroiding",
+                "allowed_values": ["lmp", "cwt", "gaussian"],
+            },
+        },
+    )
+
+    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 optional types
+        if isinstance(expected_dtype, str) and expected_dtype.startswith("Optional"):
+            if value is None:
+                return True
+            # Extract the inner type for validation
+            if "int" in expected_dtype:
+                expected_dtype = int
+            elif "str" in expected_dtype:
+                expected_dtype = str
+            elif "bool" in expected_dtype:
+                expected_dtype = bool
+
+        # Type checking
+        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
+        elif expected_dtype is bool:
+            if not isinstance(value, bool):
+                return False
+        elif expected_dtype is str:
+            if not isinstance(value, str):
+                return False
+        elif expected_dtype is list:
+            if not isinstance(value, list):
+                return False
+
+        # Range validation for numeric types
+        if expected_dtype in (int, float) and isinstance(value, (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
+
+        # Allowed values validation for strings
+        if expected_dtype is str and "allowed_values" in metadata:
+            if value not in metadata["allowed_values"]:
+                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"]
+
+            # Handle optional types
+            if isinstance(expected_dtype, str) and expected_dtype.startswith("Optional") and value is not None:
+                if "int" in expected_dtype and not isinstance(value, int):
+                    try:
+                        value = int(value)
+                    except (ValueError, TypeError):
+                        if validate:
+                            return False
+                elif "float" in expected_dtype 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