added has_retention_indices & has_retention_times functions.

RIAssigner/data/Data.py

@@ -118,6 +118,51 @@ def retention_indices(self, value: Iterable[RetentionIndexType]):
         """
         ...
 
+    @property
+    @abstractmethod
+    def has_retention_indices(self) -> Iterable[RetentionIndexType]:
+        """Getter for `has_retention_indices` property."""
+        ...
+
+    def check_ri_values(self) -> bool:
+        """
+        Check if all retention indices in the spectra exist.
+
+        This method iterates over the retention indices in the spectra. If it encounters a value that is None,
+        it immediately returns False. If it iterates over all retention indices without finding a None value,
+        it returns True.
+
+        Returns:
+            bool: True if all retention indices exist, False otherwise.
+        """
+        for value in self.has_retention_indices:
+            if value is None:
+                return False
+        return True
+
+    @property
+    @abstractmethod
+    def has_retention_times(self) -> Iterable[RetentionTimeType]:
+        """Getter for `has_retention_times` property."""
+        ...
+
+    def check_rt_values(self) -> bool:
+        """
+        Check if all retention times in the spectra exist.
+
+        This method iterates over the retention times in the spectra. If it encounters a value that is None,
+        it immediately returns False. If it iterates over all retention times without finding a None value,
+        it returns True.
+
+        Returns:
+            bool: True if all retention times exist, False otherwise.
+        """
+        for value in self.has_retention_times:
+            if value is None:
+                return False
+        return True
+
+
     @property
     @abstractmethod
     def comment(self) -> Iterable[CommentFieldType]:

RIAssigner/data/MatchMSData.py

@@ -123,6 +123,26 @@ def comment(self) -> Iterable[Data.CommentFieldType]:
         content = [spectrum.get(self.comment_keys, default=None) for spectrum in self._spectra]
         return content
 
+    @property
+    def has_retention_indices(self) -> Iterable[Data.RetentionIndexType]:
+        """ Check if retention indices exist in spectra."""
+        for spectrum in self._spectra:
+            ri = spectrum.get(self._ri_key, default=None)
+            if ri is None:
+                raise ValueError("Retention index does not exist in spectrum")
+        return self._spectra
+
+    @property
+    def has_retention_times(self) -> Iterable[Data.RetentionTimeType]:
+        """ Check if retention times exist in spectra."""
+        for spectrum in self._spectra:
+            ri = spectrum.get(self._rt_key, default=None)
+            if ri is None:
+                raise ValueError("Retention time does not exist in spectrum")
+        return self._spectra
+
+
+
 def safe_read_key(spectrum: Spectrum, key: str) -> Optional[float]:
     """ Read key from spectrum and convert to float or return 'None'.
     Tries to read the given key from the spectrum metadata and convert it to a float.

RIAssigner/data/PandasData.py

@@ -13,6 +13,7 @@ class PandasData(Data):
     def __init__(self, filename: str, filetype: str, rt_unit: str):
         super().__init__(filename, filetype, rt_unit)
         self._read()
+        self._rt_key = 'rt'
 
     def _read(self):
         """ Load content from file into PandasData object. """
@@ -126,5 +127,16 @@ def comment(self) -> Iterable[Data.CommentFieldType]:
         """ Get comments."""
         self._comment_keys = "comment"
         content = self._data[self._comment_keys].tolist()
-        return content
-
+        return content   
+
+    @property
+    def has_retention_indices(self) -> Iterable[Data.RetentionIndexType]:
+        pass
+
+    @property
+    def has_retention_times(self) -> Iterable[Data.RetentionTimeType]:
+        """ Check if retention times exist in data."""
+        rt = self._data[self._rt_key].tolist()
+        if rt is None:
+            raise ValueError("Retention time does not exist in data")
+        return self._data