Update documents.

ms_entropy/entropy_search/flash_entropy_search.py

@@ -19,6 +19,7 @@ def __init__(
     ):
         """
         Initialize the EntropySearch class.
+        
         :param max_ms2_tolerance_in_da:  The maximum MS2 tolerance in Da.
         :param mz_index_step:   The step size for the m/z index.
         :param low_memory:  The memory usage mode, can be 0, 1, or 2. 0 means normal mode, 1 means low memory mode, and 2 means medium memory mode.

ms_entropy/entropy_search/flash_entropy_search_core.py

@@ -18,6 +18,7 @@ def __init__(
     ) -> None:
         """
         Initialize the EntropySearch class.
+    
         :param path_array: The path array of the index files.
         :param max_ms2_tolerance_in_da: The maximum MS2 tolerance used when searching the MS/MS spectra, in Dalton. Default is 0.024.
         :param mz_index_step:   The step size of the m/z index, in Dalton. Default is 0.0001.

ms_entropy/entropy_search/flash_entropy_search_core_low_memory.py

@@ -7,6 +7,17 @@
 
 class FlashEntropySearchCoreLowMemory(FlashEntropySearchCore):
     def __init__(self, path_data, max_ms2_tolerance_in_da=0.024, mz_index_step=0.0001, intensity_weight="entropy") -> None:
+        """
+        Initialize the EntropySearch class.
+        This class use file.read function to read the data from the file, which is suitable for very low memory usage.
+        
+        :param path_data:   The path to save the index data.
+        :param max_ms2_tolerance_in_da:  The maximum MS2 tolerance in Da.
+        :param mz_index_step:   The step size for the m/z index.
+        :param intensity_weight:    The weight for the intensity in the entropy calculation, can be "entropy" or None. Default is "entropy".
+            - None: The intensity will not be weighted, then the unweighted similarity will be calculated.
+            - "entropy": The intensity will be weighted by the entropy, then the entropy similarity will be calculated.
+        """
         super().__init__(max_ms2_tolerance_in_da=max_ms2_tolerance_in_da, mz_index_step=mz_index_step, intensity_weight=intensity_weight)
         self.path_data = Path(str(path_data))
         self.path_data.mkdir(parents=True, exist_ok=True)

ms_entropy/entropy_search/flash_entropy_search_core_medium_memory.py

@@ -7,6 +7,17 @@
 
 class FlashEntropySearchCoreMediumMemory(FlashEntropySearchCore):
     def __init__(self, path_data, max_ms2_tolerance_in_da=0.024, mz_index_step=0.0001, intensity_weight="entropy") -> None:
+        """
+        Initialize the EntropySearch class.
+        This class is use memmap function to read data from the disk, which is suitable for most of the cases, unless the data is super large.
+        
+        :param path_data:   The path to save the index data.
+        :param max_ms2_tolerance_in_da:  The maximum MS2 tolerance in Da.
+        :param mz_index_step:   The step size for the m/z index.
+        :param intensity_weight:    The weight for the intensity in the entropy calculation, can be "entropy" or None. Default is "entropy".
+            - None: The intensity will not be weighted, then the unweighted similarity will be calculated.
+            - "entropy": The intensity will be weighted by the entropy, then the entropy similarity will be calculated.
+        """
         super().__init__(max_ms2_tolerance_in_da=max_ms2_tolerance_in_da, mz_index_step=mz_index_step, intensity_weight=intensity_weight)
         self.path_data = Path(str(path_data))
         self.path_data.mkdir(parents=True, exist_ok=True)