add alpharaw base format

alphadia/data/alpharaw.py

@@ -8,6 +8,7 @@
 # third party imports
 import numpy as np
 import pandas as pd
+from alpharaw import ms_data_base as alpharawms_data_base
 from alpharaw import mzml as alpharawmzml
 
 # TODO fix: "import resolves to its containing file"
@@ -338,6 +339,14 @@ def jitclass(self):
         )
 
 
+class AlphaRawBase(AlphaRaw, alpharawms_data_base.MSData_Base):
+    def __init__(self, raw_file_path: str, process_count: int = 10, **kwargs):
+        super().__init__(process_count=process_count)
+        self.load_hdf(raw_file_path)
+        self.process_alpharaw(**kwargs)
+        log_stats(self.rt_values, self.cycle)
+
+
 class MzML(AlphaRaw, alpharawmzml.MzMLReader):
     def __init__(self, raw_file_path: str, process_count: int = 10, **kwargs):
         super().__init__(process_count=process_count)

alphadia/workflow/base.py

@@ -194,13 +194,19 @@ def _get_dia_data_object(
             shutil.copyfile(dia_data_path, tmp_dia_data_path)
             dia_data_path = tmp_dia_data_path
 
-        if file_extension.lower() == ".d" or file_extension.lower() == ".hdf":
+        if file_extension.lower() == ".d":
             self.reporter.log_metric("raw_data_type", "bruker")
             dia_data = bruker.TimsTOFTranspose(
                 dia_data_path,
                 mmap_detector_events=self.config["general"]["mmap_detector_events"],
             )
 
+        elif file_extension.lower() == ".hdf":
+            self.reporter.log_metric("raw_data_type", "alpharaw")
+            dia_data = alpharaw.AlphaRawBase(
+                dia_data_path,
+            )
+
         elif file_extension.lower() == ".raw":
             self.reporter.log_metric("raw_data_type", "thermo")
             # check if cv selection exists