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deprecate the method _load_class_info
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To refactor the following when dealing with annotations:
- running of CANOPUS to predict chemical classes
- loading chemical classes to annotate spectra and moleclar families
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CunliangGeng committed Dec 19, 2023
1 parent 83f8e39 commit ecb03e8
Showing 1 changed file with 2 additions and 3 deletions.
5 changes: 2 additions & 3 deletions src/nplinker/loader.py
Original file line number Diff line number Diff line change
@@ -1,6 +1,7 @@
import glob
import os
from pathlib import Path
from deprecated import deprecated
from nplinker.class_info.chem_classes import ChemClassPredictions
from nplinker.class_info.class_matches import ClassMatches
from nplinker.class_info.runcanopus import run_canopus
Expand Down Expand Up @@ -197,9 +198,6 @@ def load(self):
if not self._load_genomics():
return False

if not self._load_class_info():
return False

self._load_optional()

# Restrict strain list to only relevant strains (those that are present
Expand Down Expand Up @@ -519,6 +517,7 @@ def _run_bigscape(self):

self.bigscape_dir = find_bigscape_dir(self.bigscape_dir)

@deprecated(reason="To be refactored. It was used in the `self.load` method before.")
def _load_class_info(self):
"""Load class match info (based on mibig) and chemical class predictions.
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