small docs updates

uio-bmi · May 28, 2024 · 114499f · 114499f
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commit 114499f
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Showing 2 changed files with 5 additions and 24 deletions.
diff --git a/docs/source/developer_docs/example_code/SillyEncoder.py b/docs/source/developer_docs/example_code/SillyEncoder.py
@@ -84,8 +84,10 @@ def encode(self, dataset, params: EncoderParams) -> Dataset:
                                                                    # make sure to use the general encoder name here
                                                                    # (e.g., OneHotEncoder.__name__, not OneHotSequenceEncoder.__name__)
 
-        return self._construct_encoded_dataset(dataset, encoded_data)
+        encoded_dataset = dataset.clone()
+        encoded_dataset.encoded_data = encoded_data
 
+        return encoded_dataset
 
     def _get_encoded_examples(self, dataset: Dataset) -> np.array:
         if isinstance(dataset, SequenceDataset):
@@ -155,25 +157,4 @@ def _get_encoded_repertoires(self, dataset: RepertoireDataset) -> np.array:
             random_encoding = np.random.rand(self.embedding_len)
             encoded_repertoires.append(random_encoding)
 
-        return np.array(encoded_repertoires)
-
-    def _construct_encoded_dataset(self, dataset, encoded_data) -> Dataset:
-        if isinstance(dataset, SequenceDataset):
-            return SequenceDataset(filenames=dataset.get_filenames(),
-                                   encoded_data=encoded_data,
-                                   labels=dataset.labels,
-                                   file_size=dataset.file_size,
-                                   dataset_file=dataset.dataset_file)
-        elif isinstance(dataset, ReceptorDataset):
-            return ReceptorDataset(filenames=dataset.get_filenames(),
-                                   encoded_data=encoded_data,
-                                   labels=dataset.labels,
-                                   file_size=dataset.file_size,
-                                   dataset_file=dataset.dataset_file)
-        elif isinstance(dataset, RepertoireDataset):
-            return RepertoireDataset(repertoires=dataset.repertoires,
-                                     encoded_data=encoded_data,
-                                     labels=dataset.labels,
-                                     metadata_file=dataset.metadata_file)
-
-
+        return np.array(encoded_repertoires)
diff --git a/docs/source/quickstart.rst b/docs/source/quickstart.rst
@@ -35,7 +35,7 @@ Lastly, this quickstart tutorial can be used when you have immuneML :ref:`instal
 
 For simulation purposes, you can try LIgO quickstart:
 
-- :ref:`Simulation quickstart`
+- :ref:`LIgO simulation quickstart`