GUI
===

Main GUI
~~~~~~~~
.. automodule:: alphastats.gui.gui
    :members:
    :undoc-members:

AlphaPeptStats GUI
~~~~~~~~~~~~~~~~~~
.. automodule:: alphastats.gui.AlphaPeptStats
    :members:
    :undoc-members:

GUI Pages
~~~~~~~~~

The GUI pages module contains Streamlit pages with spaces in filenames that cannot be directly imported as Python modules. These include:

- ``01_Home.py`` - Home page and landing interface
- ``02_Import Data.py`` - Data import interface
- ``03_Data Overview.py`` - Data exploration and quality control
- ``04_Preprocessing.py`` - Data preprocessing interface
- ``05_Analysis.py`` - Statistical analysis interface
- ``06_LLM.py`` - Large Language Model integration
- ``07_Results.py`` - Results visualization
- ``08_Upload Custom Analysis.py`` - Custom analysis upload interface

GUI Utilities
~~~~~~~~~~~~~

Analysis Helper
^^^^^^^^^^^^^^^
.. automodule:: alphastats.gui.utils.analysis_helper
    :members:
    :undoc-members:

Analysis Utilities
^^^^^^^^^^^^^^^^^^
.. automodule:: alphastats.gui.utils.analysis
    :members:
    :undoc-members:

Import Helper
^^^^^^^^^^^^^
.. automodule:: alphastats.gui.utils.import_helper
    :members:
    :undoc-members:

LLM Helper
^^^^^^^^^^
.. automodule:: alphastats.gui.utils.llm_helper
    :members:
    :undoc-members:

Options
^^^^^^^
.. automodule:: alphastats.gui.utils.options
    :members:
    :undoc-members:

Overview Helper
^^^^^^^^^^^^^^^
.. automodule:: alphastats.gui.utils.overview_helper
    :members:
    :undoc-members:

Preprocessing Helper
^^^^^^^^^^^^^^^^^^^^
.. automodule:: alphastats.gui.utils.preprocessing_helper
    :members:
    :undoc-members:

Results
^^^^^^^
.. automodule:: alphastats.gui.utils.result
    :members:
    :undoc-members:

Session Manager
^^^^^^^^^^^^^^^
.. automodule:: alphastats.gui.utils.session_manager
    :members:
    :undoc-members:

State Keys
^^^^^^^^^^
.. automodule:: alphastats.gui.utils.state_keys
    :members:
    :undoc-members:

State Utilities
^^^^^^^^^^^^^^^
.. automodule:: alphastats.gui.utils.state_utils
    :members:
    :undoc-members:

UI Helper
^^^^^^^^^
.. automodule:: alphastats.gui.utils.ui_helper
    :members:
    :undoc-members:

Upload Custom Analysis
^^^^^^^^^^^^^^^^^^^^^^
.. automodule:: alphastats.gui.utils.upload_custom_analysis
    :members:
    :undoc-members: