OpenSWATH - GUI Models ============ The main models used by the GUI are the :class:`.PeptideTree` and the :class:`MSData.DataModel <.DataModel>` models. Internally, :class:`.PeptideTree` uses :class:`.ChromatogramTransition` to store access to single rows in the tree data structure while :class:`MSData.DataModel <.DataModel>` uses :class:`.SwathRunCollection` to keep track of multiple SWATH-MS runs. :mod:`MSData Data model` Module ------------------- Contains classes that provide access to the raw data MSData ^^^^^^ .. autoclass:: openswathgui.models.MSData.DataModel :members: :undoc-members: :show-inheritance: .. PrecursorModel ^^^^^^^^^^^^^^ .. autoclass:: openswathgui.models.MSData.PrecursorModel :members: :undoc-members: :show-inheritance: :mod:`TreeModels` Module ------------------- Contains classes that provide access to the hierarhical tree container protein, precursor, peptide and transition level data. While :class:`.TreeNode` and :class:`.TreeModel` are generic models for trees and nodes, the derived classes :class:`.PeptideTreeNode` and :class:`.PeptideTree` are implementations specific to TAPIR. TreeNode ^^^^^^^^^^^^^^ .. autoclass:: openswathgui.models.TreeModels.TreeNode :undoc-members: :show-inheritance: TreeModel ^^^^^^^^^^^^^^ .. autoclass:: openswathgui.models.TreeModels.TreeModel :undoc-members: :show-inheritance: PeptideTreeNode ^^^^^^^^^^^^^^ .. autoclass:: openswathgui.models.PeptideTree.PeptideTreeNode :members: :show-inheritance: PeptideTree ^^^^^^^^^^^^^^ .. autoclass:: openswathgui.models.PeptideTree.PeptideTree :members: :undoc-members: :show-inheritance: :mod:`SWATH MS Run` Module ------------------- Raw chromatographic data is handled using the :class:`.SwathRunCollection` class which can either hold references to mzML or to SqMass data. SwathRunCollection ^^^^^^^^^^^^^^^^^^ .. autoclass:: openswathgui.models.SwathRunCollection.SwathRunCollection :members: :undoc-members: :show-inheritance: SqMass ^^^^^^ .. autoclass:: openswathgui.models.SqlSwathRun.SqlSwathRun :members: :undoc-members: :show-inheritance: .. autoclass:: openswathgui.models.SqlDataAccess.SqlDataAccess :members: :undoc-members: :show-inheritance: MzML File ^^^^^^^^^ .. autoclass:: openswathgui.models.SwathRun.SwathRun :members: :undoc-members: :show-inheritance: .. autoclass:: openswathgui.models.SingleChromatogramFile.SingleChromatogramFile :members: :undoc-members: :show-inheritance: :mod:`ChromatogramTransition` Module ------------------- ChromatogramTransition ^^^^^^^^^^^^^^^^^^^^^^ .. autoclass:: openswathgui.models.ChromatogramTransition.ChromatogramTransition :members: :undoc-members: :show-inheritance: