Reference
=========

Technical reference documentation for TanaT. This section is intended for looking up specific information about classes, methods, parameters, and return types. 

.. toctree::
   :maxdepth: 2
   :hidden:

   glossary
   metadata
   manipulation
   alignment
   criterion
   metrics
   api/index

What's in this section?
------------------------

:doc:`glossary`
   Definitions of key terms and concepts used throughout TanaT documentation.

:doc:`metadata`
   Detailed reference for TanaT's metadata system, including all update methods, 
   inspection tools, and propagation rules.

:doc:`manipulation`
   Comprehensive reference for data manipulation methods with compatibility matrices
   showing which methods work with Sequence, SequencePool, Trajectory, and TrajectoryPool.

:doc:`alignment`
   Temporal alignment and reference date (T0) management, including zeroing methods
   and temporal transformations (relative time, relative rank).

:doc:`criterion`
   Data filtering and selection criterion with detailed compatibility information
   for entity, sequence, and trajectory filtering levels.

:doc:`metrics`
   Distance metrics for entities, sequences, and trajectories, including configuration options.

:doc:`api/index`
   Complete API reference automatically generated from source code. 
   Browse by module to find all available classes, functions, and their signatures.
