straindesign.efmtool_cmp_interface
==================================

.. py:module:: straindesign.efmtool_cmp_interface

.. autoapi-nested-parse::

   EFMtool compression interface for straindesign.

   This module provides compression utilities for metabolic networks.
   By default, the pure Python 'sparse_rref' compression backend is used.
   The Java EFMTool backend is available via compression_backend='efmtool_rref' (requires jpype1).

   For the documentation of the compression API provided by StrainDesign,
   refer to straindesign.compression.compress_model.





Module Contents
---------------

.. py:function:: basic_columns_rat(mx, tolerance=0)

   Find basic columns using exact rational arithmetic (FLINT or sympy).


.. py:function:: basic_columns_rat_java(mx, tolerance=0)

   Find basic columns using Java Gaussian elimination.

   Legacy implementation using jpype and Java efmtool.
   Requires jpype1 and sympy to be installed.

   :param mx: Matrix (numpy array or Java matrix)
   :param tolerance: Tolerance (unused in exact arithmetic)

   :returns: Array of indices of basic columns


.. py:function:: compress_model_java(model)

   Legacy Java compression using jpype (requires jpype and sympy).

   :param model: COBRA model (will be modified in place)

   :returns: Reaction map from compressed to original reactions with scaling factors
   :rtype: dict


.. py:function:: jBigFraction2sympyRat(val)

   Convert Java BigFraction to sympy Rational (requires Java init).


.. py:function:: jBigIntegerPair2sympyRat(numer, denom)

   Convert Java BigInteger pair to sympy Rational (requires sympy).


.. py:function:: jpypeArrayOfArrays2numpy_mat(jmat)

   Convert jpype array of arrays to numpy matrix.


.. py:function:: numpy_mat2jpypeArrayOfArrays(npmat)

   Convert numpy matrix to jpype array of arrays (requires Java init).


.. py:function:: sympyRat2jBigIntegerPair(val)

   Convert Fraction or sympy Rational to Java BigInteger pair (requires Java init).