Documented in composition_adjustment.h. */

Documented in composition_adjustment.h. */

Documented in composition_adjustment.h. */

* Calculate the primal and dual residuals the optimization problem, * and their combined Euclidean norm. * * @param rnorm the Euclidean norm

* Compute a set of scores (scaled to lambda = 1) from a set of target * frequencies and a set of background frequencies. The target * frequencies n

* Compute the dual residual vector of the optimization problem. The * dual residual vector is also known as the gradient of the * Lagrangian functi

* Evaluate the nonlinear functions and derivatives associated with * the problem of generating optimal target frequencies. * * @param values

* Factor the linear system to be solved in this iteration of Newton's * method. * * @param newton_system holds the factorization * @param x

* * ListNodeFreeData(vnp) * frees whole chain of ListNodes * frees associated data pointers - BEWARE of this if these are not * a

Documented in nlm_linear_algebra.h. */

Documented in nlm_linear_algebra.h. */

Documented in nlm_linear_algebra.h. */

Documented in nlm_linear_algebra.h. */

* Create a new uninitialized ReNewtonSystem; the fields are * initialized by the FactorReNewtonSystem procedure. * ReNewtonSystemNew and FactorReNew

* Calculate the residuals of the linear constraints of the score * matrix optimization problem. * * @param rA the residual vector of the

Deallocate a SMessageOrigin structure * @param msgo structure to deallocate [in] * @return NULL */

* Compute the symmetric product A D A^T, where A is the matrix of * linear constraints from the problem of generating optimal target * frequencies

comments in blast_seg.h */

* Solve the linear system for this iteration of Newton's method, using * the matrix factored by the FactorReNewtonSystem routine. * * @param x