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/* $Id: optimize_target_freq.h,v 1.6 2005/12/01 13:54:04 gertz Exp $
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/* $Id: optimize_target_freq.h,v 1.7 2005/12/19 15:38:01 gertz Exp $
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* ===========================================================================
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* PUBLIC DOMAIN NOTICE
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* @file optimize_target_freq.h
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* Routines for finding an optimal set of target frequencies for the
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* purpose of generating a compositionally adjusted score matrix.
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* @author E. Michael Gertz
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* Exports for optimized_target_freq.c
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#ifndef __OPTIMIZE_TARGET_FREQ__
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* Find an optimal set of target frequencies for the purpose of
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* generating a compositionally adjusted score matrix.
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* @param x On exit, the optimal set of target frequencies,
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* interpreted as a two dimensional array in
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* row-major order. x need not be initialized on
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* entry; any initial value will be ignored.
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* @param alphsize the size of the alphabet for this optimization
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* @param *iterations the total number of iterations used in finding
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* the target frequencies
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* @param q a set of target frequencies from a standard
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* @param row_sums the required row sums for the target frequencies;
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* the composition of one of the sequences being compared.
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* @param col_sums the required column sums for the target frequencies;
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* the composition of the other sequence being compared.
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* @param constrain_rel_entropy if true, constrain the relative
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* entropy of the optimal target
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* frequencies to equal
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* @param relative_entropy if constrain_rel_entropy is true, then this
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* is the required relative entropy for the
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* optimal target frequencies. Otherwise,
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* this argument is ignored.
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* @param maxits the maximum number of iterations permitted for the
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* optimization algorithm; a good value is 2000.
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* @param tol the solution tolerance; the residuals of the optimization
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* program must have Euclidean norm <= tol for the
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* algorithm to terminate.
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* @returns if an optimal set of target frequencies is
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* found, then 0, if the iteration failed to
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* converge, then 1, if there was some error, then -1.
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Blast_OptimizeTargetFrequencies(double x[],
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algo/blast/composition_adjustment/optimize_target_freq.h
