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/* $Id: unified_pvalues.h,v 1.1 2006/05/03 14:06:10 gertz Exp $
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* ===========================================================================
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* National Center for Biotechnology Information
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* This software/database is a "United States Government Work" under the
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* terms of the United States Copyright Act. It was written as part of
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* the author's official duties as a United States Government employee and
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* thus cannot be copyrighted. This software/database is freely available
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* to the public for use. The National Library of Medicine and the U.S.
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* Government have not placed any restriction on its use or reproduction.
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* Although all reasonable efforts have been taken to ensure the accuracy
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* and reliability of the software and data, the NLM and the U.S.
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* Government do not and cannot warrant the performance or results that
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* may be obtained by using this software or data. The NLM and the U.S.
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* Government disclaim all warranties, express or implied, including
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* warranties of performance, merchantability or fitness for any particular
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* Please cite the author in any work or product based on this material.
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* ==========================================================================*/
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* @file unified_pvalues.h
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* Headers for computing a "composition" p-value of a match, and for
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* computing a unified p-value combining the customary alignment
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* p-value and the new composition p-value
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* @author Yi-Kuo Yu, Alejandro Schaffer, Mike Gertz
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#ifndef __UNIFIED_PVALUES__
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#define __UNIFIED_PVALUES__
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#include <algo/blast/core/blast_export.h>
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/** the smallest value of lambda in the table of lambda's empirical
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* distribution function. */
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#define COMPO_MIN_LAMBDA 0.034
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* Conditionally compute a compositional p-value.
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* @param length1 length of the first sequence
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* @param length2 length of the second sequence
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* @param lambda statistical parameter lambda estimated for this pair
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* @param function_index index of test to decide whether to report
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* a composition p_value.
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* @return the p-value, or -1 if the p-value should not be used.
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double Blast_CompositionPvalue(int length1,
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* This function implements the method of Fisher, R. C. Elston (1991)
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* Biometrical J. 33:339-345 and T. L. Bailey and M. Gribskov (1998)
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* Bioinformatics 14:48-54. to combine to p-values into a unified
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* p-value. The input p-values are p_comp and p_alignment. The value
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* returned, call it p_return, is the area in the unit square under
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* the curve y = p_comp*p_align.
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* @param p_comp composition p-value
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* @param p_alignment alignment p-value
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double Blast_Overall_P_Value(double p_comp,
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algo/blast/composition_adjustment/unified_pvalues.h
