1 /* $Id: compo_mode_condition.h,v 1.8 2010/03/26 14:54:33 kazimird Exp $ 2 * =========================================================================== 3 * 4 * PUBLIC DOMAIN NOTICE 5 * National Center for Biotechnology Information 6 * 7 * This software/database is a "United States Government Work" under the 8 * terms of the United States Copyright Act. It was written as part of 9 * the author's official duties as a United States Government employee and 10 * thus cannot be copyrighted. This software/database is freely available 11 * to the public for use. The National Library of Medicine and the U.S. 12 * Government have not placed any restriction on its use or reproduction. 13 * 14 * Although all reasonable efforts have been taken to ensure the accuracy 15 * and reliability of the software and data, the NLM and the U.S. 16 * Government do not and cannot warrant the performance or results that 17 * may be obtained by using this software or data. The NLM and the U.S. 18 * Government disclaim all warranties, express or implied, including 19 * warranties of performance, merchantability or fitness for any particular 20 * purpose. 21 * 22 * Please cite the author in any work or product based on this material. 23 * 24 * ===========================================================================*/ 25 /** 26 * @file compo_mode_condition.h 27 * Declarations of functions used to choose the mode for 28 * composition-based statistics. 29 * 30 * @author Alejandro Schaffer, Yi-Kuo Yu 31 */ 32 33 #ifndef __COMPO_MODE_CONDITION__ 34 #define __COMPO_MODE_CONDITION__ 35 36 #include <algo/blast/core/blast_export.h> 37 #include <algo/blast/composition_adjustment/composition_constants.h> 38 39 #ifdef __cplusplus 40 extern "C" { 41 #endif 42 43 44 /** 45 * Choose how the relative entropy should be constrained based on 46 * properties of the two sequences to be aligned. 47 * 48 * @param length1 length of the first sequence 49 * @param length2 length of the second sequence 50 * @param probArray1 arrays of probabilities for the first sequence, in 51 * a 20 letter amino-acid alphabet 52 * @param probArray2 arrays of probabilities for the other sequence 53 * @param matrixName name of the scoring matrix 54 * @param composition_adjust_mode requested mode of composition adjustment 55 */ 56 NCBI_XBLAST_EXPORT 57 EMatrixAdjustRule 58 Blast_ChooseMatrixAdjustRule(int length1, int length2, 59 const double * probArray1, 60 const double * probArray2, 61 const char * matrixName, 62 ECompoAdjustModes composition_adjust_mode); 63 64 #ifdef __cplusplus 65 } 66 #endif 67 68 #endif 69