blast_options.c

ncbi源码

   hit_params->cutoff_small_gap *= (Int4)sbp->scale_factor;
}


/*
 * ===========================================================================
 *
 * $Log: blast_options.c,v $
 * Revision 1000.6  2004/06/01 18:07:31  gouriano
 * PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.111
 *
 * Revision 1.111  2004/05/26 16:04:54  papadopo
 * fix doxygen errors
 *
 * Revision 1.110  2004/05/24 17:26:21  camacho
 * Fix PC warning
 *
 * Revision 1.109  2004/05/20 16:29:30  madden
 * Make searchsp an Int8 consistent with rest of blast
 *
 * Revision 1.108  2004/05/19 14:52:02  camacho
 * 1. Added doxygen tags to enable doxygen processing of algo/blast/core
 * 2. Standardized copyright, CVS $Id string, $Log and rcsid formatting and i
 *    location
 * 3. Added use of @todo doxygen keyword
 *
 * Revision 1.107  2004/05/17 15:30:20  madden
 * Int algorithm_type replaced with enum EBlastPrelimGapExt, removed include for blast_gapalign.h
 *
 * Revision 1.106  2004/05/14 17:11:03  dondosha
 * Minor correction in setting X-dropoffs
 *
 * Revision 1.105  2004/05/14 13:14:15  camacho
 * Use correct definition for inclusion threshold
 *
 * Revision 1.104  2004/05/12 12:18:06  madden
 * Clean out PSIBlast options, add fields to ExtensionOptions to support smith-waterman and composition-based stats
 *
 * Revision 1.103  2004/05/10 14:27:23  madden
 * Correction to CalculateLinkHSPCutoffs to use gap_trigger in calculation of small cutoff
 *
 * Revision 1.102  2004/05/07 15:22:15  papadopo
 * 1. add functions to allocate and free BlastScoringParameters structures
 * 2. apply a scaling factor to all cutoffs generated in HitSavingParameters
 *    or ExtentionParameters structures
 *
 * Revision 1.101  2004/04/29 17:41:05  papadopo
 * Scale down the search space when calculating the S2 cutoff score for a translated RPS search
 *
 * Revision 1.100  2004/04/29 15:08:43  madden
 * Add BlastScoringOptionsDup
 *
 * Revision 1.99  2004/04/23 14:02:25  papadopo
 * ignore validation of LookupTableOptions if performing an RPS search
 *
 * Revision 1.98  2004/04/22 22:18:03  dondosha
 * Set lookup table type correctly in BLAST_FillLookupTableOptions - needed for C driver only
 *
 * Revision 1.97  2004/04/21 17:00:59  madden
 * Removed set but not read variable
 *
 * Revision 1.96  2004/04/19 12:58:44  madden
 * Changed BLAST_KarlinBlk to Blast_KarlinBlk to avoid conflict with blastkar.h structure, renamed some functions to start with Blast_Karlin, made Blast_KarlinBlkDestruct public
 *
 * Revision 1.95  2004/04/16 14:17:06  papadopo
 * add use of RPS-specific defines, remove RPS argument to FillLookupTableOptions
 *
 * Revision 1.94  2004/04/07 03:06:16  camacho
 * Added blast_encoding.[hc], refactoring blast_stat.[hc]
 *
 * Revision 1.93  2004/03/26 20:46:00  dondosha
 * Made gap_trigger parameter an integer, as in the old code
 *
 * Revision 1.92  2004/03/22 20:11:37  dondosha
 * Do not allow small gaps cutoff to be less than gap trigger
 *
 * Revision 1.91  2004/03/17 15:19:10  camacho
 * Add missing casts
 *
 * Revision 1.90  2004/03/11 23:58:10  dondosha
 * Set cutoff_score to 0 before calling BLAST_Cutoffs, so it knows what to calculate
 *
 * Revision 1.89  2004/03/11 20:41:49  camacho
 * Remove dead code
 *
 * Revision 1.88  2004/03/10 17:33:10  papadopo
 * Make a separate lookup table type for RPS blast
 *
 * Revision 1.87  2004/03/09 22:37:26  dondosha
 * Added const qualifiers to parameter arguments wherever relevant
 *
 * Revision 1.86  2004/03/09 18:46:24  dondosha
 * Corrected how cutoffs are calculated
 *
 * Revision 1.85  2004/03/04 21:07:48  papadopo
 * add RPS BLAST functionality
 *
 * Revision 1.84  2004/02/27 15:56:33  papadopo
 * Mike Gertz' modifications to unify handling of gapped Karlin blocks for protein and nucleotide searches. Also modified BLAST_MainSetUp to allocate gapped Karlin blocks last
 *
 * Revision 1.83  2004/02/24 17:57:14  dondosha
 * Added function to combine all options validation functions for the C engine
 *
 * Revision 1.82  2004/02/19 21:16:48  dondosha
 * Use enum type for severity argument in Blast_MessageWrite
 *
 * Revision 1.81  2004/02/17 22:10:30  dondosha
 * Set preliminary hitlist size in options initialization
 *
 * Revision 1.80  2004/02/07 15:48:30  ucko
 * PSIBlastOptionsNew: rearrange slightly so that declarations come first.
 *
 * Revision 1.79  2004/02/06 22:49:30  dondosha
 * Check for NULL pointer in PSIBlastOptionsNew
 *
 * Revision 1.78  2004/02/03 18:33:39  dondosha
 * Correction to previous change: word size can be 11 if discontiguous words
 *
 * Revision 1.77  2004/02/03 16:17:33  dondosha
 * Require word size to be >= 12 with megablast lookup table
 *
 * Revision 1.76  2004/02/02 18:49:32  dondosha
 * Fixes for minor compiler warnings
 *
 * Revision 1.75  2003/12/31 20:04:47  dondosha
 * Round best stride to a number divisible by 4 for all values except 6 and 7
 *
 * Revision 1.74  2003/12/31 16:04:37  coulouri
 * use -1 to disable protein neighboring words
 *
 * Revision 1.73  2003/12/08 16:03:05  coulouri
 * Propagate protein neighboring threshold even if it is zero
 *
 * Revision 1.72  2003/11/24 23:18:32  dondosha
 * Added gap_decay_rate argument to BLAST_Cutoffs; removed BLAST_Cutoffs_simple
 *
 * Revision 1.71  2003/11/12 18:17:46  dondosha
 * Correction in calculating scanning stride
 *
 * Revision 1.70  2003/11/04 23:22:47  dondosha
 * Do not calculate hit saving cutoff score for PHI BLAST
 *
 * Revision 1.69  2003/10/30 19:34:01  dondosha
 * Removed gapped_calculation from BlastHitSavingOptions structure
 *
 * Revision 1.68  2003/10/24 20:55:10  camacho
 * Rename GetDefaultStride
 *
 * Revision 1.67  2003/10/22 16:44:33  dondosha
 * Added function to calculate default stride value for AG method
 *
 * Revision 1.66  2003/10/21 22:15:34  camacho
 * Rearranging of C options structures, fix seed extension method
 *
 * Revision 1.65  2003/10/17 18:20:20  dondosha
 * Use separate variables for different initial word extension options
 *
 * Revision 1.64  2003/10/15 16:59:43  coulouri
 * type correctness fixes
 *
 * Revision 1.63  2003/10/07 17:26:11  dondosha
 * Lower case mask moved from options to the sequence block
 *
 * Revision 1.62  2003/10/02 22:08:34  dondosha
 * Corrections for one-strand translated searches
 *
 * Revision 1.61  2003/10/01 22:36:52  dondosha
 * Correction of setting of e2 in revision 1.57 was wrong
 *
 * Revision 1.60  2003/09/24 19:28:20  dondosha
 * Correction in setting extend word method: unset options that are set by default but overridden
 *
 * Revision 1.59  2003/09/12 17:26:01  dondosha
 * Added check that gap extension option cannot be 0 when gap open is not 0
 *
 * Revision 1.58  2003/09/10 19:48:08  dondosha
 * Removed dependency on mb_lookup.h
 *
 * Revision 1.57  2003/09/09 22:12:02  dondosha
 * Minor correction for ungapped cutoff calculation; added freeing of PHI pattern
 *
 * Revision 1.56  2003/09/08 12:55:57  madden
 * Allow use of PSSM to construct lookup table
 *
 * Revision 1.55  2003/08/27 15:05:37  camacho
 * Use symbolic name for alphabet sizes
 *
 * Revision 1.54  2003/08/26 21:53:33  madden
 * Protein alphabet is 26 chars, not 25
 *
 * Revision 1.53  2003/08/11 15:01:59  dondosha
 * Added algo/blast/core to all #included headers
 *
 * Revision 1.52  2003/08/01 17:26:19  dondosha
 * Use renamed versions of functions from local blastkar.h
 *
 * Revision 1.51  2003/07/31 17:45:17  dondosha
 * Made use of const qualifier consistent throughout the library
 *
 * Revision 1.50  2003/07/31 14:31:41  camacho
 * Replaced Char for char
 *
 * Revision 1.49  2003/07/31 14:19:28  camacho
 * Replaced FloatHi for double
 *
 * Revision 1.48  2003/07/31 00:32:37  camacho
 * Eliminated Ptr notation
 *
 * Revision 1.47  2003/07/30 22:06:25  dondosha
 * Convert matrix name to upper case when filling scoring options
 *
 * Revision 1.46  2003/07/30 19:39:14  camacho
 * Remove PNTRs
 *
 * Revision 1.45  2003/07/30 18:58:10  dondosha
 * Removed unused member matrixname from lookup table options
 *
 * Revision 1.44  2003/07/30 17:15:00  dondosha
 * Minor fixes for very strict compiler warnings
 *
 * Revision 1.43  2003/07/30 16:32:02  madden
 * Use ansi functions when possible
 *
 * Revision 1.42  2003/07/29 14:42:31  coulouri
 * use strdup() instead of StringSave()
 *
 * Revision 1.41  2003/07/28 19:04:15  camacho
 * Replaced all MemNews for calloc
 *
 * Revision 1.40  2003/07/25 21:12:28  coulouri
 * remove constructions of the form "return sfree();" and "a=sfree(a);"
 *
 * Revision 1.39  2003/07/25 17:25:43  coulouri
 * in progres:
 *  * use malloc/calloc/realloc instead of Malloc/Calloc/Realloc
 *  * add sfree() macro and __sfree() helper function to util.[ch]
 *  * use sfree() instead of MemFree()
 *
 * Revision 1.38  2003/07/23 17:31:10  camacho
 * BlastDatabaseParameters struct is deprecated
 *
 * Revision 1.37  2003/07/23 16:42:01  dondosha
 * Formatting options moved from blast_options.c to blast_format.c
 *
 * Revision 1.36  2003/07/22 20:26:16  dondosha
 * Initialize BlastDatabaseParameters structure outside engine
 *
 * Revision 1.35  2003/07/22 15:32:55  dondosha
 * Removed dependence on readdb API
 *
 * Revision 1.34  2003/07/21 20:31:47  dondosha
 * Added BlastDatabaseParameters structure with genetic code string
 *
 * Revision 1.33  2003/06/26 21:38:05  dondosha
 * Program number is removed from options structures, and passed explicitly as a parameter to functions that need it
 *
 * Revision 1.32  2003/06/26 20:24:06  camacho
 * Do not free options structure in BlastExtensionParametersFree
 *
 * Revision 1.31  2003/06/23 21:49:11  dondosha
 * Possibility of linking HSPs for tblastn activated
 *
 * Revision 1.30  2003/06/20 21:40:21  dondosha
 * Added parameters for linking HSPs
 *
 * Revision 1.29  2003/06/20 15:20:21  dondosha
 * Memory leak fixes
 *
 * Revision 1.28  2003/06/18 12:21:01  camacho
 * Added proper return value
 *
 * Revision 1.27  2003/06/17 20:42:43  camacho
 * Moved comments to header file, fixed includes
 *
 * Revision 1.26  2003/06/11 16:14:53  dondosha
 * Added initialization of PSI-BLAST and database options
 *
 * Revision 1.25  2003/06/09 20:13:17  dondosha
 * Minor type casting compiler warnings fixes
 *
 * Revision 1.24  2003/06/06 17:02:30  dondosha
 * Typo fix
 *
 * Revision 1.23  2003/06/04 20:16:51  coulouri
 * make prototypes and definitions agree
 *
 * Revision 1.22  2003/06/03 15:50:39  coulouri
 * correct function pointer argument
 *
 * Revision 1.21  2003/05/30 15:52:11  coulouri
 * various lint-induced cleanups
 *
 * Revision 1.20  2003/05/21 22:31:53  dondosha
 * Added forcing of ungapped search for tblastx to option validation
 *
 * Revision 1.19  2003/05/18 21:57:37  camacho
 * Use Uint1 for program name whenever possible
 *
 * Revision 1.18  2003/05/15 22:01:22  coulouri
 * add rcsid string to sources
 *
 * Revision 1.17  2003/05/13 20:41:48  dondosha
 * Correction in assigning of number of db sequences for 2 sequence case
 *
 * Revision 1.16  2003/05/13 15:11:34  dondosha
 * Changed some char * arguments to const char *
 *
 * Revision 1.15  2003/05/07 17:44:31  dondosha
 * Assign ungapped xdropoff default correctly for protein programs
 *
 * Revision 1.14  2003/05/06 20:29:57  dondosha
 * Fix in filling effective length options
 *
 * Revision 1.13  2003/05/06 14:34:51  dondosha
 * Fix in comment
 *
 * Revision 1.12  2003/05/01 16:56:30  dondosha
 * Fixed strict compiler warnings
 *
 * Revision 1.11  2003/05/01 15:33:39  dondosha
 * Reorganized the setup of BLAST search
 *
 * Revision 1.10  2003/04/24 14:27:35  dondosha
 * Correction for latest changes
 *
 * Revision 1.9  2003/04/23 20:04:49  dondosha
 * Added a function BLAST_InitAllDefaultOptions to initialize all various options structures with only default values
 *
 * Revision 1.8  2003/04/17 21:14:41  dondosha
 * Added cutoff score hit parameters that is calculated from e-value
 *
 * Revision 1.7  2003/04/16 22:25:37  dondosha
 * Correction to previous change
 *
 * Revision 1.6  2003/04/16 22:20:24  dondosha
 * Correction in calculation of cutoff score for ungapped extensions
 *
 * Revision 1.5  2003/04/11 22:35:48  dondosha
 * Minor corrections for blastn
 *
 * Revision 1.4  2003/04/03 22:57:50  dondosha
 * Uninitialized variable fix
 *
 * Revision 1.3  2003/04/02 17:20:41  dondosha
 * Added calculation of ungapped cutoff score in correct place
 *
 * Revision 1.2  2003/04/01 17:42:33  dondosha
 * Added arguments to BlastExtensionParametersNew
 *
 * Revision 1.1  2003/03/31 18:22:30  camacho
 * Moved from parent directory
 *
 * Revision 1.30  2003/03/28 23:12:34  dondosha
 * Added program argument to BlastFormattingOptionsNew
 *
 * Revision 1.29  2003/03/27 20:54:19  dondosha
 * Moved ungapped cutoff from hit options to word options
 *
 * Revision 1.28  2003/03/25 16:30:25  dondosha
 * Strict compiler warning fixes
 *
 * Revision 1.27  2003/03/24 20:39:17  dondosha
 * Added BlastExtensionParameters structure to hold raw gapped X-dropoff values
 *
 * Revision 1.26  2003/03/19 19:52:42  dondosha
 * 1. Added strand option argument to BlastQuerySetUpOptionsNew
 * 2. Added check of discontiguous template parameters in LookupTableOptionsValidate
 *
 * Revision 1.25  2003/03/14 19:08:53  dondosha
 * Added arguments to various OptionsNew functions, so all initialization can be done inside
 *
 * Revision 1.24  2003/03/12 17:03:41  dondosha
 * Set believe_query in formatting options to FALSE by default
 *
 * Revision 1.23  2003/03/11 20:40:32  dondosha
 * Correction in assigning gap_x_dropoff_final
 *
 * Revision 1.22  2003/03/10 16:44:42  dondosha
 * Added functions for initialization and freeing of formatting options structure
 *
 * Revision 1.21  2003/03/07 20:41:08  dondosha
 * Small corrections in option initialization functions
 *
 * Revision 1.20  2003/03/06 19:25:52  madden
 * Include blast_util.h
 *
 * Revision 1.19  2003/03/05 21:19:09  coulouri
 * set NA_LOOKUP_TABLE flag
 *
 * Revision 1.18  2003/03/05 20:58:50  dondosha
 * Corrections for handling effective search space for multiple queries
 *
 * Revision 1.17  2003/03/05 15:36:34  madden
 * Moved BlastNumber2Program and BlastProgram2Number from blast_options to blast_util
 *
 * Revision 1.16  2003/03/03 14:43:21  madden
 * Use BlastKarlinkGapBlkFill, PrintMatrixMessage, and PrintAllowedValuesMessage
 *
 * Revision 1.15  2003/02/26 15:42:50  madden
 * const charPtr becomes const char *, add BlastExtensionOptionsValidate
 *
 * Revision 1.14  2003/02/14 16:30:19  dondosha
 * Get rid of a compiler warning for type mismatch
 *
 * Revision 1.13  2003/02/13 21:42:25  madden
 * Added validation functions
 *
 * Revision 1.12  2003/02/04 13:14:36  dondosha
 * Changed the macro definitions for 
 *
 * Revision 1.11  2003/01/31 17:00:32  dondosha
 * Do not set the scan step in LookupTableOptionsNew
 *
 * Revision 1.10  2003/01/28 15:13:25  madden
 * Added functions and structures for parameters
 *
 * Revision 1.9  2003/01/22 20:49:31  dondosha
 * Set decline_align for blastn too
 *
 * Revision 1.8  2003/01/22 15:09:55  dondosha
 * Correction for default penalty assignment
 *
 * Revision 1.7  2003/01/17 22:10:45  madden
 * Added functions for BlastExtensionOptions, BlastInitialWordOptions as well as defines for default values
 *
 * Revision 1.6  2003/01/10 18:36:40  madden
 * Change call to BlastEffectiveLengthsOptionsNew
 *
 * Revision 1.5  2003/01/02 17:09:35  dondosha
 * Fill alphabet size when creating lookup table options structure
 *
 * Revision 1.4  2002/12/24 14:49:00  madden
 * Set defaults for LookupTableOptions for protein-protein searches
 *
 * Revision 1.3  2002/12/04 13:38:21  madden
 * Add function LookupTableOptionsNew
 *
 * Revision 1.2  2002/10/17 15:45:17  madden
 * Make BLOSUM62 default
 *
 * Revision 1.1  2002/10/07 21:05:12  madden
 * Sets default option values
 *
 * ===========================================================================
 */