NCBI C Toolkit Cross Reference

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  /*****************************************************************************
  
  File name: blfmtutl.h
  
  Author: Tom Madden
  
  Contents: prototypes and defines for Blast formatting utilities
  
  ******************************************************************************/
  
  /* $Revision: 1.6 $ 
  * $Log: blfmtutl.h,v $
  * Revision 1.6  2006/04/26 12:42:36  madden
  * BlastSetUserErrorString and BlastDeleteUserErrorString moved from blastool.c to blfmtutl.c
  *
  * Revision 1.5  2005/12/29 19:55:04  madden
  * Added functions to print tabular output
  *
  * Revision 1.4  2005/05/16 17:42:19  papadopo
  * From Alejandro Schaffer: Print references for composition-based statistics
  * and for compositional score matrix adjustment, if either method was used.
  *
  * Revision 1.3  2004/10/04 17:54:14  madden
  * BlastPrintVersionInfo[Ex] now takes const char* as arg for program
  *
  * Revision 1.2  2004/06/30 13:38:18  madden
  * Add prototypes for add_string_to_buffer and add_string_to_bufferEx
  *
  * Revision 1.1  2004/06/30 12:31:30  madden
  * Structures and prototypes for blast formatting utilities
  *
   *
   * */
  #ifndef __BLFMTUTL__
  #define __BLFMTUTL__
  
  #include <ncbi.h>
  #include <objcode.h>
  #include <objseq.h>
  #include <sequtil.h>
  #include <readdb.h>
  #include <ncbithr.h>
  #include <txalign.h>
  #include <ffprint.h>
  
  
  #ifdef __cplusplus
  extern "C" {
  #endif
  
  typedef struct _txdbinfo {
     struct _txdbinfo PNTR next;
     Boolean   is_protein;
     CharPtr   name;
     CharPtr   definition;
     CharPtr   date;
     Int8   total_length;
     Int4   number_seqs;
     Boolean subset;      /* Print the subset message. */
  } TxDfDbInfo, *TxDfDbInfoPtr;
  
  /*****************************************************************
  *
  *       Used for pruing SeqALigns that are too big.
  *
  ********************************************************************/
  
  typedef struct _blast_prune_hits_from_sap {
                  SeqAlignPtr sap;
                  Int4    original_number,        /* how may unique hits were there originally. */
                          number;         /* How many hits on SeqALignPtr above. */
                  Boolean allocated; /* If FALSE, SeqAlignPtr above does NOT belong to this struc.*/
          } BlastPruneSapStruct, PNTR BlastPruneSapStructPtr;
          
  
  /*
         Allocates memory for TxDfDbInfoPtr.
         Link up new (returned) value to 'old', if non-NULL.
 */
 TxDfDbInfoPtr LIBCALL TxDfDbInfoNew PROTO((TxDfDbInfoPtr old));
 
 /*
         Deallocates memory (including strings for name, definition, and date).
 */
 TxDfDbInfoPtr LIBCALL TxDfDbInfoDestruct PROTO((TxDfDbInfoPtr dbinfo));
 
 
 /*
         Duplicate a SeqAlignPtr, keeping on the number of unique db
         hits specified.
 */
 
 BlastPruneSapStructPtr LIBCALL BlastPruneHitsFromSeqAlign PROTO((SeqAlignPtr sap, Int4 number, BlastPruneSapStructPtr prune));
 
 /* Deallocates BlastPruneSapStruct and deallocates SeqAlignSet if "allocated" flag is set. */
 BlastPruneSapStructPtr LIBCALL BlastPruneSapStructDestruct PROTO((BlastPruneSapStructPtr prune));
 
 /*
 Print a summary of the query.
 */
 Boolean LIBCALL AcknowledgeBlastQuery PROTO((BioseqPtr bsp, Int4 line_length, FILE *outfp, Boolean believe_query, Boolean html));
 
 /*
         Print a report of the database used.
 */
 Boolean LIBCALL PrintDbReport PROTO((TxDfDbInfoPtr dbinfo, Int4 line_length, FILE *outfp));
 
 /*
         print out some of the Karlin-Altschul parameters.
 */
 Boolean LIBCALL PrintKAParameters PROTO((Nlm_FloatHi Lambda, Nlm_FloatHi K, Nlm_FloatHi H, Int4 line_length, FILE *outfp, Boolean gapped));
 Boolean LIBCALL PrintKAParametersExtra PROTO((Nlm_FloatHi Lambda, Nlm_FloatHi K, Nlm_FloatHi H, Nlm_FloatHi C, Int4 line_length, FILE *outfp, Boolean gapped));
 
 /*
         Print a CharPtr (VisibleString), printing a new line every time
         a tilde is encountered.
 */
 Boolean LIBCALL PrintTildeSepLines PROTO((CharPtr buffer, Int4 line_length, FILE *outfp));
 
 
 /*
         Prints some header information.
 */
 
 CharPtr LIBCALL BlastGetVersionNumber PROTO((void));
 
 CharPtr LIBCALL BlastGetReference PROTO((Boolean html));
 
 Boolean LIBCALL BlastPrintReference PROTO((Boolean html, Int4 line_length, FILE *outfp));
 Boolean LIBCALL MegaBlastPrintReference PROTO((Boolean html, Int4 line_length, FILE *outfp));
 
 CharPtr LIBCALL BlastGetPhiReference PROTO((Boolean html));
 
 Boolean LIBCALL BlastPrintPhiReference PROTO((Boolean html, Int4 line_length, FILE *outfp));
 
 Boolean LIBCALL CBStatisticsPrintReference PROTO((Boolean html, Int4 line_length, Boolean firstRound, Boolean moreRounds, FILE *outfp));
 
 Boolean LIBCALL CAdjustmentPrintReference PROTO((Boolean html, Int4 line_length, FILE *outfp));
 
 Boolean BlastPrintVersionInfo PROTO((const char* program, Boolean html, FILE *outfp));
 Boolean BlastPrintVersionInfoEx PROTO((const char* program, Boolean html, CharPtr version, CharPtr date, FILE *outfp));
 
 CharPtr LIBCALL BlastGetReleaseDate PROTO((void));
 
 /*
         adds the new string to the buffer, separating by a tilde.
         Checks the size of the buffer for FormatBlastParameters and
         allocates longer replacement if needed.
 */
 
 Boolean LIBCALL add_string_to_bufferEx PROTO((CharPtr buffer, CharPtr *old, Int2Ptr old_length, Boolean add_tilde));
 
 Boolean LIBCALL add_string_to_buffer PROTO((CharPtr buffer, CharPtr *old, Int2Ptr old_length));
 
 
 void PrintTabularOutputHeader PROTO((CharPtr blast_database, BioseqPtr query_bsp,
                               SeqLocPtr query_slp, CharPtr blast_program,
                               Int4 iteration, Boolean believe_query,
                                      FILE *outfp));
 
 void BlastPrintTabulatedResults PROTO((SeqAlignPtr seqalign, BioseqPtr query_bsp, SeqLocPtr query_slp, Int4 num_alignments, CharPtr blast_program, Boolean is_ungapped, Boolean believe_query, Int4 q_shift, Int4 s_shift, FILE *fp, Boolean print_query_info));
 
 void BlastPrintTabulatedResultsEx PROTO((SeqAlignPtr seqalign, BioseqPtr query_bsp, SeqLocPtr query_slp, Int4 num_alignments, CharPtr blast_program, Boolean is_ungapped, Boolean believe_query, Int4 q_shift, Int4 s_shift, FILE *fp, int *num_formatted, Boolean print_query_info));
 
 void BlastPrintTabularResults(SeqAlignPtr seqalign, BioseqPtr query_bsp,
         SeqLocPtr query_slp, Int4 num_alignments, CharPtr blast_program,
         Boolean is_ungapped, Boolean is_ooframe, Boolean believe_query,
         Int4 q_shift, Int4 s_shift, FILE *fp, int *num_formatted,
         Boolean print_query_info);
 
 
 /* Functions used for printing error messages. */
 
 Uint1 BlastSetUserErrorString(CharPtr string, SeqIdPtr sip, Boolean use_id);
 void BlastDeleteUserErrorString(Uint1 err_id);
 
 #ifdef __cplusplus
 }
 #endif
 #endif /* !__BLFMTUTL__ */