NCBI C Toolkit Cross Reference

   /* $Id: actutils.h,v 6.17 2008/05/02 18:02:39 bollin Exp $
    *===========================================================================
   *
   *                            PUBLIC DOMAIN NOTICE
   *            National Center for Biotechnology Information (NCBI)
   *
   *  This software/database is a "United States Government Work" under the
   *  terms of the United States Copyright Act.  It was written as part of
   *  the author's official duties as a United States Government employee and
  *  thus cannot be copyrighted.  This software/database is freely available
  *  to the public for use. The National Library of Medicine and the U.S.
  *  Government do not place any restriction on its use or reproduction.
  *  We would, however, appreciate having the NCBI and the author cited in
  *  any work or product based on this material.
  *
  *  Although all reasonable efforts have been taken to ensure the accuracy
  *  and reliability of the software and data, the NLM and the U.S.
  *  Government do not and cannot warrant the performance or results that
  *  may be obtained by using this software or data. The NLM and the U.S.
  *  Government disclaim all warranties, express or implied, including
  *  warranties of performance, merchantability or fitness for any particular
  *  purpose.
  *
  * ===========================================================================
  *
  * File Name:  actutils.h
  *
  * Author:  Sarah Wheelan
  *
  * Version Creation Date:   2/00
  *
  * $Revision: 6.17 $
  *
  * File Description: utility functions for alignments
  *
  * Modifications:
  * --------------------------------------------------------------------------
  * $Log: actutils.h,v $
  * Revision 6.17  2008/05/02 18:02:39  bollin
  * Fixed bug in ACT_CleanUpAlignments - if an alignment span is completely
  * contained in another alignment, remove the contained alignment.
  * Also added a flag to Sqn_GlobalAlign2SeqEx for whether or not the alignment
  * should be expanded to the ends of the sequence.
  *
  * Revision 6.16  2006/01/03 15:47:25  bollin
  * allow alignment callback for ACT_FindPiece so that it can use the new BLAST
  * library
  *
  * Revision 6.15  2004/11/22 16:45:24  bollin
  * created global alignment function with callback method to allow use of new
  * BLAST library
  *
  * Revision 6.14  2004/11/02 18:53:39  bollin
  * made act_get_eval available to other libraries
  *
  * Revision 6.13  2004/07/30 13:36:47  bollin
  * created separate function for reversing features on a sequence, changed code
  * to swap plus to minus and minus to plus instead of moving all features to
  * minus strand
  *
  * Revision 6.12  2002/03/27 17:35:39  todorov
  * recreated ACT_MakeProfileFromSA
  *
  * Revision 6.11  2002/03/26 19:56:21  todorov
  * alignmgr to alignmgr2 transition
  *
  * Revision 6.10  2001/09/04 13:47:13  wheelan
  * made several functions extern
  *
  * Revision 6.9  2001/07/13 14:17:54  wheelan
  * moved Sqn_GlobalAlign2Seq and associated functions here
  *
  * Revision 6.8  2000/09/06 18:06:04  sicotte
  * Add End gaps for sequin updates
  *
  * Revision 6.7  2000/08/28 16:19:14  sicotte
  * moved AlnMgrSeqAlignMergeTwoPairwiseEx AlnMgrSeqAlignMergeTwoPairwise AlnMgrSeqAlignMergePairwiseSet to actutils.c from alignmgr.c
  *
  * Revision 6.6  2000/07/08 20:44:11  vakatov
  * Get all "#include" out of the 'extern "C" { }' scope;  other cleanup...
  *
  * Revision 6.5  2000/05/04 16:45:20  wheelan
  * changes to profile builder to accomodate IBMed BLAST results
  *
  * Revision 6.4  2000/04/18 13:57:14  wheelan
  * added AlnMgrForcePairwiseContinuousEx
  *
  * Revision 6.3  2000/03/14 11:25:48  wheelan
  * added ACT_ProfileFree functions
  *
  * Revision 6.2  2000/03/02 21:11:06  lewisg
  * use bandalign for import sequence, make standalone ddv use viewmgr, make dialogs modal, send color update
  *
  * Revision 6.1  2000/02/11 17:31:45  kans
  * initial checkin of functions depending upon blast/bandalign (SW)
  *
  * ==========================================================================
  */
  
 #ifndef __ACTUTILS__
 #define __ACTUTILS__
 
 #include <ncbi.h>
 #include <objalign.h>
 #include <alignmgr2.h>
 #include <sqnutils.h>
 #include <bandalgn.h>
 #include <needleman.h>
 #include <dotseq.h>
 #include <edutil.h>
 
 #undef NLM_EXTERN
 #ifdef NLM_IMPORT
 #define NLM_EXTERN NLM_IMPORT
 #else
 #define NLM_EXTERN extern
 #endif
 
 #ifdef __cplusplus
 extern "C" {
 #endif
 
 #define CG_WINDOWSIZE 200
 
 #define MAX_LEN 12000
 
 
 /* defines for profile builder -- how many options are allowed for
 *  protein or nucleotide sequences */
 #define ACT_NUCLEN 5
 #define ACT_PROTLEN 27
 
 typedef struct act_sitelist {
    Int4     start;
    CharPtr  name;
    struct act_sitelist PNTR next;
 } ACT_sitelist, PNTR ACT_sitelistPtr;
 
 typedef struct act_topscore {
    FloatHi  score;
    Int4     pos;
    struct act_topscore PNTR next;
 } ACT_TopScore, PNTR ACT_TopScorePtr;
 
 typedef struct act_position {
    Int4Ptr  posarray;
    FloatHi  score;
 } ACT_Position, PNTR ACT_PositionPtr;
 
 typedef struct act_profile
 {
    FloatHiPtr PNTR freq;
    Boolean    nuc;
    Int4       len;
    Int4       numseq;
    FloatHi    confidence;
    struct act_profile PNTR next;
 } ACTProfile, PNTR ACTProfilePtr;
 
 typedef struct act_placebounds {
    ACT_TopScorePtr PNTR ats;
    Int4            len;
    ACTProfilePtr   app;
    ACT_PositionPtr  apos;
    Int4Ptr         currpos;
    Int4            currprof;
    Int4            nprof;
    Int4Ptr         boundarray;
    Int4Ptr         numats;
    ACT_TopScorePtr PNTR currats;
 } ACT_PlaceBounds, PNTR ACT_PlaceBoundsPtr;
 
 
 typedef struct act_cginfo {
    Int4             from;
    Int4             to;
    Int4             length;
    Int4             cg;
    Int4             a;
    Int4             c;
    Int4             t;
    Int4             g;
    Int4             n;
    ACT_sitelistPtr  asp;
    CharPtr          sequence;
    struct act_cginfo PNTR next;
 } ACT_CGInfo, PNTR ACT_CGInfoPtr;
 
 typedef struct act_statetable
 {
    Int4Ptr PNTR  state;
 } ACT_Statetab, PNTR ACT_StatetabPtr;
 
 NLM_EXTERN ACT_CGInfoPtr ACT_FindCpG(BioseqPtr bsp);
 NLM_EXTERN Uint1 ACT_GetResidue(Int4 pos, Uint1Ptr buf, Int4Ptr offset, BioseqPtr bsp);
 NLM_EXTERN ACTProfilePtr ACT_ProfileNew(Boolean nuc);
 
 /***************************************************************************
 *
 *  ACT_ProfileFree frees a single profile; ACT_ProfileSetFree frees an
 *  entire linked list of profiles.
 *
 ***************************************************************************/
 NLM_EXTERN ACTProfilePtr ACT_ProfileFree(ACTProfilePtr app);
 NLM_EXTERN ACTProfilePtr ACT_ProfileSetFree(ACTProfilePtr app);
 
 NLM_EXTERN void ACT_BuildProfile(SeqLocPtr slp, ACTProfilePtr PNTR app, Int4Ptr count, Int4 length);
 NLM_EXTERN FloatHi ACT_ScoreProfile(BioseqPtr bsp, Int4 pos, Uint1 strand, ACTProfilePtr app);
 NLM_EXTERN void ACT_EstimateConfidence(ACTProfilePtr app);
 NLM_EXTERN ACTProfilePtr ACT_SortProfilesByConfidence(ACTProfilePtr app);
 NLM_EXTERN int LIBCALLBACK ACT_CompareProfileConfidence(VoidPtr base, VoidPtr large_son);
 NLM_EXTERN ACTProfilePtr ACT_MakeProfileFromSA(SeqAlignPtr sap);
 NLM_EXTERN ACT_TopScorePtr PNTR ACT_SortAndTruncate(ACT_TopScorePtr PNTR ats);
 NLM_EXTERN ACT_TopScorePtr ACT_FindPeakScores(FloatHiPtr scorearray, Int4 len);
 NLM_EXTERN FloatHi act_get_eval(Int4 exp);
 NLM_EXTERN ACT_PositionPtr ACT_PlaceByScore(ACT_PlaceBoundsPtr abp);
 NLM_EXTERN FloatHi ACT_CalcScore(ACT_PlaceBoundsPtr abp);
 NLM_EXTERN SeqAlignPtr Sqn_GlobalAlign2Seq (BioseqPtr bsp1, BioseqPtr bsp2, BoolPtr revcomp);
 NLM_EXTERN void ReverseBioseqFeatureStrands (BioseqPtr bsp);
 NLM_EXTERN void ACT_GetNthSeqRangeInSASet(SeqAlignPtr sap, Int4 n, Int4Ptr start, Int4Ptr stop);
 NLM_EXTERN void SQN_ExtendAlnAlg(SeqAlignPtr sap, Int4 ovl, Int4 which_side, Uint1 strand);
 NLM_EXTERN SeqAlignPtr ACT_CleanUpAlignments(SeqAlignPtr sap, Int4 len1, Int4 len2);
 extern void ACT_RemoveInconsistentAlnsFromSet (SeqAlignPtr sap, Int4 fuzz, Int4 n);
 
 typedef SeqAlignPtr (LIBCALLBACK *GetAlignmentFunc) (BioseqPtr bsp1, BioseqPtr bsp2);
 typedef SeqAlignPtr (LIBCALLBACK *GetAlignmentPieceFunc) (SeqLocPtr bsp1, SeqLocPtr bsp2);
 
 NLM_EXTERN SeqAlignPtr ACT_FindPiece(BioseqPtr bsp1, BioseqPtr bsp2, Int4 start1, Int4 stop1, Int4 start2, Int4 stop2, Uint1 strand, Int4 which_side, GetAlignmentPieceFunc aln_piece_func);
 NLM_EXTERN SeqAlignPtr 
 Sqn_GlobalAlign2SeqEx 
 (BioseqPtr bsp1,
  BioseqPtr bsp2,
  BoolPtr revcomp,
  GetAlignmentFunc aln_func,
  GetAlignmentPieceFunc aln_piece_func,
  Boolean extend_ends);
 
 
 
 /***************************************************************************
 *
 *   AlnMgr2TruncateSAP truncates a given seqalign to contain only the
 *   bioseq coordinates from start to stop on the indicated row.  Anything
 *   before those coordinates is discarded; anything remaining afterwards
 *   is made into another seqalign and put in sap->next (the original next,
 *   if any, is now at sap->next->next). Doesn't work on parent seqaligns.
 *   The function returns TRUE if the orignal alignment extended past stop.
 *
 ***************************************************************************/
 NLM_EXTERN Boolean AlnMgr2TruncateSAP(SeqAlignPtr sap, Int4 start, Int4 stop, Int4 row);
 
 
 #ifdef __cplusplus
 }
 #endif
 
 #undef NLM_EXTERN
 #ifdef NLM_EXPORT
 #define NLM_EXTERN NLM_EXPORT
 #else
 #define NLM_EXTERN
 #endif
 
 #endif