/* $Id: actutils.h,v 6.10 2001/09/04 13:47:13 wheelan 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: 6.10 $ * * File Description: utility functions for alignments * * Modifications: * -------------------------------------------------------------------------- * $Log: actutils.h,v $ * 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 #include #include #include #include #include #include #include #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 Boolean ACT_AddBioseqToSAByProfile(SeqAlignPtr sap, BioseqPtr bsp); NLM_EXTERN ACT_TopScorePtr PNTR ACT_SortAndTruncate(ACT_TopScorePtr PNTR ats); NLM_EXTERN ACT_TopScorePtr ACT_FindPeakScores(FloatHiPtr scorearray, Int4 len); NLM_EXTERN ACT_PositionPtr ACT_PlaceByScore(ACT_PlaceBoundsPtr abp); NLM_EXTERN FloatHi ACT_CalcScore(ACT_PlaceBoundsPtr abp); NLM_EXTERN SeqAlignPtr ACT_GlobalAlignSimple(BioseqPtr bsp1, BioseqPtr bsp2, Boolean Default); NLM_EXTERN SeqAlignPtr ACT_GlobalAlignTwoSeq(BioseqPtr bsp1, BioseqPtr bsp2); NLM_EXTERN SeqAlignPtr AlnMgrForcePairwiseContinuous(SeqAlignPtr sap); NLM_EXTERN SeqAlignPtr AlnMgrForcePairwiseContinuousEx(SeqAlignPtr sap, Int4 start_1, Int4 stop_1, Int4 start_2, Int4 stop_2); NLM_EXTERN SeqAlignPtr AlnMgrSeqAlignMergeTwoPairwiseEx(SeqAlignPtr sap_global,SeqAlignPtr salp1,SeqAlignPtr salp2,Int4 which_master, Uint1 strand_master, Uint1 strand_subject, Int4 startm1,Int4 stopm1, Int4 start1, Int4 stop1,Int4 startm2,Int4 stopm2, Int4 start2, Int4 stop2); NLM_EXTERN SeqAlignPtr AlnMgrSeqAlignLocalToGlobal(SeqAlignPtr sap); NLM_EXTERN SeqAlignPtr AlnMgrSeqAlignMergeTwoPairwise(SeqAlignPtr sap_global,SeqAlignPtr salp1,SeqAlignPtr salp2,Int4 which_master); NLM_EXTERN Int4 AlnMgrSeqAlignMergePairwiseSet(SeqAlignPtr PNTR sap_ptr); NLM_EXTERN SeqAlignPtr Sqn_GlobalAlign2Seq (BioseqPtr bsp1, BioseqPtr bsp2, BoolPtr revcomp); NLM_EXTERN void ACT_GetNthSeqRangeInSASet(SeqAlignPtr sap, Int4 n, Int4Ptr start, Int4Ptr stop); NLM_EXTERN SeqAlignPtr ACT_FindPiece(BioseqPtr bsp1, BioseqPtr bsp2, Int4 start1, Int4 stop1, Int4 start2, Int4 stop2, Uint1 strand, Int4 which_side); 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); #ifdef __cplusplus } #endif #undef NLM_EXTERN #ifdef NLM_EXPORT #define NLM_EXTERN NLM_EXPORT #else #define NLM_EXTERN #endif #endif