/* =========================================================================== * * 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: dotseq.h * * Author: Fasika Aklilu * * Version Creation Date: 8/9/01 * * $Revision: 6.4 $ * * File Description: computes local alignments for dot matrix * * Modifications: * -------------------------------------------------------------------------- * Date Name Description of modification * ------- ---------- ----------------------------------------------------- $Revision: 6.4 $ $Log: dotseq.h,v $ Revision 6.4 2001/08/09 16:33:18 aklilu added revision Revision 6.3 2000/07/26 18:23:10 sicotte added DOT_SPI_FindBestAlnByDotPlotEx, to return rejected alignments */ #ifndef _DOTSEQ_ #define _DOTSEQ_ #ifdef __cplusplus extern "C" { #endif /**************************************************************************** INCLUDE SECTION ***************************************************************************/ #include #include #include #include #include #include #include #include #include /**************************************************************************** DEFINES SECTION ***************************************************************************/ #define UNDEFINED 25 /* amino acids undefined in BLOSUM62 */ #define MAX_TRIM 200 /**************************************************************************** DATA STRUCTURE SECTION ***************************************************************************/ typedef struct hs_diag { Int4 q_start; /* left most value on the graph */ Int4 s_start; /* left most value on the graph */ Int4 length; Int4 score; Int4 rdmKey; } DOTDiag, PNTR DOTDiagPtr; /* coordinates of old diags -used in history binary tree */ typedef struct hist { Int4 diag_constant; Int4 q_stop; } DOTHist, PNTR DOTHistPtr; /* main struct */ typedef struct mainseqinfo { Int4Ptr PNTR matrix; /* dna matrix */ Int2 maxscore; /* highest matrix score */ Int2 minscore;/* lowest matrix score */ Boolean is_na; Int4 qlen; /* length of query sequence */ Int4 slen; /* length of subject sequence */ Uint1 qstrand; /* strand of query */ Uint1 sstrand; /* strand of subject */ BioseqPtr qbsp; /* query bioseq */ BioseqPtr sbsp; /* subject bioseq */ SeqLocPtr qslp; /* query seqloc pointer */ SeqLocPtr sslp; /* subject seqloc pointer */ Int4 q_start; /* left position on query bioseq */ Int4 q_stop; /* right position on query bioseq */ Int4 s_start; /* left position on subject bioseq */ Int4 s_stop;/* right position on subject bioseq */ Uint1Ptr qseq; /* query sequence buffer */ Uint1Ptr sseq; /* subject sequence buffer */ CharPtr qname; /* query accession */ CharPtr sname;/* subject accession */ /* hash value */ Int4 word_size; /* size of hash table index */ /* binary tree data */ Int4 cutoff_score; /* cutoff to store hits */ Avl_TreePtr tree; /* binary tree for collecting hits */ Boolean first_pass; Int4Ptr score_array;/* array by score for threshold ramp */ Int4 unique; /* binary tree variable */ Int4 tree_limit; /* upper limit for size of binary tree */ /* sorted diag data */ DOTDiagPtr PNTR hitlist; /* dotseq output data -- array of hits */ Int4 index; /* total number of stored hits in array */ } DOTMainData, PNTR DOTMainDataPtr; typedef struct dotdata { Uint1 xstrand; Uint1 ystrand; Int4 xstart; Int4 xstop; Int4 ystart; Int4 ystop; Int4 index; DOTDiagPtr PNTR hitlist; } DOTData, PNTR DOTDataPtr; /* information for history binary tree */ typedef struct info{ DOTMainDataPtr mip; Uint1Ptr qseq; Uint1Ptr sseq; Int4 q_pos; Int4 s_pos; Int4 wordsize; Avl_TreePtr tree; Boolean first_pass; } DOTInfo, PNTR DOTInfoPtr; /**************************************************************************** FUNCTION DECLARATIONS ***************************************************************************/ /* Function: Compute all matches between two sequences. Input: 2 bioseqptrs. Returns: DOTMainDataPtr with hitlist structure with start/stops in bioseq coordinates */ DOTMainDataPtr DOT_CreateAndStore (DOTMainDataPtr mip, BioseqPtr qbsp, BioseqPtr sbsp, Int4 q_start, Int4 q_stop, Int4 s_start, Int4 s_stop, Int4 word_size, Int4 tree_limit, Boolean initialize); /* Function: Compute all matches between two sequences. Input: 2 seqlocptrs (can specify plus or minus strand in slp). Returns: Filled DOTMainDataPtr with hitlist structure with start/stops in bioseq coordinates */ DOTMainDataPtr DOT_CreateAndStorebyLoc (SeqLocPtr slp1, SeqLocPtr slp2, Int4 word_size, Int4 tree_limit); Int2 DOT_BuildHitList(DOTMainDataPtr mip, Boolean do_sort, Boolean do_countscore); Boolean DOT_GetSeqs (DOTMainDataPtr mip, Boolean is_zoom); Int2 DOT_FreeMainInfo(DOTMainDataPtr mip); Int2 DOT_FreeMainInfoPtrEx (DOTMainDataPtr mip); Int2 DOT_FreeHitsArray (DOTDiagPtr PNTR hitlist, Int4 index); Boolean DOT_GetSeqs (DOTMainDataPtr mip, Boolean is_zoom); extern DOTMainDataPtr DOT_InitMainInfo (DOTMainDataPtr mip, BioseqPtr qbsp, BioseqPtr sbsp, Int4 word_size, Int4 tree_limit, Int4 qstart, Int4 qstop, Int4 sstart, Int4 sstop); SeqAlignPtr DOT_SPI_FindBestAlnByDotPlot(SeqLocPtr slp1, SeqLocPtr slp2, Int4 wordsize, Int4 num_hits); extern Uint2 DOT_AttachSeqAnnotToSeqEntry (Uint2 entityID, SeqAnnotPtr sap, BioseqPtr bsp); extern Int4Ptr PNTR DOT_DNAScoringMatrix(Int4 mismatch, Int4 reward,Int4 alsize); #ifdef __cplusplus } #endif #endif /* ndef _DOTSEQ_ */