/* $Id: blocks.h,v 6.2 1999/11/26 15:42:24 vakatov 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: blocks.h * * Author: Sarah Wheelan * * Version Creation Date: * * $Revision: 6.2 $ * * File Description: Creating an editable version of a seqalign * * Modifications: * -------------------------------------------------------------------------- * $Log: blocks.h,v $ * Revision 6.2 1999/11/26 15:42:24 vakatov * Fixed for the C++ and/or MSVC DLL compilation * * Revision 6.1 1999/07/06 19:49:14 kans * initial public checkin * * Revision 1.19 1999/07/01 20:58:34 wheelan * added include salpedit.h, added FlipSequence, CalcMinusBounds, PropagateStrandInfo, and Patrick Durand`s SABlock printing function * * Revision 1.18 1999/06/25 20:56:39 wheelan * took out unnecessary includes * * Revision 1.17 1999/06/24 20:44:45 wheelan * added IndexNewBlocks to correctly index SABlocks made from DenseDiags * * Revision 1.16 1999/06/21 12:07:28 wheelan * added SeqAlignListMergeAll function * * Revision 1.15 1999/06/11 17:02:54 wheelan * Added DeBlockify and GetSeqIdList functions * * Revision 1.13 1999/06/07 20:59:30 lewisg * fix typo in traverser fcn typedefs * * Revision 1.12 1999/05/29 00:09:15 lewisg * new editing functions * * Revision 1.11 1999/05/24 23:10:50 lewisg * more initialization for AddEmptyBlocks * * Revision 1.9 1999/05/24 15:33:20 lewisg * make Segment.gap hold gap count * * Revision 1.8 1999/05/21 14:53:59 lewisg * added functions, removed ssp * * * ========================================================================== */ #ifndef _NCBI_DDV_BLOCKS_ #define _NCBI_DDV_BLOCKS_ #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 /* Gapless segment for the Display SeqAlign */ typedef struct _segment { Int4 from; Int4 to; Int4 gap; /* lyg: we should delete sip. this is kept elsewhere */ SeqIdPtr sip; /* lyg: deleted pointer to standard seg */ Int4 BspID; struct _segment* next; struct _segment* prev; struct _segment* bsp_next; struct _segment* bsp_prev; Uint1 strand; /* lyg: visible should be deleted also */ Uint1 visible; Boolean link; Boolean move; /* lyg: does this Segment have a pending edit? */ } Segment, PNTR SegmentPtr; /* Head of Linked List for Each Segment */ typedef struct _seqalignblock { Int4 from; Int4 to; SegmentPtr segp_head; Int4 SegID; Int4 AlignID; Int4 RegionID; struct _seqalignblock* next; struct _seqalignblock* prev; Boolean aligned; /* lyg: indicates that the column is aligned */ /* lyg: visible and highlighted should be kept elsewhere */ Uint1 visible; Boolean highlighted; } SABlock, PNTR SABlockPtr; /* Anciliary Information for each "row" Bioseq : Not Part of SeqAlign */ typedef struct _ddv_seginfo { Int4 BspID; SeqPortPtr spp; SeqIdPtr sip; BioseqPtr bsp; /* Optional, Only if locked */ struct _ddv_segInfo * next; Uint2 entityID; Uint2 itemID; } DDV_SegInfo, * DDV_SegInfoPtr; /* Transform an N-dim Multiple SeqAlign into the Block SeqAlign (dsp only) */ NLM_EXTERN SABlockPtr Blockify(SeqAlignPtr sap); NLM_EXTERN SABlockPtr IndexBlocks(SABlockPtr sabp); NLM_EXTERN SABlockPtr IndexNewBlocks(SABlockPtr sabp); NLM_EXTERN void GetBlockInfo(SABlockPtr sabp, Int4Ptr length, Int4Ptr numbioseqs, Int4Ptr numblocks, Int4Ptr validate); NLM_EXTERN void CleanupBlocks(SABlockPtr sabp); NLM_EXTERN SABlockPtr SAMergeBlocks(SABlockPtr sabp1, SABlockPtr sabp2); NLM_EXTERN Int4 GetBlockOrientation(Int4Ptr shift, SegmentPtr segp1, SegmentPtr segp2, Int4 index1, Int4 index2); NLM_EXTERN SABlockPtr SquishBlocks(SABlockPtr sabp); NLM_EXTERN SABlockPtr SARemoveSequence(Int4 BspID, SeqIdPtr sip, SABlockPtr sabp); NLM_EXTERN SABlockPtr RearrangeSegments(Int4 BspID, SABlockPtr sabp, Int4 position); NLM_EXTERN SABlockPtr TeenyBlock(SABlockPtr sabp, Int4 from, Int4 to); NLM_EXTERN SABlockPtr SASplitBlock(SABlockPtr sabp, Int4 from); NLM_EXTERN SABlockPtr AddEmptyBlocks(SABlockPtr sabp, Int4 n, Boolean beginning, Boolean end); NLM_EXTERN SABlockPtr AddEmptySegments(SABlockPtr sabp); NLM_EXTERN SABlockPtr FillInUnaligned(SABlockPtr sabp); NLM_EXTERN SeqAlignPtr DeBlockify(SABlockPtr sabp); NLM_EXTERN SeqIdPtr GetSeqIdList(SABlockPtr sabp); NLM_EXTERN SeqAlignPtr SeqAlignListMergeAll(SeqAnnotPtr sap); NLM_EXTERN SegmentPtr PropagateStrandInfo(SegmentPtr segp); /******************************************************************************* Function : blk_PrintSABP() Purpose : display an indexed seqalign as a matrix (debug purpose only) Parameters : sabp;header of the indexed seqalign Return value : - *******************************************************************************/ NLM_EXTERN void blk_PrintSABP(SABlockPtr sabp); /***************************************************************************** * * Notes on changes by lyg: * - removed ssp in Segment * - initialized RegionID in Blockify * - added SAReturnBlock() and SAReturnSegment() * - added traversal routine * - set SABlock.gap equal to the length of the gap * - preserve RegionID in AddEmptyBlocks(), initialize more members * *****************************************************************************/ /***************************************************************************** * * For a given column, return a pointer to the block that contains the * position. Returns NULL if a containing block is not found. * *****************************************************************************/ NLM_EXTERN SABlock * SAReturnBlock(SABlock *sabpHead, Int4 lColumn); /***************************************************************************** * * For a given position, return a pointer to the Segment that contains the * position. Returns NULL if a containing Segment is not found. Note that * the lRow argument is position, not BspID. * *****************************************************************************/ NLM_EXTERN Segment * SAReturnSegment(SABlock *sabpHead, Int4 lColumn, Int4 lRow); /***************************************************************************** * * Generic Segment traversal function with callback * *****************************************************************************/ typedef void (*pfnSAFunction)(Segment *pSegment, void *pData); NLM_EXTERN Int4 SATraverse(SABlock *sabpHead, pfnSAFunction pFunction, void *pData); /***************************************************************************** * * Traverser to clear the move bit * *****************************************************************************/ NLM_EXTERN void SAClearMove(Segment *pSegment, void *pData); /***************************************************************************** * * Generic SABlock traversal function with callback * *****************************************************************************/ typedef void (*pfnSABlockFunction)(SABlock *sabp, void *pData); NLM_EXTERN Int4 SATraverseBlock (SABlock *sabpHead, pfnSABlockFunction pFunction, void *pData); /***************************************************************************** * * Traverser to find the highest valued RegionID * *****************************************************************************/ NLM_EXTERN void SARegionBounds(SABlock *sabp, void *pData); #ifdef __cplusplus } #endif #undef NLM_EXTERN #ifdef NLM_EXPORT #define NLM_EXTERN NLM_EXPORT #else #define NLM_EXTERN #endif #endif