/usr/include/ncbi/salstruc.h is in libncbi6-dev 6.1.20120620-7.
This file is owned by root:root, with mode 0o644.
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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 | /* salstruc.h
* ===========================================================================
*
* 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: salstruc.h
*
* Author: Colombe Chappey
*
* Version Creation Date: 1/27/96
*
* $Revision: 6.6 $
*
* File Description:
*
* Modifications:
* --------------------------------------------------------------------------
* $Log: salstruc.h,v $
* Revision 6.6 2006/07/13 17:06:39 bollin
* use Uint4 instead of Uint2 for itemID values
* removed unused variables
* resolved compiler warnings
*
* Revision 6.5 2005/11/22 21:56:23 bollin
* made function for deleting locations from alignments extern
*
* Revision 6.4 1999/11/24 21:24:29 vakatov
* Fixed for the C++ and/or MSVC DLL compilation
*
* ==========================================================================
*/
#ifndef _SALSTRUC_
#define _SALSTRUC_
#include <salsa.h>
#include <txalign.h>
#undef NLM_EXTERN
#ifdef NLM_IMPORT
#define NLM_EXTERN NLM_IMPORT
#else
#define NLM_EXTERN extern
#endif
#ifdef __cplusplus
extern "C" {
#endif
/**********************************************************************/
NLM_EXTERN SelStructPtr BufferFree (SelStructPtr ssp);
NLM_EXTERN EditAlignDataPtr SetupDataBuffer (EditAlignDataPtr adp);
NLM_EXTERN EditAlignDataPtr SetupDataPanel (EditAlignDataPtr adp);
NLM_EXTERN CharPtr next_notemptyline (ValNodePtr anp_list, ValNodePtr linebuff, Int2 numberalignline, Int2 *index, Int4 start, Int4 *drw_width, TextAlignBufPtr *tdp, AlignNodePtr *anp);
NLM_EXTERN SelEdStructPtr is_feature_to_buffer (ValNodePtr vnphead, Uint4 bspitemID, Uint2 entityID, Int4 from, Int4 drw_width, SeqAlignPtr salp, Uint2 seqedit, ValNodePtr sqloc_list);
NLM_EXTERN ByteStorePtr cds_to_pept (SeqLocPtr slp, Uint1 frame, Int2 gencode, Boolean include_stop);
NLM_EXTERN void data_collect_arrange (EditAlignDataPtr adp, Boolean recollect);
NLM_EXTERN CharPtr get_master (ValNodePtr linebuff, Uint2 entityID, Uint4 itemID, Uint2 itemtype);
NLM_EXTERN Boolean read_buffer_fromalignnode (EditAlignDataPtr adp, ValNodePtr *linebuff, Int4 bufferstart, Int4 minbufferlength, Int2 *numberalignline);
/**********************************
***
*** BioseqTrimN
*** truncates the nnn's at the extremities of a bioseq bsp
*** providing TopSeqEntry sep allows to modify the SeqAlign if any
***
***********************************/
NLM_EXTERN Boolean BioseqTrimN (BioseqPtr bsp, SeqEntryPtr sep);
/* Function removes location from alignment */
NLM_EXTERN void SeqAlignDeleteByLocCallback (SeqEntryPtr sep, Pointer mydata,
Int4 index, Int2 indent);
/*******************************************************************
*** AddFeatFunc
******************************************************************/
NLM_EXTERN ValNodePtr AddFeatFunc (SelEdStructPtr feat, ValNodePtr *featlist, Uint2 itemsubtype);
/******************************************************************
*
*** CollectFeatureForEditor
*** slp: the target Seq-loc
*** anp: the AlignNode belong to the target Seq-loc
*** csop: the option for gathering the features
******************************************************************/
NLM_EXTERN ValNodePtr CollectFeatureForEditor (SeqLocPtr slp, ValNodePtr seqfeat, Uint2 seq_entityID, Uint4 bsp_itemID, Uint1 *featOrder, Boolean all_feat);
/**********************************************************************
*** Display alignment in several formats
***
**********************************************************************/
NLM_EXTERN void ShowAlignmentText (FILE *fout, EditAlignDataPtr adp, SelStructPtr ssp, Int2 leftmargin, Int4 printfrom, Int4 printto, Boolean html_option);
NLM_EXTERN void showfastagap_fromalign (SeqAlignPtr salp, Int4 line, FILE *f);
#ifdef __cplusplus
}
#endif
#undef NLM_EXTERN
#ifdef NLM_EXPORT
#define NLM_EXTERN NLM_EXPORT
#else
#define NLM_EXTERN
#endif
#endif
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