/usr/include/ncbi/seqcons.h is in libvibrant6-dev 6.1.20110713-3ubuntu2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 | /* $Id: seqcons.h,v 6.15 2000/04/27 13:36:19 thiessen 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: $Id: seqcons.h,v 6.15 2000/04/27 13:36:19 thiessen Exp $
*
* Authors: Paul Thiessen
*
* Version Creation Date: 2/10/2000
*
* File Description: to calculate colors for columns to visualize
* sequence conservation
*
* Modifications:
* --------------------------------------------------------------------------
* $Log: seqcons.h,v $
* Revision 6.15 2000/04/27 13:36:19 thiessen
* change algorithm GUI names
*
* Revision 6.14 2000/04/06 19:03:20 thiessen
* new BLOSUM62 conservation coloring
*
* Revision 6.13 2000/03/16 20:31:45 thiessen
* fixes to color; new color-by-variety algorithm
*
* Revision 6.12 2000/03/14 18:03:14 thiessen
* add target row to MMD; remove rowmgr
*
* Revision 6.11 2000/03/03 20:05:17 thiessen
* removal of palette-building pass if in 24-bit color
*
* Revision 6.10 2000/03/03 14:13:42 thiessen
* moved back into ncbicn3d
*
* Revision 1.1 2000/03/02 21:20:41 thiessen
* many improvements, moved into object library
*
* Revision 6.8 2000/02/25 02:53:15 thiessen
* check AlignMgr rather than bAligned flag to see if a residue is aligned
*
* Revision 6.7 2000/02/19 21:25:58 thiessen
* split of cn3dmodl into cn3dmodl and cn3dstyl
*
* Revision 6.6 2000/02/17 15:41:11 thiessen
* added CSC algorithm selection submenu
*
* Revision 6.5 2000/02/16 21:25:32 thiessen
* new row manager module; made Cn3D use row-wise color storage for aligned strucs
*
* Revision 6.4 2000/02/16 14:02:01 thiessen
* further progress on seqcons module
*
* Revision 6.3 2000/02/14 20:04:24 thiessen
* another fix for solvent; more filling in of seqcons
*
* Revision 6.2 2000/02/14 12:32:31 thiessen
* fix solvent identification; progress on seqcons module
*
* Revision 6.1 2000/02/11 01:12:35 thiessen
* new module for sequence conservation coloring
*
*
*
* ==========================================================================
*/
#ifndef _SEQCONS_
#define _SEQCONS_ 1
#include <objalign.h>
#include <mmdbapi.h>
#include <ddvcolor.h>
#ifdef __cplusplus
extern "C" {
#endif
/**** identities and number of available algorithms ****/
enum {
CSC_BYVARIETY=0, /* first one must be 0 */
CSC_BYBLOSUM62,
CSC_SHOWIDENTITY,
CSC_SHOWALIGNED,
CSC_NUMALGORITHMS
};
/**** public module functions ****/
/*
* Returns the string name for the specified algorithm type; NULL if invalid type.
*/
extern const Nlm_Char * CSC_GetAlgorithmName(Nlm_Int2);
/*
* Calculates (with the given algorithm) colors for all aligned colums.
* Returns TRUE on success, FALSE on error. Should be called before any colors
* are read or a different coloring algorithm is desired.
*/
extern Nlm_Boolean CSC_CalculateColumnColors(SeqAlignPtr, Nlm_Int2 useAlgorithm);
/*
* Returns a color given a row and a bioseq coordinate. Returns CSC_COLOR_ERROR
* upon error; if successful, the returned color is a packed 3-byte RGB color
* where
* red = (color & 0x00FF0000) >> 16
* green = (color & 0x0000FF00) >> 8
* blue = (color & 0x000000FF)
*
* Expects the "seqLoc" numbering to start at 0.
*/
#define CSC_COLOR_ERROR (0xFF222222)
extern Nlm_Int4 CSC_GetColumnColorByRow(Nlm_Int4 row, Nlm_Int4 seqLoc);
/*
* Goes over a given row, applying appropriate capitalization and,
* depending on whether the boolean passed is TRUE, color to a residue.
* The "unalignedColor" gets applied to unaligned residues.
*/
extern void CSC_SetDDVRowCells(Nlm_Int4 row,
Nlm_Boolean applyColumnColor,
Nlm_Uint1 *unalignedColor,
DDV_ColorGlobal *pDDVCG);
/*
* Given a PMSD, scans through it and current SeqAlign to find rows that
* don't have associated structure, and applying CSC_SetDDVRowCells.
*/
extern void CSC_SetNonStructureDDVRowCells(PMSD pmsd,
Nlm_Boolean applyColumnColor,
Nlm_Uint1 *unalignedColor,
DDV_ColorGlobal *pDDVCG);
/*
* Same as above, just does all rows.
*/
extern void CSC_SetAllDDVRowCells(Nlm_Boolean applyColumnColor,
Nlm_Uint1 *unalignedColor,
DDV_ColorGlobal *pDDVCG);
#ifdef __cplusplus
}
#endif
#endif /* _SEQCONS_ */
|