/usr/include/ncbi/seqcons.h is in libvibrant6-dev 6.1.20170106-2.
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* ===========================================================================
*
* 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_ */
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