NCBI C Toolkit Cross Reference

   /*   $Id: seqcons.h,v 6.15 2000/04/27 13:36:19 thiessen Exp $
   * ===========================================================================
   *
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   *            National Center for Biotechnology Information (NCBI)
   *
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  *
  * 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_ */